NeurIPS 2025 Papers

Language-guided object recognition in remote sensing imagery is crucial for large-scale mapping and automated data annotation. However, existing open-vocabulary and visual grounding methods rely on explicit category cues, limiting their ability to handle complex or implicit queries that require advanced reasoning. To address this issue, we introduce a new suite of tasks, including Instruction-Oriented Object Counting, Detection, and Segmentation (InstructCDS), covering open-vocabulary, open-ended, and open-subclass scenarios. We further present EarthInstruct, the first InstructCDS benchmark for earth observation. It is constructed from two diverse remote sensing datasets with varying spatial resolutions and annotation rules across 20 categories, necessitating models to interpret dataset-specific instructions. Given the scarcity of semantically rich labeled data in remote sensing, we propose InstructSAM, a training-free framework for instruction-driven object recognition. InstructSAM leverages large vision-language models to interpret user instructions and estimate object counts, employs SAM2 for mask proposal, and formulates mask-label assignment as a binary integer programming problem. By integrating semantic similarity with counting constraints, InstructSAM efficiently assigns categories to predicted masks without relying on confidence thresholds. Experiments demonstrate that InstructSAM matches or surpasses specialized baselines across multiple tasks while maintaining near-constant inference time regardless of object count, reducing output tokens by 89\% and overall runtime by over 32\% compared to direct generation approaches. We believe the contributions of the proposed tasks, benchmark, and effective approach will advance future research in developing versatile object recognition systems. The code is available at https://VoyagerXvoyagerx.github.io/InstructSAM.

We present BrainODE, a neural ordinary differential equation (ODE)-based framework for modeling continuous longitudinal deformations of brain shapes. BrainODE learns a deformation space over anatomically meaningful brain regions to facilitate early prediction of neurodegenerative disease progression. Addressing inherent challenges of longitudinal neuroimaging data-such as limited sample sizes, irregular temporal sampling, and substantial inter-subject variability-we propose a conditional neural ODE architecture that models shape dynamics with subject-specific age and cognitive status. To enable autoregressive forecasting of brain morphology from a single observation, we propose a pseudo-cognitive status embedding that allows progressive shape prediction across intermediate time points with predicted cognitive decline. Experiments show that BrainODE outperforms time-aware baselines in predicting future brain shapes, demonstrating strong generalization across longitudinal datasets with both regular and irregular time intervals.

Multi-modality object Re-IDentification (ReID) targets to retrieve special objects by integrating complementary information from diverse visual sources. However, existing models that are trained on modality-complete datasets typically exhibit significantly degraded discrimination during inference with modality-incomplete inputs. This disparity highlights the necessity of developing a robust multi-modality ReID model that remains effective in real-world applications. For that, this paper delivers a flexible framework tailored for more realistic multi-modality retrieval scenario, dubbed as Miss-ReID, which is the first work to friendly support both the modality-missing training and inference conditions. The core of Miss-ReID lies in compensating for missing visual cues via vision-text knowledge transfer driven by Vision-Language foundation Models (VLMs), effectively mitigating performance degradation. In brief, we capture diverse visual features from accessible modalities first, and then build memory banks to store heterogeneous prototypes for each identity, preserving multi-modality characteristics. Afterwards, we employ structure-aware query interactions to dynamically distill modality-invariant object structures from existing localized visual patches, which are further reversed into pseudo-word tokens that encapsulate the identity-relevant structural semantics. In tandem, the inverted tokens, integrated with learnable modality prompts, are embedded into crafted textual template to form the personalized linguistic descriptions tailored for diverse modalities. Ultimately, harnessing VLMs' inherent vision-text alignment capability, the resulting textual features effectively function as compensatory semantic representations for missing visual modalities, after being optimized with some memory-based alignment constraints. Extensive experiments demonstrate our model's efficacy and superiority over state-of-the-art methods in various modality-missing scenarios, and our endeavors further propel multi-modality ReID into real-world applications.

