NeurIPS 2025 Papers

Graph Transformers (GTs) have shown strong empirical performance, yet current architectures vary widely in their use of attention mechanisms, positional embeddings (PEs), and expressivity. Existing expressivity results are often tied to specific design choices and lack comprehensive empirical validation on large-scale data. This leaves a gap between theory and practice, preventing generalizable insights that exceed particular application domains. Here, we propose the Generalized-Distance Transformer (GDT), a GT architecture using standard attention that incorporates many advancements for GTs from recent years, and develop a fine-grained understanding of the GDT's representation power in terms of attention and PEs. Through extensive experiments, we identify design choices that consistently perform well across various applications, tasks, and model scales, demonstrating strong performance in a few-shot transfer setting without fine-tuning. Our evaluation covers over eight million graphs with roughly 270M tokens across diverse domains, including image-based object detection, molecular property prediction, code summarization, and out-of-distribution algorithmic reasoning. We distill our theoretical and practical findings into several generalizable insights about effective GT design, training, and inference.

Reliable uncertainty quantification is crucial for reinforcement learning (RL) in high-stakes settings. We propose a unified conformal prediction framework for infinite-horizon policy evaluation that constructs distribution-free prediction intervals for returns in both on-policy and off-policy settings. Our method integrates distributional RL with conformal calibration, addressing challenges such as unobserved returns, temporal dependencies, and distributional shifts. We propose a modular pseudo-return construction based on truncated rollouts and a time-aware calibration strategy using experience replay and weighted subsampling. These innovations mitigate model bias and restore approximate exchangeability, enabling uncertainty quantification even under policy shifts. Our theoretical analysis provides coverage guarantees that account for model misspecification and importance weight estimation. Empirical results, including experiments in synthetic and benchmark environments like Mountain Car, show that our method significantly improves coverage and reliability over standard distributional RL baselines.

Multiple Instance Learning (MIL) is a standard weakly supervised approach for Whole Slide Image (WSI) classification, where performance hinges on both feature representation and MIL pooling strategies. Recent research has predominantly focused on Transformer-based architectures adapted for WSIs. However, we argue that this trend faces a fundamental limitation: data scarcity. In typical settings, Transformer models yield only marginal gains without access to large-scale datasets—resources that are virtually inaccessible to all but a few well-funded research labs. Motivated by this, we revisit simple, non-attention MIL with unsupervised slide features and analyze temperature-$\beta$-controlled log-sum-exp (LSE) pooling. For slides partitioned into $N$ patches, we theoretically show that LSE has a smooth transition at a critical $\beta_{\mathrm{crit}}=\mathcal{O}(\log N)$ threshold, interpolating between mean-like aggregation (stable, better generalization but less sensitive) and max-like aggregation (more sensitive but looser generalization bounds). Grounded in this analysis, we introduce Maxsoft—a novel MIL pooling function that enables flexible control over this trade-off, allowing adaptation to specific tasks and datasets. To further tackle real-world deployment challenges such as specimen heterogeneity, we propose PerPatch augmentation—a simple yet effective technique that enhances model robustness. Empirically, Maxsoft achieves state-of-the-art performance in low-data regimes across four major benchmarks (CAMELYON16, CAMELYON17, TCGA-Lung, and SICAP-MIL), often matching or surpassing large-scale foundation models. When combined with PerPatch augmentation, this performance is further improved through increased robustness. Code is available at \href{https://github.com/jafarinia/maxsoft}{\texttt{https://github.com/jafarinia/maxsoft}}

We present CrypticBio, the largest publicly available multimodal dataset of visually confusing species, specifically curated to support the development of AI models in the context of biodiversity applications. Visually confusing or cryptic species are groups of two or more taxa that are nearly indistinguishable based on visual characteristics alone. While much existing work addresses taxonomic identification in a broad sense, datasets that directly address the morphological confusion of cryptic species are small, manually curated, and target only a single taxon. Thus, the challenge of identifying such subtle differences in a wide range of taxa remains unaddressed. Curated from real-world trends in species misidentification among community annotators of iNaturalist, CrypticBio contains 52K unique cryptic groups spanning 67K species represented in 166 million images. Records in the dataset include research-grade image annotations—scientific, multicultural, and multilingual species terminology, hierarchical taxonomy, spatiotemporal context, and associated cryptic groups. To facilitate easy subset curation from CrypticBio, we provide an open-source pipeline, CrypticBio-Curate. The multimodal design of the dataset provides complementary cues such as spatiotemporal context that support the identification of cryptic species. To highlight the importance of the dataset, we benchmark a suite of state-of-the-art foundation models across CrypticBio subsets of common, unseen, endangered, and invasive species, and demonstrate the substantial impact of spatiotemporal context on vision-language zero-shot learning for cryptic species. By introducing CrypticBio, we aim to catalyze progress toward real-world-ready fine-grained species classification models for biodiversity monitoring capable of handling the nuanced challenges of species ambiguity. The data and the code are publicly available in the project website https://georgianagmanolache.github.io/crypticbio.

