Boolean networks (BNs) are widely used to model biological regulatory networks. Attractors here hold significant meaning as they represent long-term behaviors such as homeostasis and the results of cell differentiation. As such, computing attractors is of critical importance to guarantee the validity of a model or to assess its stability and robustness. However, this problem is quite challenging when it comes to large real-world models. To overcome the limits of state-of-the-art BDD-based or ASP-based enumeration approaches, we introduce a SAT-based approach to compute fixed points (singleton attractors) of BN and exhibit its merits for counting the number of singleton attractors of large-scale benchmarks well established in the literature.
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Tackling Long-Tailed Data Challenges in Spiking Neural Networks via Heterogeneous Knowledge Distillation
PDF ↗Spiking Neural Networks (SNNs), inspired by the behavior of biological neurons, have gained significant research interest for resource-constrained edge devices and neuromorphic hardware due to their use of binary spike signals for inter-unit communication with low power consumption. However, the absence of research on spiking neural networks on long-tailed data has severely limited the deployment and application of this emerging network in practical scenarios. To fill this gap, this paper proposes a long-tail learning framework based on spiking neural networks, named LT-SpikingFormer, to alleviate the distribution bias between head and tail classes. LT-SpikingFormer adopts a widely trained Convolutional Neural Network to construct a heterogeneous knowledge distillation paradigm, offering balanced and reliable prior knowledge. Moreover, a multi-granularity hierarchical feature distillation objective is proposed to leverage cross-layer local features and network global predictions to facilitate refined information distillation to optimize the network, specifically for the performance of the tailed classes. Extensive experimental results demonstrate that our method performs well on several benchmark datasets.
Biological neural systems often represent information on low-dimensional manifolds that reflect the topology of their encoded variables. This suggests that neural activity can be naturally organized in geometrically meaningful ways, as seen in rodent head direction cells forming circular manifolds. This proposal examines whether artificial neural networks (ANNs) trained on tasks with well-defined topologies—such as planar or spherical coordinates from autonomous driving datasets like Apolloscape, cyclic temporal variables, or graph-structured road networks—develop similar low-dimensional representations aligned with the variables' inherent topology. We consider convolutional and vision transformer models for image data, graph neural networks for road network graphs, and 3D or point-based models for LIDAR point clouds, analyzing their internal activations with dimensionality reduction and topological data analysis. If successful, this approach not only elucidates the nature of internal representations in ANNs but also offers insights into the computational principles that bridge artificial systems and biological cognition.
Scientific discovery serves as the cornerstone for advances in various fields, from the fundamental laws of physics to the intricate mechanisms of biology. However, two existing mainstream methods---symbolic regression and dimensional analysis, are significantly limited in this task: the former suffers from low computational efficiency due to the vast search space and often results in formulas without physical meaning; the latter provides a useful theoretical framework but also struggles in searching in a huge space because of lacking effective analysis for the latent variables. To address this issue, here we propose a framework for efficiently discovering underlying formulas in data, named FIND. We draw inspiration from Buckingham’s Pi theorem, imposing dimensional constraints on the input and output, thereby ensuring discovered expressions possess physical meaning. Additionally, we propose a theoretical scheme for identifying the latent structure as well as a coarse-to-fine framework, significantly reducing the search space of latent variables. This framework not only improves computational efficiency but also enhances model interpretability. From comprehensive experimental validation, FIND showcases its potential to uncover meaningful scientific insights across various domains, providing a robust tool for advancing our understanding of unknown systems.
