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Bernardo Taveira, Carl Lindström, Maryam Fatemi, Lars Hammarstrand, Fredrik Kahl

Voronoi diagrams, and their more general weighted counterpart, power diagrams, are fundamental geometric constructs with wide-ranging applications in biology, physics simulation, and computer graphics. Recently, they have gained renewed attention in mesh-based neural rendering. Despite being extensively studied, the construction of 3D Voronoi diagrams for large-scale point sets remains computationally expensive, limiting their adoption in large-scale applications. Existing CPU-based approaches typically rely on computing its dual, the Delaunay tetrahedralization, but are prohibitively slow for large diagrams, while GPU-based methods either struggle to scale efficiently to large point sets or assume homogeneous point distributions. The weighted case, power diagrams, is even less explored in this context. Existing approaches are typically tailored to the application at hand, assuming homogeneous point distributions and small weight variations, making them unsuitable for general use in more complex heterogeneous data. In this paper, we present a highly parallelizable GPU algorithm for the fast construction of large-scale 3D Voronoi and power diagrams. Our approach constructs each convex cell from a weighted 3D point by progressively clipping an initial cell volume against bisecting planes induced by candidate neighboring points. To efficiently identify candidate neighbors under arbitrary spatial distributions, we introduce a culling criterion based on directional geometric bounds of the evolving cell, combined with a hierarchical best-first traversal of bounding volumes. We achieve performance on par with state-of-the-art Delaunay tetrahedralization methods on small and moderate problem sizes, while exhibiting robust scalability to large point sets and diverse spatial distributions. Moreover, our method naturally generalizes to power diagrams without additional assumptions. To facilitate reproducibility and future research, we release our source code, see https://research.zenseact.com/publications/paragram.

Hongbo Xia, Shengxin Liu, Zhaoquan Gu

Extracting cohesive subgraphs from complex networks is a fundamental task in graph analytics and is essential for understanding biological, social, and web graphs. The edge-based γ-quasi-clique model offers a flexible alternative by identifying subgraphs whose edge densities exceed a specified threshold γ. However, finding the exact maximum edge-based quasi-clique is computationally challenging, as the problem is NP-hard and lacks the hereditary property. These characteristics limit the effectiveness of conventional pruning methods and the development of efficient reduction rules. As a result, existing algorithms, such as QClique and FPCE, struggle to scale to large graphs. In this paper, we revisit the problem and propose a novel iterative framework that reformulates the problem as a sequence of hereditary subproblems, enabling more effective pruning and reduction strategies and improving the worst-case time complexity. Furthermore, we redesign the iterative process and introduce a novel heuristic to further improve practical efficiency. Extensive experiments on 253 large-scale real-world graphs demonstrate that our proposed algorithm EQC-Pro outperforms existing methods by up to four orders of magnitude.

Mohammad Rostami

Continual learning (CL) is a prerequisite for autonomous intelligence. Despite decades of progress, the field has operated largely without a mechanistic account of \emph{where} and \emph{why} forgetting occurs, treating it as a monolithic phenomenon to be suppressed rather than a structured process to be understood. We argue that three recent shifts are collectively redefining the field: (1) a mechanistic turn that localizes forgetting to specific computational circuits; (2) the emergence of foundation models that change the problem entirely; and (3) the imperative to move beyond task-bounded protocols toward genuinely autonomous, boundary-free learning. Grounded in Complementary Learning Systems (CLS) theory, this work identifies fast and slow learning pathways inside large language models, characterizes the structural geometry of forgetting, and constructs deployable CL pipelines with biologically motivated signatures. These directions chart a path toward autonomous learning systems that regulate their own consolidation.

