论文检索

Applications · Chemistry, Physics, and Earth Sciences

Pengkang Guo, Bruno Correia, Pierre Vandergheynst, Daniel Probst

Machine learning for protein modeling faces significant challenges due to proteins' inherently dynamic nature, yet most graph-based machine learning methods rely solely on static structural information. Recently, the growing availability of molecular dynamics trajectories provides new opportunities for understanding the dynamic behavior of proteins; however, computational methods for utilizing this dynamic information remain limited. We propose a novel graph representation that integrates both static structural information and dynamic correlations from molecular dynamics trajectories, enabling more comprehensive modeling of proteins. By applying relational graph neural networks (RGNNs) to process this heterogeneous representation, we demonstrate significant improvements over structure-based approaches across three distinct tasks: atomic adaptability prediction, binding site detection, and binding affinity prediction. Our results validate that combining static and dynamic information provides complementary signals for understanding protein-ligand interactions, offering new possibilities for drug design and structural biology applications.

Applications · Chemistry, Physics, and Earth Sciences

Sanjeev Raja, Martin Šípka, Michael Psenka, Tobias Kreiman, Michal Pavelka, Aditi Krishnapriyan

Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches rely on expensive training procedures and under-utilize growing quantities of atomistic data, limiting scalability and generalization. Generative models of atomistic conformational ensembles sample temporally independent states from energy landscapes, but their application to TPS remains mostly unexplored. In this work, we address TPS by interpreting candidate paths as trajectories sampled from stochastic dynamics induced by the learned score function of generative models, namely denoising diffusion and flow matching. Under these dynamics, finding high-likelihood transition paths becomes equivalent to minimizing the Onsager-Machlup (OM) action functional, enabling us to repurpose pre-trained generative models for TPS in a zero-shot fashion. We demonstrate our approach on a Müller-Brown potential and several fast-folding proteins, where we obtain diverse, physically realistic transition pathways, as well as tetrapeptides, where we demonstrate successful TPS on systems not seen by the generative model during training. Our method can be easily incorporated into new generative models, making it practically relevant as models continue to scale and improve.

Applications · Chemistry, Physics, and Earth Sciences

Xiang Fu, Brandon Wood, Luis Barroso-Luque, Daniel S. Levine, Meng Gao, Misko Dzamba, Larry Zitnick

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

Applications · Chemistry, Physics, and Earth Sciences

Qingpo Wuwu, Chonghan Gao, Tianyu Chen, Yihang Huang, Yuekai Zhang, Jianing Wang, Jianxin Li, Haoyi Zhou, Shanghang Zhang

Solving partial differential equations (PDEs) using neural methods has been a long-standing scientific and engineering research pursuit. Physics-Informed Neural Networks (PINNs) have emerged as a promising alternative to traditional numerical methods for solving PDEs. However, the gap between domain-specific knowledge and deep learning expertise often limits the practical application of PINNs. Previous works typically involve manually conducting extensive PINNs experiments and summarizing heuristic rules for hyperparameter tuning. In this work, we introduce PINNsAgent, a novel surrogation framework that leverages large language models (LLMs) to bridge the gap between domain-specific knowledge and deep learning. PINNsAgent integrates Physics-Guided Knowledge Replay (PGKR) for efficient knowledge transfer from solved PDEs to similar problems, and Memory Tree Reasoning for exploring the search space of optimal PINNs architectures. We evaluate PINNsAgent on 14 benchmark PDEs, demonstrating its effectiveness in automating the surrogation process and significantly improving the accuracy of PINNs-based solutions.

Social Aspects · Privacy

David Geissbühler, Hatef Otroshi Shahreza, Sébastien Marcel

Face recognition models are trained on large-scale datasets, which have privacy and ethical concerns. Lately, the use of synthetic data to complement or replace genuine data for the training of face recognition models has been proposed. While promising results have been obtained, it still remains unclear if generative models can yield diverse enough data for such tasks. In this work, we introduce a new method, inspired by the physical motion of soft particles subjected to stochastic Brownian forces, allowing us to sample identities distributions in a latent space under various constraints. We introduce three complementary algorithms, called Langevin, Dispersion, and DisCo, aimed at generating large synthetic face datasets. With this in hands, we generate several face datasets and benchmark them by training face recognition models, showing that data generated with our method exceeds the performance of previously GAN-based datasets and achieves competitive performance with state-of-the-art diffusion-based synthetic datasets. While diffusion models are shown to memorize training data, we prevent leakage in our new synthetic datasets, paving the way for more responsible synthetic datasets. Project page: https://www.idiap.ch/paper/synthetics-disco

