AI4S

Artificial intelligence is rapidly reshaping the natural sciences, with weather forecasting emerging as a flagship AI4Science application where machine learning models can now rival and even surpass traditional numerical simulations. Following the success of the landmark models Pangu Weather and Graphcast, outperforming traditional numerical methods for global medium-range forecasting, many novel data-driven methods have emerged. A common limitation shared by many of these models is their reliance on an equiangular discretization of the sphere which suffers from a much finer grid at the poles than around the equator. In contrast, in the Hierarchical Equal Area iso-Latitude Pixelization (HEALPix) of the sphere, each pixel covers the same surface area, removing unphysical biases. Motivated by a growing support for this grid in meteorology and climate sciences, we propose to perform weather forecasting with deep learning models which natively operate on the HEALPix grid. To this end, we introduce Pangu Equal ARea (PEAR), a transformer-based weather forecasting model which operates directly on HEALPix-features and outperforms the corresponding model on an equiangular grid without any computational overhead.

To address the global health threat of antimicrobial resistance, antimicrobial peptides (AMP) are being explored for their potent and promising ability to fight resistant pathogens. While artificial intelligence (AI) is being employed to advance AMP discovery and design, most AMP design models struggle to balance key goals like activity, toxicity, and novelty, using rigid or unclear scoring methods that make results hard to interpret and optimize. As the capabilities of Large Language Models (LLM) advance and evolve swiftly, we turn to AI multi-agent collaboration based on such models (multi-agent LLMs), which show rapidly rising potential in complex scientific design scenarios. Based on this, we introduce MAC-AMP, a closed-loop multi-agent collaboration (MAC) system for multi-objective AMP design. The system implements a fully autonomous simulated peer review-adaptive reinforcement learning framework that requires only a task description and example dataset to design novel AMPs. The novelty of our work lies in introducing a closed-loop multi-agent system for AMP design, with cross-domain transferability, that supports multi-objective optimization while remaining explainable rather than a'black box'. Experiments show that MAC-AMP outperforms other AMP generative models by effectively optimizing AMP generation for multiple key molecular properties, demonstrating exceptional results in antibacterial activity, AMP likeliness, toxicity compliance, and structural reliability.

The capacity to transfer knowledge across scientific domains relies on shared organizational principles. However, existing transfer-learning methodologies often fail to bridge radically heterogeneous systems, particularly under severe data scarcity or stochastic noise. This study formalizes Explainable Cross-Domain Transfer Learning (X-CDTL), a framework unifying network science and explainable artificial intelligence to identify structural invariants that generalize across biological, linguistic, molecular, and social networks. By introducing the Importance Inversion Transfer (IIT) mechanism, the framework prioritizes domain-invariant structural anchors over idiosyncratic, highly discriminative features. In anomaly detection tasks, models guided by these principles achieve significant performance gains - exhibiting a 56% relative improvement in decision stability under extreme noise - over traditional baselines. These results provide evidence for a shared organizational signature across heterogeneous domains, establishing a principled paradigm for cross-disciplinary knowledge propagation. By shifting from opaque latent representations to explicit structural laws, this work advances machine learning as a robust engine for scientific discovery.

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30$\times$ speedup in data preparation.

Artificial intelligence (AI) is rapidly emerging as a new paradigm of scientific discovery, namely data-driven science, across nearly all scientific disciplines. In materials science and engineering, AI has already begun to exert a transformative influence, making it both timely and necessary to examine its interaction with materials plasticity. In this study, we present a holistic survey of the convergence between AI and plasticity, highlighting state-of-the-art AI methodologies employed to discover, construct surrogate models for, and emulate the plastic behavior of materials. From a materials science perspective, we examine cause-and-effect relationships governing plastic deformation, including microstructural characterization and macroscopic responses described through plasticity constitutive models. From the perspective of AI methodology, we review a broad spectrum of applied approaches, ranging from frequentist techniques such as classical machine learning (ML), deep learning (DL), and physics-informed models to probabilistic frameworks that incorporate uncertainty quantification and generative AI methods. These data-driven approaches are discussed in the context of materials characterization and plasticity-related applications. The primary objective of this survey is to develop a comprehensive and well-organized taxonomy grounded in AI methodologies, with particular emphasis on distinguishing critical aspects of these techniques, including model architectures, data requirements, and predictive performance within the specific domain of materials plasticity. By doing so, this work aims to provide a clear road map for researchers and practitioners in the materials community, while offering deeper physical insight and intuition into the role of AI in advancing materials plasticity and characterization, an area of growing importance in the emerging AI-driven era.

We present an integrated multiagent AI ecosystem for polymer discovery that unifies high-throughput materials workflows, artificial intelligence, and computational modeling within a single Polymer Research Lifecycle (PRL) pipeline. The system orchestrates specialized agents powered by state-of-the-art large language models (DeepSeek-V2 and DeepSeek-Coder) to retrieve and reason over scientific resources, invoke external tools, execute domain-specific code, and perform metacognitive self-assessment for robust end-to-end task execution. We demonstrate three practical capabilities: a high-fidelity polymer property prediction and generative design pipeline, a fully automated multimodal workflow for biopolymer structure characterization, and a metacognitive agent framework that can monitor performance and improve execution strategies over time. On a held-out test set of 1,251 polymers, our PolyGNN agent achieves strong predictive accuracy, reaching R2 = 0.89 for glass-transition temperature (Tg ), R2 = 0.82 for tensile strength, R2 = 0.75 for elongation, and R2 = 0.91 for density. The framework also provides uncertainty estimates via multiagent consensus and scales with linear complexity to at least 10,000 polymers, enabling high-throughput screening at low computational cost. For a representative workload, the system completes inference in 16.3 s using about 2 GB of memory and 0.1 GPU hours, at an estimated cost of about $0.08. On a dedicated Tg benchmark, our approach attains R2 = 0.78, outperforming strong baselines including single-LLM prediction (R2 = 0.67), group-contribution methods (R2 = 0.71), and ChemCrow (R2 = 0.66). We further demonstrate metacognitive control in a polystyrene case study, where the system not only produces domain-level scientific outputs but continually monitors and optimizes its own behavior through tactical, strategic, and meta-strategic self-assessment.

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will produce unprecedented volumes of heterogeneous astronomical data (images, catalogs, and alerts) that challenge traditional analysis pipelines. The LSST Dark Energy Science Collaboration (DESC) aims to derive robust constraints on dark energy and dark matter from these data, requiring methods that are statistically powerful, scalable, and operationally reliable. Artificial intelligence and machine learning (AI/ML) are already embedded across DESC science workflows, from photometric redshifts and transient classification to weak lensing inference and cosmological simulations. Yet their utility for precision cosmology hinges on trustworthy uncertainty quantification, robustness to covariate shift and model misspecification, and reproducible integration within scientific pipelines. This white paper surveys the current landscape of AI/ML across DESC's primary cosmological probes and cross-cutting analyses, revealing that the same core methodologies and fundamental challenges recur across disparate science cases. Since progress on these cross-cutting challenges would benefit multiple probes simultaneously, we identify key methodological research priorities, including Bayesian inference at scale, physics-informed methods, validation frameworks, and active learning for discovery. With an eye on emerging techniques, we also explore the potential of the latest foundation model methodologies and LLM-driven agentic AI systems to reshape DESC workflows, provided their deployment is coupled with rigorous evaluation and governance. Finally, we discuss critical software, computing, data infrastructure, and human capital requirements for the successful deployment of these new methodologies, and consider associated risks and opportunities for broader coordination with external actors.

We propose Enginuity - the first open, large-scale, multi-domain engineering diagram dataset with comprehensive structural annotations designed for automated diagram parsing. By capturing hierarchical component relationships, connections, and semantic elements across diverse engineering domains, our proposed dataset would enable multimodal large language models to address critical downstream tasks including structured diagram parsing, cross-modal information retrieval, and AI-assisted engineering simulation. Enginuity would be transformative for AI for Scientific Discovery by enabling artificial intelligence systems to comprehend and manipulate the visual-structural knowledge embedded in engineering diagrams, breaking down a fundamental barrier that currently prevents AI from fully participating in scientific workflows where diagram interpretation, technical drawing analysis, and visual reasoning are essential for hypothesis generation, experimental design, and discovery.

