Applications · chemistry physics and earth sciences

Designing microstructures with coupled cross-physics objectives is a fundamental challenge where traditional topology optimization is often computationally prohibitive and deep generative models frequently suffer from physical hallucinations. We introduce AutoMS, a multi-agent neuro-symbolic framework that reformulates inverse design as an LLM-driven evolutionary search. AutoMS leverages LLMs as semantic navigators to decompose complex requirements and coordinate agent workflows, while a novel Simulation-Aware Evolutionary Search (SAES) mechanism handles low-level numerical optimization via local gradient approximation and directed parameter updates. This architecture achieves a state-of-the-art 83.8\% success rate on 17 diverse cross-physics tasks, significantly outperforming both traditional evolutionary algorithms and existing agentic baselines. By decoupling open-ended semantic orchestration from simulation-grounded numerical search, AutoMS provides a robust pathway for navigating complex physical landscapes that remain intractable for standard generative or purely linguistic approaches.

Short-term precipitation nowcasting is inherently under-constrained due to limited historical observation windows: identical observations can lead to multiple plausible future trajectories, especially for extreme events. Existing generative methods rely solely on visual features and lack explicit constraints on precipitation motion semantics, resulting in ambiguous dynamics, blurred details, and unstable predictions. We propose LangPrecip, the first language-guided precipitation nowcasting framework, and contribute LangPrecip-160K, a large-scale radar-text paired dataset with 160K annotated sequences. LangPrecip addresses the under-constrained challenge by leveraging natural-language motion descriptions as explicit semantic constraints to reduce motion ambiguity and introducing a dual-path wavelet consistency unfolding decoder that enforces physical data fidelity during latent-to-pixel reconstruction. By reformulating nowcasting as semantically constrained trajectory generation under the Rectified Flow paradigm with model-based decoder optimization, LangPrecip produces sharper and more physically consistent forecasts. Experiments on Swedish and MRMS benchmarks demonstrate substantial improvements over state-of-the-art vision-only methods, achieving over 60\% and 19\% relative gains in heavy-rainfall CSI at 80-minute lead time with enhanced spatial detail preservation. Dataset is available at https://github.com/UESTC-LXD/LangPrecip.

Chaos arises in many complex dynamical systems, from weather to power grids, but is difficult to accurately model with data-driven methods such as machine learning emulators. While emulators are promising tools for accelerating simulations and solving inverse problems, they still struggle to learn chaotic dynamics, where sensitivity to initial conditions renders exact long-term forecasts infeasible, especially given noisy data. Recent work instead trains emulators to match the statistical properties of chaotic attractors, but these approaches often rely on handcrafted summary statistics or large, diverse multi-environment datasets. In this work, we propose a family of adversarial optimal transport objectives that can jointly learn high-quality summary statistics and a physically consistent emulator from a single noisy trajectory. We theoretically analyze and experimentally validate a Sinkhorn divergence formulation (2-Wasserstein) and a WGAN-style dual formulation (1-Wasserstein) of our approach. Numerical experiments across a variety of chaotic systems, including ones with high-dimensional spatiotemporal chaos, show that emulators trained using our proposed objectives have significantly improved long-term statistical fidelity.

Low-precision arithmetic is pervasive in neural network training and deployment, yet its effect on prediction \textit{confidence}, not just accuracy, remains unexamined. We show that the softmax function amplifies logit-space quantization errors in an input-dependent manner: confidence distortion scales with the product of precision-dependent error bound $\epsilon$ and logit norm, peaking when the model is confident but not saturated. This explains why identical models report different confidence values across precisions, a phenomenon we term \textit{Precision Split}. During training, the same mechanism causes gradient underflow: when logit margins exceed a precision-dependent threshold, gradients vanish and samples silently stop contributing to learning. Since logit norm serves as a computable proxy for precision-induced risk, we propose Precision-Aware Confidence Scaling (PACS), which applies sample-adaptive temperature inversely related to this risk, with sub-one-percent overhead and no full-precision computation required. On ImageNet with mixed-precision ResNet-50, PACS reduces Expected Calibration Error from 5.82\% to 1.92\% while maintaining accuracy, with consistent improvements across architectures, precision formats, and modalities.