Kerui Xu, Keyuan Xu, Shuheng Yin, Hang Qiu

Drug repositioning has emerged as an attractive drug development strategy with deep learning-based computational methods showing great potential in predicting Drug-Disease Associations (DDAs). However, dominant computational paradigms typically rely on Random Negative Sampling (RNS) and static embedding fusion, leading to two fundamental limitations. First, RNS treats unobserved pairs uniformly, resulting in coarse decision boundaries that fail to distinguish true associations from ambiguous candidates. Second, static fusion applies a monolithic combination of heterogeneous features, failing to adapt to the sample-specific dominance of different biological mechanisms. To address these issues, we propose DIAM, which establishes a mechanism-adaptive paradigm by explicitly decoupling structural and molecular signals. Specifically, DIAM introduces a Dual-Stream Biological Mechanism Decoupling module to construct global structural propagation and local molecular interaction views explicitly. Leveraging these views, we design a biological plausibility score to guide the hard negative sampling, enforcing finer-grained decision boundaries. Furthermore, an Adaptive Residual Gating (ARG) is devised to perform instance-aware modulation, dynamically weighing the contribution of global and local views for each specific pair. Extensive experiments on three benchmark datasets demonstrate that DIAM outperforms seven state-of-the-art methods. A case study on Alzheimer's disease further validates the model's effectiveness in identifying potential candidate drugs for practical application.

Zizhe Jin, Yizhen Zheng, Huan Yee Koh, Jiaxin Ju, Jiapu Wang, Shirui Pan

Generating protein sequences that reliably fold into target structures is a central challenge in computational biology and protein design. Progress in protein inverse folding (PIF), however, is fundamentally constrained by the scarcity of high-quality structural data, which limits the effectiveness of existing models. In this work, we propose TTS-Design, a test-time compute scaling framework that enhances protein sequence design without retraining models or relying on larger training data. For TTS-Design, its core design is a dedicated inverse folding reward model named IF-RM, which quantitatively evaluates structure–sequence compatibility and enables effective selection among multiple candidate sequences at inference time. By integrating IF-RM into existing PIF models, TTS-Design leverages additional computation during inference stage to explore and refine candidate solutions. Extensive experiments on the CATH 4.2 and CATH 4.3 demonstrate that TTS-Design consistently improves sequence recovery and structural reliability across different backbone models, without retraining or increasing model size. Case studies on real-world proteins further confirm its practical effectiveness. Overall, our results highlight test-time compute scaling as a promising and effective paradigm for advancing protein inverse folding and other scientific problems under data-limited scenarios.

Weiliang Huo, Shuo Yu, Qingchen Zhang

Spatial transcriptomics has significantly advanced tissue biology and makes it possible to study the spatial interactions of cells in the microenvironment of complex tissues. However, accurately inferring intercellular communication from these data remains challenging due to the need to effectively integrate spatial topology with high-dimensional gene expression information. To address this challenge, we propose DAHGT-CCI, a novel method for inferring intercellular communication from spatial transcriptomics data. By fusing multimodal heterogeneous features to construct a unified node representation and introducing a meta-relation-aware dynamic attention mechanism, DAHGT-CCI can adaptively learn the weights of edges in the graph, thereby achieving superior precision and fine-grained inference of intercellular interactions. We evaluated the performance of DAHGT-CCI on six different spatial transcriptomics datasets. In these benchmarks, DAHGT-CCI outperformed existing graph-based learning methods and cell-cell communication inference models in terms of accuracy, AUROC, recall, and F1 score. These results demonstrate that DAHGT-CCI can more accurately reconstruct cell communication networks in complex tissue microenvironments, offering an indispensable computational tool for studying developmental processes, disease mechanisms, and potential therapeutic targets from a spatially resolved perspective.

Zequan Xie, Weiming Zeng, Yunhua Chen, Sichang Lin, Tongyang Chen, Jinsheng Xiao

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain’s predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

Hua Xu

While deep learning excels at decoding neural signals, the opacity of state-of-the-art models limits their scientific utility and clinical trustworthiness. We propose a research that bridges this gap by integrating high-performance architectures—specifically Transformers and Graph Neural Networks—with mechanistic interpretability and neuro-symbolic reasoning. This proposal aims to uncover verifiable mappings between artificial computational circuits and biological dynamics without compromising decoding accuracy. Validated through rigorous benchmarking and wet-lab experiments, this work establishes a foundation for transparent brain-computer interfaces and accelerates fundamental neuroscience research.

