论文检索

Applications · Chemistry, Physics, and Earth Sciences

Minghan Li, fengji Li, Yilin Tao, Yue Deng

Computational protein design typically employs a sequential workflow of structure generation followed by sequence (re)design. While structure generators can be explicitly conditioned on functional objectives, inverse folding models are constrained by their function-agnostic nature and sequence-structure degeneracy. More critically, the associated training objectives do not account for the *Best-of-N* (BoN) inference protocol, resulting in a fundamental training-inference misalignment. Here, we propose FIDIA, a reinforcement learning framework that enables **F**unction-**I**nformed sequence **D**esign via **I**nference-**A**ligned policy optimization. Specifically, FIDIA integrates functional constraints into composite rewards and explicitly optimize the induced policy under BoN toward high-fitness sequence regions. We achieve this via a grounded gradient estimator that directly maximizes the expected maximum reward. FIDIA consistently outperforms both standard and RL-optimized baselines in success rate and precision on a general motif scaffolding benchmark. Further experiments on realworld cases including vaccine and affinity-enhancing enzyme design validate FIDIA’s efficacy in complex therapeutic and biocatalytic contexts.

Applications · Chemistry, Physics, and Earth Sciences

Kevin Han, Haolin Cong, Bowen Deng, Amir Barati Farimani

Machine learning interatomic potentials (MLIPs) have proven to be wildly useful for molecular dynamics simulations, powering countless drug and materials discovery applications. However, MLIPs face two primary bottlenecks preventing them from reaching realistic simulation scales: inference time and memory consumption. In this work, we address both issues by challenging the long-held belief that the cutoff radius for the MLIP must be held to a fixed, constant value. For the first time, we introduce a **dynamic** cutoff formulation that still leads to stable, long timescale molecular dynamics simulation. In introducing the dynamic cutoff, we are able to induce sparsity onto the underlying atom graph by targeting a specific number of neighbors per atom, significantly reducing both memory consumption and inference time. We show the effectiveness of a dynamic cutoff by implementing it onto 4 state of the art MLIPs: MACE, Nequip, Orbv3, and TensorNet, leading to **2.26x** less memory consumption and **2.04x** faster inference time, depending on the model and atomic system. We also perform an extensive error analysis and find that the dynamic cutoff models exhibit minimal accuracy dropoff compared to their fixed cutoff counterparts on both materials and molecular datasets. All model implementations and training code will be fully open sourced.

Applications · Chemistry, Physics, and Earth Sciences

Jiyeon Kim, Youngjoon Hong, Won-Yong Shin

Mesh-based simulations provide high-fidelity solutions to partial differential equations (PDEs), but achieving such accuracy typically requires fine meshes, leading to substantial computational overhead. Super-resolution techniques aim to mitigate this cost by reconstructing high-resolution (HR), high-fidelity solutions from low-cost, low-resolution (LR) counterparts. However, training neural networks for super-resolution often demands large amounts of expensive HR supervision data. To address this challenge, we propose SuperMeshNet, an HR data-efficient super-resolution framework for mesh-based simulations aided by message passing neural networks (MPNNs). As its core, SuperMeshNet introduces complementary learning, a semi-supervised approach that effectively leverages both 1) a small amount of paired LR-HR data and 2) abundant unpaired LR data via two jointly trained, complementary MPNN-based models. Additionally, our model is enriched by inductive biases, which is empirically shown to further improve super-resolution performance. Extensive experiments demonstrate that SuperMeshNet requires 90% less HR data to achieve even lower root mean square error (RMSE) than that of the fully supervised benchmark without the inductive biases. The source code and datasets are available at https://anonymous.4open.science/r/SuperMeshNet/README.md.

Applications · Chemistry, Physics, and Earth Sciences

Jiyeon Kim, Byungju Lee, Won-Yong Shin

Unlike most static material properties widely studied in the machine learning literature, ionic transport properties are inherently dynamic, making their fast and accurate prediction from static atomic structures challenging. The current standard approach, molecular dynamics (MD) simulations, suffers from prohibitively high computational cost. Recent autoregressive learning-based MD acceleration methods requiring sequential inference remain slow and prone to error accumulation; in contrast, existing non-autoregressive material property prediction models are less accurate because they fail to exploit dynamics. Moreover, existing methods typically benefit from datasets either with or without atomic trajectories, but not both. To overcome these limitations, we propose a non-autoregressive learning framework based on modality reduction, which treats atomic trajectories as an auxiliary modality during training but does not require them at inference. This enables a predictor to learn dynamics without requiring sequential inference and to benefit from both types of datasets. As a result, our framework achieves over 200 times speedup compared to autoregressive models on the dataset with atomic trajectories while substantially reducing prediction error relative to non-autoregressive benchmarks across both types of datasets. Our code is available at https://anonymous.4open.science/r/2026.

