NeurIPS 2025 Papers

Matrix factorization is a fundamental method in statistics and machine learning for inferring and summarizing structure in multivariate data. Modern data sets often come with "side information" of various forms (images, text, graphs) that can be leveraged to improve estimation of the underlying structure. However, existing methods that leverage side information are limited in the types of data they can incorporate, and they assume specific parametric models. Here, we introduce a novel method for this problem, *covariate-moderated empirical Bayes matrix factorization* (cEBMF). cEBMF is a modular framework that accepts any type of side information that is processable by a probabilistic model or a neural network. The cEBMF framework can accommodate different assumptions and constraints on the factors through the use of different priors, and it adapts these priors to the data. We demonstrate the benefits of cEBMF in simulations and in analyses of spatial transcriptomics and collaborative filtering data. A PyTorch-based implementation of cEBMF with flexible priors is available at https://github.com/william-denault/cebmf_torch.

We present in this paper a novel post-training quantization (PTQ) method, dubbed AccuQuant, for diffusion models. We show analytically and empirically that quantization errors for diffusion models are accumulated over denoising steps in a sampling process. To alleviate the error accumulation problem, AccuQuant minimizes the discrepancies between outputs of a full-precision diffusion model and its quantized version within a couple of denoising steps. That is, it simulates multiple denoising steps of a diffusion sampling process explicitly for quantization, accounting the accumulated errors over multiple denoising steps, which is in contrast to previous approaches to imitating a training process of diffusion models, namely, minimizing the discrepancies independently for each step. We also present an efficient implementation technique for AccuQuant, together with a novel objective, which reduces a memory complexity significantly from $\mathcal{O}(n)$ to $\mathcal{O}(1)$, where $n$ is the number of denoising steps. We demonstrate the efficacy and efficiency of AccuQuant across various tasks and diffusion models on standard benchmarks.

Large language models (LLMs) have shown remarkable progress in mathematical problem-solving, but evaluation has largely focused on problems that have exact analytical solutions or involve formal proofs, often overlooking approximation-based problems ubiquitous in applied science and engineering. To fill this gap, we build on prior work and present $\textbf{HARDMath2}$, a dataset of 211 original problems covering the core topics in an introductory graduate applied math class, including boundary-layer analysis, WKB methods, asymptotic solutions of nonlinear partial differential equations, and the asymptotics of oscillatory integrals. This dataset was designed and verified by the students and instructors of a core graduate applied mathematics course at Harvard. We build the dataset through a novel collaborative environment that challenges students to write and refine difficult problems consistent with the class syllabus, peer-validate solutions, test different models, and automatically check LLM-generated solutions against their own answers and numerical ground truths. Evaluation results show that leading frontier models still struggle with many of the problems in the dataset, highlighting a gap in the mathematical reasoning skills of current LLMs. Importantly, students identified strategies to create increasingly difficult problems by interacting with the models and exploiting common failure modes. This back-and-forth with the models not only resulted in a richer and more challenging benchmark but also led to qualitative improvements in the students' understanding of the course material, which is increasingly important as we enter an age where state-of-the-art language models can solve many challenging problems across a wide domain of fields.

The physical sciences are replete with dynamical systems that require the resolution of a wide range of length and time scales. This presents significant computational challenges since direct numerical simulation requires discretization at the finest relevant scales, leading to a high-dimensional state space. In this work, we propose an approach to learn stochastic multiscale models in the form of stochastic differential equations directly from observational data. Drawing inspiration from physics-based multiscale modeling approaches, we resolve the macroscale state on a coarse mesh while introducing a microscale latent state to explicitly model unresolved dynamics. We learn the parameters of the multiscale model using a simulator-free amortized variational inference method with a Product of Experts likelihood that enforces scale separation. We present detailed numerical studies to demonstrate that our learned multiscale models achieve superior predictive accuracy compared to under-resolved direct numerical simulation and closure-type models at equivalent resolution, as well as reduced-order modeling approaches.

