NeurIPS 2025 Papers

This paper proposes **$\mathcal{X}^2$-DFD**, an **e$\mathcal{X}$plainable** and **e$\mathcal{X}$tendable** framework based on multimodal large-language models (MLLMs) for deepfake detection, consisting of three key stages. The first stage, *Model Feature Assessment*, systematically evaluates the detectability of forgery-related features for the MLLM, generating a prioritized ranking of features based on their intrinsic importance to the model. The second stage, *Explainable Dataset Construction*, consists of two key modules: *Strong Feature Strengthening*, which is designed to enhance the model’s existing detection and explanation capabilities by reinforcing its well-learned features, and *Weak Feature Supplementing*, which addresses gaps by integrating specific feature detectors (e.g., low-level artifact analyzers) to compensate for the MLLM’s limitations. The third stage, Fine-tuning and Inference, involves fine-tuning the MLLM on the constructed dataset and deploying it for final detection and explanation. By integrating these three stages, our approach enhances the MLLM's strengths while supplementing its weaknesses, ultimately improving both the detectability and explainability. Extensive experiments and ablations, followed by a comprehensive human study, validate the improved performance of our approach compared to the original MLLMs. More encouragingly, our framework is designed to be plug-and-play, allowing it to seamlessly integrate with future more advanced MLLMs and specific feature detectors, leading to continual improvement and extension to face the challenges of rapidly evolving deepfakes. Code can be found on https://github.com/chenyize111/X2DFD.

Chain-of-thought (CoT) reasoning in large language models (LLMs) can be formalized as a latent variable problem, where the model needs to generate intermediate reasoning steps. While prior approaches such as iterative reward-ranked fine-tuning (RAFT) have relied on such formulations, they typically apply uniform inference budgets across prompts, which fails to account for variability in difficulty and convergence behavior. This work identifies the main bottleneck in CoT training as inefficient stochastic gradient estimation due to static sampling strategies. We propose GVM-RAFT, a prompt-specific Dynamic Sample Allocation Strategy designed to minimize stochastic gradient variance under a computational budget constraint. The method dynamically allocates computational resources by monitoring prompt acceptance rates and stochastic gradient norms, ensuring that the resulting gradient variance is minimized. Our theoretical analysis shows that the proposed dynamic sampling strategy leads to accelerated convergence guarantees under suitable conditions. Experiments on mathematical reasoning show that GVM-RAFT achieves a 2-4x speedup and considerable accuracy improvements over vanilla RAFT. The proposed dynamic sampling strategy is general and can be incorporated into other reinforcement learning algorithms, such as GRPO, leading to similar improvements in convergence and test accuracy.

Language models deployed in real-world systems often require post-hoc updates to incorporate new or corrected knowledge. However, editing such models efficiently and reliably—without retraining or forgetting previous information—remains a major challenge. Existing methods for lifelong model editing either compromise generalization, interfere with past edits, or fail to scale to long editing sequences. We propose MEMOIR, a novel scalable framework that injects knowledge through a residual memory, i.e., a dedicated parameter module, while preserving the core capabilities of the pre-trained model. By sparsifying input activations through data-dependent masks, MEMOIR confines each edit to a distinct subset of the memory parameters, minimizing interference among edits. At inference, it identifies relevant edits by comparing the sparse activation patterns of new queries to those stored during editing. This enables generalization to rephrased queries by activating only the relevant knowledge while suppressing unnecessary memory activation for unrelated prompts. Experiments on question answering, hallucination correction, and out-of-distribution generalization benchmarks across LLaMA-3 and Mistral demonstrate that MEMOIR achieves state-of-the-art performance across reliability, generalization, and locality metrics, scaling to thousands of sequential edits with minimal forgetting.

