NeurIPS 2025 Papers

The bisimulation metric (BSM) is a powerful tool for computing state similarities within a Markov decision process (MDP), revealing that states closer in BSM have more similar optimal value functions. While BSM has been successfully utilized in reinforcement learning (RL) for tasks like state representation learning and policy exploration, its application to multiple-MDP scenarios, such as policy transfer, remains challenging. Prior work has attempted to generalize BSM to pairs of MDPs, but a lack of rigorous analysis of its mathematical properties has limited further theoretical progress. In this work, we formally establish a generalized bisimulation metric (GBSM) between pairs of MDPs, which is rigorously proven with the three fundamental properties: GBSM symmetry, inter-MDP triangle inequality, and the distance bound on identical states. Leveraging these properties, we theoretically analyse policy transfer, state aggregation, and sampling-based estimation in MDPs, obtaining explicit bounds that are strictly tighter than those derived from the standard BSM. Additionally, GBSM provides a closed-form sample complexity for estimation, improving upon existing asymptotic results based on BSM. Numerical results validate our theoretical findings and demonstrate the effectiveness of GBSM in multi-MDP scenarios.

Vehicle GPS trajectories provide valuable movement information that supports various downstream tasks and applications. A desirable trajectory learning model should be able to transfer across regions and tasks without retraining, avoiding the need to maintain multiple specialized models and subpar performance with limited training data. However, each region has its unique spatial features and contexts, which are reflected in vehicle movement patterns and are difficult to generalize. Additionally, transferring across different tasks faces technical challenges due to the varying input-output structures required for each task. Existing efforts towards transferability primarily involve learning embedding vectors for trajectories, which perform poorly in region transfer and require retraining of prediction modules for task transfer. To address these challenges, we propose $\textit{TransferTraj}$, a vehicle GPS trajectory learning model that excels in both region and task transferability. For region transferability, we introduce RTTE as the main learnable module within TransferTraj. It integrates spatial, temporal, POI, and road network modalities of trajectories to effectively manage variations in spatial context distribution across regions. It also introduces a TRIE module for incorporating relative information of spatial features and a spatial context MoE module for handling movement patterns in diverse contexts. For task transferability, we propose a task-transferable input-output scheme that unifies the input-output structure of different tasks into the masking and recovery of modalities and trajectory points. This approach allows TransferTraj to be pre-trained once and transferred to different tasks without retraining. We conduct extensive experiments on three real-world vehicle trajectory datasets under various transfer settings, including task transfer, zero-shot region transfer, and few-shot region transfer. Experimental results demonstrate that TransferTraj significantly outperforms state-of-the-art baselines in different scenarios, validating its effectiveness in region and task transfer. Code is available at https://github.com/wtl52656/TransferTraj.

Adam is the de facto optimization algorithm for several deep learning applications, but an understanding of its implicit bias and how it differs from other algorithms, particularly standard first-order methods such as (stochastic) gradient descent (GD), remains limited. In practice, neural networks (NNs) trained with SGD are known to exhibit simplicity bias --- a tendency to find simple solutions. In contrast, we show that Adam is more resistant to such simplicity bias. First, we investigate the differences in the implicit biases of Adam and GD when training two-layer ReLU NNs on a binary classification task with Gaussian data. We find that GD exhibits a simplicity bias, resulting in a linear decision boundary with a suboptimal margin, whereas Adam leads to much richer and more diverse features, producing a nonlinear boundary that is closer to the Bayes' optimal predictor. This richer decision boundary also allows Adam to achieve higher test accuracy both in-distribution and under certain distribution shifts. We theoretically prove these results by analyzing the population gradients. Next, to corroborate our theoretical findings, we present extensive empirical results showing that this property of Adam leads to superior generalization across various datasets with spurious correlations where NNs trained with SGD are known to show simplicity bias and do not generalize well under certain distributional shifts.

Artificial intelligence (AI) has played a transformative role in chemical research, greatly facilitating the prediction of small molecule properties, simulation of catalytic processes, and material design. These advances are driven by increases in computing power, open source machine learning frameworks, and extensive chemical datasets. However, a persistent challenge is the limited amount of high-quality real-world data, while models calculated based on large amounts of theoretical data are often costly and difficult to deploy, which hinders the applicability of AI models in real-world scenarios. In this study, we enhance the prediction of solute-solvent properties by proposing a novel sample selection method: the iterative core subset extraction (CSIE) framework. CSIE iteratively updates the core sample subset based on information gain to remove redundant features in theoretical data and optimize the performance of the model on real chemical datasets. Furthermore, we introduce an asymmetric molecular interaction graph neural network (AMGNN) that combines positional information and bidirectional edge connections to simulate real-world chemical reaction scenarios to better capture solute-solvent interactions. Experimental results show that our method can accurately extract the core subset and improve the prediction accuracy.

