Daily Papers

Weight sharing is a fundamental concept in neural architecture search (NAS), enabling gradient-based methods to explore cell-based architecture spaces significantly faster than traditional blackbox approaches. In parallel, weight entanglement has emerged as a technique for intricate parameter sharing among architectures within macro-level search spaces. %However, the macro structure of such spaces poses compatibility challenges for gradient-based NAS methods. %As a result, blackbox optimization methods have been commonly employed, particularly in conjunction with supernet training, to maintain search efficiency. %Due to the inherent differences in the structure of these search spaces, these Since weight-entanglement poses compatibility challenges for gradient-based NAS methods, these two paradigms have largely developed independently in parallel sub-communities. This paper aims to bridge the gap between these sub-communities by proposing a novel scheme to adapt gradient-based methods for weight-entangled spaces. This enables us to conduct an in-depth comparative assessment and analysis of the performance of gradient-based NAS in weight-entangled search spaces. Our findings reveal that this integration of weight-entanglement and gradient-based NAS brings forth the various benefits of gradient-based methods (enhanced performance, improved supernet training properties and superior any-time performance), while preserving the memory efficiency of weight-entangled spaces. The code for our work is openly accessible https://anonymous.4open.science/r/TangleNAS-527C{here}

Neural Architecture Search (NAS) is an exciting new field which promises to be as much as a game-changer as Convolutional Neural Networks were in 2012. Despite many great works leading to substantial improvements on a variety of tasks, comparison between different methods is still very much an open issue. While most algorithms are tested on the same datasets, there is no shared experimental protocol followed by all. As such, and due to the under-use of ablation studies, there is a lack of clarity regarding why certain methods are more effective than others. Our first contribution is a benchmark of 8 NAS methods on 5 datasets. To overcome the hurdle of comparing methods with different search spaces, we propose using a method's relative improvement over the randomly sampled average architecture, which effectively removes advantages arising from expertly engineered search spaces or training protocols. Surprisingly, we find that many NAS techniques struggle to significantly beat the average architecture baseline. We perform further experiments with the commonly used DARTS search space in order to understand the contribution of each component in the NAS pipeline. These experiments highlight that: (i) the use of tricks in the evaluation protocol has a predominant impact on the reported performance of architectures; (ii) the cell-based search space has a very narrow accuracy range, such that the seed has a considerable impact on architecture rankings; (iii) the hand-designed macro-structure (cells) is more important than the searched micro-structure (operations); and (iv) the depth-gap is a real phenomenon, evidenced by the change in rankings between 8 and 20 cell architectures. To conclude, we suggest best practices, that we hope will prove useful for the community and help mitigate current NAS pitfalls. The code used is available at https://github.com/antoyang/NAS-Benchmark.

In deep learning, performance is strongly affected by the choice of architecture and hyperparameters. While there has been extensive work on automatic hyperparameter optimization for simple spaces, complex spaces such as the space of deep architectures remain largely unexplored. As a result, the choice of architecture is done manually by the human expert through a slow trial and error process guided mainly by intuition. In this paper we describe a framework for automatically designing and training deep models. We propose an extensible and modular language that allows the human expert to compactly represent complex search spaces over architectures and their hyperparameters. The resulting search spaces are tree-structured and therefore easy to traverse. Models can be automatically compiled to computational graphs once values for all hyperparameters have been chosen. We can leverage the structure of the search space to introduce different model search algorithms, such as random search, Monte Carlo tree search (MCTS), and sequential model-based optimization (SMBO). We present experiments comparing the different algorithms on CIFAR-10 and show that MCTS and SMBO outperform random search. In addition, these experiments show that our framework can be used effectively for model discovery, as it is possible to describe expressive search spaces and discover competitive models without much effort from the human expert. Code for our framework and experiments has been made publicly available.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Techniques for automatically designing deep neural network architectures such as reinforcement learning based approaches have recently shown promising results. However, their success is based on vast computational resources (e.g. hundreds of GPUs), making them difficult to be widely used. A noticeable limitation is that they still design and train each network from scratch during the exploration of the architecture space, which is highly inefficient. In this paper, we propose a new framework toward efficient architecture search by exploring the architecture space based on the current network and reusing its weights. We employ a reinforcement learning agent as the meta-controller, whose action is to grow the network depth or layer width with function-preserving transformations. As such, the previously validated networks can be reused for further exploration, thus saves a large amount of computational cost. We apply our method to explore the architecture space of the plain convolutional neural networks (no skip-connections, branching etc.) on image benchmark datasets (CIFAR-10, SVHN) with restricted computational resources (5 GPUs). Our method can design highly competitive networks that outperform existing networks using the same design scheme. On CIFAR-10, our model without skip-connections achieves 4.23\% test error rate, exceeding a vast majority of modern architectures and approaching DenseNet. Furthermore, by applying our method to explore the DenseNet architecture space, we are able to achieve more accurate networks with fewer parameters.

Multi-cellular robot design aims to create robots comprised of numerous cells that can be efficiently controlled to perform diverse tasks. Previous research has demonstrated the ability to generate robots for various tasks, but these approaches often optimize robots directly in the vast design space, resulting in robots with complicated morphologies that are hard to control. In response, this paper presents a novel coarse-to-fine method for designing multi-cellular robots. Initially, this strategy seeks optimal coarse-grained robots and progressively refines them. To mitigate the challenge of determining the precise refinement juncture during the coarse-to-fine transition, we introduce the Hyperbolic Embeddings for Robot Design (HERD) framework. HERD unifies robots of various granularity within a shared hyperbolic space and leverages a refined Cross-Entropy Method for optimization. This framework enables our method to autonomously identify areas of exploration in hyperbolic space and concentrate on regions demonstrating promise. Finally, the extensive empirical studies on various challenging tasks sourced from EvoGym show our approach's superior efficiency and generalization capability.

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

Creating large-scale interactive 3D environments is essential for the development of Robotics and Embodied AI research. Current methods, including manual design, procedural generation, diffusion-based scene generation, and large language model (LLM) guided scene design, are hindered by limitations such as excessive human effort, reliance on predefined rules or training datasets, and limited 3D spatial reasoning ability. Since pre-trained 2D image generative models better capture scene and object configuration than LLMs, we address these challenges by introducing Architect, a generative framework that creates complex and realistic 3D embodied environments leveraging diffusion-based 2D image inpainting. In detail, we utilize foundation visual perception models to obtain each generated object from the image and leverage pre-trained depth estimation models to lift the generated 2D image to 3D space. Our pipeline is further extended to a hierarchical and iterative inpainting process to continuously generate placement of large furniture and small objects to enrich the scene. This iterative structure brings the flexibility for our method to generate or refine scenes from various starting points, such as text, floor plans, or pre-arranged environments.

Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).

Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities.

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

Not yet. We present SPACE, a benchmark that systematically evaluates spatial cognition in frontier models. Our benchmark builds on decades of research in cognitive science. It evaluates large-scale mapping abilities that are brought to bear when an organism traverses physical environments, smaller-scale reasoning about object shapes and layouts, and cognitive infrastructure such as spatial attention and memory. For many tasks, we instantiate parallel presentations via text and images, allowing us to benchmark both large language models and large multimodal models. Results suggest that contemporary frontier models fall short of the spatial intelligence of animals, performing near chance level on a number of classic tests of animal cognition.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

Differentiable ARchiTecture Search (DARTS) is one of the most trending Neural Architecture Search (NAS) methods. It drastically reduces search cost by resorting to weight-sharing. However, it also dramatically reduces the search space, thus excluding potential promising architectures. In this article, we propose D-DARTS, a solution that addresses this problem by nesting neural networks at the cell level instead of using weight-sharing to produce more diversified and specialized architectures. Moreover, we introduce a novel algorithm that can derive deeper architectures from a few trained cells, increasing performance and saving computation time. In addition, we also present an alternative search space (DARTOpti) in which we optimize existing handcrafted architectures (e.g., ResNet) rather than starting from scratch. This approach is accompanied by a novel metric that measures the distance between architectures inside our custom search space. Our solution reaches competitive performance on multiple computer vision tasks. Code and pretrained models can be accessed at https://github.com/aheuillet/D-DARTS.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (e.g., foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Designing 3D indoor layouts is a crucial task with significant applications in virtual reality, interior design, and automated space planning. Existing methods for 3D layout design either rely on diffusion models, which utilize spatial relationship priors, or heavily leverage the inferential capabilities of proprietary Large Language Models (LLMs), which require extensive prompt engineering and in-context exemplars via black-box trials. These methods often face limitations in generalization and dynamic scene editing. In this paper, we introduce LLplace, a novel 3D indoor scene layout designer based on lightweight fine-tuned open-source LLM Llama3. LLplace circumvents the need for spatial relationship priors and in-context exemplars, enabling efficient and credible room layout generation based solely on user inputs specifying the room type and desired objects. We curated a new dialogue dataset based on the 3D-Front dataset, expanding the original data volume and incorporating dialogue data for adding and removing objects. This dataset can enhance the LLM's spatial understanding. Furthermore, through dialogue, LLplace activates the LLM's capability to understand 3D layouts and perform dynamic scene editing, enabling the addition and removal of objects. Our approach demonstrates that LLplace can effectively generate and edit 3D indoor layouts interactively and outperform existing methods in delivering high-quality 3D design solutions. Code and dataset will be released.

Inspired by cognitive theories, we introduce AnyHome, a framework that translates any text into well-structured and textured indoor scenes at a house-scale. By prompting Large Language Models (LLMs) with designed templates, our approach converts provided textual narratives into amodal structured representations. These representations guarantee consistent and realistic spatial layouts by directing the synthesis of a geometry mesh within defined constraints. A Score Distillation Sampling process is then employed to refine the geometry, followed by an egocentric inpainting process that adds lifelike textures to it. AnyHome stands out with its editability, customizability, diversity, and realism. The structured representations for scenes allow for extensive editing at varying levels of granularity. Capable of interpreting texts ranging from simple labels to detailed narratives, AnyHome generates detailed geometries and textures that outperform existing methods in both quantitative and qualitative measures.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

A myriad of recent breakthroughs in hand-crafted neural architectures for visual recognition have highlighted the urgent need to explore hybrid architectures consisting of diversified building blocks. Meanwhile, neural architecture search methods are surging with an expectation to reduce human efforts. However, whether NAS methods can efficiently and effectively handle diversified search spaces with disparate candidates (e.g. CNNs and transformers) is still an open question. In this work, we present Block-wisely Self-supervised Neural Architecture Search (BossNAS), an unsupervised NAS method that addresses the problem of inaccurate architecture rating caused by large weight-sharing space and biased supervision in previous methods. More specifically, we factorize the search space into blocks and utilize a novel self-supervised training scheme, named ensemble bootstrapping, to train each block separately before searching them as a whole towards the population center. Additionally, we present HyTra search space, a fabric-like hybrid CNN-transformer search space with searchable down-sampling positions. On this challenging search space, our searched model, BossNet-T, achieves up to 82.5% accuracy on ImageNet, surpassing EfficientNet by 2.4% with comparable compute time. Moreover, our method achieves superior architecture rating accuracy with 0.78 and 0.76 Spearman correlation on the canonical MBConv search space with ImageNet and on NATS-Bench size search space with CIFAR-100, respectively, surpassing state-of-the-art NAS methods. Code: https://github.com/changlin31/BossNAS

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.

We introduce Habitat 2.0 (H2.0), a simulation platform for training virtual robots in interactive 3D environments and complex physics-enabled scenarios. We make comprehensive contributions to all levels of the embodied AI stack - data, simulation, and benchmark tasks. Specifically, we present: (i) ReplicaCAD: an artist-authored, annotated, reconfigurable 3D dataset of apartments (matching real spaces) with articulated objects (e.g. cabinets and drawers that can open/close); (ii) H2.0: a high-performance physics-enabled 3D simulator with speeds exceeding 25,000 simulation steps per second (850x real-time) on an 8-GPU node, representing 100x speed-ups over prior work; and, (iii) Home Assistant Benchmark (HAB): a suite of common tasks for assistive robots (tidy the house, prepare groceries, set the table) that test a range of mobile manipulation capabilities. These large-scale engineering contributions allow us to systematically compare deep reinforcement learning (RL) at scale and classical sense-plan-act (SPA) pipelines in long-horizon structured tasks, with an emphasis on generalization to new objects, receptacles, and layouts. We find that (1) flat RL policies struggle on HAB compared to hierarchical ones; (2) a hierarchy with independent skills suffers from 'hand-off problems', and (3) SPA pipelines are more brittle than RL policies.