Identifying the Markov properties or conditional independencies of a collection of random variables is a fundamental task in statistics for modeling and inference. Existing approaches often learn the structure of a probabilistic graph, which encodes these dependencies, by assuming that the variables follow a distribution with a simple parametric form. Moreover, the computational cost of many algorithms scales poorly for high-dimensional distributions, as they need to estimate all the edges in the graph simultaneously. In this work, we propose a scalable algorithm to infer the conditional independence relationships of each variable by exploiting the local Markov property. The proposed method, named Localized Sparsity Identification for Non-Gaussian Distributions (L-SING), estimates the graph by using flexible classes of transport maps to represent the conditional distribution for each variable. We show that L-SING includes existing approaches, such as neighborhood selection with Lasso, as a special case. We demonstrate the effectiveness of our algorithm in both Gaussian and non-Gaussian settings by comparing it to existing methods. Lastly, we show the scalability of the proposed approach by applying it to high-dimensional non-Gaussian examples, including a biological dataset with more than 150 variables.
Spiking neural networks (SNNs), inspired by the inherent spiking computation paradigm of the biological neural systems, have exhibited superior energy efficiency in 2D classification tasks over traditional artificial neural networks (ANNs). However, the regression potential of SNNs has not been well explored, especially in 3D point cloud processing. In this paper, we propose noise-injected spiking graph convolutional networks to leverage the full regression potential of SNNs in 3D point cloud denoising. Specifically, we first emulate the noise-injected neuronal dynamics to build noise-injected spiking neurons. On this basis, we design noise-injected spiking graph convolution for promoting disturbance-aware spiking representation learning on 3D points. Starting from the spiking graph convolution, we build two SNN-based denoising networks. One is a purely spiking graph convolutional network, which achieves low accuracy loss compared with some ANN-based alternatives, while resulting in significantly reduced energy consumption on two benchmark datasets, PU-Net and PC-Net. The other is a hybrid architecture, which integrates some ANN-based learning operations and exhibits a high performance-efficiency trade-off with only a few time steps. Our work lights up SNN’s potential for 3D point cloud denoising, injecting new perspectives of exploring the deployment on neuromorphic chips while paving the way for developing energy-efficient 3D data acquisition devices.
We introduce a biologically plausible RL framework for solving tasks in partially observable Markov decision processes (POMDPs). The proposed algorithm combines three integral parts: (1) A Meta-RL architecture, resembling the mammalian basal ganglia; (2) A biologically plausible reinforcement learning algorithm, exploiting temporal difference learning and eligibility traces to train the policy and the value-function; (3) An online automatic differentiation algorithm for computing the gradients with respect to parameters of a shared recurrent network backbone. Our experimental results show that the method is capable of solving a diverse set of partially observable reinforcement learning tasks. The algorithm we call real-time recurrent reinforcement learning (RTRRL) serves as a model of learning in biological neural networks, mimicking reward pathways in the basal ganglia.
This work introduces IsUMap, a novel manifold learning technique that enhances data representation by integrating aspects of UMAP and Isomap with Vietoris-Rips filtrations and metric realization of one-parameter filtrations of simplicial complexes. Inferring topological information from combinatorial models which have been built according to metric relations (Vietoris-Rips complexes) has proven useful in topological data analysis and general machine learning applications. This encourages the use of such objects for geometric inference. We extend this research direction by proposing a clear theoretical pipeline that not only provides a comprehensive guide for assigning a (triangulated) metric space to every admissible one- parameter filtration of simplicial complexes but also offers a method for merging these objects. With this, our method presents a systematic and detailed construction of a metric representation for locally distorted metric spaces that captures complex data structures more accurately than the previous schemes. Our approach addresses limitations in existing methods by accommodating non-uniform data distributions and intricate local geometries. We validate its performance through extensive experiments on examples with known geometries and in applications to data, in particular from computational biology.
