Daily Papers

The recently launched James Webb Space Telescope (JWST) is opening new observing windows on the distant universe. Among JWST's instruments, the Mid Infrared Instrument (MIRI) offers the unique capability of imaging observations at wavelengths lambda > 5mum. This enables unique access to the rest frame near infra-red (NIR, lambda ge 1\mum) emission from galaxies at redshifts z>4 and the visual (lambda gtrsim 5000\AA) rest frame for z>9. We here report on the guaranteed time observations (GTO) from the MIRI European Consortium, of the Hubble Ultra Deep Field (HUDF), forming the MIRI Deep Imaging Survey (MIDIS), consisting of an on source integration time of sim41 hours in the MIRI/F560W (5.6 mum) filter. To our knowledge, this constitutes the longest single filter exposure obtained with JWST of an extragalactic field as yet.

We present an overview of the James Webb Space Telescope (JWST) Advanced Deep Extragalactic Survey (JADES), an ambitious program of infrared imaging and spectroscopy in the GOODS-S and GOODS-N deep fields, designed to study galaxy evolution from high redshift to cosmic noon. JADES uses about 770 hours of Cycle 1 guaranteed time largely from the Near-Infrared Camera (NIRCam) and Near-Infrared Spectrograph (NIRSpec) instrument teams. In GOODS-S, in and around the Hubble Ultra Deep Field and Chandra Deep Field South, JADES produces a deep imaging region of ~45 arcmin^2 with an average of 130 hrs of exposure time spread over 9 NIRCam filters. This is extended at medium depth in GOODS-S and GOODS-N with NIRCam imaging of ~175 arcmin^2 with an average exposure time of 20 hrs spread over 8-10 filters. In both fields, we conduct extensive NIRSpec multi-object spectroscopy, including 2 deep pointings of 55 hrs exposure time, 14 medium pointings of ~12 hrs, and 15 shallower pointings of ~4 hrs, targeting over 5000 HST and JWST-detected faint sources with 5 low, medium, and high-resolution dispersers covering 0.6-5.3 microns. Finally, JADES extends redward via coordinated parallels with the JWST Mid-Infrared Instrument (MIRI), featuring ~9 arcmin^2 with 43 hours of exposure at 7.7 microns and twice that area with 2-6.5 hours of exposure at 12.8 microns For nearly 30 years, the GOODS-S and GOODS-N fields have been developed as the premier deep fields on the sky; JADES is now providing a compelling start on the JWST legacy in these fields.

The statistical power of weak lensing measurements is principally driven by the number of high redshift galaxies whose shapes are resolved. Conventional wisdom and physical intuition suggest this is optimised by deep imaging at long (red or near IR) wavelengths, to avoid losing redshifted Balmer break and Lyman break galaxies. We use the synthetic Emission Line EL-COSMOS catalogue to simulate lensing observations using different filters, from various altitudes. Here were predict the number of exposures to achieve a target z > 0.3 source density, using off-the-shelf and custom filters. Ground-based observations are easily better at red wavelengths, as (more narrowly) are space-based observations. However, we find that SuperBIT, a diffraction-limited observatory operating in the stratosphere, should instead perform its lensing-quality observations at blue wavelengths.

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.

Intravascular ultrasound (IVUS) offers a unique perspective in the treatment of vascular diseases by creating a sequence of ultrasound-slices acquired from within the vessel. However, unlike conventional hand-held ultrasound, the thin catheter only provides room for a small number of physical channels for signal transfer from a transducer-array at the tip. For continued improvement of image quality and frame rate, we present the use of deep reinforcement learning to deal with the current physical information bottleneck. Valuable inspiration has come from the field of magnetic resonance imaging (MRI), where learned acquisition schemes have brought significant acceleration in image acquisition at competing image quality. To efficiently accelerate IVUS imaging, we propose a framework that utilizes deep reinforcement learning for an optimal adaptive acquisition policy on a per-frame basis enabled by actor-critic methods and Gumbel top-K sampling.

Faint tidal features around galaxies record their merger and interaction histories over cosmic time. Due to their low surface brightnesses and complex morphologies, existing automated methods struggle to detect such features and most work to date has heavily relied on visual inspection. This presents a major obstacle to quantitative study of tidal debris features in large statistical samples, and hence the ability to be able to use these features to advance understanding of the galaxy population as a whole. This paper uses convolutional neural networks (CNNs) with dropout and augmentation to identify galaxies in the CFHTLS-Wide Survey that have faint tidal features. Evaluating the performance of the CNNs against previously-published expert visual classifications, we find that our method achieves high (76%) completeness and low (20%) contamination, and also performs considerably better than other automated methods recently applied in the literature. We argue that CNNs offer a promising approach to effective automatic identification of low surface brightness tidal debris features in and around galaxies. When applied to forthcoming deep wide-field imaging surveys (e.g. LSST, Euclid), CNNs have the potential to provide a several order-of-magnitude increase in the sample size of morphologically-perturbed galaxies and thereby facilitate a much-anticipated revolution in terms of quantitative low surface brightness science.

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

Near-field radar imaging systems are recently used in a wide range of applications, such as medical diagnosis, through-wall imaging, concealed weapon detection, and nondestructive evaluation. In this paper, we consider the problem of reconstructing the three-dimensional (3D) complex-valued reflectivity distribution of the near-field scene from sparse multiple-input multiple-output (MIMO) array measurements. Using the alternating direction method of multipliers (ADMM) framework, we solve this inverse problem by enforcing regularization on the magnitude of the complex-valued reflectivity distribution. For this, we provide a general expression for the proximal mapping associated with such regularization functionals. This equivalently corresponds to the solution of a complex-valued denoising problem which involves regularization on the magnitude. By utilizing this expression, we develop a novel and efficient plug-and-play (PnP) reconstruction method that consists of simple update steps. Due to the success of data-adaptive deep priors in various imaging problems, we also train a 3D deep denoiser to exploit within the developed PnP framework for MIMO imaging. The effectiveness of the developed learning-based PnP approach is illustrated under various compressive and noisy observation scenarios using both simulated data and experimental measurements. The performance is also compared with sparsity priors and the commonly used analytical approaches such as back-projection and Kirchhoff migration. The results demonstrate that the developed technique not only provides state-of-the-art reconstruction performance for 3D real-world targets, but also enables fast computation. Our approach provides a unified general framework to effectively handle arbitrary regularization on the magnitude of a complex-valued unknown and is equally applicable to other radar image formation problems (including SAR).

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

Hyperspectral imaging (HSI) has recently emerged as a promising tool for many agricultural applications; however, the technology cannot be directly used in a real-time system due to the extensive time needed to process large volumes of data. Consequently, the development of a simple, compact, and cost-effective imaging system is not possible with the current HSI systems. Therefore, the overall goal of this study was to reconstruct hyperspectral images from RGB images through deep learning for agricultural applications. Specifically, this study used Hyperspectral Convolutional Neural Network - Dense (HSCNN-D) to reconstruct hyperspectral images from RGB images for predicting soluble solid content (SSC) in sweet potatoes. The algorithm accurately reconstructed the hyperspectral images from RGB images, with the resulting spectra closely matching the ground-truth. The partial least squares regression (PLSR) model based on reconstructed spectra outperformed the model using the full spectral range, demonstrating its potential for SSC prediction in sweet potatoes. These findings highlight the potential of deep learning-based hyperspectral image reconstruction as a low-cost, efficient tool for various agricultural uses.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Nowadays, the enhanced capabilities of in-expensive imaging devices have led to a tremendous increase in the acquisition and sharing of multimedia content over the Internet. Despite advances in imaging sensor technology, annoying conditions like occlusions hamper photography and may deteriorate the performance of applications such as surveillance, detection, and recognition. Occlusion segmentation is difficult because of scale variations, illumination changes, and so on. Similarly, recovering a scene from foreground occlusions also poses significant challenges due to the complexity of accurately estimating the occluded regions and maintaining coherence with the surrounding context. In particular, image de-fencing presents its own set of challenges because of the diverse variations in shape, texture, color, patterns, and the often cluttered environment. This study focuses on the automatic detection and removal of occlusions from a single image. We propose a fully automatic, two-stage convolutional neural network for fence segmentation and occlusion completion. We leverage generative adversarial networks (GANs) to synthesize realistic content, including both structure and texture, in a single shot for inpainting. To assess zero-shot generalization, we evaluated our trained occlusion detection model on our proposed fence-like occlusion segmentation dataset. The dataset can be found on GitHub.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Coronavirus disease 2019 (Covid-19) is highly contagious with limited treatment options. Early and accurate diagnosis of Covid-19 is crucial in reducing the spread of the disease and its accompanied mortality. Currently, detection by reverse transcriptase polymerase chain reaction (RT-PCR) is the gold standard of outpatient and inpatient detection of Covid-19. RT-PCR is a rapid method, however, its accuracy in detection is only ~70-75%. Another approved strategy is computed tomography (CT) imaging. CT imaging has a much higher sensitivity of ~80-98%, but similar accuracy of 70%. To enhance the accuracy of CT imaging detection, we developed an open-source set of algorithms called CovidCTNet that successfully differentiates Covid-19 from community-acquired pneumonia (CAP) and other lung diseases. CovidCTNet increases the accuracy of CT imaging detection to 90% compared to radiologists (70%). The model is designed to work with heterogeneous and small sample sizes independent of the CT imaging hardware. In order to facilitate the detection of Covid-19 globally and assist radiologists and physicians in the screening process, we are releasing all algorithms and parametric details in an open-source format. Open-source sharing of our CovidCTNet enables developers to rapidly improve and optimize services, while preserving user privacy and data ownership.

Intrinsic imaging or intrinsic image decomposition has traditionally been described as the problem of decomposing an image into two layers: a reflectance, the albedo invariant color of the material; and a shading, produced by the interaction between light and geometry. Deep learning techniques have been broadly applied in recent years to increase the accuracy of those separations. In this survey, we overview those results in context of well-known intrinsic image data sets and relevant metrics used in the literature, discussing their suitability to predict a desirable intrinsic image decomposition. Although the Lambertian assumption is still a foundational basis for many methods, we show that there is increasing awareness on the potential of more sophisticated physically-principled components of the image formation process, that is, optically accurate material models and geometry, and more complete inverse light transport estimations. We classify these methods in terms of the type of decomposition, considering the priors and models used, as well as the learning architecture and methodology driving the decomposition process. We also provide insights about future directions for research, given the recent advances in neural, inverse and differentiable rendering techniques.

Deep learning-based vision is characterized by intricate frameworks that often necessitate a profound understanding, presenting a barrier to newcomers and limiting broad adoption. With many researchers grappling with the constraints of smaller datasets, there's a pronounced reliance on pre-trained neural networks, especially for tasks such as image classification. This reliance is further intensified in niche imaging areas where obtaining vast datasets is challenging. Despite the widespread use of transfer learning as a remedy to the small dataset dilemma, a conspicuous absence of tailored auto-ML solutions persists. Addressing these challenges is "Deep Fast Vision", a python library that streamlines the deep learning process. This tool offers a user-friendly experience, enabling results through a simple nested dictionary definition, helping to democratize deep learning for non-experts. Designed for simplicity and scalability, Deep Fast Vision appears as a bridge, connecting the complexities of existing deep learning frameworks with the needs of a diverse user base.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

Wrist Fracture is the most common type of fracture with a high incidence rate. Conventional radiography (i.e. X-ray imaging) is used for wrist fracture detection routinely, but occasionally fracture delineation poses issues and an additional confirmation by computed tomography (CT) is needed for diagnosis. Recent advances in the field of Deep Learning (DL), a subfield of Artificial Intelligence (AI), have shown that wrist fracture detection can be automated using Convolutional Neural Networks. However, previous studies did not pay close attention to the difficult cases which can only be confirmed via CT imaging. In this study, we have developed and analyzed a state-of-the-art DL-based pipeline for wrist (distal radius) fracture detection -- DeepWrist, and evaluated it against one general population test set, and one challenging test set comprising only cases requiring confirmation by CT. Our results reveal that a typical state-of-the-art approach, such as DeepWrist, while having a near-perfect performance on the general independent test set, has a substantially lower performance on the challenging test set -- average precision of 0.99 (0.99-0.99) vs 0.64 (0.46-0.83), respectively. Similarly, the area under the ROC curve was of 0.99 (0.98-0.99) vs 0.84 (0.72-0.93), respectively. Our findings highlight the importance of a meticulous analysis of DL-based models before clinical use, and unearth the need for more challenging settings for testing medical AI systems.

The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosing infected patients. Medical imaging, such as X-ray and Computed Tomography (CT), combined with the potential of Artificial Intelligence (AI), plays an essential role in supporting medical personnel in the diagnosis process. Thus, in this article five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2 and DenseNet161) and their ensemble, using majority voting have been used to classify COVID-19, pneumoni{\ae} and healthy subjects using chest X-ray images. Multilabel classification was performed to predict multiple pathologies for each patient, if present. Firstly, the interpretability of each of the networks was thoroughly studied using local interpretability methods - occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT, and using a global technique - neuron activation profiles. The mean Micro-F1 score of the models for COVID-19 classifications ranges from 0.66 to 0.875, and is 0.89 for the ensemble of the network models. The qualitative results showed that the ResNets were the most interpretable models. This research demonstrates the importance of using interpretability methods to compare different models before making a decision regarding the best performing model.

Quality control is of vital importance during electronics production. As the methods of producing electronic circuits improve, there is an increasing chance of solder defects during assembling the printed circuit board (PCB). Many technologies have been incorporated for inspecting failed soldering, such as X-ray imaging, optical imaging, and thermal imaging. With some advanced algorithms, the new technologies are expected to control the production quality based on the digital images. However, current algorithms sometimes are not accurate enough to meet the quality control. Specialists are needed to do a follow-up checking. For automated X-ray inspection, joint of interest on the X-ray image is located by region of interest (ROI) and inspected by some algorithms. Some incorrect ROIs deteriorate the inspection algorithm. The high dimension of X-ray images and the varying sizes of image dimensions also challenge the inspection algorithms. On the other hand, recent advances on deep learning shed light on image-based tasks and are competitive to human levels. In this paper, deep learning is incorporated in X-ray imaging based quality control during PCB quality inspection. Two artificial intelligence (AI) based models are proposed and compared for joint defect detection. The noised ROI problem and the varying sizes of imaging dimension problem are addressed. The efficacy of the proposed methods are verified through experimenting on a real-world 3D X-ray dataset. By incorporating the proposed methods, specialist inspection workload is largely saved.

Capturing real world lighting is a long standing challenge in imaging and most practical methods acquire High Dynamic Range (HDR) images by either fusing multiple exposures, or boosting the dynamic range of Standard Dynamic Range (SDR) images. Multiple exposure capture is problematic as it requires longer capture times which can often lead to ghosting problems. The main alternative, inverse tone mapping is an ill-defined problem that is especially challenging as single captured exposures usually contain clipped and quantized values, and are therefore missing substantial amounts of content. To alleviate this, we propose a new approach, High Dynamic Range Thermal (HDRT), for HDR acquisition using a separate, commonly available, thermal infrared (IR) sensor. We propose a novel deep neural method (HDRTNet) which combines IR and SDR content to generate HDR images. HDRTNet learns to exploit IR features linked to the RGB image and the IR-specific parameters are subsequently used in a dual branch method that fuses features at shallow layers. This produces an HDR image that is significantly superior to that generated using naive fusion approaches. To validate our method, we have created the first HDR and thermal dataset, and performed extensive experiments comparing HDRTNet with the state-of-the-art. We show substantial quantitative and qualitative quality improvements on both over- and under-exposed images, showing that our approach is robust to capturing in multiple different lighting conditions.

In breast cancer imaging, there has been a trend to directly predict pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) from histological images based on deep learning (DL). However, it has been a commonly known problem that the constructed DL-based models numerically have better performances in internal validation than in external validation. The primary reason for this situation lies in that the distribution of the external data for validation is different from the distribution of the training data for the construction of the predictive model. In this paper, we aim to alleviate this situation with a more intrinsic approach. We propose an experts' cognition-driven ensemble deep learning (ECDEDL) approach for external validation of predicting pCR to NAC from histological images in breast cancer. The proposed ECDEDL, which takes the cognition of both pathology and artificial intelligence experts into consideration to improve the generalization of the predictive model to the external validation, more intrinsically approximates the working paradigm of a human being which will refer to his various working experiences to make decisions. The proposed ECDEDL approach was validated with 695 WSIs collected from the same center as the primary dataset to develop the predictive model and perform the internal validation, and 340 WSIs collected from other three centers as the external dataset to perform the external validation. In external validation, the proposed ECDEDL approach improves the AUCs of pCR prediction from 61.52(59.80-63.26) to 67.75(66.74-68.80) and the Accuracies of pCR prediction from 56.09(49.39-62.79) to 71.01(69.44-72.58). The proposed ECDEDL was quite effective for external validation, numerically more approximating the internal validation.

Point-spread-function (PSF) engineering is a powerful computational imaging techniques wherein a custom phase mask is integrated into an optical system to encode additional information into captured images. Used in combination with deep learning, such systems now offer state-of-the-art performance at monocular depth estimation, extended depth-of-field imaging, lensless imaging, and other tasks. Inspired by recent advances in spatial light modulator (SLM) technology, this paper answers a natural question: Can one encode additional information and achieve superior performance by changing a phase mask dynamically over time? We first prove that the set of PSFs described by static phase masks is non-convex and that, as a result, time-averaged PSFs generated by dynamic phase masks are fundamentally more expressive. We then demonstrate, in simulation, that time-averaged dynamic (TiDy) phase masks can offer substantially improved monocular depth estimation and extended depth-of-field imaging performance.

We report the results of deep H-alpha and [O III] images of the bright WN7/WC4 Wolf-Rayet star WR 8 (HD 62910). These data show considerably more surrounding nebulosity than seen in prior imaging. The brighter portions of the nebula span 6' in diameter and exhibit considerable fine-scale structure including numerous emission clumps and bright head-tail like features presumably due to the effects of the WR star's stellar winds. Due to the overlap of a relatively bright band of unrelated foreground diffuse interstellar H-alpha emission, WR 8's nebula is best viewed via its [O III] emission. A faint 9' x 13' diffuse outer nebulosity is detected surrounding the nebula's main ring of emission. The nebula's optical structure is substantially different from that of its thermal continuum dust emission seen in WISE 22 micron infrared images which show a smaller and sharply defined emission shell.

Merging multi-exposure images is a common approach for obtaining high dynamic range (HDR) images, with the primary challenge being the avoidance of ghosting artifacts in dynamic scenes. Recent methods have proposed using deep neural networks for deghosting. However, the methods typically rely on sufficient data with HDR ground-truths, which are difficult and costly to collect. In this work, to eliminate the need for labeled data, we propose SelfHDR, a self-supervised HDR reconstruction method that only requires dynamic multi-exposure images during training. Specifically, SelfHDR learns a reconstruction network under the supervision of two complementary components, which can be constructed from multi-exposure images and focus on HDR color as well as structure, respectively. The color component is estimated from aligned multi-exposure images, while the structure one is generated through a structure-focused network that is supervised by the color component and an input reference (\eg, medium-exposure) image. During testing, the learned reconstruction network is directly deployed to predict an HDR image. Experiments on real-world images demonstrate our SelfHDR achieves superior results against the state-of-the-art self-supervised methods, and comparable performance to supervised ones. Codes are available at https://github.com/cszhilu1998/SelfHDR

Fluorescence Lifetime Imaging (FLI) is a critical molecular imaging modality that provides unique information about the tissue microenvironment, which is invaluable for biomedical applications. FLI operates by acquiring and analyzing photon time-of-arrival histograms to extract quantitative parameters associated with temporal fluorescence decay. These histograms are influenced by the intrinsic properties of the fluorophore, instrument parameters, time-of-flight distributions associated with pixel-wise variations in the topographic and optical characteristics of the sample. Recent advancements in Deep Learning (DL) have enabled improved fluorescence lifetime parameter estimation. However, existing models are primarily designed for planar surface samples, limiting their applicability in translational scenarios involving complex surface profiles, such as in-vivo whole-animal or imaged guided surgical applications. To address this limitation, we present MFliNet (Macroscopic FLI Network), a novel DL architecture that integrates the Instrument Response Function (IRF) as an additional input alongside experimental photon time-of-arrival histograms. Leveraging the capabilities of a Differential Transformer encoder-decoder architecture, MFliNet effectively focuses on critical input features, such as variations in photon time-of-arrival distributions. We evaluate MFliNet using rigorously designed tissue-mimicking phantoms and preclinical in-vivo cancer xenograft models. Our results demonstrate the model's robustness and suitability for complex macroscopic FLI applications, offering new opportunities for advanced biomedical imaging in diverse and challenging settings.

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

The rapid advancement of deep learning has facilitated the automated processing of electron microscopy (EM) big data stacks. However, designing a framework that eliminates manual labeling and adapts to domain gaps remains challenging. Current research remains entangled in the dilemma of pursuing complete automation while still requiring simulations or slight manual annotations. Here we demonstrate tandem generative adversarial network (tGAN), a fully label-free and simulation-free pipeline capable of generating EM images for computer vision training. The tGAN can assimilate key features from new data stacks, thus producing a tailored virtual dataset for the training of automated EM analysis tools. Using segmenting nanoparticles for analyzing size distribution of supported catalysts as the demonstration, our findings showcased that the recognition accuracy of tGAN even exceeds the manually-labeling method by 5%. It can also be adaptively deployed to various data domains without further manual manipulation, which is verified by transfer learning from HAADF-STEM to BF-TEM. This generalizability may enable it to extend its application to a broader range of imaging characterizations, liberating microscopists and materials scientists from tedious dataset annotations.

