NeurIPS 2025 论文列表

General intelligence requires systems that acquire new skills efficiently and generalize beyond their training distributions. Although program synthesis approaches have strong generalization power, they face scaling issues due to large combinatorial spaces that quickly make them impractical and require human-generated DSLs or pre-trained priors to narrow this search space. On the other hand, deep learning methods have had high successes, but they lack structured test-time adaptation and rely on heavy stochastic sampling or expensive gradient updates for fine-tuning. In this work, we propose the Latent Program Network (LPN), a new architecture that builds in test-time search directly into neural models. LPN learns a latent space of implicit programs---neurally mapping inputs to outputs---through which it can search using gradients at test time. LPN combines the adaptability of symbolic approaches and the scalability of neural methods. It searches through a compact latent space at test time and bypasses the need for pre-defined domain-specific languages. On a range of programming-by-examples tasks, LPN either outperforms or matches performance compared to in-context learning and test-time training methods. Tested on the ARC-AGI benchmark, we demonstrate that LPN can both learn a compact program space and search through it at test time to adapt to novel tasks. LPN doubles its performance on out-of-distribution tasks when test-time search is switched on.

Predicting changes in binding free energy ($\Delta\Delta G$) is essential for understanding protein-protein interactions, which are critical in drug design and protein engineering. However, existing methods often rely on pre-trained knowledge and heuristic features, limiting their ability to accurately model complex mutation effects, particularly higher-order and many-body interactions. To address these challenges, we propose H3-DDG, a Hypergraph-driven Hierarchical network to capture Higher-order many-body interactions across multiple scales. By introducing a hierarchical communication mechanism, H3-DDG effectively models both local and global mutational effects. Experimental results demonstrate state-of-the-art performance on multiple benchmarks. On the SKEMPI v2 dataset, H3-DDG achieves a Pearson correlation of 0.75, improving multi-point mutations prediction by 12.10%. On the challenging BindingGYM dataset, it outperforms Prompt-DDG and BA-DDG by 62.61% and 34.26%, respectively. Ablation and efficiency analyses demonstrate its robustness and scalability, while a case study on SARS-CoV-2 antibodies highlights its practical value in improving binding affinity for therapeutic design.

In this paper, we examine the convergence landscape of multi-agent learning under uncertainty. Specifically, we analyze two stochastic models of regularized learning in continuous games—one in continuous and one in discrete time—with the aim of characterizing the long run behavior of the induced sequence of play. In stark contrast to deterministic, full-information models of learning (or models with a vanishing learning rate), we show that the resulting dynamics do not converge in general. In lieu of this, we ask instead which actions are played more often in the long run, and by how much. We show that, in strongly monotone games, the dynamics of regularized learning may wander away from equilibrium infinitely often, but they always return to its vicinity in finite time (which we estimate), and their long-run distribution is sharply concentrated around a neighborhood thereof. We quantify the degree of this concentration, and we show that these favorable properties may all break down if the underlying game is not strongly monotone—underscoring in this way the limits of regularized learning in the presence of persistent randomness and uncertainty

Dynamic coreset selection is a promising approach for improving the training efficiency of deep neural networks by periodically selecting a small subset of the most representative or informative samples, thereby avoiding the need to train on the entire dataset. However, it remains inherently challenging due not only to the complex interdependencies among samples and the evolving nature of model training, but also to a critical *coreset representativeness degradation issue* identified and explored in-depth in this paper, that is, the representativeness or information content of the coreset degrades over time as training progresses. Therefore, we argue that, in addition to designing accurate selection rules, it is equally important to endow the algorithms with the ability to assess the quality of the current coreset. Such awareness enables timely re-selection, mitigating the risk of overfitting to stale subsets—a limitation often overlooked by existing methods. To this end, this paper proposes an **E**fficient **R**epresentativeness-**A**ware **C**oreset **S**election method for deep neural networks, a lightweight framework that enables dynamic tracking and maintenance of coreset quality during training. While the ideal criterion—gradient discrepancy between the coreset and the full dataset—is computationally prohibitive, we introduce a scalable surrogate based on the signal-to-noise ratio (SNR) of gradients within the coreset, which is the main technical contribution of this paper and is also supported by our theoretical analysis. Intuitively, a decline in SNR indicates overfitting to the subset and declining representativeness. Leveraging this observation, our method triggers coreset updates without requiring costly Hessian or full-batch gradient computations, maintaining minimal computational overhead. Experiments on multiple datasets confirm the effectiveness of our approach. Notably, compared with existing gradient-based dynamic coreset selection baselines, our method achieves up to a 5.4\% improvement in test accuracy across multiple datasets.

