NeurIPS 2025 论文列表

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained molecular annotations across multiple levels, bridging the gap between molecules and textual descriptions. Additionally, we propose chemically-informative molecular representation, effectively addressing limitations in existing molecular representation strategies. Building upon these innovations, we develop KnowMol, a state-of-the-art multi-modal molecular large language model. Extensive experiments demonstrate that KnowMol achieves superior performance across molecular understanding and generation tasks.

Interpretable machine learning is essential in high-stakes domains like healthcare. Rule lists are a popular choice due to their transparency and accuracy, but learning them effectively remains a challenge. Existing methods require feature pre-discretization, constrain rule complexity or ordering, or struggle to scale. We present NeuRules, a novel end-to-end framework that overcomes these limitations. At its core, NeuRules transforms the inherently combinatorial task of rule list learning into a differentiable optimization problem, enabling gradient-based learning. It simultaneously discovers feature conditions, assembles them into conjunctive rules, and determines their order—without pre-processing or manual constraints. A key contribution here is a gradient shaping technique that steers learning toward sparse rules with strong predictive performance. To produce ordered lists, we introduce a differentiable relaxation that, through simulated annealing, converges to a strict rule list. Extensive experiments show that NeuRules consistently outperforms combinatorial and neural baselines on binary as well as multi-class classification tasks across a wide range of datasets.

The discovery of the *lazy neuron phenomenon* (Li et al., 2022), where fewer than 10% of the feedforward networks (FFN) parameters in trained Transformers are activated per token, has spurred significant interests in *activation sparsity* for enhancing large model efficiency. While notable progress has been made in translating such sparsity to wall-time benefits across CPUs, GPUs, and TPUs, modern Transformers have moved away from the ReLU activation function crucial to this phenomenon. Existing efforts on re-introducing activation sparsity, e.g., by reverting to ReLU or applying top-k masking, often degrade model quality, increase parameter count, or complicate training. Sparse attention, the application of sparse activation to the attention mechanism, often face similar challenges. This paper introduces the Spark Transformer, a novel architecture that achieves high activation sparsity in both FFN and the attention mechanism while maintaining model quality, parameter count, and standard training procedures. Our method realizes sparsity via top-$k$ masking for explicit control over sparsity level. Crucially, we introduce *statistical top-k*, a hardware-accelerator-friendly, linear-time approximate algorithm that avoids costly sorting and mitigates significant training slowdown from standard top-k operators. Furthermore, Spark Transformer reallocates existing FFN parameters and attention key embeddings to form a low-cost predictor for identifying activated entries. This design not only mitigates quality loss from enforced sparsity, but also enhances wall-time benefit. Pretrained with the Gemma-2 recipe, Spark Transformer demonstrates competitive performance on standard benchmarks while exhibiting significant sparsity: only 8\% of FFN neurons are activated, and each token attends to a maximum of 256 tokens. This translates to a 2.5x reduction in FLOPs, leading to decoding wall-time speedups of up to 1.79x on CPU and 1.40xon GPU.

Large language model (LLM) evaluation is increasingly costly, prompting interest in methods that speed up evaluation by shrinking benchmark datasets. Benchmark prediction (also called efficient LLM evaluation) aims to select a small subset of evaluation points and predict overall benchmark performance from that subset. In this paper, we systematically assess the strengths and limitations of 11 benchmark prediction methods across 19 diverse benchmarks. First, we identify a highly competitive baseline: Take a random sample and fit a regression model on the sample to predict missing entries. Outperforming most existing methods, this baseline challenges the assumption that careful subset selection is necessary for benchmark prediction. Second, we discover that all existing methods crucially depend on model similarity. They work best when interpolating scores among similar models. The effectiveness of benchmark prediction sharply declines when new models have higher accuracy than previously seen models. In this setting of extrapolation, none of the previous methods consistently beat a simple average over random samples. To improve over the sample average, we introduce a new method inspired by augmented inverse propensity weighting. This method consistently outperforms the random sample average even for extrapolation. However, its performance still relies on model similarity and the gains are modest in general. This shows that benchmark prediction fails just when it is most needed: at the evaluation frontier, where the goal is to evaluate new models of unknown capabilities.