Auditory attention detection (AAD) aims to decode listeners' focus in complex auditory environments from electroencephalography (EEG) recordings, which is crucial for developing neuro-steered hearing devices. Despite recent advancements, EEG-based AAD remains hindered by the absence of synergistic frameworks that can fully leverage complementary EEG features under energy-efficiency constraints. We propose ***S$^2$M-Former***, a novel ***s***piking ***s***ymmetric ***m***ixing framework to address this limitation through two key innovations: i) Presenting a spike-driven symmetric architecture composed of parallel spatial and frequency branches with mirrored modular design, leveraging biologically plausible token-channel mixers to enhance complementary learning across branches; ii) Introducing lightweight 1D token sequences to replace conventional 3D operations, reducing parameters by 14.7$\times$. The brain-inspired spiking architecture further reduces power consumption, achieving a 5.8$\times$ energy reduction compared to recent ANN methods, while also surpassing existing SNN baselines in terms of parameter efficiency and performance. Comprehensive experiments on three AAD benchmarks (KUL, DTU and AV-GC-AAD) across three settings (within-trial, cross-trial and cross-subject) demonstrate that S$^2$M-Former achieves comparable state-of-the-art (SOTA) decoding accuracy, making it a promising low-power, high-performance solution for AAD tasks. Code is available at https://github.com/JackieWang9811/S2M-Former.

The ability to continually learn new skills, retain, and flexibly deploy them to accomplish goals is a key feature of intelligent and efficient behavior. However, the neural mechanisms facilitating the continual learning and flexible (re-)composition of skills remain elusive. Here, we study continual learning and the compositional reuse of learned computations in recurrent neural network (RNN) models using a novel two-system approach: one system that infers 'what' computation to perform, and one that implements 'how' to perform it. We focus on a set of compositional cognitive tasks commonly studied in neuroscience. To construct the 'what' system, we first show that a large family of tasks can be systematically described by a probabilistic generative model, where compositionality stems from a shared underlying vocabulary of discrete task-epochs. The shared epoch structure makes these tasks inherently compositional. We first show that this compositionality can be systematically described by a probabilistic generative model. Furthermore, we develop an unsupervised online learning approach that can learn this model on a single-trial basis, building its vocabulary incrementally as it is exposed to new tasks, and inferring the latent epoch structure as a time-varying computational context within a trial. We implement the 'how' system as an RNN whose low-rank components are composed according to the context inferred by the 'what' system. The contextual inference facilitates the creation, learning, and reuse of the low-rank RNN components as new tasks are introduced sequentially, enabling continual learning without catastrophic forgetting. Using an example task set, we demonstrate the efficacy and competitive performance of this two-system learning framework, its potential for forward and backward transfer, as well as few-shot learning via re-composition.

Modern interactive applications increasingly demand dynamic 3D content, yet the transformation of static 3D models into animated assets constitutes a significant bottleneck in content creation pipelines. While recent advances in generative AI have revolutionized static 3D model creation, rigging and animation continue to depend heavily on expert intervention. We present \textbf{Puppeteer}, a comprehensive framework that addresses both automatic rigging and animation for diverse 3D objects. Our system first predicts plausible skeletal structures via an auto-regressive transformer that introduces a joint-based tokenization strategy for compact representation and a hierarchical ordering methodology with stochastic perturbation that enhances bidirectional learning capabilities. It then infers skinning weights via an attention-based architecture incorporating topology-aware joint attention that explicitly encodes inter-joint relationships based on skeletal graph distances. Finally, we complement these rigging advances with a differentiable optimization-based animation pipeline that generates stable, high-fidelity animations while being computationally more efficient than existing approaches. Extensive evaluations across multiple benchmarks demonstrate that our method significantly outperforms state-of-the-art techniques in both skeletal prediction accuracy and skinning quality. The system robustly processes diverse 3D content, ranging from professionally designed game assets to AI-generated shapes, producing temporally coherent animations that eliminate the jittering issues common in existing methods.