There is extensive literature on accelerating first-order optimization methods in an Euclidean setting. Under which conditions such acceleration is feasible in Riemannian optimization problems is an active area of research. Motivated by the recent success of silver stepsize methods in the Euclidean setting, we undertake a study of such algorithms in the Riemannian setting. We provide the new class of algorithms determined by the choice of vector transport that allows the silver stepsize acceleration on Riemannian manifolds for the function classes associated with the corresponding vector transport. As a core application, we show that our algorithm recovers the standard Wasserstein gradient descent on the 2-Wasserstein space and, as a result, provides the first provable accelerated gradient method for potential functional optimization problems in the Wasserstein space. In addition, we validate the numerical strength of the algorithm for standard benchmark tasks on the space of symmetric positive definite matrices.

Earth observation foundation models have shown strong generalization across multiple Earth observation tasks, but their robustness under real-world perturbations remains underexplored. To bridge this gap, we introduce REOBench, the first comprehensive benchmark for evaluating the robustness of Earth observation foundation models across six tasks and twelve types of image corruptions, including both appearance-based and geometric perturbations. To ensure realistic and fine-grained evaluation, our benchmark focuses on high-resolution optical remote sensing images, which are widely used in critical applications such as urban planning and disaster response. We conduct a systematic evaluation of a broad range of models trained using masked image modeling, contrastive learning, and vision-language pre-training paradigms. Our results reveal that (1) existing Earth observation foundation models experience significant performance degradation when exposed to input corruptions. (2) The severity of degradation varies across tasks, model architectures, backbone sizes, and types of corruption, with performance drop varying from less than 1% to over 25%. (3) Vision-language models show enhanced robustness, particularly in multimodal tasks. REOBench underscores the vulnerability of current Earth observation foundation models to real-world corruptions and provides actionable insights for developing more robust and reliable models.

Perceiving the shape and material of an object from a single image is inherently ambiguous, especially when lighting is unknown and unconstrained. Despite this, humans can often disentangle shape and material, and when they are uncertain, they often move their head slightly or rotate the object to help resolve the ambiguities. Inspired by this behavior, we introduce a novel conditional denoising-diffusion model that generates samples of shape-and-material maps from a short video of an object undergoing differential motions. Our parameter-efficient architecture allows training directly in pixel-space, and it generates many disentangled attributes of an object simultaneously. Trained on a modest number of synthetic object-motion videos with supervision on shape and material, the model exhibits compelling emergent behavior: For static observations, it produces diverse, multimodal predictions of plausible shape-and-material maps that capture the inherent ambiguities; and when objects move, the distributions converge to more accurate explanations. The model also produces high-quality shape-and-material estimates for less ambiguous, real-world objects. By moving beyond single-view to continuous motion observations, and by using generative perception to capture visual ambiguities, our work suggests ways to improve visual reasoning in physically-embodied systems.

Forecasting real-world time series requires modeling both short-term fluctuations and long-term evolutions, as these signals typically exhibit multiscale temporal structures. A core challenge lies in reconciling such dynamics: high-frequency seasonality demands local precision, while low-frequency trends require global robustness. However, most existing methods adopt a unified loss function across all temporal components, overlooking their structural differences. This misalignment often causes overfitting to seasonal noise or underfitting of long-term trends, leading to suboptimal forecasting performance. To address this issue, we propose a Physics-guided Multiscale Loss Framework (PMLF) that decomposes time series into seasonal and trend components and assigns component-specific objectives grounded in the distinct energy responses of oscillatory and drift dynamics. Specifically, we assign a quadratic loss to seasonal components, reflecting the quadratic potential energy profile of molecular vibration, while a logarithmic loss is used for trend components to capture the sublinear energy profile of molecular drift under sustained external forces. Furthermore, we introduce a softmax-based strategy that adaptively balances the unequal energetic responses of these two physical processes. Experiments on different public benchmarks show that PMLF improves the performance of diverse baselines, demonstrating the effectiveness of physics-guided loss design in modeling structural heterogeneity in time series forecasting.