Scientific Artificial Intelligence (AI) applications require models that deliver trustworthy uncertainty estimates while respecting domain constraints. Existing uncertainty quantification methods lack mechanisms to incorporate symbolic scientific knowledge, while neurosymbolic approaches operate deterministically without principled uncertainty modeling. We introduce the Constraint-Aware Neurosymbolic Uncertainty Framework (CANUF), unifying Bayesian deep learning with differentiable symbolic reasoning. The architecture comprises three components: automated constraint extraction from scientific literature, probabilistic neural backbone with variational inference, and differentiable constraint satisfaction layer ensuring physical consistency. Experiments on Materials Project (140,000+ materials), QM9 molecular properties, and climate benchmarks show CANUF reduces Expected Calibration Error by 34.7% versus Bayesian neural networks while maintaining 99.2% constraint satisfaction. Ablations reveal constraint-guided recalibration contributes 18.3% performance gain, with constraint extraction achieving 91.4% precision. CANUF provides the first end-to-end differentiable pipeline simultaneously addressing uncertainty quantification, constraint satisfaction, and interpretable explanations for scientific predictions.

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding real-time researcher guidance. This paper introduces Deep Research, a multi-agent system enabling interactive scientific investigation with turnaround times measured in minutes. The architecture comprises specialized agents for planning, data analysis, literature search, and novelty detection, unified through a persistent world state that maintains context across iterative research cycles. Two operational modes support different workflows: semi-autonomous mode with selective human checkpoints, and fully autonomous mode for extended investigations. Evaluation on the BixBench computational biology benchmark demonstrated state-of-the-art performance, achieving 48.8% accuracy on open response and 64.4% on multiple-choice evaluation, exceeding existing baselines by 14 to 26 percentage points. Analysis of architectural constraints, including open access literature limitations and challenges inherent to automated novelty assessment, informs practical deployment considerations for AI-assisted scientific workflows.

The advancement of artificial intelligence toward agentic science is currently bottlenecked by the challenge of ultra-long-horizon autonomy, the ability to sustain strategic coherence and iterative correction over experimental cycles spanning days or weeks. While Large Language Models (LLMs) have demonstrated prowess in short-horizon reasoning, they are easily overwhelmed by execution details in the high-dimensional, delayed-feedback environments of real-world research, failing to consolidate sparse feedback into coherent long-term guidance. Here, we present ML-Master 2.0, an autonomous agent that masters ultra-long-horizon machine learning engineering (MLE) which is a representative microcosm of scientific discovery. By reframing context management as a process of cognitive accumulation, our approach introduces Hierarchical Cognitive Caching (HCC), a multi-tiered architecture inspired by computer systems that enables the structural differentiation of experience over time. By dynamically distilling transient execution traces into stable knowledge and cross-task wisdom, HCC allows agents to decouple immediate execution from long-term experimental strategy, effectively overcoming the scaling limits of static context windows. In evaluations on OpenAI's MLE-Bench under 24-hour budgets, ML-Master 2.0 achieves a state-of-the-art medal rate of 56.44%. Our findings demonstrate that ultra-long-horizon autonomy provides a scalable blueprint for AI capable of autonomous exploration beyond human-precedent complexities.

Autonomous experimentation holds the potential to accelerate materials development by combining artificial intelligence (AI) with modular robotic platforms to explore extensive combinatorial chemical and processing spaces. Such self-driving laboratories can not only increase the throughput of repetitive experiments, but also incorporate human domain expertise to drive the search towards user-defined objectives, including improved materials performance metrics. We present an autonomous materials synthesis extension to SARA, the Scientific Autonomous Reasoning Agent, utilizing phase information provided by an automated probabilistic phase labeling algorithm to expedite the search for targeted phase regions. By incorporating human input into an expanded SARA-H (SARA with human-in-the-loop) framework, we enhance the efficiency of the underlying reasoning process. Using synthetic benchmarks, we demonstrate the efficiency of our AI implementation and show that the human input can contribute to significant improvement in sampling efficiency. We conduct experimental active learning campaigns using robotic processing of thin-film samples of several oxide material systems, including Bi$_2$O$_3$, SnO$_x$, and Bi-Ti-O, using lateral-gradient laser spike annealing to synthesize and kinetically trap metastable phases. We showcase the utility of human-in-the-loop autonomous experimentation for the Bi-Ti-O system, where we identify extensive processing domains that stabilize $\delta$-Bi$_2$O$_3$ and Bi$_2$Ti$_2$O$_7$, explore dwell-dependent ternary oxide phase behavior, and provide evidence confirming predictions that cationic substitutional doping of TiO$_2$ with Bi inhibits the unfavorable transformation of the metastable anatase to the ground-state rutile phase. The autonomous methods we have developed enable the discovery of new materials and new understanding of materials synthesis and properties.

Artificial intelligence now outperforms humans in several scientific and engineering tasks, yet its internal representations often remain opaque. In this Perspective, we argue that explainable artificial intelligence (XAI), combined with causal reasoning, enables {\it learning from the learners}. Focusing on discovery, optimization and certification, we show how the combination of foundation models and explainability methods allows the extraction of causal mechanisms, guides robust design and control, and supports trust and accountability in high-stakes applications. We discuss challenges in faithfulness, generalization and usability of explanations, and propose XAI as a unifying framework for human-AI collaboration in science and engineering.

Artificial Intelligence (AI) is transforming domains from healthcare and agriculture to finance and industry. As progress on Earth meets growing constraints, the next frontier is outer space, where AI can enable autonomous, resilient operations under extreme uncertainty and limited human oversight. This paper introduces Space AI as a unified interdisciplinary field at the intersection of artificial intelligence and space science and technology. We consolidate historical developments and contemporary progress, and propose a systematic framework that organises Space AI into four mission contexts: 1 AI on Earth, covering intelligent mission planning, spacecraft design optimisation, simulation, and ground-based data analytics; 2 AI in Orbit, focusing on satellite and station autonomy, space robotics, on-board/near-real-time data processing, communication optimisation, and orbital safety; 3 AI in Deep Space, enabling autonomous navigation, adaptive scientific discovery, resource mapping, and long-duration human-AI collaboration under communication constraints; and 4 AI for Multi-Planetary Life, supporting in-situ resource utilisation, habitat and infrastructure construction, life-support and ecological management, and resilient interplanetary networks. Ultimately, Space AI can accelerate humanity's capability to explore and operate in space, while translating advances in sensing, robotics, optimisation, and trustworthy AI into broad societal impact on Earth.

Automated scientific discovery with large language models is transforming the research lifecycle from ideation to experimentation, yet existing agents struggle to autonomously process raw data collected from scientific experiments. We introduce SciDER, a data-centric end-to-end system that automates the research lifecycle. Unlike traditional frameworks, our specialized agents collaboratively parse and analyze raw scientific data, generate hypotheses and experimental designs grounded in specific data characteristics, and write and execute corresponding code. Evaluation on three benchmarks shows SciDER excels in specialized data-driven scientific discovery and outperforms general-purpose agents and state-of-the-art models through its self-evolving memory and critic-led feedback loop. Distributed as a modular Python package, we also provide easy-to-use PyPI packages with a lightweight web interface to accelerate autonomous, data-driven research and aim to be accessible to all researchers and developers.

Fluid-solid interaction (FSI) problems are fundamental in many scientific and engineering applications, yet effectively capturing the highly nonlinear two-way interactions remains a significant challenge. Most existing deep learning methods are limited to simplified one-way FSI scenarios, often assuming rigid and static solid to reduce complexity. Even in two-way setups, prevailing approaches struggle to capture dynamic, heterogeneous interactions due to the lack of cross-domain awareness. In this paper, we introduce \textbf{Fisale}, a data-driven framework for handling complex two-way \textbf{FSI} problems. It is inspired by classical numerical methods, namely the Arbitrary Lagrangian-Eulerian (\textbf{ALE}) method and the partitioned coupling algorithm. Fisale explicitly models the coupling interface as a distinct component and leverages multiscale latent ALE grids to provide unified, geometry-aware embeddings across domains. A partitioned coupling module (PCM) further decomposes the problem into structured substeps, enabling progressive modeling of nonlinear interdependencies. Compared to existing models, Fisale introduces a more flexible framework that iteratively handles complex dynamics of solid, fluid and their coupling interface on a unified representation, and enables scalable learning of complex two-way FSI behaviors. Experimentally, Fisale excels in three reality-related challenging FSI scenarios, covering 2D, 3D and various tasks. The code is available at \href{https://github.com/therontau0054/Fisale}.