Since the seminal work of TabPFN, research on tabular foundation models (TFMs) based on in-context learning (ICL) has challenged long-standing paradigms in machine learning. Without seeing any real-world data, models pretrained on purely synthetic datasets generalize remarkably well across diverse datasets, often using only a moderate number of in-context examples. This shifts the focus in tabular machine learning from model architecture design to the design of synthetic datasets, or, more precisely, to the prior distributions that generate them. Yet the guiding principles for prior design remain poorly understood. This work marks the first attempt to address the gap. We systematically investigate and identify key properties of synthetic priors that allow pretrained TFMs to generalize well. Based on these insights, we introduce Mitra, a TFM trained on a curated mixture of synthetic priors selected for their diversity, distinctiveness, and performance on real-world tabular data. Mitra consistently outperforms state-of-the-art TFMs, such as TabPFNv2 and TabICL, across both classification and regression benchmarks, with better sample efficiency.

We introduce **MLRC-Bench**, a benchmark designed to quantify how effectively language agents can tackle challenging **M**achine **L**earning (ML) **R**esearch **C**ompetitions, with a focus on open research problems that demand novel methodologies. Unlike prior work, e.g., AI Scientist, which evaluates the end-to-end agentic pipeline by using LLM-as-a-judge, MLRC-Bench measures the key steps of proposing and implementing novel research methods and evaluates them with rigorous protocol and objective metrics. Our curated suite of 7 competition tasks reveals significant challenges for LLM agents. Even the best-performing tested agent (gemini-exp-1206 under MLAB) closes only 9.3% of the gap between baseline and top human participant scores. Furthermore, our analysis reveals a misalignment between the *LLM-judged* innovation and their *actual* performance on cutting-edge ML research problems. MLRC-Bench is a dynamic benchmark, which is designed to continually grow with new ML competitions to encourage rigorous and objective evaluations of AI’s research capabilities. Our leaderboard and code are publicly available at https://huggingface.co/spaces/launch/MLRC_Bench.

Coreset selection methods have shown promise in reducing the training data size while maintaining model performance for data-efficient machine learning. However, many large real-world datasets suffer from unknown spurious correlations and hidden biases. Therefore, it is crucial to understand how such biases would affect downstream tasks via the selected coresets. In this work, we conduct the first comprehensive analysis of the implications of data selection on the bias levels of the selected coresets and the robustness of downstream models trained on them. We use an extensive experimental setting spanning ten different spurious correlations benchmarks, five score metrics to characterize sample importance/ difficulty, and five data selection policies across a broad range of coreset sizes to identify important patterns and derive insights. Thereby, we unravel a series of nontrivial nuances in well-known interactions between sample difficulty and bias alignment, as well as dataset bias and resultant model robustness. For example, we show that embedding-based sample characterizations run a comparatively lower risk of inadvertently exacerbating bias when used for selecting coresets compared to characterizations based on learning dynamics. Our analysis also reveals that lower bias levels achieved by coresets of difficult samples do not reliably guarantee downstream robustness. Most importantly, we show that special considerations need to be made when the coreset size is very small, since there is a unique risk of highly prototypical coresets reaching high average performance while obscuring their low group-robustness.

Learning dynamics is essential for model-based control and Reinforcement Learning in systems operating in changing environments, such as robotics, autonomous vehicles, and power systems. However, limited system measurements, such as those from low-resolution meters, demand sample-efficient learning. Symmetry provides a powerful inductive bias by characterizing equivalent relations in system behavior to improve sample efficiency. While recent methods attempt to discover symmetries from data, they typically assume a single global symmetry group and treat symmetry discovery and dynamic learning as separate tasks, leading to limited expressiveness and error accumulation. In this paper, we propose the Latent Mixture of Symmetries (Latent MoS), an expressive model that captures symmetry-governed latent factors from complex dynamical measurements. Latent MoS focuses on dynamic learning while locally preserving the underlying symmetric transformations. To further capture long-range temporal equivalence, we introduce a hierarchical architecture that stacks Latent MoS blocks across multiple time scales. Numerical experiments across diverse physical systems demonstrate that Latent MoS significantly outperforms state-of-the-art baselines in interpolation and extrapolation tasks while offering interpretable latent representations suitable for future geometric and safety-critical analysis.