Subcellular structure segmentation is a fundamental task in biological imaging. Existing self-supervised representation learning combined with classical k-means clustering achieved unsupervised image segmentation, but it was constrained by time-consuming test-time pixel-wise feature extraction and clustering synchronization. This study introduces SCCS, a lightweight graph neural network-based spectral clustering framework for end-to-end subcellular structure segmentation upon superpixel graphs, greatly relieving the computational complexity in test-time numerical spectral clustering and inter-graph label inconsistency. Specifically, SCCS exploits the self-supervised masked autoencoder for representation learning and the construction of superpixel graphs (spG). Unlike per-graph scalar affinity-based spectral clustering, the proposed SCCS parameterizes the mapping from learned deep spG representations to coordinates in the spectral embedding space and the clustering assignments. The SCCS is optimized under unsupervised eigendecomposition and incremental clustering criteria, which synchronize the intra- and inter-graph spectral clustering. The proposed approach is evaluated on a publicly available volumetric electron microscopy dataset. Experiments demonstrate the effectiveness and performance gains of the proposed SCCS over the state-of-the-art in discovering a variety of subcellular structures.
Large language models and other highly capable AI systems ease the burdens of deciding what to say or do, but this very ease can undermine the effectiveness of our actions in social contexts. We explain this apparent tension by introducing the integrative theoretical concept of "mental proof," which occurs when observable actions are used to certify unobservable mental facts. From hiring to dating, mental proofs enable people to credibly communicate values, intentions, states of knowledge, and other private features of their minds to one another in low-trust environments where honesty cannot be easily enforced. Drawing on results from economics, theoretical biology, and computer science, we describe the core theoretical mechanisms that enable people to effect mental proofs. An analysis of these mechanisms clarifies when and how artificial intelligence can make low-trust cooperation harder despite making thinking easier.
Spiking Neural Networks (SNNs) are seen as an energy-efficient alternative to traditional Artificial Neural Networks (ANNs), but the performance gap remains a challenge. While this gap is narrowing through ANN-to-SNN conversion, substantial computational resources are still needed, and the energy efficiency of converted SNNs cannot be ensured. To address this, we present a unified training-free conversion framework that significantly enhances both the performance and efficiency of converted SNNs. Inspired by the biological nervous system, we propose a novel Adaptive-Firing Neuron Model (AdaFire), which dynamically adjusts firing patterns across different layers to substantially reduce the Unevenness Error - the primary source of error of converted SNNs within limited inference timesteps. We further introduce two efficiency-enhancing techniques: the Sensitivity Spike Compression (SSC) technique for reducing spike operations, and the Input-aware Adaptive Timesteps (IAT) technique for decreasing latency. These methods collectively enable our approach to achieve state-of-the-art performance with significant energy savings of up to 70.1%, 60.3%, and 43.1% on CIFAR-10, CIFAR-100, and ImageNet datasets, respectively. Extensive experiments across 2D, 3D, event-driven classification tasks, object detection, and segmentation tasks, demonstrate the effectiveness of our method in various domains.
Missense mutations could affect the Liquid-Liquid Phase Separation (LLPS) propensity of proteins and lead to aberrant phase-separating behaviours, which are recently found to be associated with many diseases including Alzheimer's and cancer. However, the regulatory role of mutations in LLPS remains unclear due to challenges in accurately characterizing the LLPS ability of mutants, including the high similarity in features, lack of labeled data, and vast amounts of data involved. To bridge this gap and facilitate the discovery of therapeutic strategies, we propose the first machine learning-based guider for protein phase-separating behaviour alteration, PScalpel. PScalpel leverages both structural information and an auxiliary tasks-based graph contrastive learning framework to distinguish the mutants’ LLPS ability, and incorporates a genetic algorithms-based recommendation method to identify mutants with desired LLPS properties. Comprehensive computational and biological experiments validate the effectiveness of PScalpel as a versatile tool for guiding alterations in protein phase separation behavior.