Nastaran Darabi, Devashri Naik, Sina Tayebati, Dinithi Jayasuriya, Amit Ranjan Trivedi

Large Language Model (LLM) agents are now widely deployed in Ambient Intelligence (AmI) environments, where autonomous agents must sense, act, and coordinate at scale. As agent capabilities and interdependence increase, traditional reliability strategies such as isolated adaptive control, anomaly detection, or trust modeling have proven inadequate due to their fragmented and scenario-specific nature. Comprehensive architectures that enable integrated self-management, collective anomaly response, robust information dissemination, and privacy-preserving adaptation remain scarce. We propose a bio-autonomic framework for decentralized resilience in multi-agent LLM systems where a unified architecture systematically applies principles from biological autonomic systems to LLM-based multi-agent environments. Specifically, each agent implements an autonomic control loop, formally structured as Monitor-Analyze-Plan-Execute over a shared Knowledge base (MAPE-K), for self-regulation. At the system level, the framework integrates immune-inspired anomaly detection using the Dendritic Cell Algorithm, probabilistic computational trust, decentralized gossip for robust information sharing, and federated learning with homomorphic encryption for collaborative, privacy-preserving adaptation. This holistic approach enables LLM agent ecosystems to self-organize, detect and isolate faults, and collectively adapt as system complexity increases. Empirical evaluations show that our framework achieves substantially improved resilience and recovery compared to state-of-the-art multi-agent baselines.

Jiangshuai Xu, Peiyun Xue, Jiacheng Song, Xuhui Huang, Qingshan Hou

Catastrophic forgetting remains a fundamental barrier to artificial continual learning (CL) - a capability innate to humans. Existing CL methods often incur prohibitive computational costs in resource-constrained scenarios. Spiking neural networks (SNNs), with their biological plausibility and energy efficiency, offer distinct advantages for CL. Inspired by cortico-hippocampal memory mechanisms, we propose a spiking neural network framework integrating Hebbian plasticity with meta-learning, named HLML-SNN. This architecture emulates a dual-phase CL process: (1) In the short-term phase, sample-level Hebbian learning rapidly adapts to new inputs through local synaptic updates; (2) In the long-term phase, task-level meta-learning optimizes cross-task parameters using consolidated synaptic weights, mimicking cortical memory integration to refine shared representations and initialize subsequent Hebbian learning. HLML-SNN incrementally transforms short-term adaptations into stable long-term knowledge, where the synergy of rapid synaptic updates and meta-driven global optimization enables efficient continual learning while balancing stability and plasticity. Empirical results establish HLML-SNN's state-of-the-art performance across split-MNIST/CIFAR10/CIFAR100/TinyImageNet while markedly reducing training time compared to existing methods, demonstrating substantial practical potential for rapid deployment scenarios. The code and appendix are available on https://github.com/JiangshuaiXu/HLML SNN.

Kushal Kapoor, Wyatt Mackey, Yiannis Aloimonos, Xiaomin Lin

We propose HiCL, a novel hippocampal-inspired dual-memory continual learning architecture designed to mitigate catastrophic forgetting by using elements inspired by the hippocampal circuitry. Our system encodes inputs through a grid-cell-like layer, followed by sparse pattern separation using a dentate gyrus-inspired module with top-k sparsity. Episodic memory traces are maintained in a CA3-like autoassociative memory. Task-specific processing is dynamically managed via a DG-gated mixture-of-experts mechanism, wherein inputs are routed to experts based on cosine similarity between their normalized sparse DG representations and learned task-specific DG prototypes computed through online exponential moving averages. This biologically grounded yet mathematically principled gating strategy enables differentiable, scalable task-routing without relying on a separate gating network, and enhances the model's adaptability and efficiency in learning multiple sequential tasks. Cortical outputs are consolidated using Elastic Weight Consolidation weighted by inter-task similarity. Crucially, we incorporate prioritized replay of stored patterns to reinforce essential past experiences. Evaluations on standard continual learning benchmarks demonstrate the effectiveness of our architecture in reducing task interference, achieving near state-of-the-art results in continual learning tasks at lower computational costs.