Buildings are primary components of cities, often featuring repeated elements such as windows and doors. Traditional 3D building asset creation is labor-intensive and requires specialized skills to develop design rules. Recent generative models for building creation often overlook these patterns, leading to low visual fidelity and limited scalability. Drawing inspiration from procedural modeling techniques used in the gaming and visual effects industry, our method, Proc-GS, integrates procedural code into the 3D Gaussian Splatting (3D-GS) framework, leveraging their advantages in high-fidelity rendering and efficient asset management from both worlds. By manipulating procedural code, we can streamline this process and generate an infinite variety of buildings. This integration significantly reduces model size by utilizing shared foundational assets, enabling scalable generation with precise control over building assembly. We showcase the potential for expansive cityscape generation while maintaining high rendering fidelity and precise control on both real and synthetic cases.

We introduce 3D-FRONT (3D Furnished Rooms with layOuts and semaNTics), a new, large-scale, and comprehensive repository of synthetic indoor scenes highlighted by professionally designed layouts and a large number of rooms populated by high-quality textured 3D models with style compatibility. From layout semantics down to texture details of individual objects, our dataset is freely available to the academic community and beyond. Currently, 3D-FRONT contains 18,968 rooms diversely furnished by 3D objects, far surpassing all publicly available scene datasets. In addition, the 13,151 furniture objects all come with high-quality textures. While the floorplans and layout designs are directly sourced from professional creations, the interior designs in terms of furniture styles, color, and textures have been carefully curated based on a recommender system we develop to attain consistent styles as expert designs. Furthermore, we release Trescope, a light-weight rendering tool, to support benchmark rendering of 2D images and annotations from 3D-FRONT. We demonstrate two applications, interior scene synthesis and texture synthesis, that are especially tailored to the strengths of our new dataset. The project page is at: https://tianchi.aliyun.com/specials/promotion/alibaba-3d-scene-dataset.

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).

In this paper, we propose a hybrid approach for multi-object microbial cell segmentation. The approach combines an ML-based detection with a geometry-aware variational-based segmentation using B-splines that are parametrized based on a geometric model of the cell shape. The detection is done first using YOLOv5. In a second step, each detected cell is segmented individually. Thus, the segmentation only needs to be done on a per-cell basis, which makes it amenable to a variational approach that incorporates prior knowledge on the geometry. Here, the contour of the segmentation is modelled as closed uniform cubic B-spline, whose control points are parametrized using the known cell geometry. Compared to purely ML-based segmentation approaches, which need accurate segmentation maps as training data that are very laborious to produce, our method just needs bounding boxes as training data. Still, the proposed method performs on par with ML-based segmentation approaches usually used in this context. We study the performance of the proposed method on time-lapse microscopy data of Corynebacterium glutamicum.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).

The creation of complex 3D scenes tailored to user specifications has been a tedious and challenging task with traditional 3D modeling tools. Although some pioneering methods have achieved automatic text-to-3D generation, they are generally limited to small-scale scenes with restricted control over the shape and texture. We introduce SceneCraft, a novel method for generating detailed indoor scenes that adhere to textual descriptions and spatial layout preferences provided by users. Central to our method is a rendering-based technique, which converts 3D semantic layouts into multi-view 2D proxy maps. Furthermore, we design a semantic and depth conditioned diffusion model to generate multi-view images, which are used to learn a neural radiance field (NeRF) as the final scene representation. Without the constraints of panorama image generation, we surpass previous methods in supporting complicated indoor space generation beyond a single room, even as complicated as a whole multi-bedroom apartment with irregular shapes and layouts. Through experimental analysis, we demonstrate that our method significantly outperforms existing approaches in complex indoor scene generation with diverse textures, consistent geometry, and realistic visual quality. Code and more results are available at: https://orangesodahub.github.io/SceneCraft

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

We investigate the construction of latent spaces through self-supervised learning to support semantically meaningful operations. Analogous to operational amplifiers, these "operational latent spaces" (OpLaS) not only demonstrate semantic structure such as clustering but also support common transformational operations with inherent semantic meaning. Some operational latent spaces are found to have arisen "unintentionally" in the progress toward some (other) self-supervised learning objective, in which unintended but still useful properties are discovered among the relationships of points in the space. Other spaces may be constructed "intentionally" by developers stipulating certain kinds of clustering or transformations intended to produce the desired structure. We focus on the intentional creation of operational latent spaces via self-supervised learning, including the introduction of rotation operators via a novel "FiLMR" layer, which can be used to enable ring-like symmetries found in some musical constructions.

Large pre-trained models, or foundation models, have shown impressive performance when adapted to a variety of downstream tasks, often out-performing specialized models. Hypernetworks, neural networks that generate some or all of the parameters of another neural network, have become an increasingly important technique for conditioning and generalizing implicit neural representations (INRs), which represent signals or objects such as audio or 3D shapes using a neural network. However, despite the potential benefits of incorporating foundation models in hypernetwork methods, this research direction has not been investigated, likely due to the dissimilarity of the weight generation task with other visual tasks. To address this gap, we (1) show how foundation models can improve hypernetworks with Transformer-based architectures, (2) provide an empirical analysis of the benefits of foundation models for hypernetworks through the lens of the generalizable INR task, showing that leveraging foundation models improves performance, generalizability, and data efficiency across a variety of algorithms and modalities. We also provide further analysis in examining the design space of foundation model-based hypernetworks, including examining the choice of foundation models, algorithms, and the effect of scaling foundation models.

Designing machine learning architectures for processing neural networks in their raw weight matrix form is a newly introduced research direction. Unfortunately, the unique symmetry structure of deep weight spaces makes this design very challenging. If successful, such architectures would be capable of performing a wide range of intriguing tasks, from adapting a pre-trained network to a new domain to editing objects represented as functions (INRs or NeRFs). As a first step towards this goal, we present here a novel network architecture for learning in deep weight spaces. It takes as input a concatenation of weights and biases of a pre-trained MLP and processes it using a composition of layers that are equivariant to the natural permutation symmetry of the MLP's weights: Changing the order of neurons in intermediate layers of the MLP does not affect the function it represents. We provide a full characterization of all affine equivariant and invariant layers for these symmetries and show how these layers can be implemented using three basic operations: pooling, broadcasting, and fully connected layers applied to the input in an appropriate manner. We demonstrate the effectiveness of our architecture and its advantages over natural baselines in a variety of learning tasks.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

3D simulated environments play a critical role in Embodied AI, but their creation requires expertise and extensive manual effort, restricting their diversity and scope. To mitigate this limitation, we present Holodeck, a system that generates 3D environments to match a user-supplied prompt fully automatedly. Holodeck can generate diverse scenes, e.g., arcades, spas, and museums, adjust the designs for styles, and can capture the semantics of complex queries such as "apartment for a researcher with a cat" and "office of a professor who is a fan of Star Wars". Holodeck leverages a large language model (GPT-4) for common sense knowledge about what the scene might look like and uses a large collection of 3D assets from Objaverse to populate the scene with diverse objects. To address the challenge of positioning objects correctly, we prompt GPT-4 to generate spatial relational constraints between objects and then optimize the layout to satisfy those constraints. Our large-scale human evaluation shows that annotators prefer Holodeck over manually designed procedural baselines in residential scenes and that Holodeck can produce high-quality outputs for diverse scene types. We also demonstrate an exciting application of Holodeck in Embodied AI, training agents to navigate in novel scenes like music rooms and daycares without human-constructed data, which is a significant step forward in developing general-purpose embodied agents.

Recently, there has been growing interest in developing learning-based methods to detect and utilize salient semi-global or global structures, such as junctions, lines, planes, cuboids, smooth surfaces, and all types of symmetries, for 3D scene modeling and understanding. However, the ground truth annotations are often obtained via human labor, which is particularly challenging and inefficient for such tasks due to the large number of 3D structure instances (e.g., line segments) and other factors such as viewpoints and occlusions. In this paper, we present a new synthetic dataset, Structured3D, with the aim of providing large-scale photo-realistic images with rich 3D structure annotations for a wide spectrum of structured 3D modeling tasks. We take advantage of the availability of professional interior designs and automatically extract 3D structures from them. We generate high-quality images with an industry-leading rendering engine. We use our synthetic dataset in combination with real images to train deep networks for room layout estimation and demonstrate improved performance on benchmark datasets.

We explore efficient neural architecture search methods and show that a simple yet powerful evolutionary algorithm can discover new architectures with excellent performance. Our approach combines a novel hierarchical genetic representation scheme that imitates the modularized design pattern commonly adopted by human experts, and an expressive search space that supports complex topologies. Our algorithm efficiently discovers architectures that outperform a large number of manually designed models for image classification, obtaining top-1 error of 3.6% on CIFAR-10 and 20.3% when transferred to ImageNet, which is competitive with the best existing neural architecture search approaches. We also present results using random search, achieving 0.3% less top-1 accuracy on CIFAR-10 and 0.1% less on ImageNet whilst reducing the search time from 36 hours down to 1 hour.

Developing neural network image classification models often requires significant architecture engineering. In this paper, we study a method to learn the model architectures directly on the dataset of interest. As this approach is expensive when the dataset is large, we propose to search for an architectural building block on a small dataset and then transfer the block to a larger dataset. The key contribution of this work is the design of a new search space (the "NASNet search space") which enables transferability. In our experiments, we search for the best convolutional layer (or "cell") on the CIFAR-10 dataset and then apply this cell to the ImageNet dataset by stacking together more copies of this cell, each with their own parameters to design a convolutional architecture, named "NASNet architecture". We also introduce a new regularization technique called ScheduledDropPath that significantly improves generalization in the NASNet models. On CIFAR-10 itself, NASNet achieves 2.4% error rate, which is state-of-the-art. On ImageNet, NASNet achieves, among the published works, state-of-the-art accuracy of 82.7% top-1 and 96.2% top-5 on ImageNet. Our model is 1.2% better in top-1 accuracy than the best human-invented architectures while having 9 billion fewer FLOPS - a reduction of 28% in computational demand from the previous state-of-the-art model. When evaluated at different levels of computational cost, accuracies of NASNets exceed those of the state-of-the-art human-designed models. For instance, a small version of NASNet also achieves 74% top-1 accuracy, which is 3.1% better than equivalently-sized, state-of-the-art models for mobile platforms. Finally, the learned features by NASNet used with the Faster-RCNN framework surpass state-of-the-art by 4.0% achieving 43.1% mAP on the COCO dataset.

Neural Architecture Search (NAS) has been a source of dramatic improvements in neural network design, with recent results meeting or exceeding the performance of hand-tuned architectures. However, our understanding of how to represent the search space for neural net architectures and how to search that space efficiently are both still in their infancy. We have performed an in-depth analysis to identify limitations in a widely used search space and a recent architecture search method, Differentiable Architecture Search (DARTS). These findings led us to introduce novel network blocks with a more general, balanced, and consistent design; a better-optimized Cosine Power Annealing learning rate schedule; and other improvements. Our resulting sharpDARTS search is 50% faster with a 20-30% relative improvement in final model error on CIFAR-10 when compared to DARTS. Our best single model run has 1.93% (1.98+/-0.07) validation error on CIFAR-10 and 5.5% error (5.8+/-0.3) on the recently released CIFAR-10.1 test set. To our knowledge, both are state of the art for models of similar size. This model also generalizes competitively to ImageNet at 25.1% top-1 (7.8% top-5) error. We found improvements for existing search spaces but does DARTS generalize to new domains? We propose Differentiable Hyperparameter Grid Search and the HyperCuboid search space, which are representations designed to leverage DARTS for more general parameter optimization. Here we find that DARTS fails to generalize when compared against a human's one shot choice of models. We look back to the DARTS and sharpDARTS search spaces to understand why, and an ablation study reveals an unusual generalization gap. We finally propose Max-W regularization to solve this problem, which proves significantly better than the handmade design. Code will be made available.

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

With the advent of specialized hardware such as Graphics Processing Units (GPUs), large scale image localization, classification and retrieval have seen increased prevalence. Designing scalable software architecture that co-evolves with such specialized hardware is a challenge in the commercial setting. In this paper, we describe one such architecture (Cortexica) that leverages scalability of GPUs and sandboxing offered by docker containers. This allows for the flexibility of mixing different computer architectures as well as computational algorithms with the security of a trusted environment. We illustrate the utility of this framework in a commercial setting i.e., searching for multiple products in an image by combining image localisation and retrieval.

