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Mar 11

SR-CACO-2: A Dataset for Confocal Fluorescence Microscopy Image Super-Resolution

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

Designing a Practical Degradation Model for Deep Blind Image Super-Resolution

It is widely acknowledged that single image super-resolution (SISR) methods would not perform well if the assumed degradation model deviates from those in real images. Although several degradation models take additional factors into consideration, such as blur, they are still not effective enough to cover the diverse degradations of real images. To address this issue, this paper proposes to design a more complex but practical degradation model that consists of randomly shuffled blur, downsampling and noise degradations. Specifically, the blur is approximated by two convolutions with isotropic and anisotropic Gaussian kernels; the downsampling is randomly chosen from nearest, bilinear and bicubic interpolations; the noise is synthesized by adding Gaussian noise with different noise levels, adopting JPEG compression with different quality factors, and generating processed camera sensor noise via reverse-forward camera image signal processing (ISP) pipeline model and RAW image noise model. To verify the effectiveness of the new degradation model, we have trained a deep blind ESRGAN super-resolver and then applied it to super-resolve both synthetic and real images with diverse degradations. The experimental results demonstrate that the new degradation model can help to significantly improve the practicability of deep super-resolvers, thus providing a powerful alternative solution for real SISR applications.

Feature Modulation Transformer: Cross-Refinement of Global Representation via High-Frequency Prior for Image Super-Resolution

Transformer-based methods have exhibited remarkable potential in single image super-resolution (SISR) by effectively extracting long-range dependencies. However, most of the current research in this area has prioritized the design of transformer blocks to capture global information, while overlooking the importance of incorporating high-frequency priors, which we believe could be beneficial. In our study, we conducted a series of experiments and found that transformer structures are more adept at capturing low-frequency information, but have limited capacity in constructing high-frequency representations when compared to their convolutional counterparts. Our proposed solution, the cross-refinement adaptive feature modulation transformer (CRAFT), integrates the strengths of both convolutional and transformer structures. It comprises three key components: the high-frequency enhancement residual block (HFERB) for extracting high-frequency information, the shift rectangle window attention block (SRWAB) for capturing global information, and the hybrid fusion block (HFB) for refining the global representation. Our experiments on multiple datasets demonstrate that CRAFT outperforms state-of-the-art methods by up to 0.29dB while using fewer parameters. The source code will be made available at: https://github.com/AVC2-UESTC/CRAFT-SR.git.

Transforming Image Super-Resolution: A ConvFormer-based Efficient Approach

Recent progress in single-image super-resolution (SISR) has achieved remarkable performance, yet the computational costs of these methods remain a challenge for deployment on resource-constrained devices. Especially for transformer-based methods, the self-attention mechanism in such models brings great breakthroughs while incurring substantial computational costs. To tackle this issue, we introduce the Convolutional Transformer layer (ConvFormer) and the ConvFormer-based Super-Resolution network (CFSR), which offer an effective and efficient solution for lightweight image super-resolution tasks. In detail, CFSR leverages the large kernel convolution as the feature mixer to replace the self-attention module, efficiently modeling long-range dependencies and extensive receptive fields with a slight computational cost. Furthermore, we propose an edge-preserving feed-forward network, simplified as EFN, to obtain local feature aggregation and simultaneously preserve more high-frequency information. Extensive experiments demonstrate that CFSR can achieve an advanced trade-off between computational cost and performance when compared to existing lightweight SR methods. Compared to state-of-the-art methods, e.g. ShuffleMixer, the proposed CFSR achieves 0.39 dB gains on Urban100 dataset for x2 SR task while containing 26% and 31% fewer parameters and FLOPs, respectively. Code and pre-trained models are available at https://github.com/Aitical/CFSR.

Interferometer response characterization algorithm for multi-aperture Fabry-Perot imaging spectrometers

In recent years, the demand for hyperspectral imaging devices has grown significantly, driven by their ability of capturing high-resolution spectral information. Among the several possible optical designs for acquiring hyperspectral images, there is a growing interest in interferometric spectral imaging systems based on division of aperture. These systems have the advantage of capturing snapshot acquisitions while maintaining a compact design. However, they require a careful calibration to operate properly. In this work, we present the interferometer response characterization algorithm (IRCA), a robust three-step procedure designed to characterize the transmittance response of multi-aperture imaging spectrometers based on the interferometry of Fabry-Perot. Additionally, we propose a formulation of the image formation model for such devices suitable to estimate the parameters of interest by considering the model under various regimes of finesse. The proposed algorithm processes the image output obtained from a set of monochromatic light sources and refines the results using nonlinear regression after an ad-hoc initialization. Through experimental analysis conducted on four different prototypes from the Image SPectrometer On Chip (ImSPOC) family, we validate the performance of our approach for characterization. The associated source code for this paper is available at https://github.com/danaroth83/irca.

