NeurIPS 2025 Papers

U‑shaped networks output logits at multiple spatial scales, each capturing a different blend of coarse context and fine detail. Yet, training still treats these logits in isolation—either supervising only the final, highest‑resolution logits or applying deep supervision with identical loss weights at every scale—without exploring *mixed‑scale* combinations. Consequently, the decoder output misses the complementary cues that arise only when coarse and fine predictions are fused. To address this issue, we introduce LoMix ($\underline{Lo}$gits $\underline{Mix}$ing), a Neural Architecture Search (NAS)‑inspired, differentiable plug-and-play module that **generates** new mixed‑scale outputs and **learns** how exactly each of them should guide the training process. More precisely, LoMix mixes the multi-scale decoder logits with four lightweight fusion operators: addition, multiplication, concatenation, and attention-based weighted fusion, yielding a rich set of synthetic “mutant’’ maps. Every original or mutant map is given a softplus loss weight that is co‑optimized with network parameters, mimicking a one‑step architecture search that automatically discovers the most useful scales, mixtures, and operators. Plugging LoMix into recent U-shaped architectures (i.e., PVT‑V2‑B2 backbone with EMCAD decoder) on Synapse 8‑organ dataset improves DICE by +4.2\% over single‑output supervision, +2.2\% over deep supervision, and +1.5\% over equally weighted additive fusion, all with **zero** inference overhead. When training data are scarce (e.g., one or two labeled scans, 5\% of the trainset), the advantage grows to +9.23\%, underscoring LoMix’s data efficiency. Across four benchmarks and diverse U-shaped networks, LoMiX improves DICE by up to +13.5\% over single-output supervision, confirming that learnable weighted mixed‑scale fusion generalizes broadly while remaining data efficient, fully interpretable, and overhead-free at inference. Our implementation is available at https://github.com/SLDGroup/LoMix.

Accurate video forecasting enables autonomous vehicles to anticipate hazards, robotics and surveillance systems to predict human intent, and environmental models to issue timely warnings for extreme weather events. However, existing methods remain limited: transformers rely on global attention with quadratic complexity, making them impractical for high-resolution, long-horizon video prediction, while convolutional and recurrent networks suffer from short-range receptive fields and vanishing gradients, losing key information over extended sequences. To overcome these challenges, we introduce VideoTitans, the first architecture to adapt the gradient-driven Titans memory—originally designed for language modelling to video prediction. VideoTitans integrates three core ideas: (i) a sliding-window attention core that scales linearly with sequence length and spatial resolution, (ii) an episodic memory that dynamically retains only informative tokens based on a gradient-based surprise signal, and (iii) a small set of persistent tokens encoding task-specific priors that stabilize training and enhance generalization. Extensive experiments on Moving-MNIST, Human3.6M, TrafficBJ and WeatherBench benchmarks show that VideoTitans consistently reduces computation (FLOPs) and achieves competitive visual fidelity compared to state-of-the-art recurrent, convolutional, and efficient-transformer methods. Comprehensive ablations confirm that each proposed component contributes significantly.

As large language models (LLMs) become increasingly integrated into applications serving users across diverse cultures, communities, and demographics, it is critical to align LLMs with pluralistic human values beyond average principles (e.g., HHH). In psychological and social value theories such as Schwartz’s Value Theory, pluralistic values are represented by multiple value dimensions paired with various priorities. However, existing methods encounter two challenges when aligning with such fine-grained value objectives: 1) they often treat multiple values as independent and equally important, ignoring their interdependence and relative priorities (value complexity); 2) they struggle to precisely control nuanced value priorities, especially those underrepresented ones (value steerability). To handle these challenges, we propose COUPLE, a COUnterfactual reasoning framework for PLuralistic valuE alignment. It introduces a structural causal model (SCM) to feature complex interdependency and prioritization among features, as well as the causal relationship between high-level value dimensions and behaviors. Moreover, it applies counterfactual reasoning to generate outputs aligned with any desired value objectives. Benefitting from explicit causal modeling, COUPLE also provides better interpretability. We evaluate COUPLE on two datasets with different value systems and demonstrate that COUPLE advances other baselines across diverse types of value objectives. Our code is available at https://github.com/microsoft/COUPLE.

Floorplanning is the initial step in the physical design process of Electronic Design Automation (EDA), directly influencing subsequent placement, routing, and final power of the chip. However, the solution space in floorplanning is vast, and current algorithms often struggle to explore it sufficiently, making them prone to getting trapped in local optima. To achieve efficient floorplanning, we propose **CORE**, a general and effective solution optimization framework that synergizes Evolutionary Algorithms (EAs) and Reinforcement Learning (RL) for high-quality layout search and optimization. Specifically, we propose the Clustering-based Diversified Evolutionary Search that directly perturbs layouts and evolves them based on novelty and performance. Additionally, we model the floorplanning problem as a sequential decision problem with B*-Tree representation and employ RL for efficient learning. To efficiently coordinate EAs and RL, we propose the reinforcement-driven mechanism and evolution-guided mechanism. The former accelerates population evolution through RL, while the latter guides RL learning through EAs. The experimental results on the MCNC and GSRC benchmarks demonstrate that CORE outperforms other strong baselines in terms of wirelength and area utilization metrics, achieving a 12.9\% improvement in wirelength. CORE represents the first evolutionary reinforcement learning (ERL) algorithm for floorplanning, surpassing existing RL-based methods. The code is available at https://github.com/yeshenpy/CORE.