The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein design. However, its direct use in training deep models that are sensitive to fine-grained atomic geometry—such as inverse folding—exposes a critical limitation. Comparative analysis of structural feature distributions reveals that AFDB structures exhibit distinct statistical regularities, reflecting a systematic geometric bias that deviates from the conformational diversity found in experimentally determined structures from the Protein Data Bank (PDB). While AFDB structures are cleaner and more idealized, PDB structures capture the intrinsic variability and physical realism essential for generalization in downstream tasks. To address this discrepancy, we introduce a Debiasing Structure AutoEncoder (DeSAE) that learns to reconstruct native-like conformations from intentionally corrupted backbone geometries. By training the model to recover plausible structural states, DeSAE implicitly captures a more robust and natural structural manifold. At inference, applying DeSAE to AFDB structures produces debiased structures that significantly improve inverse folding performance across multiple benchmarks. This work highlights the critical impact of subtle systematic biases in predicted structures and presents a principled framework for debiasing, significantly boosting the performance of structure-based learning tasks like inverse folding.

Vision-Language Models (VLMs) have achieved remarkable progress, yet their large scale often renders them impractical for resource-constrained environments. This paper introduces Unified Reinforcement and Imitation Learning (RIL), a novel and efficient training algorithm designed to create powerful, lightweight VLMs. RIL distinctively combines the strengths of reinforcement learning with adversarial imitation learning. This enables smaller student VLMs not only to mimic the sophisticated text generation of large teacher models but also to systematically improve their generative capabilities through reinforcement signals. Key to our imitation framework is a LLM-based discriminator that adeptly distinguishes between student and teacher outputs, complemented by guidance from multiple large teacher VLMs to ensure diverse learning. This unified learning strategy, leveraging both reinforcement and imitation, empowers student models to achieve significant performance gains, making them competitive with leading closed-source VLMs. Extensive experiments on diverse vision-language benchmarks demonstrate that RIL significantly narrows the performance gap with state-of-the-art open- and closed-source VLMs and, in several instances, surpasses them.

Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies. KINDLE trains a teacher model that integrates prior knowledge with temporal gene expression dynamics and subsequently distills this encoded knowledge to a student model, enabling accurate GRN inference solely from expression data without access to any prior. KINDLE achieves state-of-the-art performance across four benchmark datasets. Notably, it successfully identifies key transcription factors governing mouse embryonic development and precisely characterizes their functional roles. In mouse hematopoietic stem cell data, KINDLE accurately predicts fate transition outcomes following knockout of two critical regulators (Gata1 and Spi1). These biological validations demonstrate our framework's dual capability in maintaining topological inference precision while preserving discovery potential for novel biological mechanisms.

We propose Graph Consistency Regularization (GCR), a novel framework that injects relational graph structures, derived from model predictions, into the learning process to promote class-aware, semantically meaningful feature representations. Functioning as a form of *self-prompting*, GCR enables the model to refine its internal structure using its own outputs. While deep networks learn rich representations, these often capture noisy inter-class similarities that contradict the model's predicted semantics. GCR addresses this issue by introducing parameter-free *Graph Consistency Layers* (GCLs) at arbitrary depths. Each GCL builds a batch-level feature similarity graph and aligns it with a global, class-aware masked prediction graph, derived by modulating softmax prediction similarities with intra-class indicators. This alignment enforces that feature-level relationships reflect class-consistent prediction behavior, acting as a *semantic regularizer* throughout the network. Unlike prior work, GCR introduces a multi-layer, cross-space graph alignment mechanism with adaptive weighting, where layer importance is learned from graph discrepancy magnitudes. This allows the model to prioritize semantically reliable layers and suppress noisy ones, enhancing feature quality without modifying the architecture or training procedure. GCR is model-agnostic, lightweight, and improves semantic structure across various networks and datasets. Experiments show that GCR promotes cleaner feature structure, stronger intra-class cohesion, and improved generalization, offering a new perspective on learning from prediction structure.

Given an undirected, weighted $n$-vertex graph $G = (V, E, w)$, a Gomory-Hu tree $T$ is a weighted tree on $V$ that preserves the Min-$s$-$t$-Cut between any pair of vertices $s, t \in V$. Finding cuts in graphs is a key primitive in problems such as bipartite matching, spectral and correlation clustering, and community detection. We design a differentially private (DP) algorithm that computes an approximate Gomory-Hu tree. Our algorithm is $\varepsilon$-DP, runs in polynomial time, and can be used to compute $s$-$t$ cuts that are $\tilde{O}(n/\varepsilon)$-additive approximations of the Min-$s$-$t$-Cuts in $G$ for all distinct $s, t \in V$ with high probability. Our error bound is essentially optimal, since [Dalirrooyfard, Mitrovic and Nevmyvaka, Neurips 2023] showed that privately outputting a single Min-$s$-$t$-Cut requires $\Omega(n)$ additive error even with $(\varepsilon, \delta)$-DP and allowing for multiplicative error. Prior to our work, the best additive error bounds for approximate all-pairs Min-$s$-$t$-Cuts were $O(n^{3/2}/\varepsilon)$ for $\varepsilon$-DP [Gupta, Roth, Ullman, TCC 2009] and $\tilde{O}(\sqrt{mn}/ \varepsilon)$ for $(\varepsilon, \delta)$-DP [Liu, Upadhyay and Zou, SODA 2024], both achieved by DP algorithms that preserve all cuts in the graph. To achieve our result, we develop an $\varepsilon$-DP algorithm for the Minimum Isolating Cuts problem with near-linear error, and introduce a novel privacy composition technique combining elements of both parallel and basic composition to handle `bounded overlap' computational branches in recursive algorithms, which maybe of independent interest.