We present the Next Generation Deep Extragalactic Exploratory Public (NGDEEP) Survey, a deep slitless spectroscopic and imaging Cycle 1 JWST treasury survey designed to constrain feedback mechanisms in low-mass galaxies across cosmic time. NGDEEP targets the Hubble Ultra Deep Field (HUDF) with NIRISS slitless spectroscopy (f~1.2e-18 erg/s/cm^2, 5sigma) to measure metallicities and star-formation rates (SFRs) for low-mass galaxies through the peak of the cosmic SFR density (0.5<z<4). In parallel, NGDEEP targets the HUDF-Par2 parallel field with NIRCam (m=30.6-30.9, 5sigma) to discover galaxies to z>12, constraining the slope of the faint-end of the rest-ultraviolet luminosity function. NGDEEP overlaps with the deepest HST ACS optical imaging in the sky: F435W in the HUDF (m=29.6), and F814W in HUDF-Par2 (m=30), making this a premier HST+JWST Deep Field. As a treasury survey, NGDEEP data is public immediately, and we will rapidly release data products and catalogs in the spirit of previous deep field initiatives. In this paper we present the NGDEEP survey design, summarize the science goals, and detail plans for the public release of NGDEEP reduced data products.

Although deep learning (DL) has received much attention in accelerated magnetic resonance imaging (MRI), recent studies show that tiny input perturbations may lead to instabilities of DL-based MRI reconstruction models. However, the approaches of robustifying these models are underdeveloped. Compared to image classification, it could be much more challenging to achieve a robust MRI image reconstruction network considering its regression-based learning objective, limited amount of training data, and lack of efficient robustness metrics. To circumvent the above limitations, our work revisits the problem of DL-based image reconstruction through the lens of robust machine learning. We find a new instability source of MRI image reconstruction, i.e., the lack of reconstruction robustness against spatial transformations of an input, e.g., rotation and cutout. Inspired by this new robustness metric, we develop a robustness-aware image reconstruction method that can defend against both pixel-wise adversarial perturbations as well as spatial transformations. Extensive experiments are also conducted to demonstrate the effectiveness of our proposed approaches.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between T_1 relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

Lung cancer stands as the preeminent cause of cancer-related mortality globally. Prompt and precise diagnosis, coupled with effective treatment, is imperative to reduce the fatality rates associated with this formidable disease. This study introduces a cutting-edge deep learning framework for the classification of lung cancer from CT scan imagery. The research encompasses a suite of image pre-processing strategies, notably Canny edge detection, and wavelet transformations, which precede the extraction of salient features and subsequent classification via a Multi-Layer Perceptron (MLP). The optimization process is further refined using the Dragonfly Algorithm (DA). The methodology put forth has attained an impressive training and testing accuracy of 99.82\%, underscoring its efficacy and reliability in the accurate diagnosis of lung cancer.

Advances in underwater imaging enable the collection of extensive seafloor image datasets that are necessary for monitoring important benthic ecosystems. The ability to collect seafloor imagery has outpaced our capacity to analyze it, hindering expedient mobilization of this crucial environmental information. Recent machine learning approaches provide opportunities to increase the efficiency with which seafloor image datasets are analyzed, yet large and consistent datasets necessary to support development of such approaches are scarce. Here we present BenthicNet: a global compilation of seafloor imagery designed to support the training and evaluation of large-scale image recognition models. An initial set of over 11.4 million images was collected and curated to represent a diversity of seafloor environments using a representative subset of 1.3 million images. These are accompanied by 2.6 million annotations translated to the CATAMI scheme, which span 190,000 of the images. A large deep learning model was trained on this compilation and preliminary results suggest it has utility for automating large and small-scale image analysis tasks. The compilation and model are made openly available for use by the scientific community at https://doi.org/10.20383/103.0614.

Breast cancer is a major cause of cancer death among women, emphasising the importance of early detection for improved treatment outcomes and quality of life. Mammography, the primary diagnostic imaging test, poses challenges due to the high variability and patterns in mammograms. Double reading of mammograms is recommended in many screening programs to improve diagnostic accuracy but increases radiologists' workload. Researchers explore Machine Learning models to support expert decision-making. Stand-alone models have shown comparable or superior performance to radiologists, but some studies note decreased sensitivity with multiple datasets, indicating the need for high generalisation and robustness models. This work devises MammoDG, a novel deep-learning framework for generalisable and reliable analysis of cross-domain multi-center mammography data. MammoDG leverages multi-view mammograms and a novel contrastive mechanism to enhance generalisation capabilities. Extensive validation demonstrates MammoDG's superiority, highlighting the critical importance of domain generalisation for trustworthy mammography analysis in imaging protocol variations.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Convolutional Neural Networks have demonstrated dermatologist-level performance in the classification of melanoma from skin lesion images, but prediction irregularities due to biases seen within the training data are an issue that should be addressed before widespread deployment is possible. In this work, we robustly remove bias and spurious variation from an automated melanoma classification pipeline using two leading bias unlearning techniques. We show that the biases introduced by surgical markings and rulers presented in previous studies can be reasonably mitigated using these bias removal methods. We also demonstrate the generalisation benefits of unlearning spurious variation relating to the imaging instrument used to capture lesion images. Our experimental results provide evidence that the effects of each of the aforementioned biases are notably reduced, with different debiasing techniques excelling at different tasks.

While deep learning technologies are now capable of generating realistic images confusing humans, the research efforts are turning to the synthesis of images for more concrete and application-specific purposes. Facial image generation based on vocal characteristics from speech is one of such important yet challenging tasks. It is the key enabler to influential use cases of image generation, especially for business in public security and entertainment. Existing solutions to the problem of speech2face renders limited image quality and fails to preserve facial similarity due to the lack of quality dataset for training and appropriate integration of vocal features. In this paper, we investigate these key technical challenges and propose Speech Fusion to Face, or SF2F in short, attempting to address the issue of facial image quality and the poor connection between vocal feature domain and modern image generation models. By adopting new strategies on data model and training, we demonstrate dramatic performance boost over state-of-the-art solution, by doubling the recall of individual identity, and lifting the quality score from 15 to 19 based on the mutual information score with VGGFace classifier.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 1600 high-resolution OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.

The retina is the only part of the human body in which blood vessels can be accessed non-invasively using imaging techniques such as digital fundus images (DFI). The spatial distribution of the retinal microvasculature may change with cardiovascular diseases and thus the eyes may be regarded as a window to our hearts. Computerized segmentation of the retinal arterioles and venules (A/V) is essential for automated microvasculature analysis. Using active learning, we created a new DFI dataset containing 240 crowd-sourced manual A/V segmentations performed by fifteen medical students and reviewed by an ophthalmologist, and developed LUNet, a novel deep learning architecture for high resolution A/V segmentation. LUNet architecture includes a double dilated convolutional block that aims to enhance the receptive field of the model and reduce its parameter count. Furthermore, LUNet has a long tail that operates at high resolution to refine the segmentation. The custom loss function emphasizes the continuity of the blood vessels. LUNet is shown to significantly outperform two state-of-the-art segmentation algorithms on the local test set as well as on four external test sets simulating distribution shifts across ethnicity, comorbidities, and annotators. We make the newly created dataset open access (upon publication).

Insect-pests significantly impact global agricultural productivity and quality. Effective management involves identifying the full insect community, including beneficial insects and harmful pests, to develop and implement integrated pest management strategies. Automated identification of insects under real-world conditions presents several challenges, including differentiating similar-looking species, intra-species dissimilarity and inter-species similarity, several life cycle stages, camouflage, diverse imaging conditions, and variability in insect orientation. A deep-learning model, InsectNet, is proposed to address these challenges. InsectNet is endowed with five key features: (a) utilization of a large dataset of insect images collected through citizen science; (b) label-free self-supervised learning for large models; (c) improving prediction accuracy for species with a small sample size; (d) enhancing model trustworthiness; and (e) democratizing access through streamlined MLOps. This approach allows accurate identification (>96% accuracy) of over 2500 insect species, including pollinator (e.g., butterflies, bees), parasitoid (e.g., some wasps and flies), predator species (e.g., lady beetles, mantises, dragonflies) and harmful pest species (e.g., armyworms, cutworms, grasshoppers, stink bugs). InsectNet can identify invasive species, provide fine-grained insect species identification, and work effectively in challenging backgrounds. It also can abstain from making predictions when uncertain, facilitating seamless human intervention and making it a practical and trustworthy tool. InsectNet can guide citizen science data collection, especially for invasive species where early detection is crucial. Similar approaches may transform other agricultural challenges like disease detection and underscore the importance of data collection, particularly through citizen science efforts..

Inpainting has recently been proposed as a successful deep learning technique for unsupervised medical image model discovery. The masks used for inpainting are generally independent of the dataset and are not tailored to perform on different given classes of anatomy. In this work, we introduce a method for generating shape-aware masks for inpainting, which aims at learning the statistical shape prior. We hypothesize that although the variation of masks improves the generalizability of inpainting models, the shape of the masks should follow the topology of the organs of interest. Hence, we propose an unsupervised guided masking approach based on an off-the-shelf inpainting model and a superpixel over-segmentation algorithm to generate a wide range of shape-dependent masks. Experimental results on abdominal MR image reconstruction show the superiority of our proposed masking method over standard methods using square-shaped or dataset of irregular shape masks.

With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse solvers, the throughput of QPM is currently limited by the speed of electronic hardware. Complementarily, to improve throughput further, here we propose to acquire images in a compressed form such that more information can be transferred beyond the existing electronic hardware bottleneck. To this end, we present a learnable optical compression-decompression framework that learns content-specific features. The proposed differentiable quantitative phase microscopy (partial mu) first uses learnable optical feature extractors as image compressors. The intensity representation produced by these networks is then captured by the imaging sensor. Finally, a reconstruction network running on electronic hardware decompresses the QPM images. In numerical experiments, the proposed system achieves compression of times 64 while maintaining the SSIM of sim 0.90 and PSNR of sim 30 dB on cells. The results demonstrated by our experiments open up a new pathway for achieving end-to-end optimized (i.e., optics and electronic) compact QPM systems that may provide unprecedented throughput improvements.

Accurate prediction of knee osteoarthritis (KOA) progression from structural MRI has a potential to enhance disease understanding and support clinical trials. Prior art focused on manually designed imaging biomarkers, which may not fully exploit all disease-related information present in MRI scan. In contrast, our method learns relevant representations from raw data end-to-end using Deep Learning, and uses them for progression prediction. The method employs a 2D CNN to process the data slice-wise and aggregate the extracted features using a Transformer. Evaluated on a large cohort (n=4,866), the proposed method outperforms conventional 2D and 3D CNN-based models and achieves average precision of 0.58pm0.03 and ROC AUC of 0.78pm0.01. This paper sets a baseline on end-to-end KOA progression prediction from structural MRI. Our code is publicly available at https://github.com/MIPT-Oulu/OAProgressionMR.

Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible for live-cell imaging. However, the reconstruction of SIM images is often slow and prone to artefacts. Here we propose a versatile reconstruction method, ML-SIM, which makes use of machine learning. The model is an end-to-end deep residual neural network that is trained on a simulated data set to be free of common SIM artefacts. ML-SIM is thus robust to noise and irregularities in the illumination patterns of the raw SIM input frames. The reconstruction method is widely applicable and does not require the acquisition of experimental training data. Since the training data are generated from simulations of the SIM process on images from generic libraries the method can be efficiently adapted to specific experimental SIM implementations. The reconstruction quality enabled by our method is compared with traditional SIM reconstruction methods, and we demonstrate advantages in terms of noise, reconstruction fidelity and contrast for both simulated and experimental inputs. In addition, reconstruction of one SIM frame typically only takes ~100ms to perform on PCs with modern Nvidia graphics cards, making the technique compatible with real-time imaging. The full implementation and the trained networks are available at http://ML-SIM.com.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Purpose: This study aims to explore training strategies to improve convolutional neural network-based image-to-image deformable registration for abdominal imaging. Methods: Different training strategies, loss functions, and transfer learning schemes were considered. Furthermore, an augmentation layer which generates artificial training image pairs on-the-fly was proposed, in addition to a loss layer that enables dynamic loss weighting. Results: Guiding registration using segmentations in the training step proved beneficial for deep-learning-based image registration. Finetuning the pretrained model from the brain MRI dataset to the abdominal CT dataset further improved performance on the latter application, removing the need for a large dataset to yield satisfactory performance. Dynamic loss weighting also marginally improved performance, all without impacting inference runtime. Conclusion: Using simple concepts, we improved the performance of a commonly used deep image registration architecture, VoxelMorph. In future work, our framework, DDMR, should be validated on different datasets to further assess its value.

The detection and removal of landmines is a complex and risky task that requires advanced remote sensing techniques to reduce the risk for the professionals involved in this task. In this paper, we propose a novel synthetic dataset for buried landmine detection to provide researchers with a valuable resource to observe, measure, locate, and address issues in landmine detection. The dataset consists of 41,800 microwave holographic images (2D) and their holographic inverted scans (3D) of different types of buried objects, including landmines, clutter, and pottery objects, and is collected by means of a microwave holography sensor. We evaluate the performance of several state-of-the-art deep learning models trained on our synthetic dataset for various classification tasks. While the results do not yield yet high performances, showing the difficulty of the proposed task, we believe that our dataset has significant potential to drive progress in the field of landmine detection thanks to the accuracy and resolution obtainable using holographic radars. To the best of our knowledge, our dataset is the first of its kind and will help drive further research on computer vision methods to automatize mine detection, with the overall goal of reducing the risks and the costs of the demining process.

Atrial fibrillation (AFib) is the prominent cardiac arrhythmia in the world. It affects mostly the elderly population, with potential consequences such as stroke and heart failure in the absence of necessary treatments as soon as possible. The importance of atrial scarring in the development and progression of AFib has gained recognition, positioning late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) as a crucial technique for the non-invasive evaluation of atrial scar tissue. This review delves into the recent progress in segmenting atrial scars using LGE-MRIs, emphasizing the importance of precise scar measurement in the treatment and management of AFib. Initially, it provides a detailed examination of AFib. Subsequently, it explores the application of deep learning in this domain. The review culminates in a discussion of the latest research advancements in atrial scar segmentation using deep learning methods. By offering a thorough analysis of current technologies and their impact on AFib management strategies, this review highlights the integral role of deep learning in enhancing atrial scar segmentation and its implications for future therapeutic approaches.

We present detailed morphology measurements for 8.67 million galaxies in the DESI Legacy Imaging Surveys (DECaLS, MzLS, and BASS, plus DES). These are automated measurements made by deep learning models trained on Galaxy Zoo volunteer votes. Our models typically predict the fraction of volunteers selecting each answer to within 5-10\% for every answer to every GZ question. The models are trained on newly-collected votes for DESI-LS DR8 images as well as historical votes from GZ DECaLS. We also release the newly-collected votes. Extending our morphology measurements outside of the previously-released DECaLS/SDSS intersection increases our sky coverage by a factor of 4 (5,000 to 19,000 deg^2) and allows for full overlap with complementary surveys including ALFALFA and MaNGA.

Digital agriculture has evolved significantly over the last few years due to the technological developments in automation and computational intelligence applied to the agricultural sector, including vineyards which are a relevant crop in the Mediterranean region. In this work, a study is presented of semantic segmentation for vine detection in real-world vineyards by exploring state-of-the-art deep segmentation networks and conventional unsupervised methods. Camera data have been collected on vineyards using an Unmanned Aerial System (UAS) equipped with a dual imaging sensor payload, namely a high-definition RGB camera and a five-band multispectral and thermal camera. Extensive experiments using deep-segmentation networks and unsupervised methods have been performed on multimodal datasets representing four distinct vineyards located in the central region of Portugal. The reported results indicate that SegNet, U-Net, and ModSegNet have equivalent overall performance in vine segmentation. The results also show that multimodality slightly improves the performance of vine segmentation, but the NIR spectrum alone generally is sufficient on most of the datasets. Furthermore, results suggest that high-definition RGB images produce equivalent or higher performance than any lower resolution multispectral band combination. Lastly, Deep Learning (DL) networks have higher overall performance than classical methods. The code and dataset are publicly available at https://github.com/Cybonic/DL_vineyard_segmentation_study.git

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

Large-scale medical imaging datasets have accelerated development of artificial intelligence tools for clinical decision support. However, the large size of these datasets is a bottleneck for users with limited storage and bandwidth. Many users may not even require such large datasets as AI models are often trained on lower resolution images. If users could directly download at their desired resolution, storage and bandwidth requirements would significantly decrease. However, it is impossible to anticipate every users' requirements and impractical to store the data at multiple resolutions. What if we could store images at a single resolution but send them at different ones? We propose MIST, an open-source framework to operationalize progressive resolution for streaming medical images at multiple resolutions from a single high-resolution copy. We demonstrate that MIST can dramatically reduce imaging infrastructure inefficiencies for hosting and streaming medical images by >90%, while maintaining diagnostic quality for deep learning applications.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

With recent advances in computing hardware and surges of deep-learning architectures, learning-based deep image registration methods have surpassed their traditional counterparts, in terms of metric performance and inference time. However, these methods focus on improving performance measurements such as Dice, resulting in less attention given to model behaviors that are equally desirable for registrations, especially for medical imaging. This paper investigates these behaviors for popular learning-based deep registrations under a sanity-checking microscope. We find that most existing registrations suffer from low inverse consistency and nondiscrimination of identical pairs due to overly optimized image similarities. To rectify these behaviors, we propose a novel regularization-based sanity-enforcer method that imposes two sanity checks on the deep model to reduce its inverse consistency errors and increase its discriminative power simultaneously. Moreover, we derive a set of theoretical guarantees for our sanity-checked image registration method, with experimental results supporting our theoretical findings and their effectiveness in increasing the sanity of models without sacrificing any performance. Our code and models are available at https://github.com/tuffr5/Saner-deep-registration.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Deep learning expresses a category of machine learning algorithms that have the capability to combine raw inputs into intermediate features layers. These deep learning algorithms have demonstrated great results in different fields. Deep learning has particularly witnessed for a great achievement of human level performance across a number of domains in computer vision and pattern recognition. For the achievement of state-of-the-art performances in diverse domains, the deep learning used different architectures and these architectures used activation functions to perform various computations between hidden and output layers of any architecture. This paper presents a survey on the existing studies of deep learning in handwriting recognition field. Even though the recent progress indicates that the deep learning methods has provided valuable means for speeding up or proving accurate results in handwriting recognition, but following from the extensive literature survey, the present study finds that the deep learning has yet to revolutionize more and has to resolve many of the most pressing challenges in this field, but promising advances have been made on the prior state of the art. Additionally, an inadequate availability of labelled data to train presents problems in this domain. Nevertheless, the present handwriting recognition survey foresees deep learning enabling changes at both bench and bedside with the potential to transform several domains as image processing, speech recognition, computer vision, machine translation, robotics and control, medical imaging, medical information processing, bio-informatics, natural language processing, cyber security, and many others.

Near-field multiple-input multiple-output (MIMO) radar imaging systems have recently gained significant attention. In this paper, we develop novel non-iterative deep learning-based reconstruction methods for real-time near-field MIMO imaging. The goal is to achieve high image quality with low computational cost at compressive settings. The developed approaches have two stages. In the first approach, physics-based initial stage performs adjoint operation to back-project the measurements to the image-space, and deep neural network (DNN)-based second stage converts the 3D backprojected measurements to a magnitude-only reflectivity image. Since scene reflectivities often have random phase, DNN processes directly the magnitude of the adjoint result. As DNN, 3D U-Net is used to jointly exploit range and cross-range correlations. To comparatively evaluate the significance of exploiting physics in a learning-based approach, two additional approaches that replace the physics-based first stage with fully connected layers are also developed as purely learning-based methods. The performance is also analyzed by changing the DNN architecture for the second stage to include complex-valued processing (instead of magnitude-only processing), 2D convolution kernels (instead of 3D), and ResNet architecture (instead of U-Net). Moreover, we develop a synthesizer to generate large-scale dataset for training with 3D extended targets. We illustrate the performance through experimental data and extensive simulations. The results show the effectiveness of the developed physics-based learned reconstruction approach in terms of both run-time and image quality at highly compressive settings. Our source codes and dataset are made available at GitHub.

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

We consider the problem of video snapshot compressive imaging (SCI), where sequential high-speed frames are modulated by different masks and captured by a single measurement. The underlying principle of reconstructing multi-frame images from only one single measurement is to solve an ill-posed problem. By combining optimization algorithms and neural networks, deep unfolding networks (DUNs) score tremendous achievements in solving inverse problems. In this paper, our proposed model is under the DUN framework and we propose a 3D Convolution-Transformer Mixture (CTM) module with a 3D efficient and scalable attention model plugged in, which helps fully learn the correlation between temporal and spatial dimensions by virtue of Transformer. To our best knowledge, this is the first time that Transformer is employed to video SCI reconstruction. Besides, to further investigate the high-frequency information during the reconstruction process which are neglected in previous studies, we introduce variance estimation characterizing the uncertainty on a pixel-by-pixel basis. Extensive experimental results demonstrate that our proposed method achieves state-of-the-art (SOTA) (with a 1.2dB gain in PSNR over previous SOTA algorithm) results. We will release the code.

Speckle fluctuations seriously limit the interpretability of synthetic aperture radar (SAR) images. Speckle reduction has thus been the subject of numerous works spanning at least four decades. Techniques based on deep neural networks have recently achieved a new level of performance in terms of SAR image restoration quality. Beyond the design of suitable network architectures or the selection of adequate loss functions, the construction of training sets is of uttermost importance. So far, most approaches have considered a supervised training strategy: the networks are trained to produce outputs as close as possible to speckle-free reference images. Speckle-free images are generally not available, which requires resorting to natural or optical images or the selection of stable areas in long time series to circumvent the lack of ground truth. Self-supervision, on the other hand, avoids the use of speckle-free images. We introduce a self-supervised strategy based on the separation of the real and imaginary parts of single-look complex SAR images, called MERLIN (coMplex sElf-supeRvised despeckLINg), and show that it offers a straightforward way to train all kinds of deep despeckling networks. Networks trained with MERLIN take into account the spatial correlations due to the SAR transfer function specific to a given sensor and imaging mode. By requiring only a single image, and possibly exploiting large archives, MERLIN opens the door to hassle-free as well as large-scale training of despeckling networks. The code of the trained models is made freely available at https://gitlab.telecom-paris.fr/RING/MERLIN.