Collapsible Linear Blocks for Super-Efficient Super Resolution

With the advent of smart devices that support 4K and 8K resolution, Single Image Super Resolution (SISR) has become an important computer vision problem. However, most super resolution deep networks are computationally very expensive. In this paper, we propose Super-Efficient Super Resolution (SESR) networks that establish a new state-of-the-art for efficient super resolution. Our approach is based on linear overparameterization of CNNs and creates an efficient model architecture for SISR. With theoretical analysis, we uncover the limitations of existing overparameterization methods and show how the proposed method alleviates them. Detailed experiments across six benchmark datasets demonstrate that SESR achieves similar or better image quality than state-of-the-art models while requiring 2x to 330x fewer Multiply-Accumulate (MAC) operations. As a result, SESR can be used on constrained hardware to perform x2 (1080p to 4K) and x4 (1080p to 8K) SISR. Towards this, we estimate hardware performance numbers for a commercial Arm mobile-Neural Processing Unit (NPU) for 1080p to 4K (x2) and 1080p to 8K (x4) SISR. Our results highlight the challenges faced by super resolution on AI accelerators and demonstrate that SESR is significantly faster (e.g., 6x-8x higher FPS) than existing models on mobile-NPU. Finally, SESR outperforms prior models by 1.5x-2x in latency on Arm CPU and GPU when deployed on a real mobile device. The code for this work is available at https://github.com/ARM-software/sesr.

Accelerating Image Super-Resolution Networks with Pixel-Level Classification

In recent times, the need for effective super-resolution (SR) techniques has surged, especially for large-scale images ranging 2K to 8K resolutions. For DNN-based SISR, decomposing images into overlapping patches is typically necessary due to computational constraints. In such patch-decomposing scheme, one can allocate computational resources differently based on each patch's difficulty to further improve efficiency while maintaining SR performance. However, this approach has a limitation: computational resources is uniformly allocated within a patch, leading to lower efficiency when the patch contain pixels with varying levels of restoration difficulty. To address the issue, we propose the Pixel-level Classifier for Single Image Super-Resolution (PCSR), a novel method designed to distribute computational resources adaptively at the pixel level. A PCSR model comprises a backbone, a pixel-level classifier, and a set of pixel-level upsamplers with varying capacities. The pixel-level classifier assigns each pixel to an appropriate upsampler based on its restoration difficulty, thereby optimizing computational resource usage. Our method allows for performance and computational cost balance during inference without re-training. Our experiments demonstrate PCSR's advantage over existing patch-distributing methods in PSNR-FLOP trade-offs across different backbone models and benchmarks. The code is available at https://github.com/3587jjh/PCSR.

ESSAformer: Efficient Transformer for Hyperspectral Image Super-resolution

Single hyperspectral image super-resolution (single-HSI-SR) aims to restore a high-resolution hyperspectral image from a low-resolution observation. However, the prevailing CNN-based approaches have shown limitations in building long-range dependencies and capturing interaction information between spectral features. This results in inadequate utilization of spectral information and artifacts after upsampling. To address this issue, we propose ESSAformer, an ESSA attention-embedded Transformer network for single-HSI-SR with an iterative refining structure. Specifically, we first introduce a robust and spectral-friendly similarity metric, \ie, the spectral correlation coefficient of the spectrum (SCC), to replace the original attention matrix and incorporates inductive biases into the model to facilitate training. Built upon it, we further utilize the kernelizable attention technique with theoretical support to form a novel efficient SCC-kernel-based self-attention (ESSA) and reduce attention computation to linear complexity. ESSA enlarges the receptive field for features after upsampling without bringing much computation and allows the model to effectively utilize spatial-spectral information from different scales, resulting in the generation of more natural high-resolution images. Without the need for pretraining on large-scale datasets, our experiments demonstrate ESSA's effectiveness in both visual quality and quantitative results.

