NeurIPS 2025 Papers

Visual generative and understanding models typically rely on distinct tokenizers to process images, presenting a key challenge for unifying them within a single framework. Recent studies attempt to address this by connecting the training of VQVAE (for autoregressive generation) and CLIP (for understanding) to build a unified tokenizer. However, directly combining these training objectives has been observed to cause severe loss conflicts. In this paper, we show that reconstruction and semantic supervision do not inherently conflict. Instead, the underlying bottleneck stems from limited representational capacity of discrete token space. Building on these insights, we introduce UniTok, a unified tokenizer featuring a novel multi-codebook quantization mechanism that effectively scales up the vocabulary size and bottleneck dimension. In terms of final performance, UniTok sets a new record of 0.38 rFID and 78.6\% zero-shot accuracy on ImageNet. Besides, UniTok can be seamlessly integrated into MLLMs to unlock native visual generation capability, without compromising the understanding performance. Additionally, we show that UniTok favors cfg-free generation, reducing gFID from 14.6 to 2.5 on ImageNet 256$\times$256 benchmark. All codes and models have been made publicly available.

The ubiquity of dynamic data in domains such as weather, healthcare, and energy underscores a growing need for effective interpretation and retrieval of time-series data. These data are inherently tied to domain-specific contexts, such as clinical notes or weather narratives, making cross-modal retrieval essential not only for downstream tasks but also for developing robust time-series foundation models by retrieval-augmented generation (RAG). Despite the increasing demand, time-series retrieval remains largely underexplored. Existing methods often lack semantic grounding, struggle to align heterogeneous modalities, and have limited capacity for handling multi-channel signals. To address this gap, we propose TRACE, a generic multimodal retriever that grounds time-series embeddings in aligned textual context. TRACE enables fine-grained channel-level alignment and employs hard negative mining to facilitate semantically meaningful retrieval. It supports flexible cross-modal retrieval modes, including Text-to-Timeseries and Timeseries-to-Text, effectively linking linguistic descriptions with complex temporal patterns. By retrieving semantically relevant pairs, TRACE enriches downstream models with informative context, leading to improved predictive accuracy and interpretability. Beyond a static retrieval engine, TRACE also serves as a powerful standalone encoder, with lightweight task-specific tuning that refines context-aware representations while maintaining strong cross-modal alignment. These representations achieve state-of-the-art performance on downstream forecasting and classification tasks. Extensive experiments across multiple domains highlight its dual utility, as both an effective encoder for downstream applications and a general-purpose retriever to enhance time-series models.

Spurious correlations occur when models rely on non-essential features that coincidentally co-vary with target labels, leading to incorrect reasoning under distribution shift. We consider spurious correlations in multi-modal Large Vision Language Models (LVLMs) pretrained on extensive and diverse datasets without explicit task supervision. We develop a benchmark by sourcing GPT-4o errors on real-world visual-question-answering (VQA) benchmarks, then curating a subset through LVLM-human annotation and synthetic counterfactual evaluation to identify errors caused by spurious correlations. This process yields SpuriVerse, a novel benchmark comprised of 124 distinct types of spurious correlations extracted from real-world datasets, each containing 1 realistic and 10 synthetic VQA samples for a total of 1364 multiple choice questions. We evaluate 15 open and closed-source LVLMs on SpuriVerse, finding that even state-of-the-art closed-source models struggle significantly, achieving at best only 35.0\% accuracy. Fine-tuning on synthetic examples that emphasize the spurious correlation improves performance to 78.4\%, suggesting that training on diverse spurious patterns generalizes to unseen situations: models appear to learn to avoid "shortcuts" and attend to the overall image context.

Large Language Models (LLMs) excel at natural language processing tasks, but their massive size leads to high computational and storage demands. Recent works have sought to reduce their model size through layer-wise structured pruning. However, they tend to ignore retaining the capabilities in the pruned part. In this work, we re-examine structured pruning paradigms and uncover several key limitations: 1) notable performance degradation due to direct layer removal, 2) incompetent linear weighted layer aggregation, and 3) the lack of effective post-training recovery mechanisms. To address these limitations, we propose CoMe, including a progressive layer pruning framework with a Concatenation-based Merging technology and a hierarchical distillation post-training process. Specifically, we introduce a channel sensitivity metric that utilizes activation intensity and weight norms for fine-grained channel selection. Subsequently, we employ a concatenation-based layer merging method to fuse the most critical channels in the adjacent layers, enabling a progressive model size reduction. Finally, we propose a hierarchical distillation protocol, which leverages the correspondences between the original and pruned model layers established during pruning, enabling efficient knowledge transfer. Experiments on seven benchmarks show that CoMe achieves state-of-the-art performance; when pruning 30% of LLaMA-2-7b's parameters, the pruned model retains 83% of its original average accuracy.