Applications · Chemistry, Physics, and Earth Sciences

Yi He, Yiming Yang, Xiaoyuan Cheng, Hai Wang, Xiao Xue, Boli Chen, Yukun Hu

Generating long-term trajectories of dissipative chaotic systems autoregressively is a highly challenging task. The inherent positive Lyapunov exponents amplify prediction errors over time.Many chaotic systems possess a crucial property — ergodicity on their attractors, which makes long-term prediction possible. State-of-the-art methods address ergodicity by preserving statistical properties using optimal transport techniques. However, these methods face scalability challenges due to the curse of dimensionality when matching distributions. To overcome this bottleneck, we propose a scalable transformer-based framework capable of stably generating long-term high-dimensional and high-resolution chaotic dynamics while preserving ergodicity. Our method is grounded in a physical perspective, revisiting the Von Neumann mean ergodic theorem to ensure the preservation of long-term statistics in the $\mathcal{L}^2$ space. We introduce novel modifications to the attention mechanism, making the transformer architecture well-suited for learning large-scale chaotic systems. Compared to operator-based and transformer-based methods, our model achieves better performances across five metrics, from short-term prediction accuracy to long-term statistics. In addition to our methodological contributions, we introduce new chaotic system benchmarks: a machine learning dataset of 140$k$ snapshots of turbulent channel flow and a processed high-dimensional Kolmogorov Flow dataset, along with various evaluation metrics for both short- and long-term performances. Both are well-suited for machine learning research on chaotic systems.

Deep Learning · Foundation Models

Keyon Vafa, Peter Chang, Ashesh Rambachan, Sendhil Mullainathan

Foundation models are premised on the idea that sequence prediction can uncover deeper domain understanding, much like how Kepler's predictions of planetary motion later led to the discovery of Newtonian mechanics. However, evaluating whether these models truly capture deeper structure remains a challenge. We develop a technique for evaluating foundation models that examines how they adapt to synthetic datasets generated from some postulated world model. Our technique measures whether the foundation model's inductive bias aligns with the world model, and so we refer to it as an inductive bias probe. Across multiple domains, we find that foundation models can excel at their training tasks yet fail to develop inductive biases towards the underlying world model when adapted to new tasks. We particularly find that foundation models trained on orbital trajectories consistently fail to apply Newtonian mechanics when adapted to new physics tasks. Further analysis reveals that these models behave as if they develop task-specific heuristics that fail to generalize.

Probabilistic Methods · Monte Carlo and Sampling Methods

Onat Dalmaz, Arjun Desai, Reinhard Heckel, Tolga Cukur, Akshay Chaudhari, Brian Hargreaves

Accelerated MRI reconstruction involves solving an ill-posed inverse problem where noise in acquired data propagates to the reconstructed images. Noise analyses are central to MRI reconstruction for providing an explicit measure of solution fidelity and for guiding the design and deployment of novel reconstruction methods. However, deep learning (DL)-based reconstruction methods have often overlooked noise propagation due to inherent analytical and computational challenges, despite its critical importance. This work proposes a theoretically grounded, memory-efficient technique to calculate *voxel-wise variance* for quantifying uncertainty due to acquisition noise in accelerated MRI reconstructions. Our approach is based on approximating the noise covariance using the DL network's Jacobian, which is intractable to calculate. To circumvent this, we derive an *unbiased estimator* for the diagonal of this covariance matrix—voxel-wise variance—, and introduce a Jacobian sketching technique to efficiently implement it. We evaluate our method on knee and brain MRI datasets for both data-driven and physics-driven networks trained in supervised and unsupervised manners. Compared to empirical references obtained via Monte-Carlo simulations, our technique achieves near-equivalent performance while reducing computational and memory demands by an order of magnitude or more. Furthermore, our method is robust across varying input noise levels, acceleration factors, and diverse undersampling schemes, highlighting its broad applicability. Our work *reintroduces* accurate and efficient noise analysis as a central tenet of reconstruction algorithms, holding promise to reshape how we evaluate and deploy DL-based MRI.