Designing high-quality indoor 3D scenes is important in many practical applications, such as room planning or game development. Conventionally, this has been a time-consuming process which requires both artistic skill and familiarity with professional software, making it hardly accessible for layman users. However, recent advances in generative AI have established solid foundation for democratizing 3D design. In this paper, we propose a pioneering approach for text-based 3D room design. Given a prompt in natural language describing the object placement in the room, our method produces a high-quality 3D scene corresponding to it. With an additional text prompt the users can change the appearance of the entire scene or of individual objects in it. Built using in-context learning, CAD model retrieval and 3D-Gaussian-Splatting-based stylization, our turnkey pipeline produces state-of-the-art 3D scenes, while being easy to use even for novices. Our project page is available at https://sceneteller.github.io/.

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Selecting appropriate datasets is critical in modern computer vision. However, no general-purpose tools exist to evaluate the extent to which two datasets differ. For this, we propose representing images - and by extension datasets - using Distributions of Neuron Activations (DNAs). DNAs fit distributions, such as histograms or Gaussians, to activations of neurons in a pre-trained feature extractor through which we pass the image(s) to represent. This extractor is frozen for all datasets, and we rely on its generally expressive power in feature space. By comparing two DNAs, we can evaluate the extent to which two datasets differ with granular control over the comparison attributes of interest, providing the ability to customise the way distances are measured to suit the requirements of the task at hand. Furthermore, DNAs are compact, representing datasets of any size with less than 15 megabytes. We demonstrate the value of DNAs by evaluating their applicability on several tasks, including conditional dataset comparison, synthetic image evaluation, and transfer learning, and across diverse datasets, ranging from synthetic cat images to celebrity faces and urban driving scenes.

Text-driven 3D indoor scene generation could be useful for gaming, film industry, and AR/VR applications. However, existing methods cannot faithfully capture the room layout, nor do they allow flexible editing of individual objects in the room. To address these problems, we present Ctrl-Room, which is able to generate convincing 3D rooms with designer-style layouts and high-fidelity textures from just a text prompt. Moreover, Ctrl-Room enables versatile interactive editing operations such as resizing or moving individual furniture items. Our key insight is to separate the modeling of layouts and appearance. %how to model the room that takes into account both scene texture and geometry at the same time. To this end, Our proposed method consists of two stages, a `Layout Generation Stage' and an `Appearance Generation Stage'. The `Layout Generation Stage' trains a text-conditional diffusion model to learn the layout distribution with our holistic scene code parameterization. Next, the `Appearance Generation Stage' employs a fine-tuned ControlNet to produce a vivid panoramic image of the room guided by the 3D scene layout and text prompt. In this way, we achieve a high-quality 3D room with convincing layouts and lively textures. Benefiting from the scene code parameterization, we can easily edit the generated room model through our mask-guided editing module, without expensive editing-specific training. Extensive experiments on the Structured3D dataset demonstrate that our method outperforms existing methods in producing more reasonable, view-consistent, and editable 3D rooms from natural language prompts.

Within the complex neuroarchitecture of the brain, astrocytes play crucial roles in development, structure, and metabolism. These cells regulate neural activity through tripartite synapses, directly impacting cognitive processes such as learning and memory. Despite the growing recognition of astrocytes' significance, traditional Spiking Neural Network (SNN) models remain predominantly neuron-centric, overlooking the profound influence of astrocytes on neural dynamics. Inspired by these biological insights, we have developed an Astrocyte-Modulated Spiking Unit (AM-SU), an innovative framework that integrates neuron-astrocyte interactions into the computational paradigm, demonstrating wide applicability across various hardware platforms. Our Astrocyte-Modulated Spiking Neural Network (AstroSNN) exhibits exceptional performance in tasks involving memory retention and natural language generation, particularly in handling long-term dependencies and complex linguistic structures. The design of AstroSNN not only enhances its biological authenticity but also introduces novel computational dynamics, enabling more effective processing of complex temporal dependencies. Furthermore, AstroSNN shows low latency, high throughput, and reduced memory usage in practical applications, making it highly suitable for resource-constrained environments. By successfully integrating astrocytic dynamics into intelligent neural networks, our work narrows the gap between biological plausibility and neural modeling, laying the groundwork for future biologically-inspired neural computing research that includes both neurons and astrocytes.

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.

Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

Designing architectures for deep neural networks requires expert knowledge and substantial computation time. We propose a technique to accelerate architecture selection by learning an auxiliary HyperNet that generates the weights of a main model conditioned on that model's architecture. By comparing the relative validation performance of networks with HyperNet-generated weights, we can effectively search over a wide range of architectures at the cost of a single training run. To facilitate this search, we develop a flexible mechanism based on memory read-writes that allows us to define a wide range of network connectivity patterns, with ResNet, DenseNet, and FractalNet blocks as special cases. We validate our method (SMASH) on CIFAR-10 and CIFAR-100, STL-10, ModelNet10, and Imagenet32x32, achieving competitive performance with similarly-sized hand-designed networks. Our code is available at https://github.com/ajbrock/SMASH

We introduce EnerVerse, a comprehensive framework for embodied future space generation specifically designed for robotic manipulation tasks. EnerVerse seamlessly integrates convolutional and bidirectional attention mechanisms for inner-chunk space modeling, ensuring low-level consistency and continuity. Recognizing the inherent redundancy in video data, we propose a sparse memory context combined with a chunkwise unidirectional generative paradigm to enable the generation of infinitely long sequences. To further augment robotic capabilities, we introduce the Free Anchor View (FAV) space, which provides flexible perspectives to enhance observation and analysis. The FAV space mitigates motion modeling ambiguity, removes physical constraints in confined environments, and significantly improves the robot's generalization and adaptability across various tasks and settings. To address the prohibitive costs and labor intensity of acquiring multi-camera observations, we present a data engine pipeline that integrates a generative model with 4D Gaussian Splatting (4DGS). This pipeline leverages the generative model's robust generalization capabilities and the spatial constraints provided by 4DGS, enabling an iterative enhancement of data quality and diversity, thus creating a data flywheel effect that effectively narrows the sim-to-real gap. Finally, our experiments demonstrate that the embodied future space generation prior substantially enhances policy predictive capabilities, resulting in improved overall performance, particularly in long-range robotic manipulation tasks.

Developing deep learning models that effectively learn object-centric representations, akin to human cognition, remains a challenging task. Existing approaches facilitate object discovery by representing objects as fixed-size vectors, called ``slots'' or ``object files''. While these approaches have shown promise in certain scenarios, they still exhibit certain limitations. First, they rely on architectural priors which can be unreliable and usually require meticulous engineering to identify the correct objects. Second, there has been a notable gap in investigating the practical utility of these representations in downstream tasks. To address the first limitation, we introduce a method that explicitly optimizes the constraint that each object in a scene should be associated with a distinct slot. We formalize this constraint by introducing consistency objectives which are cyclic in nature. By integrating these consistency objectives into various existing slot-based object-centric methods, we showcase substantial improvements in object-discovery performance. These enhancements consistently hold true across both synthetic and real-world scenes, underscoring the effectiveness and adaptability of the proposed approach. To tackle the second limitation, we apply the learned object-centric representations from the proposed method to two downstream reinforcement learning tasks, demonstrating considerable performance enhancements compared to conventional slot-based and monolithic representation learning methods. Our results suggest that the proposed approach not only improves object discovery, but also provides richer features for downstream tasks.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

Current neural architecture search (NAS) strategies focus only on finding a single, good, architecture. They offer little insight into why a specific network is performing well, or how we should modify the architecture if we want further improvements. We propose a Bayesian optimisation (BO) approach for NAS that combines the Weisfeiler-Lehman graph kernel with a Gaussian process surrogate. Our method optimises the architecture in a highly data-efficient manner: it is capable of capturing the topological structures of the architectures and is scalable to large graphs, thus making the high-dimensional and graph-like search spaces amenable to BO. More importantly, our method affords interpretability by discovering useful network features and their corresponding impact on the network performance. Indeed, we demonstrate empirically that our surrogate model is capable of identifying useful motifs which can guide the generation of new architectures. We finally show that our method outperforms existing NAS approaches to achieve the state of the art on both closed- and open-domain search spaces.

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset that comprises Cell Painting features for 11,000 genes and 3,600 compounds along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

We present the Habitat-Matterport 3D (HM3D) dataset. HM3D is a large-scale dataset of 1,000 building-scale 3D reconstructions from a diverse set of real-world locations. Each scene in the dataset consists of a textured 3D mesh reconstruction of interiors such as multi-floor residences, stores, and other private indoor spaces. HM3D surpasses existing datasets available for academic research in terms of physical scale, completeness of the reconstruction, and visual fidelity. HM3D contains 112.5k m^2 of navigable space, which is 1.4 - 3.7x larger than other building-scale datasets such as MP3D and Gibson. When compared to existing photorealistic 3D datasets such as Replica, MP3D, Gibson, and ScanNet, images rendered from HM3D have 20 - 85% higher visual fidelity w.r.t. counterpart images captured with real cameras, and HM3D meshes have 34 - 91% fewer artifacts due to incomplete surface reconstruction. The increased scale, fidelity, and diversity of HM3D directly impacts the performance of embodied AI agents trained using it. In fact, we find that HM3D is `pareto optimal' in the following sense -- agents trained to perform PointGoal navigation on HM3D achieve the highest performance regardless of whether they are evaluated on HM3D, Gibson, or MP3D. No similar claim can be made about training on other datasets. HM3D-trained PointNav agents achieve 100% performance on Gibson-test dataset, suggesting that it might be time to retire that episode dataset.

Manually creating 3D environments for AR/VR applications is a complex process requiring expert knowledge in 3D modeling software. Pioneering works facilitate this process by generating room meshes conditioned on textual style descriptions. Yet, many of these automatically generated 3D meshes do not adhere to typical room layouts, compromising their plausibility, e.g., by placing several beds in one bedroom. To address these challenges, we present ControlRoom3D, a novel method to generate high-quality room meshes. Central to our approach is a user-defined 3D semantic proxy room that outlines a rough room layout based on semantic bounding boxes and a textual description of the overall room style. Our key insight is that when rendered to 2D, this 3D representation provides valuable geometric and semantic information to control powerful 2D models to generate 3D consistent textures and geometry that aligns well with the proxy room. Backed up by an extensive study including quantitative metrics and qualitative user evaluations, our method generates diverse and globally plausible 3D room meshes, thus empowering users to design 3D rooms effortlessly without specialized knowledge.

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

The techniques for 3D indoor scene capturing are widely used, but the meshes produced leave much to be desired. In this paper, we propose "RoomDreamer", which leverages powerful natural language to synthesize a new room with a different style. Unlike existing image synthesis methods, our work addresses the challenge of synthesizing both geometry and texture aligned to the input scene structure and prompt simultaneously. The key insight is that a scene should be treated as a whole, taking into account both scene texture and geometry. The proposed framework consists of two significant components: Geometry Guided Diffusion and Mesh Optimization. Geometry Guided Diffusion for 3D Scene guarantees the consistency of the scene style by applying the 2D prior to the entire scene simultaneously. Mesh Optimization improves the geometry and texture jointly and eliminates the artifacts in the scanned scene. To validate the proposed method, real indoor scenes scanned with smartphones are used for extensive experiments, through which the effectiveness of our method is demonstrated.