As Large Language Models (LLMs) more deeply integrate into human life across various regions, aligning them with pluralistic cultures is crucial for improving user engagement and mitigating cultural conflicts. For this purpose, recently, different culture-specific corpora have been carefully curated, either synthesized or manually annotated. Nevertheless, inspired by culture theories, we identify two key challenges faced by these datasets: (1) Representativeness: These corpora fail to fully capture the target culture's core characteristics, causing insufficient cultural coverage with redundancy; (2) Distinctiveness: They struggle to distinguish the unique nuances of a given culture from shared patterns across other relevant ones, hindering precise cultural modelling. To handle these challenges, we introduce CAReDiO, a novel data optimization framework, which alternatively refines culture-sensitive questions and responses according to information-theoretic objectives in an in-context optimization manner, enhancing the cultural informativeness and distinguishability of constructed data. Extensive experiments on 15 distinct cultures demonstrate that CAReDiO can create high-quality data with richer cultural information and enable efficient alignment of small open-source or large proprietary LLMs with as few as 200 training samples, consistently outperforming previous datasets in both multi-choice and open-ended cultural benchmarks.

Accurate precipitation nowcasting is vital for disaster mitigation, but deep learning methods face a key trade-off: regression models produce over-smoothed, spectrally decaying predictions that blur convective details and violate turbulence power laws; diffusion models generate realistic yet unanchored hallucinations lacking physical grounding. We propose Spectral-Decoupled Iterative Refinement (SDIR), a deterministic framework that reformulates nowcasting as progressive frequency-decoupled refinement. SDIR first extracts a stable low-frequency synoptic skeleton, then iteratively refines high-frequency textures under physical constraints, eliminating both blurring and hallucinations. It features a dual-path design: the Synoptic Frequency-Guided Former (SFG-Former) with Scale-Adaptive Transformers for global structure, and the Fourier Residual Refiner (FR-Refiner) with Scale-Conditioned Fourier Neural Operators for fine residuals. A Physically Consistent Power Spectral Density (PCPSD) loss with dynamic masking enforces a turbulence-consistent spectral distribution. Experiments on three benchmarks show SDIR significantly outperforms SOTA methods in spatial accuracy while achieving spectral fidelity competitive with diffusion-based methods, enabling reliable high-resolution operational nowcasting. Code link: https://github.com/RuntimeWarning/SDIR.

Modeling recognition between T-cell receptors (TCRs) and peptide-MHC (pMHC) complexes is a fundamental challenge in computational immunology, constrained by sparse paired interaction data relative to abundant unpaired sequences. We introduce DecoderTCR, a masked language model framework that addresses this through two contributions: (1) a compositional continual pre-training curriculum that learns component representations from marginal data before refining cross-chain dependencies, and (2) Iterative Entropy-Guided Refinement (IEGR), a non-autoregressive decoding algorithm that resolves high-confidence positions first to provide context for uncertain regions. On held-out benchmarks, DecoderTCR achieves 0.96 AUROC for zero-shot pMHC binding prediction and 0.76 AUROC for epitope-specific TCR recognition, approaching supervised baselines without epitope-specific training. Learned representations recover structural contacts without coordinate supervision, and generated sequences exhibit realistic recombination statistics. Experimental validation across two rounds of wet-lab screening reveals a prediction-generation gap that can be narrowed via a lab-in-the-loop paradigm for TCR design.