Data integration approaches are increasingly used to enhance the efficiency and generalizability of studies. However, a key limitation of these methods is the assumption that outcome measures are identical across datasets -- an assumption that often does not hold in practice. Consider the following opioid use disorder (OUD) studies: the XBOT trial and the POAT study, both evaluating the effect of medications for OUD on withdrawal symptom severity (not the primary outcome of either trial). While XBOT measures withdrawal severity using the subjective opiate withdrawal scale, POAT uses the clinical opiate withdrawal scale. We analyze this realistic yet challenging setting where outcome measures differ across studies and where neither study records both types of outcomes. Our paper studies whether and when integrating studies with disparate outcome measures leads to efficiency gains. We introduce three sets of assumptions -- with varying degrees of strength -- linking both outcome measures. Our theoretical and empirical results highlight a cautionary tale: integration can improve asymptotic efficiency only under the strongest assumption linking the outcomes. However, misspecification of this assumption leads to bias. In contrast, a milder assumption may yield finite-sample efficiency gains, yet these benefits diminish as sample size increases. We illustrate these trade-offs via a case study integrating the XBOT and POAT datasets to estimate the comparative effect of two medications for opioid use disorder on withdrawal symptoms. By systematically varying the assumptions linking the SOW and COW scales, we show potential efficiency gains and the risks of bias. Our findings emphasize the need for careful assumption selection when fusing datasets with differing outcome measures, offering guidance for researchers navigating this common challenge in modern data integration.

Large Language Models (LLMs) have demonstrated remarkable capabilities across numerous tasks, yet principled explanations for their underlying mechanisms and several phenomena, such as scaling laws, hallucinations, and related behaviors, remain elusive. In this work, we revisit the classical relationship between compression and prediction, grounded in Kolmogorov complexity and Shannon information theory, to provide deeper insights into LLM behaviors. By leveraging the Kolmogorov Structure Function and interpreting LLM compression as a two-part coding process, we offer a detailed view of how LLMs acquire and store information across increasing model and data scales -- from pervasive syntactic patterns to progressively rarer knowledge elements. Motivated by this theoretical perspective and natural assumptions inspired by Heap’s and Zipf’s laws, we introduce a simplified yet representative hierarchical data-generation framework called the Syntax-Knowledge model. Under the Bayesian setting, we show that prediction and compression within this model naturally lead to diverse learning and scaling behaviors of LLMs. In particular, our theoretical analysis offers intuitive and principled explanations for both data and model scaling laws, the dynamics of knowledge acquisition during training and fine-tuning, factual knowledge hallucinations in LLMs. The experimental results validate our theoretical predictions.

Proprietary large language models (LLMs) exhibit strong generalization capabilities across diverse tasks and are increasingly deployed on edge devices for efficiency and privacy reasons. However, deploying proprietary LLMs at the edge without adequate protection introduces critical security threats. Attackers can extract model weights and architectures, enabling unauthorized copying and misuse. Even when protective measures prevent full extraction of model weights, attackers may still perform advanced attacks, such as fine-tuning, to further exploit the model. Existing defenses against these threats typically incur significant computational and communication overhead, making them impractical for edge deployment. To safeguard the edge-deployed LLMs, we introduce CoreGuard, a computation- and communication-efficient protection method. CoreGuard employs an efficient protection protocol to reduce computational overhead and minimize communication overhead via a propagation protocol. Extensive experiments show that CoreGuard achieves upper-bound security protection with negligible overhead.

Audio captioning systems face a fundamental challenge: teacher-forcing training creates exposure bias that leads to caption degeneration during inference. While contrastive methods have been proposed as solutions, they typically fail to capture the crucial temporal relationships between acoustic and linguistic modalities. We address this limitation by introducing the unbiased sliced Wasserstein RBF (USW-RBF) kernel with rotary positional embedding, specifically designed to preserve temporal information across modalities. Our approach offers a practical advantage: the kernel enables efficient stochastic gradient optimization, making it computationally feasible for real-world applications. Building on this foundation, we develop a complete audio captioning framework that integrates stochastic decoding to further mitigate caption degeneration. Extensive experiments on AudioCaps and Clotho datasets demonstrate that our method significantly improves caption quality, lexical diversity, and text-to-audio retrieval accuracy. Furthermore, we demonstrate the generalizability of our USW-RBF kernel by applying it to audio reasoning tasks, where it enhances the reasoning capabilities of large audio language models on the CompA-R in terms of correctness and quality. Our kernel also improves the reasoning accuracy of the MMAU-test-mini benchmarks by $4\%$. These results establish our approach as a powerful and generalizable solution for cross-modal alignment challenges in audio-language tasks.