Air pollution was responsible for 2.6 million deaths across South Asia in 2021 alone, with brick manufacturing contributing significantly to this burden. In particular, the Indo-Gangetic Plain; a densely populated and highly polluted region spanning northern India, Pakistan, Bangladesh, and parts of Afghanistan sees brick kilns contributing 8–14% of ambient air pollution. Traditional monitoring approaches, such as field surveys and manual annotation using tools like Google Earth Pro, are time and labor-intensive. Prior ML-based efforts for automated detection have relied on costly high-resolution commercial imagery and non-public datasets, limiting reproducibility and scalability. In this work, we introduce SENTINELKILNDB, a publicly available, hand-validated benchmark of 62,671 brick kilns spanning three kiln types Fixed Chimney Bull’s Trench Kiln (FCBK), Circular FCBK (CFCBK), and Zigzag kilns - annotated with oriented bounding boxes (OBBs) across 2.8 million km2 using free and globally accessible Sentinel-2 imagery. We benchmark state-of-the-art oriented object detection models and evaluate generalization across in-region, out-of-region, and super-resolution settings. SENTINELKILNDB enables rigorous evaluation of geospatial generalization and robustness for low-resolution object detection, and provides a new testbed for ML models addressing real-world environmental and remote sensing challenges at a continental scale. Datasets and code are available in SentinelKilnDB Dataset and SentinelKilnDB Bench- mark, under the Creative Commons Attribution–NonCommercial 4.0 International License.

Building state-of-the-art Vision-Language Models (VLMs) with strong captioning capabilities typically necessitates training on billions of high-quality image-text pairs, requiring millions of GPU hours. This paper introduces the Vision-Language-Vision **(VLV)** auto-encoder framework, which strategically leverages key pretrained components: a vision encoder, the decoder of a Text-to-Image (T2I) diffusion model, and subsequently, a Large Language Model (LLM). Specifically, we establish an information bottleneck by regularizing the language representation space, achieved through freezing the pretrained T2I diffusion decoder. Our VLV pipeline effectively distills knowledge from the text-conditioned diffusion model using continuous embeddings, demonstrating comprehensive semantic understanding via high-quality reconstructions. Furthermore, by fine-tuning a pretrained LLM to decode the intermediate language representations into detailed descriptions, we construct a state-of-the-art (SoTA) captioner comparable to leading models like GPT-4o and Gemini 2.0 Flash. Our method demonstrates exceptional cost-efficiency and significantly reduces data requirements; by primarily utilizing single-modal images for training and maximizing the utility of existing pretrained models (image encoder, T2I diffusion model, and LLM), it circumvents the need for massive paired image-text datasets, keeping the total training expenditure under $1,000 USD.

Neurosymbolic AI is growing in popularity thanks to its ability to combine neural perception and symbolic reasoning in end-to-end trainable models. However, recent findings reveal these are prone to shortcut reasoning, i.e., to learning unindented concepts--or neural predicates--which exploit spurious correlations to satisfy the symbolic constraints. In this paper, we address reasoning shortcuts at their root cause and we introduce prototypical neurosymbolic architectures. These models are able to satisfy the symbolic constraints (be right) because they have learnt the correct basic concepts (for the right reasons) and not because of spurious correlations, even in extremely low data regimes. Leveraging the theory of prototypical learning, we demonstrate that we can effectively avoid reasoning shortcuts by training the models to satisfy the background knowledge while taking into account the similarity of the input with respect to the handful of labelled datapoints. We extensively validate our approach on the recently proposed rsbench benchmark suite in a variety of settings and tasks with very scarce supervision: we show significant improvements in learning the right concepts both in synthetic tasks (MNIST-EvenOdd and Kand-Logic) and real-world, high-stake ones (BDD-OIA). Our findings pave the way to prototype grounding as an effective, annotation-efficient strategy for safe and reliable neurosymbolic learning.