Multiplex immunofluorescence and immunohistochemistry benefit patients by allowing cancer pathologists to identify several proteins expressed on the surface of cells, enabling cell classification, better understanding of the tumour micro-environment, more accurate diagnoses, prognoses, and tailored immunotherapy based on the immune status of individual patients. However, they are expensive and time consuming processes which require complex staining and imaging techniques by expert technicians. Hoechst staining is much cheaper and easier to perform, but is not typically used in this case as it binds to DNA rather than to the proteins targeted by immunofluorescent techniques, and it was not previously thought possible to differentiate cells expressing these proteins based only on DNA morphology. In this work we show otherwise, training a deep convolutional neural network to identify cells expressing three proteins (T lymphocyte markers CD3 and CD8, and the B lymphocyte marker CD20) with greater than 90% precision and recall, from Hoechst 33342 stained tissue only. Our model learns previously unknown morphological features associated with expression of these proteins which can be used to accurately differentiate lymphocyte subtypes for use in key prognostic metrics such as assessment of immune cell infiltration,and thereby predict and improve patient outcomes without the need for costly multiplex immunofluorescence.

This work investigates the production of high-resolution images of typical support elements in concrete structures by means of the muon tomography (muography). By exploiting detailed Monte Carlo radiation-matter simulations, we demonstrate the feasibility of the reconstruction of 1 cm--thick iron tubes inside 30 cm--deep concrete blocks, regarded as an important testbed within the structural diagnostics community. In addition, we present a new method for integrating simulated data with advanced deep learning techniques in order to improve the muon imaging of concrete structures. Through deep learning enhancement techniques, this results into a dramatic improvement of the image quality, as well as into a significant reduction of the data acquisition time, which are two critical limitations within the usual practice of muography for civil engineering diagnostics.

Self-supervised pre-training of deep learning models with contrastive learning is a widely used technique in image analysis. Current findings indicate a strong potential for contrastive pre-training on medical images. However, further research is necessary to incorporate the particular characteristics of these images. We hypothesize that the similarity of medical images hinders the success of contrastive learning in the medical imaging domain. To this end, we investigate different strategies based on deep embedding, information theory, and hashing in order to identify and reduce redundancy in medical pre-training datasets. The effect of these different reduction strategies on contrastive learning is evaluated on two pre-training datasets and several downstream classification tasks. In all of our experiments, dataset reduction leads to a considerable performance gain in downstream tasks, e.g., an AUC score improvement from 0.78 to 0.83 for the COVID CT Classification Grand Challenge, 0.97 to 0.98 for the OrganSMNIST Classification Challenge and 0.73 to 0.83 for a brain hemorrhage classification task. Furthermore, pre-training is up to nine times faster due to the dataset reduction. In conclusion, the proposed approach highlights the importance of dataset quality and provides a transferable approach to improve contrastive pre-training for classification downstream tasks on medical images.

Chest X-rays (CXR) are the most common medical imaging study and are used to diagnose multiple medical conditions. This study examines the impact of synthetic data supplementation, using diffusion models, on the performance of deep learning (DL) classifiers for CXR analysis. We employed three datasets: CheXpert, MIMIC-CXR, and Emory Chest X-ray, training conditional denoising diffusion probabilistic models (DDPMs) to generate synthetic frontal radiographs. Our approach ensured that synthetic images mirrored the demographic and pathological traits of the original data. Evaluating the classifiers' performance on internal and external datasets revealed that synthetic data supplementation enhances model accuracy, particularly in detecting less prevalent pathologies. Furthermore, models trained on synthetic data alone approached the performance of those trained on real data. This suggests that synthetic data can potentially compensate for real data shortages in training robust DL models. However, despite promising outcomes, the superiority of real data persists.

PURPOSE: Subarachnoid hemorrhage (SAH) entails high morbidity and mortality rates. Convolutional neural networks (CNN), a form of deep learning, are capable of generating highly accurate predictions from imaging data. Our objective was to predict mortality in SAH patients by processing the initial CT scan on a CNN based algorithm. METHODS: Retrospective multicentric study of a consecutive cohort of patients with SAH between 2011-2022. Demographic, clinical and radiological variables were analyzed. Pre-processed baseline CT scan images were used as the input for training a CNN using AUCMEDI Framework. Our model's architecture leverages the DenseNet-121 structure, employing transfer learning principles. The output variable was mortality in the first three months. Performance of the model was evaluated by statistical parameters conventionally used in studies involving artificial intelligence methods. RESULTS: Images from 219 patients were processed, 175 for training and validation of the CNN and 44 for its evaluation. 52%(115/219) of patients were female, and the median age was 58(SD=13.06) years. 18.5%(39/219) were idiopathic SAH. Mortality rate was 28.5%(63/219). The model showed good accuracy at predicting mortality in SAH patients exclusively using the images of the initial CT scan (Accuracy=74%, F1=75% and AUC=82%). CONCLUSION: Modern image processing techniques based on AI and CNN make possible to predict mortality in SAH patients with high accuracy using CT scan images as the only input. These models might be optimized by including more data and patients resulting in better training, development and performance on tasks which are beyond the skills of conventional clinical knowledge.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Breast density estimation is one of the key tasks in recognizing individuals predisposed to breast cancer. It is often challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Most of the time, the breast density is estimated manually where a radiologist assigns one of the four density categories decided by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts in the direction of automating a breast density classification pipeline. Breast density estimation is one of the key tasks performed during a screening exam. Dense breasts are more susceptible to breast cancer. The density estimation is challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Traditional mammograms are being replaced by tomosynthesis and its other low radiation dose variants (for example Hologic' Intelligent 2D and C-View). Because of the low-dose requirement, increasingly more screening centers are favoring the Intelligent 2D view and C-View. Deep-learning studies for breast density estimation use only a single modality for training a neural network. However, doing so restricts the number of images in the dataset. In this paper, we show that a neural network trained on all the modalities at once performs better than a neural network trained on any single modality. We discuss these results using the area under the receiver operator characteristics curves.

Deep learning has demonstrated tremendous success in variety of application domains in the past few years. This new field of machine learning has been growing rapidly and applied in most of the application domains with some new modalities of applications, which helps to open new opportunity. There are different methods have been proposed on different category of learning approaches, which includes supervised, semi-supervised and un-supervised learning. The experimental results show state-of-the-art performance of deep learning over traditional machine learning approaches in the field of Image Processing, Computer Vision, Speech Recognition, Machine Translation, Art, Medical imaging, Medical information processing, Robotics and control, Bio-informatics, Natural Language Processing (NLP), Cyber security, and many more. This report presents a brief survey on development of DL approaches, including Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) including Long Short Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). In addition, we have included recent development of proposed advanced variant DL techniques based on the mentioned DL approaches. Furthermore, DL approaches have explored and evaluated in different application domains are also included in this survey. We have also comprised recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys have published on Deep Learning in Neural Networks [1, 38] and a survey on RL [234]. However, those papers have not discussed the individual advanced techniques for training large scale deep learning models and the recently developed method of generative models [1].

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r=23.6 vs. r=22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314,000 galaxies. 140,000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314,000 galaxies. When measured against confident volunteer classifications, the networks are approximately 99% accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

In this paper, for the first time, we propose an evaluation method for deep learning models that assesses the performance of a model not only in an unseen test scenario, but also in extreme cases of noise, outliers and ambiguous input data. To this end, we utilize adversarial examples, images that fool machine learning models, while looking imperceptibly different from original data, as a measure to evaluate the robustness of a variety of medical imaging models. Through extensive experiments on skin lesion classification and whole brain segmentation with state-of-the-art networks such as Inception and UNet, we show that models that achieve comparable performance regarding generalizability may have significant variations in their perception of the underlying data manifold, leading to an extensive performance gap in their robustness.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

Deep learning methods have shown outstanding classification accuracy in medical imaging problems, which is largely attributed to the availability of large-scale datasets manually annotated with clean labels. However, given the high cost of such manual annotation, new medical imaging classification problems may need to rely on machine-generated noisy labels extracted from radiology reports. Indeed, many Chest X-ray (CXR) classifiers have already been modelled from datasets with noisy labels, but their training procedure is in general not robust to noisy-label samples, leading to sub-optimal models. Furthermore, CXR datasets are mostly multi-label, so current noisy-label learning methods designed for multi-class problems cannot be easily adapted. In this paper, we propose a new method designed for the noisy multi-label CXR learning, which detects and smoothly re-labels samples from the dataset, which is then used to train common multi-label classifiers. The proposed method optimises a bag of multi-label descriptors (BoMD) to promote their similarity with the semantic descriptors produced by BERT models from the multi-label image annotation. Our experiments on diverse noisy multi-label training sets and clean testing sets show that our model has state-of-the-art accuracy and robustness in many CXR multi-label classification benchmarks.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Deep neural networks (DNNs) offer significant promise for improving breast cancer diagnosis in medical imaging. However, these models are highly susceptible to adversarial attacks--small, imperceptible changes that can mislead classifiers--raising critical concerns about their reliability and security. Traditional attacks rely on fixed-norm perturbations, misaligning with human perception. In contrast, diffusion-based attacks require pre-trained models, demanding substantial data when these models are unavailable, limiting practical use in data-scarce scenarios. In medical imaging, however, this is often unfeasible due to the limited availability of datasets. Building on recent advancements in learnable prompts, we propose Prompt2Perturb (P2P), a novel language-guided attack method capable of generating meaningful attack examples driven by text instructions. During the prompt learning phase, our approach leverages learnable prompts within the text encoder to create subtle, yet impactful, perturbations that remain imperceptible while guiding the model towards targeted outcomes. In contrast to current prompt learning-based approaches, our P2P stands out by directly updating text embeddings, avoiding the need for retraining diffusion models. Further, we leverage the finding that optimizing only the early reverse diffusion steps boosts efficiency while ensuring that the generated adversarial examples incorporate subtle noise, thus preserving ultrasound image quality without introducing noticeable artifacts. We show that our method outperforms state-of-the-art attack techniques across three breast ultrasound datasets in FID and LPIPS. Moreover, the generated images are both more natural in appearance and more effective compared to existing adversarial attacks. Our code will be publicly available https://github.com/yasamin-med/P2P.

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

Multiparametric magnetic resonance imaging (mpMRI) has demonstrated promising results in prostate cancer (PCa) detection using deep convolutional neural networks (CNNs). Recently, transformers have achieved competitive performance compared to CNNs in computer vision. Large-scale transformers need abundant annotated data for training, which are difficult to obtain in medical imaging. Self-supervised learning can effectively leverage unlabeled data to extract useful semantic representations without annotation and its associated costs. This can improve model performance on downstream tasks with limited labelled data and increase generalizability. We introduce a novel end-to-end Cross-Shaped windows (CSwin) transformer UNet model, CSwin UNet, to detect clinically significant prostate cancer (csPCa) in prostate bi-parametric MR imaging (bpMRI) and demonstrate the effectiveness of our proposed self-supervised pre-training framework. Using a large prostate bpMRI dataset with 1500 patients, we first pre-train CSwin transformer using multi-task self-supervised learning to improve data-efficiency and network generalizability. We then finetuned using lesion annotations to perform csPCa detection. Five-fold cross validation shows that self-supervised CSwin UNet achieves 0.888 AUC and 0.545 Average Precision (AP), significantly outperforming four state-of-the-art models (Swin UNETR, DynUNet, Attention UNet, UNet). Using a separate bpMRI dataset with 158 patients, we evaluated our model robustness to external hold-out data. Self-supervised CSwin UNet achieves 0.79 AUC and 0.45 AP, still outperforming all other comparable methods and demonstrating generalization to a dataset shift.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Explainable Deep Learning has gained significant attention in the field of artificial intelligence (AI), particularly in domains such as medical imaging, where accurate and interpretable machine learning models are crucial for effective diagnosis and treatment planning. Grad-CAM is a baseline that highlights the most critical regions of an image used in a deep learning model's decision-making process, increasing interpretability and trust in the results. It is applied in many computer vision (CV) tasks such as classification and explanation. This study explores the principles of Explainable Deep Learning and its relevance to medical imaging, discusses various explainability techniques and their limitations, and examines medical imaging applications of Grad-CAM. The findings highlight the potential of Explainable Deep Learning and Grad-CAM in improving the accuracy and interpretability of deep learning models in medical imaging. The code is available in (will be available).

Despite the ever-increasing interest in applying deep learning (DL) models to medical imaging, the typical scarcity and imbalance of medical datasets can severely impact the performance of DL models. The generation of synthetic data that might be freely shared without compromising patient privacy is a well-known technique for addressing these difficulties. Inpainting algorithms are a subset of DL generative models that can alter one or more regions of an input image while matching its surrounding context and, in certain cases, non-imaging input conditions. Although the majority of inpainting techniques for medical imaging data use generative adversarial networks (GANs), the performance of these algorithms is frequently suboptimal due to their limited output variety, a problem that is already well-known for GANs. Denoising diffusion probabilistic models (DDPMs) are a recently introduced family of generative networks that can generate results of comparable quality to GANs, but with diverse outputs. In this paper, we describe a DDPM to execute multiple inpainting tasks on 2D axial slices of brain MRI with various sequences, and present proof-of-concept examples of its performance in a variety of evaluation scenarios. Our model and a public online interface to try our tool are available at: https://github.com/Mayo-Radiology-Informatics-Lab/MBTI

The rise of deep learning has marked significant progress in fields such as computer vision, natural language processing, and medical imaging, primarily through the adaptation of pre-trained models for specific tasks. Traditional fine-tuning methods, involving adjustments to all parameters, face challenges due to high computational and memory demands. This has led to the development of Parameter Efficient Fine-Tuning (PEFT) techniques, which selectively update parameters to balance computational efficiency with performance. This review examines PEFT approaches, offering a detailed comparison of various strategies highlighting applications across different domains, including text generation, medical imaging, protein modeling, and speech synthesis. By assessing the effectiveness of PEFT methods in reducing computational load, speeding up training, and lowering memory usage, this paper contributes to making deep learning more accessible and adaptable, facilitating its wider application and encouraging innovation in model optimization. Ultimately, the paper aims to contribute towards insights into PEFT's evolving landscape, guiding researchers and practitioners in overcoming the limitations of conventional fine-tuning approaches.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

The Superpressure Balloon-borne Imaging Telescope (SuperBIT) is a diffraction-limited, wide-field, 0.5 m, near-infrared to near-ultraviolet observatory designed to exploit the stratosphere's space-like conditions. SuperBIT's 2023 science flight will deliver deep, blue imaging of galaxy clusters for gravitational lensing analysis. In preparation, we have developed a weak lensing measurement pipeline with modern algorithms for PSF characterization, shape measurement, and shear calibration. We validate our pipeline and forecast SuperBIT survey properties with simulated galaxy cluster observations in SuperBIT's near-UV and blue bandpasses. We predict imaging depth, galaxy number (source) density, and redshift distribution for observations in SuperBIT's three bluest filters; the effect of lensing sample selections is also considered. We find that in three hours of on-sky integration, SuperBIT can attain a depth of b = 26 mag and a total source density exceeding 40 galaxies per square arcminute. Even with the application of lensing-analysis catalog selections, we find b-band source densities between 25 and 30 galaxies per square arcminute with a median redshift of z = 1.1. Our analysis confirms SuperBIT's capability for weak gravitational lensing measurements in the blue.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

We use deep, mu_{r} lesssim 28,mag,arcsec^{-2}, r-band imaging from the Dark Energy Camera Legacy Survey (DECaLS) to search for past, or ongoing, merger activity in a sample of 282 Low Excitation Radio Galaxies (LERGs) at z<0.07. Our principle aim is to assess the the role of mergers in the evolution of LERGs. Exploiting the imaging depth, we classify tidal remnants around galaxies as both minor and major morphological disturbances for our LERG sample and 1,622 control galaxies matched in redshift, stellar mass, and environment. In groups and in the field, the LERG minor merger fraction is consistent with the control population. In galaxy clusters, 8.8 pm 2.9, % of LERGs show evidence of recent minor mergers in contrast to 23.0pm 2.0, % of controls. This sim 4 sigma deficit of minor mergers in cluster LERGs suggests these events may inhibit this type of nuclear activity for galaxies within the cluster environment. We observe a > 4sigma excess of major mergers in the LERGs with M_{*} lesssim 10^{11},M_{odot}, with 10 pm 1.5, % of these AGN involved in such large-scale interactions compared to 3.2 pm 0.4,% of control galaxies. This excess of major mergers in LERGs decreases with increasing stellar mass, vanishing by M_{*} > 10^{11.3},M_{odot}. These observations show that minor mergers do not fuel LERGs, and are consistent with typical LERGs being powered by accretion of matter from their halo. Where LERGs are associated with major mergers, these objects may evolve into more efficiently accreting active galactic nuclei as the merger progresses and more gas falls on to the central engine.

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Giant Star-forming Clumps (GSFCs) are areas of intensive star-formation that are commonly observed in high-redshift (z>1) galaxies but their formation and role in galaxy evolution remain unclear. High-resolution observations of low-redshift clumpy galaxy analogues are rare and restricted to a limited set of galaxies but the increasing availability of wide-field galaxy survey data makes the detection of large clumpy galaxy samples increasingly feasible. Deep Learning, and in particular CNNs, have been successfully applied to image classification tasks in astrophysical data analysis. However, one application of DL that remains relatively unexplored is that of automatically identifying and localising specific objects or features in astrophysical imaging data. In this paper we demonstrate the feasibility of using Deep learning-based object detection models to localise GSFCs in astrophysical imaging data. We apply the Faster R-CNN object detection framework (FRCNN) to identify GSFCs in low redshift (z<0.3) galaxies. Unlike other studies, we train different FRCNN models not on simulated images with known labels but on real observational data that was collected by the Sloan Digital Sky Survey Legacy Survey and labelled by volunteers from the citizen science project `Galaxy Zoo: Clump Scout'. The FRCNN model relies on a CNN component as a `backbone' feature extractor. We show that CNNs, that have been pre-trained for image classification using astrophysical images, outperform those that have been pre-trained on terrestrial images. In particular, we compare a domain-specific CNN -`Zoobot' - with a generic classification backbone and find that Zoobot achieves higher detection performance and also requires smaller training data sets to do so. Our final model is capable of producing GSFC detections with a completeness and purity of >=0.8 while only being trained on ~5,000 galaxy images.

Three-dimensional microscopy is often limited by anisotropic spatial resolution, resulting in lower axial resolution than lateral resolution. Current State-of-The-Art (SoTA) isotropic reconstruction methods utilizing deep neural networks can achieve impressive super-resolution performance in fixed imaging settings. However, their generality in practical use is limited by degraded performance caused by artifacts and blurring when facing unseen anisotropic factors. To address these issues, we propose DiffuseIR, an unsupervised method for isotropic reconstruction based on diffusion models. First, we pre-train a diffusion model to learn the structural distribution of biological tissue from lateral microscopic images, resulting in generating naturally high-resolution images. Then we use low-axial-resolution microscopy images to condition the generation process of the diffusion model and generate high-axial-resolution reconstruction results. Since the diffusion model learns the universal structural distribution of biological tissues, which is independent of the axial resolution, DiffuseIR can reconstruct authentic images with unseen low-axial resolutions into a high-axial resolution without requiring re-training. The proposed DiffuseIR achieves SoTA performance in experiments on EM data and can even compete with supervised methods.

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

In recent years, the integration of advanced imaging techniques and deep learning methods has significantly advanced computer-aided diagnosis (CAD) systems for breast cancer detection and classification. Transformers, which have shown great promise in computer vision, are now being applied to medical image analysis. However, their application to histopathological images presents challenges due to the need for extensive manual annotations of whole-slide images (WSIs), as these models require large amounts of data to work effectively, which is costly and time-consuming. Furthermore, the quadratic computational cost of Vision Transformers (ViTs) is particularly prohibitive for large, high-resolution histopathological images, especially on edge devices with limited computational resources. In this study, we introduce a novel lightweight breast cancer classification approach using transformers that operates effectively without large datasets. By incorporating parallel processing pathways for Discrete Cosine Transform (DCT) Attention and MobileConv, we convert image data from the spatial domain to the frequency domain to utilize the benefits such as filtering out high frequencies in the image, which reduces computational cost. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets. Our proposed model achieves an accuracy of 96.00% pm 0.48% for binary classification and 87.85% pm 0.93% for multiclass classification, which is comparable to state-of-the-art models while significantly reducing computational costs. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets.

Data diversity and volume are crucial to the success of training deep learning models, while in the medical imaging field, the difficulty and cost of data collection and annotation are especially huge. Specifically in robotic surgery, data scarcity and imbalance have heavily affected the model accuracy and limited the design and deployment of deep learning-based surgical applications such as surgical instrument segmentation. Considering this, we rethink the surgical instrument segmentation task and propose a one-to-many data generation solution that gets rid of the complicated and expensive process of data collection and annotation from robotic surgery. In our method, we only utilize a single surgical background tissue image and a few open-source instrument images as the seed images and apply multiple augmentations and blending techniques to synthesize amounts of image variations. In addition, we also introduce the chained augmentation mixing during training to further enhance the data diversities. The proposed approach is evaluated on the real datasets of the EndoVis-2018 and EndoVis-2017 surgical scene segmentation. Our empirical analysis suggests that without the high cost of data collection and annotation, we can achieve decent surgical instrument segmentation performance. Moreover, we also observe that our method can deal with novel instrument prediction in the deployment domain. We hope our inspiring results will encourage researchers to emphasize data-centric methods to overcome demanding deep learning limitations besides data shortage, such as class imbalance, domain adaptation, and incremental learning. Our code is available at https://github.com/lofrienger/Single_SurgicalScene_For_Segmentation.

Detecting out-of-distribution (OOD) samples in medical imaging plays an important role for downstream medical diagnosis. However, existing OOD detectors are demonstrated on natural images composed of inter-classes and have difficulty generalizing to medical images. The key issue is the granularity of OOD data in the medical domain, where intra-class OOD samples are predominant. We focus on the generalizability of OOD detection for medical images and propose a self-supervised Cascade Variational autoencoder-based Anomaly Detector (CVAD). We use a variational autoencoders' cascade architecture, which combines latent representation at multiple scales, before being fed to a discriminator to distinguish the OOD data from the in-distribution (ID) data. Finally, both the reconstruction error and the OOD probability predicted by the binary discriminator are used to determine the anomalies. We compare the performance with the state-of-the-art deep learning models to demonstrate our model's efficacy on various open-access medical imaging datasets for both intra- and inter-class OOD. Further extensive results on datasets including common natural datasets show our model's effectiveness and generalizability. The code is available at https://github.com/XiaoyuanGuo/CVAD.