Recent advancements in Long Chain-of-Thought (CoT) reasoning models have improved performance on complex tasks, but they suffer from overthinking, which generates redundant reasoning steps, especially for simple questions. This paper revisits the reasoning patterns of Long and Short CoT models, observing that the Short CoT patterns offer concise reasoning efficiently, while the Long CoT patterns excel in challenging scenarios where the Short CoT patterns struggle. To enable models to leverage both patterns, we propose Question-Free Fine-Tuning (QFFT), a fine-tuning approach that removes the input question during training and learns exclusively from Long CoT responses. This approach enables the model to adaptively employ both reasoning patterns: it prioritizes the Short CoT patterns and activates the Long CoT patterns only when necessary. Experiments on various mathematical datasets demonstrate that QFFT reduces average response length by more than 50\%, while achieving performance comparable to Supervised Fine-Tuning (SFT). Additionally, QFFT exhibits superior performance compared to SFT in noisy, out-of-domain, and low-resource scenarios.

Multi-modal image segmentation faces real-world deployment challenges from incomplete/corrupted modalities degrading performance. While existing methods address training-inference modality gaps via specialized per-combination models, they introduce high deployment costs by requiring exhaustive model subsets and model-modality matching. In this work, we propose a unified modality-relax segmentation network (UniMRSeg) through hierarchical self-supervised compensation (HSSC). Our approach hierarchically bridges representation gaps between complete and incomplete modalities across input, feature and output levels. First, we adopt modality reconstruction with the hybrid shuffled-masking augmentation, encouraging the model to learn the intrinsic modality characteristics and generate meaningful representations for missing modalities through cross-modal fusion. Next, modality-invariant contrastive learning implicitly compensates the feature space distance among incomplete-complete modality pairs. Furthermore, the proposed lightweight reverse attention adapter explicitly compensates for the weak perceptual semantics in the frozen encoder. Last, UniMRSeg is fine-tuned under the hybrid consistency constraint to ensure stable prediction under all modality combinations without large performance fluctuations. Without bells and whistles, UniMRSeg significantly outperforms the state-of-the-art methods under diverse missing modality scenarios on MRI-based brain tumor segmentation, RGB-D semantic segmentation, RGB-D/T salient object segmentation. The code will be released at \url{https://github.com/Xiaoqi-Zhao-DLUT/UniMRSeg}.

Information seeking demands iterative evidence gathering and reflective reasoning, yet large language models (LLMs) still struggle with it in open-web question answering. Existing prompting and supervised fine-tuning (SFT) methods remain fixed by prompt rules or training corpora, and are usually benchmarked only on well-structured wiki sources, limiting real-world adaptability. We introduce $\textbf{WebPuzzle}$, a 24k-sample training and 275-sample test benchmark that evaluates information seeking on the live internet, across both wiki and open-domain queries. Leveraging 7k WebPuzzle instances, we develop $\textbf{DeepDiver}$, a reinforcement-learning (RL) framework that cultivates $\textbf{Search Intensity Scaling (SIS)}$—an emergent ability to escalate search frequency and depth instead of settling on overconfident, under-evidenced answers. With SIS, Qwen2.5-7B-Instruct and Pangu-7B-Reasoner attain performance on real-web tasks comparable to the 671B-parameter DeepSeek-R1. We detail DeepDiver’s curriculum from cold-start SFT to a well designed RL procedure, and show that its seeking policy generalized from closed-ended queries to open-ended generation such as long-form writing. Our results advance adaptive information seeking in LLMs and provide a rigorous benchmark for future work.