Vision–language models (VLMs) excel at zero-shot inference but often degrade under test-time domain shifts. For this reason, episodic test-time adaptation strategies have recently emerged as powerful techniques for adapting VLMs to a single unlabeled image. However, existing adaptation strategies, such as test-time prompt tuning, typically require backpropagating through large encoder weights or altering core model components. In this work, we introduce \textbf{S}pectrum-Aware \textbf{T}est-Time \textbf{S}teering (\textbf{STS}), a \textit{lightweight adaptation framework} that extracts a spectral subspace from the textual embeddings to define principal semantic directions, and learns to steer latent representations in a spectrum-aware manner by adapting a small number of per-sample shift parameters to minimize entropy across augmented views. STS operates entirely at inference in the latent space, without backpropagation through or modification of the frozen encoders. Building on standard evaluation protocols, our comprehensive experiments demonstrate that STS largely surpasses or compares favorably against state-of-the-art test-time adaptation methods, while introducing only a handful of additional parameters and achieving inference speeds up to 8× faster with a 12× smaller memory footprint than conventional test-time prompt tuning. The code is available at \url{https://github.com/kdafnis/STS}.

Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80.000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.56% relative average improvement in mean Average Precision over the second-best method adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.

The task of geometry problem solving has been a long-standing focus in the automated mathematics community and draws growing attention due to its complexity for both symbolic and neural models. Although prior studies have explored various effective approaches for enhancing problem solving performances, two fundamental challenges remain unaddressed, which are essential to the application in practical scenarios. First, the multi-step reasoning gap between the initial geometric conditions and ultimate problem goal leads to a great search space for solution exploration. Second, obtaining multiple interpretable and shorter solutions remains an open problem. In this work, we introduce the Causal-Reasoning Geometry Problem Solver to overcome these challenges. Specifically, the Causal Graph Reasoning theory is proposed to perform symbolic reasoning before problem solving. Several causal graphs are constructed according to predefined rule base, where each graph is composed of primitive nodes, causal edges and prerequisite edges. By applying causal graph deduction from initial conditions, the reachability status of nodes are iteratively conveyed by causal edges until reaching the target nodes, representing feasible causal deduction paths. In this way, the search space of solutions is compressed from the beginning, the end and intermediate reasoning paths, while ensuring the interpretability and variety of solutions. To achieve this, we further propose Forward Matrix Deduction which transforms the causal graphs into matrices and vectors, and applies matrix operations to update the status value of reachable nodes in iterations. Finally, multiple solutions can be generated by tracing back from the target nodes after validation. Experiments demonstrate the effectiveness of our method to obtain multiple shorter and interpretable solutions. Code is available after acceptance.

Out-of-distribution (OOD) detection, recognized for its ability to identify samples of unknown classes, provides solid advantages in ensuring the reliability of machine learning models. Among existing OOD detection methods, pre-trained vision-language models have emerged as powerful post-hoc OOD detectors by leveraging textual and visual information. Despite the empirical success, there still remains a lack of research on a formal understanding of their effectiveness. This paper bridges the gap by theoretically demonstrating that existing CLIP-based post-hoc methods effectively perform a stochastic estimation of the point-wise mutual information (PMI) between the input image and each in-distribution label. This estimation is then utilized to construct energy functions for modeling in-distribution distributions. Different from prior methods that inherently consider PMI estimation as a whole task, we, motivated by the divide-and-conquer philosophy, decompose PMI estimation into multiple easier sub-tasks by applying the chain rule of PMI, which not only reduces the estimation complexity but also provably increases the estimation upper bound to reduce the underestimation bias. Extensive evaluations across mainstream benchmarks empirically manifest that our method establishes a new state-of-the-art in a variety of OOD detection setups.

Recent multimodal embedding approaches leveraging multimodal large language models (MLLMs) fine-tuned with contrastive learning (CL) have shown promising results, yet the underlying reasons behind their superiority remain underexplored. This work argues that a crucial advantage of MLLM-based approaches stems from implicit cross-modal alignment achieved during generative pretraining, where the language decoder learns to exploit multimodal signals within a shared representation space for generating unimodal outputs. Through analysis of anisotropy and kernel similarity structure, we empirically confirm that latent alignment emerges within MLLM representations, allowing CL to serve as a lightweight refinement stage. Leveraging this insight, we propose a Language-Centric Omnimodal Embedding framework, termed LCO-Embed. Extensive experiments across diverse backbones and benchmarks demonstrate its effectiveness, achieving state-of-the-art performance across modalities. Furthermore, we identify a Generation-Representation Scaling Law (GRSL), showing that the representational capabilities gained through contrastive refinement scale positively with the MLLM's generative capabilities. This suggests that improving generative abilities evolves as an effective paradigm for enhancing representation quality. We provide a theoretical explanation of GRSL, which formally links the MLLM's generative quality to the upper bound on its representation performance, and validate it on a challenging, low-resource visual-document retrieval task, showing that continual generative pretraining before CL can further enhance the potential of a model's embedding capabilities. Codes, models, and resources are available at https://github.com/LCO-Embedding/LCO-Embedding.