Heteroscedasticity -- where the variance of a variable changes with other variables -- is pervasive in real data, and elucidating why it arises from the perspective of statistical moments is crucial in scientific knowledge discovery and decision-making. However, standard causal discovery does not reveal which causes act on the mean versus the variance, as it returns a single moment-agnostic graph, limiting interpretability and downstream intervention design. We propose a Bayesian, moment-driven causal discovery framework that infers separate \textit{mean} and \textit{variance} causal graphs from observational heteroscedastic data. We first derive the identification results by establishing sufficient conditions under which these two graphs are separately identifiable. Building on this theory, we develop a variational inference method that learns a posterior distribution over both graphs, enabling principled uncertainty quantification of structural features (e.g., edges, paths, and subgraphs). To address the challenges of parameter optimization in heteroscedastic models with two graph structures, we take a curvature-aware optimization approach and develop a prior incorporation technique that leverages domain knowledge on node orderings, improving sample efficiency. Experiments on synthetic, semi-synthetic, and real data show that our approach accurately recovers mean and variance structures and outperforms state-of-the-art baselines.

A central challenge in scientific machine learning (ML) is the correct representation of physical systems governed by multi-regime behaviours. In these scenarios, standard data analysis techniques often fail to capture the nature of the data, as the system's response varies significantly across the state space due to its stochasticity and the different physical regimes. Uncertainty quantification (UQ) should thus not be viewed merely as a safety assessment, but as a support to the learning task itself, guiding the model to internalise the behaviour of the data. We address this by focusing on the Critical Heat Flux (CHF) benchmark and dataset presented by the OECD/NEA Expert Group on Reactor Systems Multi-Physics. This case study represents a test for scientific ML due to the non-linear dependence of CHF on the inputs and the existence of distinct microscopic physical regimes. These regimes exhibit diverse statistical profiles, a complexity that requires UQ techniques to internalise the data behaviour and ensure reliable predictions. In this work, we conduct a comparative analysis of UQ methodologies to determine their impact on physical representation. We contrast post-hoc methods, specifically conformal prediction, against end-to-end coverage-oriented pipelines, including (Bayesian) heteroscedastic regression and quality-driven losses. These approaches treat uncertainty not as a final metric, but as an active component of the optimisation process, modelling the prediction and its behaviour simultaneously. We show that while post-hoc methods ensure statistical calibration, coverage-oriented learning effectively reshapes the model's representation to match the complex physical regimes. The result is a model that delivers not only high predictive accuracy but also a physically consistent uncertainty estimation that adapts dynamically to the intrinsic variability of the CHF.

Urban Villages (UVs) represent a distinctive form of high-density informal settlement embedded within China's rapidly urbanizing cities. Accurate identification of UVs is critical for urban governance, renewal, and sustainable development. But due to the pronounced heterogeneity and diversity of UVs across China's vast territory, a consistent and reliable nationwide dataset has been lacking. In this work, we present GeoLink-UV, a high-resolution nationwide UV mapping product that clearly delineates the locations and boundaries of UVs in 342 Chinese cities. The dataset is derived from multisource geospatial data, including optical remote sensing images and geo-vector data, and is generated through a foundation model-driven mapping framework designed to address the generalization issues and improve the product quality. A geographically stratified accuracy assessment based on independent samples from 28 cities confirms the reliability and scientific credibility of the nationwide dataset across heterogeneous urban contexts. Based on this nationwide product, we reveal substantial interregional disparities in UV prevalence and spatial configuration. On average, UV areas account for 8 % of built-up land, with marked clustering in central and south China. Building-level analysis further confirms a consistent low-rise, high-density development pattern of UVs nationwide, while highlighting regionally differentiated morphological characteristics. The GeoLink-UV dataset provides an open and systematically validated geospatial foundation for urban studies, informal settlement monitoring, and evidence-based urban renewal planning, and contributes directly to large-scale assessments aligned with Sustainable Development Goal 11. The GeoLink-UV dataset introduced in this article is freely available at https://doi.org/10.5281/zenodo.18688062.

Accurate long-horizon prediction of spatiotemporal fields on complex geometries is a fundamental challenge in scientific machine learning, with applications such as additive manufacturing where temperature histories govern defect formation and mechanical properties. High-fidelity simulations are accurate but computationally costly, and despite recent advances, machine learning methods remain challenged by long-horizon temperature and gradient prediction. We propose a deep learning framework for predicting full temperature histories directly on meshes, conditioned on geometry and process parameters, while maintaining stability over thousands of time steps and generalizing across heterogeneous geometries. The framework adopts a temporal multiscale architecture composed of two coupled models operating at complementary time scales. Both models rely on a latent recurrent graph neural network to capture spatiotemporal dynamics on meshes, while a variational graph autoencoder provides a compact latent representation that reduces memory usage and improves training stability. Experiments on simulated powder bed fusion data demonstrate accurate and temporally stable long-horizon predictions across diverse geometries, outperforming existing baseline. Although evaluated in two dimensions, the framework is general and extensible to physics-driven systems with multiscale dynamics and to three-dimensional geometries.

Accurate prediction of main engine power is essential for vessel performance optimization, fuel efficiency, and compliance with emission regulations. Conventional machine learning approaches, such as Support Vector Machines, variants of Artificial Neural Networks (ANNs), and tree-based methods like Random Forests, Extra Tree Regressors, and XGBoost, can capture nonlinearities but often struggle to respect the fundamental propeller law relationship between power and speed, resulting in poor extrapolation outside the training envelope. This study introduces a hybrid modeling framework that integrates physics-based knowledge from sea trials with data-driven residual learning. The baseline component, derived from calm-water power curves of the form $P = cV^n$, captures the dominant power-speed dependence, while another, nonlinear, regressor is then trained to predict the residual power, representing deviations caused by environmental and operational conditions. By constraining the machine learning task to residual corrections, the hybrid model simplifies learning, improves generalization, and ensures consistency with the underlying physics. In this study, an XGBoost, a simple Neural Network, and a Physics-Informed Neural Network (PINN) coupled with the baseline component were compared to identical models without the baseline component. Validation on in-service data demonstrates that the hybrid model consistently outperformed a pure data-driven baseline in sparse data regions while maintaining similar performance in populated ones. The proposed framework provides a practical and computationally efficient tool for vessel performance monitoring, with applications in weather routing, trim optimization, and energy efficiency planning.

The preservation of cultural heritage is increasingly transitioning towards data-driven predictive maintenance and"Digital Twin"construction. However, the mechanical constitutive models required for high-fidelity simulations remain fragmented across decades of unstructured scientific literature, creating a"Data Silo"that hinders conservation engineering. To address this, we present an automated, two-stage agentic framework leveraging Large Language Models (LLMs) to extract mechanical constitutive equations, calibrated parameters, and metadata from PDF documents. The workflow employs a resource-efficient"Gatekeeper"agent for relevance filtering and a high-capability"Analyst"agent for fine-grained extraction, featuring a novel Context-Aware Symbolic Grounding mechanism to resolve mathematical ambiguities. Applied to a corpus of over 2,000 research papers, the system successfully isolated 113 core documents and constructed a structured database containing 185 constitutive model instances and over 450 calibrated parameters. The extraction precision reached 80.4\%, establishing a highly efficient"Human-in-the-loop"workflow that reduces manual data curation time by approximately 90\%. We demonstrate the system's utility through a web-based Knowledge Retrieval Platform, which enables rapid parameter discovery for computational modeling. This work transforms scattered literature into a queryable digital asset, laying the data foundation for the"Digital Material Twin"of built heritage.

Automating scientific discovery in complex, experiment-driven domains requires more than iterative mutation of programs; it demands structured hypothesis management, environment interaction, and principled reflection. We present OR-Agent, a configurable multi-agent research framework designed for automated exploration in rich experimental environments. OR-Agent organizes research as a structured tree-based workflow that explicitly models branching hypothesis generation and systematic backtracking, enabling controlled management of research trajectories beyond simple mutation-crossover loops. At its core, we introduce an evolutionary-systematic ideation mechanism that unifies evolutionary selection of research starting points, comprehensive research plan generation, and coordinated exploration within a research tree. We introduce a hierarchical optimization-inspired reflection system in which short-term reflections act as verbal gradients, long-term reflections as verbal momentum, and memory compression as semantic weight decay, collectively forming a principled mechanism for governing research dynamics. We conduct extensive experiments across classical combinatorial optimization benchmarks as well as simulation-based cooperative driving scenarios. Results demonstrate that OR-Agent outperforms strong evolutionary baselines while providing a general, extensible, and inspectable framework for AI-assisted scientific discovery. All code and experimental data are publicly available at https://github.com/qiliuchn/OR-Agent.