Partial differential equations (PDEs) are fundamental for modeling complex natural and physical phenomena. In many real-world applications, however, observational data are \textbf{extremely sparse}, which severely limits the applicability of both classical numerical solvers and existing neural approaches. While neural methods have shown promising results under moderately sparse observations, their inference efficiency at high resolutions is limited, and their accuracy degrades substantially in the extremely sparse regime. In this work, we propose the \textbf{Di-BiLPS}, a unified neural framework that effectively handle \textbf{both forward and inverse} PDE problems under extremely sparse observations. Di-BiLPS combines a variational autoencoder to compress high-dimensional inputs into a compact latent space, a latent diffusion module to model uncertainty, and contrastive learning to align representations. Operating entirely in this latent space, the framework achieves efficient inference while retaining flexible input–output mapping. In addition, we introduce a \textbf{PDE-informed denoising algorithm} based on a variance-preserving diffusion process, which further improves inference efficiency. Extensive experiments on multiple PDE benchmarks demonstrate that Di-BiLPS consistently achieves \textbf{SOTA performance under extremely sparse inputs (as low as 3\%)}, while substantially reducing computational cost. Moreover, Di-BiLPS enables \textbf{zero-shot super-resolution}, as it allows predictions over continuous spatial–temporal domains.

Deep learning methods based on backward stochastic differential equations (BSDEs) have emerged as competitive alternatives to physics-informed neural networks (PINNs) for solving high-dimensional partial differential equations (PDEs). By leveraging probabilistic representations, BSDE approaches can avoid the curse of dimensionality and often admit second-order-free training objectives that do not require explicit Hessian evaluations. It has recently been established that the commonly used Euler–Maruyama (EM) time discretization induces an intrinsic bias in BSDE training losses. While high-order schemes such as Heun can fully eliminate this bias, such schemes re-introduce second-order spatial derivatives and incur substantial computational overhead. In this work, we provide a principled analysis of EM-induced loss bias and propose an unbiased, second-order-free training framework that preserves the computational advantages of BSDE methods. Our code is available at https://github.com/seojaemin22/Un-EM-BSDE.

Physics-Informed Neural Networks (PINNs) often train slowly or fail to converge on challenging partial differential equations (PDEs), a behavior recently linked to severely ill-conditioned loss landscapes inherited from the underlying differential operator. We study PINNs augmented with a pointwise data-fidelity term, added at a few points in the domain to the standard residual and boundary losses. We show that this supervision term acts as an operator-level preconditioner: for suitable weights, our comparison bounds guarantee a substantially smaller condition number than under the standard PINN loss, independently of how the pointwise labels are obtained. For a broad class of PDEs admitting a Feynman-Kac (FK) representation, we generate such labels by Monte Carlo averages of the FK functional, resulting in what we call "FK-PINNs", and using the excess risk decomposition approach, we derive non-asymptotic $L^2(\Omega)$-error bounds for FK-PINNs with $\tanh$ activation trained by finitely many steps of gradient descent. Along the way, we establish pseudo-dimension bounds for first- and second-order derivatives of $\tanh$ neural networks, which are of independent interest and, to the best of our knowledge, new. Numerical experiments on Poisson, Schrödinger, mean exit time, and committor problems corroborate the theory, and show that FK-PINNs can successfully solve PDEs for which standard PINNs exhibit severe failure modes.

Determining where to execute the manipulation policy is a fundamental challenge in mobile manipulation. Most approaches have formulated this as a geometric search problem, prioritizing physical reachability. However, given the high sensitivity of modern learning-based manipulation policies, geometric criteria alone are insufficient. Optimal performance requires base positioning that is aware of the policy's preference. While recent works have attempted to address this, they remain limited in practicality due to reliance on pre-built scene reconstruction and slow inference. In this work, we introduce **N2M** that systematically reformulates the approach to base positioning problem, naturally overcoming limitations of previous methods. Our key insight is that policy preferences are inherent to the local scene structure and can be effectively learned from the policy rollouts. Technically, we propose a novel *viewpoint augmentation* strategy that enables the model to learn robust, viewpoint-invariant pose preferences with remarkable data efficiency. Extensive experiments demonstrate that N2M achieves state-of-the-art performance, outperforming both non-policy-aware baselines and recent policy-aware alternatives. Furthermore, we provide a comprehensive analysis highlighting N2M’s broad applicability, generalization capabilities, and data efficiency. Project website: https://clvrai.github.io/N2M/