We present a system for generating indoor scenes in response to text prompts. The prompts are not limited to a fixed vocabulary of scene descriptions, and the objects in generated scenes are not restricted to a fixed set of object categories -- we call this setting indoor scene generation. Unlike most prior work on indoor scene generation, our system does not require a large training dataset of existing 3D scenes. Instead, it leverages the world knowledge encoded in pre-trained large language models (LLMs) to synthesize programs in a domain-specific layout language that describe objects and spatial relations between them. Executing such a program produces a specification of a constraint satisfaction problem, which the system solves using a gradient-based optimization scheme to produce object positions and orientations. To produce object geometry, the system retrieves 3D meshes from a database. Unlike prior work which uses databases of category-annotated, mutually-aligned meshes, we develop a pipeline using vision-language models (VLMs) to retrieve meshes from massive databases of un-annotated, inconsistently-aligned meshes. Experimental evaluations show that our system outperforms generative models trained on 3D data for traditional, closed-universe scene generation tasks; it also outperforms a recent LLM-based layout generation method on open-universe scene generation.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

Animating portraits using speech has received growing attention in recent years, with various creative and practical use cases. An ideal generated video should have good lip sync with the audio, natural facial expressions and head motions, and high frame quality. In this work, we present SPACE, which uses speech and a single image to generate high-resolution, and expressive videos with realistic head pose, without requiring a driving video. It uses a multi-stage approach, combining the controllability of facial landmarks with the high-quality synthesis power of a pretrained face generator. SPACE also allows for the control of emotions and their intensities. Our method outperforms prior methods in objective metrics for image quality and facial motions and is strongly preferred by users in pair-wise comparisons. The project website is available at https://deepimagination.cc/SPACE/

Diffusion-based methods have achieved prominent success in generating 2D media. However, accomplishing similar proficiencies for scene-level mesh texturing in 3D spatial applications, e.g., XR/VR, remains constrained, primarily due to the intricate nature of 3D geometry and the necessity for immersive free-viewpoint rendering. In this paper, we propose a novel indoor scene texturing framework, which delivers text-driven texture generation with enchanting details and authentic spatial coherence. The key insight is to first imagine a stylized 360{\deg} panoramic texture from the central viewpoint of the scene, and then propagate it to the rest areas with inpainting and imitating techniques. To ensure meaningful and aligned textures to the scene, we develop a novel coarse-to-fine panoramic texture generation approach with dual texture alignment, which both considers the geometry and texture cues of the captured scenes. To survive from cluttered geometries during texture propagation, we design a separated strategy, which conducts texture inpainting in confidential regions and then learns an implicit imitating network to synthesize textures in occluded and tiny structural areas. Extensive experiments and the immersive VR application on real-world indoor scenes demonstrate the high quality of the generated textures and the engaging experience on VR headsets. Project webpage: https://ybbbbt.com/publication/dreamspace

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Spatial control is a core capability in controllable image generation. Advancements in layout-guided image generation have shown promising results on in-distribution (ID) datasets with similar spatial configurations. However, it is unclear how these models perform when facing out-of-distribution (OOD) samples with arbitrary, unseen layouts. In this paper, we propose LayoutBench, a diagnostic benchmark for layout-guided image generation that examines four categories of spatial control skills: number, position, size, and shape. We benchmark two recent representative layout-guided image generation methods and observe that the good ID layout control may not generalize well to arbitrary layouts in the wild (e.g., objects at the boundary). Next, we propose IterInpaint, a new baseline that generates foreground and background regions in a step-by-step manner via inpainting, demonstrating stronger generalizability than existing models on OOD layouts in LayoutBench. We perform quantitative and qualitative evaluation and fine-grained analysis on the four LayoutBench skills to pinpoint the weaknesses of existing models. Lastly, we show comprehensive ablation studies on IterInpaint, including training task ratio, crop&paste vs. repaint, and generation order. Project website: https://layoutbench.github.io

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

While high-quality texture maps are essential for realistic 3D asset rendering, few studies have explored learning directly in the texture space, especially on large-scale datasets. In this work, we depart from the conventional approach of relying on pre-trained 2D diffusion models for test-time optimization of 3D textures. Instead, we focus on the fundamental problem of learning in the UV texture space itself. For the first time, we train a large diffusion model capable of directly generating high-resolution texture maps in a feed-forward manner. To facilitate efficient learning in high-resolution UV spaces, we propose a scalable network architecture that interleaves convolutions on UV maps with attention layers on point clouds. Leveraging this architectural design, we train a 700 million parameter diffusion model that can generate UV texture maps guided by text prompts and single-view images. Once trained, our model naturally supports various extended applications, including text-guided texture inpainting, sparse-view texture completion, and text-driven texture synthesis. Project page is at http://cvmi-lab.github.io/TEXGen/.

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization.

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

Polygonal meshes are ubiquitous, but have only played a relatively minor role in the deep learning revolution. State-of-the-art neural generative models for 3D shapes learn implicit functions and generate meshes via expensive iso-surfacing. We overcome these challenges by employing a classical spatial data structure from computer graphics, Binary Space Partitioning (BSP), to facilitate 3D learning. The core operation of BSP involves recursive subdivision of 3D space to obtain convex sets. By exploiting this property, we devise BSP-Net, a network that learns to represent a 3D shape via convex decomposition without supervision. The network is trained to reconstruct a shape using a set of convexes obtained from a BSP-tree built over a set of planes, where the planes and convexes are both defined by learned network weights. BSP-Net directly outputs polygonal meshes from the inferred convexes. The generated meshes are watertight, compact (i.e., low-poly), and well suited to represent sharp geometry. We show that the reconstruction quality by BSP-Net is competitive with those from state-of-the-art methods while using much fewer primitives. We also explore variations to BSP-Net including using a more generic decoder for reconstruction, more general primitives than planes, as well as training a generative model with variational auto-encoders. Code is available at https://github.com/czq142857/BSP-NET-original.

Better understanding and modelling of building interiors and the emergence of more impressive AR/VR technology has brought up the need for automatic parsing of floorplan images. However, there is a clear lack of representative datasets to investigate the problem further. To address this shortcoming, this paper presents a novel image dataset called CubiCasa5K, a large-scale floorplan image dataset containing 5000 samples annotated into over 80 floorplan object categories. The dataset annotations are performed in a dense and versatile manner by using polygons for separating the different objects. Diverging from the classical approaches based on strong heuristics and low-level pixel operations, we present a method relying on an improved multi-task convolutional neural network. By releasing the novel dataset and our implementations, this study significantly boosts the research on automatic floorplan image analysis as it provides a richer set of tools for investigating the problem in a more comprehensive manner.

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

Imaging systems consist of cameras to encode visual information about the world and perception models to interpret this encoding. Cameras contain (1) illumination sources, (2) optical elements, and (3) sensors, while perception models use (4) algorithms. Directly searching over all combinations of these four building blocks to design an imaging system is challenging due to the size of the search space. Moreover, cameras and perception models are often designed independently, leading to sub-optimal task performance. In this paper, we formulate these four building blocks of imaging systems as a context-free grammar (CFG), which can be automatically searched over with a learned camera designer to jointly optimize the imaging system with task-specific perception models. By transforming the CFG to a state-action space, we then show how the camera designer can be implemented with reinforcement learning to intelligently search over the combinatorial space of possible imaging system configurations. We demonstrate our approach on two tasks, depth estimation and camera rig design for autonomous vehicles, showing that our method yields rigs that outperform industry-wide standards. We believe that our proposed approach is an important step towards automating imaging system design.

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

Learning in weight spaces, where neural networks process the weights of other deep neural networks, has emerged as a promising research direction with applications in various fields, from analyzing and editing neural fields and implicit neural representations, to network pruning and quantization. Recent works designed architectures for effective learning in that space, which takes into account its unique, permutation-equivariant, structure. Unfortunately, so far these architectures suffer from severe overfitting and were shown to benefit from large datasets. This poses a significant challenge because generating data for this learning setup is laborious and time-consuming since each data sample is a full set of network weights that has to be trained. In this paper, we address this difficulty by investigating data augmentations for weight spaces, a set of techniques that enable generating new data examples on the fly without having to train additional input weight space elements. We first review several recently proposed data augmentation schemes %that were proposed recently and divide them into categories. We then introduce a novel augmentation scheme based on the Mixup method. We evaluate the performance of these techniques on existing benchmarks as well as new benchmarks we generate, which can be valuable for future studies.

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and complexity of the problem, this manual architecture exploration likely exceeds human design abilities. In this paper, we propose a principled approach, rooted in differentiable neural architecture search, to automatically define branching (tree-like) structures in the encoding stage of a multi-task neural network. To allow flexibility within resource-constrained environments, we introduce a proxyless, resource-aware loss that dynamically controls the model size. Evaluations across a variety of dense prediction tasks show that our approach consistently finds high-performing branching structures within limited resource budgets.

Neural Architecture Search (NAS) has gained significant popularity as an effective tool for designing high performance deep neural networks (DNNs). NAS can be performed via policy gradient, evolutionary algorithms, differentiable architecture search or tree-search methods. While significant progress has been made for both policy gradient and differentiable architecture search, tree-search methods have so far failed to achieve comparable accuracy or search efficiency. In this paper, we formulate NAS as a Combinatorial Multi-Armed Bandit (CMAB) problem (CMAB-NAS). This allows the decomposition of a large search space into smaller blocks where tree-search methods can be applied more effectively and efficiently. We further leverage a tree-based method called Nested Monte-Carlo Search to tackle the CMAB-NAS problem. On CIFAR-10, our approach discovers a cell structure that achieves a low error rate that is comparable to the state-of-the-art, using only 0.58 GPU days, which is 20 times faster than current tree-search methods. Moreover, the discovered structure transfers well to large-scale datasets such as ImageNet.

We present Text2Room, a method for generating room-scale textured 3D meshes from a given text prompt as input. To this end, we leverage pre-trained 2D text-to-image models to synthesize a sequence of images from different poses. In order to lift these outputs into a consistent 3D scene representation, we combine monocular depth estimation with a text-conditioned inpainting model. The core idea of our approach is a tailored viewpoint selection such that the content of each image can be fused into a seamless, textured 3D mesh. More specifically, we propose a continuous alignment strategy that iteratively fuses scene frames with the existing geometry to create a seamless mesh. Unlike existing works that focus on generating single objects or zoom-out trajectories from text, our method generates complete 3D scenes with multiple objects and explicit 3D geometry. We evaluate our approach using qualitative and quantitative metrics, demonstrating it as the first method to generate room-scale 3D geometry with compelling textures from only text as input.

Internet image collections containing photos captured by crowds of photographers show promise for enabling digital exploration of large-scale tourist landmarks. However, prior works focus primarily on geometric reconstruction and visualization, neglecting the key role of language in providing a semantic interface for navigation and fine-grained understanding. In constrained 3D domains, recent methods have leveraged vision-and-language models as a strong prior of 2D visual semantics. While these models display an excellent understanding of broad visual semantics, they struggle with unconstrained photo collections depicting such tourist landmarks, as they lack expert knowledge of the architectural domain. In this work, we present a localization system that connects neural representations of scenes depicting large-scale landmarks with text describing a semantic region within the scene, by harnessing the power of SOTA vision-and-language models with adaptations for understanding landmark scene semantics. To bolster such models with fine-grained knowledge, we leverage large-scale Internet data containing images of similar landmarks along with weakly-related textual information. Our approach is built upon the premise that images physically grounded in space can provide a powerful supervision signal for localizing new concepts, whose semantics may be unlocked from Internet textual metadata with large language models. We use correspondences between views of scenes to bootstrap spatial understanding of these semantics, providing guidance for 3D-compatible segmentation that ultimately lifts to a volumetric scene representation. Our results show that HaLo-NeRF can accurately localize a variety of semantic concepts related to architectural landmarks, surpassing the results of other 3D models as well as strong 2D segmentation baselines. Our project page is at https://tau-vailab.github.io/HaLo-NeRF/.

Constructing compact and informative 3D scene representations is essential for effective embodied exploration and reasoning, especially in complex environments over extended periods. Existing representations, such as object-centric 3D scene graphs, oversimplify spatial relationships by modeling scenes as isolated objects with restrictive textual relationships, making it difficult to address queries requiring nuanced spatial understanding. Moreover, these representations lack natural mechanisms for active exploration and memory management, hindering their application to lifelong autonomy. In this work, we propose 3D-Mem, a novel 3D scene memory framework for embodied agents. 3D-Mem employs informative multi-view images, termed Memory Snapshots, to represent the scene and capture rich visual information of explored regions. It further integrates frontier-based exploration by introducing Frontier Snapshots-glimpses of unexplored areas-enabling agents to make informed decisions by considering both known and potential new information. To support lifelong memory in active exploration settings, we present an incremental construction pipeline for 3D-Mem, as well as a memory retrieval technique for memory management. Experimental results on three benchmarks demonstrate that 3D-Mem significantly enhances agents' exploration and reasoning capabilities in 3D environments, highlighting its potential for advancing applications in embodied AI.

We introduce SceneScript, a method that directly produces full scene models as a sequence of structured language commands using an autoregressive, token-based approach. Our proposed scene representation is inspired by recent successes in transformers & LLMs, and departs from more traditional methods which commonly describe scenes as meshes, voxel grids, point clouds or radiance fields. Our method infers the set of structured language commands directly from encoded visual data using a scene language encoder-decoder architecture. To train SceneScript, we generate and release a large-scale synthetic dataset called Aria Synthetic Environments consisting of 100k high-quality in-door scenes, with photorealistic and ground-truth annotated renders of egocentric scene walkthroughs. Our method gives state-of-the art results in architectural layout estimation, and competitive results in 3D object detection. Lastly, we explore an advantage for SceneScript, which is the ability to readily adapt to new commands via simple additions to the structured language, which we illustrate for tasks such as coarse 3D object part reconstruction.