Designing optimal Bayes filters for nonlinear non-Gaussian systems is a challenging task. The main difficulties are: 1) representing complex beliefs, 2) handling non-Gaussian noise, and 3) marginalizing past states. To address these challenges, we focus on polynomial systems and propose the Max Entropy Moment Kalman Filter (MEM-KF). To address 1), we represent arbitrary beliefs by a Moment-Constrained Max-Entropy Distribution (MED). The MED can asymptotically approximate almost any distribution given an increasing number of moment constraints. To address 2), we model the noise in the process and observation model as MED. To address 3), we propagate the moments through the process model and recover the distribution as MED, thus avoiding symbolic integration, which is generally intractable. All the steps in MEM-KF, including the extraction of a point estimate, can be solved via convex optimization. We showcase the MEM-KF in challenging robotics tasks, such as localization with unknown data association.

Speculative decoding is an effective and lossless method for Large Language Model (LLM) inference acceleration. It employs a smaller model to generate a draft token sequence, which is then verified by the original base model. In multi-GPU systems, inference latency can be further reduced through tensor parallelism (TP), while the optimal TP size of the draft model is typically smaller than that of the base model, leading to GPU idling during the drafting stage. We observe that such inefficiency stems from the sequential execution of layers, which is seemingly natural but actually unnecessary. Therefore, we propose EasySpec, a layer-parallel speculation strategy that optimizes the efficiency of multi-GPU utilization. EasySpec breaks the inter-layer data dependencies in the draft model, enabling multiple layers to run simultaneously across multiple devices as ``fuzzy'' speculation. After each drafting-and-verification iteration, the draft model’s key-value cache is calibrated in a single forward pass, preventing long-term fuzzy-error accumulation at minimal additional latency. EasySpec is a training-free and plug-in method. We evaluated EasySpec on several mainstream open-source LLMs, using smaller versions of models from the same series as drafters. The results demonstrate that EasySpec can achieve a peak speedup of 4.17x compared to vanilla decoding, while preserving the original distributions of the base LLMs. Specifically, the drafting stage can be accelerated by up to 1.62x with a maximum speculation accuracy drop of only 7\%. The code is available at https://github.com/Yize-Wu/EasySpec.

Linear Mode Connectivity (LMC) is a notable phenomenon in the loss landscapes of neural networks, wherein independently trained models have been observed to be connected—up to permutation symmetries—by linear paths in parameter space along which the loss remains consistently low. This observation challenges classical views of non-convex optimization and has implications for model ensembling, generalization, and our understanding of neural loss geometry. Inspired by recent studies on LMC in standard neural networks, we systematically investigate this phenomenon within Mixture-of-Experts (MoE) architectures—a class of models known for their scalability and computational efficiency, which combine traditional neural networks—referred to as experts—through a learnable gating mechanism. We begin by conducting a comprehensive analysis of both dense and sparse gating regimes, demonstrating that the symmetries inherent to MoE architectures are fully characterized by permutations acting on both the expert components and the gating function. Building on these foundational findings, we propose a matching algorithm that enables alignment between independently trained MoEs, thereby facilitating the discovery of LMC. Finally, we empirically validate the presence of LMC using our proposed algorithm across diverse MoE configurations—including dense, sparse, and shared-expert variants—under a wide range of model settings and datasets of varying scales and modalities. Our results confirm the existence of LMC in MoE architectures and offer fundamental insights into the functional landscape and optimization dynamics of deep learning models.

