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Applications · Chemistry, Physics, and Earth Sciences

Lingshi MENG, Haosen Shi, Sinno Jialin Pan

Physics-Informed Neural Networks (PINNs) represent a significant advancement in computational methods for solving partial differential equations (PDEs). However, the adoption of deeper neural network architectures presents significant challenges, as they struggle to address differential-related complications that arise during the computation of derivatives over the input of PINNs. These complications extend beyond traditional vanishing and exploding gradients to include vanishing and exploding differentials, with both phenomena becoming more severe as networks grow deeper. By examining the computation graph of derivatives in deep neural networks, we identify key bottlenecks causing numerical instabilities in deep architectures. In response, we introduce a novel approach that utilizes Coupling Layers with carefully regulated spectral norms of Jacobian matrices to stabilize and facilitate deep PINN training, effectively addressing differential-related challenges and improving model stability. Our proposed architecture successfully mitigates the fundamental constraints of deeper PINNs while maximizing their capabilities through consistent differential propagation. Comprehensive evaluations show that our approach surpasses conventional shallow PINN methods and alternative deep PINN designs across a range of challenging problems, particularly in cases featuring high-frequency solution components.

Applications · Chemistry, Physics, and Earth Sciences

Miruna Cretu, John Bradshaw, Patricia Suriana, Saeed Saremi, Omar Mahmood, Kirill Shmilovich, Kangway Chuang, Vishnu Sresht, Colin A. Grambow

We present SynLaD, a latent diffusion framework for small-molecule generation that unifies 3D design objectives (what to make) with synthetic accessibility (how to make it). Current models typically optimize one objective at the expense of the other, creating a bottleneck for discovering high-scoring and experimentally testable molecules. SynLaD combines reaction-constrained generation with pharmacophore-conditioned 3D design by learning a latent space that decodes to both 3D structures and synthesis pathways. An encoder maps molecules to a latent representation used by two decoder heads: (i) a geometric head that reconstructs atom types and coordinates and (ii) an autoregressive synthesis head that outputs synthetic routes in a serialized, reaction-based notation. A diffusion transformer generates novel latents in the learned space, conditioned on pharmacophore profiles. Across analogue-generation tasks for bioactive ligands, SynLaD outperforms existing baselines in synthesizable and diverse hit generation, demonstrating that a single model can produce shape-accurate molecules with feasible synthesis plans.

Applications · Chemistry, Physics, and Earth Sciences

Jiahao Chen, Letian Gao, Yanhaozhu, Wenbiao Zhou, Bing Su, Zhi Lu, Bo Huang

Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for \textit{de novo} drug design. We consider two types of ED—calculated and cryo-EM/X-ray—obtainable from computational or experimental sources, supporting unified pre-training and experimental integration. Compared with rigid pocket representations, experimental ED naturally captures conformational flexibility and provides a more faithful description of the binding environment. Based on this, we introduce EDMolGPT, a decoder-only autoregressive framework that generates molecules from low-resolution ED point clouds. By grounding generation in physically meaningful density signals, EDMolGPT mitigates structural bias and produces molecules with 3D conformations. Evaluations on 101 biological targets verify the effectiveness. Code will be released upon acceptance.

Applications · Chemistry, Physics, and Earth Sciences

Hao Wei, Björn List, Nils Thuerey

Physics obeys strict symmetries like rotational equivariance. However, the standard Transformer architectures widely used in physics foundation models do not enforce these constraints by construction. We introduce ReViT, a rotationally equivariant Vision Transformer framework for neural PDE solvers operating on grid-based physical fields that strictly enforces rotational equivariance. ReViT maps scalar and vector inputs into locally invariant representations derived from physics-based canonical bases, enabling the use of standard self-attention without symmetry violations. Built on a hierarchical Swin-style backbone with a precomputed reference basis pyramid, ReViT preserves equivariance across multi-scale operations. We evaluate ReViT on a wide range of 2D and 3D PDE benchmarks, such as Magnetohydrodynamics and Turbulent Channel Flows, demonstrating significant gains over state-of-the-art baselines. ReViT exhibits strong generalization, and reduces MSE by up to 65\% compared with the best-performing alternatives.