Indoor scene synthesis involves automatically picking and placing furniture appropriately on a floor plan, so that the scene looks realistic and is functionally plausible. Such scenes can serve as homes for immersive 3D experiences, or be used to train embodied agents. Existing methods for this task rely on labeled categories of furniture, e.g. bed, chair or table, to generate contextually relevant combinations of furniture. Whether heuristic or learned, these methods ignore instance-level visual attributes of objects, and as a result may produce visually less coherent scenes. In this paper, we introduce an auto-regressive scene model which can output instance-level predictions, using general purpose image embedding based on CLIP. This allows us to learn visual correspondences such as matching color and style, and produce more functionally plausible and aesthetically pleasing scenes. Evaluated on the 3D-FRONT dataset, our model achieves SOTA results in scene synthesis and improves auto-completion metrics by over 50%. Moreover, our embedding-based approach enables zero-shot text-guided scene synthesis and editing, which easily generalizes to furniture not seen during training.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

The visual examination of tissue biopsy sections is fundamental for cancer diagnosis, with pathologists analyzing sections at multiple magnifications to discern tumor cells and their subtypes. However, existing attention-based multiple instance learning (MIL) models, used for analyzing Whole Slide Images (WSIs) in cancer diagnostics, often overlook the contextual information of tumor and neighboring tiles, leading to misclassifications. To address this, we propose the Context-Aware Multiple Instance Learning (CAMIL) architecture. CAMIL incorporates neighbor-constrained attention to consider dependencies among tiles within a WSI and integrates contextual constraints as prior knowledge into the MIL model. We evaluated CAMIL on subtyping non-small cell lung cancer (TCGA-NSCLC) and detecting lymph node (CAMELYON16) metastasis, achieving test AUCs of 0.959\% and 0.975\%, respectively, outperforming other state-of-the-art methods. Additionally, CAMIL enhances model interpretability by identifying regions of high diagnostic value.

Efficient Human Epithelial-2 (HEp-2) cell image classification can facilitate the diagnosis of many autoimmune diseases. This paper presents an automatic framework for this classification task, by utilizing the deep convolutional neural networks (CNNs) which have recently attracted intensive attention in visual recognition. This paper elaborates the important components of this framework, discusses multiple key factors that impact the efficiency of training a deep CNN, and systematically compares this framework with the well-established image classification models in the literature. Experiments on benchmark datasets show that i) the proposed framework can effectively outperform existing models by properly applying data augmentation; ii) our CNN-based framework demonstrates excellent adaptability across different datasets, which is highly desirable for classification under varying laboratory settings. Our system is ranked high in the cell image classification competition hosted by ICPR 2014.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

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.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

We investigate the problem of training generative models on a very sparse collection of 3D models. We use geometrically motivated energies to augment and thus boost a sparse collection of example (training) models. We analyze the Hessian of the as-rigid-as-possible (ARAP) energy to sample from and project to the underlying (local) shape space, and use the augmented dataset to train a variational autoencoder (VAE). We iterate the process of building latent spaces of VAE and augmenting the associated dataset, to progressively reveal a richer and more expressive generative space for creating geometrically and semantically valid samples. Our framework allows us to train generative 3D models even with a small set of good quality 3D models, which are typically hard to curate. We extensively evaluate our method against a set of strong baselines, provide ablation studies and demonstrate application towards establishing shape correspondences. We present multiple examples of interesting and meaningful shape variations even when starting from as few as 3-10 training shapes.

We address 2D floorplan reconstruction from 3D scans. Existing approaches typically employ heuristically designed multi-stage pipelines. Instead, we formulate floorplan reconstruction as a single-stage structured prediction task: find a variable-size set of polygons, which in turn are variable-length sequences of ordered vertices. To solve it we develop a novel Transformer architecture that generates polygons of multiple rooms in parallel, in a holistic manner without hand-crafted intermediate stages. The model features two-level queries for polygons and corners, and includes polygon matching to make the network end-to-end trainable. Our method achieves a new state-of-the-art for two challenging datasets, Structured3D and SceneCAD, along with significantly faster inference than previous methods. Moreover, it can readily be extended to predict additional information, i.e., semantic room types and architectural elements like doors and windows. Our code and models are available at: https://github.com/ywyue/RoomFormer.

Developing accurate machine learning models for oncology requires large-scale, high-quality multimodal datasets. However, creating such datasets remains challenging due to the complexity and heterogeneity of medical data. To address this challenge, we introduce HoneyBee, a scalable modular framework for building multimodal oncology datasets that leverages foundational models to generate representative embeddings. HoneyBee integrates various data modalities, including clinical records, imaging data, and patient outcomes. It employs data preprocessing techniques and transformer-based architectures to generate embeddings that capture the essential features and relationships within the raw medical data. The generated embeddings are stored in a structured format using Hugging Face datasets and PyTorch dataloaders for accessibility. Vector databases enable efficient querying and retrieval for machine learning applications. We demonstrate the effectiveness of HoneyBee through experiments assessing the quality and representativeness of the embeddings. The framework is designed to be extensible to other medical domains and aims to accelerate oncology research by providing high-quality, machine learning-ready datasets. HoneyBee is an ongoing open-source effort, and the code, datasets, and models are available at the project repository.

Task-specific deep learning models in histopathology offer promising opportunities for improving diagnosis, clinical research, and precision medicine. However, development of such models is often limited by availability of high-quality data. Foundation models in histopathology that learn general representations across a wide range of tissue types, diagnoses, and magnifications offer the potential to reduce the data, compute, and technical expertise necessary to develop task-specific deep learning models with the required level of model performance. In this work, we describe the development and evaluation of foundation models for histopathology via self-supervised learning (SSL). We first establish a diverse set of benchmark tasks involving 17 unique tissue types and 12 unique cancer types and spanning different optimal magnifications and task types. Next, we use this benchmark to explore and evaluate histopathology-specific SSL methods followed by further evaluation on held out patch-level and weakly supervised tasks. We found that standard SSL methods thoughtfully applied to histopathology images are performant across our benchmark tasks and that domain-specific methodological improvements can further increase performance. Our findings reinforce the value of using domain-specific SSL methods in pathology, and establish a set of high quality foundation models to enable further research across diverse applications.

Few-shot image generation is a challenging task since it aims to generate diverse new images for an unseen category with only a few images. Existing methods suffer from the trade-off between the quality and diversity of generated images. To tackle this problem, we propose Hyperbolic Attribute Editing~(HAE), a simple yet effective method. Unlike other methods that work in Euclidean space, HAE captures the hierarchy among images using data from seen categories in hyperbolic space. Given a well-trained HAE, images of unseen categories can be generated by moving the latent code of a given image toward any meaningful directions in the Poincar\'e disk with a fixing radius. Most importantly, the hyperbolic space allows us to control the semantic diversity of the generated images by setting different radii in the disk. Extensive experiments and visualizations demonstrate that HAE is capable of not only generating images with promising quality and diversity using limited data but achieving a highly controllable and interpretable editing process.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

High-fidelity human 3D models can now be learned directly from videos, typically by combining a template-based surface model with neural representations. However, obtaining a template surface requires expensive multi-view capture systems, laser scans, or strictly controlled conditions. Previous methods avoid using a template but rely on a costly or ill-posed mapping from observation to canonical space. We propose a hybrid point-based representation for reconstructing animatable characters that does not require an explicit surface model, while being generalizable to novel poses. For a given video, our method automatically produces an explicit set of 3D points representing approximate canonical geometry, and learns an articulated deformation model that produces pose-dependent point transformations. The points serve both as a scaffold for high-frequency neural features and an anchor for efficiently mapping between observation and canonical space. We demonstrate on established benchmarks that our representation overcomes limitations of prior work operating in either canonical or in observation space. Moreover, our automatic point extraction approach enables learning models of human and animal characters alike, matching the performance of the methods using rigged surface templates despite being more general. Project website: https://lemonatsu.github.io/npc/

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

Coarse architectural models are often generated at scales ranging from individual buildings to scenes for downstream applications such as Digital Twin City, Metaverse, LODs, etc. Such piece-wise planar models can be abstracted as twins from 3D dense reconstructions. However, these models typically lack realistic texture relative to the real building or scene, making them unsuitable for vivid display or direct reference. In this paper, we present TwinTex, the first automatic texture mapping framework to generate a photo-realistic texture for a piece-wise planar proxy. Our method addresses most challenges occurring in such twin texture generation. Specifically, for each primitive plane, we first select a small set of photos with greedy heuristics considering photometric quality, perspective quality and facade texture completeness. Then, different levels of line features (LoLs) are extracted from the set of selected photos to generate guidance for later steps. With LoLs, we employ optimization algorithms to align texture with geometry from local to global. Finally, we fine-tune a diffusion model with a multi-mask initialization component and a new dataset to inpaint the missing region. Experimental results on many buildings, indoor scenes and man-made objects of varying complexity demonstrate the generalization ability of our algorithm. Our approach surpasses state-of-the-art texture mapping methods in terms of high-fidelity quality and reaches a human-expert production level with much less effort. Project page: https://vcc.tech/research/2023/TwinTex.

Toward infinite-scale 3D city synthesis, we propose a novel framework, InfiniCity, which constructs and renders an unconstrainedly large and 3D-grounded environment from random noises. InfiniCity decomposes the seemingly impractical task into three feasible modules, taking advantage of both 2D and 3D data. First, an infinite-pixel image synthesis module generates arbitrary-scale 2D maps from the bird's-eye view. Next, an octree-based voxel completion module lifts the generated 2D map to 3D octrees. Finally, a voxel-based neural rendering module texturizes the voxels and renders 2D images. InfiniCity can thus synthesize arbitrary-scale and traversable 3D city environments, and allow flexible and interactive editing from users. We quantitatively and qualitatively demonstrate the efficacy of the proposed framework. Project page: https://hubert0527.github.io/infinicity/

Efforts to overcome catastrophic forgetting have primarily centered around developing more effective Continual Learning (CL) methods. In contrast, less attention was devoted to analyzing the role of network architecture design (e.g., network depth, width, and components) in contributing to CL. This paper seeks to bridge this gap between network architecture design and CL, and to present a holistic study on the impact of network architectures on CL. This work considers architecture design at the network scaling level, i.e., width and depth, and also at the network components, i.e., skip connections, global pooling layers, and down-sampling. In both cases, we first derive insights through systematically exploring how architectural designs affect CL. Then, grounded in these insights, we craft a specialized search space for CL and further propose a simple yet effective ArchCraft method to steer a CL-friendly architecture, namely, this method recrafts AlexNet/ResNet into AlexAC/ResAC. Experimental validation across various CL settings and scenarios demonstrates that improved architectures are parameter-efficient, achieving state-of-the-art performance of CL while being 86%, 61%, and 97% more compact in terms of parameters than the naive CL architecture in Task IL and Class IL. Code is available at https://github.com/byyx666/ArchCraft.

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership i in S and estimating set intersection sizes |X cap Y| for two sets of symbols X and Y, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters.

Human intelligence emerged through the process of natural selection and evolution on Earth. We investigate what it would take to re-create this process in silico. While past work has often focused on low-level processes (such as simulating physics or chemistry), we instead take a more targeted approach, aiming to evolve agents that can accumulate open-ended culture and technologies across generations. Towards this, we present JaxLife: an artificial life simulator in which embodied agents, parameterized by deep neural networks, must learn to survive in an expressive world containing programmable systems. First, we describe the environment and show that it can facilitate meaningful Turing-complete computation. We then analyze the evolved emergent agents' behavior, such as rudimentary communication protocols, agriculture, and tool use. Finally, we investigate how complexity scales with the amount of compute used. We believe JaxLife takes a step towards studying evolved behavior in more open-ended simulations. Our code is available at https://github.com/luchris429/JaxLife

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70% test accuracy on CIFAR-10 with 14.3M parameters and 74.6% top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures.