Paired RGB-thermal data is crucial for visual-thermal sensor fusion and cross-modality tasks, including important applications such as multi-modal image alignment and retrieval. However, the scarcity of synchronized and calibrated RGB-thermal image pairs presents a major obstacle to progress in these areas. To overcome this challenge, RGB-to-Thermal (RGB-T) image translation has emerged as a promising solution, enabling the synthesis of thermal images from abundant RGB datasets for training purposes. In this study, we propose ThermalGen, an adaptive flow-based generative model for RGB-T image translation, incorporating an RGB image conditioning architecture and a style-disentangled mechanism. To support large-scale training, we curated eight public satellite-aerial, aerial, and ground RGB-T paired datasets, and introduced three new large-scale satellite-aerial RGB-T datasets--DJI-day, Bosonplus-day, and Bosonplus-night--captured across diverse times, sensor types, and geographic regions. Extensive evaluations across multiple RGB-T benchmarks demonstrate that ThermalGen achieves comparable or superior translation performance compared to existing GAN-based and diffusion-based methods. To our knowledge, ThermalGen is the first RGB-T image translation model capable of synthesizing thermal images that reflect significant variations in viewpoints, sensor characteristics, and environmental conditions. Project page: http://xjh19971.github.io/ThermalGen

In the era of large-scale foundation models, fully fine-tuning pretrained networks for each downstream task is often prohibitively resource-intensive. Prompt tuning offers a lightweight alternative by introducing tunable prompts while keeping the backbone frozen. However, existing visual prompt tuning methods often fail to specialize the prompts or enrich the representation space--especially when applied to self-supervised backbones. We show that these limitations become especially pronounced in challenging tasks and data-scarce settings, where effective adaptation is most critical. In this work, we introduce VIPAMIN, a visual prompt initialization strategy that enhances adaptation of self-supervised models by (1) aligning prompts with semantically informative regions in the embedding space, and (2) injecting novel representational directions beyond the pretrained subspace. Despite its simplicity--requiring only a single forward pass and lightweight operations--VIPAMIN consistently improves performance across diverse tasks and dataset sizes, setting a new state of the art in visual prompt tuning.

Recent advances in large vision-language models (LVLMs) have demonstrated strong performance on general-purpose medical tasks. However, their effectiveness in specialized domains such as dentistry remains underexplored. In particular, panoramic X-rays, a widely used imaging modality in oral radiology, pose interpretative challenges due to dense anatomical structures and subtle pathological cues, which are not captured by existing medical benchmarks or instruction datasets. To this end, we introduce MMOral, the first large-scale multimodal instruction dataset and benchmark tailored for panoramic X-ray interpretation. MMOral consists of 20,563 annotated images paired with 1.3 million instruction-following instances across diverse task types, including attribute extraction, report generation, visual question answering, and image-grounded dialogue. In addition, we present MMOral-Bench, a comprehensive evaluation suite covering five key diagnostic dimensions in dentistry. We evaluate 64 LVLMs on MMOral-Bench and find that even the best-performing model, i.e., GPT-4o, only achieves 43.31% accuracy, revealing significant limitations of current models in this domain. To promote the progress of this specific domain, we provide the supervised fine-tuning (SFT) process utilizing our meticulously curated MMOral instruction dataset. Remarkably, a single epoch of SFT yields substantial performance enhancements for LVLMs, e.g., Qwen2.5-VL-7B demonstrates a 24.73% improvement. MMOral holds significant potential as a critical foundation for intelligent dentistry and enables more clinically impactful multimodal AI systems in the dental field.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis across diverse models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had a high probability of being mutagenic. In this work, we introduce Medex, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. Medex consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or RefSeq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLaVA architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). Medex is highly effective for creating models with strong priors: in supervised prediction problems that use our data for pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with Medex can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset on HuggingFace at https://huggingface.co/datasets/DocAndDesign/Medex, and will provide expanded versions as the available literature grows.