Applications · Chemistry, Physics, and Earth Sciences

Dingling Yao, Andrea Polesello, Adeel Pervez, Caroline Muller, Francesco Locatello

While Vision Foundation Models (VFMs) excel at predictive tasks on satellite imagery, their performance can arise from visual correlations rather than underlying structural invariants, making certain perception-based out-of-distribution accuracy a poor proxy for scientific utility. As a result, models may look correct without reasoning correctly—a discrepancy we term the *Perception–Physics Paradox*. To address this gap, we introduce *Scientific Alignment* as an implicit objective for representation learning in scientific domains. We study a principled, testable aspect of scientific alignment through *Structural Isomorphism*, which requires latent representations to uniquely identify physical systems up to a linear reparameterization. This perspective induces a hierarchy of necessary conditions and yields a systematic probing protocol for physical and causal interpretability. To operationalize this framework, we release *TC-Atlas*, a foundational global dataset and automated construction pipeline for tropical cyclone research, and show that current VFMs rely on visual shortcuts that collapse in extreme regimes, indicating that scientific alignment does not arise as a natural byproduct of visual scaling alone.

Applications · Chemistry, Physics, and Earth Sciences

Michael Aich, Andreas Fürst, Florian Sestak, Carlos Ruiz-Gonzalez, Niklas Boers, Johannes Brandstetter

Deep learning has revolutionized weather and climate modeling, yet the current landscape remains fragmented: highly specialized models are typically trained individually for distinct tasks. To unify this landscape, we introduce WIND, a single pre-trained foundation model capable of replacing specialized baselines across a vast array of tasks. Crucially, in contrast to previous atmospheric foundation models, we achieve this without any task-specific fine-tuning. To learn a robust, task-agnostic prior of the atmosphere, we pre-train WIND with a self-supervised video reconstruction objective, utilizing an unconditional video diffusion model to iteratively reconstruct atmospheric dynamics from a noisy state. At inference, we frame diverse domain-specific problems strictly as inverse problems and solve them via posterior sampling. This unified approach allows us to tackle highly relevant weather and climate problems, including probabilistic forecasting, spatial and temporal downscaling, sparse reconstruction and enforcing conservation laws purely with our pre-trained model. We further demonstrate the model's capacity to generate physically consistent counterfactual storylines of extreme weather events under global warming scenarios. By combining generative video modeling with inverse problem solving, WIND offers a computationally efficient paradigm shift in AI-based atmospheric modeling.

Applications · Chemistry, Physics, and Earth Sciences

Dongzhe Zheng, Tao Zhong, Christine Allen-Blanchette

In this paper, we study solution operators of physical field equations on geometric meshes from a function-space perspective. We reveal that Hodge orthogonality fundamentally resolves spectral interference by isolating unlearnable topological degrees of freedom from learnable geometric dynamics, enabling an additive approximation confined to structure-preserving subspaces. Building on Hodge theory and operator splitting, we derive a principled operator-level decomposition. The result is a Hybrid Eulerian-Lagrangian architecture with an algebraic-level inductive bias we call Hodge Spectral Duality (HSD). In our framework, we use discrete differential forms to capture topology-dominated components and an orthogonal auxiliary ambient space to represent complex local dynamics. Our method achieves superior accuracy and efficiency on geometric graphs with enhanced fidelity to physical invariants.

Applications · Chemistry, Physics, and Earth Sciences

Daria Ledneva, Mikhail Nuridinov, Denis Kuznetsov

Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model scale, architecture, tokenization, and pretraining data while explicitly exposing task-level trade-offs. Our analysis shows that aggregate leaderboards are unstable: model rankings vary sharply across task categories, scale provides only modest and inconsistent gains, and architectural and pretraining alignment frequently outweigh parameter count. These results highlight limitations of current evaluation practices and position GENEB as a reference framework for principled comparison and category-aware model selection in genomic machine learning.

Applications · Chemistry, Physics, and Earth Sciences

Daria Ledneva, Denis Kuznetsov

Genomic foundation models increasingly adopt large language model architectures, yet almost universally rely on fixed tokenization schemes such as $k$-mers or BPE, which impose arbitrary sequence boundaries and may obscure biologically relevant structure. Although recent work has demonstrated the feasibility of adaptive hierarchical tokenization in autoregressive settings, its extension to masked language modeling and systematic downstream evaluation remain underexplored. We present \textbf{LDARNet}, a 120M-parameter hierarchical genomic foundation model that integrates learnable sequence compression into the masked language modeling paradigm by combining BiMamba-2 state-space layers with selective attention and ratio-based regularization to induce stable token boundaries without supervision. We evaluate LDARNet by fine-tuning on 27 tasks from the Genomics Benchmarks and Nucleotide Transformer suites, covering regulatory, epigenetic, and sequence-level prediction problems, and compare it against state-of-the-art models ranging from 8M to 2.5B parameters. LDARNet achieves 11 out of 18 wins among models under 300M parameters and attains state-of-the-art performance on 5 histone modification tasks, outperforming even substantially larger models on several long-range epigenetic benchmarks. These results indicate that adaptive hierarchical tokenization under masked language modeling can capture long-range genomic dependencies relevant to regulatory biology and highlight learnable compression as a promising direction for efficient and scalable genomic foundation models.