Neural Architecture Search (NAS) algorithms automate the task of finding optimal deep learning architectures given an initial search space of possible operations. Developing these search spaces is usually a manual affair with pre-optimized search spaces being more efficient, rather than searching from scratch. In this paper we present a new framework called Neural Architecture Type System (NeuralArTS) that categorizes the infinite set of network operations in a structured type system. We further demonstrate how NeuralArTS can be applied to convolutional layers and propose several future directions.

Object-centric architectures usually apply a differentiable module to the entire feature map to decompose it into sets of entity representations called slots. Some of these methods structurally resemble clustering algorithms, where the cluster's center in latent space serves as a slot representation. Slot Attention is an example of such a method, acting as a learnable analog of the soft k-means algorithm. Our work employs a learnable clustering method based on the Gaussian Mixture Model. Unlike other approaches, we represent slots not only as centers of clusters but also incorporate information about the distance between clusters and assigned vectors, leading to more expressive slot representations. Our experiments demonstrate that using this approach instead of Slot Attention improves performance in object-centric scenarios, achieving state-of-the-art results in the set property prediction task.

We present a method for creating 3D indoor scenes with a generative model learned from a collection of semantic-segmented depth images captured from different unknown scenes. Given a room with a specified size, our method automatically generates 3D objects in a room from a randomly sampled latent code. Different from existing methods that represent an indoor scene with the type, location, and other properties of objects in the room and learn the scene layout from a collection of complete 3D indoor scenes, our method models each indoor scene as a 3D semantic scene volume and learns a volumetric generative adversarial network (GAN) from a collection of 2.5D partial observations of 3D scenes. To this end, we apply a differentiable projection layer to project the generated 3D semantic scene volumes into semantic-segmented depth images and design a new multiple-view discriminator for learning the complete 3D scene volume from 2.5D semantic-segmented depth images. Compared to existing methods, our method not only efficiently reduces the workload of modeling and acquiring 3D scenes for training, but also produces better object shapes and their detailed layouts in the scene. We evaluate our method with different indoor scene datasets and demonstrate the advantages of our method. We also extend our method for generating 3D indoor scenes from semantic-segmented depth images inferred from RGB images of real scenes.

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding and interaction within human-AI and multi-agent AI frameworks. A key innovation of Cephalo is its advanced dataset generation method, which employs a sophisticated algorithm to accurately detect and separate images and their corresponding textual descriptions from PDF documents, such as scientific papers. The method includes a careful refinement of image-text pairs through integrated vision and language processing, ensuring high-quality, contextually relevant, and well reasoned training data. Cephalo is trained on integrated image and text data extracted from thousands of scientific papers and science-focused Wikipedia pages demonstrates can interpret complex visual scenes, generate precise language descriptions, and answer queries about images effectively. The combination of a vision encoder with an autoregressive transformer supports complex natural language understanding in an integrated model, which can be coupled with other generative methods to create an image-to-text-to-image or image-to-text-to-3D pipeline. To explore the development of larger models from smaller ones, we merge sets of layers that originate from different pre-trained source models. This hybrid approach allows us to leverage the domain-specific expertise and general conversational capabilities to harness the strengths of multiple models. We examine the models in diverse use cases that incorporate biological materials, fracture and engineering analysis, protein biophysics, and bio-inspired design based on insect behavior. Generative applications include bio-inspired designs, including pollen-inspired architected materials, as well as the synthesis of bio-inspired material microstructures from a photograph of a solar eclipse.

Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several fine-tuning techniques have been developed to update the pre-trained model weights in a more resource-efficient manner, such as through low-rank adjustments. Yet, almost all of these methods focus on linear weights, neglecting the intricacies of parameter spaces in higher dimensions like 4D. Alternatively, some methods can be adapted for high-dimensional parameter space by compressing changes in the original space into two dimensions and then employing low-rank matrix decomposition. However, these approaches destructs the structural integrity of the involved high-dimensional spaces. To tackle the diversity of dimensional spaces across different foundation models and provide a more precise representation of the changes within these spaces, this paper introduces a generalized parameter-efficient fine-tuning framework, FLoRA, designed for various dimensional parameter space. Specifically, utilizing Tucker decomposition, FLoRA asserts that changes in each dimensional parameter space are based on a low-rank core space which maintains the consistent topological structure with the original space. It then models the changes through this core space alongside corresponding weights to reconstruct alterations in the original space. FLoRA effectively preserves the structural integrity of the change of original N-dimensional parameter space, meanwhile decomposes it via low-rank tensor decomposition. Extensive experiments on computer vision, natural language processing and multi-modal tasks validate FLoRA's effectiveness. Codes are available at https://github.com/SJTU-DeepVisionLab/FLoRA.

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.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .

We present Galactic, a large-scale simulation and reinforcement-learning (RL) framework for robotic mobile manipulation in indoor environments. Specifically, a Fetch robot (equipped with a mobile base, 7DoF arm, RGBD camera, egomotion, and onboard sensing) is spawned in a home environment and asked to rearrange objects - by navigating to an object, picking it up, navigating to a target location, and then placing the object at the target location. Galactic is fast. In terms of simulation speed (rendering + physics), Galactic achieves over 421,000 steps-per-second (SPS) on an 8-GPU node, which is 54x faster than Habitat 2.0 (7699 SPS). More importantly, Galactic was designed to optimize the entire rendering + physics + RL interplay since any bottleneck in the interplay slows down training. In terms of simulation+RL speed (rendering + physics + inference + learning), Galactic achieves over 108,000 SPS, which 88x faster than Habitat 2.0 (1243 SPS). These massive speed-ups not only drastically cut the wall-clock training time of existing experiments, but also unlock an unprecedented scale of new experiments. First, Galactic can train a mobile pick skill to >80% accuracy in under 16 minutes, a 100x speedup compared to the over 24 hours it takes to train the same skill in Habitat 2.0. Second, we use Galactic to perform the largest-scale experiment to date for rearrangement using 5B steps of experience in 46 hours, which is equivalent to 20 years of robot experience. This scaling results in a single neural network composed of task-agnostic components achieving 85% success in GeometricGoal rearrangement, compared to 0% success reported in Habitat 2.0 for the same approach. The code is available at github.com/facebookresearch/galactic.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Recent advancements in implicit 3D representations and generative models have markedly propelled the field of 3D object generation forward. However, it remains a significant challenge to accurately model geometries with defined sharp features under parametric controls, which is crucial in fields like industrial design and manufacturing. To bridge this gap, we introduce a framework that employs Large Language Models (LLMs) to generate text-driven 3D shapes, manipulating 3D software via program synthesis. We present 3D-PreMise, a dataset specifically tailored for 3D parametric modeling of industrial shapes, designed to explore state-of-the-art LLMs within our proposed pipeline. Our work reveals effective generation strategies and delves into the self-correction capabilities of LLMs using a visual interface. Our work highlights both the potential and limitations of LLMs in 3D parametric modeling for industrial applications.

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

Interior design allows us to be who we are and live how we want - each design is as unique as our distinct personality. However, it is not trivial for non-professionals to express and materialize this since it requires aligning functional and visual expectations with the constraints of physical space; this renders interior design a luxury. To make it more accessible, we present I-Design, a personalized interior designer that allows users to generate and visualize their design goals through natural language communication. I-Design starts with a team of large language model agents that engage in dialogues and logical reasoning with one another, transforming textual user input into feasible scene graph designs with relative object relationships. Subsequently, an effective placement algorithm determines optimal locations for each object within the scene. The final design is then constructed in 3D by retrieving and integrating assets from an existing object database. Additionally, we propose a new evaluation protocol that utilizes a vision-language model and complements the design pipeline. Extensive quantitative and qualitative experiments show that I-Design outperforms existing methods in delivering high-quality 3D design solutions and aligning with abstract concepts that match user input, showcasing its advantages across detailed 3D arrangement and conceptual fidelity.

In this paper, we propose Img2CAD, the first approach to our knowledge that uses 2D image inputs to generate CAD models with editable parameters. Unlike existing AI methods for 3D model generation using text or image inputs often rely on mesh-based representations, which are incompatible with CAD tools and lack editability and fine control, Img2CAD enables seamless integration between AI-based 3D reconstruction and CAD software. We have identified an innovative intermediate representation called Structured Visual Geometry (SVG), characterized by vectorized wireframes extracted from objects. This representation significantly enhances the performance of generating conditioned CAD models. Additionally, we introduce two new datasets to further support research in this area: ABC-mono, the largest known dataset comprising over 200,000 3D CAD models with rendered images, and KOCAD, the first dataset featuring real-world captured objects alongside their ground truth CAD models, supporting further research in conditioned CAD model generation.

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

The advancement of diffusion models has pushed the boundary of text-to-3D object generation. While it is straightforward to composite objects into a scene with reasonable geometry, it is nontrivial to texture such a scene perfectly due to style inconsistency and occlusions between objects. To tackle these problems, we propose a coarse-to-fine 3D scene texturing framework, referred to as RoomTex, to generate high-fidelity and style-consistent textures for untextured compositional scene meshes. In the coarse stage, RoomTex first unwraps the scene mesh to a panoramic depth map and leverages ControlNet to generate a room panorama, which is regarded as the coarse reference to ensure the global texture consistency. In the fine stage, based on the panoramic image and perspective depth maps, RoomTex will refine and texture every single object in the room iteratively along a series of selected camera views, until this object is completely painted. Moreover, we propose to maintain superior alignment between RGB and depth spaces via subtle edge detection methods. Extensive experiments show our method is capable of generating high-quality and diverse room textures, and more importantly, supporting interactive fine-grained texture control and flexible scene editing thanks to our inpainting-based framework and compositional mesh input. Our project page is available at https://qwang666.github.io/RoomTex/.

Embodiment co-design aims to optimize a robot's morphology and control policy simultaneously. While prior work has demonstrated its potential for generating environment-adaptive robots, this field still faces persistent challenges in optimization efficiency due to the (i) combinatorial nature of morphological search spaces and (ii) intricate dependencies between morphology and control. We prove that the ineffective morphology representation and unbalanced reward signals between the design and control stages are key obstacles to efficiency. To advance towards efficient embodiment co-design, we propose BodyGen, which utilizes (1) topology-aware self-attention for both design and control, enabling efficient morphology representation with lightweight model sizes; (2) a temporal credit assignment mechanism that ensures balanced reward signals for optimization. With our findings, Body achieves an average 60.03% performance improvement against state-of-the-art baselines. We provide codes and more results on the website: https://genesisorigin.github.io.

3D scene generation has garnered growing attention in recent years and has made significant progress. Generating 4D cities is more challenging than 3D scenes due to the presence of structurally complex, visually diverse objects like buildings and vehicles, and heightened human sensitivity to distortions in urban environments. To tackle these issues, we propose CityDreamer4D, a compositional generative model specifically tailored for generating unbounded 4D cities. Our main insights are 1) 4D city generation should separate dynamic objects (e.g., vehicles) from static scenes (e.g., buildings and roads), and 2) all objects in the 4D scene should be composed of different types of neural fields for buildings, vehicles, and background stuff. Specifically, we propose Traffic Scenario Generator and Unbounded Layout Generator to produce dynamic traffic scenarios and static city layouts using a highly compact BEV representation. Objects in 4D cities are generated by combining stuff-oriented and instance-oriented neural fields for background stuff, buildings, and vehicles. To suit the distinct characteristics of background stuff and instances, the neural fields employ customized generative hash grids and periodic positional embeddings as scene parameterizations. Furthermore, we offer a comprehensive suite of datasets for city generation, including OSM, GoogleEarth, and CityTopia. The OSM dataset provides a variety of real-world city layouts, while the Google Earth and CityTopia datasets deliver large-scale, high-quality city imagery complete with 3D instance annotations. Leveraging its compositional design, CityDreamer4D supports a range of downstream applications, such as instance editing, city stylization, and urban simulation, while delivering state-of-the-art performance in generating realistic 4D cities.

The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While neural docking techniques have exhibited promising outcomes in binary protein docking, the application of advanced neural architectures to multimeric protein docking remains uncertain. This study introduces SyNDock, an automated framework that swiftly assembles precise multimeric complexes within seconds, showcasing performance that can potentially surpass or be on par with recent advanced approaches. SyNDock possesses several appealing advantages not present in previous approaches. Firstly, SyNDock formulates multimeric protein docking as a problem of learning global transformations to holistically depict the placement of chain units of a complex, enabling a learning-centric solution. Secondly, SyNDock proposes a trainable two-step SE(3) algorithm, involving initial pairwise transformation and confidence estimation, followed by global transformation synchronization. This enables effective learning for assembling the complex in a globally consistent manner. Lastly, extensive experiments conducted on our proposed benchmark dataset demonstrate that SyNDock outperforms existing docking software in crucial performance metrics, including accuracy and runtime. For instance, it achieves a 4.5% improvement in performance and a remarkable millionfold acceleration in speed.