Applications · Robotics

Jianke Zhang, Yanjiang Guo, Yucheng Hu, Xiaoyu Chen, Xiang Zhu, Jianyu Chen

Recent advancements in Vision-Language-Action (VLA) models have leveraged pre-trained Vision-Language Models (VLMs) to improve the generalization capabilities.VLMs, typically pre-trained on vision-language understanding tasks, provide rich semantic knowledge and reasoning abilities. However, prior research has shown that VLMs often focus onhigh-level semantic content and neglect low-level features, limiting their ability to capture detailed spatial information and understand physical dynamics.These aspects, which are crucial for embodied control tasks, remain underexplored in existing pre-training paradigms.In this paper, we investigate the training paradigm for VLAs, and introduce \textbf{UP-VLA}, a \textbf{U}nified VLA model training with both multi-modal \textbf{U}nderstanding and future \textbf{P}rediction objectives, enhancing both high-level semantic comprehension and low-level spatial understanding. Experimental results show that UP-VLA achieves a 33\% improvement on the Calvin ABC-D benchmark compared to the previous state-of-the-art method. Additionally, UP-VLA demonstrates improved success rates in real-world manipulation tasks, particularly those requiring precise spatial information.

Deep Learning · Large Language Models

Nolan Koblischke, Hyunseok Jang, Kristen Menou, Mohamad Ali-Dib

Modern science emerged from reasoning over repeatedly-observed planetary motions. We present Gravity-Bench-v1, an environment-based benchmark that challenges AI agents on tasks that parallel this historical development. Gravity-Bench-v1 evaluates agents on the discovery of physics concealed within a dynamic environment, using rigorous gravitational dynamics simulations. Gravity-Bench includes out-of-distribution cases, i.e. with physics that deviates from the real world, to evaluate true scientific generalization capabilities. Agents must plan to collect data within an experimental budget and must perform a dynamic form of data analysis and reasoning to solve tasks efficiently. Our benchmark admits an open-ended space of solutions. Reference solutions for each task are provided to calibrate AI performance against human expertise. Technically at an upper-undergraduate level, our benchmark proves challenging to baseline AI agents. Gravity-Bench-v1 and planned extensions should help map out AI progress towards scientific discovery capabilities.

Applications · Chemistry, Physics, and Earth Sciences

Ziyang Yu, Wenbing Huang, Yang Liu

Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based improvements have mostly focused on single-domain molecules, lacking transferability to unfamiliar molecular systems. Therefore, we propose **Uni**fied **Sim**ulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions. First, we employ a multi-head pretraining approach to learn a unified atomic representation model from a large and diverse set of molecular data. Then, based on the stochastic interpolant framework, we learn the state transition patterns over long timesteps from MD trajectories, and introduce a force guidance module for rapidly adapting to different chemical environments. Our experiments demonstrate that UniSim achieves highly competitive performance across small molecules, peptides, and proteins.

Applications · Everything Else

Yuxiang Zhao, zhuomin chai, Xun Jiang, Qiang Xu, Runsheng Wang, Yibo Lin

Recent advancements have integrated various deep-learning methodologies into physical design, aiming for workflows acceleration and surpasses human-devised solutions. However, prior research has primarily concentrated on developing task-specific networks, which necessitate a significant investment of time to construct large, specialized datasets, and the unintended isolation of models across different tasks. In this paper, we introduce DeepLayout, the first general representation learning framework specifically designed for backend circuit design. To address the distinct characteristics of post-placement circuits, including topological connectivity and geometric distribution, we propose a hybrid encoding architecture that integrates GNN with spatial transformers. Additionally, the framework includes a flexible decoder module that accommodates a variety of task types, supporting multiple hierarchical outputs such as nets and layouts. To mitigate the high annotation costs associated with layout data, we introduce a mask-based self-supervised learning approach designed explicitly for layout representation. This strategy involves a carefully devised masking approach tailored to layout features, precise reconstruction guidance, and most critically—two key supervised learning tasks. We conduct extensive experiments on large-scale industrial datasets, demonstrating that DeepLayout surpasses state-of-the-art (SOTA) methods specialized for individual tasks on two crucial layout quality assessment benchmarks. The experiment results underscore the framework’s robust capability to learn the intrinsic properties of circuits.