Stellarators are magnetic confinement devices under active development to deliver steady-state carbon-free fusion energy. Their design involves a high-dimensional, constrained optimization problem that requires expensive physics simulations and significant domain expertise. Recent advances in plasma physics and open-source tools have made stellarator optimization more accessible. However, broader community progress is currently bottlenecked by the lack of standardized optimization problems with strong baselines and datasets that enable data-driven approaches, particularly for quasi-isodynamic (QI) stellarator configurations, considered as a promising path to commercial fusion due to their inherent resilience to current-driven disruptions. Here, we release an open dataset of diverse QI-like stellarator plasma boundary shapes, paired with their ideal magnetohydrodynamic (MHD) equilibria and performance metrics. We generated this dataset by sampling a variety of QI fields and optimizing corresponding stellarator plasma boundaries. We introduce three optimization benchmarks of increasing complexity: (1) a single-objective geometric optimization problem, (2) a "simple-to-build" QI stellarator, and (3) a multi-objective ideal-MHD stable QI stellarator that investigates trade-offs between compactness and coil simplicity. For every benchmark, we provide reference code, evaluation scripts, and strong baselines based on classical optimization techniques. Finally, we show how learned models trained on our dataset can efficiently generate novel, feasible configurations without querying expensive physics oracles. By openly releasing the dataset (https://huggingface.co/datasets/proxima-fusion/constellaration) along with benchmark problems and baselines (https://github.com/proximafusion/constellaration), we aim to lower the entry barrier for optimization and machine learning researchers to engage in stellarator design and to accelerate cross-disciplinary progress toward bringing fusion energy to the grid.

The Johnson-Lindenstrauss (JL) lemma is a cornerstone of dimensionality reduction in Euclidean space, but its applicability to non-Euclidean data has remained limited. This paper extends the JL lemma beyond Euclidean geometry to handle general dissimilarity matrices that are prevalent in real-world applications. We present two complementary approaches: First, we show how the JL transform can be applied to vectors in pseudo-Euclidean space with signature $(p,q)$, providing theoretical guarantees that depend on the ratio of the $(p, q)$ norm and Euclidean norm of two vectors, measuring the deviation from Euclidean geometry. Second, we prove that any symmetric hollow dissimilarity matrix can be represented as a matrix of generalized power distances, with an additional parameter representing the uncertainty level within the data. In this representation, applying the JL transform yields multiplicative approximation with a controlled additive error term proportional to the deviation from Euclidean geometry. Our theoretical results provide fine-grained performance analysis based on the degree to which the input data deviates from Euclidean geometry, making practical and meaningful reduction in dimensionality accessible to a wider class of data. We validate our approaches on both synthetic and real-world datasets, demonstrating the effectiveness of extending the JL lemma to non-Euclidean settings.

Mass spectrometry (MS) plays a critical role in molecular identification, significantly advancing scientific discovery. However, structure elucidation from MS data remains challenging due to the scarcity of annotated spectra. While large-scale pretraining has proven effective in addressing data scarcity in other domains, applying this paradigm to mass spectrometry is hindered by the complexity and heterogeneity of raw spectral signals. To address this, we propose MS-BART, a unified modeling framework that maps mass spectra and molecular structures into a shared token vocabulary, enabling cross-modal learning through large-scale pretraining on reliably computed fingerprint–molecule datasets. Multi-task pretraining objectives further enhance MS-BART's generalization by jointly optimizing denoising and translation task. The pretrained model is subsequently transferred to experimental spectra through finetuning on fingerprint predictions generated with MIST, a pre-trained spectral inference model, thereby enhancing robustness to real-world spectral variability. While finetuning alleviates the distributional difference, MS-BART still suffers molecular hallucination and requires further alignment. We therefore introduce a chemical feedback mechanism that guides the model toward generating molecules closer to the reference structure. Extensive evaluations demonstrate that MS-BART achieves SOTA performance across 5/12 key metrics on MassSpecGym and NPLIB1 and is faster by one order of magnitude than competing diffusion-based methods, while comprehensive ablation studies systematically validate the model's effectiveness and robustness. We provide the data and code at [https://github.com/OpenDFM/MS-BART](https://github.com/OpenDFM/MS-BART).