The emerging field of Diverse Intelligence seeks to identify, formalize, and understand commonalities in behavioral competencies across a wide range of implementations. Especially interesting are simple systems that provide unexpected examples of memory, decision-making, or problem-solving in substrates that at first glance do not appear to be complex enough to implement such capabilities. We seek to develop tools to help understand the minimal requirements for such capabilities, and to learn to recognize and predict basal forms of intelligence in unconventional substrates. Here, we apply novel analyses to the behavior of classical sorting algorithms, short pieces of code which have been studied for many decades. To study these sorting algorithms as a model of biological morphogenesis and its competencies, we break two formerly-ubiquitous assumptions: top-down control (instead, showing how each element within a array of numbers can exert minimal agency and implement sorting policies from the bottom up), and fully reliable hardware (instead, allowing some of the elements to be "damaged" and fail to execute the algorithm). We quantitatively characterize sorting activity as the traversal of a problem space, showing that arrays of autonomous elements sort themselves more reliably and robustly than traditional implementations in the presence of errors. Moreover, we find the ability to temporarily reduce progress in order to navigate around a defect, and unexpected clustering behavior among the elements in chimeric arrays whose elements follow one of two different algorithms. The discovery of emergent problem-solving capacities in simple, familiar algorithms contributes a new perspective to the field of Diverse Intelligence, showing how basal forms of intelligence can emerge in simple systems without being explicitly encoded in their underlying mechanics.

A comprehensive semantic understanding of a scene is important for many applications - but in what space should diverse semantic information (e.g., objects, scene categories, material types, texture, etc.) be grounded and what should be its structure? Aspiring to have one unified structure that hosts diverse types of semantics, we follow the Scene Graph paradigm in 3D, generating a 3D Scene Graph. Given a 3D mesh and registered panoramic images, we construct a graph that spans the entire building and includes semantics on objects (e.g., class, material, and other attributes), rooms (e.g., scene category, volume, etc.) and cameras (e.g., location, etc.), as well as the relationships among these entities. However, this process is prohibitively labor heavy if done manually. To alleviate this we devise a semi-automatic framework that employs existing detection methods and enhances them using two main constraints: I. framing of query images sampled on panoramas to maximize the performance of 2D detectors, and II. multi-view consistency enforcement across 2D detections that originate in different camera locations.

Much of the success of deep learning is drawn from building architectures that properly respect underlying symmetry and structure in the data on which they operate - a set of considerations that have been united under the banner of geometric deep learning. Often problems in the physical sciences deal with relatively small sets of points in two- or three-dimensional space wherein translation, rotation, and permutation equivariance are important or even vital for models to be useful in practice. In this work, we present rotation- and permutation-equivariant architectures for deep learning on these small point clouds, composed of a set of products of terms from the geometric algebra and reductions over those products using an attention mechanism. The geometric algebra provides valuable mathematical structure by which to combine vector, scalar, and other types of geometric inputs in a systematic way to account for rotation invariance or covariance, while attention yields a powerful way to impose permutation equivariance. We demonstrate the usefulness of these architectures by training models to solve sample problems relevant to physics, chemistry, and biology.

The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H&E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

We target a 3D generative model for general natural scenes that are typically unique and intricate. Lacking the necessary volumes of training data, along with the difficulties of having ad hoc designs in presence of varying scene characteristics, renders existing setups intractable. Inspired by classical patch-based image models, we advocate for synthesizing 3D scenes at the patch level, given a single example. At the core of this work lies important algorithmic designs w.r.t the scene representation and generative patch nearest-neighbor module, that address unique challenges arising from lifting classical 2D patch-based framework to 3D generation. These design choices, on a collective level, contribute to a robust, effective, and efficient model that can generate high-quality general natural scenes with both realistic geometric structure and visual appearance, in large quantities and varieties, as demonstrated upon a variety of exemplar scenes.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

3D generation guided by text-to-image diffusion models enables the creation of visually compelling assets. However previous methods explore generation based on image or text. The boundaries of creativity are limited by what can be expressed through words or the images that can be sourced. We present YouDream, a method to generate high-quality anatomically controllable animals. YouDream is guided using a text-to-image diffusion model controlled by 2D views of a 3D pose prior. Our method generates 3D animals that are not possible to create using previous text-to-3D generative methods. Additionally, our method is capable of preserving anatomic consistency in the generated animals, an area where prior text-to-3D approaches often struggle. Moreover, we design a fully automated pipeline for generating commonly found animals. To circumvent the need for human intervention to create a 3D pose, we propose a multi-agent LLM that adapts poses from a limited library of animal 3D poses to represent the desired animal. A user study conducted on the outcomes of YouDream demonstrates the preference of the animal models generated by our method over others. Turntable results and code are released at https://youdream3d.github.io/

This paper focuses on the task of room layout estimation from a monocular RGB image. Prior works break the problem into two sub-tasks: semantic segmentation of floor, walls, ceiling to produce layout hypotheses, followed by an iterative optimization step to rank these hypotheses. In contrast, we adopt a more direct formulation of this problem as one of estimating an ordered set of room layout keypoints. The room layout and the corresponding segmentation is completely specified given the locations of these ordered keypoints. We predict the locations of the room layout keypoints using RoomNet, an end-to-end trainable encoder-decoder network. On the challenging benchmark datasets Hedau and LSUN, we achieve state-of-the-art performance along with 200x to 600x speedup compared to the most recent work. Additionally, we present optional extensions to the RoomNet architecture such as including recurrent computations and memory units to refine the keypoint locations under the same parametric capacity.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

There is increased interest in using generative AI to create 3D spaces for Virtual Reality (VR) applications. However, today's models produce artificial environments, falling short of supporting collaborative tasks that benefit from incorporating the user's physical context. To generate environments that support VR telepresence, we introduce SpaceBlender, a novel pipeline that utilizes generative AI techniques to blend users' physical surroundings into unified virtual spaces. This pipeline transforms user-provided 2D images into context-rich 3D environments through an iterative process consisting of depth estimation, mesh alignment, and diffusion-based space completion guided by geometric priors and adaptive text prompts. In a preliminary within-subjects study, where 20 participants performed a collaborative VR affinity diagramming task in pairs, we compared SpaceBlender with a generic virtual environment and a state-of-the-art scene generation framework, evaluating its ability to create virtual spaces suitable for collaboration. Participants appreciated the enhanced familiarity and context provided by SpaceBlender but also noted complexities in the generative environments that could detract from task focus. Drawing on participant feedback, we propose directions for improving the pipeline and discuss the value and design of blended spaces for different scenarios.

Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabeled data into a foundation model before learning from, potentially limited, labeled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 103k slides corresponding to 750 million image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

We present APT, an advanced Large Language Model (LLM)-driven framework that enables autonomous agents to construct complex and creative structures within the Minecraft environment. Unlike previous approaches that primarily concentrate on skill-based open-world tasks or rely on image-based diffusion models for generating voxel-based structures, our method leverages the intrinsic spatial reasoning capabilities of LLMs. By employing chain-of-thought decomposition along with multimodal inputs, the framework generates detailed architectural layouts and blueprints that the agent can execute under zero-shot or few-shot learning scenarios. Our agent incorporates both memory and reflection modules to facilitate lifelong learning, adaptive refinement, and error correction throughout the building process. To rigorously evaluate the agent's performance in this emerging research area, we introduce a comprehensive benchmark consisting of diverse construction tasks designed to test creativity, spatial reasoning, adherence to in-game rules, and the effective integration of multimodal instructions. Experimental results using various GPT-based LLM backends and agent configurations demonstrate the agent's capacity to accurately interpret extensive instructions involving numerous items, their positions, and orientations. The agent successfully produces complex structures complete with internal functionalities such as Redstone-powered systems. A/B testing indicates that the inclusion of a memory module leads to a significant increase in performance, emphasizing its role in enabling continuous learning and the reuse of accumulated experience. Additionally, the agent's unexpected emergence of scaffolding behavior highlights the potential of future LLM-driven agents to utilize subroutine planning and leverage the emergence ability of LLMs to autonomously develop human-like problem-solving techniques.

Point cloud analysis (such as 3D segmentation and detection) is a challenging task, because of not only the irregular geometries of many millions of unordered points, but also the great variations caused by depth, viewpoint, occlusion, etc. Current studies put much focus on the adaption of neural networks to the complex geometries of point clouds, but are blind to a fundamental question: how to learn an appropriate point embedding space that is aware of both discriminative semantics and challenging variations? As a response, we propose a clustering based supervised learning scheme for point cloud analysis. Unlike current de-facto, scene-wise training paradigm, our algorithm conducts within-class clustering on the point embedding space for automatically discovering subclass patterns which are latent yet representative across scenes. The mined patterns are, in turn, used to repaint the embedding space, so as to respect the underlying distribution of the entire training dataset and improve the robustness to the variations. Our algorithm is principled and readily pluggable to modern point cloud segmentation networks during training, without extra overhead during testing. With various 3D network architectures (i.e., voxel-based, point-based, Transformer-based, automatically searched), our algorithm shows notable improvements on famous point cloud segmentation datasets (i.e.,2.0-2.6% on single-scan and 2.0-2.2% multi-scan of SemanticKITTI, 1.8-1.9% on S3DIS, in terms of mIoU). Our algorithm also demonstrates utility in 3D detection, showing 2.0-3.4% mAP gains on KITTI.

Spatial confounding poses a significant challenge in scientific studies involving spatial data, where unobserved spatial variables can influence both treatment and outcome, possibly leading to spurious associations. To address this problem, we introduce SpaCE: The Spatial Confounding Environment, the first toolkit to provide realistic benchmark datasets and tools for systematically evaluating causal inference methods designed to alleviate spatial confounding. Each dataset includes training data, true counterfactuals, a spatial graph with coordinates, and smoothness and confounding scores characterizing the effect of a missing spatial confounder. It also includes realistic semi-synthetic outcomes and counterfactuals, generated using state-of-the-art machine learning ensembles, following best practices for causal inference benchmarks. The datasets cover real treatment and covariates from diverse domains, including climate, health and social sciences. SpaCE facilitates an automated end-to-end pipeline, simplifying data loading, experimental setup, and evaluating machine learning and causal inference models. The SpaCE project provides several dozens of datasets of diverse sizes and spatial complexity. It is publicly available as a Python package, encouraging community feedback and contributions.

Visual environments are structured, consisting of distinct objects or entities. These entities have properties -- both visible and latent -- that determine the manner in which they interact with one another. To partition images into entities, deep-learning researchers have proposed structural inductive biases such as slot-based architectures. To model interactions among entities, equivariant graph neural nets (GNNs) are used, but these are not particularly well suited to the task for two reasons. First, GNNs do not predispose interactions to be sparse, as relationships among independent entities are likely to be. Second, GNNs do not factorize knowledge about interactions in an entity-conditional manner. As an alternative, we take inspiration from cognitive science and resurrect a classic approach, production systems, which consist of a set of rule templates that are applied by binding placeholder variables in the rules to specific entities. Rules are scored on their match to entities, and the best fitting rules are applied to update entity properties. In a series of experiments, we demonstrate that this architecture achieves a flexible, dynamic flow of control and serves to factorize entity-specific and rule-based information. This disentangling of knowledge achieves robust future-state prediction in rich visual environments, outperforming state-of-the-art methods using GNNs, and allows for the extrapolation from simple (few object) environments to more complex environments.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

Humans and animals have a rich and flexible understanding of the physical world, which enables them to infer the underlying dynamical trajectories of objects and events, plausible future states, and use that to plan and anticipate the consequences of actions. However, the neural mechanisms underlying these computations are unclear. We combine a goal-driven modeling approach with dense neurophysiological data and high-throughput human behavioral readouts to directly impinge on this question. Specifically, we construct and evaluate several classes of sensory-cognitive networks to predict the future state of rich, ethologically-relevant environments, ranging from self-supervised end-to-end models with pixel-wise or object-centric objectives, to models that future predict in the latent space of purely static image-based or dynamic video-based pretrained foundation models. We find strong differentiation across these model classes in their ability to predict neural and behavioral data both within and across diverse environments. In particular, we find that neural responses are currently best predicted by models trained to predict the future state of their environment in the latent space of pretrained foundation models optimized for dynamic scenes in a self-supervised manner. Notably, models that future predict in the latent space of video foundation models that are optimized to support a diverse range of sensorimotor tasks, reasonably match both human behavioral error patterns and neural dynamics across all environmental scenarios that we were able to test. Overall, these findings suggest that the neural mechanisms and behaviors of primate mental simulation are thus far most consistent with being optimized to future predict on dynamic, reusable visual representations that are useful for embodied AI more generally.