Misinformation detectors often rely on superficial cues (i.e., shortcuts) that correlate with misinformation in training data but fail to generalize to the diverse and evolving nature of real-world misinformation. This issue is exacerbated by large language models (LLMs), which can easily generate convincing misinformation using simple prompts. We introduce TruthOverTricks, a unified evaluation paradigm for measuring shortcut learning in misinformation detection. TruthOverTricks categorizes shortcut behaviors into intrinsic shortcut induction and extrinsic shortcut injection, and evaluates seven representative detectors across 14 popular benchmarks, along with two new factual misinformation datasets, NQ-Misinfo and Streaming-Misinfo. Empirical results reveal that existing detectors suffer severe performance degradation when exposed to both naturally occurring and adversarially crafted shortcuts. To address this, we propose the Shortcut Mitigation Framework (SMF), an LLM-augmented data augmentation framework that mitigates shortcut reliance through paraphrasing, factual summarization, and sentiment normalization. SMF consistently enhances robustness across 16 benchmarks, forcing models to rely on deeper semantic understanding rather than shortcut cues.

Local convergence has emerged as a fundamental tool for analyzing sparse random graph models. We introduce a new notion of local convergence, _color convergence_, based on the Weisfeiler–Leman algorithm. Color convergence fully characterizes the class of random graphs that are well-behaved in the limit for message-passing graph neural networks. Building on this, we propose the _Refined Configuration Model_ (RCM), a random graph model that generalizes the configuration model. The RCM is universal with respect to local convergence among locally tree-like random graph models, including Erdős–Rényi, stochastic block and configuration models. Finally, this framework enables a complete characterization of the random trees that arise as local limits of such graphs.

Large language models (LLMs) process entire input contexts indiscriminately, which is inefficient when the information required to answer a query is localized within the context. We present dynamic context cutoff, a novel method enabling LLMs to self-terminate processing upon acquiring sufficient task-relevant information. Through analysis of model internals, we discover that specific attention heads inherently encode "sufficiency signals" -- detectable through lightweight classifiers -- that predict when critical information has been processed. This reveals a new efficiency paradigm: models' internal understanding naturally dictates processing needs rather than external compression heuristics. Comprehensive experiments across six QA datasets (up to 40K tokens) with three model families (LLaMA/Qwen/Mistral, 1B-70B) demonstrate 3.4% accuracy improvement while achieving 1.33x token reduction on average. Furthermore, our method demonstrates superior performance compared to other context efficiency methods at equivalent token reduction rates. Additionally, we observe an emergent scaling phenomenon: while smaller models require probing for sufficiency detection, larger models exhibit intrinsic self-assessment capabilities through prompting.

LLM-based agents have shown promising capabilities in a growing range of software engineering (SWE) tasks. However, advancing this field faces two critical challenges. First, high-quality training data is scarce, especially data that reflects real-world SWE scenarios, where agents must interact with development environments, execute code and adapt behavior based on the outcomes of their actions. Existing datasets are either limited to one-shot code generation or comprise small, manually curated collections of interactive tasks, lacking both scale and diversity. Second, the lack of fresh interactive SWE tasks affects evaluation of rapidly improving models, as static benchmarks quickly become outdated due to contamination issues. To address these limitations, we introduce a novel, automated, and scalable pipeline to continuously extract real-world interactive SWE tasks from diverse GitHub repositories. Using this pipeline, we construct SWE-rebench, a public dataset comprising over 21,000 interactive Python-based SWE tasks, suitable for reinforcement learning of SWE agents at scale. Additionally, we use continuous supply of fresh tasks collected using SWE-rebench methodology to build a contamination-free benchmark for agentic software engineering. We compare results of various LLMs on this benchmark to results on SWE-bench Verified and show that performance of some language models might be inflated due to contamination issues.

The rapid advancement of native multi-modal models and omni-models, exemplified by GPT-4o, Gemini and o3 with their capability to process and generate content across modalities such as text and images, marks a significant milestone in the evolution of intelligence. Systematic evaluation of their multi-modal output capabilities in visual thinking process (a.k.a., multi-modal chain of thought, M-CoT) becomes critically important. However, existing benchmarks for evaluating multi-modal models primarily focus on assessing multi-modal inputs and text-only reasoning process while neglecting the importance of reasoning through multi-modal outputs. In this paper, we present a benchmark, dubbed as RBench-V, designed to assess models’ vision-indispensable reasoning. To conduct RBench-V, we carefully hand-pick 803 questions covering math, physics, counting and games. Unlike problems in previous benchmarks, which typically specify certain input modalities, RBench-V presents problems centered on multi-modal outputs, which require image manipulation, such as generating novel images and constructing auxiliary lines to support reasoning process. We evaluate numerous open- and closed-source models on RBench-V, including o3, Gemini 2.5 pro, Qwen2.5-VL, etc. Even the best-performing model, o3, achieves only 25.8% accuracy on RBench-V, far below the human score of 82.3%, which shows current models struggle to leverage multi-modal reasoning. Data and code are available at https://evalmodels.github.io/rbenchv.