Relighting is a crucial task with both practical demand and artistic value, and recent diffusion models have shown strong potential by enabling rich and controllable lighting effects. However, as they are typically optimized in semantic latent space, where proximity does not guarantee physical correctness in visual space, they often produce unrealistic results—such as overexposed highlights, misaligned shadows, and incorrect occlusions. We address this with **UniLumos**, a unified relighting framework for both images and videos that brings RGB-space geometry feedback into a flow-matching backbone. By supervising the model with depth and normal maps extracted from its outputs, we explicitly align lighting effects with the scene structure, enhancing physical plausibility. Nevertheless, this feedback requires high-quality outputs for supervision in visual space, making standard multi-step denoising computationally expensive. To mitigate this, we employ path consistency learning, allowing supervision to remain effective even under few-step training regimes. To enable fine-grained relighting control and supervision, we design a structured six-dimensional annotation protocol capturing core illumination attributes. Building upon this, we propose **LumosBench**, a disentangled attribute-level benchmark that evaluates lighting controllability via large vision-language models, enabling automatic and interpretable assessment of relighting precision across individual dimensions. Extensive experiments demonstrate that UniLumos achieves state-of-the-art relighting quality with significantly improved physical consistency, while delivering a 20x speedup for both image and video relighting. Code is available at https://github.com/alibaba-damo-academy/Lumos-Custom.

Group Relative Policy Optimization (GRPO) fine-tuning has been empirically shown to significantly enhance the reasoning abilities of language models. However, it often relies on large-scale, high-quality labeled data, which is typically difficult to obtain. To address this challenge, we introduce the Noise-Aware Dual-Reward Optimization (NaDRO) , which effectively enhances LLMs training in environments where data is noisy or imperfect. NaDRO operates through two key components: \textbf{(1) Preference-based Outcome Reward (POR)}, which extracts reliable preference signals from noisy data, guiding LLMs towards more effective decisions instead of relying on specific noisy scores; and \textbf{(2) a Context Perception Reward (CPR) mechanism}, which ensures that LLMs conduct necessary qualitative assessment of the current problem state, rewarding accurate judgments to foster better cognitive understanding before decision-making. In the context of combinatorial optimization problems, where dynamically selecting heuristic algorithms is challenging due to large problem scales and the difficulty of obtaining accurate decision data, we designed experiments to test our approach. Our results indicate that the fine-tuned Qwen 7B and Llama 3-8B models outperform mainstream large language models (LLMs) training in this task. Code is released at \url{https://anonymous.4open.science/r/NaDRO-D34D}

Large language models (LLMs) have achieved impressive results on complex reasoning tasks, but their high inference cost remains a major barrier to real-world deployment. A promising solution is to use cascaded inference, where small, cheap models handle easy queries, and only the hardest examples are escalated to more powerful models. However, existing cascade methods typically rely on supervised training with labeled data, offer no theoretical generalization guarantees, and provide limited control over test-time computational cost. We introduce **C3PO** (*Cost Controlled Cascaded Prediction Optimization*), a self-supervised framework for optimizing LLM cascades under probabilistic cost constraints. By focusing on minimizing regret with respect to the most powerful model (MPM), C3PO avoids the need for labeled data by constructing a cascade using only unlabeled model outputs. It leverages conformal prediction to bound the probability that inference cost exceeds a user-specified budget. We provide theoretical guarantees on both cost control and generalization error, and show that our optimization procedure is effective even with small calibration sets. Empirically, C3PO achieves state-of-the-art performance across a diverse set of reasoning benchmarks including GSM8K, MATH-500, BigBench-Hard and AIME, outperforming strong LLM cascading baselines in both accuracy and cost-efficiency. Our results demonstrate that principled, label-free cascade optimization can enable scalable LLM deployment.