Applications · Chemistry, Physics, and Earth Sciences

Jinjin He, Zhiqi Li, Sinan Wang, Bo Zhu

We propose Hermite-NGP, a gradient-augmented multi-resolution hash encoding designed to enable fast and accurate computation of spatial derivatives for neural PDE solvers. Unlike existing NGP-based approaches that rely on automatic differentiation or finite differences and suffer from instability or high cost, Hermite-NGP explicitly stores function values and mixed partial derivatives at hash grid vertices, allowing fully analytic evaluation of gradients, Jacobians, and Hessians via Hermite interpolation. This design preserves the efficiency and spatial adaptivity of NGP while supporting exact differential operators up to second order. We further introduce a multi-resolution curriculum training strategy analogous to multigrid V-cycles to enable coarse-to-fine optimization. Across a range of 2D and 3D PDE benchmarks, Hermite-NGP achieves up to an order-of-magnitude lower error than prior neural PDE methods, and reduces wall-clock convergence time by $2$ – $10\times$ compared to other solvers, with per-epoch training times as low as $3.5 \mathrm{ms}$ for models with up to $17$M parameters.

Applications · Chemistry, Physics, and Earth Sciences

Yongqi Jin, Yecheng Wang, Jun-jie Wang, Rong Zhu, Guolin Ke, Weinan E

Accurate prediction of nuclear magnetic resonance (NMR) chemical shifts is fundamental to spectral analysis and molecular structure elucidation, yet existing machine learning methods rely on limited, labor-intensive atom-assigned datasets. We propose a semi-supervised framework that learns NMR chemical shifts from millions of literature-extracted spectra without explicit atom-level assignments, integrating a small amount of labeled data with large-scale unassigned spectra. We formulate chemical shift prediction from literature spectra as a permutation-invariant set supervision problem, and show that under commonly satisfied conditions on the loss function, optimal bipartite matching reduces to a sorting-based loss, enabling stable large-scale semi-supervised training beyond traditional curated datasets. Our models achieve substantially improved accuracy and robustness over state-of-the-art methods and exhibit stronger generalization on significantly larger and more diverse molecular datasets. Moreover, by incorporating solvent information at scale, our approach captures systematic solvent effects across common NMR solvents for the first time. Overall, our results demonstrate that large-scale unlabeled spectra mined from the literature can serve as a practical and effective data source for training NMR shift models, suggesting a broader role of literature-derived, weakly structured data in data-centric AI for science.

Applications · Chemistry, Physics, and Earth Sciences

Benjamin Shaffer, Shawn Koohy, Brooks Kinch, M. Ani Hsieh, Nathaniel Trask

We aim to develop physics foundation models for science and engineering that provide real-time solutions to Partial Differential Equations (PDEs) which preserve structure and accuracy under adaptation to unseen geometries. To this end, we introduce General-Geometry Neural Whitney Forms (Geo-NeWF): a data-driven finite element method. We jointly learn a differential operator and compatible reduced finite element spaces defined on the underlying geometry. The resulting model is solved to generate predictions, while exactly preserving physical conservation laws through Finite Element Exterior Calculus. Geometry enters the model as a discretized mesh both through a transformer-based encoding and as the basis for the learned finite element spaces. This explicitly connects the underlying geometry and imposed boundary conditions to the solution, providing a powerful inductive bias for learning neural PDEs which we demonstrate improves generalization to unseen domains. We provide a novel parameterization of the constitutive model ensuring existence and uniqueness of the solution. Our approach demonstrates state-of-the-art performance on several steady-state PDE benchmarks and provides a significant improvement over conventional baselines on out-of-distribution geometries.

Applications · Chemistry, Physics, and Earth Sciences

Arthur Kosmala, Stephan Günnemann, Meng Gao, Brandon Wood

Molecular dynamics (MD) is a key tool for simulating the dynamical behavior of atomic systems. However, MD is inherently serial, which makes it difficult to increase single-system throughput with concurrent compute. To address this, we introduce **L**angevin **S**peculative **D**ynamics (**LSD**), a distributed and model-agnostic speculative sampler for accelerating MD *without adding relative error*. Inspired by speculative methods in language and diffusion modeling, LSD uses a draft model to propose fast simulation steps and verifies them in parallel with a slower target model, applying a transport map from the draft to the target distribution. We extend speculative sampling to second-order Langevin dynamics, derive the achievable speedup as a function of physical parameters, show that LSD generalizes across different systems and draft-target combinations with a 3-9x speedup, and confirm theoretically and empirically that LSD samples trajectories from the same distribution as its target model.