Multi-view 3D human pose estimation (HPE) leverages complementary information across views to improve accuracy and robustness. Traditional methods rely on camera calibration to establish geometric correspondences, which is sensitive to calibration accuracy and lacks flexibility in dynamic settings. Calibration-free approaches address these limitations by learning adaptive view interactions, typically leveraging expressive and flexible continuous representations. However, as the multiview interaction relationship is learned entirely from data without constraint, they are vulnerable to noisy input, which can propagate, amplify and accumulate errors across all views, severely corrupting the final estimated pose. To mitigate this, we propose a novel framework that integrates a noise-resilient discrete prior into the continuous representation-based model. Specifically, we introduce the \textit{UniCodebook}, a unified, compact, robust, and discrete representation complementary to continuous features, allowing the model to benefit from robustness to noise while preserving regression capability. Furthermore, we further propose an attribute-preserving and complementarity-enhancing Discrete-Continuous Spatial Attention (DCSA) mechanism to facilitate interaction between discrete priors and continuous pose features. Extensive experiments on three representative datasets demonstrate that our approach outperforms both calibration-required and calibration-free methods, achieving state-of-the-art performance.

Accurate, high-resolution ocean forecasting is crucial for maritime operations and environmental monitoring. While traditional numerical models are capable of producing sub-daily, eddy-resolving forecasts, they are computationally intensive and face challenges in maintaining accuracy at fine spatial and temporal scales. In contrast, recent data-driven approaches offer improved computational efficiency and emerging potential, yet typically operate at daily resolution and struggle with sub-daily predictions due to error accumulation over time. We introduce FuXi-Ocean, the first data-driven global ocean forecasting model achieving six-hourly predictions at eddy-resolving 1/12° spatial resolution, reaching depths of up to 1500 meters. The model architecture integrates a context-aware feature extraction module with a predictive network employing stacked attention blocks. The core innovation is the Mixture-of-Time (MoT) module, which adaptively integrates predictions from multiple temporal contexts by learning variable-specific reliability , mitigating cumulative errors in sequential forecasting. Through comprehensive experimental evaluation, FuXi-Ocean demonstrates superior skill in predicting key variables, including temperature, salinity, and currents, across multiple depths.

Path integration is essential for spatial navigation. Experimental studies have identified neural correlates for path integration, but exactly how the neural system accomplishes this computation remains unresolved. Here, we adopt recurrent neural networks (RNNs) trained to perform a path integration task to explore this issue. After training, we borrow neuroscience prior knowledge and methods to unfold the black box of the trained model, including: clarifying neuron types based on their receptive fields, dissecting information flows between neuron groups by pruning their connections, and analyzing internal dynamics of neuron groups using the attractor framework. Intriguingly, we uncover a hierarchical information processing pathway embedded in the RNN model, along which velocity information of an agent is first forwarded to band cells, band and grid cells then coordinate to carry out path integration, and finally grid cells output the agent location. Inspired by the RNN-based study, we construct a neural circuit model, in which band cells form one-dimensional (1D) continuous attractor neural networks (CANNs) and serve as upstream neurons to support downstream grid cells to carry out path integration in the 2D space. Our study challenges the conventional view of considering grid cells as the principal velocity integrator, and supports a neural circuit model with the hierarchy of band and grid cells.

We present scPilot, the first systematic framework to practice \textit{omics-native reasoning}: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and on-demand bioinformatics tools. scPilot converts core single-cell analyses, i.e., cell-type annotation, developmental-trajectory reconstruction, and transcription-factor targeting, into step-by-step reasoning problems that the model must solve, justify, and, when needed, revise with new evidence. To measure progress, we release \scbench, a suite of 9 expertly curated datasets and graders that faithfully evaluate the omics-native reasoning capability of scPilot w.r.t various LLMs. Experiments with o1 show that \textit{iterative} omics-native reasoning lifts average accuracy by 11\% for cell-type annotation and Gemini 2.5 Pro cuts trajectory graph-edit distance by 30\% versus one-shot prompting, while generating transparent reasoning traces that explain marker gene ambiguity and regulatory logic. By grounding LLMs in raw omics data, scPilot enables auditable, interpretable, and diagnostically informative single-cell analyses.

We introduce TAPIP3D, a novel approach for long-term 3D point tracking in monocular RGB and RGB-D videos. TAPIP3D represents videos as camera-stabilized spatio-temporal feature clouds, leveraging depth and camera motion information to lift 2D video features into a 3D world space where camera movement is effectively canceled out. Within this stabilized 3D representation, TAPIP3D iteratively refines multi-frame motion estimates, enabling robust point tracking over long time horizons. To handle the irregular structure of 3D point distributions, we propose a 3D Neighborhood-to-Neighborhood (N2N) attention mechanism—a 3D-aware contextualization strategy that builds informative, spatially coherent feature neighborhoods to support precise trajectory estimation. Our 3D-centric formulation significantly improves performance over existing 3D point tracking methods and even surpasses state-of-the-art 2D pixel trackers in accuracy when reliable depth is available. The model supports inference in both camera-centric (unstabilized) and world-centric (stabilized) coordinates, with experiments showing that compensating for camera motion leads to substantial gains in tracking robustness. By replacing the conventional 2D square correlation windows used in prior 2D and 3D trackers with a spatially grounded 3D attention mechanism, TAPIP3D achieves strong and consistent results across multiple 3D point tracking benchmarks. Our code and trained checkpoints will be public.