We study the problem of efficiently estimating the mean of a $k$-class random variable, $Y$, using a limited number of labels, $N$, in settings where the analyst has access to auxiliary information (i.e.: covariates) $X$ that may be informative about $Y$. We propose an active learning algorithm ("PartiBandits") to estimate $\mathbb{E}[Y]$. The algorithm yields an estimate, $\widehat{\mu}_{\text{PB}}$, such that $\left( \widehat{\mu}_{\text{PB}} - \mathbb{E}[Y]\right)^2$ is $\tilde{\mathcal{O}}\left( \frac{\nu + \exp(c \cdot (-N/\log(N))) }{N} \right)$, where $c > 0$ is a constant and $\nu$ is the risk of the Bayes-optimal classifier. PartiBandits is essentially a two-stage algorithm. In the first stage, it learns a partition of the unlabeled data that shrinks the average conditional variance of $Y$. In the second stage it uses a UCB-style subroutine ("WarmStart-UCB") to request labels from each stratum round-by-round. Both the main algorithm's and the subroutine's convergence rates are minimax optimal in classical settings. PartiBandits bridges the UCB and disagreement-based approaches to active learning despite these two approaches being designed to tackle very different tasks. We illustrate our methods through simulation using nationwide electronic health records. Our methods can be implemented using the \textbf{PartiBandits} package in R.

Decoding natural language text from non-invasive brain signals, such as functional magnetic resonance imaging (fMRI), remains a central challenge in brain-computer interface research. While recent advances in large language models (LLMs) have enabled open-vocabulary fMRI-to-text decoding, existing frameworks typically process the entire fMRI sequence in a single step, leading to performance degradation when handling long input sequences due to memory overload and semantic drift. To address this limitation, we propose a brain-inspired sequential fMRI-to-text decoding framework that mimics the human cognitive strategy of segmented and inductive language processing. Specifically, we divide long fMRI time series into consecutive segments aligned with optimal language comprehension length. Each segment is decoded incrementally, followed by a wrap-up mechanism that summarizes the semantic content and incorporates it as prior knowledge into subsequent decoding steps. This sequence-wise approach alleviates memory burden and ensures semantic continuity across segments. In addition, we introduce a text-guided masking strategy integrated with a masked autoencoder (MAE) framework for fMRI representation learning. This method leverages attention distributions over key semantic tokens to selectively mask the corresponding fMRI time points, and employs MAE to guide the model toward focusing on neural activity at semantically salient moments, thereby enhancing the capability of fMRI embeddings to represent textual information. Experimental results on the two datasets demonstrate that our method significantly outperforms state-of-the-art approaches, with performance gains increasing as decoding length grows.

There is growing interest in leveraging mechanistic interpretability and controllability to better understand and influence the internal dynamics of large language models (LLMs). However, current methods face fundamental challenges in reliably localizing and manipulating feature representations. Sparse Autoencoders (SAEs) have recently emerged as a promising direction for feature extraction at scale, yet they, too, are limited by incomplete feature isolation and unreliable monosemanticity. To systematically quantify these limitations, we introduce Feature Monosemanticity Score (FMS), a novel metric to quantify feature monosemanticity in latent representation. Building on these insights, we propose Guided Sparse Autoencoders (G-SAE), a method that conditions latent representations on labeled concepts during training. We demonstrate that reliable localization and disentanglement of target concepts within the latent space improve interpretability, detection of behavior, and control. Specifically, our evaluations on toxicity detection, writing style identification, and privacy attribute recognition show that G-SAE not only enhances monosemanticity but also enables more effective and fine-grained steering with less quality degradation. Our findings provide actionable guidelines for measuring and advancing mechanistic interpretability and control of LLMs.

There has recently been a surge of interest in Wearable Assistant Agents: agents embodied in a wearable form factor such as smart glasses, who can take actions toward a user’s stated goal — a high-level language-expressed command such as “where did I leave my keys?”, “Text Alice I will be late”, or “What’s the weather in Cancun?”. In this work, we consider the complementary problem of eliminating the effort required to interact with such an agent by proactively inferring the user’s goal from multimodal contextual observations. As vision-language models (VLMs) hold strong potential to ultimately solve this problem, our work focuses on creating a strong benchmark to measure progress toward this end. Given the limited prior work in this area, establishing the benchmark required collecting a novel multimodal goal-inference dataset; our dataset comprises ~30 hours of data from 363 participants across 3,482 recordings, featuring ground-truth reference goals alongside accompanying visual, audio, digital, and longitudinal contextual observations. We ran a human predictability study, where we found that humans set a strong baseline that comprises a de facto upper bound on model performance: they show multiple choice question (MCQ) accuracy of 93%, with the best VLM achieving about 84% accuracy. However, MCQ assesses discrimination, not the model’s ultimate task of generating the goal through open-ended text generation. Through a meta-evaluation, we find that a VLM judging the generated goals is as good as a human judge if it has access to a human-authored script of the video or a correct reference goal. Finally, we evaluate several families of modern vision-language models on the benchmark, showing that larger models have a significant performance advantage, but are still far from being practically useful, as they produce relevant goals only ~57% of the time. The best-performing smaller models—whose size makes them better suited to wearable applications—perform significantly worse than their counterparts, generating ~49% accuracy on the benchmark. Through a modality ablation, we show that models benefit from extra information in relevant modalities with minimal performance degradation from irrelevant modalities, but don’t gain as much when noisy modalities are included (e.g., in the case of digital context when most of the app state is irrelevant).