Knee Osteoarthritis (KOA) is a highly prevalent chronic musculoskeletal condition with no currently available treatment. The manifestation of KOA is heterogeneous and prediction of its progression is challenging. Current literature suggests that the use of multi-modal data and advanced modeling methods, such as the ones based on Deep Learning, has promise in tackling this challenge. To date, however, the evidence on the efficacy of this approach is limited. In this study, we leveraged recent advances in Deep Learning and, using a Transformer approach, developed a unified framework for the multi-modal fusion of knee imaging data. Subsequently, we analyzed its performance across a range of scenarios by investigating multiple progression horizons -- from short-term to long-term. We report our findings using a large cohort (n=2421-3967) derived from the Osteoarthritis Initiative dataset. We show that structural knee MRI allows identifying radiographic KOA progressors on par with multi-modal fusion approaches, achieving an area under the ROC curve (ROC AUC) of 0.70-0.76 and Average Precision (AP) of 0.15-0.54 in 2-8 year horizons. Progression within 1 year was better predicted with a multi-modal method using X-ray, structural, and compositional MR images -- ROC AUC of 0.76(0.04), AP of 0.13(0.04) -- or via clinical data. Our follow-up analysis generally shows that prediction from the imaging data is more accurate for post-traumatic subjects, and we further investigate which subject subgroups may benefit the most. The present study provides novel insights into multi-modal imaging of KOA and brings a unified data-driven framework for studying its progression in an end-to-end manner, providing new tools for the design of more efficient clinical trials. The source code of our framework and the pre-trained models are made publicly available.

Nematode worms are one of most abundant metazoan groups on the earth, occupying diverse ecological niches. Accurate recognition or identification of nematodes are of great importance for pest control, soil ecology, bio-geography, habitat conservation and against climate changes. Computer vision and image processing have witnessed a few successes in species recognition of nematodes; however, it is still in great demand. In this paper, we identify two main bottlenecks: (1) the lack of a publicly available imaging dataset for diverse species of nematodes (especially the species only found in natural environment) which requires considerable human resources in field work and experts in taxonomy, and (2) the lack of a standard benchmark of state-of-the-art deep learning techniques on this dataset which demands the discipline background in computer science. With these in mind, we propose an image dataset consisting of diverse nematodes (both laboratory cultured and naturally isolated), which, to our knowledge, is the first time in the community. We further set up a species recognition benchmark by employing state-of-the-art deep learning networks on this dataset. We discuss the experimental results, compare the recognition accuracy of different networks, and show the challenges of our dataset. We make our dataset publicly available at: https://github.com/xuequanlu/I-Nema

Global floods, exacerbated by climate change, pose severe threats to human life, infrastructure, and the environment. Recent catastrophic events in Pakistan and New Zealand underscore the urgent need for precise flood mapping to guide restoration efforts, understand vulnerabilities, and prepare for future occurrences. While Synthetic Aperture Radar (SAR) remote sensing offers day-and-night, all-weather imaging capabilities, its application in deep learning for flood segmentation is limited by the lack of large annotated datasets. To address this, we introduce Kuro Siwo, a manually annotated multi-temporal dataset, spanning 43 flood events globally. Our dataset maps more than 338 billion m^2 of land, with 33 billion designated as either flooded areas or permanent water bodies. Kuro Siwo includes a highly processed product optimized for flood mapping based on SAR Ground Range Detected, and a primal SAR Single Look Complex product with minimal preprocessing, designed to promote research on the exploitation of both the phase and amplitude information and to offer maximum flexibility for downstream task preprocessing. To leverage advances in large scale self-supervised pretraining methods for remote sensing data, we augment Kuro Siwo with a large unlabeled set of SAR samples. Finally, we provide an extensive benchmark, namely BlackBench, offering strong baselines for a diverse set of flood events from Europe, America, Africa, Asia and Australia.

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.

Deep convolutional networks have become a popular tool for image generation and restoration. Generally, their excellent performance is imputed to their ability to learn realistic image priors from a large number of example images. In this paper, we show that, on the contrary, the structure of a generator network is sufficient to capture a great deal of low-level image statistics prior to any learning. In order to do so, we show that a randomly-initialized neural network can be used as a handcrafted prior with excellent results in standard inverse problems such as denoising, super-resolution, and inpainting. Furthermore, the same prior can be used to invert deep neural representations to diagnose them, and to restore images based on flash-no flash input pairs. Apart from its diverse applications, our approach highlights the inductive bias captured by standard generator network architectures. It also bridges the gap between two very popular families of image restoration methods: learning-based methods using deep convolutional networks and learning-free methods based on handcrafted image priors such as self-similarity. Code and supplementary material are available at https://dmitryulyanov.github.io/deep_image_prior .

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

In this work, we introduce a deep-learning framework designed for estimating dense image correspondences. Our fully convolutional model generates dense feature maps for images, where each pixel is associated with a descriptor that can be matched across multiple images. Unlike previous methods, our model is trained on synthetic data that includes significant distortions, such as perspective changes, illumination variations, shadows, and specular highlights. Utilizing contrastive learning, our feature maps achieve greater invariance to these distortions, enabling robust matching. Notably, our method eliminates the need for a keypoint detector, setting it apart from many existing image-matching techniques.

In recent years, deep learning methods have been successfully applied to single-image super-resolution tasks. Despite their great performances, deep learning methods cannot be easily applied to real-world applications due to the requirement of heavy computation. In this paper, we address this issue by proposing an accurate and lightweight deep network for image super-resolution. In detail, we design an architecture that implements a cascading mechanism upon a residual network. We also present variant models of the proposed cascading residual network to further improve efficiency. Our extensive experiments show that even with much fewer parameters and operations, our models achieve performance comparable to that of state-of-the-art methods.

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

We propose a deep learning method for single image super-resolution (SR). Our method directly learns an end-to-end mapping between the low/high-resolution images. The mapping is represented as a deep convolutional neural network (CNN) that takes the low-resolution image as the input and outputs the high-resolution one. We further show that traditional sparse-coding-based SR methods can also be viewed as a deep convolutional network. But unlike traditional methods that handle each component separately, our method jointly optimizes all layers. Our deep CNN has a lightweight structure, yet demonstrates state-of-the-art restoration quality, and achieves fast speed for practical on-line usage. We explore different network structures and parameter settings to achieve trade-offs between performance and speed. Moreover, we extend our network to cope with three color channels simultaneously, and show better overall reconstruction quality.

Image-generating machine learning models are typically trained with loss functions based on distance in the image space. This often leads to over-smoothed results. We propose a class of loss functions, which we call deep perceptual similarity metrics (DeePSiM), that mitigate this problem. Instead of computing distances in the image space, we compute distances between image features extracted by deep neural networks. This metric better reflects perceptually similarity of images and thus leads to better results. We show three applications: autoencoder training, a modification of a variational autoencoder, and inversion of deep convolutional networks. In all cases, the generated images look sharp and resemble natural images.

A significant weakness of most current deep Convolutional Neural Networks is the need to train them using vast amounts of manu- ally labelled data. In this work we propose a unsupervised framework to learn a deep convolutional neural network for single view depth predic- tion, without requiring a pre-training stage or annotated ground truth depths. We achieve this by training the network in a manner analogous to an autoencoder. At training time we consider a pair of images, source and target, with small, known camera motion between the two such as a stereo pair. We train the convolutional encoder for the task of predicting the depth map for the source image. To do so, we explicitly generate an inverse warp of the target image using the predicted depth and known inter-view displacement, to reconstruct the source image; the photomet- ric error in the reconstruction is the reconstruction loss for the encoder. The acquisition of this training data is considerably simpler than for equivalent systems, requiring no manual annotation, nor calibration of depth sensor to camera. We show that our network trained on less than half of the KITTI dataset (without any further augmentation) gives com- parable performance to that of the state of art supervised methods for single view depth estimation.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_{data}) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_{data}, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic ``label sharpness'' (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model's adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_{data} formalism to the related metric of learned representation intrinsic dimension (d_{repr}), derive a generalization scaling law with respect to d_{repr}, and show that d_{data} serves as an upper bound for d_{repr}. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties

Deep networks are increasingly being applied to problems involving image synthesis, e.g., generating images from textual descriptions and reconstructing an input image from a compact representation. Supervised training of image-synthesis networks typically uses a pixel-wise loss (PL) to indicate the mismatch between a generated image and its corresponding target image. We propose instead to use a loss function that is better calibrated to human perceptual judgments of image quality: the multiscale structural-similarity score (MS-SSIM). Because MS-SSIM is differentiable, it is easily incorporated into gradient-descent learning. We compare the consequences of using MS-SSIM versus PL loss on training deterministic and stochastic autoencoders. For three different architectures, we collected human judgments of the quality of image reconstructions. Observers reliably prefer images synthesized by MS-SSIM-optimized models over those synthesized by PL-optimized models, for two distinct PL measures (ell_1 and ell_2 distances). We also explore the effect of training objective on image encoding and analyze conditions under which perceptually-optimized representations yield better performance on image classification. Finally, we demonstrate the superiority of perceptually-optimized networks for super-resolution imaging. Just as computer vision has advanced through the use of convolutional architectures that mimic the structure of the mammalian visual system, we argue that significant additional advances can be made in modeling images through the use of training objectives that are well aligned to characteristics of human perception.

Cardiac MRI allows for a comprehensive assessment of myocardial structure, function, and tissue characteristics. Here we describe a foundational vision system for cardiac MRI, capable of representing the breadth of human cardiovascular disease and health. Our deep learning model is trained via self-supervised contrastive learning, by which visual concepts in cine-sequence cardiac MRI scans are learned from the raw text of the accompanying radiology reports. We train and evaluate our model on data from four large academic clinical institutions in the United States. We additionally showcase the performance of our models on the UK BioBank, and two additional publicly available external datasets. We explore emergent zero-shot capabilities of our system, and demonstrate remarkable performance across a range of tasks; including the problem of left ventricular ejection fraction regression, and the diagnosis of 35 different conditions such as cardiac amyloidosis and hypertrophic cardiomyopathy. We show that our deep learning system is capable of not only understanding the staggering complexity of human cardiovascular disease, but can be directed towards clinical problems of interest yielding impressive, clinical grade diagnostic accuracy with a fraction of the training data typically required for such tasks.

In this work we investigate the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting. Our main contribution is a thorough evaluation of networks of increasing depth using an architecture with very small (3x3) convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers. These findings were the basis of our ImageNet Challenge 2014 submission, where our team secured the first and the second places in the localisation and classification tracks respectively. We also show that our representations generalise well to other datasets, where they achieve state-of-the-art results. We have made our two best-performing ConvNet models publicly available to facilitate further research on the use of deep visual representations in computer vision.

Feature representations, both hand-designed and learned ones, are often hard to analyze and interpret, even when they are extracted from visual data. We propose a new approach to study image representations by inverting them with an up-convolutional neural network. We apply the method to shallow representations (HOG, SIFT, LBP), as well as to deep networks. For shallow representations our approach provides significantly better reconstructions than existing methods, revealing that there is surprisingly rich information contained in these features. Inverting a deep network trained on ImageNet provides several insights into the properties of the feature representation learned by the network. Most strikingly, the colors and the rough contours of an image can be reconstructed from activations in higher network layers and even from the predicted class probabilities.

Deformable image registration (DIR) is an active research topic in biomedical imaging. There is a growing interest in developing DIR methods based on deep learning (DL). A traditional DL approach to DIR is based on training a convolutional neural network (CNN) to estimate the registration field between two input images. While conceptually simple, this approach comes with a limitation that it exclusively relies on a pre-trained CNN without explicitly enforcing fidelity between the registered image and the reference. We present plug-and-play image registration network (PIRATE) as a new DIR method that addresses this issue by integrating an explicit data-fidelity penalty and a CNN prior. PIRATE pre-trains a CNN denoiser on the registration field and "plugs" it into an iterative method as a regularizer. We additionally present PIRATE+ that fine-tunes the CNN prior in PIRATE using deep equilibrium models (DEQ). PIRATE+ interprets the fixed-point iteration of PIRATE as a network with effectively infinite layers and then trains the resulting network end-to-end, enabling it to learn more task-specific information and boosting its performance. Our numerical results on OASIS and CANDI datasets show that our methods achieve state-of-the-art performance on DIR.

The success of deep learning in vision can be attributed to: (a) models with high capacity; (b) increased computational power; and (c) availability of large-scale labeled data. Since 2012, there have been significant advances in representation capabilities of the models and computational capabilities of GPUs. But the size of the biggest dataset has surprisingly remained constant. What will happen if we increase the dataset size by 10x or 100x? This paper takes a step towards clearing the clouds of mystery surrounding the relationship between `enormous data' and visual deep learning. By exploiting the JFT-300M dataset which has more than 375M noisy labels for 300M images, we investigate how the performance of current vision tasks would change if this data was used for representation learning. Our paper delivers some surprising (and some expected) findings. First, we find that the performance on vision tasks increases logarithmically based on volume of training data size. Second, we show that representation learning (or pre-training) still holds a lot of promise. One can improve performance on many vision tasks by just training a better base model. Finally, as expected, we present new state-of-the-art results for different vision tasks including image classification, object detection, semantic segmentation and human pose estimation. Our sincere hope is that this inspires vision community to not undervalue the data and develop collective efforts in building larger datasets.

This paper addresses the challenge of grading visual features in lumbar spine MRI using Deep Learning. Such a method is essential for the automatic quantification of structural changes in the spine, which is valuable for understanding low back pain. Multiple recent studies investigated different architecture designs, and the most recent success has been attributed to the use of transformer architectures. In this work, we argue that with a well-tuned three-stage pipeline comprising semantic segmentation, localization, and classification, convolutional networks outperform the state-of-the-art approaches. We conducted an ablation study of the existing methods in a population cohort, and report performance generalization across various subgroups. Our code is publicly available to advance research on disc degeneration and low back pain.

Capturing photographs with wrong exposures remains a major source of errors in camera-based imaging. Exposure problems are categorized as either: (i) overexposed, where the camera exposure was too long, resulting in bright and washed-out image regions, or (ii) underexposed, where the exposure was too short, resulting in dark regions. Both under- and overexposure greatly reduce the contrast and visual appeal of an image. Prior work mainly focuses on underexposed images or general image enhancement. In contrast, our proposed method targets both over- and underexposure errors in photographs. We formulate the exposure correction problem as two main sub-problems: (i) color enhancement and (ii) detail enhancement. Accordingly, we propose a coarse-to-fine deep neural network (DNN) model, trainable in an end-to-end manner, that addresses each sub-problem separately. A key aspect of our solution is a new dataset of over 24,000 images exhibiting the broadest range of exposure values to date with a corresponding properly exposed image. Our method achieves results on par with existing state-of-the-art methods on underexposed images and yields significant improvements for images suffering from overexposure errors.

The recent explosion in applications of machine learning to satellite imagery often rely on visible images and therefore suffer from a lack of data during the night. The gap can be filled by employing available infra-red observations to generate visible images. This work presents how deep learning can be applied successfully to create those images by using U-Net based architectures. The proposed methods show promising results, achieving a structural similarity index (SSIM) up to 86\% on an independent test set and providing visually convincing output images, generated from infra-red observations.

Estimating accurate depth from a single image is challenging because it is an ill-posed problem as infinitely many 3D scenes can be projected to the same 2D scene. However, recent works based on deep convolutional neural networks show great progress with plausible results. The convolutional neural networks are generally composed of two parts: an encoder for dense feature extraction and a decoder for predicting the desired depth. In the encoder-decoder schemes, repeated strided convolution and spatial pooling layers lower the spatial resolution of transitional outputs, and several techniques such as skip connections or multi-layer deconvolutional networks are adopted to recover the original resolution for effective dense prediction. In this paper, for more effective guidance of densely encoded features to the desired depth prediction, we propose a network architecture that utilizes novel local planar guidance layers located at multiple stages in the decoding phase. We show that the proposed method outperforms the state-of-the-art works with significant margin evaluating on challenging benchmarks. We also provide results from an ablation study to validate the effectiveness of the proposed method.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

The advent of deep perceptual networks brought about a paradigm shift in machine vision and image perception. Image apprehension lately carried out by hand-crafted features in the latent space have been replaced by deep features acquired from supervised networks for improved understanding. However, such deep networks require strict supervision with a substantial amount of the labeled data for authentic training process. These methods perform poorly in domains lacking labeled data especially in case of remote sensing image retrieval. Resolving this, we propose an unsupervised encoder-decoder feature for remote sensing image matching (RSIM). Moreover, we replace the conventional distance metrics with a deep discriminator network to identify the similarity of the image pairs. To the best of our knowledge, discriminator network has never been used before for solving RSIM problem. Results have been validated with two publicly available benchmark remote sensing image datasets. The technique has also been investigated for content-based remote sensing image retrieval (CBRSIR); one of the widely used applications of RSIM. Results demonstrate that our technique supersedes the state-of-the-art methods used for unsupervised image matching with mean average precision (mAP) of 81%, and image retrieval with an overall improvement in mAP score of about 12%.

Convolutional Neural Networks have demonstrated superior performance on single image depth estimation in recent years. These works usually use stacked spatial pooling or strided convolution to get high-level information which are common practices in classification task. However, depth estimation is a dense prediction problem and low-resolution feature maps usually generate blurred depth map which is undesirable in application. In order to produce high quality depth map, say clean and accurate, we propose a network consists of a Dense Feature Extractor (DFE) and a Depth Map Generator (DMG). The DFE combines ResNet and dilated convolutions. It extracts multi-scale information from input image while keeping the feature maps dense. As for DMG, we use attention mechanism to fuse multi-scale features produced in DFE. Our Network is trained end-to-end and does not need any post-processing. Hence, it runs fast and can predict depth map in about 15 fps. Experiment results show that our method is competitive with the state-of-the-art in quantitative evaluation, but can preserve better structural details of the scene depth.

Deep neural networks have become a standard building block for designing models that can perform multiple dense computer vision tasks such as depth estimation and semantic segmentation thanks to their ability to capture complex correlations in high dimensional feature space across tasks. However, the cross-task correlations that are learned in the unstructured feature space can be extremely noisy and susceptible to overfitting, consequently hurting performance. We propose to address this problem by introducing a structured 3D-aware regularizer which interfaces multiple tasks through the projection of features extracted from an image encoder to a shared 3D feature space and decodes them into their task output space through differentiable rendering. We show that the proposed method is architecture agnostic and can be plugged into various prior multi-task backbones to improve their performance; as we evidence using standard benchmarks NYUv2 and PASCAL-Context.

In MRI, motion artefacts are among the most common types of artefacts. They can degrade images and render them unusable for accurate diagnosis. Traditional methods, such as prospective or retrospective motion correction, have been proposed to avoid or alleviate motion artefacts. Recently, several other methods based on deep learning approaches have been proposed to solve this problem. This work proposes to enhance the performance of existing deep learning models by the inclusion of additional information present as image priors. The proposed approach has shown promising results and will be further investigated for clinical validity.

Deep convolutional neural networks achieve remarkable visual recognition performance, at the cost of high computational complexity. In this paper, we have a new design of efficient convolutional layers based on three schemes. The 3D convolution operation in a convolutional layer can be considered as performing spatial convolution in each channel and linear projection across channels simultaneously. By unravelling them and arranging the spatial convolution sequentially, the proposed layer is composed of a single intra-channel convolution, of which the computation is negligible, and a linear channel projection. A topological subdivisioning is adopted to reduce the connection between the input channels and output channels. Additionally, we also introduce a spatial "bottleneck" structure that utilizes a convolution-projection-deconvolution pipeline to take advantage of the correlation between adjacent pixels in the input. Our experiments demonstrate that the proposed layers remarkably outperform the standard convolutional layers with regard to accuracy/complexity ratio. Our models achieve similar accuracy to VGG, ResNet-50, ResNet-101 while requiring 42, 4.5, 6.5 times less computation respectively.

Medical Image Analysis (MedIA) has become an essential tool in medicine and healthcare, aiding in disease diagnosis, prognosis, and treatment planning, and recent successes in deep learning (DL) have made significant contributions to its advances. However, DL models for MedIA remain challenging to deploy in real-world situations, failing for generalization under the distributional gap between training and testing samples, known as a distribution shift problem. Researchers have dedicated their efforts to developing various DL methods to adapt and perform robustly on unknown and out-of-distribution data distributions. This paper comprehensively reviews domain generalization studies specifically tailored for MedIA. We provide a holistic view of how domain generalization techniques interact within the broader MedIA system, going beyond methodologies to consider the operational implications on the entire MedIA workflow. Specifically, we categorize domain generalization methods into data-level, feature-level, model-level, and analysis-level methods. We show how those methods can be used in various stages of the MedIA workflow with DL equipped from data acquisition to model prediction and analysis. Furthermore, we include benchmark datasets and applications used to evaluate these approaches and analyze the strengths and weaknesses of various methods, unveiling future research opportunities.

Recent advances in deep learning have shown exciting promise in filling large holes in natural images with semantically plausible and context aware details, impacting fundamental image manipulation tasks such as object removal. While these learning-based methods are significantly more effective in capturing high-level features than prior techniques, they can only handle very low-resolution inputs due to memory limitations and difficulty in training. Even for slightly larger images, the inpainted regions would appear blurry and unpleasant boundaries become visible. We propose a multi-scale neural patch synthesis approach based on joint optimization of image content and texture constraints, which not only preserves contextual structures but also produces high-frequency details by matching and adapting patches with the most similar mid-layer feature correlations of a deep classification network. We evaluate our method on the ImageNet and Paris Streetview datasets and achieved state-of-the-art inpainting accuracy. We show our approach produces sharper and more coherent results than prior methods, especially for high-resolution images.