Applications · Robotics

Yufei Xue, Yunfeng Lin, Wentao Dong, Yang Tang, Jingbo Wang, Jiangmiao Pang, Ming Zhou, Minghuan Liu, Weinan Zhang

Learning-based whole-body controllers have become a key driver for humanoid robots, yet most existing approaches require robot-specific training. In this paper, we study the problem of cross-embodiment humanoid control and show that a single policy can robustly generalize across a wide range of humanoid robot designs with one-time training. We introduce XHugWBC, a novel cross-embodiment training framework that enables generalist humanoid control through: (1) physics-consistent morphological randomization, (2) semantically aligned observation and action spaces across diverse humanoid robots, and (3) effective policy architectures modeling morphological and dynamical properties. XHugWBC is not tied to any specific robot. Instead, it internalizes a broad distribution of morphological and dynamical characteristics during training. By learning motion priors from diverse randomized embodiments, the policy acquires a strong structural bias that supports zero-shot transfer to previously unseen robots. Experiments on twelve simulated humanoids and seven real-world robots demonstrate the strong generalization and robustness of the resulting universal controller.

Keyue Qiu, Xintong Wang, Zhilong Zhang, Hao Zhou, Wei-Ying Ma

Biomolecules such as proteins and small-molecule ligands play a central role in biological systems, arising from the tight interplay between sequence and three-dimensional structure. Recent generative models for biomolecular co-design aim to capture this interplay by jointly modeling coupled modalities. However, existing approaches largely adopt a parallel execution of marginal generative processes, implicitly enforcing fixed synchronous coupling. We argue that a critical but overlooked degree of freedom lies in how these marginal processes are \emph{temporally coupled} during training and generation, where inappropriate coupling can introduce high-variance supervision and inconsistent intermediate states, affecting modality consistency. To address this, we introduce GeoCoupling, a systematic framework that optimizes for temporal couplings between heterogeneous modalities. Empirical results across structure-based drug design and unconditional protein design demonstrate the learned couplings consistently outperform synchronous and randomly coupled baselines, yielding biomolecules with improved physical validity and diversity.

Applications · Chemistry, Physics, and Earth Sciences

Paul Collart, Juergen Gall, Andrea Schnepf, Holger Pagel, Lars Doorenbos

Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Representing microbial dynamics in process-based soil models is therefore critical to predict carbon cycling in soils, albeit highly challenging to inform from data. One promising approach to improve their parametrisation is the integration of genomic data, yet modelling the complex and unknown relationship between genomes and the processes the microbes are driving is an unsolved problem. In this work, we present the first hybrid modeling framework for deriving biokinetic parameter values of a process-based soil organic matter turnover model from metagenome-inferred functional traits based on DNA sequencing data. Our model predicts biokinetic parameters of the process-based model from genomic trait data with a neural network and integrates constraints from ecological theory and literature to ensure realistic behavior, even of non-observed state variables. We evaluate our method on synthetic genomic trait datasets of varying complexity, showing that our approach improves performance, reduces model equifinality, and learns the dynamics of unmeasurable components of the process-based model effectively, even for small training datasets.

Deep Learning · Self-Supervised Learning

Yongchao Huang

Joint Embedding Predictive Architectures (JEPA) offer a scalable paradigm for self-supervised learning by predicting latent representations rather than reconstructing high-entropy observations. However, existing formulations rely on deterministic regression objectives, which masks probabilistic semantics and limits its applicability in stochastic control. We introduce \emph{Variational JEPA (VJEPA)}, a probabilistic generalization that learns a predictive distribution over future latent states via a variational objective. We show that VJEPA unifies representation learning with Predictive State Representations (PSRs) and Bayesian filtering, establishing that sequential modeling does not require autoregressive observation likelihoods. Theoretically, we prove that VJEPA representations serve as sufficient information states for optimal control without pixel reconstruction, while providing formal guarantees for collapse avoidance. We further propose \emph{Bayesian JEPA (BJEPA)}, which extends the VJEPA framework to factorize predictive belief into a learned dynamics expert and a modular prior expert, enabling zero-shot task transfer and constraints satisfactions (e.g., goals, physics) via a Product of Experts. Empirically, VJEPA filters out high-variance nuisance distractors that cause representation collapse in generative baselines. By enabling principled uncertainty estimation (e.g. constructing credible intervals via sampling) while remaining likelihood-free regarding observations, VJEPA provides a foundational framework for scalable, robust, uncertainty-aware planning in high-dimensional, noisy environments.