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction
PDF ↗Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to capture the binding mechanisms comprehensively. The recent emerging pre-trained language models trained on massive unsupervised sequences of protein and RNA have shown strong representation ability for various in-domain downstream tasks, including binding site prediction. However, applying different-domain language models collaboratively for complex-level tasks remains unexplored. In this paper, we propose CoPRA to bridge pre-trained language models from different biological domains via Complex structure for Protein-RNA binding Affinity prediction. We demonstrate for the first time that cross-biological modal language models can collaborate to improve binding affinity prediction. We propose a Co-Former to combine the cross-modal sequence and structure information and a bi-scope pre-training strategy for improving Co-Former's interaction understanding. Meanwhile, we build the largest protein-RNA binding affinity dataset PRA310 for performance evaluation. We also test our model on a public dataset for mutation effect prediction. CoPRA reaches state-of-the-art performance on all the datasets. We provide extensive analyses and verify that CoPRA can (1) accurately predict the protein-RNA binding affinity; (2) understand the binding affinity change caused by mutations; and (3) benefit from scaling data and model size.
While computer vision models have made incredible strides in static image recognition, they still do not match human performance in tasks that require the understanding of complex, dynamic motion. This is notably true for real-world scenarios where embodied agents face complex and motion-rich environments. Our approach, BrainNRDS (Brain-Neural Representations of Dynamic Stimuli), leverages state-of-the-art video diffusion models to decouple static image representation from motion generation, enabling us to utilize fMRI brain activity for a deeper understanding of human responses to dynamic visual stimuli. Conversely, we also demonstrate that information about the brain's representation of motion can enhance the prediction of optical flow in artificial systems. Our novel approach leads to four main findings: (1) Visual motion, represented as fine-grained, object-level resolution optical flow, can be decoded from brain activity generated by participants viewing video stimuli; (2) Video encoders outperform image-based models in predicting video-driven brain activity; (3) Brain-decoded motion signals enable realistic video reanimation based only on the initial frame of the video; and (4) We extend prior work to achieve full video decoding from video-driven brain activity. BrainNRDS advances our understanding of how the brain represents spatial and temporal information in dynamic visual scenes. Our findings demonstrate the potential of combining brain imaging with video diffusion models for developing more robust and biologically-inspired computer vision systems. We show additional decoding and encoding examples on this site: https://brain-nrds.github.io/.
BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature
PDF ↗The development of vision-language models (VLMs) is driven by large-scale and diverse multi-modal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are limited to narrow domains, missing the opportunity to leverage the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA: a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset. Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are additionally provided. We demonstrate the utility and accessibility of our resource by releasing BMC-CLIP, a suite of CLIP-style models continuously pre-trained on BIOMEDICA dataset via streaming (eliminating the need to download 27 TB of data locally). On average, our models achieve state-of-the-art performance across 40 tasks -- spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology -- excelling in zero-shot classification with 6.56% average improvement (as high as 29.8% and 17.5% gains in dermatology and ophthalmology, respectively) and stronger image-text retrieval while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset to the broader research community
Physiological activities can be manifested by the sensitive changes in facial imaging. While they are barely observable to our eyes, computer vision manners can, and the derived remote photoplethysmography (rPPG) has shown considerable promise. However, existing studies mainly rely on spatial skin recognition and temporal rhythmic interactions, so they focus on identifying explicit features under ideal light conditions, but perform poorly in-the-wild with intricate obstacles and extreme illumination exposure. In this paper, we propose an end-to-end video transformer model for rPPG. It strives to eliminate complex and unknown external time-varying interferences, whether they are sufficient to occupy subtle biosignal amplitudes or exist as periodic perturbations that hinder network training. In the specific implementation, we utilize global interference sharing, subject background reference, and self-supervised disentanglement to eliminate interference, and further guide learning based on spatiotemporal filtering, reconstruction guidance, and frequency domain and biological prior constraints to achieve effective rPPG. To the best of our knowledge, this is the first robust rPPG model for real outdoor scenarios based on natural face videos, and is lightweight to deploy. Extensive experiments show the competitiveness and performance of our model in rPPG prediction across datasets and scenes.