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems. We evaluated six frontier LLMs on 137 small systems, and released a total of 350 systems at https://huggingface.co/datasets/h4duan/scigym-sbml. Our evaluation shows that while more capable models demonstrated superior performance, all models' performance declined significantly as system complexity increased, suggesting substantial room for improvement in the scientific capabilities of LLM agents.

Characterizing the cellular properties of neurons is fundamental to understanding their function in the brain. In this quest, the generation of bio-realistic models is central towards integrating multimodal cellular data sets and establishing causal relationships. However, current modeling approaches remain constrained by the limited availability and intrinsic variability of experimental neuronal data. The deterministic formalism of bio-realistic models currently precludes accounting for the natural variability observed experimentally. While deep learning is becoming increasingly relevant in this space, it fails to capture the full biophysical complexity of neurons, their nonlinear voltage dynamics, and variability. To address these shortcomings, we introduce $\texttt{NOBLE}$, a neural operator framework that learns a mapping from a continuous frequency-modulated embedding of interpretable neuron features to the somatic voltage response induced by current injection. Trained on synthetic data generated from bio-realistic neuron models, $\texttt{NOBLE}$ predicts distributions of neural dynamics accounting for the intrinsic experimental variability. Unlike conventional bio-realistic neuron models, interpolating within the embedding space offers models whose dynamics are consistent with experimentally observed responses. $\texttt{NOBLE}$ enables the efficient generation of synthetic neurons that closely resemble experimental data and exhibit trial-to-trial variability, offering a $4200$× speedup over the numerical solver. $\texttt{NOBLE}$ is the first scaled-up deep learning framework that validates its generalization with real experimental data. To this end, $\texttt{NOBLE}$ captures fundamental neural properties in a unique and emergent manner that opens the door to a better understanding of cellular composition and computations, neuromorphic architectures, large-scale brain circuits, and general neuroAI applications.

Accurate prediction of continuous properties is essential to many scientific and engineering tasks. Although deep-learning regressors excel with abundant labels, their accuracy deteriorates in data-scarce regimes. We introduce RankRefine, a model-agnostic, plug-and-play post-hoc refinement technique that injects expert knowledge through pairwise rankings. Given a query item and a small reference set with known properties, RankRefine combines the base regressor’s output with a rank-based estimate via inverse-variance weighting, requiring no retraining. In molecular property prediction task, RankRefine achieves up to 10\% relative reduction in mean absolute error using only 20 pairwise comparisons obtained through a general-purpose large language model (LLM) with no finetuning. As rankings provided by human experts or general-purpose LLMs are sufficient for improving regression across diverse domains, RankRefine offers practicality and broad applicability, especially in low-data settings.

Many real-world control problems require continual policy adjustments to balance multiple objectives, which requires the acquisition of high-quality policies to cover diverse preferences. Multi-Objective Reinforcement Learning (MORL) provides a general framework to solve such problems. However, current MORL methods suffer from high sample complexity, primarily due to the neglect of efficient knowledge sharing and conflicts in optimization with different preferences. To this end, this paper introduces a novel framework, Conflict Objective Regularization in Latent Space (**COLA**). To enable efficient knowledge sharing, COLA establishes a shared latent representation space for common knowledge, which can avoid redundant learning under different preferences. Besides, COLA introduces a regularization term for the value function to mitigate the negative effects of conflicting preferences on the value function approximation, thereby improving the accuracy of value estimation. The experimental results across various multi-objective continuous control tasks demonstrate the significant superiority of COLA over the state-of-the-art MORL baselines. Code is available at https://github.com/yeshenpy/COLA.

We present SpecMAS, a novel multi-agent system that autonomously constructs and formally verifies executable system models from natural language specifications. Given a Standard Operating Procedure (SOP) describing a target system, SpecMAS parses the specification, identifies relevant operational modes, variables, transitions, and properties, and generates a formal model in NuSMV code syntax, an industry-standard symbolic model checker. A dedicated reasoning agent extracts both explicit and implicit properties from the SOP, and verification is performed via temporal logic model checking. If any properties fail to verify, an autonomous debugging agent analyzes counterexamples and iteratively corrects the model until all properties are satisfied. This closed-loop system design guarantees provable correctness by construction and advances the state of the art in automated, interpretable, and deployable verification pipelines. We demonstrate the generality, correctness, and practical feasibility of SpecMAS across a set of representative case studies and propose a new benchmark dataset for the evaluation and comparison of model checking performance.