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

Deep Image Prior (DIP) shows that some network architectures naturally bias towards smooth images and resist noises, a phenomenon known as spectral bias. Image denoising is an immediate application of this property. Although DIP has removed the requirement of large training sets, it still presents two practical challenges for denoising: architectural design and noise-fitting, which are often intertwined. Existing methods mostly handcraft or search for the architecture from a large design space, due to the lack of understanding on how the architectural choice corresponds to the image. In this study, we analyze from a frequency perspective to demonstrate that the unlearnt upsampling is the main driving force behind the denoising phenomenon in DIP. This finding then leads to strategies for estimating a suitable architecture for every image without a laborious search. Extensive experiments show that the estimated architectures denoise and preserve the textural details better than current methods with up to 95% fewer parameters. The under-parameterized nature also makes them especially robust to a higher level of noise.

Deeper neural networks are more difficult to train. We present a residual learning framework to ease the training of networks that are substantially deeper than those used previously. We explicitly reformulate the layers as learning residual functions with reference to the layer inputs, instead of learning unreferenced functions. We provide comprehensive empirical evidence showing that these residual networks are easier to optimize, and can gain accuracy from considerably increased depth. On the ImageNet dataset we evaluate residual nets with a depth of up to 152 layers---8x deeper than VGG nets but still having lower complexity. An ensemble of these residual nets achieves 3.57% error on the ImageNet test set. This result won the 1st place on the ILSVRC 2015 classification task. We also present analysis on CIFAR-10 with 100 and 1000 layers. The depth of representations is of central importance for many visual recognition tasks. Solely due to our extremely deep representations, we obtain a 28% relative improvement on the COCO object detection dataset. Deep residual nets are foundations of our submissions to ILSVRC & COCO 2015 competitions, where we also won the 1st places on the tasks of ImageNet detection, ImageNet localization, COCO detection, and COCO segmentation.

Deep learning is commonly used to reconstruct HDR images from LDR images. LDR stack-based methods are used for single-image HDR reconstruction, generating an HDR image from a deep learning-generated LDR stack. However, current methods generate the stack with predetermined exposure values (EVs), which may limit the quality of HDR reconstruction. To address this, we propose the continuous exposure value representation (CEVR), which uses an implicit function to generate LDR images with arbitrary EVs, including those unseen during training. Our approach generates a continuous stack with more images containing diverse EVs, significantly improving HDR reconstruction. We use a cycle training strategy to supervise the model in generating continuous EV LDR images without corresponding ground truths. Our CEVR model outperforms existing methods, as demonstrated by experimental results.

We present deepflash2, a deep learning solution that facilitates the objective and reliable segmentation of ambiguous bioimages through multi-expert annotations and integrated quality assurance. Thereby, deepflash2 addresses typical challenges that arise during training, evaluation, and application of deep learning models in bioimaging. The tool is embedded in an easy-to-use graphical user interface and offers best-in-class predictive performance for semantic and instance segmentation under economical usage of computational resources.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

We present a method that achieves state-of-the-art results for synthesizing novel views of complex scenes by optimizing an underlying continuous volumetric scene function using a sparse set of input views. Our algorithm represents a scene using a fully-connected (non-convolutional) deep network, whose input is a single continuous 5D coordinate (spatial location (x,y,z) and viewing direction (theta, phi)) and whose output is the volume density and view-dependent emitted radiance at that spatial location. We synthesize views by querying 5D coordinates along camera rays and use classic volume rendering techniques to project the output colors and densities into an image. Because volume rendering is naturally differentiable, the only input required to optimize our representation is a set of images with known camera poses. We describe how to effectively optimize neural radiance fields to render photorealistic novel views of scenes with complicated geometry and appearance, and demonstrate results that outperform prior work on neural rendering and view synthesis. View synthesis results are best viewed as videos, so we urge readers to view our supplementary video for convincing comparisons.

We present an approach to enhancing the realism of synthetic images. The images are enhanced by a convolutional network that leverages intermediate representations produced by conventional rendering pipelines. The network is trained via a novel adversarial objective, which provides strong supervision at multiple perceptual levels. We analyze scene layout distributions in commonly used datasets and find that they differ in important ways. We hypothesize that this is one of the causes of strong artifacts that can be observed in the results of many prior methods. To address this we propose a new strategy for sampling image patches during training. We also introduce multiple architectural improvements in the deep network modules used for photorealism enhancement. We confirm the benefits of our contributions in controlled experiments and report substantial gains in stability and realism in comparison to recent image-to-image translation methods and a variety of other baselines.

The interest of the deep learning community in image synthesis has grown massively in recent years. Nowadays, deep generative methods, and especially Generative Adversarial Networks (GANs), are leading to state-of-the-art performance, capable of synthesizing images that appear realistic. While the efforts for improving the quality of the generated images are extensive, most attempts still consider the generator part as an uncorroborated "black-box". In this paper, we aim to provide a better understanding and design of the image generation process. We interpret existing generators as implicitly relying on sparsity-inspired models. More specifically, we show that generators can be viewed as manifestations of the Convolutional Sparse Coding (CSC) and its Multi-Layered version (ML-CSC) synthesis processes. We leverage this observation by explicitly enforcing a sparsifying regularization on appropriately chosen activation layers in the generator, and demonstrate that this leads to improved image synthesis. Furthermore, we show that the same rationale and benefits apply to generators serving inverse problems, demonstrated on the Deep Image Prior (DIP) method.

Recent research on super-resolution has progressed with the development of deep convolutional neural networks (DCNN). In particular, residual learning techniques exhibit improved performance. In this paper, we develop an enhanced deep super-resolution network (EDSR) with performance exceeding those of current state-of-the-art SR methods. The significant performance improvement of our model is due to optimization by removing unnecessary modules in conventional residual networks. The performance is further improved by expanding the model size while we stabilize the training procedure. We also propose a new multi-scale deep super-resolution system (MDSR) and training method, which can reconstruct high-resolution images of different upscaling factors in a single model. The proposed methods show superior performance over the state-of-the-art methods on benchmark datasets and prove its excellence by winning the NTIRE2017 Super-Resolution Challenge.

It is widely believed that the success of deep convolutional networks is based on progressively discarding uninformative variability about the input with respect to the problem at hand. This is supported empirically by the difficulty of recovering images from their hidden representations, in most commonly used network architectures. In this paper we show via a one-to-one mapping that this loss of information is not a necessary condition to learn representations that generalize well on complicated problems, such as ImageNet. Via a cascade of homeomorphic layers, we build the i-RevNet, a network that can be fully inverted up to the final projection onto the classes, i.e. no information is discarded. Building an invertible architecture is difficult, for one, because the local inversion is ill-conditioned, we overcome this by providing an explicit inverse. An analysis of i-RevNets learned representations suggests an alternative explanation for the success of deep networks by a progressive contraction and linear separation with depth. To shed light on the nature of the model learned by the i-RevNet we reconstruct linear interpolations between natural image representations.

Deep networks have achieved great success in image rescaling (IR) task that seeks to learn the optimal downscaled representations, i.e., low-resolution (LR) images, to reconstruct the original high-resolution (HR) images. Compared with super-resolution methods that consider a fixed downscaling scheme, e.g., bicubic, IR often achieves significantly better reconstruction performance thanks to the learned downscaled representations. This highlights the importance of a good downscaled representation in image reconstruction tasks. Existing IR methods mainly learn the downscaled representation by jointly optimizing the downscaling and upscaling models. Unlike them, we seek to improve the downscaled representation through a different and more direct way: optimizing the downscaled image itself instead of the down-/upscaling models. Specifically, we propose a collaborative downscaling scheme that directly generates the collaborative LR examples by descending the gradient w.r.t. the reconstruction loss on them to benefit the IR process. Furthermore, since LR images are downscaled from the corresponding HR images, one can also improve the downscaled representation if we have a better representation in the HR domain. Inspired by this, we propose a Hierarchical Collaborative Downscaling (HCD) method that performs gradient descent in both HR and LR domains to improve the downscaled representations. Extensive experiments show that our HCD significantly improves the reconstruction performance both quantitatively and qualitatively. Moreover, we also highlight the flexibility of our HCD since it can generalize well across diverse IR models.

When capturing and storing images, devices inevitably introduce noise. Reducing this noise is a critical task called image denoising. Deep learning has become the de facto method for image denoising, especially with the emergence of Transformer-based models that have achieved notable state-of-the-art results on various image tasks. However, deep learning-based methods often suffer from a lack of generalization ability. For example, deep models trained on Gaussian noise may perform poorly when tested on other noise distributions. To address this issue, we present a novel approach to enhance the generalization performance of denoising networks, known as masked training. Our method involves masking random pixels of the input image and reconstructing the missing information during training. We also mask out the features in the self-attention layers to avoid the impact of training-testing inconsistency. Our approach exhibits better generalization ability than other deep learning models and is directly applicable to real-world scenarios. Additionally, our interpretability analysis demonstrates the superiority of our method.

Deep learning (DL) has proven highly effective for ultrasound-based computer-aided diagnosis (CAD) of breast cancers. In an automaticCAD system, lesion detection is critical for the following diagnosis. However, existing DL-based methods generally require voluminous manually-annotated region of interest (ROI) labels and class labels to train both the lesion detection and diagnosis models. In clinical practice, the ROI labels, i.e. ground truths, may not always be optimal for the classification task due to individual experience of sonologists, resulting in the issue of coarse annotation that limits the diagnosis performance of a CAD model. To address this issue, a novel Two-Stage Detection and Diagnosis Network (TSDDNet) is proposed based on weakly supervised learning to enhance diagnostic accuracy of the ultrasound-based CAD for breast cancers. In particular, all the ROI-level labels are considered as coarse labels in the first training stage, and then a candidate selection mechanism is designed to identify optimallesion areas for both the fully and partially annotated samples. It refines the current ROI-level labels in the fully annotated images and the detected ROIs in the partially annotated samples with a weakly supervised manner under the guidance of class labels. In the second training stage, a self-distillation strategy further is further proposed to integrate the detection network and classification network into a unified framework as the final CAD model for joint optimization, which then further improves the diagnosis performance. The proposed TSDDNet is evaluated on a B-mode ultrasound dataset, and the experimental results show that it achieves the best performance on both lesion detection and diagnosis tasks, suggesting promising application potential.

With its significant performance improvements, the deep learning paradigm has become a standard tool for modern image denoisers. While promising performance has been shown on seen noise distributions, existing approaches often suffer from generalisation to unseen noise types or general and real noise. It is understandable as the model is designed to learn paired mapping (e.g. from a noisy image to its clean version). In this paper, we instead propose to learn to disentangle the noisy image, under the intuitive assumption that different corrupted versions of the same clean image share a common latent space. A self-supervised learning framework is proposed to achieve the goal, without looking at the latent clean image. By taking two different corrupted versions of the same image as input, the proposed Multi-view Self-supervised Disentanglement (MeD) approach learns to disentangle the latent clean features from the corruptions and recover the clean image consequently. Extensive experimental analysis on both synthetic and real noise shows the superiority of the proposed method over prior self-supervised approaches, especially on unseen novel noise types. On real noise, the proposed method even outperforms its supervised counterparts by over 3 dB.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

In the field of medical sciences, reliable detection and classification of brain tumors from images remains a formidable challenge due to the rarity of tumors within the population of patients. Therefore, the ability to detect tumors in anomaly scenarios is paramount for ensuring timely interventions and improved patient outcomes. This study addresses the issue by leveraging deep learning (DL) techniques to detect and classify brain tumors in challenging situations. The curated data set from the National Brain Mapping Lab (NBML) comprises 81 patients, including 30 Tumor cases and 51 Normal cases. The detection and classification pipelines are separated into two consecutive tasks. The detection phase involved comprehensive data analysis and pre-processing to modify the number of image samples and the number of patients of each class to anomaly distribution (9 Normal per 1 Tumor) to comply with real world scenarios. Next, in addition to common evaluation metrics for the testing, we employed a novel performance evaluation method called Patient to Patient (PTP), focusing on the realistic evaluation of the model. In the detection phase, we fine-tuned a YOLOv8n detection model to detect the tumor region. Subsequent testing and evaluation yielded competitive performance both in Common Evaluation Metrics and PTP metrics. Furthermore, using the Data Efficient Image Transformer (DeiT) module, we distilled a Vision Transformer (ViT) model from a fine-tuned ResNet152 as a teacher in the classification phase. This approach demonstrates promising strides in reliable tumor detection and classification, offering potential advancements in tumor diagnosis for real-world medical imaging scenarios.

Deep models have achieved significant process on single image super-resolution (SISR) tasks, in particular large models with large kernel (3times3 or more). However, the heavy computational footprint of such models prevents their deployment in real-time, resource-constrained environments. Conversely, 1times1 convolutions bring substantial computational efficiency, but struggle with aggregating local spatial representations, an essential capability to SISR models. In response to this dichotomy, we propose to harmonize the merits of both 3times3 and 1times1 kernels, and exploit a great potential for lightweight SISR tasks. Specifically, we propose a simple yet effective fully 1times1 convolutional network, named Shift-Conv-based Network (SCNet). By incorporating a parameter-free spatial-shift operation, it equips the fully 1times1 convolutional network with powerful representation capability while impressive computational efficiency. Extensive experiments demonstrate that SCNets, despite its fully 1times1 convolutional structure, consistently matches or even surpasses the performance of existing lightweight SR models that employ regular convolutions.

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

Deep neural networks that achieve remarkable performance in image classification have previously been shown to be easily fooled by tiny transformations such as a one pixel translation of the input image. In order to address this problem, two approaches have been proposed in recent years. The first approach suggests using huge datasets together with data augmentation in the hope that a highly varied training set will teach the network to learn to be invariant. The second approach suggests using architectural modifications based on sampling theory to deal explicitly with image translations. In this paper, we show that these approaches still fall short in robustly handling 'natural' image translations that simulate a subtle change in camera orientation. Our findings reveal that a mere one-pixel translation can result in a significant change in the predicted image representation for approximately 40% of the test images in state-of-the-art models (e.g. open-CLIP trained on LAION-2B or DINO-v2) , while models that are explicitly constructed to be robust to cyclic translations can still be fooled with 1 pixel realistic (non-cyclic) translations 11% of the time. We present Robust Inference by Crop Selection: a simple method that can be proven to achieve any desired level of consistency, although with a modest tradeoff with the model's accuracy. Importantly, we demonstrate how employing this method reduces the ability to fool state-of-the-art models with a 1 pixel translation to less than 5% while suffering from only a 1% drop in classification accuracy. Additionally, we show that our method can be easy adjusted to deal with circular shifts as well. In such case we achieve 100% robustness to integer shifts with state-of-the-art accuracy, and with no need for any further training.

The rapid advancement of Artificial Intelligence (AI) in biomedical imaging and radiotherapy is hindered by the limited availability of large imaging data repositories. With recent research and improvements in denoising diffusion probabilistic models (DDPM), high quality synthetic medical scans are now possible. Despite this, there is currently no way of generating multiple related images, such as a corresponding ground truth which can be used to train models, so synthetic scans are often manually annotated before use. This research introduces a novel architecture that is able to generate multiple, related PET-CT-tumour mask pairs using paired networks and conditional encoders. Our approach includes innovative, time step-controlled mechanisms and a `noise-seeding' strategy to improve DDPM sampling consistency. While our model requires a modified perceptual loss function to ensure accurate feature alignment we show generation of clearly aligned synthetic images and improvement in segmentation accuracy with generated images.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

We address the long-standing problem of how to learn effective pixel-based image diffusion models at scale, introducing a remarkably simple greedy growing method for stable training of large-scale, high-resolution models. without the needs for cascaded super-resolution components. The key insight stems from careful pre-training of core components, namely, those responsible for text-to-image alignment {\it vs.} high-resolution rendering. We first demonstrate the benefits of scaling a {\it Shallow UNet}, with no down(up)-sampling enc(dec)oder. Scaling its deep core layers is shown to improve alignment, object structure, and composition. Building on this core model, we propose a greedy algorithm that grows the architecture into high-resolution end-to-end models, while preserving the integrity of the pre-trained representation, stabilizing training, and reducing the need for large high-resolution datasets. This enables a single stage model capable of generating high-resolution images without the need of a super-resolution cascade. Our key results rely on public datasets and show that we are able to train non-cascaded models up to 8B parameters with no further regularization schemes. Vermeer, our full pipeline model trained with internal datasets to produce 1024x1024 images, without cascades, is preferred by 44.0% vs. 21.4% human evaluators over SDXL.

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Low-Light Image Enhancement is a computer vision task which intensifies the dark images to appropriate brightness. It can also be seen as an ill-posed problem in image restoration domain. With the success of deep neural networks, the convolutional neural networks surpass the traditional algorithm-based methods and become the mainstream in the computer vision area. To advance the performance of enhancement algorithms, we propose an image enhancement network (HWMNet) based on an improved hierarchical model: M-Net+. Specifically, we use a half wavelet attention block on M-Net+ to enrich the features from wavelet domain. Furthermore, our HWMNet has competitive performance results on two image enhancement datasets in terms of quantitative metrics and visual quality. The source code and pretrained model are available at https://github.com/FanChiMao/HWMNet.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Large-scale labeled data are generally required to train deep neural networks in order to obtain better performance in visual feature learning from images or videos for computer vision applications. To avoid extensive cost of collecting and annotating large-scale datasets, as a subset of unsupervised learning methods, self-supervised learning methods are proposed to learn general image and video features from large-scale unlabeled data without using any human-annotated labels. This paper provides an extensive review of deep learning-based self-supervised general visual feature learning methods from images or videos. First, the motivation, general pipeline, and terminologies of this field are described. Then the common deep neural network architectures that used for self-supervised learning are summarized. Next, the main components and evaluation metrics of self-supervised learning methods are reviewed followed by the commonly used image and video datasets and the existing self-supervised visual feature learning methods. Finally, quantitative performance comparisons of the reviewed methods on benchmark datasets are summarized and discussed for both image and video feature learning. At last, this paper is concluded and lists a set of promising future directions for self-supervised visual feature learning.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

Hyperthermia (HT) in combination with radio- and/or chemotherapy has become an accepted cancer treatment for distinct solid tumour entities. In HT, tumour tissue is exogenously heated to temperatures between 39 and 43 ^circC for 60 minutes. Temperature monitoring can be performed non-invasively using dynamic magnetic resonance imaging (MRI). However, the slow nature of MRI leads to motion artefacts in the images due to the movements of patients during image acquisition. By discarding parts of the data, the speed of the acquisition can be increased - known as undersampling. However, due to the invalidation of the Nyquist criterion, the acquired images might be blurry and can also produce aliasing artefacts. The aim of this work was, therefore, to reconstruct highly undersampled MR thermometry acquisitions with better resolution and with fewer artefacts compared to conventional methods. The use of deep learning in the medical field has emerged in recent times, and various studies have shown that deep learning has the potential to solve inverse problems such as MR image reconstruction. However, most of the published work only focuses on the magnitude images, while the phase images are ignored, which are fundamental requirements for MR thermometry. This work, for the first time, presents deep learning-based solutions for reconstructing undersampled MR thermometry data. Two different deep learning models have been employed here, the Fourier Primal-Dual network and the Fourier Primal-Dual UNet, to reconstruct highly undersampled complex images of MR thermometry. The method reduced the temperature difference between the undersampled MRIs and the fully sampled MRIs from 1.3 ^circC to 0.6 ^circC in full volume and 0.49 ^circC to 0.06 ^circC in the tumour region for an acceleration factor of 10.

In recent years, supervised learning with convolutional networks (CNNs) has seen huge adoption in computer vision applications. Comparatively, unsupervised learning with CNNs has received less attention. In this work we hope to help bridge the gap between the success of CNNs for supervised learning and unsupervised learning. We introduce a class of CNNs called deep convolutional generative adversarial networks (DCGANs), that have certain architectural constraints, and demonstrate that they are a strong candidate for unsupervised learning. Training on various image datasets, we show convincing evidence that our deep convolutional adversarial pair learns a hierarchy of representations from object parts to scenes in both the generator and discriminator. Additionally, we use the learned features for novel tasks - demonstrating their applicability as general image representations.

Image and video inpainting is a classic problem in computer vision and computer graphics, aiming to fill in the plausible and realistic content in the missing areas of images and videos. With the advance of deep learning, this problem has achieved significant progress recently. The goal of this paper is to comprehensively review the deep learning-based methods for image and video inpainting. Specifically, we sort existing methods into different categories from the perspective of their high-level inpainting pipeline, present different deep learning architectures, including CNN, VAE, GAN, diffusion models, etc., and summarize techniques for module design. We review the training objectives and the common benchmark datasets. We present evaluation metrics for low-level pixel and high-level perceptional similarity, conduct a performance evaluation, and discuss the strengths and weaknesses of representative inpainting methods. We also discuss related real-world applications. Finally, we discuss open challenges and suggest potential future research directions.

Deep learning in computer vision has achieved great success with the price of large-scale labeled training data. However, exhaustive data annotation is impracticable for each task of all domains of interest, due to high labor costs and unguaranteed labeling accuracy. Besides, the uncontrollable data collection process produces non-IID training and test data, where undesired duplication may exist. All these nuisances may hinder the verification of typical theories and exposure to new findings. To circumvent them, an alternative is to generate synthetic data via 3D rendering with domain randomization. We in this work push forward along this line by doing profound and extensive research on bare supervised learning and downstream domain adaptation. Specifically, under the well-controlled, IID data setting enabled by 3D rendering, we systematically verify the typical, important learning insights, e.g., shortcut learning, and discover the new laws of various data regimes and network architectures in generalization. We further investigate the effect of image formation factors on generalization, e.g., object scale, material texture, illumination, camera viewpoint, and background in a 3D scene. Moreover, we use the simulation-to-reality adaptation as a downstream task for comparing the transferability between synthetic and real data when used for pre-training, which demonstrates that synthetic data pre-training is also promising to improve real test results. Lastly, to promote future research, we develop a new large-scale synthetic-to-real benchmark for image classification, termed S2RDA, which provides more significant challenges for transfer from simulation to reality. The code and datasets are available at https://github.com/huitangtang/On_the_Utility_of_Synthetic_Data.