We tackle the task of recovering an animatable 3D human avatar from a single or a sparse set of images. For this task, beyond a set of images, many prior state-of-the-art methods use accurate “ground-truth” camera poses and human poses as input to guide reconstruction at test-time. We show that pose‑dependent reconstruction degrades results significantly if pose estimates are noisy. To overcome this, we introduce NoPo-Avatar, which reconstructs avatars solely from images, without any pose input. By removing the dependence of test-time reconstruction on human poses, NoPo-Avatar is not affected by noisy human pose estimates, making it more widely applicable. Experiments on challenging THuman2.0, XHuman, and HuGe100K data show that NoPo-Avatar outperforms existing baselines in practical settings (without ground‑truth poses) and delivers comparable results in lab settings (with ground‑truth poses).

Reasoning models are large language models that use extra "thought tokens" before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained in scientific domains without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 577,790 experimentally-grounded chemistry tasks involving synthesized organic molecules. Our model outperforms all previous general-purpose chemistry models, frontier models, and humans, and is more data efficient relative to specialized models. We anticipate that this method can be applied to train highly data-efficient language models specialized for predictive and generative tasks across a wide variety of scientific domains.

Temporally consistent depth estimation from stereo video is critical for real-world applications such as augmented reality, where inconsistent depth estimation disrupts the immersion of users. Despite its importance, this task remains challenging due to the difficulty in modeling long-term temporal consistency in a computationally efficient manner. Previous methods attempt to address this by aggregating spatio-temporal information but face a fundamental trade-off: limited temporal modeling provides only modest gains, whereas capturing long-range dependencies significantly increases computational cost. To address this limitation, we introduce a memory buffer for modeling long-range spatio-temporal consistency while achieving efficient dynamic stereo matching. Inspired by the two-stage decision-making process in humans, we propose a Pick-and-Play Memory (PPM) construction module for dynamic Stereo matching, dubbed as PPMStereo. PPM consists of a pick process that identifies the most relevant frames and a play process that weights the selected frames adaptively for spatio-temporal aggregation. This two-stage collaborative process maintains a compact yet highly informative memory buffer while achieving temporally consistent information aggregation. Extensive experiments validate the effectiveness of PPMStereo, demonstrating state-of-the-art performance in both accuracy and temporal consistency.Codes are available at \textcolor{blue}{https://github.com/cocowy1/PPMStereo}.

Recent deep learning approaches for river discharge forecasting have improved the accuracy and efficiency in flood forecasting, enabling more reliable early warning systems for risk management. Nevertheless, existing deep learning approaches in hydrology remain largely confined to local-scale applications and do not leverage the inherent spatial connections of bodies of water. Thus, there is a strong need for new deep learning methodologies that are capable of modeling spatio-temporal relations to improve river discharge and flood forecasting for scientific and operational applications. To address this, we present RiverMamba, a novel deep learning model that is pretrained with long-term reanalysis data and that can forecast global river discharge and floods on a $0.05^\circ$ grid up to 7 days lead time, which is of high relevance in early warning. To achieve this, RiverMamba leverages efficient Mamba blocks that enable the model to capture spatio-temporal relations in very large river networks and enhance its forecast capability for longer lead times. The forecast blocks integrate ECMWF HRES meteorological forecasts, while accounting for their inaccuracies through spatio-temporal modeling. Our analysis demonstrates that RiverMamba provides reliable predictions of river discharge across various flood return periods, including extreme floods, and lead times, surpassing both AI- and physics-based models. The source code and datasets are publicly available at the project page https://hakamshams.github.io/RiverMamba.