What features neural networks learn, and how, remains an open question. In this paper, we introduce Alternating Gradient Flows (AGF), an algorithmic framework that describes the dynamics of feature learning in two-layer networks trained from small initialization. Prior works have shown that gradient flow in this regime exhibits a staircase-like loss curve, alternating between plateaus where neurons slowly align to useful directions and sharp drops where neurons rapidly grow in norm. AGF approximates this behavior as an alternating two-step process: maximizing a utility function over dormant neurons and minimizing a cost function over active ones. AGF begins with all neurons dormant, corresponding to an initialization at the origin. At each iteration, a dormant neuron activates, triggering the acquisition of a feature and a drop in the loss. AGF quantifies the order, timing, and magnitude of these drops, matching experiments across several commonly studied architectures. We show that AGF unifies and extends existing saddle-to-saddle analyses in fully connected linear networks and attention-only linear transformers, where the learned features are singular modes and principal components, respectively. In diagonal linear networks, we prove AGF converges to gradient flow in the limit of vanishing initialization. Applying AGF to quadratic networks trained to perform modular addition, we give the first complete characterization of the training dynamics, revealing that networks learn Fourier features in decreasing order of coefficient magnitude. Altogether, AGF offers a promising step towards understanding feature learning in neural networks.

Modern neural networks often encode unwanted concepts alongside task-relevant information, leading to fairness and interpretability concerns. Existing post-hoc approaches can remove undesired concepts but often degrade useful signals. We introduce SPLINCE—Simultaneous Projection for LINear concept removal and Covariance prEservation—which eliminates sensitive concepts from representations while exactly preserving their covariance with a target label. SPLINCE achieves this via an oblique projection that ``splices out'' the unwanted direction yet protects important label correlations. Theoretically, it is the unique solution that removes linear concept predictability and maintains target covariance with minimal embedding distortion. Empirically, SPLINCE outperforms baselines on benchmarks such as Bias in Bios and Winobias, removing protected attributes while minimally damaging main-task information.

Accurate prediction of ionic conductivity in electrolyte systems is crucial for advancing numerous scientific and technological applications. While significant progress has been made, current research faces two fundamental challenges: (1) the lack of high-quality standardized benchmarks, and (2) inadequate modeling of geometric structure and intermolecular interactions in mixture systems. To address these limitations, we first reorganize and enhance the CALiSol and DiffMix electrolyte datasets by incorporating geometric graph representations of molecules. We then propose GeoMix, a novel geometry-aware framework that preserves Set-SE(3) equivariance—an essential but challenging property for mixture systems. At the heart of GeoMix lies the Geometric Interaction Network (GIN), an equivariant module specifically designed for intermolecular geometric message passing. Comprehensive experiments demonstrate that GeoMix consistently outperforms diverse baselines (including MLPs, GNNs, and geometric GNNs) across both datasets, validating the importance of cross-molecular geometric interactions and equivariant message passing for accurate property prediction. This work not only establishes new benchmarks for electrolyte research but also provides a general geometric learning framework that advances modeling of mixture systems in energy materials, pharmaceutical development, and beyond.

Expensive communication cost is a common performance bottleneck in Federated Learning (FL), which makes it less appealing in real-world applications. Many communication-efficient FL methods focus on discarding a part of model updates mostly based on gradient magnitude. In this study, we find that recycling previous updates, rather than simply dropping them, more effectively reduces the communication cost while maintaining FL performance. We propose *FedLUAR*, a Layer-wise Update Aggregation with Recycling scheme for communication-efficient FL. We first define a useful metric that quantifies the extent to which the aggregated gradients influences the model parameter values in each layer. *FedLUAR* selects a few layers based on the metric and recycles their previous updates on the server side. Our extensive empirical study demonstrates that the update recycling scheme significantly reduces the communication cost while maintaining model accuracy. For example, our method achieves nearly the same AG News accuracy as FedAvg, while reducing the communication cost to just 17%.

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome. The implementation of ChromFound is available via https://github.com/JohnsonKlose/ChromFound.