Offline reinforcement learning (RL) aims to learn a policy from a fixed dataset without additional environment interaction. However, effective offline policy learning often requires a large and diverse dataset to mitigate epistemic uncertainty. Collecting such data demands substantial online interactions, which are costly or infeasible in many real-world domains. Therefore, improving policy learning from limited offline data—achieving high data efficiency—is critical for practical offline RL. In this paper, we propose a simple yet effective plug-and-play pretraining framework that initializes the feature representation of a $Q$-network to enhance data efficiency in offline RL. Our approach employs a shared $Q$-network architecture trained in two stages: pretraining a backbone feature extractor with a transition prediction head; training a $Q$-network—combining the backbone feature extractor and a $Q$-value head—with *any* offline RL objective. Extensive experiments on the D4RL, Robomimic, V-D4RL, and ExoRL benchmarks show that our method substantially improves both performance and data efficiency across diverse datasets and domains. Remarkably, with only **10\%** of the dataset, our approach outperforms standard offline RL baselines trained on the full data.

Generating hyperspectral images (HSIs) from RGB images through spectral reconstruction can significantly reduce the cost of HSI acquisition. In this paper, we propose a Fractal-Based Recursive Spectral Reconstruction Network (FRN), which differs from existing paradigms that attempt to directly integrate the full-spectrum information from the R, G, and B channels in a one-shot manner. Instead, it treats spectral reconstruction as a progressive process, predicting from broad to narrow bands or employing a coarse-to-fine approach for predicting the next wavelength. Inspired by fractals in mathematics, FRN establishes a novel spectral reconstruction paradigm by recursively invoking an atomic reconstruction module. In each invocation, only the spectral information from neighboring bands is used to provide clues for the generation of the image at the next wavelength, which follows the low-rank property of spectral data. Moreover, we design a band-aware state space model that employs a pixel-differentiated scanning strategy at different stages of the generation process, further suppressing interference from low-correlation regions caused by reflectance differences. Through extensive experimentation across different datasets, FRN achieves superior reconstruction performance compared to state-of-the-art methods. Code is available at https://github.com/mongko007/frn.

Optimization modeling is fundamental to decision-making in fields such as supply chain management, logistics, and financial engineering, but its complexity presents a major barrier to adoption. Automating model creation from natural language is key to improving efficiency and access. However, while Large Language Models (LLMs) are a promising tool for this, they often produce flawed or infeasible results due to errors and hallucinations. To address this issue, we propose Solver-Informed Reinforcement Learning (SIRL), a framework that uses Reinforcement Learning with Verifiable Reward to improve LLMs’ ability to generate accurate and executable optimization models. Specifically, SIRL automatically assesses the executable code and the instance-level mathematical model represented by the associated .lp files. This process yields precise feedback on syntactic validity, feasibility, and solution quality, which serves as a direct reward signal to guide the reinforcement learning process. Furthermore, this verification mechanism also supports our instance-enhanced self-consistency method for creating high-quality training data. Extensive experiments on diverse public benchmarks demonstrate that models trained with our SIRL framework achieve state-of-the-art performance, substantially outperforming existing methods in generating accurate and executable optimization models. Specifically, our SIRL-32B model surpasses DeepSeek-V3 and OpenAI-o3 on the majority of these benchmarks. Our code is publicly available at https://github.com/Cardinal-Operations/SIRL.

Humans continuously infer the states, goals, and behaviors of others by perceiving their surroundings in dynamic, real-world social interactions. However, most Theory of Mind (ToM) benchmarks only evaluate static, text-based scenarios, which have a significant gap compared to real interactions. We propose the SoMi-ToM benchmark, designed to evaluate multi-perspective ToM in embodied multi-agent complex social interactions. This benchmark is based on rich multimodal interaction data generated by the interaction environment SoMi, covering diverse crafting goals and social relationships. Our framework supports multi-level evaluation: (1) first-person evaluation provides multimodal (visual, dialogue, action, etc.) input from a first-person perspective during a task for real-time state inference, (2) third-person evaluation provides complete third-person perspective video and text records after a task for goal and behavior inference. This evaluation method allows for a more comprehensive examination of a model's ToM capabilities from both the subjective immediate experience and the objective global observation. We constructed a challenging dataset containing 35 third-person perspective videos, 363 first-person perspective images, and 1225 expert-annotated multiple-choice questions (three options). On this dataset, we systematically evaluated the performance of human subjects and several state-of-the-art large vision-language models (LVLMs). The results show that LVLMs perform significantly worse than humans on SoMi-ToM: the average accuracy gap between humans and models is 40.1% in first-person evaluation and 26.4% in third-person evaluation. This indicates that future LVLMs need to further improve their ToM capabilities in embodied, complex social interactions.

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.