Urban computing harnesses big data to decode complex urban dynamics and revolutionize location-based services. Traditional approaches have treated geospatial prediction tasks (e.g., estimating socio-economic indicators) and retrieval tasks (e.g., querying geographic objects) as isolated challenges, necessitating separate models with distinct training objectives. This fragmentation imposes significant computational burdens and limits cross-task synergy, despite advances in representation learning and multi-task foundation models. We present UrbanSparse, a pioneering framework that unifies geospatial prediction and retrieval through a novel sparse-dense representation architecture. By synergistically combining these tasks, UrbanSparse eliminates redundant systems while amplifying their mutual strengths. Our approach introduces two innovations: (1) Bloom filter-based sparse encodings that compress high-sparsity geographic queries and fine-grained text terms for retrieval effectiveness, and (2) a dense semantic codebook that captures granular urban features to boost prediction accuracy. A two-view contrastive learning mechanism further bridges urban objects, regions, and contexts. Experiments on real-world datasets demonstrate 25.16% gains in prediction accuracy and 20.76% improvements in retrieval precision over state-of-the-art baselines, alongside 65.97% faster training. These advantages position UrbanSparse as a scalable solution for large urban datasets. To our knowledge, this is the first unified framework bridging geospatial prediction and retrieval, opening new frontiers in data-driven urban intelligence.

Virtual footwear try-on (VFTON), a critical yet underexplored area in virtual try-on (VTON), aims to synthesize faithful try-on results given diverse footwear and model images while maintaining 3D consistency and texture authenticity. Unlike conventional garment-focused VTON methods, VFTON presents unique challenges due to (1) Data Scarcity, which arises from the difficulty of perfectly matching product shoes with models wearing the identical ones, (2) Viewpoint Misalignment, where the target foot pose and source shoe views are always misaligned, leading to incomplete texture information and detail distortion, and (3) Background-induced Color Distortion, where complex material of footwear interacts with environmental lighting, causing unintended color contamination. To address these challenges, we introduce MVShoes, a multi-view shoe try-on dataset consisting of 7305 well-annotated image triplets, covering diverse footwear categories and challenging try-on scenarios. Furthermore, we propose a dual-stream DiT architecture, ShoeFit, designed to mitigate viewpoint misalignment through Multi-View Conditioning with 3D Rotary Position Embedding, and alleviate background-induced distortion using the LayeredRefAttention which leverages background features to modulate footwear latents. The proposed framework effectively decouples shoe appearance from environmental interferences while preserving high-quality texture detail through decoupled denoising and conditioning branches. Extensive quantitative and qualitative experiments demonstrate that our method substantially improves rendering fidelity and robustness under challenging real-world product shoes, establishing a new benchmark in high-fidelity footwear try-on synthesis. The dataset and benchmark will be publicly available upon acceptance of the paper.

We consider the problem of identifying the best arm in a multi-armed bandit model. Despite a wealth of literature in the traditional fixed budget and fixed confidence regimes of the best arm identification problem, it still remains a mystery to most practitioners as to how to choose an approach and corresponding budget or confidence parameter. We propose a new formalism to avoid this dilemma altogether by minimizing a risk functional which explicitly balances the performance of the recommended arm and the cost incurred by learning this arm. In this framework, a cost is incurred for each observation during the sampling phase, and upon recommending an arm, a performance penalty is incurred for identifying a suboptimal arm. The learner's goal is to minimize the sum of the penalty and cost. This new regime mirrors the priorities of many practitioners, e.g. maximizing profit in an A/B testing framework, better than classical fixed budget or confidence settings. We derive theoretical lower bounds for the risk of each of two choices for the performance penalty, the probability of misidentification and the simple regret, and propose an algorithm called DBCARE to match these lower bounds up to polylog factors on nearly all problem instances. We then demonstrate the performance of DBCARE on a number of simulated models, comparing to fixed budget and confidence algorithms to show the shortfalls of existing BAI paradigms on this problem.