Linear attention has attracted interest as a computationally efficient approximation to softmax attention, especially for long sequences. Recent studies has explored distilling softmax attention in pre-trained Transformers into linear attention. However, a critical challenge remains: *how to choose the feature dimension that governs the approximation quality*. Existing methods fix this dimension uniformly across all attention layers, overlooking the diverse roles and complexities of them. In this paper, we propose a principled method to automatically determine the feature dimension in linear attention using the concept of statistical *degrees of freedom*, which represent the effective dimensionality of the inputs. We provide a theoretical bound on the approximation error and show that the dimension chosen by our method achieves smaller errors under a fixed computational budget. Furthermore, we introduce an efficient layerwise training strategy to learn nonlinear features tailored to each layer. Experiments on multiple pre-trained transformers demonstrate that our method improves the performance of distilled models compared to baselines without increasing the inference cost. Our findings also provide insight into how the complexity of the attention mechanism evolves across layers.

Securing personal identity against deepfake attacks is increasingly critical in the digital age, especially for celebrities and political figures whose faces are easily accessible and frequently targeted. Most existing deepfake detection methods focus on general-purpose scenarios and often ignore the valuable prior knowledge of known facial identities, e.g., "VIP individuals" whose authentic facial data are already available. In this paper, we propose **VIPGuard**, a unified multimodal framework designed to capture fine-grained and comprehensive facial representations of a given identity, compare them against potentially fake or similar-looking faces, and reason over these comparisons to make accurate and explainable predictions. Specifically, our framework consists of three main stages. First, we fine-tune a multimodal large language model (MLLM) to learn detailed and structural facial attributes. Second, we perform identity-level discriminative learning to enable the model to distinguish subtle differences between highly similar faces, including real and fake variations. Finally, we introduce user-specific customization, where we model the unique characteristics of the target face identity and perform semantic reasoning via MLLM to enable personalized and explainable deepfake detection. Our framework shows clear advantages over previous detection works, where traditional detectors mainly rely on low-level visual cues and provide no human-understandable explanations, while other MLLM-based models often lack a detailed understanding of specific face identities. To facilitate the evaluation of our method, we build a comprehensive identity-aware benchmark called **VIPBench** for personalized deepfake detection, involving the latest 7 face-swapping and 7 entire face synthesis techniques for generation. Extensive experiments show that our model outperforms existing methods in both detection and explanation. The code is available at https://github.com/KQL11/VIPGuard .

The fundamental challenge of long video understanding, e.g., question answering, lies in the extensive number of frames, making it infeasible to densely understand the local details while comprehensively digest the global contexts, especially within a limited context length. To address this problem, our insight is to process short video segments individually and combine these segment-level analyses into a final response. This intuition is noted in the well-established MapReduce principle in big data processing and is naturally compatible with inference scaling at the system level. Motivated by this, we propose MR. Video (pronounced as "mister video"), a long video understanding framework adopting the MapReduce principle. We define the standard operations of MapReduce in a long video understanding context: the Map steps conduct independent and sequence-parallel dense perception on short video segments, covering local details, while the Reduce steps comprehensively aggregate the segment-level results into an answer with global contexts. Thanks to the low cost and convenience of building video agents, we instantiate such Map and Reduce operations as an effective video agent capable of attending to local details and global contexts. Based on such abilities, we further introduce two critical yet previously under-explored long video understanding designs: (a) consistent character/object names in the captions, benefiting the reasoning of actions and stories across long horizons; (b) question intention analysis, which changes the key-frame retrieval in previous video agents to localizing the relevant information via jointly reasoning the whole video contexts and questions. Our MR. Video achieves a >7% accuracy improvement on the challenging LVBench over state-of-the-art video agents and vision-language models (VLMs) and demonstrates a clear advantage on multiple long video benchmarks, highlighting the potential of the MapReduce principle. The code is at https://github.com/ziqipang/MR-Video}{https://github.com/ziqipang/MR-Video.