Applications · Chemistry, Physics, and Earth Sciences

Jiahua Rao, Dahao Xu, Wentao Wei, Yicong Chen, Mingjun Yang, Yuedong Yang

While Graph Neural Networks and Transformers have shown promise in predicting molecular properties, they struggle with directly modeling complex many-body interactions. Current methods often approximate interactions like three- and four-body terms in message passing, while attention-based models, despite enabling direct atom communication, are typically limited to triplets, making higher-order interactions computationally demanding. To address the limitations, we introduce MABNet, a geometric attention framework designed to model four-body interactions by facilitating direct communication among atomic quartets. This approach bypasses the computational bottlenecks associated with traditional triplet-based attention mechanisms, allowing for the efficient handling of higher-order interactions. MABNet achieves state-of-the-art performance on benchmarks like MD22 and SPICE. These improvements underscore its capability to accurately capture intricate many-body interactions in large molecules. By unifying rigorous many-body physics with computational efficiency, MABNet advances molecular simulations for applications in drug design and materials discovery, while its extensible framework paves the way for modeling higher-order quantum effects.

Applications

Stathi Fotiadis, Noah Brenowitz, Tomas Geffner, Yair Cohen, Michael Pritchard, Arash Vahdat, Morteza Mardani

Conditional diffusion and flow models are effective for super-resolving small-scale details in natural images. However, in physical sciences such as weather, three major challenges arise: (i) spatially misaligned input-output distributions (PDEs at different resolutions lead to divergent trajectories), (ii) misaligned and distinct input-output channels (channel synthesis), (iii) several channels with diverse stochasticity scales (multiscale). To address these, we propose to first encode inputs into a latent base distribution that is closer to the target, then apply Flow Matching to generate small-scale physics. The encoder captures deterministic components, while Flow Matching adds stochastic details. To handle uncertainty in the deterministic part, we inject noise via an adaptive noise scaling mechanism, dynamically adjusted by maximum-likelihood estimates of the encoder’s predictions. Experiments on real-world weather data (including super-resolution from 25 km to 2 km scales in Taiwan) and in synthetic Kolmogorov flow datasets show that our proposed Adaptive Flow Matching (AFM) framework outperforms existing methods and produces better-calibrated ensembles.

Applications · Chemistry, Physics, and Earth Sciences

Muhammed Göktepe, Amir Hossein Shamseddin, Erencan Uysal, Javier Monteagudo, Lukas Drees, Aysim Toker, Senthold Asseng, Malte von Bloh

Satellite imagery is essential for Earth observation, enabling applications like crop yield prediction, environmental monitoring, and climatechange assessment. However, integrating satellite imagery with climate data remains a challenge, limiting its utility for forecasting and scenario analysis. We introduce a novel dataset of 2.9 million Sentinel-2 images spanning 15 land cover types with corresponding climate records, forming the foundation for two satellite image generation approaches using fine-tuned Stable Diffusion 3 models. The first is a text-to-image generation model that uses textual prompts with climate and land cover details to produce realistic synthetic imagery for specific regions. The second leverages ControlNet for multi-conditional image generation, preserving spatial structures while mapping climate data or generating time-series to simulate landscape evolution. By combining synthetic image generation with climate and land cover data, our work advances generative modeling in remote sensing, offering realistic inputs for environmental forecasting and new possibilities for climate adaptation and geospatial analysis.

Applications · Chemistry, Physics, and Earth Sciences

Vignesh Gopakumar, Ander Gray, Lorenzo Zanisi, Timothy Nunn, Daniel Giles, Matt Kusner, Stanislas Pamela, Marc Deisenroth

Simulating complex physical systems is crucial for understanding and predicting phenomena across diverse fields, such as fluid dynamics and heat transfer, as well as plasma physics and structural mechanics. Traditional approaches rely on solving partial differential equations (PDEs) using numerical methods, which are computationally expensive and often prohibitively slow for real-time applications or large-scale simulations. Neural PDEs have emerged as efficient alternatives to these costly numerical solvers, offering significant computational speed-ups. However, their lack of robust uncertainty quantification (UQ) limits deployment in critical applications. We introduce a model-agnostic, physics-informed conformal prediction (CP) framework that provides guaranteed uncertainty estimates without requiring labelled data. By utilising a physics-based approach, we can quantify and calibrate the model's inconsistencies with the physics rather than the uncertainty arising from the data. Our approach utilises convolutional layers as finite-difference stencils and leverages physics residual errors as nonconformity scores, enabling data-free UQ with marginal and joint coverage guarantees across prediction domains for a range of complex PDEs. We further validate the efficacy of our method on neural PDE models for plasma modelling and shot design in fusion reactors.