Machine learning research has advanced in multiple aspects, including model structures and learning methods. The effort to automate such research, known as AutoML, has also made significant progress. However, this progress has largely focused on the architecture of neural networks, where it has relied on sophisticated expert-designed layers as building blocks---or similarly restrictive search spaces. Our goal is to show that AutoML can go further: it is possible today to automatically discover complete machine learning algorithms just using basic mathematical operations as building blocks. We demonstrate this by introducing a novel framework that significantly reduces human bias through a generic search space. Despite the vastness of this space, evolutionary search can still discover two-layer neural networks trained by backpropagation. These simple neural networks can then be surpassed by evolving directly on tasks of interest, e.g. CIFAR-10 variants, where modern techniques emerge in the top algorithms, such as bilinear interactions, normalized gradients, and weight averaging. Moreover, evolution adapts algorithms to different task types: e.g., dropout-like techniques appear when little data is available. We believe these preliminary successes in discovering machine learning algorithms from scratch indicate a promising new direction for the field.

We present a simple, highly modularized network architecture for image classification. Our network is constructed by repeating a building block that aggregates a set of transformations with the same topology. Our simple design results in a homogeneous, multi-branch architecture that has only a few hyper-parameters to set. This strategy exposes a new dimension, which we call "cardinality" (the size of the set of transformations), as an essential factor in addition to the dimensions of depth and width. On the ImageNet-1K dataset, we empirically show that even under the restricted condition of maintaining complexity, increasing cardinality is able to improve classification accuracy. Moreover, increasing cardinality is more effective than going deeper or wider when we increase the capacity. Our models, named ResNeXt, are the foundations of our entry to the ILSVRC 2016 classification task in which we secured 2nd place. We further investigate ResNeXt on an ImageNet-5K set and the COCO detection set, also showing better results than its ResNet counterpart. The code and models are publicly available online.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.

Real-time rendering and animation of humans is a core function in games, movies, and telepresence applications. Existing methods have a number of drawbacks we aim to address with our work. Triangle meshes have difficulty modeling thin structures like hair, volumetric representations like Neural Volumes are too low-resolution given a reasonable memory budget, and high-resolution implicit representations like Neural Radiance Fields are too slow for use in real-time applications. We present Mixture of Volumetric Primitives (MVP), a representation for rendering dynamic 3D content that combines the completeness of volumetric representations with the efficiency of primitive-based rendering, e.g., point-based or mesh-based methods. Our approach achieves this by leveraging spatially shared computation with a deconvolutional architecture and by minimizing computation in empty regions of space with volumetric primitives that can move to cover only occupied regions. Our parameterization supports the integration of correspondence and tracking constraints, while being robust to areas where classical tracking fails, such as around thin or translucent structures and areas with large topological variability. MVP is a hybrid that generalizes both volumetric and primitive-based representations. Through a series of extensive experiments we demonstrate that it inherits the strengths of each, while avoiding many of their limitations. We also compare our approach to several state-of-the-art methods and demonstrate that MVP produces superior results in terms of quality and runtime performance.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Learning-based methods have become increasingly popular in 3D indoor scene synthesis (ISS), showing superior performance over traditional optimization-based approaches. These learning-based methods typically model distributions on simple yet explicit scene representations using generative models. However, due to the oversimplified explicit representations that overlook detailed information and the lack of guidance from multimodal relationships within the scene, most learning-based methods struggle to generate indoor scenes with realistic object arrangements and styles. In this paper, we introduce a new method, Scene Implicit Neural Field (S-INF), for indoor scene synthesis, aiming to learn meaningful representations of multimodal relationships, to enhance the realism of indoor scene synthesis. S-INF assumes that the scene layout is often related to the object-detailed information. It disentangles the multimodal relationships into scene layout relationships and detailed object relationships, fusing them later through implicit neural fields (INFs). By learning specialized scene layout relationships and projecting them into S-INF, we achieve a realistic generation of scene layout. Additionally, S-INF captures dense and detailed object relationships through differentiable rendering, ensuring stylistic consistency across objects. Through extensive experiments on the benchmark 3D-FRONT dataset, we demonstrate that our method consistently achieves state-of-the-art performance under different types of ISS.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Modularization is a cornerstone of computer science, abstracting complex functions into atomic building blocks. In this paper, we introduce a new level of modularization by abstracting generative models into atomic generative modules. Analogous to fractals in mathematics, our method constructs a new type of generative model by recursively invoking atomic generative modules, resulting in self-similar fractal architectures that we call fractal generative models. As a running example, we instantiate our fractal framework using autoregressive models as the atomic generative modules and examine it on the challenging task of pixel-by-pixel image generation, demonstrating strong performance in both likelihood estimation and generation quality. We hope this work could open a new paradigm in generative modeling and provide a fertile ground for future research. Code is available at https://github.com/LTH14/fractalgen.

This paper presents a new approach to recognize elements in floor plan layouts. Besides walls and rooms, we aim to recognize diverse floor plan elements, such as doors, windows and different types of rooms, in the floor layouts. To this end, we model a hierarchy of floor plan elements and design a deep multi-task neural network with two tasks: one to learn to predict room-boundary elements, and the other to predict rooms with types. More importantly, we formulate the room-boundary-guided attention mechanism in our spatial contextual module to carefully take room-boundary features into account to enhance the room-type predictions. Furthermore, we design a cross-and-within-task weighted loss to balance the multi-label tasks and prepare two new datasets for floor plan recognition. Experimental results demonstrate the superiority and effectiveness of our network over the state-of-the-art methods.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

In Marius von Senden's Space and Sight, a newly sighted blind patient describes the experience of a corner as lemon-like, because corners "prick" sight like lemons prick the tongue. Prickliness, here, is a dimension in the feature space of sensory experience, an effect of the perceived on the perceiver that arises where the two interact. In the account of the newly sighted, an effect familiar from one interaction translates to a novel context. Perception serves as the vehicle for generalization, in that an effect shared across different experiences produces a concrete abstraction grounded in those experiences. Cezanne and the post-impressionists, fluent in the language of experience translation, realized that the way to paint a concrete form that best reflected reality was to paint not what they saw, but what it was like to see. We envision a future of creation using AI where what it is like to see is replicable, transferrable, manipulable - part of the artist's palette that is both grounded in a particular context, and generalizable beyond it. An active line of research maps human-interpretable features onto directions in GAN latent space. Supervised and self-supervised approaches that search for anticipated directions or use off-the-shelf classifiers to drive image manipulation in embedding space are limited in the variety of features they can uncover. Unsupervised approaches that discover useful new directions show that the space of perceptually meaningful directions is nowhere close to being fully mapped. As this space is broad and full of creative potential, we want tools for direction discovery that capture the richness and generalizability of human perception. Our approach puts creators in the discovery loop during real-time tool use, in order to identify directions that are perceptually meaningful to them, and generate interpretable image translations along those directions.

Training a high-quality deep neural network requires choosing suitable hyperparameters, which is a non-trivial and expensive process. Current works try to automatically optimize or design principles of hyperparameters, such that they can generalize to diverse unseen scenarios. However, most designs or optimization methods are agnostic to the choice of network structures, and thus largely ignore the impact of neural architectures on hyperparameters. In this work, we precisely characterize the dependence of initializations and maximal learning rates on the network architecture, which includes the network depth, width, convolutional kernel size, and connectivity patterns. By pursuing every parameter to be maximally updated with the same mean squared change in pre-activations, we can generalize our initialization and learning rates across MLPs (multi-layer perception) and CNNs (convolutional neural network) with sophisticated graph topologies. We verify our principles with comprehensive experiments. More importantly, our strategy further sheds light on advancing current benchmarks for architecture design. A fair comparison of AutoML algorithms requires accurate network rankings. However, we demonstrate that network rankings can be easily changed by better training networks in benchmarks with our architecture-aware learning rates and initialization.

Open-universe 3D layout generation arranges unlabeled 3D assets conditioned on language instruction. Large language models (LLMs) struggle with generating physically plausible 3D scenes and adherence to input instructions, particularly in cluttered scenes. We introduce LayoutVLM, a framework and scene layout representation that exploits the semantic knowledge of Vision-Language Models (VLMs) and supports differentiable optimization to ensure physical plausibility. LayoutVLM employs VLMs to generate two mutually reinforcing representations from visually marked images, and a self-consistent decoding process to improve VLMs spatial planning. Our experiments show that LayoutVLM addresses the limitations of existing LLM and constraint-based approaches, producing physically plausible 3D layouts better aligned with the semantic intent of input language instructions. We also demonstrate that fine-tuning VLMs with the proposed scene layout representation extracted from existing scene datasets can improve performance.

We introduce a new approach for generating realistic 3D models with UV maps through a representation termed "Object Images." This approach encapsulates surface geometry, appearance, and patch structures within a 64x64 pixel image, effectively converting complex 3D shapes into a more manageable 2D format. By doing so, we address the challenges of both geometric and semantic irregularity inherent in polygonal meshes. This method allows us to use image generation models, such as Diffusion Transformers, directly for 3D shape generation. Evaluated on the ABO dataset, our generated shapes with patch structures achieve point cloud FID comparable to recent 3D generative models, while naturally supporting PBR material generation.

Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a new platform, FastPathology, using the FAST framework and C++. It minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results. Runtime experiments were conducted on four different use cases, using different architectures, inference engines, hardware configurations and operating systems. Memory usage for reading, visualizing, zooming and panning a WSI were measured, using FastPathology and three existing platforms. FastPathology performed similarly in terms of memory to the other C++ based application, while using considerably less than the two Java-based platforms. The choice of neural network model, inference engine, hardware and processors influenced runtime considerably. Thus, FastPathology includes all steps needed for efficient visualization and processing of WSIs in a single application, including inference of CNNs with real-time display of the results. Source code, binary releases and test data can be found online on GitHub at https://github.com/SINTEFMedtek/FAST-Pathology/.

Personalized generation paradigms empower designers to customize visual intellectual properties with the help of textual descriptions by tuning or adapting pre-trained text-to-image models on a few images. Recent works explore approaches for concurrently customizing both content and detailed visual style appearance. However, these existing approaches often generate images where the content and style are entangled. In this study, we reconsider the customization of content and style concepts from the perspective of parameter space construction. Unlike existing methods that utilize a shared parameter space for content and style, we propose a learning framework that separates the parameter space to facilitate individual learning of content and style, thereby enabling disentangled content and style. To achieve this goal, we introduce "partly learnable projection" (PLP) matrices to separate the original adapters into divided sub-parameter spaces. We propose "break-for-make" customization learning pipeline based on PLP, which is simple yet effective. We break the original adapters into "up projection" and "down projection", train content and style PLPs individually with the guidance of corresponding textual prompts in the separate adapters, and maintain generalization by employing a multi-correspondence projection learning strategy. Based on the adapters broken apart for separate training content and style, we then make the entity parameter space by reconstructing the content and style PLPs matrices, followed by fine-tuning the combined adapter to generate the target object with the desired appearance. Experiments on various styles, including textures, materials, and artistic style, show that our method outperforms state-of-the-art single/multiple concept learning pipelines in terms of content-style-prompt alignment.

Real-world applications often require a large gallery of 3D assets that share a consistent theme. While remarkable advances have been made in general 3D content creation from text or image, synthesizing customized 3D assets following the shared theme of input 3D exemplars remains an open and challenging problem. In this work, we present ThemeStation, a novel approach for theme-aware 3D-to-3D generation. ThemeStation synthesizes customized 3D assets based on given few exemplars with two goals: 1) unity for generating 3D assets that thematically align with the given exemplars and 2) diversity for generating 3D assets with a high degree of variations. To this end, we design a two-stage framework that draws a concept image first, followed by a reference-informed 3D modeling stage. We propose a novel dual score distillation (DSD) loss to jointly leverage priors from both the input exemplars and the synthesized concept image. Extensive experiments and user studies confirm that ThemeStation surpasses prior works in producing diverse theme-aware 3D models with impressive quality. ThemeStation also enables various applications such as controllable 3D-to-3D generation.