Discrete state space diffusion models have shown significant advantages in applications involving discrete data, such as text and image generation. It has also been observed that their performance is highly sensitive to the choice of rate matrices, particularly between uniform and absorbing rate matrices. While empirical results suggest that absorbing rate matrices often yield better generation quality compared to uniform rate matrices, existing theoretical works have largely focused on the uniform rate matrices case. Notably, convergence guarantees and error analyses for absorbing diffusion models are still missing. In this work, we provide the first finite-time error bounds and convergence rate analysis for discrete diffusion models using absorbing rate matrices. We begin by deriving an upper bound on the KL divergence of the forward process, introducing a surrogate initialization distribution to address the challenge posed by the absorbing stationary distribution, which is a singleton and causes the KL divergence to be ill-defined. We then establish the first convergence guarantees for both the $\tau$-leaping and uniformization samplers under absorbing rate matrices, demonstrating improved rates over their counterparts using uniform rate matrices. Furthermore, under suitable assumptions, we provide convergence guarantees without early stopping. Our analysis introduces several new technical tools to address challenges unique to absorbing rate matrices. These include a Jensen-type argument for bounding forward process convergence, novel techniques for bounding absorbing score functions, and a non-divergent upper bound on the score near initialization that removes the need of early-stopping.

Breast cancer remains a leading cause of death among women, with early detection significantly improving prognosis. Non-contrast computed tomography (NCCT) scans of the chest, routinely acquired for thoracic assessments, often capture the breast region incidentally, presenting an underexplored opportunity for opportunistic breast lesion detection without additional imaging cost or radiation. However, the subtle appearance of lesions in NCCT and the difficulty of jointly modeling lesion detection and malignancy classification pose unique challenges. In this work, we propose Dual-Res Tandem Mamba-3D (DRT-M3D), a novel multitask framework for opportunistic breast cancer analysis on NCCT scans. DRT-M3D introduces a dual-resolution architecture, which captures fine-grained spatial details for segmentation-based lesion detection and global contextual features for breast-level cancer classification. It further incorporates a tandem input mechanism that models bilateral breast regions jointly through Mamba-3D blocks, enabling cross-breast feature interaction by leveraging subtle asymmetries between the two sides. Our approach achieves state-of-the-art performance in both tasks across multi-institutional NCCT datasets spanning four medical centers. Extensive experiments and ablation studies validate the effectiveness of each key component.

Foundation models have enabled rapid progress across many specialized domains by leveraging large-scale pre-training on unlabeled data, demonstrating strong generalization to a variety of downstream tasks. While such models have gained significant attention in fields like Earth Observation, their application to Mars science remains limited. A key enabler of progress in other domains has been the availability of standardized benchmarks that support systematic evaluation. In contrast, Mars science lacks such benchmarks and standardized evaluation frameworks, which have limited progress toward developing foundation models for Martian tasks. To address this gap, we introduce Mars-Bench, the first benchmark designed to systematically evaluate models across a broad range of Mars-related tasks using both orbital and surface imagery. Mars-Bench comprises 20 datasets spanning classification, segmentation, and object detection, focused on key geologic features such as craters, cones, boulders, and frost. We provide standardized, ready-to-use datasets and baseline evaluations using models pre-trained on natural images, Earth satellite data, and state-of-the-art vision-language models. Results from all analyses suggest that Mars-specific foundation models may offer advantages over general-domain counterparts, motivating further exploration of domain-adapted pre-training. Mars-Bench aims to establish a standardized foundation for developing and comparing machine learning models for Mars science. Our data, models, and code are available at: https://mars-bench.github.io/.