Applications · Everything Else

Ke Liu, Hao Chen, Chunhua Shen

Developing models for protein-ligand interactions holds substantial significance for drug discovery. Supervised methods often failed due to the lack of labeled data for predicting the protein-ligand binding energy, like antibodies. Therefore, unsupervised approaches are urged to make full use of the unlabeled data. To tackle the problem, we propose an efficient, unsupervised protein-ligand binding energy prediction model via the conservation of energy (CEBind), which follows the physical laws. Specifically, given a protein-ligand complex, we randomly sample forces for each atom in the ligand. Then these forces are applied rigidly to the ligand to perturb its position, following the law of rigid body dynamics. Finally, CEBind predicts the energy of both the unperturbed complex and the perturbed complex. The energy gap between two complexes equals the work of the outer forces, following the law of conservation of energy. Extensive experiments are conducted on the unsupervised protein-ligand binding energy prediction benchmarks, comparing them with previous works. Empirical results and theoretic analysis demonstrate that CEBind is more efficient and outperforms previous unsupervised models on benchmarks.

Applications · Robotics

junmin zhong, Emiliano Quinones Yumbla, Seyed Yousef Soltanian, Ruofan Wu, Wenlong Zhang, Jennie Si

This study presents an innovative reinforcement learning (RL) control approach to facilitate soft exosuit-assisted human walking. Our goal is to address the ongoing challenges in developing reliable RL-based methods for controlling physical devices. To overcome key obstacles—such as limited data, the absence of a simulator for human-robot interaction during walking, the need for low computational overhead in real-time deployment, and the demand for rapid adaptation to achieve personalized control while ensuring human safety—we propose an online Adaptation from an offline Imitating Expert Policy (AIP) approach. Our offline learning mimics human expert actions through real human walking demonstrations without robot assistance. The resulted policy is then used to initialize online actor-critic learning, the goal of which is to optimally personalize robot assistance. In addition to being fast and robust, our online RL method also posses important properties such as learning convergence, dynamic stability, and solution optimality. We have successfully demonstrated our simpleand robust framework for safe robot control on all five tested human participants, without selectively presenting results. The qualitative performance guarantees provided by our online RL, along with the consistent experimental validation of AIP control, represent the first demonstration of online adaptation for softsuit control personalization and serve as important evidence for the use of online RL in controlling a physical device to solve a real-life problem.

Applications · Chemistry, Physics, and Earth Sciences

Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities—continuous 3D positions and discrete 2D topologies—which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9\% on CrossDock, more than 10\% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Applications · Chemistry, Physics, and Earth Sciences

Yiming Yang, Xiaoyuan Cheng, Daniel Giles, Sibo Cheng, Yi He, Xiao Xue, Boli Chen, Yukun Hu

Variational data assimilation estimates the dynamical system states by minimizing a cost function that fits the numerical models with the observational data. Although four-dimensional variational assimilation (4D-Var) is widely used, it faces high computational costs in complex nonlinear systems and depends on imperfect state-observation mappings. Deep learning (DL) offers more expressive approximators, while integrating DL models into 4D-Var is challenging due to their nonlinearities and lack of theoretical guarantees in assimilation results. In this paper, we propose \textit{Tensor-Var}, a novel framework that integrates kernel conditional mean embedding (CME) with 4D-Var to linearize nonlinear dynamics, achieving convex optimization in a learned feature space. Moreover, our method provides a new perspective for solving 4D-Var in a linear way, offering theoretical guarantees of consistent assimilation results between the original and feature spaces. To handle large-scale problems, we propose a method to learn deep features (DFs) using neural networks within the Tensor-Var framework. Experiments on chaotic systems and global weather prediction with real-time observations show that Tensor-Var outperforms conventional and DL hybrid 4D-Var baselines in accuracy while achieving a 10- to 20-fold speed improvement.