Reconstructing dynamical evolution from limited observations is a fundamental challenge in single-cell biology, where dynamic unbalanced optimal transport (OT) provides a principled framework for modeling coupled transport and mass variation. However, existing approaches rely on trajectory simulation at inference time, making inference a key bottleneck for scalable applications. In this work, we propose a mean-flow framework for unbalanced flow matching that summarizes both transport and mass-growth dynamics over arbitrary time intervals using mean velocity and mass-growth fields, enabling fast one-step generation without trajectory simulation. To solve dynamic unbalanced OT under the Wasserstein-Fisher-Rao geometry, we further build on this framework to develop **Wasserstein-Fisher-Rao Mean Flow Matching (WFR-MFM)**. Across synthetic and real single-cell RNA sequencing datasets, WFR-MFM achieves orders-of-magnitude faster inference than a range of existing baselines while maintaining high predictive accuracy, and enables efficient perturbation response prediction on large synthetic datasets with thousands of conditions.

Deep learning-based methods have shown remarkable effectiveness in solving PDEs, largely due to their ability to enable fast simulations once trained. However, despite the availability of high-performance computing infrastructure, many critical applications remain constrained by the substantial computational costs associated with generating large-scale, high-quality datasets and training models. In this work, inspired by studies on the structure of Green's functions for elliptic PDEs, we introduce Neural-HSS, a parameter-efficient architecture built upon the Hierarchical Semi-Separable (HSS) matrix structure that is provably data-efficient for a broad class of PDEs. We theoretically analyze the proposed architecture, proving that it satisfies exactness properties even in very low-data regimes. We also investigate its connections with other architectural primitives, such as the Fourier neural operator layer and convolutional layers. We experimentally validate the data efficiency of Neural-HSS on the three-dimensional Poisson equation over a grid of two million points, demonstrating its superior ability to learn from data generated by elliptic PDEs in the low-data regime while outperforming baseline methods. Finally, we demonstrate its capability to learn from data arising from a broad class of PDEs in diverse domains, including electromagnetism, fluid dynamics, and biology.

We present SoftMatcha 2, an ultra-fast and flexible search algorithm that enables search over trillion-scale natural language corpora in under 0.3 seconds while allowing semantic variations in the form of substitution, insertion, and deletion. Our approach employs string matching based on suffix arrays that scales well with corpus size, and represents words as vectors, which underpin its semantic flexibility. To mitigate the combinatorial explosion induced by the semantic relaxation of queries, our method is built on two key algorithmic ideas: dynamic corpus-aware pruning and fast exact lookup enabled by a disk-aware design. We theoretically analyze the efficiency of the proposed method, indicating that it can mitigate exponential growth in the search space. Empirically, on FineWeb-Edu (Lozhkov et al., 2024) (1.4T tokens), it attains substantially lower search latency than existing methods: infini-gram (Liu et al., 2024), infini-gram mini (Xu et al., 2025), and SoftMatcha (Deguchi et al., 2025). As a practical application, our method uncovers benchmark contamination in training corpora that existing approaches miss, and it also benefits information retrieval and paraphrase detection. We also provide an online demo of fast, soft search across corpora in seven languages.

High-precision robotic manipulation requires fine-grained spatial reasoning that is often difficult to achieve with RGB-only policies due to depth ambiguity and perspective scale issues. Policies that leverage 3D information directly, such as those based on point clouds, offer a stronger geometric prior over purely image-based ones, yet their performance remains highly task-dependent. We hypothesize that this discrepancy may be due to the spectral bias of neural networks towards learning low frequency functions, which especially affects architectures conditioned on slow-moving Cartesian features. We thus propose to map point clouds from Cartesian space into high-dimensional Fourier space, effectively equipping the point cloud encoder with direct access to high-frequency features. We experimentally validate the use of Fourier features on challenging manipulation tasks from the RoboCasa and ManiSkill3 benchmarks and on a real robot setup. Despite their simplicity, we find that Fourier features provide significant benefits across diverse encoder architectures and benchmarks and are robust across hyperparameters. Our results indicate that Fourier features let policies leverage geometric details more effectively than Cartesian features, showing their potential as a general-purpose tool for point cloud-based imitation learning. We provide source code and videos on our project page: https://fourier-il.github.io/fourier-il.