Clustering is a class of unsupervised learning methods that has been extensively applied and studied in computer vision. Little work has been done to adapt it to the end-to-end training of visual features on large scale datasets. In this work, we present DeepCluster, a clustering method that jointly learns the parameters of a neural network and the cluster assignments of the resulting features. DeepCluster iteratively groups the features with a standard clustering algorithm, k-means, and uses the subsequent assignments as supervision to update the weights of the network. We apply DeepCluster to the unsupervised training of convolutional neural networks on large datasets like ImageNet and YFCC100M. The resulting model outperforms the current state of the art by a significant margin on all the standard benchmarks.

Deep neural networks have achieved impressive experimental results in image classification, but can surprisingly be unstable with respect to adversarial perturbations, that is, minimal changes to the input image that cause the network to misclassify it. With potential applications including perception modules and end-to-end controllers for self-driving cars, this raises concerns about their safety. We develop a novel automated verification framework for feed-forward multi-layer neural networks based on Satisfiability Modulo Theory (SMT). We focus on safety of image classification decisions with respect to image manipulations, such as scratches or changes to camera angle or lighting conditions that would result in the same class being assigned by a human, and define safety for an individual decision in terms of invariance of the classification within a small neighbourhood of the original image. We enable exhaustive search of the region by employing discretisation, and propagate the analysis layer by layer. Our method works directly with the network code and, in contrast to existing methods, can guarantee that adversarial examples, if they exist, are found for the given region and family of manipulations. If found, adversarial examples can be shown to human testers and/or used to fine-tune the network. We implement the techniques using Z3 and evaluate them on state-of-the-art networks, including regularised and deep learning networks. We also compare against existing techniques to search for adversarial examples and estimate network robustness.

Large-scale models pre-trained on large-scale datasets have profoundly advanced the development of deep learning. However, the state-of-the-art models for medical image segmentation are still small-scale, with their parameters only in the tens of millions. Further scaling them up to higher orders of magnitude is rarely explored. An overarching goal of exploring large-scale models is to train them on large-scale medical segmentation datasets for better transfer capacities. In this work, we design a series of Scalable and Transferable U-Net (STU-Net) models, with parameter sizes ranging from 14 million to 1.4 billion. Notably, the 1.4B STU-Net is the largest medical image segmentation model to date. Our STU-Net is based on nnU-Net framework due to its popularity and impressive performance. We first refine the default convolutional blocks in nnU-Net to make them scalable. Then, we empirically evaluate different scaling combinations of network depth and width, discovering that it is optimal to scale model depth and width together. We train our scalable STU-Net models on a large-scale TotalSegmentator dataset and find that increasing model size brings a stronger performance gain. This observation reveals that a large model is promising in medical image segmentation. Furthermore, we evaluate the transferability of our model on 14 downstream datasets for direct inference and 3 datasets for further fine-tuning, covering various modalities and segmentation targets. We observe good performance of our pre-trained model in both direct inference and fine-tuning. The code and pre-trained models are available at https://github.com/Ziyan-Huang/STU-Net.

Recent deep learning based approaches have shown promising results for the challenging task of inpainting large missing regions in an image. These methods can generate visually plausible image structures and textures, but often create distorted structures or blurry textures inconsistent with surrounding areas. This is mainly due to ineffectiveness of convolutional neural networks in explicitly borrowing or copying information from distant spatial locations. On the other hand, traditional texture and patch synthesis approaches are particularly suitable when it needs to borrow textures from the surrounding regions. Motivated by these observations, we propose a new deep generative model-based approach which can not only synthesize novel image structures but also explicitly utilize surrounding image features as references during network training to make better predictions. The model is a feed-forward, fully convolutional neural network which can process images with multiple holes at arbitrary locations and with variable sizes during the test time. Experiments on multiple datasets including faces (CelebA, CelebA-HQ), textures (DTD) and natural images (ImageNet, Places2) demonstrate that our proposed approach generates higher-quality inpainting results than existing ones. Code, demo and models are available at: https://github.com/JiahuiYu/generative_inpainting.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

While deep neural networks (NN) significantly advance image compressed sensing (CS) by improving reconstruction quality, the necessity of training current CS NNs from scratch constrains their effectiveness and hampers rapid deployment. Although recent methods utilize pre-trained diffusion models for image reconstruction, they struggle with slow inference and restricted adaptability to CS. To tackle these challenges, this paper proposes Invertible Diffusion Models (IDM), a novel efficient, end-to-end diffusion-based CS method. IDM repurposes a large-scale diffusion sampling process as a reconstruction model, and fine-tunes it end-to-end to recover original images directly from CS measurements, moving beyond the traditional paradigm of one-step noise estimation learning. To enable such memory-intensive end-to-end fine-tuning, we propose a novel two-level invertible design to transform both (1) multi-step sampling process and (2) noise estimation U-Net in each step into invertible networks. As a result, most intermediate features are cleared during training to reduce up to 93.8% GPU memory. In addition, we develop a set of lightweight modules to inject measurements into noise estimator to further facilitate reconstruction. Experiments demonstrate that IDM outperforms existing state-of-the-art CS networks by up to 2.64dB in PSNR. Compared to the recent diffusion-based approach DDNM, our IDM achieves up to 10.09dB PSNR gain and 14.54 times faster inference. Code is available at https://github.com/Guaishou74851/IDM.

Deep neural networks excel at finding hierarchical representations that solve complex tasks over large data sets. How can we humans understand these learned representations? In this work, we present network dissection, an analytic framework to systematically identify the semantics of individual hidden units within image classification and image generation networks. First, we analyze a convolutional neural network (CNN) trained on scene classification and discover units that match a diverse set of object concepts. We find evidence that the network has learned many object classes that play crucial roles in classifying scene classes. Second, we use a similar analytic method to analyze a generative adversarial network (GAN) model trained to generate scenes. By analyzing changes made when small sets of units are activated or deactivated, we find that objects can be added and removed from the output scenes while adapting to the context. Finally, we apply our analytic framework to understanding adversarial attacks and to semantic image editing.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990pm0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968pm0.005) and 17 for radially (0.962pm0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

Photography during night or in dark conditions typically suffers from noise, low light and blurring issues due to the dim environment and the common use of long exposure. Although Deblurring and Low-light Image Enhancement (LLIE) are related under these conditions, most approaches in image restoration solve these tasks separately. In this paper, we present an efficient and robust neural network for multi-task low-light image restoration. Instead of following the current tendency of Transformer-based models, we propose new attention mechanisms to enhance the receptive field of efficient CNNs. Our method reduces the computational costs in terms of parameters and MAC operations compared to previous methods. Our model, DarkIR, achieves new state-of-the-art results on the popular LOLBlur, LOLv2 and Real-LOLBlur datasets, being able to generalize on real-world night and dark images. Code and models at https://github.com/cidautai/DarkIR

We study the task of image inpainting, which is to fill in the missing region of an incomplete image with plausible contents. To this end, we propose a learning-based approach to generate visually coherent completion given a high-resolution image with missing components. In order to overcome the difficulty to directly learn the distribution of high-dimensional image data, we divide the task into inference and translation as two separate steps and model each step with a deep neural network. We also use simple heuristics to guide the propagation of local textures from the boundary to the hole. We show that, by using such techniques, inpainting reduces to the problem of learning two image-feature translation functions in much smaller space and hence easier to train. We evaluate our method on several public datasets and show that we generate results of better visual quality than previous state-of-the-art methods.

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.

We consider the training of the first layer of vision models and notice the clear relationship between pixel values and gradient update magnitudes: the gradients arriving at the weights of a first layer are by definition directly proportional to (normalized) input pixel values. Thus, an image with low contrast has a smaller impact on learning than an image with higher contrast, and a very bright or very dark image has a stronger impact on the weights than an image with moderate brightness. In this work, we propose performing gradient descent on the embeddings produced by the first layer of the model. However, switching to discrete inputs with an embedding layer is not a reasonable option for vision models. Thus, we propose the conceptual procedure of (i) a gradient descent step on first layer activations to construct an activation proposal, and (ii) finding the optimal weights of the first layer, i.e., those weights which minimize the squared distance to the activation proposal. We provide a closed form solution of the procedure and adjust it for robust stochastic training while computing everything efficiently. Empirically, we find that TrAct (Training Activations) speeds up training by factors between 1.25x and 4x while requiring only a small computational overhead. We demonstrate the utility of TrAct with different optimizers for a range of different vision models including convolutional and transformer architectures.

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Deep learning has been successful in automating the design of features in machine learning pipelines. However, the algorithms optimizing neural network parameters remain largely hand-designed and computationally inefficient. We study if we can use deep learning to directly predict these parameters by exploiting the past knowledge of training other networks. We introduce a large-scale dataset of diverse computational graphs of neural architectures - DeepNets-1M - and use it to explore parameter prediction on CIFAR-10 and ImageNet. By leveraging advances in graph neural networks, we propose a hypernetwork that can predict performant parameters in a single forward pass taking a fraction of a second, even on a CPU. The proposed model achieves surprisingly good performance on unseen and diverse networks. For example, it is able to predict all 24 million parameters of a ResNet-50 achieving a 60% accuracy on CIFAR-10. On ImageNet, top-5 accuracy of some of our networks approaches 50%. Our task along with the model and results can potentially lead to a new, more computationally efficient paradigm of training networks. Our model also learns a strong representation of neural architectures enabling their analysis.

Deep neural networks (DNNs) trained for image denoising are able to generate high-quality samples with score-based reverse diffusion algorithms. These impressive capabilities seem to imply an escape from the curse of dimensionality, but recent reports of memorization of the training set raise the question of whether these networks are learning the "true" continuous density of the data. Here, we show that two DNNs trained on non-overlapping subsets of a dataset learn nearly the same score function, and thus the same density, when the number of training images is large enough. In this regime of strong generalization, diffusion-generated images are distinct from the training set, and are of high visual quality, suggesting that the inductive biases of the DNNs are well-aligned with the data density. We analyze the learned denoising functions and show that the inductive biases give rise to a shrinkage operation in a basis adapted to the underlying image. Examination of these bases reveals oscillating harmonic structures along contours and in homogeneous regions. We demonstrate that trained denoisers are inductively biased towards these geometry-adaptive harmonic bases since they arise not only when the network is trained on photographic images, but also when it is trained on image classes supported on low-dimensional manifolds for which the harmonic basis is suboptimal. Finally, we show that when trained on regular image classes for which the optimal basis is known to be geometry-adaptive and harmonic, the denoising performance of the networks is near-optimal.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

Image representations, from SIFT and Bag of Visual Words to Convolutional Neural Networks (CNNs), are a crucial component of almost any image understanding system. Nevertheless, our understanding of them remains limited. In this paper we conduct a direct analysis of the visual information contained in representations by asking the following question: given an encoding of an image, to which extent is it possible to reconstruct the image itself? To answer this question we contribute a general framework to invert representations. We show that this method can invert representations such as HOG and SIFT more accurately than recent alternatives while being applicable to CNNs too. We then use this technique to study the inverse of recent state-of-the-art CNN image representations for the first time. Among our findings, we show that several layers in CNNs retain photographically accurate information about the image, with different degrees of geometric and photometric invariance.

Extracting useful visual cues for the downstream tasks is especially challenging under low-light vision. Prior works create enhanced representations by either correlating visual quality with machine perception or designing illumination-degrading transformation methods that require pre-training on synthetic datasets. We argue that optimizing enhanced image representation pertaining to the loss of the downstream task can result in more expressive representations. Therefore, in this work, we propose a novel module, FeatEnHancer, that hierarchically combines multiscale features using multiheaded attention guided by task-related loss function to create suitable representations. Furthermore, our intra-scale enhancement improves the quality of features extracted at each scale or level, as well as combines features from different scales in a way that reflects their relative importance for the task at hand. FeatEnHancer is a general-purpose plug-and-play module and can be incorporated into any low-light vision pipeline. We show with extensive experimentation that the enhanced representation produced with FeatEnHancer significantly and consistently improves results in several low-light vision tasks, including dark object detection (+5.7 mAP on ExDark), face detection (+1.5 mAPon DARK FACE), nighttime semantic segmentation (+5.1 mIoU on ACDC ), and video object detection (+1.8 mAP on DarkVision), highlighting the effectiveness of enhancing hierarchical features under low-light vision.

We present a simple baseline for directly estimating the relative pose (rotation and translation, including scale) between two images. Deep methods have recently shown strong progress but often require complex or multi-stage architectures. We show that a handful of modifications can be applied to a Vision Transformer (ViT) to bring its computations close to the Eight-Point Algorithm. This inductive bias enables a simple method to be competitive in multiple settings, often substantially improving over the state of the art with strong performance gains in limited data regimes.

Deep neural network (DNN) inference has become an important part of many data-center workloads. This has prompted focused efforts to design ever-faster deep learning accelerators such as GPUs and TPUs. However, an end-to-end DNN-based vision application contains more than just DNN inference, including input decompression, resizing, sampling, normalization, and data transfer. In this paper, we perform a thorough evaluation of computer vision inference requests performed on a throughput-optimized serving system. We quantify the performance impact of server overheads such as data movement, preprocessing, and message brokers between two DNNs producing outputs at different rates. Our empirical analysis encompasses many computer vision tasks including image classification, segmentation, detection, depth-estimation, and more complex processing pipelines with multiple DNNs. Our results consistently demonstrate that end-to-end application performance can easily be dominated by data processing and data movement functions (up to 56% of end-to-end latency in a medium-sized image, and sim 80% impact on system throughput in a large image), even though these functions have been conventionally overlooked in deep learning system design. Our work identifies important performance bottlenecks in different application scenarios, achieves 2.25times better throughput compared to prior work, and paves the way for more holistic deep learning system design.

DeepLab2 is a TensorFlow library for deep labeling, aiming to provide a state-of-the-art and easy-to-use TensorFlow codebase for general dense pixel prediction problems in computer vision. DeepLab2 includes all our recently developed DeepLab model variants with pretrained checkpoints as well as model training and evaluation code, allowing the community to reproduce and further improve upon the state-of-art systems. To showcase the effectiveness of DeepLab2, our Panoptic-DeepLab employing Axial-SWideRNet as network backbone achieves 68.0% PQ or 83.5% mIoU on Cityscaspes validation set, with only single-scale inference and ImageNet-1K pretrained checkpoints. We hope that publicly sharing our library could facilitate future research on dense pixel labeling tasks and envision new applications of this technology. Code is made publicly available at https://github.com/google-research/deeplab2.

We present a one-shot text-to-image diffusion model that can generate high-resolution images from natural language descriptions. Our model employs a layered U-Net architecture that simultaneously synthesizes images at multiple resolution scales. We show that this method outperforms the baseline of synthesizing images only at the target resolution, while reducing the computational cost per step. We demonstrate that higher resolution synthesis can be achieved by layering convolutions at additional resolution scales, in contrast to other methods which require additional models for super-resolution synthesis.

With the goal of recovering high-quality image content from its degraded version, image restoration enjoys numerous applications, such as in surveillance, computational photography, medical imaging, and remote sensing. Recently, convolutional neural networks (CNNs) have achieved dramatic improvements over conventional approaches for image restoration task. Existing CNN-based methods typically operate either on full-resolution or on progressively low-resolution representations. In the former case, spatially precise but contextually less robust results are achieved, while in the latter case, semantically reliable but spatially less accurate outputs are generated. In this paper, we present a novel architecture with the collective goals of maintaining spatially-precise high-resolution representations through the entire network and receiving strong contextual information from the low-resolution representations. The core of our approach is a multi-scale residual block containing several key elements: (a) parallel multi-resolution convolution streams for extracting multi-scale features, (b) information exchange across the multi-resolution streams, (c) spatial and channel attention mechanisms for capturing contextual information, and (d) attention based multi-scale feature aggregation. In a nutshell, our approach learns an enriched set of features that combines contextual information from multiple scales, while simultaneously preserving the high-resolution spatial details. Extensive experiments on five real image benchmark datasets demonstrate that our method, named as MIRNet, achieves state-of-the-art results for a variety of image processing tasks, including image denoising, super-resolution, and image enhancement. The source code and pre-trained models are available at https://github.com/swz30/MIRNet.

Recently, stereo vision based on lightweight RGBD cameras has been widely used in various fields. However, limited by the imaging principles, the commonly used RGB-D cameras based on TOF, structured light, or binocular vision acquire some invalid data inevitably, such as weak reflection, boundary shadows, and artifacts, which may bring adverse impacts to the follow-up work. In this paper, we propose a new model for depth image completion based on the Attention Guided Gated-convolutional Network (AGG-Net), through which more accurate and reliable depth images can be obtained from the raw depth maps and the corresponding RGB images. Our model employs a UNet-like architecture which consists of two parallel branches of depth and color features. In the encoding stage, an Attention Guided Gated-Convolution (AG-GConv) module is proposed to realize the fusion of depth and color features at different scales, which can effectively reduce the negative impacts of invalid depth data on the reconstruction. In the decoding stage, an Attention Guided Skip Connection (AG-SC) module is presented to avoid introducing too many depth-irrelevant features to the reconstruction. The experimental results demonstrate that our method outperforms the state-of-the-art methods on the popular benchmarks NYU-Depth V2, DIML, and SUN RGB-D.

We look critically at popular self-supervision techniques for learning deep convolutional neural networks without manual labels. We show that three different and representative methods, BiGAN, RotNet and DeepCluster, can learn the first few layers of a convolutional network from a single image as well as using millions of images and manual labels, provided that strong data augmentation is used. However, for deeper layers the gap with manual supervision cannot be closed even if millions of unlabelled images are used for training. We conclude that: (1) the weights of the early layers of deep networks contain limited information about the statistics of natural images, that (2) such low-level statistics can be learned through self-supervision just as well as through strong supervision, and that (3) the low-level statistics can be captured via synthetic transformations instead of using a large image dataset.

Vision Transformer (ViT) has become one of the most popular neural architectures due to its great scalability, computational efficiency, and compelling performance in many vision tasks. However, ViT has shown inferior performance to Convolutional Neural Network (CNN) on medical tasks due to its data-hungry nature and the lack of annotated medical data. In this paper, we pre-train ViTs on 266,340 chest X-rays using Masked Autoencoders (MAE) which reconstruct missing pixels from a small part of each image. For comparison, CNNs are also pre-trained on the same 266,340 X-rays using advanced self-supervised methods (e.g., MoCo v2). The results show that our pre-trained ViT performs comparably (sometimes better) to the state-of-the-art CNN (DenseNet-121) for multi-label thorax disease classification. This performance is attributed to the strong recipes extracted from our empirical studies for pre-training and fine-tuning ViT. The pre-training recipe signifies that medical reconstruction requires a much smaller proportion of an image (10% vs. 25%) and a more moderate random resized crop range (0.5~1.0 vs. 0.2~1.0) compared with natural imaging. Furthermore, we remark that in-domain transfer learning is preferred whenever possible. The fine-tuning recipe discloses that layer-wise LR decay, RandAug magnitude, and DropPath rate are significant factors to consider. We hope that this study can direct future research on the application of Transformers to a larger variety of medical imaging tasks.

Recent advances in deep learning have shown exciting promise in filling large holes and lead to another orientation for image inpainting. However, existing learning-based methods often create artifacts and fallacious textures because of insufficient cognition understanding. Previous generative networks are limited with single receptive type and give up pooling in consideration of detail sharpness. Human cognition is constant regardless of the target attribute. As multiple receptive fields improve the ability of abstract image characterization and pooling can keep feature invariant, specifically, deep inception learning is adopted to promote high-level feature representation and enhance model learning capacity for local patches. Moreover, approaches for generating diverse mask images are introduced and a random mask dataset is created. We benchmark our methods on ImageNet, Places2 dataset, and CelebA-HQ. Experiments for regular, irregular, and custom regions completion are all performed and free-style image inpainting is also presented. Quantitative comparisons with previous state-of-the-art methods show that ours obtain much more natural image completions.

Deep Convolutional Neural Networks (DCNNs) have recently shown state of the art performance in high level vision tasks, such as image classification and object detection. This work brings together methods from DCNNs and probabilistic graphical models for addressing the task of pixel-level classification (also called "semantic image segmentation"). We show that responses at the final layer of DCNNs are not sufficiently localized for accurate object segmentation. This is due to the very invariance properties that make DCNNs good for high level tasks. We overcome this poor localization property of deep networks by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF). Qualitatively, our "DeepLab" system is able to localize segment boundaries at a level of accuracy which is beyond previous methods. Quantitatively, our method sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 71.6% IOU accuracy in the test set. We show how these results can be obtained efficiently: Careful network re-purposing and a novel application of the 'hole' algorithm from the wavelet community allow dense computation of neural net responses at 8 frames per second on a modern GPU.

High dynamic range (HDR) images capture much more intensity levels than standard ones. Current methods predominantly generate HDR images from 8-bit low dynamic range (LDR) sRGB images that have been degraded by the camera processing pipeline. However, it becomes a formidable task to retrieve extremely high dynamic range scenes from such limited bit-depth data. Unlike existing methods, the core idea of this work is to incorporate more informative Raw sensor data to generate HDR images, aiming to recover scene information in hard regions (the darkest and brightest areas of an HDR scene). To this end, we propose a model tailor-made for Raw images, harnessing the unique features of Raw data to facilitate the Raw-to-HDR mapping. Specifically, we learn exposure masks to separate the hard and easy regions of a high dynamic scene. Then, we introduce two important guidances, dual intensity guidance, which guides less informative channels with more informative ones, and global spatial guidance, which extrapolates scene specifics over an extended spatial domain. To verify our Raw-to-HDR approach, we collect a large Raw/HDR paired dataset for both training and testing. Our empirical evaluations validate the superiority of the proposed Raw-to-HDR reconstruction model, as well as our newly captured dataset in the experiments.

