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Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models

Neural Information Processing Systems

In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular systems. However, while classical diffusion sampling usually recovers the training distribution, the corresponding energy-based interpretation of the learned score is often inconsistent with this distribution, even for low-dimensional toy systems. We trace this inconsistency to inaccuracies of the learned score at very small diffusion timesteps, where the model must capture the correct evolution of the data distribution. In this regime, diffusion models fail to satisfy the Fokker-Planck equation, which governs the evolution of the score. We interpret this deviation as one source of the observed inconsistencies and propose an energy-based diffusion model with a Fokker-Planck-derived regularization term to enforce consistency. We demonstrate our approach by sampling and simulating multiple biomolecular systems, including fast-folding proteins, and by introducing a state-of-the-art transferable Boltzmann emulator for dipeptides that supports simulation and achieves improved consistency and efficient sampling.


Theoretical Benefit and Limitation of Diffusion Language Model

Neural Information Processing Systems

Diffusion language models have emerged as a new approach for text generation. By enabling the parallel sampling of multiple tokens in each diffusion step, they appear to offer a more efficient alternative to auto-regressive models. However, our observations show that current open-sourced diffusion language models require more sampling steps to achieve comparable accuracy on representative tasks-resulting in even higher inference costs than their auto-regressive counterparts. To investigate whether this is an inherent limitation, we conduct a rigorous theoretical analysis of a widely adopted variant: the Masked Diffusion Model (MDM). Surprisingly, our analysis reveals that the conclusion is highly sensitive to the choice of evaluation metric. Under mild conditions, we prove that when the target is near-optimal perplexity, MDMs can achieve this goal in a constant number of sampling steps, independent of sequence length. This result demonstrates that efficiency can, in principle, be attained without compromising generation quality. However, when targeting low sequence error rate-which is important for assessing the "correctness" of a generated sequence, such as a reasoning chain-we show that in the worst case, the required sampling steps must scale linearly with sequence length, thereby eliminating the efficiency advantage. Our analysis establishes the first theoretical foundation for understanding the comparative strengths and limitations of MDMs, offering practical guidance on when to favor MDMs over auto-regressive models and vice versa.


Elastic ViTs from Pretrained Models without Retraining

Neural Information Processing Systems

Vision foundation models achieve remarkable performance but are only available in a limited set of pre-determined sizes, forcing sub-optimal deployment choices under real-world constraints. We introduce SnapViT: single-shot network approximation for pruned Vision Transformers, a new post-pretraining structured pruning method that enables elastic inference across a continuum of compute budgets. Our approach efficiently combines gradient information with cross-network structure correlations, approximated via an evolutionary algorithm, does not require labeled data, generalizes to models without a classification head, and is retraining-free. Experiments on DINO, SigLIPv2, DeIT, and AugReg models demonstrate superior performance over state-of-the-art methods across various sparsities, requiring less than five minutes on a single A100 GPU to generate elastic models that can be adjusted to any computational budget. Our key contributions include an efficient pruning strategy for pretrained Vision Transformers, a novel evolutionary approximation of Hessian off-diagonal structures, and a self-supervised importance scoring mechanism that maintains strong performance without requiring retraining or labels. Code and pruned models are available at: https://elastic.ashita.nl/


Spectral Analysis of Representational Similarity with Limited Neurons

Neural Information Processing Systems

Understanding representational similarity between neural recordings and computational models is essential for neuroscience, yet remains challenging to measure reliably due to the constraints on the number of neurons that can be recorded simultaneously. In this work, we apply tools from Random Matrix Theory to investigate how such limitations affect similarity measures, focusing on Centered Kernel Alignment (CKA) and Canonical Correlation Analysis (CCA). We propose an analytical framework for representational similarity analysis that relates measured similarities to the spectral properties of the underlying representations. We demonstrate that neural similarities are systematically underestimated under finite neuron sampling, mainly due to eigenvector delocalization. Moreover, for power-law population spectra, we show that the number of localized eigenvectors scales as the square root of the number of recorded neurons, providing a simple rule of thumb for practitioners. To overcome sampling bias, we introduce a denoising method to infer population-level similarity, enabling accurate analysis even with small neuron samples. Theoretical predictions are validated on synthetic and real datasets, offering practical strategies for interpreting neural data under finite sampling constraints.


Learning Generalizable Shape Completion with SIM(3) Equivariance

Neural Information Processing Systems

This leaks pose and scale cues that networks may exploit to memorize absolute positions rather than inferring intrinsic geometry. When such alignment is absent in real data, performance collapses. We argue that robust generalization demands architectural equivariance to the similarity group, SIM(3), so the model remains agnostic to pose and scale. Following this principle, we introduce the first SIM(3)-equivariant shape completion network, whose modular layers successively canonicalize features, reason over similarity-invariant geometry, and restore the original frame. Under a de-biased evaluation protocol that removes the hidden cues, our model outperforms both equivariant and augmentation baselines on the PCN benchmark. It also sets new cross-domain records on real driving and indoor scans, lowering minimal matching distance on KITTI by 17%and Chamfer distance ℓ1on OmniObject3D by 14%. Perhaps surprisingly, ours under the stricter protocol still outperforms competitors under their biased settings. These results establish full SIM(3) equivariance as an effective route to truly generalizable shape completion.