Bridging the gap between visual realism and physical understanding is a core challenge for video-based world models. We study the structural identifiability of continuous-time physical laws from raw pixels, focusing on whether an encoder-only pipeline can uniquely recover the parameters of second-order linear ODEs. We prove that a level-set slope-coverage condition ensures the learned latent space is locally affine to the true physical state, enabling exact parameter recovery. Our theory provides the first characterization of minimal data requirements across damping regimes, establishing that underdamped systems are identifiable from a single video clip, whereas other regimes require three diverse trajectories. We further introduce a variance-floor regularizer to stabilize the decoder-free objective and prevent latent collapse. Validated on synthetic and real-world data, our approach demonstrates that interpretable physical constants can be reliably estimated from video without the need for compute-intensive pixel reconstruction, ensuring both physical correctness and transparency. Code is available at https://github.com/wenjiewang3/PhysicsFromVideo.

We present a unified algorithmic framework for the numerical solution, constrained optimization, and physics-informed learning of PDEs with a variational structure. Our framework is based on a Galerkin discretization of the underlying variational forms, and its high efficiency stems from a novel highly-optimized and GPU-compliant TensorGalerkin framework for linear system assembly (stiffness matrices and load vectors). TensorGalerkin operates by tensorizing element-wise operations within a Python-level Map stage and then performs global reduction with a sparse matrix multiplication that performs message passing on the mesh-induced sparsity graph. The Map and Reduce stages are co-designed inside PyTorch's autograd so that the assembly graph contains $O(1)$ nodes regardless of how the number of elements and local DoFs scale. We validate this $O(1)$-graph property by deploying TensorGalerkin downstream as i) a highly-efficient numerical PDEs solver, ii) an end-to-end differentiable framework for PDE-constrained optimization, and iii) a physics-informed operator learning algorithm for PDEs. With multiple benchmarks, including 2D and 3D elliptic, parabolic, and hyperbolic PDEs on unstructured meshes, we demonstrate that the proposed framework provides significant computational efficiency and accuracy gains over a variety of baselines in all the targeted downstream applications.

In this paper, we study dynamic regret in unconstrained online convex optimization (OCO) with movement costs. Specifically, we generalize the standard setting by allowing the movement cost coefficients $\lambda_t$ to vary arbitrarily over time. Our main contribution is a novel algorithm that establishes the first comparator-adaptive dynamic regret bound for this setting, guaranteeing $\widetilde{\mathcal{O}}(\sqrt{(M^2+MP_T)(T+\sum_t \lambda_t)})$ regret, where $P_T$ is the path length of the comparator sequence over $T$ rounds and $M$ is the maximal comparator norm. Our result recovers the optimal adaptive rates for both static and dynamic regret in OCO as the special case where $\lambda_t=0$ for all rounds. To demonstrate the versatility of our results, we consider two applications: *OCO with delayed feedback* and *OCO with time-varying memory*. We show that both problems can be translated into time-varying movement costs, establishing a novel reduction specifically for the delayed feedback setting that is of independent interest. A crucial observation is that the first-order dependence on movement costs in our regret bound plays a key role in enabling optimal comparator-adaptive dynamic regret guarantees in both settings.

We present SynLaD, a latent diffusion framework for small-molecule generation that unifies ligand-based drug 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 synthesizable 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-aligned molecules with feasible synthesis plans.

We present TerraBind, 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. TerraBind 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, TerraBind matches diffusion-based baselines in ligand pose accuracy. For binding affinity, TerraBind 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.