Data attribution methods quantify the influence of training data on model outputs and are becoming increasingly relevant for a wide range of LLM research and applications, including dataset curation, model interpretability, data valuation. However, there remain critical gaps in systematic LLM-centric evaluation of data attribution methods. To this end, we introduce DATE-LM (Data Attribution Evaluation in Language Models), a unified benchmark for evaluating data attribution methods through real-world LLM applications. DATE-LM measures attribution quality through three key tasks — training data selection, toxicity/bias filtering, and factual attribution. Our benchmark is designed for ease of use, enabling researchers to configure and run large-scale evaluations across diverse tasks and LLM architectures. Furthermore, we use DATE-LM to conduct a large-scale evaluation of existing data attribution methods. Our findings show that no single method dominates across all tasks, data attribution methods have trade-offs with simpler baselines, and method performance is sensitive to task-specific evaluation design. Finally, we release a public leaderboard for quick comparison of methods and to facilitate community engagement. We hope DATE-LM serves as a foundation for future data attribution research in LLMs.

In the molecular domain, numerous studies have explored the use of multimodal large language models (LLMs) to construct a general-purpose, multi-task molecular model. However, these efforts are still far from achieving a truly universal molecular model. We identify three key challenges in this endeavor: (1) Existing molecular task datasets are typically small in scale and lack comprehensive domain coverage. (2) Tasks from different molecular subfields are difficult to effectively learn jointly through LLMs due to significant distributional shifts and competition among tasks, which introduces instability in the learning process. (3) Both inter-task and intra-task molecular representations demand different intrinsic dimensions in the language space, making it challenging to balance between redundancy and insufficiency in language model representations. To address these challenges, we innovatively categorize existing small-molecule tasks into four types: Mol2Mol, Mol2Text, Mol2Num, and Text2Mol. We then collect a dataset encompassing over 16 tasks with more than 1.4 million samples, making it the largest molecular instruction-tuning dataset to date. Leveraging the extensive pretraining of LLMs on existing chemical literature, we propose a novel multimodal LLM framework, named **Omni-Mol**, which unifies all small-molecule tasks and supports both molecular generation and understanding. The core of Omni-Mol is our proposed MoGE, which dynamically adapts to the intrinsic rank of different tasks. This mixture-of-experts architecture enhances the model's ability to handle diverse tasks and modalities effectively. Our model achieves unified instruction tuning across 16 tasks and attains state-of-the-art performance on 13 of them. Extensive experiments further demonstrate the scalability and versatility of Omni-Mol.

Vision-language-action models (VLAs) show potential as generalist robot policies. However, these models pose extreme safety challenges during real-world deployment, including the risk of harm to the environment, the robot itself, and humans. *How can safety constraints be explicitly integrated into VLAs?* We address this by exploring an integrated safety approach (ISA), systematically **modeling** safety requirements, then actively **eliciting** diverse unsafe behaviors, effectively **constraining** VLA policies via safe reinforcement learning, and rigorously **assuring** their safety through targeted evaluations. Leveraging the constrained Markov decision process (CMDP) paradigm, ISA optimizes VLAs from a min-max perspective against elicited safety risks. Thus, policies aligned through this comprehensive approach achieve the following key features: (I) effective **safety-performance trade-offs**, reducing the cumulative cost of safety violations by 83.58\% compared to the state-of-the-art method, while also maintaining task success rate (+3.85\%). (II) strong **safety assurance**, with the ability to mitigate long-tail risks and handle extreme failure scenarios. (III) robust **generalization** of learned safety behaviors to various out-of-distribution perturbations. The effectiveness is evaluated on long-horizon mobile manipulation tasks.

Recent advances in vision language models (VLM) have been driven by contrastive models such as CLIP, which learn to associate visual information with their corresponding text descriptions. However, these models have limitations in understanding complex compositional scenes involving multiple objects and their spatial relationships. To address these challenges, we propose a novel approach that diverges from commonly used strategies that rely on the design of finegrained hard-negative augmentations. Instead, our work focuses on integrating inductive biases into the pretraining of CLIP-like models to improve their compositional understanding. To that end, we introduce a binding module that connects a scene graph, derived from a text description, with a slot-structured image representation, facilitating a structured similarity assessment between the two modalities. We also leverage relationships as text-conditioned visual constraints, thereby capturing the intricate interactions between objects and their contextual relationships more effectively. Our resulting model not only enhances the performance of CLIP-based models in multi-object compositional understanding but also paves the way towards more accurate and sample-efficient image-text matching of complex scenes.