Large Language Models (LLMs) offer substantial promise for clinical natural language processing (NLP); however, a lack of standardized benchmarking methodologies limits their objective evaluation and practical translation. To address this gap, we introduce ClinBench, an open-source, multi-model, multi-domain benchmarking framework. ClinBench is designed for the rigorous evaluation of LLMs on important structured information extraction tasks (e.g., tumor staging, histologic diagnoses, atrial fibrillation, and social determinants of health) from unstructured clinical notes. The framework standardizes the evaluation pipeline by: (i) operating on consistently structured input datasets; (ii) employing dynamic, YAML-based prompting for uniform task definition; and (iii) enforcing output validation via JSON schemas, supporting robust comparison across diverse LLM architectures. We demonstrate ClinBench through a large-scale study of 11 prominent LLMs (e.g., GPT-4o series, LLaMA3 variants, Mixtral) across three clinical domains using configurations of public datasets (TCGA for lung cancer, MIMIC-IV-ECG for atrial fibrillation, and MIMIC notes for SDOH). Our results reveal significant performance-efficiency trade-offs. For example, when averaged across the four benchmarked clinical extraction tasks, GPT-3.5-turbo achieved a mean F1 score of 0.83 with a mean runtime of 16.8 minutes. In comparison, LLaMA3.1-70b obtained a similar mean F1 of 0.82 but required a substantially longer mean runtime of 42.7 minutes. GPT-4o-mini also presented a favorable balance with a mean F1 of 0.81 and a mean runtime of 13.4 minutes. ClinBench provides a unified, extensible framework and empirical insights for reproducible, fair LLM benchmarking in clinical NLP. By enabling transparent and standardized evaluation, this work advances data-centric AI research, informs model selection based on performance, cost, and clinical priorities, and supports the effective integration of LLMs into healthcare. The framework and evaluation code are publicly available at https://github.com/ismaelvillanuevamiranda/ClinBench/.

The practical use of reinforcement learning (RL) requires handling diverse settings, including online, offline, and offline-to-online learning. Instead of developing separate algorithms for each setting, we propose Uni-RL, a unified model-free RL framework that addresses all these scenarios within a single formulation. Uni-RL builds on the Implicit Value Regularization (IVR) framework and generalizes its dataset behavior constraint to the constraint w.r.t a reference policy, yielding an unified value learning objective for general settings. The reference policy is chosen to be the target policy in the online setting and the behavior policy in the offline setting. Using an iteratively refined behavior policy solves the over-constrained problem of directly applying IVR in the online setting, it provides an implicit trust-region style update through the value function while being off-policy. Uni-RL also introduces an unified policy extraction objective that estimates in-sample policy gradient using only actions from the reference policy. This supports various policy classes and theoretically guaranntees less value estimation error and larger performance improvement over the reference policy. We evaluate Uni-RL on a range of standard RL benchmarks across online, offline, and offline-to-online settings. In online RL, Uni-RL achieves higher sample efficiency than both off-policy methods without trust-region updates and on-policy methods with trust-region updates. In offline RL, Uni-RL retains the benefits of in-sample learning while outperforming IVR through better policy extraction. In offline-to-online RL, Uni-RL beats both constraint-based methods and unconstrained approaches by effectively balancing stability and adaptability.

Evaluating large language models (LLMs) is crucial for both assessing their capabilities and identifying safety or robustness issues prior to deployment. Reliably measuring abstract and complex phenomena such as `safety' and `robustness' requires strong construct validity, that is, having measures that represent what matters to the phenomenon. With a team of 29 expert reviewers, we conduct a systematic review of 445 LLM benchmarks from leading conferences in natural language processing and machine learning. Across the reviewed articles, we find patterns related to the measured phenomena, tasks, and scoring metrics which undermine the validity of the resulting claims. To address these shortcomings, we provide eight key recommendations and detailed actionable guidance to researchers and practitioners in developing LLM benchmarks.