Wenjiang Zhang, Sifeng Wang, Yuwei Su, Xinyu Li, Chen Zhang, Suyu Zhong

Visual neural decoding seeks to reconstruct or infer perceived visual stimuli from brain activity patterns, providing critical insights into human cognition and enabling transformative applications in brain-computer interfaces and artificial intelligence. Current approaches, however, remain constrained by the scarcity of high-quality stimulus-brain response pairs and the inherent semantic mismatch between neural representations and visual content. Inspired by perceptual variability and co-adaptive strategy of the biological systems, we propose a novel self-supervised architecture, named NeuroBridge, which integrates Cognitive Prior Augmentation (CPA) with Shared Semantic Projector (SSP) to promote effective cross-modality alignment. Specifically, CPA simulates perceptual variability by applying asymmetric, modality-specific transformations to both EEG signals and images, enhancing semantic diversity. Unlike previous approaches, SSP establishes a bidirectional alignment process through a co-adaptive strategy, which mutually aligns features from two modalities into a shared semantic space for effective cross-modal learning. NeuroBridge surpasses previous state-of-the-art methods under both intra-subject and inter-subject settings. In the intra-subject scenario, it achieves the improvements of 12.3% in top-1 accuracy and 10.2% in top-5 accuracy, reaching 63.2% and 89.9% respectively on a 200-way zero-shot retrieval task. Extensive experiments demonstrate the effectiveness, robustness, and scalability of the proposed framework for neural visual decoding.

Jiajun Ma, Yongchao Zhang, Chao Zhang, Zhao Lv, Shengbing Pei

Graph Transformer shows remarkable potential in brain network analysis due to its ability to model graph structures and complex node relationships. Most existing methods typically model the brain as a flat network, ignoring its modular structure, and their attention mechanisms treat all brain region connections equally, ignoring distance-related node connection patterns. However, brain information processing is a hierarchical process that involves local and long-range interactions between brain regions, interactions between regions and sub-functional modules, and interactions among functional modules themselves. This hierarchical interaction mechanism enables the brain to efficiently integrate local computations and global information flow, supporting the execution of complex cognitive functions. To address this issue, we propose BrainHGT, a hierarchical Graph Transformer that simulates the brain’s natural information processing from local regions to global communities. Specifically, we design a novel long-short range attention encoder that utilizes parallel pathways to handle dense local interactions and sparse long-range connections, thereby effectively alleviating the over-globalizing issue. To further capture the brain’s modular architecture, we designe a prior-guided clustering module that utilizes a cross-attention mechanism to group brain regions into functional communities and leverage neuroanatomical prior to guide the clustering process, thereby improving the biological plausibility and interpretability. Experimental results indicate that our proposed method significantly improves performance of disease identification, and can reliably capture the sub-functional modules of the brain, demonstrating its interpretability.

Yousef Yeganeh, Goktug Guvercin, Nassir Navab, Azade Farshad

While conventional computer vision emphasizes pixel-level and feature-based objectives, medical image analysis of intricate biological structures necessitates explicit representation of their complex topological properties. Despite their successes, deep learning models often struggle to accurately capture the connectivity and continuity of fine, sometimes pixel-thin, yet critical structures due to their reliance on implicit learning from data. To address this challenge, we introduce Conformable Convolution, a novel convolutional layer designed to explicitly impose topological consistency. Conformable Convolution learns adaptive kernel offsets that focus on regions of high topological significance within an image. This prioritization is guided by our proposed Topological Posterior Generator (TPG) module, which leverages persistent homology. The TPG module identifies key topological features and guides the convolutional layers by applying persistent homology to feature maps transformed into cubical complexes. Unlike existing approaches that are merely aware of topology, our method explicitly constrains the learning process to ensure topological correctness. The proposed modules are architecture-agnostic, enabling them to be integrated seamlessly into various architectures. We showcase the effectiveness of our framework in the segmentation task, where preserving the interconnectedness of structures is critical. The results on three diverse datasets demonstrate that our framework effectively preserves the topology both quantitatively and qualitatively.