In this work, we investigate the use of data-driven equation discovery for dynamical systems to model and forecast continuous-time dynamics of unconstrained optimization problems. To avoid expensive evaluations of the objective function and its gradient, we leverage trajectory data on the optimization variables to learn the continuous-time dynamics associated with gradient descent, Newton's method, and ADAM optimization. The discovered gradient flows are then solved as a surrogate for the original optimization problem. To this end, we introduce the Learned Gradient Flow (LGF) optimizer, which is equipped to build surrogate models of variable polynomial order in full- or reduced-dimensional spaces at user-defined intervals in the optimization process. We demonstrate the efficacy of this approach on several standard problems from engineering mechanics and scientific machine learning, including two inverse problems, structural topology optimization, and two forward solves with different discretizations. Our results suggest that the learned gradient flows can significantly expedite convergence by capturing critical features of the optimization trajectory while avoiding expensive evaluations of the objective and its gradient.

Learning solution operators for systems with complex, varying geometries and parametric physical settings is a central challenge in scientific machine learning. In many-query regimes such as design optimization, control and inverse problems, surrogate modeling must generalize across geometries while allowing flexible evaluation at arbitrary spatial locations. In this work, we propose Arbitrary Geometry-encoded Transformer (ArGEnT), a geometry-aware attention-based architecture for operator learning on arbitrary domains. ArGEnT employs Transformer attention mechanisms to encode geometric information directly from point-cloud representations with three variants-self-attention, cross-attention, and hybrid-attention-that incorporates different strategies for incorporating geometric features. By integrating ArGEnT into DeepONet as the trunk network, we develop a surrogate modeling framework capable of learning operator mappings that depend on both geometric and non-geometric inputs without the need to explicitly parametrize geometry as a branch network input. Evaluation on benchmark problems spanning fluid dynamics, solid mechanics and electrochemical systems, we demonstrate significantly improved prediction accuracy and generalization performance compared with the standard DeepONet and other existing geometry-aware saurrogates. In particular, the cross-attention transformer variant enables accurate geometry-conditioned predictions with reduced reliance on signed distance functions. By combining flexible geometry encoding with operator-learning capabilities, ArGEnT provides a scalable surrogate modeling framework for optimization, uncertainty quantification, and data-driven modeling of complex physical systems.

Robotic assistance in scientific laboratories requires procedurally correct long-horizon manipulation, reliable execution under limited supervision, and robustness in low-demonstration regimes. Such conditions greatly challenge end-to-end vision-language-action (VLA) models, whose assumptions of recoverable errors and data-driven policy learning often break down in protocol-sensitive experiments. We propose CAPER, a framework for Constrained And ProcEdural Reasoning for robotic scientific experiments, which explicitly restricts where learning and reasoning occur in the planning and control pipeline. Rather than strengthening end-to-end policies, CAPER enforces a responsibility-separated structure: task-level reasoning generates procedurally valid action sequences under explicit constraints, mid-level multimodal grounding realizes subtasks without delegating spatial decision-making to large language models, and low-level control adapts to physical uncertainty via reinforcement learning with minimal demonstrations. By encoding procedural commitments through interpretable intermediate representations, CAPER prevents execution-time violations of experimental logic, improving controllability, robustness, and data efficiency. Experiments on a scientific workflow benchmark and a public long-horizon manipulation dataset demonstrate consistent improvements in success rate and procedural correctness, particularly in low-data and long-horizon settings.

Molecule generation and optimization is a fundamental task in chemical domain. The rapid development of intelligent tools, especially large language models (LLMs) with powerful knowledge reserves and interactive capabilities, has provided new paradigms for it. Nevertheless, the intrinsic challenge for LLMs lies in the complex implicit relationship between molecular structure and pharmacological properties and the lack of corresponding labeled data. To bridge this gap, we propose DrugR, an LLM-based method that introduces explicit, step-by-step pharmacological reasoning into the optimization process. Our approach integrates domain-specific continual pretraining, supervised fine-tuning via reverse data engineering, and self-balanced multi-granular reinforcement learning. This framework enables DrugR to effectively improve key ADMET properties while preserving the original molecule's core efficacy. Experimental results demonstrate that DrugR achieves comprehensive enhancement across multiple properties without compromising structural similarity or target binding affinity. Importantly, its explicit reasoning process provides clear, interpretable rationales for each optimization step, yielding actionable design insights and advancing toward automated, knowledge-driven scientific discovery. Our code and model checkpoints are open-sourced to foster future research.

Accurate simulation of turbulent flows is fundamental to scientific and engineering applications. Direct numerical simulation (DNS) offers the highest fidelity but is computationally prohibitive, while existing data-driven alternatives struggle with stable long-horizon rollouts, physical consistency, and faithful simulation of small-scale structures. These challenges are particularly acute in three-dimensional (3D) settings, where the cubic growth of spatial degrees of freedom dramatically amplifies computational cost, memory demand, and the difficulty of capturing multi-scale interactions. To address these challenges, we propose a Physics-Enhanced Swin Transformer (PEST) for 3D turbulence simulation. PEST leverages a window-based self-attention mechanism to effectively model localized PDE interactions while maintaining computational efficiency. We introduce a frequency-domain adaptive loss that explicitly emphasizes small-scale structures, enabling more faithful simulation of high-frequency dynamics. To improve physical consistency, we incorporate Navier--Stokes residual constraints and divergence-free regularization directly into the learning objective. Extensive experiments on two representative turbulent flow configurations demonstrate that PEST achieves accurate, physically consistent, and stable autoregressive long-term simulations, outperforming existing data-driven baselines.

This work presents a finite element-guided physics-informed operator learning framework for multiphysics problems with coupled partial differential equations (PDEs) on arbitrary domains. The proposed framework learns an operator from the input space to the solution space with a weighted residual formulation based on the finite element method, enabling discretization-independent prediction beyond the training resolution without relying on labeled simulation data. The present framework for multiphysics problems is implemented in Folax, a JAX-based operator learning platform, and is verified on nonlinear coupled thermo-mechanical problems. Two- and three-dimensional representative volume elements with varying heterogeneous microstructures, and a close-to-reality industrial casting example under varying boundary conditions are investigated as the example problems. We investigate the potential of several neural operators combined with the proposed finite element-guided approach, including Fourier neural operators (FNOs), deep operator networks (DeepONets), and a newly proposed implicit finite operator learning (iFOL) approach based on conditional neural fields. The results demonstrate that FNOs yield highly accurate solution operators on regular domains, where the global features can be efficiently learned in the spectral domain, and iFOL offers efficient parametric operator learning capabilities for complex and irregular geometries. Furthermore, studies on training strategies, network decomposition, and training sample quality reveal that a monolithic training strategy using a single network is sufficient for accurate predictions, while training sample quality strongly influences performance. Overall, the present approach highlights the potential of physics-informed operator learning with a finite element-based loss as a unified and scalable approach for coupled multiphysics simulations.

The Bayesian update step poses significant computational challenges in high-dimensional nonlinear estimation. While log-homotopy particle flow filters offer an alternative to stochastic sampling, existing formulations usually yield stiff differential equations. Conversely, existing deep learning approximations typically treat the update as a black-box task or rely on asymptotic relaxation, neglecting the exact geometric structure of the finite-horizon probability transport. In this work, we propose a physics-informed neural particle flow, which is an amortized inference framework. To construct the flow, we couple the log-homotopy trajectory of the prior to posterior density function with the continuity equation describing the density evolution. This derivation yields a governing partial differential equation (PDE), referred to as the master PDE. By embedding this PDE as a physical constraint into the loss function, we train a neural network to approximate the transport velocity field. This approach enables purely unsupervised training, eliminating the need for ground-truth posterior samples. We demonstrate that the neural parameterization acts as an implicit regularizer, mitigating the numerical stiffness inherent to analytic flows and reducing online computational complexity. Experimental validation on multimodal benchmarks and a challenging nonlinear scenario confirms better mode coverage and robustness compared to state-of-the-art baselines.

Operator learning has the potential to strongly impact scientific computing by learning solution operators for differential equations, potentially accelerating multi-query tasks such as design optimization and uncertainty quantification by orders of magnitude. Despite proven universal approximation properties, deep operator networks (DeepONets) often exhibit limited accuracy and generalization in practice, which hinders their adoption. Understanding these limitations is therefore crucial for further advancing the approach. This work analyzes performance limitations of the classical DeepONet architecture. It is shown that the approximation error is dominated by the branch network when the internal dimension is sufficiently large, and that the learned trunk basis can often be replaced by classical basis functions without a significant impact on performance. To investigate this further, a modified DeepONet is constructed in which the trunk network is replaced by the left singular vectors of the training solution matrix. This modification yields several key insights. First, a spectral bias in the branch network is observed, with coefficients of dominant, low-frequency modes learned more effectively. Second, due to singular-value scaling of the branch coefficients, the overall branch error is dominated by modes with intermediate singular values rather than the smallest ones. Third, using a shared branch network for all mode coefficients, as in the standard architecture, improves generalization of small modes compared to a stacked architecture in which coefficients are computed separately. Finally, strong and detrimental coupling between modes in parameter space is identified.