Occupancy prediction infers fine-grained 3D geometry and semantics from camera images of the surrounding environment, making it a critical perception task for autonomous driving. Existing methods either adopt dense grids as scene representation which is difficult to scale to high resolution, or learn the entire scene using a single set of sparse queries, which is insufficient to handle the various object characteristics. In this paper, we present ODG, a hierarchical dual sparse Gaussian representation to effectively capture complex scene dynamics. Building upon the observation that driving scenes can be universally decomposed into static and dynamic counterparts, we define dual Gaussian queries to better model the diverse scene objects. We utilize a hierarchical Gaussian transformer to predict the occupied voxel centers and semantic classes along with the Gaussian parameters. Leveraging the real-time rendering capability of 3D Gaussian Splatting, we also impose rendering supervision with available depth and semantic map annotations injecting pixel-level alignment to boost occupancy learning. Extensive experiments on the Occ3D-nuScenes and Occ3D-Waymo benchmarks demonstrate our proposed method sets new state-of-the-art results while maintaining low inference cost.

Surface electromyography (sEMG) at the wrists could enable natural, keyboard‑free text entry, yet the state‑of‑the‑art emg2qwerty baseline still misrecognizes 51.8\% of characters zero‑shot on unseen users and 7.0\% after user‑specific fine‑tuning. We trace much of these errors to mismatched cross‑user signal statistics, fragile reliance on high‑order feature dependencies, and the absence of architectural inductive biases aligned with the bilateral nature of typing. To address these issues, we introduce three simple modifications: (i) Rolling Time Normalization which adaptively aligns input distributions across users; (ii) Aggressive Channel Masking, which encourages reliance on low‑order feature combinations more likely to generalize across users; and (iii) a Split‑and‑Share encoder that processes each hand independently with weight‑shared streams to reflect the bilateral symmetry of the neuromuscular system. Combined with a five‑fold reduction in spectral resolution (33$\rightarrow$6 frequency bands), these components yield a compact Split-and-Share model, SplashNet‑mini, which uses only ¼ the parameters and 0.6× the FLOPs of the baseline while reducing character error rate (CER) to 36.4\% zero‑shot and 5.9\% after fine‑tuning. An upscaled variant, SplashNet (½ parameters, 1.15× FLOPs of the baseline), further lowers error to 35.7\% and 5.5\%, representing 31\% and 21\% relative improvements in the zero-shot and finetuned settings, respectively. SplashNet therefore establishes a new state-of-the-art without requiring additional data.

Recent advances in video diffusion models have driven rapid progress in video editing techniques. However, video object removal, a critical subtask of video editing, remains challenging due to issues such as hallucinated objects and visual artifacts. Furthermore, existing methods often rely on computationally expensive sampling procedures and classifier-free guidance (CFG), resulting in slow inference. To address these limitations, we propose **MiniMax-Remover**, a novel two-stage video object removal approach. Motivated by the observation that text condition is not best suited for this task, we simplify the pretrained video generation model by removing textual input and cross-attention layers. In this way, we obtain a more lightweight and efficient model architecture in the first stage. In the second stage, we proposed a minimax optimization strategy to further distill the remover with the successful videos produced by stage-1 model. Specifically, the inner maximization identifies adversarial input noise ("bad noise'') that leads to failure removals, while the outer minimization trains the model to generate high-quality removal results even under such challenging conditions. As a result, our method achieves a state-of-the-art video object removal results using as few as 6 sampling steps without CFG usage. Extensive experiments demonstrate the effectiveness and superiority of MiniMax-Remover compared to existing methods. Codes and Videos are available at: **https://minimax-remover.github.io**.