Ziqiao Weng, Yaoyu Fang, Jiahe Qian, Xinkun Wang, Lee A D Cooper, Weidong Cai, Bo Zhou

Spatial transcriptomics (ST) bridges gene expression and tissue morphology but faces clinical adoption barriers due to technical complexity and prohibitive costs. While computational methods predict gene expression from H&E-stained whole-slide images (WSIs), existing approaches often fail to capture the intricate biological heterogeneity within spots and are susceptible to morphological noise when integrating contextual information from surrounding tissue. To overcome these limitations, we propose HiFusion, a novel deep learning framework that integrates two complementary components. First, we introduce the Hierarchical Intra-Spot Modeling module that extracts fine-grained morphological representations through multi-resolution sub-patch decomposition, guided by a feature alignment loss to ensure semantic consistency across scales. Concurrently, we present the Context-aware Cross-scale Fusion module, which employs cross-attention to selectively incorporate biologically relevant regional context, thereby enhancing representational capacity. This architecture enables comprehensive modeling of both cellular-level features and tissue microenvironmental cues, which are essential for accurate gene expression prediction. Extensive experiments on two benchmark ST datasets demonstrate that HiFusion achieves state-of-the-art performance across both 2D slide-wise cross-validation and more challenging 3D sample-specific scenarios. These results underscore HiFusion’s potential as a robust, accurate, and scalable solution for ST inference from routine histopathology.

Zhenzhe Hou, Xiaohui Chu, Runze Hu, Yang Li, Yutao Liu

Efficient visual backbone design remains crucial for resource-constrained computer vision applications. Inspired by the adaptive continuous-time dynamics observed in biological neurons, we propose FVNet, a novel lightweight architecture that integrates liquid neural dynamics for efficient and dynamic visual feature extraction. Central to FVNet is the Fluid Temporal Flow Unit (FTFU), which employs continuous-time equations with learnable time constants to capture spatio-temporal dependencies adaptively. By further stacking these units in a Multi-Phase Fluid Block (MPFB), our model processes features across parallel temporal scales, enabling context-aware feature encoding without incurring excessive computational overhead. Through a discrete closed-form solution, FVNet achieves the representational power of continuous-time models while avoiding the instability and overhead of iterative numerical solvers. Extensive experiments on various vision tasks demonstrate that FVNet achieves superior performance and efficiency over existing state-of-the-art lightweight networks.

Deming Zhou, Yuetong Fang, Zhaorui Wang, Renjing Xu

The primate visual cortex exhibits topographic organization, where functionally similar neurons are spatially clustered, a structure widely believed to enhance neural processing efficiency. While prior works have demonstrated that conventional deep ANNs can develop topographic representations, these models largely neglect crucial temporal dynamics. This oversight often leads to significant performance degradation in tasks like object recognition and compromises their biological fidelity. To address this, we leverage spiking neural networks (SNNs), which inherently capture spike-based temporal dynamics and offer enhanced biological plausibility. We propose a novel Spatio-Temporal Constraints (STC) loss function for topographic deep spiking neural networks (TDSNNs), successfully replicating the hierarchical spatial functional organization observed in the primate visual cortex from low-level sensory input to high-level abstract representations. Our results show that STC effectively generates representative topographic features across simulated visual cortical areas. While introducing topography typically leads to significant performance degradation in ANNs, our spiking architecture exhibits a remarkably small performance drop (No drop in ImageNet top-1 accuracy, compared to a 3% drop observed in TopoNet, which is the best-performing topographic ANN so far) and outperforms topographic ANNs in brain-likeness. We also reveal that topographic organization facilitates efficient and stable temporal information processing via the spike mechanism in TDSNNs, contributing to model robustness. These findings suggest that TDSNNs offer a compelling balance between computational performance and brain-like features, providing not only a framework for interpreting neural science phenomena but also novel insights for designing more efficient and robust deep learning models.