Language model outputs are not always reliable, thus prompting research into how to adapt model responses based on uncertainty. Common approaches include: abstention, where models refrain from generating responses when uncertain; and linguistic calibration, where models hedge their statements using uncertainty quantifiers. However, abstention can withhold valuable information, while linguistically calibrated responses are often challenging to leverage in downstream tasks. We propose a unified view, Conformal Linguistic Calibration (CLC), which reinterprets linguistic calibration as answer set prediction. First we present a framework connecting abstention and linguistic calibration through the lens of linguistic pragmatics. We then describe an implementation of CLC that allows for controlling the level of imprecision in model responses. Results demonstrate our method produces calibrated outputs with conformal guarantees on factual accuracy. Further, our approach enables fine-tuning models to perform uncertainty-aware adaptive claim rewriting, offering a controllable balance between factuality and specificity.

This paper proposes a neural rendering approach that represents a scene as "compressed light-field tokens (CLiFTs)", retaining rich appearance and geometric information of a scene. CLiFT enables compute-efficient rendering by compressed tokens, while being capable of changing the number of tokens to represent a scene or render a novel view with one trained network. Concretely, given a set of images, multi-view encoder tokenizes the images with the camera poses. Latent-space K-means selects a reduced set of rays as cluster centroids using the tokens. The multi-view ``condenser'' compresses the information of all the tokens into the centroid tokens to construct CLiFTs. At test time, given a target view and a compute budget (i.e., the number of CLiFTs), the system collects the specified number of nearby tokens and synthesizes a novel view using a compute-adaptive renderer. trained to handle a variable number of tokens. Extensive experiments on RealEstate10K and DL3DV datasets quantitatively and qualitatively validate our approach, achieving significant data reduction with comparable rendering quality and the highest overall rendering score, while providing trade-offs of data size, rendering quality, and rendering speed.

Diffusion models hold great potential for accelerating antibody design, but their performance is so far limited by the number of antibody-antigen complexes used for model training. Meanwhile, AlphaFold3-like protein folding models, pre-trained on a large corpus of crystal structures, have acquired a broad understanding of biomolecular interaction. Based on this insight, we develop a new antigen-conditioned antibody design model by adapting the diffusion module of AlphaFold3-like models for sequence-structure co-diffusion. Specifically, we extend their structure diffusion module with a sequence diffusion head and fine-tune the entire protein folding model for antibody sequence-structure co-design. Our benchmark results show that sequence-structure co-diffusion models not only surpass state-of-the-art antibody design methods in performance but also maintain structure prediction accuracy comparable to the original folding model. Notably, in the antibody co-design task, our method achieves a CDR-H3 recovery rate of 65% for typical antibodies, outperforming the baselines by 87%, and attains a remarkable 63% recovery rate for nanobodies.

Contrastive learning (CL) is a prevalent technique for training embedding models, which pulls semantically similar examples (positives) closer in the representation space while pushing dissimilar ones (negatives) further apart. A key source of negatives are "in-batch" examples, i.e., positives from other examples in the batch. Effectiveness of such models is hence strongly influenced by the size and quality of training batches. In this work, we propose *Breaking the Batch Barrier* (B3), a novel batch construction strategy designed to curate high-quality batches for CL. Our approach begins by using a pretrained teacher embedding model to rank all examples in the dataset, from which a sparse similarity graph is constructed. A community detection algorithm is then applied to this graph to identify clusters of examples that serve as strong negatives for one another. The clusters are then used to construct batches that are rich in in-batch negatives. Empirical results on the MMEB multimodal embedding benchmark (36 tasks) demonstrate that our method sets a new state of the art, outperforming previous best methods by +1.3 and +2.9 points at the 7B and 2B model scales, respectively. Notably, models trained with B3 surpass existing state-of-the-art results even with a batch size as small as 64, which is 4–16× smaller than that required by other methods. Moreover, experiments show that B3 generalizes well across domains and tasks, maintaining strong performance even when trained with considerably weaker teachers.