Conventional Computed Tomography (CT) methods require large numbers of noise-free projections for accurate density reconstructions, limiting their applicability to the more complex class of Cone Beam Geometry CT (CBCT) reconstruction. Recently, deep learning methods have been proposed to overcome these limitations, with methods based on neural fields (NF) showing strong performance, by approximating the reconstructed density through a continuous-in-space coordinate based neural network. Our focus is on improving such methods, however, unlike previous work, which requires training an NF from scratch for each new set of projections, we instead propose to leverage anatomical consistencies over different scans by training a single conditional NF on a dataset of projections. We propose a novel conditioning method where local modulations are modeled per patient as a field over the input domain through a Neural Modulation Field (NMF). The resulting Conditional Cone Beam Neural Tomography (CondCBNT) shows improved performance for both high and low numbers of available projections on noise-free and noisy data.

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

The ability to describe images with natural language sentences is the hallmark for image and language understanding. Such a system has wide ranging applications such as annotating images and using natural sentences to search for images.In this project we focus on the task of bidirectional image retrieval: such asystem is capable of retrieving an image based on a sentence (image search) andretrieve sentence based on an image query (image annotation). We present asystem based on a global ranking objective function which uses a combinationof convolutional neural networks (CNN) and multi layer perceptrons (MLP).It takes a pair of image and sentence and processes them in different channels,finally embedding it into a common multimodal vector space. These embeddingsencode abstract semantic information about the two inputs and can be comparedusing traditional information retrieval approaches. For each such pair, the modelreturns a score which is interpretted as a similarity metric. If this score is high,the image and sentence are likely to convey similar meaning, and if the score is low then they are likely not to. The visual input is modeled via deep convolutional neural network. On theother hand we explore three models for the textual module. The first one isbag of words with an MLP. The second one uses n-grams (bigram, trigrams,and a combination of trigram & skip-grams) with an MLP. The third is morespecialized deep network specific for modeling variable length sequences (SSE).We report comparable performance to recent work in the field, even though ouroverall model is simpler. We also show that the training time choice of how wecan generate our negative samples has a significant impact on performance, and can be used to specialize the bi-directional system in one particular task.

In medical vision, different imaging modalities provide complementary information. However, in practice, not all modalities may be available during inference or even training. Previous approaches, e.g., knowledge distillation or image synthesis, often assume the availability of full modalities for all patients during training; this is unrealistic and impractical due to the variability in data collection across sites. We propose a novel approach to learn enhanced modality-agnostic representations by employing a meta-learning strategy in training, even when only limited full modality samples are available. Meta-learning enhances partial modality representations to full modality representations by meta-training on partial modality data and meta-testing on limited full modality samples. Additionally, we co-supervise this feature enrichment by introducing an auxiliary adversarial learning branch. More specifically, a missing modality detector is used as a discriminator to mimic the full modality setting. Our segmentation framework significantly outperforms state-of-the-art brain tumor segmentation techniques in missing modality scenarios.

Image matching, which aims to identify corresponding pixel locations between images, is crucial in a wide range of scientific disciplines, aiding in image registration, fusion, and analysis. In recent years, deep learning-based image matching algorithms have dramatically outperformed humans in rapidly and accurately finding large amounts of correspondences. However, when dealing with images captured under different imaging modalities that result in significant appearance changes, the performance of these algorithms often deteriorates due to the scarcity of annotated cross-modal training data. This limitation hinders applications in various fields that rely on multiple image modalities to obtain complementary information. To address this challenge, we propose a large-scale pre-training framework that utilizes synthetic cross-modal training signals, incorporating diverse data from various sources, to train models to recognize and match fundamental structures across images. This capability is transferable to real-world, unseen cross-modality image matching tasks. Our key finding is that the matching model trained with our framework achieves remarkable generalizability across more than eight unseen cross-modality registration tasks using the same network weight, substantially outperforming existing methods, whether designed for generalization or tailored for specific tasks. This advancement significantly enhances the applicability of image matching technologies across various scientific disciplines and paves the way for new applications in multi-modality human and artificial intelligence analysis and beyond.

Non-linear manifold learning enables high-dimensional data analysis, but requires out-of-sample-extension methods to process new data points. In this paper, we propose a manifold learning algorithm based on deep learning to create an encoder, which maps a high-dimensional dataset and its low-dimensional embedding, and a decoder, which takes the embedded data back to the high-dimensional space. Stacking the encoder and decoder together constructs an autoencoder, which we term a diffusion net, that performs out-of-sample-extension as well as outlier detection. We introduce new neural net constraints for the encoder, which preserves the local geometry of the points, and we prove rates of convergence for the encoder. Also, our approach is efficient in both computational complexity and memory requirements, as opposed to previous methods that require storage of all training points in both the high-dimensional and the low-dimensional spaces to calculate the out-of-sample-extension and the pre-image.

Images fed to a deep neural network have in general undergone several handcrafted image signal processing (ISP) operations, all of which have been optimized to produce visually pleasing images. In this work, we investigate the hypothesis that the intermediate representation of visually pleasing images is sub-optimal for downstream computer vision tasks compared to the RAW image representation. We suggest that the operations of the ISP instead should be optimized towards the end task, by learning the parameters of the operations jointly during training. We extend previous works on this topic and propose a new learnable operation that enables an object detector to achieve superior performance when compared to both previous works and traditional RGB images. In experiments on the open PASCALRAW dataset, we empirically confirm our hypothesis.

Cancer is a complex disease, the understanding and treatment of which are being aided through increases in the volume of collected data and in the scale of deployed computing power. Consequently, there is a growing need for the development of data-driven and, in particular, deep learning methods for various tasks such as cancer diagnosis, detection, prognosis, and prediction. Despite recent successes, however, designing high-performing deep learning models for nonimage and nontext cancer data is a time-consuming, trial-and-error, manual task that requires both cancer domain and deep learning expertise. To that end, we develop a reinforcement-learning-based neural architecture search to automate deep-learning-based predictive model development for a class of representative cancer data. We develop custom building blocks that allow domain experts to incorporate the cancer-data-specific characteristics. We show that our approach discovers deep neural network architectures that have significantly fewer trainable parameters, shorter training time, and accuracy similar to or higher than those of manually designed architectures. We study and demonstrate the scalability of our approach on up to 1,024 Intel Knights Landing nodes of the Theta supercomputer at the Argonne Leadership Computing Facility.

Depth is the hallmark of deep neural networks. But more depth means more sequential computation and higher latency. This begs the question -- is it possible to build high-performing "non-deep" neural networks? We show that it is. To do so, we use parallel subnetworks instead of stacking one layer after another. This helps effectively reduce depth while maintaining high performance. By utilizing parallel substructures, we show, for the first time, that a network with a depth of just 12 can achieve top-1 accuracy over 80% on ImageNet, 96% on CIFAR10, and 81% on CIFAR100. We also show that a network with a low-depth (12) backbone can achieve an AP of 48% on MS-COCO. We analyze the scaling rules for our design and show how to increase performance without changing the network's depth. Finally, we provide a proof of concept for how non-deep networks could be used to build low-latency recognition systems. Code is available at https://github.com/imankgoyal/NonDeepNetworks.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

High dynamic range (HDR) imaging aims to retrieve information from multiple low-dynamic range inputs to generate realistic output. The essence is to leverage the contextual information, including both dynamic and static semantics, for better image generation. Existing methods often focus on the spatial misalignment across input frames caused by the foreground and/or camera motion. However, there is no research on jointly leveraging the dynamic and static context in a simultaneous manner. To delve into this problem, we propose a novel alignment-free network with a Semantics Consistent Transformer (SCTNet) with both spatial and channel attention modules in the network. The spatial attention aims to deal with the intra-image correlation to model the dynamic motion, while the channel attention enables the inter-image intertwining to enhance the semantic consistency across frames. Aside from this, we introduce a novel realistic HDR dataset with more variations in foreground objects, environmental factors, and larger motions. Extensive comparisons on both conventional datasets and ours validate the effectiveness of our method, achieving the best trade-off on the performance and the computational cost.

With the development of Deep Neural Networks (DNNs), plenty of methods based on DNNs have been proposed for Single Image Super-Resolution (SISR). However, existing methods mostly train the DNNs on uniformly sampled LR-HR patch pairs, which makes them fail to fully exploit informative patches within the image. In this paper, we present a simple yet effective data augmentation method. We first devise a heuristic metric to evaluate the informative importance of each patch pair. In order to reduce the computational cost for all patch pairs, we further propose to optimize the calculation of our metric by integral image, achieving about two orders of magnitude speedup. The training patch pairs are sampled according to their informative importance with our method. Extensive experiments show our sampling augmentation can consistently improve the convergence and boost the performance of various SISR architectures, including EDSR, RCAN, RDN, SRCNN and ESPCN across different scaling factors (x2, x3, x4). Code is available at https://github.com/littlepure2333/SamplingAug

For convolutional neural network models that optimize an image embedding, we propose a method to highlight the regions of images that contribute most to pairwise similarity. This work is a corollary to the visualization tools developed for classification networks, but applicable to the problem domains better suited to similarity learning. The visualization shows how similarity networks that are fine-tuned learn to focus on different features. We also generalize our approach to embedding networks that use different pooling strategies and provide a simple mechanism to support image similarity searches on objects or sub-regions in the query image.

Deep learning-based methods have achieved remarkable success in image restoration and enhancement, but are they still competitive when there is a lack of paired training data? As one such example, this paper explores the low-light image enhancement problem, where in practice it is extremely challenging to simultaneously take a low-light and a normal-light photo of the same visual scene. We propose a highly effective unsupervised generative adversarial network, dubbed EnlightenGAN, that can be trained without low/normal-light image pairs, yet proves to generalize very well on various real-world test images. Instead of supervising the learning using ground truth data, we propose to regularize the unpaired training using the information extracted from the input itself, and benchmark a series of innovations for the low-light image enhancement problem, including a global-local discriminator structure, a self-regularized perceptual loss fusion, and attention mechanism. Through extensive experiments, our proposed approach outperforms recent methods under a variety of metrics in terms of visual quality and subjective user study. Thanks to the great flexibility brought by unpaired training, EnlightenGAN is demonstrated to be easily adaptable to enhancing real-world images from various domains. The code is available at https://github.com/yueruchen/EnlightenGAN

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large computational costs. In this work, we address the challenge of downsizing medical images in order to improve downstream computational efficiency while preserving clinically-relevant features. We introduce MedVAE, a family of six large-scale 2D and 3D autoencoders capable of encoding medical images as downsized latent representations and decoding latent representations back to high-resolution images. We train MedVAE autoencoders using a novel two-stage training approach with 1,052,730 medical images. Across diverse tasks obtained from 20 medical image datasets, we demonstrate that (1) utilizing MedVAE latent representations in place of high-resolution images when training downstream models can lead to efficiency benefits (up to 70x improvement in throughput) while simultaneously preserving clinically-relevant features and (2) MedVAE can decode latent representations back to high-resolution images with high fidelity. Our work demonstrates that large-scale, generalizable autoencoders can help address critical efficiency challenges in the medical domain. Our code is available at https://github.com/StanfordMIMI/MedVAE.

Building AI models with trustworthiness is important especially in regulated areas such as healthcare. In tackling COVID-19, previous work uses convolutional neural networks as the backbone architecture, which has shown to be prone to over-caution and overconfidence in making decisions, rendering them less trustworthy -- a crucial flaw in the context of medical imaging. In this study, we propose a feature learning approach using Vision Transformers, which use an attention-based mechanism, and examine the representation learning capability of Transformers as a new backbone architecture for medical imaging. Through the task of classifying COVID-19 chest radiographs, we investigate into whether generalization capabilities benefit solely from Vision Transformers' architectural advances. Quantitative and qualitative evaluations are conducted on the trustworthiness of the models, through the use of "trust score" computation and a visual explainability technique. We conclude that the attention-based feature learning approach is promising in building trustworthy deep learning models for healthcare.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Deep learning classifiers face significant challenges when dealing with heterogeneous multi-modal and multi-organ biomedical datasets. The low-level feature distinguishability limited to imaging-modality hinders the classifiers' ability to learn high-level semantic relationships, resulting in sub-optimal performance. To address this issue, image augmentation strategies are employed as regularization techniques. While additive noise input during network training is a well-established augmentation as regularization method, modern pipelines often favor more robust techniques such as dropout and weight decay. This preference stems from the observation that combining these established techniques with noise input can adversely affect model performance. In this study, we propose a novel pretraining pipeline that learns to generate conditional noise mask specifically tailored to improve performance on multi-modal and multi-organ datasets. As a reinforcement learning algorithm, our approach employs a dual-component system comprising a very light-weight policy network that learns to sample conditional noise using a differentiable beta distribution as well as a classifier network. The policy network is trained using the reinforce algorithm to generate image-specific noise masks that regularize the classifier during pretraining. A key aspect is that the policy network's role is limited to obtaining an intermediate (or heated) model before fine-tuning. During inference, the policy network is omitted, allowing direct comparison between the baseline and noise-regularized models. We conducted experiments and related analyses on RadImageNet datasets. Results demonstrate that fine-tuning the intermediate models consistently outperforms conventional training algorithms on both classification and generalization to unseen concept tasks.

Standard training datasets for deep learning often contain objects in common settings (e.g., "a horse on grass" or "a ship in water") since they are usually collected by randomly scraping the web. Uncommon and rare settings (e.g., "a plane on water", "a car in snowy weather") are thus severely under-represented in the training data. This can lead to an undesirable bias in model predictions towards common settings and create a false sense of accuracy. In this paper, we introduce FOCUS (Familiar Objects in Common and Uncommon Settings), a dataset for stress-testing the generalization power of deep image classifiers. By leveraging the power of modern search engines, we deliberately gather data containing objects in common and uncommon settings in a wide range of locations, weather conditions, and time of day. We present a detailed analysis of the performance of various popular image classifiers on our dataset and demonstrate a clear drop in performance when classifying images in uncommon settings. By analyzing deep features of these models, we show that such errors can be due to the use of spurious features in model predictions. We believe that our dataset will aid researchers in understanding the inability of deep models to generalize well to uncommon settings and drive future work on improving their distributional robustness.

The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particularly benefited: the use of deep learning models trained on large amounts of natural images has greatly improved its quality, and approaches that combine the diverse information contained in visual experiences have proliferated rapidly in recent years. In this technical paper, by taking advantage of the simple and generic framework that we proposed (Takagi and Nishimoto, CVPR 2023), we examine the extent to which various additional decoding techniques affect the performance of visual experience reconstruction. Specifically, we combined our earlier work with the following three techniques: using decoded text from brain activity, nonlinear optimization for structural image reconstruction, and using decoded depth information from brain activity. We confirmed that these techniques contributed to improving accuracy over the baseline. We also discuss what researchers should consider when performing visual reconstruction using deep generative models trained on large datasets. Please check our webpage at https://sites.google.com/view/stablediffusion-with-brain/. Code is also available at https://github.com/yu-takagi/StableDiffusionReconstruction.

We have witnessed significant progress in deep learning-based 3D vision, ranging from neural radiance field (NeRF) based 3D representation learning to applications in novel view synthesis (NVS). However, existing scene-level datasets for deep learning-based 3D vision, limited to either synthetic environments or a narrow selection of real-world scenes, are quite insufficient. This insufficiency not only hinders a comprehensive benchmark of existing methods but also caps what could be explored in deep learning-based 3D analysis. To address this critical gap, we present DL3DV-10K, a large-scale scene dataset, featuring 51.2 million frames from 10,510 videos captured from 65 types of point-of-interest (POI) locations, covering both bounded and unbounded scenes, with different levels of reflection, transparency, and lighting. We conducted a comprehensive benchmark of recent NVS methods on DL3DV-10K, which revealed valuable insights for future research in NVS. In addition, we have obtained encouraging results in a pilot study to learn generalizable NeRF from DL3DV-10K, which manifests the necessity of a large-scale scene-level dataset to forge a path toward a foundation model for learning 3D representation. Our DL3DV-10K dataset, benchmark results, and models will be publicly accessible at https://dl3dv-10k.github.io/DL3DV-10K/.

There has been much interest in deploying deep learning algorithms on low-powered devices, including smartphones, drones, and medical sensors. However, full-scale deep neural networks are often too resource-intensive in terms of energy and storage. As a result, the bulk part of the machine learning operation is therefore often carried out on an edge server, where the data is compressed and transmitted. However, compressing data (such as images) leads to transmitting information irrelevant to the supervised task. Another popular approach is to split the deep network between the device and the server while compressing intermediate features. To date, however, such split computing strategies have barely outperformed the aforementioned naive data compression baselines due to their inefficient approaches to feature compression. This paper adopts ideas from knowledge distillation and neural image compression to compress intermediate feature representations more efficiently. Our supervised compression approach uses a teacher model and a student model with a stochastic bottleneck and learnable prior for entropy coding (Entropic Student). We compare our approach to various neural image and feature compression baselines in three vision tasks and found that it achieves better supervised rate-distortion performance while maintaining smaller end-to-end latency. We furthermore show that the learned feature representations can be tuned to serve multiple downstream tasks.

Deep learning has proven to be a highly effective problem-solving tool for object detection and image segmentation across various domains such as healthcare and autonomous driving. At the heart of this performance lies neural architecture design which relies heavily on domain knowledge and prior experience on the researchers' behalf. More recently, this process of finding the most optimal architectures, given an initial search space of possible operations, was automated by Neural Architecture Search (NAS). In this paper, we evaluate the robustness of one such algorithm known as Efficient NAS (ENAS) against data agnostic poisoning attacks on the original search space with carefully designed ineffective operations. By evaluating algorithm performance on the CIFAR-10 dataset, we empirically demonstrate how our novel search space poisoning (SSP) approach and multiple-instance poisoning attacks exploit design flaws in the ENAS controller to result in inflated prediction error rates for child networks. Our results provide insights into the challenges to surmount in using NAS for more adversarially robust architecture search.

Very deep convolutional networks with hundreds of layers have led to significant reductions in error on competitive benchmarks. Although the unmatched expressiveness of the many layers can be highly desirable at test time, training very deep networks comes with its own set of challenges. The gradients can vanish, the forward flow often diminishes, and the training time can be painfully slow. To address these problems, we propose stochastic depth, a training procedure that enables the seemingly contradictory setup to train short networks and use deep networks at test time. We start with very deep networks but during training, for each mini-batch, randomly drop a subset of layers and bypass them with the identity function. This simple approach complements the recent success of residual networks. It reduces training time substantially and improves the test error significantly on almost all data sets that we used for evaluation. With stochastic depth we can increase the depth of residual networks even beyond 1200 layers and still yield meaningful improvements in test error (4.91% on CIFAR-10).

Training deep neural networks on images represented as grids of pixels has brought to light an interesting phenomenon known as adversarial examples. Inspired by how humans reconstruct abstract concepts, we attempt to codify the input bitmap image into a set of compact, interpretable elements to avoid being fooled by the adversarial structures. We take the first step in this direction by experimenting with image vectorization as an input transformation step to map the adversarial examples back into the natural manifold of MNIST handwritten digits. We compare our method vs. state-of-the-art input transformations and further discuss the trade-offs between a hand-designed and a learned transformation defense.

Incorporating a deep generative model as the prior distribution in inverse problems has established substantial success in reconstructing images from corrupted observations. Notwithstanding, the existing optimization approaches use gradient descent largely without adapting to the non-convex nature of the problem and can be sensitive to initial values, impeding further performance improvement. In this paper, we propose an efficient amortized optimization scheme for inverse problems with a deep generative prior. Specifically, the optimization task with high degrees of difficulty is decomposed into optimizing a sequence of much easier ones. We provide a theoretical guarantee of the proposed algorithm and empirically validate it on different inverse problems. As a result, our approach outperforms baseline methods qualitatively and quantitatively by a large margin.

Generating a description of an image is called image captioning. Image captioning requires to recognize the important objects, their attributes and their relationships in an image. It also needs to generate syntactically and semantically correct sentences. Deep learning-based techniques are capable of handling the complexities and challenges of image captioning. In this survey paper, we aim to present a comprehensive review of existing deep learning-based image captioning techniques. We discuss the foundation of the techniques to analyze their performances, strengths and limitations. We also discuss the datasets and the evaluation metrics popularly used in deep learning based automatic image captioning.

Blind image deconvolution (BID) is a classic yet challenging problem in the field of image processing. Recent advances in deep image prior (DIP) have motivated a series of DIP-based approaches, demonstrating remarkable success in BID. However, due to the high non-convexity of the inherent optimization process, these methods are notorious for their sensitivity to the initialized kernel. To alleviate this issue and further improve their performance, we propose a new framework for BID that better considers the prior modeling and the initialization for blur kernels, leveraging a deep generative model. The proposed approach pre-trains a generative adversarial network-based kernel generator that aptly characterizes the kernel priors and a kernel initializer that facilitates a well-informed initialization for the blur kernel through latent space encoding. With the pre-trained kernel generator and initializer, one can obtain a high-quality initialization of the blur kernel, and enable optimization within a compact latent kernel manifold. Such a framework results in an evident performance improvement over existing DIP-based BID methods. Extensive experiments on different datasets demonstrate the effectiveness of the proposed method.

Deep Neural Networks (DNNs) require large amounts of annotated training data for a good performance. Often this data is generated using manual labeling (error-prone and time-consuming) or rendering (requiring geometry and material information). Both approaches make it difficult or uneconomic to apply them to many small-scale applications. A fast and straightforward approach of acquiring the necessary training data would allow the adoption of deep learning to even the smallest of applications. Chroma keying is the process of replacing a color (usually blue or green) with another background. Instead of chroma keying, we propose luminance keying for fast and straightforward training image acquisition. We deploy a black screen with high light absorption (99.99\%) to record roughly 1-minute long videos of our target objects, circumventing typical problems of chroma keying, such as color bleeding or color overlap between background color and object color. Next we automatically mask our objects using simple brightness thresholding, saving the need for manual annotation. Finally, we automatically place the objects on random backgrounds and train a 2D object detector. We do extensive evaluation of the performance on the widely-used YCB-V object set and compare favourably to other conventional techniques such as rendering, without needing 3D meshes, materials or any other information of our target objects and in a fraction of the time needed for other approaches. Our work demonstrates highly accurate training data acquisition allowing to start training state-of-the-art networks within minutes.