Physics-informed neural networks (PINNs) have emerged as a promising mesh-free paradigm for solving partial differential equations, yet adoption in science and engineering is limited by slow training and modest accuracy relative to modern numerical solvers. We introduce the Sequential Correction Algorithm for Learning Efficient PINN (Scale-PINN), a learning strategy that bridges modern physics-informed learning with numerical algorithms. Scale-PINN incorporates the iterative residual-correction principle, a cornerstone of numerical solvers, directly into the loss formulation, marking a paradigm shift in how PINN losses can be conceived and constructed. This integration enables Scale-PINN to achieve unprecedented convergence speed across PDE problems from different physics domain, including reducing training time on a challenging fluid-dynamics problem for state-of-the-art PINN from hours to sub-2 minutes while maintaining superior accuracy, and enabling application to representative problems in aerodynamics and urban science. By uniting the rigor of numerical methods with the flexibility of deep learning, Scale-PINN marks a significant leap toward the practical adoption of PINNs in science and engineering through scalable, physics-informed learning. Codes are available at https://github.com/chiuph/SCALE-PINN.

Understanding and predicting microstructure evolution is fundamental to materials science, as it governs the resulting properties and performance of materials. Traditional simulation methods, such as phase-field models, offer high-fidelity results but are computationally expensive due to the need to solve complex partial differential equations at fine spatiotemporal resolutions. To address this challenge, we propose a deep learning-based framework that accelerates microstructure evolution predictions while maintaining high accuracy. Our approach utilizes a fully convolutional spatiotemporal model trained in a self-supervised manner using sequential images generated from simulations of microstructural processes, including grain growth and spinodal decomposition. The trained neural network effectively learns the underlying physical dynamics and can accurately capture both short-term local behaviors and long-term statistical properties of evolving microstructures, while also demonstrating generalization to unseen spatiotemporal domains and variations in configuration and material parameters. Compared to recurrent neural architectures, our model achieves state-of-the-art predictive performance with significantly reduced computational cost in both training and inference. This work establishes a robust baseline for spatiotemporal learning in materials science and offers a scalable, data-driven alternative for fast and reliable microstructure simulations.

Partial differential equations (PDEs) form a central component of scientific computing. Among recent advances in deep learning, evolutionary neural networks have been developed to successively capture the temporal dynamics of time-dependent PDEs via parameter evolution. The parameter updates are obtained by solving a linear system derived from the governing equation residuals at each time step. However, strong-form evolutionary approaches can yield ill-conditioned linear systems due to pointwise residual discretization, and their computational cost scales unfavorably with the number of training samples. To address these limitations, we propose a weak-form evolutionary Kolmogorov-Arnold Network (KAN) for the scalable and accurate prediction of PDE solutions. We decouple the linear system size from the number of training samples through the weak formulation, leading to improved scalability compared to strong-form approaches. We also rigorously enforce boundary conditions by constructing the trial space with boundary-constrained KANs to satisfy Dirichlet and periodic conditions, and by incorporating derivative boundary conditions directly into the weak formulation for Neumann conditions. In conclusion, the proposed weak-form evolutionary KAN framework provides a stable and scalable approach for PDEs and contributes to scientific machine learning with potential relevance to future engineering applications.

The traditional limitations of neural networks in reliably generalizing beyond the convex hulls of their training data present a significant problem for computational physics, in which one often wishes to solve PDEs in regimes far beyond anything which can be experimentally or analytically validated. In this paper, we show how it is possible to circumvent these limitations by constructing formally-verified neural network solvers for PDEs, with rigorous convergence, stability, and conservation properties, whose correctness can therefore be guaranteed even in extrapolatory regimes. By using the method of characteristics to predict the analytical properties of PDE solutions a priori (even in regions arbitrarily far from the training domain), we show how it is possible to construct rigorous extrapolatory bounds on the worst-case L^inf errors of shallow neural network approximations. Then, by decomposing PDE solutions into compositions of simpler functions, we show how it is possible to compose these shallow neural networks together to form deep architectures, based on ideas from compositional deep learning, in which the large L^inf errors in the approximations have been suppressed. The resulting framework, called BEACONS (Bounded-Error, Algebraically-COmposable Neural Solvers), comprises both an automatic code-generator for the neural solvers themselves, as well as a bespoke automated theorem-proving system for producing machine-checkable certificates of correctness. We apply the framework to a variety of linear and non-linear PDEs, including the linear advection and inviscid Burgers'equations, as well as the full compressible Euler equations, in both 1D and 2D, and illustrate how BEACONS architectures are able to extrapolate solutions far beyond the training data in a reliable and bounded way. Various advantages of the approach over the classical PINN approach are discussed.

Numerical solution of partial differential equations (PDEs) plays a vital role in various fields of science and engineering. In recent years, deep neural networks (DNNs) have emerged as a powerful tool for solving PDEs, leveraging their approximation capabilities to handle complex domains and high-dimensional problems. Among these, operator learning has gained increasing attention by learning mappings between function spaces using DNNs. This paper proposes a novel approach, termed the Neural Evolutionary Kernel Method (NEKM), for solving a class of time-dependent partial differential equations (PDEs) via deep neural network (DNN)-based kernel representations. By integrating boundary integral techniques with operator learning, prior mathematical information of time-dependent partial differential equations (PDEs) is embedded into the design of neural network architectures for predicting their solutions, enhancing both computational efficiency and solution accuracy. Numerical experiments on the heat, wave, and Schr\"{o}dinger equations demonstrate that the Neural Evolutionary Kernel Method (NEKM) achieves high accuracy and favorable computational efficiency. Furthermore, the operator learning framework inherently supports the simultaneous prediction of solutions to multiple PDEs with different coefficients, rendering its capability for solving random PDEs.

Solving Partial Differential Equations (PDEs) is fundamental to numerous scientific and engineering disciplines. A common challenge arises from solving the PDE families, which are characterized by sharing an identical mathematical structure but varying in specific parameters. Traditional numerical methods, such as the finite element method, need to independently solve each instance within a PDE family, which incurs massive computational cost. On the other hand, while recent advancements in machine learning PDE solvers offer impressive computational speed and accuracy, their inherent ``black-box"nature presents a considerable limitation. These methods primarily yield numerical approximations, thereby lacking the crucial interpretability provided by analytical expressions, which are essential for deeper scientific insight. To address these limitations, we propose a neuro-assisted multitasking symbolic PDE solver framework for PDE family solving, dubbed NMIPS. In particular, we employ multifactorial optimization to simultaneously discover the analytical solutions of PDEs. To enhance computational efficiency, we devise an affine transfer method by transferring learned mathematical structures among PDEs in a family, avoiding solving each PDE from scratch. Experimental results across multiple cases demonstrate promising improvements over existing baselines, achieving up to a $\sim$35.7% increase in accuracy while providing interpretable analytical solutions.

We study the problem of learning the law of linear stochastic partial differential equations (SPDEs) with additive Gaussian forcing from spatiotemporal observations. Most existing deep learning approaches either assume access to the driving noise or initial condition, or rely on deterministic surrogate models that fail to capture intrinsic stochasticity. We propose a structured latent-variable formulation that requires only observations of solution realizations and learns the underlying randomly forced dynamics. Our approach combines a spectral Galerkin projection with a truncated Wiener chaos expansion, yielding a principled separation between deterministic evolution and stochastic forcing. This reduces the infinite-dimensional SPDE to a finite system of parametrized ordinary differential equations governing latent temporal dynamics. The latent dynamics and stochastic forcing are jointly inferred through variational learning, allowing recovery of stochastic structure without explicit observation or simulation of noise during training. Empirical evaluation on synthetic data demonstrates state-of-the-art performance under comparable modeling assumptions across bounded and unbounded one-dimensional spatial domains.

We propose an optimization-informed deep neural network approach, named iUzawa-Net, aiming for the first solver that enables real-time solutions for a class of nonsmooth optimal control problems of linear partial differential equations (PDEs). The iUzawa-Net unrolls an inexact Uzawa method for saddle point problems, replacing classical preconditioners and PDE solvers with specifically designed learnable neural networks. We prove universal approximation properties and establish the asymptotic $\varepsilon$-optimality for the iUzawa-Net, and validate its promising numerical efficiency through nonsmooth elliptic and parabolic optimal control problems. Our techniques offer a versatile framework for designing and analyzing various optimization-informed deep learning approaches to optimal control and other PDE-constrained optimization problems. The proposed learning-to-control approach synergizes model-based optimization algorithms and data-driven deep learning techniques, inheriting the merits of both methodologies.