Social Aspects · Safety

Dongwook Choi, Taeyoon Kwon, Bogyung Jeong, Minju Kim, Yeonjun Hwang, Hyojun Kim, Byungchul Kim, Young Kyun Jang, Jinyoung Yeo

MLLM-powered embodied agents deployed in real-world environments encounter physical hazards. However, existing approaches lack explicit mechanisms for identifying hazards and reasoning about action-conditioned risks, leading agents to either miss risky interactions or over-identify risks. To address this, we propose EMBGUARD, the first MLLM-based safety guardrail for embodied agents designed to decouple physical risk reasoning from agent policy. By evaluating a (visual observation, action) pair, EMBGUARD identifies hazardous configurations and provides natural language explanations of potential risks. Alongside EMBGUARD, we contribute EMBHAZARD, a training dataset of 17K action-conditioned pairs, and EMBGUARDTEST, a benchmark of 189 manually curated real-world scenarios spanning seven physical risk categories. Through compositional variation of hazards and actions, we generate diverse risky and benign scenarios that agents may encounter during planning. Despite its compact size (2B, 4B), EMBGUARD achieves performance competitive with proprietary MLLMs (e.g., GPT-5.1, Gemini-2.5-Pro) while significantly reducing the false-positive rates that hinder realtime deployment. We make the code, data, and models publicly available at https://anonymous.4open.science/r/EMBGuard-742D.

Deep Learning · Self-Supervised Learning

Yaoqi Liu, Jin Wang, Chunchen Wang, Hui Wang, Chuan Shi

In recent years, wireless signal recognition (WSR), which leverages artificial intelligence (AI) to identify properties of passively received radio signals, has garnered significant attention due to its broad applications, such as spectrum management. Existing WSR methods typically learn directly from received signals, which are distorted by physical wireless channel effects such as fading, and current denoising diffusion models lack de-channeling capabilities, which leads to performance degradation. Therefore, we propose PWC-Diff, a novel framework that integrates prior Physical Wireless Channels into the denoising Diffusion process. The framework employs a dedicated architecture named FusedFormer, which contains a fusion module and a self-attention module that jointly capture the temporal and spectral characteristics of the signals throughout the diffusion trajectory. By leveraging prior wireless channels, PWC-Diff learns to progressively “de-channel” the received signal and recover a representation closer to the transmitted signal. Extensive experiments on several datasets across three WSR tasks have achieved state-of-the-art (SOTA) performance, which demonstrates the rationality of our theory, and ablation experiments further illustrate the effectiveness of our proposed PWC-Diff.

Applications · Chemistry, Physics, and Earth Sciences

Yitian Wang, Zhao Yang, Angxiao Yue, Wentao Guo, Yaning Cui, Hongteng Xu

Modeling peptide cyclization is critical for the virtual screening of candidate peptides with desirable physical and pharmaceutical properties. This task is challenging because a cyclic peptide often exhibits diverse, ring-shaped conformations, which cannot be well captured by deterministic prediction models derived from linear peptide folding. In this study, we propose MuCO (Multi-stage Conformation Optimization), a generative peptide cyclization method that models the distribution of cyclic peptide conformations conditioned on the corresponding linear peptide. In principle, MuCO decouples the peptide cyclization task into three stages: topology-aware backbone design, generative side-chain packing, and physics-aware all-atom optimization, thereby generating and optimizing conformations of cyclic peptides in a coarse-to-fine manner. This multi-stage framework enables an efficient parallel sampling strategy for conformation generation and allows for rapid exploration of diverse, low-energy conformations. Experiments on the large-scale CPSea dataset demonstrate that MuCO significantly outperforms state-of-the-art methods in consistently in physical stability, structural diversity, secondary structure recovery, and computational efficiency, making it a promising computational tool for exploring and designing cyclic peptides.

Applications · Chemistry, Physics, and Earth Sciences

Yi Zhang, Peng Wang, Difan Zou

Diffusion models show growing promise for generative modeling of physical systems, but enforcing partial differential equation (PDE) constraints directly is infeasible during the stochastic denoising process. Current methods apply constraints to the expected clean sample, incurring a Jensen’s Gap that forces a trade-off between PDE satisfaction and generative accuracy. To bridge this gap, we propose Physics-Informed Distillation of Diffusion Models (PIDDM), a simple yet effective post-hoc distillation strategy that enforces PDE constraints after training. PIDDM enables fast single-step generation while improving both physical consistency and sample quality, supporting forward/inverse problems and reconstruction from partial observations. Extensive experiments across PDE benchmarks show PIDDM outperforms recent baselines, such as PIDM, DiffusionPDE, and ECI-sampling, in both accuracy and constraint satisfaction, with lower computation and minimal hyperparameter tuning, offering a more efficient pathway to physics-informed diffusion models.