Spatial transcriptomics (ST) are emerging technologies that reveal spatial distributions of gene expressions within tissues, serving as important ways to uncover biological insights. However, the irregular spatial profiles and variability of genes make it challenging to integrate spatial information with gene expression under a computational framework. Current algorithms mostly utilize spatial graph neural networks to encode spatial information, which may incur increased computational costs and may not be flexible enough to depict complex spatial configurations. In this study, we introduce a concise yet effective representation framework, STINR, for deciphering ST data. STINR leverages an implicit neural representation (INR) to continuously represent ST data, which efficiently characterizes spatial and slice-wise correlations of ST data by inheriting the implicit smoothness of INR. STINR allows easier integration of multiple slices and multi-omics without any alignment, and serves as a potent tool for various biological tasks including gene imputation, gene denoising, spatial domain detection, and cell-type deconvolution stemed from ST data. In particular, STINR identifies the thinnest cortex layer in the dorsolateral prefrontal cortex which previous methods were unable to achieve, and more accurately identifies tumor regions in the human squamous cell carcinoma, showcasing its practical value for biological discoveries.
Obtaining high-quality, practically usable 3D models of biological plants remains a significant challenge in computer vision and graphics. In this paper, we present a novel method for generating realistic 3D plant models from single-view photographs. Our approach employs a neural decomposition technique to learn a lightweight hierarchical box representation from the image, effectively capturing the structures and botanical features of plants. Then, this representation can be subsequently refined through a shape-guided parametric modeling module to produce complete 3D plant models. By combining hierarchical learning and parametric modeling, our method generates structured 3D plant assets with fine geometric details. Notably, through learning the decomposition in different levels of detail, our method can adapt to two distinct plant categories: outdoor trees and houseplants, each with unique appearance features. Within the scope of plant modeling, our method is the first comprehensive solution capable of reconstructing both plant categories from single-view images.
VISTREAM: Improving Computation Efficiency of Visual Streaming Perception via Law-of-Charge-Conservation Inspired Spiking Neural Network
PDF ↗Visual streaming perception (VSP) involves online intelligent processing of sequential frames captured by vision sensors, enabling real-time decision-making in applications such as autonomous driving, UAVs, and AR/VR. However, the computational efficiency of VSP on edge devices remains a challenge due to power constraints and the underutilization of temporal dependencies between frames. While spiking neural networks (SNNs) offer biologically inspired event-driven processing with potential energy benefits, their practical advantage over artificial neural networks (ANNs) for VSP tasks remains unproven.In this work, we introduce a novel framework, VISTREAM, which leverages the Law of Charge Conservation (LoCC) property in ST-BIF neurons and a differential encoding (DiffEncode) scheme to optimize SNN inference for VSP. By encoding temporal differences between neighboring frames and eliminating frequent membrane resets, VISTREAM achieves significant computational efficiency while maintaining accuracy equivalent to its ANN counterpart. We provide theoretical proofs of equivalence and validate VISTREAM across diverse VSP tasks, including object detection, tracking, and segmentation, demonstrating substantial energy savings without compromising performance.
BioX-CPath: Biologically-driven Explainable Diagnostics for Multistain IHC Computational Pathology
PDF ↗The development of biologically interpretable and explainable models remains a key challenge in computational pathology, particularly for multistain immunohistochemistry (IHC) analysis. We present BioX-CPath, an explainable graph neural network architecture for whole slide image (WSI) classification that leverages both spatial and semantic features across multiple stains. At its core, BioXCPath introduces a novel Stain-Aware Attention Pooling (SAAP) module that generates biologically meaningful, stain-aware patient embeddings. Our approach achieves state-of-the-art performance on both Rheumatoid Arthritis and Sjogren's Disease multistain datasets. Beyond performance metrics, BioX-CPath provides interpretable insights through stain attention scores, entropy measures, and stain interaction scores, that permit measuring model alignment with known pathological mechanisms. This biological grounding, combined with strong classification performance, makes BioX-CPath particularly suitable for clinical applications where interpretability is key. Source code and documentation can be found at: https://github.com/AmayaGS/BioX-CPath.