Entropy Minimization (EM) is beneficial to reducing class overlap, bridging domain gap, and restricting uncertainty for various tasks in machine learning, yet its potential is limited. To study the internal mechanism of EM, we reformulate and decouple the classical EM into two parts with opposite effects: cluster aggregation driving factor (CADF) rewards dominant classes and prompts a peaked output distribution, while gradient mitigation calibrator (GMC) penalizes high-confidence classes based on predicted probabilities. Furthermore, we reveal the limitations of classical EM caused by its coupled formulation: 1) reward collapse impedes the contribution of high-certainty samples in the learning process, and 2) easy-class bias induces misalignment between output distribution and label distribution. To address these issues, we propose Adaptive Decoupled Entropy Minimization (AdaDEM), which normalizes the reward brought from CADF and employs a marginal entropy calibrator (MEC) to replace GMC. AdaDEM outperforms DEM*, an upper-bound variant of classical EM, and achieves superior performance across various imperfectly supervised learning tasks in noisy and dynamic environments.

Generalist Graph Anomaly Detection (GGAD) extends traditional Graph Anomaly Detection (GAD) from one-for-one to one-for-all scenarios, posing significant challenges due to Feature Space Shift (FSS) and Graph Structure Shift (GSS). This paper first formalizes these challenges and proposes quantitative metrics to measure their severity. To tackle FSS, we develop an anomaly-driven graph invariant learning module that learns domain-invariant node representations. To address GSS, a novel structure-insensitive affinity learning module is introduced, capturing cross-domain structural correspondences via affinity-based features. Our unified framework, IA-GGAD, integrates these modules, enabling anomaly prediction on unseen graphs without target-domain retraining or fine-tuning. Extensive experiments on benchmark datasets from varied domains demonstrate IA-GGAD’s superior performance, significantly outperforming state-of-the-art methods (e.g., achieving up to +12.28\% AUROC over ARC on ACM). Ablation studies further confirm the effectiveness of each proposed module. The code is available at \url{https://github.com/kg-cc/IA-GGAD/}.

Stochastic Natural Gradient Variational Inference (NGVI) is a widely used method for approximating posterior distribution in probabilistic models. Despite its empirical success and foundational role in variational inference, its theoretical underpinnings remain limited, particularly in the case of non-conjugate likelihoods. While NGVI has been shown to be a special instance of Stochastic Mirror Descent, and recent work has provided convergence guarantees using relative smoothness and strong convexity for conjugate models, these results do not extend to the non-conjugate setting, where the variational loss becomes non-convex and harder to analyze. In this work, we focus on mean-field parameterization and advance the theoretical understanding of NGVI in three key directions. First, we derive sufficient conditions under which the variational loss satisfies relative smoothness with respect to a suitable mirror map. Second, leveraging this structure, we propose a modified NGVI algorithm incorporating non-Euclidean projections and prove its global non-asymptotic convergence to a stationary point. Finally, under additional structural assumptions about the likelihood, we uncover hidden convexity properties of the variational loss and establish fast global convergence of NGVI to a global optimum. These results provide new insights into the geometry and convergence behavior of NGVI in challenging inference settings.

Cyclic peptides exhibit better binding affinity and proteolytic stability compared to their linear counterparts. However, the development of cyclic peptide design models is hindered by the scarcity of data. To address this, we introduce **CPSea**(**C**yclic **P**eptide **Sea**), a dataset of 2.71 million cyclic peptide-receptor complexes, curated through systematic mining of the AlphaFold Database (AFDB). Our pipeline extracts compact domains from AFDB, identifies cyclization sites using the $\beta$-carbon (C$_\beta$) distance thresholds, and applies multi-stage filtering to ensure structure fidelity and binding compatibility. Compared with experimental data of cyclic peptides, CPSea shows similar distributions in metrics on structure fidelity and wet-lab compatibility. To our knowledge, CPSea is the largest cyclic peptide-receptor dataset to date, enabling end-to-end model training for the first time. The dataset also showcases the feasibility of simulating inter-chain interactions using intra-chain interactions, expanding available resources for machine-learning models on protein-protein interactions. The dataset and relevant scripts are accessible on GitHub ([https://github.com/YZY010418/CPSea](https://github.com/YZY010418/CPSea)).