Unifying Multimodal Retrieval via Document Screenshot Embedding

In the real world, documents are organized in different formats and varied modalities. Traditional retrieval pipelines require tailored document parsing techniques and content extraction modules to prepare input for indexing. This process is tedious, prone to errors, and has information loss. To this end, we propose Document Screenshot Embedding} (DSE), a novel retrieval paradigm that regards document screenshots as a unified input format, which does not require any content extraction preprocess and preserves all the information in a document (e.g., text, image and layout). DSE leverages a large vision-language model to directly encode document screenshots into dense representations for retrieval. To evaluate our method, we first craft the dataset of Wiki-SS, a 1.3M Wikipedia web page screenshots as the corpus to answer the questions from the Natural Questions dataset. In such a text-intensive document retrieval setting, DSE shows competitive effectiveness compared to other text retrieval methods relying on parsing. For example, DSE outperforms BM25 by 17 points in top-1 retrieval accuracy. Additionally, in a mixed-modality task of slide retrieval, DSE significantly outperforms OCR text retrieval methods by over 15 points in nDCG@10. These experiments show that DSE is an effective document retrieval paradigm for diverse types of documents. Model checkpoints, code, and Wiki-SS collection will be released.

Rethinking Symbolic Regression Datasets and Benchmarks for Scientific Discovery

This paper revisits datasets and evaluation criteria for Symbolic Regression, a task of expressing given data using mathematical equations, specifically focused on its potential for scientific discovery. Focused on a set of formulas used in the existing datasets based on Feynman Lectures on Physics, we recreate 120 datasets to discuss the performance of symbolic regression for scientific discovery (SRSD). For each of the 120 SRSD datasets, we carefully review the properties of the formula and its variables to design reasonably realistic sampling range of values so that our new SRSD datasets can be used for evaluating the potential of SRSD such as whether or not an SR method can (re)discover physical laws from such datasets. As an evaluation metric, we also propose to use normalized edit distances between a predicted equation and the ground-truth equation trees. While existing metrics are either binary or errors between the target values and an SR model's predicted values for a given input, normalized edit distances evaluate a sort of similarity between the ground-truth and predicted equation trees. We have conducted experiments on our new SRSD datasets using five state-of-the-art SR methods in SRBench and a simple baseline based on a recent Transformer architecture. The results show that we provide a more realistic performance evaluation and open up a new machine learning-based approach for scientific discovery. Our datasets and code repository are publicly available.

On the Parameterization and Initialization of Diagonal State Space Models

State space models (SSM) have recently been shown to be very effective as a deep learning layer as a promising alternative to sequence models such as RNNs, CNNs, or Transformers. The first version to show this potential was the S4 model, which is particularly effective on tasks involving long-range dependencies by using a prescribed state matrix called the HiPPO matrix. While this has an interpretable mathematical mechanism for modeling long dependencies, it introduces a custom representation and algorithm that can be difficult to implement. On the other hand, a recent variant of S4 called DSS showed that restricting the state matrix to be fully diagonal can still preserve the performance of the original model when using a specific initialization based on approximating S4's matrix. This work seeks to systematically understand how to parameterize and initialize such diagonal state space models. While it follows from classical results that almost all SSMs have an equivalent diagonal form, we show that the initialization is critical for performance. We explain why DSS works mathematically, by showing that the diagonal restriction of S4's matrix surprisingly recovers the same kernel in the limit of infinite state dimension. We also systematically describe various design choices in parameterizing and computing diagonal SSMs, and perform a controlled empirical study ablating the effects of these choices. Our final model S4D is a simple diagonal version of S4 whose kernel computation requires just 2 lines of code and performs comparably to S4 in almost all settings, with state-of-the-art results for image, audio, and medical time-series domains, and averaging 85\% on the Long Range Arena benchmark.

A Survey of Graph Neural Networks for Social Recommender Systems

Social recommender systems (SocialRS) simultaneously leverage user-to-item interactions as well as user-to-user social relations for the task of generating item recommendations to users. Additionally exploiting social relations is clearly effective in understanding users' tastes due to the effects of homophily and social influence. For this reason, SocialRS has increasingly attracted attention. In particular, with the advance of Graph Neural Networks (GNN), many GNN-based SocialRS methods have been developed recently. Therefore, we conduct a comprehensive and systematic review of the literature on GNN-based SocialRS. In this survey, we first identify 80 papers on GNN-based SocialRS after annotating 2151 papers by following the PRISMA framework (Preferred Reporting Items for Systematic Reviews and Meta-Analysis). Then, we comprehensively review them in terms of their inputs and architectures to propose a novel taxonomy: (1) input taxonomy includes 5 groups of input type notations and 7 groups of input representation notations; (2) architecture taxonomy includes 8 groups of GNN encoder, 2 groups of decoder, and 12 groups of loss function notations. We classify the GNN-based SocialRS methods into several categories as per the taxonomy and describe their details. Furthermore, we summarize the benchmark datasets and metrics widely used to evaluate the GNN-based SocialRS methods. Finally, we conclude this survey by presenting some future research directions.