Deep learning has emerged as a transformative tool for the neural surrogate modeling of partial differential equations (PDEs), known as neural PDE solvers. However, scaling these solvers to industrial-scale geometries with over $10^8$ cells remains a fundamental challenge due to the prohibitive memory complexity of processing high-resolution meshes. We present Transolver-3, a new member of the Transolver family as a highly scalable framework designed for high-fidelity physics simulations. To bridge the gap between limited GPU capacity and the resolution requirements of complex engineering tasks, we introduce two key architectural optimizations: faster slice and deslice by exploiting matrix multiplication associative property and geometry slice tiling to partition the computation of physical states. Combined with an amortized training strategy by learning on random subsets of original high-resolution meshes and a physical state caching technique during inference, Transolver-3 enables high-fidelity field prediction on industrial-scale meshes. Extensive experiments demonstrate that Transolver-3 is capable of handling meshes with over 160 million cells, achieving impressive performance across three challenging simulation benchmarks, including aircraft and automotive design tasks.

We propose SymPlex, a reinforcement learning framework for discovering analytical symbolic solutions to partial differential equations (PDEs) without access to ground-truth expressions. SymPlex formulates symbolic PDE solving as tree-structured decision-making and optimizes candidate solutions using only the PDE and its boundary conditions. At its core is SymFormer, a structure-aware Transformer that models hierarchical symbolic dependencies via tree-relative self-attention and enforces syntactic validity through grammar-constrained autoregressive decoding, overcoming the limited expressivity of sequence-based generators. Unlike numerical and neural approaches that approximate solutions in discretized or implicit function spaces, SymPlex operates directly in symbolic expression space, enabling interpretable and human-readable solutions that naturally represent non-smooth behavior and explicit parametric dependence. Empirical results demonstrate exact recovery of non-smooth and parametric PDE solutions using deep learning-based symbolic methods.

Accurate estimation of tacrolimus exposure, quantified by the area under the concentration-time curve (AUC), is essential for precision dosing after renal transplantation. Current practice relies on population pharmacokinetic (PopPK) models based on nonlinear mixed-effects (NLME) methods. However, these models depend on rigid, pre-specified assumptions and may struggle to capture complex, patient-specific dynamics, leading to model misspecification. In this study, we introduce a novel data-driven alternative based on Latent Ordinary Differential Equations (Latent ODEs) for tacrolimus AUC prediction. This deep learning approach learns individualized pharmacokinetic dynamics directly from sparse clinical data, enabling greater flexibility in modeling complex biological behavior. The model was evaluated through extensive simulations across multiple scenarios and benchmarked against two standard approaches: NLME-based estimation and the iterative two-stage Bayesian (it2B) method. We further performed a rigorous clinical validation using a development dataset (n = 178) and a completely independent external dataset (n = 75). In simulation, the Latent ODE model demonstrated superior robustness, maintaining high accuracy even when underlying biological mechanisms deviated from standard assumptions. Regarding experiments on clinical datasets, in internal validation, it achieved significantly higher precision with a mean RMSPE of 7.99% compared with 9.24% for it2B (p<0.001). On the external cohort, it achieved an RMSPE of 10.82%, comparable to the two standard estimators (11.48% and 11.54%). These results establish the Latent ODE as a powerful and reliable tool for AUC prediction. Its flexible architecture provides a promising foundation for next-generation, multi-modal models in personalized medicine.

Neural operators have emerged as powerful deep learning frameworks for approximating solution operators of parameterized partial differential equations (PDE). However, current methods predominantly rely on multilayer perceptrons (MLPs) for mapping inputs to solutions, which impairs training robustness in physics-informed settings due to inherent spectral biases and fixed activation functions. To overcome the architectural limitations, we introduce the Physics-Informed Chebyshev Polynomial Neural Operator (CPNO), a novel mesh-free framework that leverages a basis transformation to replace unstable monomial expansions with the numerically stable Chebyshev spectral basis. By integrating parameter dependent modulation mechanism to main net, CPNO constructs PDE solutions in a near-optimal functional space, decoupling the model from MLP-specific constraints and enhancing multi-scale representation. Theoretical analysis demonstrates the Chebyshev basis's near-minimax uniform approximation properties and superior conditioning, with Lebesgue constants growing logarithmically with degree, thereby mitigating spectral bias and ensuring stable gradient flow during optimization. Numerical experiments on benchmark parameterized PDEs show that CPNO achieves superior accuracy, faster convergence, and enhanced robustness to hyperparameters. The experiment of transonic airfoil flow has demonstrated the capability of CPNO in characterizing complex geometric problems.

Modeling distributed dynamical systems governed by hyperbolic partial differential equations (PDEs) remains challenging due to discontinuities and shocks that hinder the convergence of traditional physics-informed neural networks (PINNs). The recently proposed vanishing stacked residual PINN (VSR-PINN) embeds a vanishing-viscosity mechanism within stacked residual refinements to enable a smooth transition from the parabolic to hyperbolic regime. This paper integrates three curriculum-learning methods as primal-dual (PD) optimization, causality progression, and adaptive sampling into the VSR-PINN. The PD strategy balances physics and data losses, the causality scheme unlocks deeper stacks by respecting temporal and gradient evolution, and adaptive sampling targets high residuals. Numerical experiments on traffic reconstruction confirm that enforcing causality systematically reduces the median point-wise MSE and its variability across runs, yielding improvements of nearly one order of magnitude over non-causal training in both the baseline and PD variants.

From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.

Machine learning accelerates molecular property prediction, yet state-of-the-art Large Language Models and Graph Neural Networks operate as black boxes. In drug discovery, where safety is critical, this opacity risks masking false correlations and excluding human expertise. Existing interpretability methods suffer from the effectiveness-trustworthiness trade-off: explanations may fail to reflect a model's true reasoning, degrade performance, or lack domain grounding. Concept Bottleneck Models (CBMs) offer a solution by projecting inputs to human-interpretable concepts before readout, ensuring that explanations are inherently faithful to the decision process. However, adapting CBMs to chemistry faces three challenges: the Relevance Gap (selecting task-relevant concepts from a large descriptor space), the Annotation Gap (obtaining concept supervision for molecular data), and the Capacity Gap (degrading performance due to bottleneck constraints). We introduce GlassMol, a model-agnostic CBM that addresses these gaps through automated concept curation and LLM-guided concept selection. Experiments across thirteen benchmarks demonstrate that \method generally matches or exceeds black-box baselines, suggesting that interpretability does not sacrifice performance and challenging the commonly assumed trade-off. Code is available at https://github.com/walleio/GlassMol.

Deep generative modeling to stochastically design small molecules is an emerging technology for accelerating drug discovery and development. However, one major issue in molecular generative models is their lower frequency of drug-like compounds. To resolve this problem, we developed a novel framework for optimization of deep generative models integrated with a D-Wave quantum annealing computer, where our Neural Hash Function (NHF) presented herein is used both as the regularization and binarization schemes simultaneously, of which the latter is for transformation between continuous and discrete signals of the classical and quantum neural networks, respectively, in the error evaluation (i.e., objective) function. The compounds generated via the quantum-annealing generative models exhibited higher quality in both validity and drug-likeness than those generated via the fully-classical models, and was further indicated to exceed even the training data in terms of drug-likeness features, without any restraints and conditions to deliberately induce such an optimization. These results indicated an advantage of quantum annealing to aim at a stochastic generator integrated with our novel neural network architectures, for the extended performance of feature space sampling and extraction of characteristic features in drug design.

Molecular crystal structure prediction represents a grand challenge in computational chemistry due to large sizes of constituent molecules and complex intra- and intermolecular interactions. While generative modeling has revolutionized structure discovery for molecules, inorganic solids, and metal-organic frameworks, extending such approaches to fully periodic molecular crystals is still elusive. Here, we present MolCrystalFlow, a flow-based generative model for molecular crystal structure prediction. The framework disentangles intramolecular complexity from intermolecular packing by embedding molecules as rigid bodies and jointly learning the lattice matrix, molecular orientations, and centroid positions. Centroids and orientations are represented on their native Riemannian manifolds, allowing geodesic flow construction and graph neural network operations that respects geometric symmetries. We benchmark our model against a state-of-the-art generative model (MOFFlow) for large-size periodic crystals and a rule-based structure generation method (Genarris) on two open-source molecular crystal datasets. MolCrystalFlow outperforms MOFFlow while achieving competitive performance against Genarris. We also demonstrate an integration of MolCrystalFlow model with universal machine learning potential to accelerate molecular crystal structure prediction, paving the way for data-driven generative discovery of molecular crystals.