Applications · Chemistry, Physics, and Earth Sciences

Zhaoxin Yu, Nan Xu, Kun Chen, Jiahao Zhao, Lei Wang, Wenji Mao

With the continuous advancement of reasoning abilities in Large Language Models (LLMs), their application to scientific reasoning tasks has gained significant research attention. Current research primarily emphasizes boosting LLMs' performances on scientific QA benchmarks by training on larger, more comprehensive datasets with extended reasoning chains. However, these approaches neglect the essence of scientific reasoning process -- logicality, which is the rational foundation to ensure the validity of reasoning steps leading to reliable conclusions. In this work, we make the first systematic investigation into the internal logicality underlying LLM scientific reasoning, and develop a scientific logicality enriched methodology, including a set of assessment criteria and data sampling methods for logicality-guided training, to improve the logical faithfulness as well as task performance. Further, we take physics, characterized by its diverse logical structures and formalisms, as an exemplar discipline to practise the above methodology. For data construction, we extract scientific problems from academic literature and sample a high-quality dataset exhibiting strong logicality. Experiments based on three different backbone LLMs reveal that: 1) the training data we constructed can effectively improve the scientific logicality in LLM reasoning; and 2) the enriched scientific logicality plays a critical role in solving scientific problems.

Applications · Chemistry, Physics, and Earth Sciences

Luca Anthony Thiede, Abdulrahman Aldossary, Andreas Burger, Jorge Campos-Gonzalez-Angulo, Alex Zook, Melisa Alkan, KOHEI NAKAJI, Jérôme F. Gonthier, Taylor Patti, Mohammad Vakili 等

Density functional theory (DFT) is the most widely used method for calculating molecular properties; however, its accuracy is often insufficient for quantitative predictions. Coupled cluster (CC) theory is the most successful method for achieving accuracy beyond DFT and predicting properties that closely align with experiment. It is known as the ``gold standard'' of quantum chemistry. Unfortunately, the high computational cost of CC limits its widespread applicability. In this work, we present the Molecular Orbital Learning Model (MoLe), an equivariant machine learning model that directly predicts CC's core mathematical objects, the excitation amplitudes, from the mean-field Hartree-Fock molecular orbitals as inputs. We test various aspects of our model and demonstrate its very high data efficiency and remarkable out-of-distribution generalization to larger molecules and off-equilibrium geometries, despite being trained only on small equilibrium geometries. Finally, we also examine its ability to reduce the number of cycles required to converge CC calculations. MoLe can set the foundations for high-accuracy wavefunction-based ML architectures to accelerate molecular design and complement force-field approaches.

Reinforcement Learning · Deep RL

John Wikman, Alexandre Proutiere, David Broman

In standard reinforcement learning (RL) settings, the interaction between the agent and the environment is typically modeled as a Markov decision process (MDP), which assumes that the agent observes the system state instantaneously, selects an action without delay, and executes it immediately. In real-world dynamic environments, such as cyber-physical systems, this assumption often breaks down due to delays in the interaction between the agent and the system. These delays can vary stochastically over time and are typically _unobservable_ when deciding on an action. Existing methods deal with this uncertainty conservatively by assuming a known fixed upper bound on the delay, even if the delay is often much lower. In this work, we introduce the _interaction layer_, a general framework that enables agents to adaptively handle unobservable and time-varying delays. Specifically, the agent generates a matrix of possible future actions, anticipating a horizon of potential delays, to handle both unpredictable delays and lost action packets sent over networks. Building on this framework, we develop a model-based algorithm, _Actor-Critic with Delay Adaptation (ACDA)_, which dynamically adjusts to delay patterns. Our method significantly outperforms state-of-the-art approaches across a wide range of locomotion benchmark environments, including real-world measured delays.

Deep Learning · Foundation Models

Xindi Wu, Despoina Paschalidou, Jun Gao, Antonio Torralba, Laura Leal-Taixé, Olga Russakovsky, Sanja Fidler, Jonathan Lorraine

Despite the rapid progress of video generation models, the role of data in influencing motion is poorly understood. We present Motive (MOTIon attribution for Video gEneration), a motion-centric, gradient-based data attribution framework that scales to modern, large, high-quality video datasets and models. We use this to study which fine-tuning clips improve or degrade temporal dynamics. Motive isolates temporal dynamics from static appearance via motion-weighted loss masks, yielding efficient and scalable motion-specific influence computation. On text-to-video models, Motive identifies clips that strongly affect motion and guides data curation that improves temporal consistency and physical plausibility. With Motive-selected high-influence data, we improve both motion smoothness and dynamic degree on VBench, achieving a 74.1% human preference win rate compared with the pretrained base model. To our knowledge, this is the first framework to attribute motion rather than visual appearance in video generative models and to use it to curate fine-tuning data.