Recent 6D pose estimation methods demonstrate notable performance but still face some practical limitations. For instance, many of them rely heavily on sensor depth, which may fail with challenging surface conditions, such as transparent or highly reflective materials. In the meantime, RGB-based solutions provide less robust matching performance in low-light and texture-less scenes due to the lack of geometry information. Motivated by these, we propose **SingRef6D**, a lightweight pipeline requiring only a **single RGB** image as a reference, eliminating the need for costly depth sensors, multi-view image acquisition, or training view synthesis models and neural fields. This enables SingRef6D to remain robust and capable even under resource-limited settings where depth or dense templates are unavailable. Our framework incorporates two key innovations. First, we propose a token-scaler-based fine-tuning mechanism with a novel optimization loss on top of Depth-Anything v2 to enhance its ability to predict accurate depth, even for challenging surfaces. Our results show a 14.41% improvement (in $\delta_{1.05}$) on REAL275 depth prediction compared to Depth-Anything v2 (with fine-tuned head). Second, benefiting from depth availability, we introduce a depth-aware matching process that effectively integrates spatial relationships within LoFTR, enabling our system to handle matching for challenging materials and lighting conditions. Evaluations of pose estimation on the REAL275, ClearPose, and Toyota-Light datasets show that our approach surpasses state-of-the-art methods, achieving a 6.1% improvement in average recall.

Large Language Models exhibit logical inconsistency across multi-turn inference processes, undermining correctness in complex inferential tasks. Challenges arise from ensuring that outputs align with both factual correctness and human intent. Approaches like single-agent reflection and multi-agent debate frequently prioritize consistency, but at the expense of accuracy. To address this problem, we propose a novel game-theoretic consensus mechanism that enables LLMs to self-check their outputs during the decoding stage of output generation. Our method models the decoding process as a multistage Bayesian Decoding Game, where strategic interactions dynamically converge to a consensus on the most reliable outputs without human feedback or additional training. Remarkably, our game design allows smaller models to outperform much larger models through game mechanisms (e.g., 78.1 LLaMA13B vs. 76.6 PaLM540B). As a model-agnostic method, our approach consistently improves even the latest models, enhancing DeepSeek-7B's performance on MMLU by 12.4%. Our framework effectively balances correctness and consistency, demonstrating that properly designed game-theoretic mechanisms can significantly enhance the self-verification capabilities of language models across various tasks and model architectures.

In cooperative Multi-Agent Reinforcement Learning (MARL), it is a common practice to tune hyperparameters in ideal simulated environments to maximize cooperative performance. However, policies tuned for cooperation often fail to maintain robustness and resilience under real-world uncertainties. Building trustworthy MARL systems requires a deep understanding of \emph{robustness}, which ensures stability under uncertainties, and \emph{resilience}, the ability to recover from disruptions—a concept extensively studied in control systems but largely overlooked in MARL. In this paper, we present a large-scale empirical study comprising over 82,620 experiments to evaluate cooperation, robustness, and resilience in MARL across 4 real-world environments, 13 uncertainty types, and 15 hyperparameters. Our key findings are: (1) Under mild uncertainty, optimizing cooperation improves robustness and resilience, but this link weakens as perturbations intensify. Robustness and resilience also varies by algorithm and uncertainty type. (2) Robustness and resilience do not generalize across uncertainty modalities or agent scopes: policies robust to action noise for all agents may fail under observation noise on a single agent. (3) Hyperparameter tuning is critical for trustworthy MARL: surprisingly, standard practices like parameter sharing, GAE, and PopArt can hurt robustness, while early stopping, high critic learning rates, and Leaky ReLU consistently help. By optimizing hyperparameters only, we observe substantial improvement in cooperation, robustness and resilience across all MARL backbones, with the phenomenon also generalizing to robust MARL methods across these backbones.