Accurate molecular property prediction is central to drug discovery, yet graph neural networks often underperform in data-scarce regimes and fail to surpass traditional fingerprints. We introduce cross-graph inter-message passing (XIMP), which performs message passing both within and across multiple related graph representations. For small molecules, we combine the molecular graph with scaffold-aware junction trees and pharmacophore-encoding extended reduced graphs, integrating complementary abstractions. While prior work is either limited to a single abstraction or non-iterative communication across graphs, XIMP supports an arbitrary number of abstractions and both direct and indirect communication between them in each layer. Across ten diverse molecular property prediction tasks, XIMP outperforms state-of-the-art baselines in most cases, leveraging interpretable abstractions as an inductive bias that guides learning toward established chemical concepts, enhancing generalization in low-data settings.

This study proposes MCEMOL (Multi-Constrained Evolutionary Molecular Design Framework), a molecular optimization approach integrating rule-based evolution with molecular crossover. MCEMOL employs dual-layer evolution: optimizing transformation rules at rule level while applying crossover and mutation to molecular structures. Unlike deep learning methods requiring large datasets and extensive training, our algorithm evolves efficiently from minimal starting molecules with low computational overhead. The framework incorporates message-passing neural networks and comprehensive chemical constraints, ensuring efficient and interpretable molecular design. Experimental results demonstrate that MCEMOL provides transparent design pathways through its evolutionary mechanism while generating valid, diverse, target-compliant molecules. The framework achieves 100% molecular validity with high structural diversity and excellent drug-likeness compliance, showing strong performance in symmetry constraints, pharmacophore optimization, and stereochemical integrity. Unlike black-box methods, MCEMOL delivers dual value: interpretable transformation rules researchers can understand and trust, alongside high-quality molecular libraries for practical applications. This establishes a paradigm where interpretable AI-driven drug design and effective molecular generation are achieved simultaneously, bridging the gap between computational innovation and practical drug discovery needs.

Experimental validation of chemical processes is slow and costly, limiting exploration in materials discovery. Machine learning can prioritize promising candidates, but existing data in patents and literature is heterogeneous and difficult to use. We introduce a universal directed-tree process-graph representation that unifies unstructured text, molecular structures, and numeric measurements into a single machine-readable format. To learn from this structured data, we developed a multi-modal graph neural network with a property-conditioned attention mechanism. Trained on approximately 700,000 process graphs from nearly 9,000 diverse documents, our model learns semantically rich embeddings that generalize across domains. When fine-tuned on compact, domain-specific datasets, the pretrained model achieves strong performance, demonstrating that universal process representations learned at scale transfer effectively to specialized prediction tasks with minimal additional data.

The discovery of next-generation photoinitiators for two-photon polymerization (TPP) is hindered by the absence of large, open datasets containing the quantum-chemical and photophysical properties required to model photodissociation and excited-state behavior. Existing molecular datasets typically provide only basic physicochemical descriptors and therefore cannot support data-driven screening or AI-assisted design of photoinitiators. To address this gap, we introduce QuantumChem-200K, a large-scale dataset of over 200,000 organic molecules annotated with eleven quantum-chemical properties, including two-photon absorption (TPA) cross sections, TPA spectral ranges, singlet-triplet intersystem crossing (ISC) energies, toxicity and synthetic accessibility scores, hydrophilicity, solubility, boiling point, molecular weight, and aromaticity. These values are computed using a hybrid workflow that integrates density function theory (DFT), semi-empirical excited-state methods, atomistic quantum solvers, and neural-network predictors. Using QuantumChem-200K, we fine tune the open-source Qwen2.5-32B large language model to create a chemistry AI assistant capable of forward property prediction from SMILES. Benchmarking on 3000 unseen molecules from VQM24 and ZINC20 demonstrates that domain-specific fine-tuning significantly improves accuracy over GPT-4o, Llama-3.1-70B, and the base Qwen2.5-32B model, particularly for TPA and ISC predictions central to photoinitiator design. QuantumChem-200K and the corresponding AI assistant together provide the first scalable platform for high-throughput, LLM-driven photoinitiator screening and accelerated discovery of photosensitive materials.

Batched synthesis and testing of molecular designs is the key bottleneck of drug development. There has been great interest in leveraging biomolecular foundation models as surrogates to accelerate this process. In this work, we show how to obtain scalable probabilistic surrogates of binding affinity for use in Batch Bayesian Optimization (Batch BO). This demands parallel acquisition functions that hedge between designs and the ability to rapidly sample from a joint predictive density to approximate them. Through the framework of Epistemic Neural Networks (ENNs), we obtain scalable joint predictive distributions of binding affinity on top of representations taken from large structure-informed models. Key to this work is an investigation into the importance of prior networks in ENNs and how to pretrain them on synthetic data to improve downstream performance in Batch BO. Their utility is demonstrated by rediscovering known potent EGFR inhibitors on a semi-synthetic benchmark in up to 5x fewer iterations, as well as potent inhibitors from a real-world small-molecule library in up to 10x fewer iterations, offering a promising solution for large-scale drug discovery applications.

The convergence of statistical learning and molecular physics is transforming our approach to modeling biomolecular systems. Physics-informed machine learning (PIML) offers a systematic framework that integrates data-driven inference with physical constraints, resulting in models that are accurate, mechanistic, generalizable, and able to extrapolate beyond observed domains. This review surveys recent advances in physics-informed neural networks and operator learning, differentiable molecular simulation, and hybrid physics-ML potentials, with emphasis on long-timescale kinetics, rare events, and free-energy estimation. We frame these approaches as solutions to the"biomolecular closure problem", recovering unresolved interactions beyond classical force fields while preserving thermodynamic consistency and mechanistic interpretability. We examine theoretical foundations, tools and frameworks, computational trade-offs, and unresolved issues, including model expressiveness and stability. We outline prospective research avenues at the intersection of machine learning, statistical physics, and computational chemistry, contending that future advancements will depend on mechanistic inductive biases, and integrated differentiable physical learning frameworks for biomolecular simulation and discovery.

The discovery of effective molecular modulators is essential for advancing perovskite solar cells (PSCs), but the research process is hindered by the vastness of chemical space and the time-consuming and expensive trial-and-error experimental screening. Concurrently, machine learning (ML) offers significant potential for accelerating materials discovery. However, applying ML to PSCs remains a major challenge due to data scarcity and limitations of traditional quantitative structure-property relationship (QSPR) models. Here, we apply a chemical informed transfer learning framework based on pre-trained deep neural networks, which achieves high accuracy in predicting the molecular modulator's effect on the power conversion efficiency (PCE) of PSCs. This framework is established through systematical benchmarking of diverse molecular representations, enabling lowcost and high-throughput virtual screening over 79,043 commercially available molecules. Furthermore, we leverage interpretability techniques to visualize the learned chemical representation and experimentally characterize the resulting modulator-perovskite interactions. The top molecular modulators identified by the framework are subsequently validated experimentally, delivering a remarkably improved champion PCE of 26.91% in PSCs.

High-energy materials (HEMs) are critical for propulsion and defense domains, yet their discovery remains constrained by experimental data and restricted access to testing facilities. This work presents a novel approach toward high-energy molecules by combining Long Short-Term Memory (LSTM) networks for molecular generation and Attentive Graph Neural Networks (GNN) for property predictions. We propose a transformative embedding space construction strategy that integrates fixed SHA-256 embeddings with partially trainable representations. Unlike conventional regularization techniques, this changes the representational basis itself, reshaping the molecular input space before learning begins. Without recourse to pretraining, the generator achieves 67.5% validity and 37.5% novelty. The generated library exhibits a mean Tanimoto coefficient of 0.214 relative to training set signifying the ability of framework to generate a diverse chemical space. We identified 37 new super explosives higher than 9 km/s predicted detonation velocity.

The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise thermodynamic calculations. Recent advancements in machine learning (ML) present an opportunity to overcome these limitations by leveraging neural networks to develop more precise implicit solvent potentials for diverse applications. A major drawback of current ML-based methods is their reliance on force-matching alone, which can lead to energy predictions that differ by an arbitrary constant and are therefore unsuitable for absolute free energy comparisons. Here, we introduce a novel methodology with a graph neural network (GNN)-based implicit solvent model, dubbed Lambda Solvation Neural Network (LSNN). In addition to force-matching, this network was trained to match the derivatives of alchemical variables, ensuring that solvation free energies can be meaningfully compared across chemical species. Trained on a dataset of approximately 300,000 small molecules, LSNN achieves free energy predictions with accuracy comparable to explicit-solvent alchemical simulations, while offering a computational speedup and establishing a foundational framework for future applications in drug discovery.