Remote physiological sensing is an evolving area of research. As systems approach clinical precision, there is increasing focus on complex applications such as cognitive state estimation. Hence, there is a need for large datasets that facilitate research into complex downstream tasks such as remote cognitive load estimation. A first-of-its-kind, our paper introduces an open-source multimodal multi-vital sign dataset consisting of concurrent recordings from RGB, NIR (near-infrared), thermal, and RF (radio-frequency) sensors alongside contact-based physiological signals, such as pulse oximeter and chest bands, providing a benchmark for cognitive state assessment. By adopting a multimodal approach to remote health sensing, our dataset and its associated hardware system excel at modeling the complexities of cognitive load. Here, cognitive load is defined as the mental effort exerted during tasks such as reading, memorizing, and solving math problems. By using the NASA-TLX survey, we set personalized thresholds for defining high/low cognitive levels, enabling a more reliable benchmark. Our benchmarking scheme bridges the gap between existing remote sensing strategies and cognitive load estimation techniques by using vital signs (such as photoplethysmography (PPG) and respiratory waveforms) and physiological signals (blink waveforms) as an intermediary. Through this paper, we focus on replacing the need for intrusive contact-based physiological measurements with more user-friendly remote sensors. Our benchmarking demonstrates that multimodal fusion significantly improves remote vital sign estimation, with our fusion model achieving $<3~BPM$ (beats per minute) error for vital sign estimation. For cognitive load classification, the combination of remote PPG, remote respiratory signals, and blink markers achieves $86.49$% accuracy, approaching the performance of contact-based sensing ($87.5$%) and validating the feasibility of non-intrusive cognitive monitoring.

Decoding visual stimuli from neural population activity is crucial for understanding the brain and for applications in brain-machine interfaces. However, such biological data is often scarce, particularly in primates or humans, where high-throughput recording techniques, such as two-photon imaging, remain challenging or impossible to apply. This, in turn, poses a challenge for deep learning decoding techniques. To overcome this, we introduce MEIcoder, a biologically informed decoding method that leverages neuron-specific most exciting inputs (MEIs), a structural similarity index measure loss, and adversarial training. MEIcoder achieves state-of-the-art performance in reconstructing visual stimuli from single-cell activity in primary visual cortex (V1), especially excelling on small datasets with fewer recorded neurons. Using ablation studies, we demonstrate that MEIs are the main drivers of the performance, and in scaling experiments, we show that MEIcoder can reconstruct high-fidelity natural-looking images from as few as 1,000-2,500 neurons and less than 1,000 training data points. We also propose a unified benchmark with over 160,000 samples to foster future research. Our results demonstrate the feasibility of reliable decoding in early visual system and provide practical insights for neuroscience and neuroengineering applications.

As large language models increasingly gain popularity in real-world applications, processing extremely long contexts, often exceeding the model’s pre-trained context limits, has emerged as a critical challenge. While existing approaches to efficient long-context processing show promise, recurrent compression-based methods struggle with information preservation, whereas random access approaches require substantial memory resources. We introduce REFORM, a novel inference framework that efficiently handles long contexts through a two-phase approach. First, it incrementally processes input chunks while maintaining a compressed KV cache, constructs cross-layer context embeddings, and utilizes early exit strategy for improved efficiency. Second, it identifies and gathers essential tokens via similarity matching and selectively recomputes the KV cache. Compared to baselines, REFORM achieves over 50% and 27% performance gains on RULER and BABILong respectively at 1M context length. It also outperforms baselines on ∞-Bench, RepoEval, and MM-NIAH, demonstrating flexibility across diverse tasks and domains. Additionally, REFORM reduces inference time by 30% and peak memory usage by 5%, achieving both efficiency and superior performance.

Variant and gene interpretation are fundamental to personalized medicine and translational biomedicine. However, traditional approaches are manual and labor-intensive. Generative language models (LMs) can facilitate this process, accelerating the translation of fundamental research into clinically-actionable insights. While existing benchmarks have attempted to quantify the capabilities of LMs for interpreting scientific data, these studies focus on narrow tasks that do not translate to real-world research. To meet these challenges, we introduce CGBench, a robust benchmark that tests reasoning capabilities of LMs on scientific publications. CGBench is built from ClinGen, a resource of expert-curated literature interpretations in clinical genetics. CGBench measures the ability to 1) extract relevant experimental results following precise protocols and guidelines, 2) judge the strength of evidence, and 3) categorize and describe the relevant outcome of experiments. We test 8 different LMs and find that while models show promise, substantial gaps exist in literature interpretation, especially on fine-grained instructions. Reasoning models excel in fine-grained tasks but non-reasoning models are better at high-level interpretations. Finally, we measure LM explanations against human explanations with an LM judge approach, revealing that models often hallucinate or misinterpret results even when correctly classifying evidence. CGBench reveals strengths and weaknesses of LMs for precise interpretation of scientific publications, opening avenues for future research in AI for clinical genetics and science more broadly.