Fine-grained open-vocabulary object detection (FG-OVD) aims to detect novel object categories described by attribute-rich texts. While existing open-vocabulary detectors show promise at the base-category level, they underperform in fine-grained settings due to the semantic entanglement of subjects and attributes in pretrained vision-language model (VLM) embeddings -- leading to over-representation of attributes, mislocalization, and semantic drift in embedding space. We propose GUIDED, a decomposition framework specifically designed to address the semantic entanglement between subjects and attributes in fine-grained prompts. By separating object localization and fine-grained recognition into distinct pathways, GUIDED aligns each subtask with the module best suited for its respective roles. Specifically, given a fine-grained class name, we first use a language model to extract a coarse-grained subject and its descriptive attributes. Then the detector is guided solely by the subject embedding, ensuring stable localization unaffected by irrelevant or overrepresented attributes. To selectively retain helpful attributes, we introduce an attribute embedding fusion module that incorporates attribute information into detection queries in an attention-based manner. This mitigates over-representation while preserving discriminative power. Finally, a region-level attribute discrimination module compares each detected region against full fine-grained class names using a refined vision-language model with a projection head for improved alignment. Extensive experiments on FG-OVD and 3F-OVD benchmarks show that GUIDED achieves new state-of-the-art results, demonstrating the benefits of disentangled modeling and modular optimization.

Complex, temporally evolving phenomena, from climate to brain activity, are governed by dynamical systems (DS). DS reconstruction (DSR) seeks to infer generative surrogate models of these from observed data, reproducing their long-term behavior. Existing DSR approaches require purpose-training for any new system observed, lacking the zero-shot and in-context inference capabilities known from LLMs. Here we introduce *DynaMix*, a novel multivariate ALRNN-based mixture-of-experts architecture pre-trained for DSR, the first DSR model able to generalize zero-shot to out-of-domain DS. Just from a provided context signal, without any re-training, DynaMix faithfully forecasts the long-term evolution of novel DS where existing time series (TS) foundation models, like Chronos, fail -- at a fraction of the number of parameters (0.1%) and orders of magnitude faster inference times. DynaMix outperforms TS foundation models in terms of long-term statistics, and often also short-term forecasts, even on real-world time series, like traffic or weather data, typically used for training and evaluating TS models, *but not at all part of DynaMix' training corpus*. We illustrate some of the failure modes of TS models for DSR problems, and conclude that models built on DS principles may bear a huge potential also for advancing the TS prediction field.

Density estimation is essential for generative modeling, particularly with the rise of modern neural networks. While existing methods capture complex data distributions, they often lack interpretability and uncertainty quantification. Bayesian nonparametric methods, especially the \polya tree, offer a robust framework that addresses these issues by accurately capturing function behavior over small intervals. Traditional techniques like Markov chain Monte Carlo (MCMC) face high computational complexity and scalability limitations, hindering the use of Bayesian nonparametric methods in deep learning. To tackle this, we introduce the variational \polya tree (VPT) model, which employs stochastic variational inference to compute posterior distributions. This model provides a flexible, nonparametric Bayesian prior that captures latent densities and works well with stochastic gradient optimization. We also leverage the joint distribution likelihood for a more precise variational posterior approximation than traditional mean-field methods. We evaluate the model performance on both real data and images, and demonstrate its competitiveness with other state-of-the-art deep density estimation methods. We also explore its ability in enhancing interpretability and uncertainty quantification. Code is available at \url{https://github.com/howardchanth/var-polya-tree}.

Decision-making models for individuals, particularly in high-stakes scenarios like vaccine uptake, often diverge from population optimal predictions. This gap arises from the uniqueness of the individual decision-making process, shaped by numerical attributes (e.g., cost, time) and linguistic influences (e.g., personal preferences and constraints). Developing upon Utility Theory and leveraging the textual-reasoning capabilities of Large Language Models (LLMs), this paper proposes an Adaptive Textual-symbolic Human-centric Reasoning framework (ATHENA) to address the optimal information integration. ATHENA uniquely integrates two stages: First, it discovers robust, group-level symbolic utility functions via LLM-augmented symbolic discovery; Second, it implements individual-level semantic adaptation, creating personalized semantic templates guided by the optimal utility to model personalized choices. Validated on real-world travel mode and vaccine choice tasks, ATHENA consistently outperforms utility-based, machine learning, and other LLM-based models, lifting F1 score by at least 6.5\% over the strongest cutting-edge models. Further, ablation studies confirm that both stages of ATHENA are critical and complementary, as removing either clearly degrades overall predictive performance. By organically integrating symbolic utility modeling and semantic adaptation, ATHENA provides a new scheme for modeling human-centric decisions. The project page can be found at https://yibozh.github.io/Athena.