Chenlin Zhou, Liutao Yu, Zhaokun Zhou, Han Zhang, Jiaqi Wang, Huihui Zhou, Zhengyu Ma, Yonghong Tian

Spiking neural networks (SNNs) offer a promising energy-efficient alternative to artificial neural networks, due to their event-driven spiking computation. However, some foundation SNN backbones (including Spikformer and SEW ResNet) suffer from non-spike computations (integer-float multiplications) caused by the structure of their residual connections. These non-spike computations increase SNNs' power consumption and make them unsuitable for deployment on mainstream neuromorphic hardware. In this paper, we analyze the spike-driven behavior of the residual connection methods in SNNs. We then present Spikingformer, a novel spiking transformer backbone that merges the MS Residual connection with Self-Attention in a biologically plausible way to address the non-spike computation challenge in Spikformer while maintaining global modeling capabilities. We evaluate Spikingformer across 13 datasets spanning large static images, neuromorphic data, and natural language tasks, and demonstrate the effectiveness and universality of Spikingformer, setting a vital benchmark for spiking neural networks. In addition, with the spike-driven features and global modeling capabilities, Spikingformer is expected to become a more efficient general-purpose SNN backbone towards energy-efficient artificial intelligence.

Jian Song, Xiangfei Yang, Shangke Lyu, Donglin Wang

Spiking neural networks (SNNs) have demonstrated significant potential in real-time multi-sensor perception tasks due to their event-driven and parameter-efficient characteristics. A key challenge is the timestep-wise iterative update of neuronal hidden states (membrane potentials), which complicates the trade-off between accuracy and latency. SNNs tend to achieve better performance with longer timesteps, inevitably resulting in higher computational overhead and latency compared to artificial neural networks (ANNs). Moreover, many recent advances in SNNs rely on architecture-specific optimizations, which, while effective with fewer timesteps, often limit generalizability and scalability across modalities and models. To address these limitations, we propose Activation-wise Membrane Potential Propagation (AMP2), a unified hidden state update mechanism for SNNs. Inspired by the spatial propagation of membrane potentials in biological neurons, AMP2 enables dynamic transmission of membrane potentials among spatially adjacent neurons, facilitating spatiotemporal integration and cooperative dynamics of hidden states, thereby improving efficiency and accuracy while reducing reliance on extended temporal updates. This simple yet effective strategy significantly enhances SNN performance across various architectures, including MLPs and CNNs for point cloud and event-based data. Furthermore, ablation studies integrating AMP2 into Transformer-based SNNs for classification tasks demonstrate its potential as a general-purpose and efficient solution for spiking neural networks.

Shanshan Qin, Joshua L. Pughe-Sanford, Alexander Genkin, Pembe Gizem Ozdil, Philip Greengard, Anirvan M. Sengupta, Dmitri Chklovskii

We introduce a biologically inspired, multilayer neural architecture composed of Rectified Spectral Units (ReSUs). Each ReSU projects a recent window of its input history onto a canonical direction obtained via canonical correlation analysis (CCA) of previously observed past–future input pairs, and then rectifies either its positive or negative component. By encoding canonical directions in synaptic weights and temporal filters, ReSUs implement a local, self-supervised algorithm for progressively constructing increasingly complex features. To evaluate both computational power and biological fidelity, we trained a two-layer ReSU network in a self-supervised regime on translating natural scenes. First-layer units, each driven by a single pixel, developed temporal filters resembling those of Drosophila post-photoreceptor neurons (L1/L2 and L3), including their empirically observed adaptation to signal-to-noise ratio (SNR). Second-layer units, which pooled spatially over the first layer, became direction-selective—analogous to T4 motion-detecting cells—with learned synaptic weight patterns approximating those derived from connectomic reconstructions. Together, these results suggest that ReSUs offer (i) a principled framework for modeling sensory circuits and (ii) a biologically grounded, backpropagation-free paradigm for constructing deep self-supervised neural networks.