Efficient Quadratic Corrections for Frank-Wolfe Algorithms

Neural Information Processing Systems

We develop a Frank-Wolfe algorithm with corrective steps, generalizing previous algorithms including Blended Conditional Gradients, Blended Pairwise Conditional Gradients, and Fully-Corrective Frank-Wolfe. For this, we prove tight convergence guarantees together with an optimal face identification property. Furthermore, we propose two highly efficient corrective steps for convex quadratic objectives based on linear optimization or linear system solving, akin to Wolfe's MinimumNorm Point algorithm, and prove finite-time convergence under suitable conditions. Beyond optimization problems that are directly quadratic, we revisit two algorithms, Split Conditional Gradient and Second-Order Conditional Gradient Sliding, which can leverage quadratic corrections to accelerate the solution of their quadratic subproblems. We show improved convergence rates for the first and prove broader applicability for the second. Finally, we demonstrate substantial computational speedups for Frank-Wolfe-based algorithms with quadratic corrections across the considered problem classes.


WorldEmbeddingVLAInstructionImageVLAActionImage/Video Generation InstructionImagePolicyVLAInstructionImageAction InstructionImageActionAction(a)(b)(c)(d)Dream Queries

Neural Information Processing Systems

Recent advances in vision-language-action (VLA) models have shown promise in integrating image generation with action prediction to improve generalization and reasoning in robot manipulation. However, existing methods are limited to challenging image-based forecasting, which suffers from redundant information and lacks comprehensive and critical world knowledge, including dynamic, spatial and semantic information. To address these limitations, we propose DreamVLA, a novel VLA framework that integrates comprehensive world knowledge forecasting to enable inverse dynamics modeling, thereby establishing a perceptionprediction-action loop for manipulation tasks. Specifically, DreamVLA introduces a dynamic-region-guided world knowledge prediction, integrated with the spatial and semantic cues, which provide compact yet comprehensive representations for action planning.


Scaling Computer-Use Grounding via User Interface Decomposition and Synthesis

Neural Information Processing Systems

Graphical user interface (GUI) grounding, the ability to map natural language instructions to specific actions on graphical user interfaces, remains a critical bottleneck in computer use agent development. Current benchmarks oversimplify grounding tasks as short referring expressions, failing to capture the complexity of real-world interactions that require software commonsense, layout understanding, and fine-grained manipulation capabilities. To address these limitations, we introduce OSWORLD-G, a comprehensive benchmark comprising 564 finely annotated samples across diverse task types including text matching, element recognition, layout understanding, and precise manipulation. Additionally, we synthesize and release the largest computer use grounding dataset JEDI, which contains 4 million examples through multi-perspective decoupling of tasks. Our multi-scale models trained on JEDI demonstrate its effectiveness by outperforming existing approaches on ScreenSpot-v2, ScreenSpot-Pro, and our OSWORLD-G. Furthermore, we demonstrate that improved grounding with JEDI directly enhances agentic capabilities of general foundation models on complex computer tasks with state-of-the-art performance, improving from 23% to 51% on OSWorld. Through detailed ablation studies, we identify key factors contributing to grounding performance and verify that combining specialized data for different interface elements enables compositional generalization to novel interfaces.


Computational Budget Should Be Considered in Data Selection

Neural Information Processing Systems

Data selection improves computational efficiency by choosing informative subsets of training samples. However, existing methods ignore the compute budget, treating data selection and importance evaluation independently of compute budget constraints. Yet empirical studies show no algorithm can consistently outperform others (or even random selection) across varying budgets. We therefore argue that compute budget must be integral to data-selection strategies, since different budgets impose distinct requirements on data quantity, quality, and distribution for effective training. To this end, we propose a novel Computational budget-Aware Data Selection (CADS) method and naturally formulate it into a bilevel optimization framework, where the inner loop trains the model within the constraints of the computational budget on some selected subset of training data, while the outer loop optimizes data selection based on model evaluation.


Rig3R: Rig-Aware Conditioning for Learned 3D Reconstruction

Neural Information Processing Systems

Estimating agent pose and 3D scene structure from multi-camera rigs is a central task in embodied AI applications such as autonomous driving. Recent learned approaches such as DUSt3R have shown impressive performance in multiview settings. However, these models treat images as unstructured collections, limiting effectiveness in scenarios where frames are captured from synchronized rigs with known or inferable structure. To this end, we introduce Rig3R, a generalization of prior multiview reconstruction models that incorporates rig structure when available, and learns to infer it when not. Rig3R conditions on optional rig metadata including camera IDs, timestamp, and rig calibrations to develop a rig-aware latent space that remains robust to missing information.