We consider off-policy evaluation (OPE) in Partially Observable Markov Decision Processes (POMDPs) with unobserved confounding. Recent advances have introduced bridge-function to circumvent unmeasured confounding and develop estimators for the policy value, yet the statistical error bounds of them related to the length of horizon $T$ and the size of the state-action space $|\mathcal{O}||\mathcal{A}|$ remain largely unexplored. In this paper, we systematically investigate the finite-sample error bounds of OPE estimators in finite-horizon tabular confounded POMDPs. Specifically, we show that under certain rank conditions, the estimation error for policy value can achieve a rate of $\mathcal{O}(T^{1.5}/\sqrt{n})$, excluding the cardinality of the observation space $|\mathcal{O}|$ and the action space $|\mathcal{A}|$. With an additional mild condition on the concentrability coefficients in confounded POMDPs, the rate of estimation error can be improved to $\mathcal{O}(T/\sqrt{n})$. We also show that for a fully history-dependent policy, the estimation error scales as $\mathcal{O}\big(T/\sqrt{n}(|\mathcal{O}| |\mathcal{A}|)^{\frac{T}{2}}\big)$, highlighting the exponential error dependence introduced by history-based proxies to infer hidden states. Furthermore, when the target policy is memoryless policy, the error bound improves to $\mathcal{O}\big(T/\sqrt{n}\sqrt{|\mathcal{O}| |\mathcal{A}|}\big)$, which matches the optimal rate known for tabular MDPs. To the best of our knowledge, this is the first work to provide a comprehensive finite-sample analysis of OPE in confounded POMDPs.

We present WUKONG, a novel training-free framework for high-fidelity textured 3D morphing that takes a pair of source and target prompts (text or images) as input. Unlike conventional methods -- which rely on manual correspondence matching and deformation trajectory estimation (limiting generalization and requiring costly preprocessing) -- WUKONG leverages the generative prior of flow-based transformers to produce high-fidelity 3D transitions with rich texture details. To ensure smooth shape transitions, we exploit the inherent continuity of flow-based generative processes and formulate morphing as an optimal transport barycenter problem. We further introduce a sequential initialization strategy to prevent abrupt geometric distortions and preserve identity coherence. For faithful texture preservation, we propose a similarity-guided semantic consistency mechanism that selectively retains high-frequency details and enables precise control over blending dynamics. This avoids common artifacts like oversmoothing while maintaining semantic fidelity. Through extensive quantitative and qualitative evaluations, we demonstrate that WUKONG significantly outperforms state-of-the-art methods, achieving superior results across diverse geometry and texture variations.

We introduce Neural Green’s Function, a neural solution operator for linear partial differential equations (PDEs) whose differential operators admit eigendecompositions. Inspired by Green’s functions, the solution operators of linear PDEs that depend exclusively on the domain geometry, we design Neural Green’s Function to imitate their behavior, achieving superior generalization across diverse irregular geometries and source and boundary functions. Specifically, Neural Green’s Function extracts per-point features from a volumetric point cloud representing the problem domain and uses them to predict a decomposition of the solution operator, which is subsequently applied to evaluate solutions via numerical integration. Unlike recent learning-based solution operators, which often struggle to generalize to unseen source or boundary functions, our framework is, by design, agnostic to the specific functions used during training, enabling robust and efficient generalization. In the steady-state thermal analysis of mechanical part geometries from the MCB dataset, Neural Green’s Function outperforms state-of-the-art neural operators, achieving an average error reduction of 13.9% across five shape categories, while being up to 350 times faster than a numerical solver that requires computationally expensive meshing.

This paper presents a novel problem, interactive anomaly detection (AD) for articulated objects, and introduces a tailored solution that detects functional anomalies by integrating vision, interaction, and anticipation. Unlike traditional AD methods that rely on passive visual observations, our approach actively manipulates objects to reveal anomalies that would otherwise remain hidden. Our method learns to generate a sequence of actions to interact exclusively with normal objects and to anticipate the resulting normal motion. During inference, the model applies predicted actions to the object and compares the observed motion with the anticipated motion to detect anomalies. Additionally, we introduce a new benchmark, PartNet-IAD, for interactive AD, which includes articulated objects with realistic functional anomalies. Experiments show strong generalization to detect anomalies in both seen and unseen object categories. Code and dataset will be released.