Applications · Chemistry, Physics, and Earth Sciences

Matteo Rossi, Ryan Pederson, Miles Wang-Henderson, Benjamin Kaufman, Edward Williams, Carl Underkoffler, Owen Howell, Adrian Layer, Stephan Thaler, Narbe Mardirossian 等

We present CoarseBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26$\times$ faster inference than state-of-the-art methods while improving affinity prediction accuracy by up to 20\%. Current deep learning approaches to structure-based drug design rely on expensive all-atom diffusion to generate 3D coordinates, creating inference bottlenecks that render large-scale compound screening computationally intractable. We challenge this paradigm with the hypothesis: full all-atom resolution is unnecessary for accurate small molecule pose and binding affinity prediction. CoarseBind tests this hypothesis through a coarse pocket-level representation (protein C$_\beta$ atoms and ligand heavy atoms only) within a multimodal architecture combining pretrained molecular encoders and ESM-2 protein embeddings that learns rich structural representations, which are used in a diffusion-free optimization module for pose generation and a binding affinity likelihood prediction module. On structure prediction benchmarks, CoarseBind matches diffusion-based baselines in ligand pose accuracy. For binding affinity, CoarseBind outperforms Boltz-2 by 16-20\% in Pearson correlation on both a public benchmark (CASP16) and a diverse private dataset (18 assays). The affinity module also provides well-calibrated uncertainty estimates, addressing a critical gap in compound prioritization for drug discovery. Furthermore, this module enables a continual learning framework and a hedged batch selection strategy that, in simulated drug discovery cycles, achieves 6$\times$ greater affinity improvement over greedy approaches.

Applications · Chemistry, Physics, and Earth Sciences

Zhenyuan Zhao, Yu Xing, Tianyang Xue, Lingxin Cao, Xin Yan, Lin Lu

Designing microstructures that satisfy coupled cross-physics objectives is a fundamental challenge in material science. This inverse design problem involves a vast, discontinuous search space where traditional topology optimization is computationally prohibitive, and deep generative models often suffer from "physical hallucinations," lacking the capability to ensure rigorous validity. To address this limitation, we introduce AutoMS, a multi-agent neuro-symbolic framework that reformulates inverse design as an LLM-driven evolutionary search. Unlike methods that treat LLMs merely as interfaces, AutoMS integrates them as "semantic navigators" to initialize search spaces and break local optima, while our novel Simulation-Aware Evolutionary Search (SAES) addresses the "blindness" of traditional evolutionary strategies. Specifically, SAES utilizes simulation feedback to perform local gradient approximation and directed parameter updates, effectively guiding the search toward physically valid Pareto frontiers. Orchestrating specialized agents (Manager, Parser, Generator, and Simulator), AutoMS achieves a state-of-the-art 83.8\% success rate on 17 diverse cross-physics tasks, nearly doubling the performance of traditional NSGA-II (43.7\%) and significantly outperforming ReAct-based LLM baselines (53.3\%). Furthermore, our hierarchical architecture reduces total execution time by 23.3\%. AutoMS demonstrates that autonomous agent systems can effectively navigate complex physical landscapes, bridging the gap between semantic design intent and rigorous physical validity.

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

Robin Winter, Julian Cremer, Djork-Arné Clevert

Virtual screening of billion-scale molecular libraries based on 3D shape similarity remains computationally prohibitive, requiring expensive conformational sampling and alignment, as done by established tools like *ROCS*. Here, we introduce *SAND* (**S**hape-**A**ware **N**eural **D**escriptor), a method that can retrieve shape similar molecules from their 2D graph alone. Our approach makes two key contributions: (1) a rank-preserving contrastive learning framework using differentiable Spearman correlation that results into representations where similarity strongly correlates with 3D molecular shape overlap (R=0.86), and (2) an end-to-end learned quantization-aware training scheme that jointly optimizes the encoder with a two-level IVF-PQ discretization step, achieving approximately $4\times$ better compression than post-hoc quantization at equivalent retrieval quality. We demonstrate that *SAND* enables searching over 10 billion molecules in less than a second on a single GPU node - a speedup of $>10^{8} \times$ compared to traditional methods. We release open-source code and trained weights to facilitate adoption.

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

Xiaochen Du, Juno Nam, Jaemoo Choi, Wei Guo, Sathya Edamadaka, Junyi Sha, Elton Pan, Yongxin Chen, Molei Tao, Rafael Gomez-Bombarelli

Sampling from discrete distributions with multiple modes and energy barriers is fundamental to machine learning and computational physics. Recent discrete neural samplers like MDNS suffer from mode collapse and fail to sample high-energy barrier regions between modes, which is critical for free energy estimation and understanding phase transitions. We propose Metadynamics Discrete Neural Sampler (MetaDNS), a general framework integrating well-tempered metadynamics into discrete diffusion or autoregressive samplers. By maintaining an adaptive, history-dependent bias potential along selected low-dimensional coordinates, MetaDNS forces exploration of previously inaccessible regions, enabling free energy reconstruction infeasible with standard neural samplers due to a lack of high-energy samples. On challenging low-temperature benchmarks including Ising, Potts, and the copper-gold binary alloy, MetaDNS reproduces the thermodynamic distribution. Compared to MCMC-based metadynamics, MetaDNS also achieves comparable exploration requiring fewer energy evaluations.