Probabilistic Partitive Partitioning (PPP)

Clustering is a NP-hard problem. Thus, no optimal algorithm exists, heuristics are applied to cluster the data. Heuristics can be very resource-intensive, if not applied properly. For substantially large data sets computational efficiencies can be achieved by reducing the input space if a minimal loss of information can be achieved. Clustering algorithms, in general, face two common problems: 1) these converge to different settings with different initial conditions and; 2) the number of clusters has to be arbitrarily decided beforehand. This problem has become critical in the realm of big data. Recently, clustering algorithms have emerged which can speedup computations using parallel processing over the grid but face the aforementioned problems. Goals: Our goals are to find methods to cluster data which: 1) guarantee convergence to the same settings irrespective of the initial conditions; 2) eliminate the need to establish the number of clusters beforehand, and 3) can be applied to cluster large datasets. Methods: We introduce a method that combines probabilistic and combinatorial clustering methods to produce repeatable and compact clusters that are not sensitive to initial conditions. This method harnesses the power of k-means (a combinatorial clustering method) to cluster/partition very large dimensional datasets and uses the Gaussian Mixture Model (a probabilistic clustering method) to validate the k-means partitions. Results: We show that this method produces very compact clusters that are not sensitive to initial conditions. This method can be used to identify the most 'separable' set in a dataset which increases the 'clusterability' of a dataset. This method also eliminates the need to specify the number of clusters in advance.

Unified Multi-Modal Interleaved Document Representation for Information Retrieval

Information Retrieval (IR) methods aim to identify relevant documents in response to a given query, which have gained remarkable attention due to their successful application in various natural language tasks. However, existing approaches typically consider only the textual information within the documents, which overlooks the fact that documents can contain multiple modalities, including texts, images, and tables. Further, they often segment each long document into multiple discrete passages for embedding, preventing them from capturing the overall document context and interactions between paragraphs. We argue that these two limitations lead to suboptimal document representations for retrieval. In this work, to address them, we aim to produce more comprehensive and nuanced document representations by holistically embedding documents interleaved with different modalities. Specifically, we achieve this by leveraging the capability of recent vision-language models that enable the processing and integration of text, images, and tables into a unified format and representation. Moreover, to mitigate the information loss from segmenting documents into passages, instead of representing and retrieving passages individually, we further merge the representations of segmented passages into one single document representation, while we additionally introduce a reranking strategy to decouple and identify the relevant passage within the document if necessary. Then, through extensive experiments on diverse information retrieval scenarios considering both the textual and multimodal queries, we show that our approach substantially outperforms relevant baselines, thanks to the consideration of the multimodal information interleaved within the documents in a unified way.

Resources for Brewing BEIR: Reproducible Reference Models and an Official Leaderboard

BEIR is a benchmark dataset for zero-shot evaluation of information retrieval models across 18 different domain/task combinations. In recent years, we have witnessed the growing popularity of a representation learning approach to building retrieval models, typically using pretrained transformers in a supervised setting. This naturally begs the question: How effective are these models when presented with queries and documents that differ from the training data? Examples include searching in different domains (e.g., medical or legal text) and with different types of queries (e.g., keywords vs. well-formed questions). While BEIR was designed to answer these questions, our work addresses two shortcomings that prevent the benchmark from achieving its full potential: First, the sophistication of modern neural methods and the complexity of current software infrastructure create barriers to entry for newcomers. To this end, we provide reproducible reference implementations that cover the two main classes of approaches: learned dense and sparse models. Second, there does not exist a single authoritative nexus for reporting the effectiveness of different models on BEIR, which has led to difficulty in comparing different methods. To remedy this, we present an official self-service BEIR leaderboard that provides fair and consistent comparisons of retrieval models. By addressing both shortcomings, our work facilitates future explorations in a range of interesting research questions that BEIR enables.