NeurIPS 2025 Papers

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.

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}.

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.

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)).

Multi-level compositional optimization is a fundamental framework in machine learning with broad applications. While recent advances have addressed compositional minimization problems, the stochastic multi-level compositional minimax problem introduces significant new challenges—most notably, the biased nature of stochastic gradients for both the primal and dual variables. In this work, we address this gap by proposing a novel stochastic multi-level compositional gradient descent-ascent algorithm, incorporating a smoothing technique under the nonconvex-PL condition. We establish a convergence rate to an $(\epsilon, \epsilon/\sqrt{\kappa})$-stationary point with improved dependence on the condition number at $O(\kappa^{3/2})$, where $\epsilon$ denotes the solution accuracy and $\kappa$ represents the condition number. Moreover, we design a novel stage-wise algorithm with variance reduction to address the biased gradient issue under the two-sided PL condition. This algorithm successfully enables a translation from and $(\epsilon, \epsilon/\sqrt{\kappa})$-stationary point to an $\epsilon$-stationary point. Finally, extensive experiments validate the effectiveness of our algorithms.

Despite the remarkable generation quality of video Diffusion Transformer (DiT) models, their practical deployment is severely hindered by extensive computational requirements. This inefficiency stems from two key challenges: the quadratic complexity of self-attention with respect to token length and the multi-step nature of diffusion models. To address these limitations, we present Jenga, a novel inference pipeline that combines dynamic attention carving with progressive resolution generation. Our approach leverages two key insights: (1) early denoising steps do not require high-resolution latents, and (2) later steps do not require dense attention. Jenga introduces a block-wise attention mechanism that dynamically selects relevant token interactions using 3D space-filling curves, alongside a progressive resolution strategy that gradually increases latent resolution during generation. Experimental results demonstrate that Jenga achieves substantial speedups across multiple state-of-the-art video diffusion models while maintaining comparable generation quality (8.83$\times$ speedup with 0.01\% performance drop on VBench). As a plug-and-play solution, Jenga enables practical, high-quality video generation on modern hardware by reducing inference time from minutes to seconds---without requiring model retraining.

We study the problem of computing the exact median by leveraging side information to minimize costly, exact comparisons. We analyze this problem in two key settings: (1) using predictions from unreliable 'weak' oracles, and (2) exploiting known structural information in the form of a partial order. In the classical setting, we introduce a modified LazySelect algorithm that combines weak comparisons with occasional strong comparisons through majority voting. We show that this hybrid strategy has near-linear running time and can achieve high-probability correctness using only sublinear strong comparisons, even when the weak oracle is only slightly better than random guessing. Our theoretical results hold under the persistent comparison model, where resampling will not amplify the probability of correctness. In the partially ordered setting, we generalize the notion of median to directed acyclic graphs (DAGs) and show that the complexity of median selection depends heavily on the DAG's width. We complement our analysis with extensive experiments on synthetic data.

Multi-agent collaboration enhances the perception capabilities of individual agents through information sharing. However, in real-world applications, differences in sensors and models across heterogeneous agents inevitably lead to domain gaps during collaboration. Existing approaches based on adaptation and reconstruction fail to support *pragmatic heterogeneous collaboration* due to two key limitations: (1) Intrusive retraining of the encoder or core modules disrupts the established semantic consistency among agents; and (2) accommodating new agents incurs high computational costs, limiting scalability. To address these challenges, we present a novel **Gen**erative **Comm**unication mechanism (GenComm) that facilitates seamless perception across heterogeneous multi-agent systems through feature generation, without altering the original network, and employs lightweight numerical alignment of spatial information to efficiently integrate new agents at minimal cost. Specifically, a tailored Deformable Message Extractor is designed to extract spatial message for each collaborator, which is then transmitted in place of intermediate features. The Spatial-Aware Feature Generator, utilizing a conditional diffusion model, generates features aligned with the ego agent's semantic space while preserving the spatial information of the collaborators. These generated features are further refined by a Channel Enhancer before fusion. Experiments conducted on the OPV2V-H, DAIR-V2X and V2X-Real datasets demonstrate that GenComm outperforms existing state-of-the-art methods, achieving an 81\% reduction in both computational cost and parameter count when incorporating new agents. Our code is available at https://github.com/jeffreychou777/GenComm.

Graph Neural Networks (GNNs) have achieved remarkable success across various domains. However, recent theoretical advances have identified fundamental limitations in their information propagation capabilities, such as over-squashing, where distant nodes fail to effectively exchange information. While extensively studied in static contexts, this issue remains unexplored in Spatiotemporal GNNs (STGNNs), which process sequences associated with graph nodes. Nonetheless, the temporal dimension amplifies this challenge by increasing the information that must be propagated. In this work, we formalize the spatiotemporal over-squashing problem and demonstrate its distinct characteristics compared to the static case. Our analysis reveals that, counterintuitively, convolutional STGNNs favor information propagation from points temporally distant rather than close in time. Moreover, we prove that architectures that follow either time-and-space or time-then-space processing paradigms are equally affected by this phenomenon, providing theoretical justification for computationally efficient implementations. We validate our findings on synthetic and real-world datasets, providing deeper insights into their operational dynamics and principled guidance for more effective designs.

To adapt kernel two-sample and independence testing to complex structured data, aggregation of multiple kernels is frequently employed to boost testing power compared to single-kernel tests. However, we observe a phenomenon that directly maximizing multiple kernel-based statistics may result in highly similar kernels that capture highly overlapping information, limiting the effectiveness of aggregation. To address this, we propose an aggregated statistic that explicitly incorporates kernel diversity based on the covariance between different kernels. Moreover, we identify a fundamental challenge: a trade-off between the diversity among kernels and the test power of individual kernels, i.e., the selected kernels should be both effective and diverse. This motivates a testing framework with selection inference, which leverages information from the training phase to select kernels with strong individual performance from the learned diverse kernel pool. We provide rigorous theoretical statements and proofs to show the consistency on the test power and control of Type-I error, along with asymptotic analysis of the proposed statistics. Lastly, we conducted extensive empirical experiments demonstrating the superior performance of our proposed approach across various benchmarks for both two-sample and independence testing.