This study addresses the issue of fusing infrared and visible images that appear differently for object detection. Aiming at generating an image of high visual quality, previous approaches discover commons underlying the two modalities and fuse upon the common space either by iterative optimization or deep networks. These approaches neglect that modality differences implying the complementary information are extremely important for both fusion and subsequent detection task. This paper proposes a bilevel optimization formulation for the joint problem of fusion and detection, and then unrolls to a target-aware Dual Adversarial Learning (TarDAL) network for fusion and a commonly used detection network. The fusion network with one generator and dual discriminators seeks commons while learning from differences, which preserves structural information of targets from the infrared and textural details from the visible. Furthermore, we build a synchronized imaging system with calibrated infrared and optical sensors, and collect currently the most comprehensive benchmark covering a wide range of scenarios. Extensive experiments on several public datasets and our benchmark demonstrate that our method outputs not only visually appealing fusion but also higher detection mAP than the state-of-the-art approaches.

Remote sensing has significantly advanced water detection by applying semantic segmentation techniques to satellite imagery. However, semantic segmentation remains challenging due to the substantial amount of annotated data required. This is particularly problematic in wetland detection, where water extent varies over time and space, necessitating multiple annotations for the same area. In this paper, we present DeepAqua, a self-supervised deep learning model that leverages knowledge distillation to eliminate the need for manual annotations during the training phase. DeepAqua utilizes the Normalized Difference Water Index (NDWI) as a teacher model to train a Convolutional Neural Network (CNN) for segmenting water from Synthetic Aperture Radar (SAR) images. To train the student model, we exploit cases where optical- and radar-based water masks coincide, enabling the detection of both open and vegetated water surfaces. Our model represents a significant advancement in computer vision techniques by effectively training semantic segmentation models without any manually annotated data. This approach offers a practical solution for monitoring wetland water extent changes without needing ground truth data, making it highly adaptable and scalable for wetland conservation efforts.

The integration of deep learning systems into the medical domain has been hindered by the resource-intensive process of data annotation and the inability of these systems to generalize to different data distributions. Foundation models, which are models pre-trained on large datasets, have emerged as a solution to reduce reliance on annotated data and enhance model generalizability and robustness. DINOv2, an open-source foundation model pre-trained with self-supervised learning on 142 million curated natural images, excels in extracting general-purpose visual representations, exhibiting promising capabilities across various vision tasks. Nevertheless, a critical question remains unanswered regarding DINOv2's adaptability to radiological imaging, and the clarity on whether its features are sufficiently general to benefit radiology image analysis is yet to be established. Therefore, this study comprehensively evaluates DINOv2 for radiology, conducting over 100 experiments across diverse modalities (X-ray, CT, and MRI). Tasks include disease classification and organ segmentation on both 2D and 3D images, evaluated under different settings like kNN, few-shot learning, linear-probing, end-to-end fine-tuning, and parameter-efficient fine-tuning, to measure the effectiveness and generalizability of the DINOv2 feature embeddings. Comparative analyses with established medical image analysis models, U-Net and TransUnet for segmentation, and CNN and ViT models pre-trained via supervised, weakly supervised, and self-supervised learning for classification, reveal DINOv2's superior performance in segmentation tasks and competitive results in disease classification. The findings contribute insights to potential avenues for optimizing pre-training strategies for medical imaging and enhancing the broader understanding of DINOv2's role in bridging the gap between natural and radiological image analysis.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

We present ZeroRF, a novel per-scene optimization method addressing the challenge of sparse view 360{\deg} reconstruction in neural field representations. Current breakthroughs like Neural Radiance Fields (NeRF) have demonstrated high-fidelity image synthesis but struggle with sparse input views. Existing methods, such as Generalizable NeRFs and per-scene optimization approaches, face limitations in data dependency, computational cost, and generalization across diverse scenarios. To overcome these challenges, we propose ZeroRF, whose key idea is to integrate a tailored Deep Image Prior into a factorized NeRF representation. Unlike traditional methods, ZeroRF parametrizes feature grids with a neural network generator, enabling efficient sparse view 360{\deg} reconstruction without any pretraining or additional regularization. Extensive experiments showcase ZeroRF's versatility and superiority in terms of both quality and speed, achieving state-of-the-art results on benchmark datasets. ZeroRF's significance extends to applications in 3D content generation and editing. Project page: https://sarahweiii.github.io/zerorf/

Deep learning based single image super-resolution models have been widely studied and superb results are achieved in upscaling low-resolution images with fixed scale factor and downscaling degradation kernel. To improve real world applicability of such models, there are growing interests to develop models optimized for arbitrary upscaling factors. Our proposed method is the first to treat arbitrary rescaling, both upscaling and downscaling, as one unified process. Using joint optimization of both directions, the proposed model is able to learn upscaling and downscaling simultaneously and achieve bidirectional arbitrary image rescaling. It improves the performance of current arbitrary upscaling models by a large margin while at the same time learns to maintain visual perception quality in downscaled images. The proposed model is further shown to be robust in cycle idempotence test, free of severe degradations in reconstruction accuracy when the downscaling-to-upscaling cycle is applied repetitively. This robustness is beneficial for image rescaling in the wild when this cycle could be applied to one image for multiple times. It also performs well on tests with arbitrary large scales and asymmetric scales, even when the model is not trained with such tasks. Extensive experiments are conducted to demonstrate the superior performance of our model.

Deep residual networks have emerged as a family of extremely deep architectures showing compelling accuracy and nice convergence behaviors. In this paper, we analyze the propagation formulations behind the residual building blocks, which suggest that the forward and backward signals can be directly propagated from one block to any other block, when using identity mappings as the skip connections and after-addition activation. A series of ablation experiments support the importance of these identity mappings. This motivates us to propose a new residual unit, which makes training easier and improves generalization. We report improved results using a 1001-layer ResNet on CIFAR-10 (4.62% error) and CIFAR-100, and a 200-layer ResNet on ImageNet. Code is available at: https://github.com/KaimingHe/resnet-1k-layers

Cardiac ultrasound (US) scanning is a commonly used techniques in cardiology to diagnose the health of the heart and its proper functioning. Therefore, it is necessary to consider ways to automate these tasks and assist medical professionals in classifying and assessing cardiac US images. Machine learning (ML) techniques are regarded as a prominent solution due to their success in numerous applications aimed at enhancing the medical field, including addressing the shortage of echography technicians. However, the limited availability of medical data presents a significant barrier to applying ML in cardiology, particularly regarding US images of the heart. This paper addresses this challenge by introducing the first open graded dataset for Cardiac Assessment and ClassificaTion of UltraSound (CACTUS), which is available online. This dataset contains images obtained from scanning a CAE Blue Phantom and representing various heart views and different quality levels, exceeding the conventional cardiac views typically found in the literature. Additionally, the paper introduces a Deep Learning (DL) framework consisting of two main components. The first component classifies cardiac US images based on the heart view using a Convolutional Neural Network (CNN). The second component uses Transfer Learning (TL) to fine-tune the knowledge from the first component and create a model for grading and assessing cardiac images. The framework demonstrates high performance in both classification and grading, achieving up to 99.43% accuracy and as low as 0.3067 error, respectively. To showcase its robustness, the framework is further fine-tuned using new images representing additional cardiac views and compared to several other state-of-the-art architectures. The framework's outcomes and performance in handling real-time scans were also assessed using a questionnaire answered by cardiac experts.

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

We present an ultra-fast, precise, parameter-free method, which we term Deep-STORM, for obtaining super-resolution images from stochastically-blinking emitters, such as fluorescent molecules used for localization microscopy. Deep-STORM uses a deep convolutional neural network that can be trained on simulated data or experimental measurements, both of which are demonstrated. The method achieves state-of-the-art resolution under challenging signal-to-noise conditions and high emitter densities, and is significantly faster than existing approaches. Additionally, no prior information on the shape of the underlying structure is required, making the method applicable to any blinking data-set. We validate our approach by super-resolution image reconstruction of simulated and experimentally obtained data.

Deep learning has recently seen rapid development and received significant attention due to its state-of-the-art performance on previously-thought hard problems. However, because of the internal complexity and nonlinear structure of deep neural networks, the underlying decision making processes for why these models are achieving such performance are challenging and sometimes mystifying to interpret. As deep learning spreads across domains, it is of paramount importance that we equip users of deep learning with tools for understanding when a model works correctly, when it fails, and ultimately how to improve its performance. Standardized toolkits for building neural networks have helped democratize deep learning; visual analytics systems have now been developed to support model explanation, interpretation, debugging, and improvement. We present a survey of the role of visual analytics in deep learning research, which highlights its short yet impactful history and thoroughly summarizes the state-of-the-art using a human-centered interrogative framework, focusing on the Five W's and How (Why, Who, What, How, When, and Where). We conclude by highlighting research directions and open research problems. This survey helps researchers and practitioners in both visual analytics and deep learning to quickly learn key aspects of this young and rapidly growing body of research, whose impact spans a diverse range of domains.

End-to-end training from scratch of current deep architectures for new computer vision problems would require Imagenet-scale datasets, and this is not always possible. In this paper we present a method that is able to take advantage of freely available multi-modal content to train computer vision algorithms without human supervision. We put forward the idea of performing self-supervised learning of visual features by mining a large scale corpus of multi-modal (text and image) documents. We show that discriminative visual features can be learnt efficiently by training a CNN to predict the semantic context in which a particular image is more probable to appear as an illustration. For this we leverage the hidden semantic structures discovered in the text corpus with a well-known topic modeling technique. Our experiments demonstrate state of the art performance in image classification, object detection, and multi-modal retrieval compared to recent self-supervised or natural-supervised approaches.

Super-Resolution convolutional neural networks have recently demonstrated high-quality restoration for single images. However, existing algorithms often require very deep architectures and long training times. Furthermore, current convolutional neural networks for super-resolution are unable to exploit features at multiple scales and weigh them equally, limiting their learning capability. In this exposition, we present a compact and accurate super-resolution algorithm namely, Densely Residual Laplacian Network (DRLN). The proposed network employs cascading residual on the residual structure to allow the flow of low-frequency information to focus on learning high and mid-level features. In addition, deep supervision is achieved via the densely concatenated residual blocks settings, which also helps in learning from high-level complex features. Moreover, we propose Laplacian attention to model the crucial features to learn the inter and intra-level dependencies between the feature maps. Furthermore, comprehensive quantitative and qualitative evaluations on low-resolution, noisy low-resolution, and real historical image benchmark datasets illustrate that our DRLN algorithm performs favorably against the state-of-the-art methods visually and accurately.

This paper presents a new state-of-the-art for document image classification and retrieval, using features learned by deep convolutional neural networks (CNNs). In object and scene analysis, deep neural nets are capable of learning a hierarchical chain of abstraction from pixel inputs to concise and descriptive representations. The current work explores this capacity in the realm of document analysis, and confirms that this representation strategy is superior to a variety of popular hand-crafted alternatives. Experiments also show that (i) features extracted from CNNs are robust to compression, (ii) CNNs trained on non-document images transfer well to document analysis tasks, and (iii) enforcing region-specific feature-learning is unnecessary given sufficient training data. This work also makes available a new labelled subset of the IIT-CDIP collection, containing 400,000 document images across 16 categories, useful for training new CNNs for document analysis.

Machine learning models, especially deep neural networks (DNNs), have been shown to be vulnerable against adversarial examples which are carefully crafted samples with a small magnitude of the perturbation. Such adversarial perturbations are usually restricted by bounding their L_p norm such that they are imperceptible, and thus many current defenses can exploit this property to reduce their adversarial impact. In this paper, we instead introduce "unrestricted" perturbations that manipulate semantically meaningful image-based visual descriptors - color and texture - in order to generate effective and photorealistic adversarial examples. We show that these semantically aware perturbations are effective against JPEG compression, feature squeezing and adversarially trained model. We also show that the proposed methods can effectively be applied to both image classification and image captioning tasks on complex datasets such as ImageNet and MSCOCO. In addition, we conduct comprehensive user studies to show that our generated semantic adversarial examples are photorealistic to humans despite large magnitude perturbations when compared to other attacks.

Unsupervised denoising is a crucial challenge in real-world imaging applications. Unsupervised deep-learning methods have demonstrated impressive performance on benchmarks based on synthetic noise. However, no metrics are available to evaluate these methods in an unsupervised fashion. This is highly problematic for the many practical applications where ground-truth clean images are not available. In this work, we propose two novel metrics: the unsupervised mean squared error (MSE) and the unsupervised peak signal-to-noise ratio (PSNR), which are computed using only noisy data. We provide a theoretical analysis of these metrics, showing that they are asymptotically consistent estimators of the supervised MSE and PSNR. Controlled numerical experiments with synthetic noise confirm that they provide accurate approximations in practice. We validate our approach on real-world data from two imaging modalities: videos in raw format and transmission electron microscopy. Our results demonstrate that the proposed metrics enable unsupervised evaluation of denoising methods based exclusively on noisy data.

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

Deep neural networks (DNNs) have demonstrated state-of-the-art results on many pattern recognition tasks, especially vision classification problems. Understanding the inner workings of such computational brains is both fascinating basic science that is interesting in its own right - similar to why we study the human brain - and will enable researchers to further improve DNNs. One path to understanding how a neural network functions internally is to study what each of its neurons has learned to detect. One such method is called activation maximization (AM), which synthesizes an input (e.g. an image) that highly activates a neuron. Here we dramatically improve the qualitative state of the art of activation maximization by harnessing a powerful, learned prior: a deep generator network (DGN). The algorithm (1) generates qualitatively state-of-the-art synthetic images that look almost real, (2) reveals the features learned by each neuron in an interpretable way, (3) generalizes well to new datasets and somewhat well to different network architectures without requiring the prior to be relearned, and (4) can be considered as a high-quality generative method (in this case, by generating novel, creative, interesting, recognizable images).

Starting with early successes in computer vision tasks, deep learning based techniques have since overtaken state of the art approaches in a multitude of domains. However, it has been demonstrated time and again that these techniques fail to capture semantic context and logical constraints, instead often relying on spurious correlations to arrive at the answer. Since application of deep learning techniques to critical scenarios are dependent on adherence to domain specific constraints, several attempts have been made to address this issue. One limitation holding back a thorough exploration of this area, is a lack of suitable datasets which feature a rich set of rules. In order to address this, we present the ChessVision Dataset, consisting of 200,000+ images of annotated chess games in progress, requiring recreation of the game state from its corresponding image. This is accompanied by a curated set of rules which constrains the set of predictions to "reasonable" game states, and are designed to probe key semantic abilities like localization and enumeration. Alongside standard metrics, additional metrics to measure performance with regards to logical consistency is presented. We analyze several popular and state of the art vision models on this task, and show that, although their performance on standard metrics are laudable, they produce a plethora of incoherent results, indicating that this dataset presents a significant challenge for future works.

We propose Deep Feature Factorization (DFF), a method capable of localizing similar semantic concepts within an image or a set of images. We use DFF to gain insight into a deep convolutional neural network's learned features, where we detect hierarchical cluster structures in feature space. This is visualized as heat maps, which highlight semantically matching regions across a set of images, revealing what the network `perceives' as similar. DFF can also be used to perform co-segmentation and co-localization, and we report state-of-the-art results on these tasks.

Deep Neural Networks (DNNs) have been a large driver and enabler for AI breakthroughs in recent years. These models have been getting larger in their attempt to become more accurate and tackle new upcoming use-cases, including AR/VR and intelligent assistants. However, the training process of such large models is a costly and time-consuming process, which typically yields a single model to fit all targets. To mitigate this, various techniques have been proposed in the literature, including pruning, sparsification or quantization of the model weights and updates. While able to achieve high compression rates, they often incur computational overheads or accuracy penalties. Alternatively, factorization methods have been leveraged to incorporate low-rank compression in the training process. Similarly, such techniques (e.g.,~SVD) frequently rely on the computationally expensive decomposition of layers and are potentially sub-optimal for non-linear models, such as DNNs. In this work, we take a further step in designing efficient low-rank models and propose Maestro, a framework for trainable low-rank layers. Instead of regularly applying a priori decompositions such as SVD, the low-rank structure is built into the training process through a generalized variant of Ordered Dropout. This method imposes an importance ordering via sampling on the decomposed DNN structure. Our theoretical analysis demonstrates that our method recovers the SVD decomposition of linear mapping on uniformly distributed data and PCA for linear autoencoders. We further apply our technique on DNNs and empirically illustrate that Maestro enables the extraction of lower footprint models that preserve model performance while allowing for graceful accuracy-latency tradeoff for the deployment to devices of different capabilities.

We present a new data-driven video inpainting method for recovering missing regions of video frames. A novel deep learning architecture is proposed which contains two sub-networks: a temporal structure inference network and a spatial detail recovering network. The temporal structure inference network is built upon a 3D fully convolutional architecture: it only learns to complete a low-resolution video volume given the expensive computational cost of 3D convolution. The low resolution result provides temporal guidance to the spatial detail recovering network, which performs image-based inpainting with a 2D fully convolutional network to produce recovered video frames in their original resolution. Such two-step network design ensures both the spatial quality of each frame and the temporal coherence across frames. Our method jointly trains both sub-networks in an end-to-end manner. We provide qualitative and quantitative evaluation on three datasets, demonstrating that our method outperforms previous learning-based video inpainting methods.

Deep features are a cornerstone of computer vision research, capturing image semantics and enabling the community to solve downstream tasks even in the zero- or few-shot regime. However, these features often lack the spatial resolution to directly perform dense prediction tasks like segmentation and depth prediction because models aggressively pool information over large areas. In this work, we introduce FeatUp, a task- and model-agnostic framework to restore lost spatial information in deep features. We introduce two variants of FeatUp: one that guides features with high-resolution signal in a single forward pass, and one that fits an implicit model to a single image to reconstruct features at any resolution. Both approaches use a multi-view consistency loss with deep analogies to NeRFs. Our features retain their original semantics and can be swapped into existing applications to yield resolution and performance gains even without re-training. We show that FeatUp significantly outperforms other feature upsampling and image super-resolution approaches in class activation map generation, transfer learning for segmentation and depth prediction, and end-to-end training for semantic segmentation.

Deep learning yields great results across many fields, from speech recognition, image classification, to translation. But for each problem, getting a deep model to work well involves research into the architecture and a long period of tuning. We present a single model that yields good results on a number of problems spanning multiple domains. In particular, this single model is trained concurrently on ImageNet, multiple translation tasks, image captioning (COCO dataset), a speech recognition corpus, and an English parsing task. Our model architecture incorporates building blocks from multiple domains. It contains convolutional layers, an attention mechanism, and sparsely-gated layers. Each of these computational blocks is crucial for a subset of the tasks we train on. Interestingly, even if a block is not crucial for a task, we observe that adding it never hurts performance and in most cases improves it on all tasks. We also show that tasks with less data benefit largely from joint training with other tasks, while performance on large tasks degrades only slightly if at all.

Convolutional networks for single-view object reconstruction have shown impressive performance and have become a popular subject of research. All existing techniques are united by the idea of having an encoder-decoder network that performs non-trivial reasoning about the 3D structure of the output space. In this work, we set up two alternative approaches that perform image classification and retrieval respectively. These simple baselines yield better results than state-of-the-art methods, both qualitatively and quantitatively. We show that encoder-decoder methods are statistically indistinguishable from these baselines, thus indicating that the current state of the art in single-view object reconstruction does not actually perform reconstruction but image classification. We identify aspects of popular experimental procedures that elicit this behavior and discuss ways to improve the current state of research.

Deep learning has been wildly successful in practice and most state-of-the-art machine learning methods are based on neural networks. Lacking, however, is a rigorous mathematical theory that adequately explains the amazing performance of deep neural networks. In this article, we present a relatively new mathematical framework that provides the beginning of a deeper understanding of deep learning. This framework precisely characterizes the functional properties of neural networks that are trained to fit to data. The key mathematical tools which support this framework include transform-domain sparse regularization, the Radon transform of computed tomography, and approximation theory, which are all techniques deeply rooted in signal processing. This framework explains the effect of weight decay regularization in neural network training, the use of skip connections and low-rank weight matrices in network architectures, the role of sparsity in neural networks, and explains why neural networks can perform well in high-dimensional problems.

Deep networks devour millions of precisely annotated images to build their complex and powerful representations. Unfortunately, tasks like autonomous driving have virtually no real-world training data. Repeatedly crashing a car into a tree is simply too expensive. The commonly prescribed solution is simple: learn a representation in simulation and transfer it to the real world. However, this transfer is challenging since simulated and real-world visual experiences vary dramatically. Our core observation is that for certain tasks, such as image recognition, datasets are plentiful. They exist in any interesting domain, simulated or real, and are easy to label and extend. We use these recognition datasets to link up a source and target domain to transfer models between them in a task distillation framework. Our method can successfully transfer navigation policies between drastically different simulators: ViZDoom, SuperTuxKart, and CARLA. Furthermore, it shows promising results on standard domain adaptation benchmarks.

The massive interest in deep neural networks (DNNs) for both computer vision and natural language processing has been sparked by the growth in computational power. However, this led to an increase in the memory footprint, to a point where it can be challenging to simply load a model on commodity devices such as mobile phones. To address this limitation, quantization is a favored solution as it maps high precision tensors to a low precision, memory efficient format. In terms of memory footprint reduction, its most effective variants are based on codebooks. These methods, however, suffer from two limitations. First, they either define a single codebook for each tensor, or use a memory-expensive mapping to multiple codebooks. Second, gradient descent optimization of the mapping favors jumps toward extreme values, hence not defining a proximal search. In this work, we propose to address these two limitations. First, we initially group similarly distributed neurons and leverage the re-ordered structure to either apply different scale factors to the different groups, or map weights that fall in these groups to several codebooks, without any mapping overhead. Second, stemming from this initialization, we propose a joint learning of the codebook and weight mappings that bears similarities with recent gradient-based post-training quantization techniques. Third, drawing estimation from straight-through estimation techniques, we introduce a novel gradient update definition to enable a proximal search of the codebooks and their mappings. The proposed jointly learnable codebooks and mappings (JLCM) method allows a very efficient approximation of any DNN: as such, a Llama 7B can be compressed down to 2Go and loaded on 5-year-old smartphones.