Multimodal large language models (MLLMs) have achieved remarkable progress in video understanding. However, hallucination, where the model generates plausible yet incorrect outputs, persists as a significant and under-addressed challenge in the video domain. Among existing solutions, activation engineering has proven successful in mitigating hallucinations in LLMs and ImageLLMs, yet its applicability to VideoLLMs remains largely unexplored. In this work, we are the first to systematically investigate the effectiveness and underlying mechanisms of activation engineering for mitigating hallucinations in VideoLLMs. We initially conduct an investigation of the key factors affecting the performance of activation engineering and find that a model’s sensitivity to hallucination depends on $\textbf{temporal variation}$ rather than task type. Moreover, selecting appropriate internal modules and dataset for activation engineering is critical for reducing hallucination. Guided by these findings, we propose a temporal-aware activation engineering framework for VideoLLMs, which adaptively identifies and manipulates hallucination-sensitive modules based on the temporal variation characteristic, substantially mitigating hallucinations without additional LLM fine-tuning. Experiments across multiple models and benchmarks demonstrate that our method markedly reduces hallucination in VideoLLMs, thereby validating the robustness of our findings.

UAV tracking can be widely applied in scenarios such as disaster rescue, environmental monitoring, and logistics transportation. However, existing UAV tracking methods predominantly emphasize speed and lack exploration in semantic awareness, which hinders the search region from extracting accurate localization information from the template. The limitation results in suboptimal performance under typical UAV tracking challenges such as camera motion, fast motion, and low resolution, etc. To address this issue, we propose a dynamic semantic aware correlation modeling tracking framework. The core of our framework is a Dynamic Semantic Relevance Generator, which, in combination with the correlation map from the Transformer, explore semantic relevance. The approach enhances the search region's ability to extract important information from the template, improving accuracy and robustness under the aforementioned challenges. Additionally, to enhance the tracking speed, we design a pruning method for the proposed framework. Therefore, we present multiple model variants that achieve trade-offs between speed and accuracy, enabling flexible deployment according to the available computational resources. Experimental results validate the effectiveness of our method, achieving competitive performance on multiple UAV tracking datasets.

Mixture-of-Experts (MoE) architectures enable efficient scaling of large language models but face prohibitive memory demands due to massive parameterization. Existing pruning methods rely on heuristic metrics or impractical enumeration of expert subsets, leading to suboptimal performance or scalability. In this paper, we propose Shapley-MoE, an efficient pruning method for MoE models inspired by cooperative game theory. By quantifying each expert’s contribution via Shapley value, our method identifies important experts without exhaustive combination evaluations. To overcome the NP-hard complexity of exact Shapley computation, we introduce a Monte Carlo sampling strategy for efficient approximation that reduces complexity to quadratic time. However, vanilla Monte Carlo sampling still faces issues of insufficient estimation accuracy and low sampling efficiency. To address these issues, we further propose two novel methods to improve sampling accuracy and efficiency: (1) Early Truncation, which early terminates unstable sampling steps caused by overly small expert subsets, and (2) Router-Guided Importance Sampling, which prioritize sampling important expert subsets using gating activation probabilities. Both theoretical and experimental analyses show that both methods can accelerate Shapley value estimation and improve accuracy. Extensive empirical evaluations demonstrate that our pruned MoE models outperform existing expert pruning methods. Notably, when applied to the Qwen2-57B-A14B model, our method reduces the number of experts by 25% with only a 0.92 increase in perplexity and over 96.4% of the average zero-shot accuracy is maintained.