Despite growing empirical evidence of bias amplification in machine learning, its theoretical foundations remain poorly understood. We develop a formal framework for majority-minority learning tasks, showing how standard training can favor majority groups and produce stereotypical predictors that neglect minority-specific features. Assuming population and variance imbalance, our analysis reveals three key findings: (i) the close proximity between "full-data" and stereotypical predictors, (ii) the dominance of a region where training the entire model tends to merely learn the majority traits, and (iii) a lower bound on the additional training required. Our results are illustrated through experiments in deep learning for tabular and image classification tasks.

Chest X-rays (CXRs) are the most frequently performed imaging examinations in clinical settings. Recent advancements in Medical Large Multimodal Models (MLMMs) have enabled automated CXR interpretation, improving diagnostic accuracy and efficiency. However, despite their strong visual understanding, current MLMMs still face two major challenges: (1) insufficient region-level understanding and interaction, and (2) limited accuracy and interpretability due to single-step prediction. In this paper, we address these challenges by empowering MLMMs with anatomy-centric reasoning capabilities to enhance their interactivity and explainability. Specifically, we propose an Anatomical Ontology-Guided Reasoning (AOR) framework that accommodates both textual and optional visual prompts, centered on region-level information to enable multimodal multi-step reasoning. We also develop AOR-Instruction, a large instruction dataset for MLMMs training, under the guidance of expert physicians. Our experiments demonstrate AOR's superior performance in both Visual Question Answering (VQA) and report generation tasks. Code and data are available at: https://github.com/Liqq1/AOR.

Modern state-space models (SSMs) often utilize structured transition matrices which enable efficient computation but pose restrictions on the model’s expressivity, as measured in terms of the ability to emulate finite-state automata (FSA). While unstructured transition matrices are optimal in terms of expressivity, they come at a prohibitively high compute and memory cost, even for moderate state sizes. We propose a structured sparse parametrization of transition matrices in SSMs that enables FSA state tracking with provably optimal state size and depth, while keeping the computational cost of the recurrence comparable to that of diagonal SSMs. Our method, \emph{PD-SSM}, parametrizes the transition matrix as the product of a column one-hot matrix ($P$) and a complex-valued diagonal matrix ($D$). As a result, the computational cost of parallel scans scales linearly with the state size. Theoretically, the model is BIBO-stable and can emulate any $N$-state FSA with one layer of dimension $N$ and a linear readout of size $N ×N$, significantly improving on all current structured SSM guarantees. Experimentally, the model significantly outperforms a wide collection of modern SSM variants on various FSA state tracking tasks. On multivariate time-series classification, it outperforms neural controlled differential equations, a paradigm explicitly built for time-series analysis. Finally, we integrate PD-SSM into a hybrid Transformer-SSM architecture and demonstrate that the model can effectively track the states of a complex FSA in which transitions are encoded into sets of variable-length English sentences. The code is available at https://github.com/IBM/expressive-sparse-state-space-model.

In machine learning, effective modeling requires a holistic consideration of how to encode inputs, make predictions (i.e., decoding), and train the model. However, in time-series forecasting, prior work has predominantly focused on encoder design, often treating prediction and training as separate or secondary concerns. In this paper, we propose TimePerceiver, a unified encoder-decoder forecasting framework that is tightly aligned with an effective training strategy. To be specific, we first generalize the forecasting task to include diverse temporal prediction objectives such as extrapolation, interpolation, and imputation. Since this generalization requires handling input and target segments that are arbitrarily positioned along the temporal axis, we design a novel encoder-decoder architecture that can flexibly perceive and adapt to these varying positions. For encoding, we introduce a set of latent bottleneck representations that can interact with all input segments to jointly capture temporal and cross-channel dependencies. For decoding, we leverage learnable queries corresponding to target timestamps to effectively retrieve relevant information. Extensive experiments demonstrate that our framework consistently and significantly outperforms prior state-of-the-art baselines across a wide range of benchmark datasets.