Structure-guided molecular generation is pivotal in early-stage drug discovery, enabling the design of compounds tailored to specific protein targets. However, despite recent advances in 3D generative modeling, particularly in improving docking scores, these methods often produce rare and intrinsically irrational molecular structures that deviate from drug-like chemical space. To quantify this issue, we propose a novel metric, the Molecule Reasonable Ratio (MRR), which measures structural rationality and reveals a critical gap between existing models and real-world approved drugs. To address this, we introduce the Collaborative Intelligence Drug Design (CIDD) framework, the first approach to unify the 3D interaction modeling capabilities of generative models with the general knowledge and reasoning power of large language models (LLMs). By leveraging LLM-based Chain-of-Thought reasoning, CIDD generates molecules that not only bind effectively to protein pockets but also exhibit strong structural drug-likeness, rationality, and synthetic accessibility. On the CrossDocked2020 benchmark, CIDD consistently improves drug-likeness metrics, including QED, SA, and MRR, across different base generative models, while maintaining competitive binding affinity. Notably, it raises the combined success rate (balancing drug-likeness and binding) from 15.72% to 34.59%, more than doubling previous results. These findings demonstrate the value of integrating knowledge reasoning with geometric generation to advance AI-driven drug design.

Intent classification models have made a significant progress in recent years. However, previous studies primarily focus on high-resource language datasets, which results in a gap for low-resource languages and for regions with high rates of illiteracy, where languages are more spoken than read or written. This is the case in Senegal, for example, where Wolof is spoken by around 90\% of the population, while the national illiteracy rate remains at of 42\%. Wolof is actually spoken by more than 10 million people in West African region. To address these limitations, we introduce the Wolof Banking Speech Intent Classification Dataset (WolBanking77), for academic research in intent classification. WolBanking77 currently contains 9,791 text sentences in the banking domain and more than 4 hours of spoken sentences. Experiments on various baselines are conducted in this work, including text and voice state-of-the-art models. The results are very promising on this current dataset. In addition, this paper presents an in-depth examination of the dataset’s contents. We report baseline F1-scores and word error rates metrics respectively on NLP and ASR models trained on WolBanking77 dataset and also comparisons between models. Dataset and code available at: [wolbanking77](https://github.com/abdoukarim/wolbanking77).

Federated Learning (FL) has emerged as a privacy-preserving framework for training models on data generated at the edge. However, the heterogeneity of data silos (e.g., label skew and domain shift) often leads to inconsistent learning objectives and suboptimal model performance. Inspired by the data-driven approach, we propose Flick, a novel data generation framework for heterogeneous **F**ederated **L**earning w**i**th **C**ommonsense **K**nowledge from Large Language Models (LLMs). In Flick, the client performs the local data summary to capture client-specific knowledge in textual form. The central server then distills task-relevant, high-quality knowledge from the out-of-the-box LLM -- guided by cross-client-specific insights -- to generate informative text prompts. These prompts direct a generative model in producing synthetic data, enabling global model fine-tuning and local data compensation. This process gradually aligns the label and feature distributions across clients. Extensive results on three datasets demonstrate that Flick improves the global model accuracy by up to 11.43\%, and accelerates convergence by up to 12.9$\times$, validating its effectiveness in addressing data heterogeneity.

Forecasting is an important task in many domains. However, existing forecasting benchmarks lack comprehensive confidence assessment, focusing on limited question types, and often consist of artificial questions that do not reflect real-world needs. To address these gaps, we introduce FOReCAst (Future Outcome Reasoning and Confidence Assessment), a benchmark that evaluates models' ability to make predictions and their confidence in them. FOReCAst spans diverse forecasting scenarios involving Boolean questions, timeframe prediction, and quantity estimation, enabling a comprehensive evaluation of both prediction accuracy and confidence calibration for real-world applications.

Clinical risk prediction plays a crucial role in early disease detection and personalized intervention. While recent models increasingly incorporate multimodal data, their development typically assumes access to large-scale, multimodal datasets and substantial computational resources. In practice, however, most clinical sites operate under resource constraints, with access limited to EHR data alone and insufficient capacity to train complicated models. This gap highlights the urgent need to democratize clinical risk prediction by enabling effective deployment in data- and resource-limited local clinical settings. In this work, we propose a cross-cohort cross-modal knowledge transfer framework that leverages the multimodal model trained on a nationwide cohort and adapts it to local cohorts with only EHR data. We focus on EHR and genetic data as representative multimodal inputs and address two key challenges. First, to mitigate the influence of noisy or less informative biological signals, we propose a novel mixture-of-aggregations design to enhance the modeling of informative and relevant genetic features. Second, to support rapid model adaptation in low-resource sites, we develop a lightweight graph-guided fine-tuning method that adapts pretrained phenotypical EHR representations to target cohorts using limited patient data. Extensive experiments on real-world clinical data validate the effectiveness of our proposed model.