A plethora of applications entail solving black-box optimization problems with high evaluation costs, including drug discovery, material design, as well as hyperparameter tuning. Toward finding the global optimum of such black-box optimization problems with sample efficiency, Bayesian optimization (BO) is a theoretically elegant framework that relies on a probabilistic surrogate model so as to iteratively select the query point with well-balanced exploration-exploitation tradeoffs. The Gaussian process (GP), as the de-facto choice for surrogate modeling, has achieved compelling performances for vanilla BO with low-dimensional continuous variables. However, GPs fall short in coping with high-dimensional counterparts with {\it irregular} variables (e.g., categorical, ordinal, etc.). To alleviate this, neural network-based surrogates have been explored. Inspired by the powerful capabilities of LLMs, we adopt the LLM as the surrogate to model the mapping from the high-dimensional input variables to the objective function. To adapt to the current problem, we leverage the low-rank adaptation (LoRA) to fine-tune the LLM parameters together with the posterior of a linear regression head via the variational Bayesian last layer (VBLL) framework. The resulting LoRA-VBLL is not only computationally light compared to existing alternatives, but also admits recursive updates. To automate the critical selection of the LoRA rank as well as other hyperparameters, a weighted ensemble (ENS) of LoRA-VBLL surrogates has been devised, which further accommodates continual update of the per-model weight and individual LoRA-VBLL parameters via recursive Bayes. Extensive experimental results demonstrate the compelling performance of the proposed (ENS-)LoRA-VBLL approaches on various high-dimensional benchmarks and the real-world molecular optimization tasks.

Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery to new material design. Current state-of-the-art models enforce roto-translational symmetries through equivariant neural network architectures, a hard-wired inductive bias that can often lead to reduced flexibility, computational efficiency, and scalability. In this work, we introduce TransIP: Transformer-based Inter-Atomic Potentials, a novel training paradigm for interatomic potentials achieving symmetry compliance without explicit architectural constraints. Our approach guides a generic non-equivariant Transformer-based model to learn SO(3)-equivariance by optimizing its representations in the embedding space. Trained on the recent Open Molecules (OMol25) collection, a large and diverse molecular dataset built specifically for MLIPs and covering different types of molecules (including small organics, biomolecular fragments, and electrolyte-like species), TransIP attains comparable performance in machine-learning force fields versus state-of-the-art equivariant baselines. Further, compared to a data augmentation baseline, TransIP achieves 40% to 60% improvement in performance across varying OMol25 dataset sizes. More broadly, our work shows that learned equivariance can be a powerful and efficient alternative to equivariant or augmentation-based MLIP models. Our code is available at: https://github.com/Ahmed-A-A-Elhag/TransIP.

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual feature engineering. However, while GNNs and self-supervised learning approaches have advanced molecular property prediction (MPP), the integration of human prior knowledge remains indispensable, as evidenced by recent methods that leverage large language models (LLMs) for knowledge extraction. Despite their strengths, LLMs are constrained by knowledge gaps and hallucinations, particularly for less-studied molecular properties. In this work, we propose a novel framework that, for the first time, integrates knowledge extracted from LLMs with structural features derived from pre-trained molecular models to enhance MPP. Our approach prompts LLMs to generate both domain-relevant knowledge and executable code for molecular vectorization, producing knowledge-based features that are subsequently fused with structural representations. We employ three state-of-the-art LLMs, GPT-4o, GPT-4.1, and DeepSeek-R1, for knowledge extraction. Extensive experiments demonstrate that our integrated method outperforms existing approaches, confirming that the combination of LLM-derived knowledge and structural information provides a robust and effective solution for MPP.

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models in published literature across several categories of drug discovery research. This paper covers the research categories comprehensively with recent papers, namely molecular property prediction, including drug-target binding affinity prediction, drug-drug interaction study, microbiome interaction prediction, drug repositioning, retrosynthesis, and new drug design, and provides guidance for future work on GNNs for drug discovery.

Graph Contrastive Learning (GCL) has emerged as a leading paradigm for self-supervised learning on graphs, with strong performance reported on standardized datasets and growing applications ranging from genomics to drug discovery. We ask a basic question: does GCL actually outperform untrained baselines? We find that GCL's advantage depends strongly on dataset size and task difficulty. On standard datasets, untrained Graph Neural Networks (GNNs), simple multilayer perceptrons, and even handcrafted statistics can rival or exceed GCL. On the large molecular dataset ogbg-molhiv, we observe a crossover: GCL lags at small scales but pulls ahead beyond a few thousand graphs, though this gain eventually plateaus. On synthetic datasets, GCL accuracy approximately scales with the logarithm of the number of graphs and its performance gap (compared with untrained GNNs) varies with respect to task complexity. Moving forward, it is crucial to identify the role of dataset size in benchmarks and applications, as well as to design GCL algorithms that avoid performance plateaus.

Graph neural networks have demonstrated remarkable success in predicting molecular properties by leveraging the rich structural information encoded in molecular graphs. However, their black-box nature reduces interpretability, which limits trust in their predictions for important applications such as drug discovery and materials design. Furthermore, existing explanation techniques often fail to reliably quantify the contribution of individual atoms or substructures due to the entangled message-passing dynamics. We introduce SEAL (Substructure Explanation via Attribution Learning), a new interpretable graph neural network that attributes model predictions to meaningful molecular subgraphs. SEAL decomposes input graphs into chemically relevant fragments and estimates their causal influence on the output. The strong alignment between fragment contributions and model predictions is achieved by explicitly reducing inter-fragment message passing in our proposed model architecture. Extensive evaluations on synthetic benchmarks and real-world molecular datasets demonstrate that SEAL outperforms other explainability methods in both quantitative attribution metrics and human-aligned interpretability. A user study further confirms that SEAL provides more intuitive and trustworthy explanations to domain experts. By bridging the gap between predictive performance and interpretability, SEAL offers a promising direction for more transparent and actionable molecular modeling.

From climate science to drug discovery, scientific computing demands have surged dramatically in recent years -- driven by larger datasets, more sophisticated models, and higher simulation fidelity. This growth rate far outpaces transistor scaling, leading to unsustainably rising costs, energy consumption, and emissions. Semiconductor manufacturing is no exception. Computational lithography -- involving transferring circuitry to silicon in diffraction-limited conditions -- is the largest workload in semiconductor manufacturing. It has also grown exceptionally complex as miniaturization has advanced in the angstrom-era, requiring more accurate modeling, intricate corrections, and broader solution-space exploration. Accelerated computing (AC) offers a solution by dramatically freeing up the compute and power envelope. AI augments these gains by serving as high-fidelity surrogates for compute-intensive steps. Together, they present a sustainable, next-generation computing platform for scientific workloads. This new paradigm needs a fundamental redesign of the software stack. For computational lithography, NVIDIA cuLitho reinvents the core primitives -- diffractive optics, computational geometry, multi-variant optimization, data processing -- to achieve a transformative 57X end-to-end acceleration. Beyond dramatically faster cycles, this expanded compute envelope enables more rigorous solutions, including curvilinear masks, high-numerical aperture extreme ultraviolet (high-NA EUV) lithography, and subatomic modeling. We reinvest a small fraction of the freed-up compute to include through-focus correction for better process resilience. Silicon experiments at IMEC show significant benefits compared to conventional methods -- 35% better process window and 19% better edge placement error. This is the first quantified chip-scale demonstration of the lithography benefits of AC and AI in silicon.

Generative foundation models have become an important tool for data reconstruction and simulation in scientific computing, showing a tight integration with traditional numerical simulations. At the same time, with the development of new hardware features, such as matrix acceleration units and high-bandwidth memory, CPU-based clusters offer promising opportunities to accelerate and scale such models, facilitating the unification of artificial intelligence and scientific computing. We present DiT-HC, the first system to train and scale the generative model DiT on a next-generation HPC CPU cluster. DiT-HC introduces three key techniques: (1) communication-free tensor parallelism (CFTP) with AutoMem for automated memory-aware dataflow, (2) HCOps, a suite of optimized GEMM and operator kernels leveraging vector and matrix acceleration units, and (3) a custom MPI backend that overlaps computation, communication, and memory movement. Experiments show 8.2 to 87.7 times speedups over native or public CPU libraries and 90.6% weak scaling efficiency on 256 nodes. These results demonstrate the feasibility of large-scale generative model training on CPU clusters and provide new insights for future HPC-AI co-design.

Artificial intelligence is reshaping scientific discovery, yet its use in materials research remains limited by fragmented computational ecosystems, reproducibility challenges, and dependence on commercial large language models (LLMs). Here we introduce AGAPI (AtomGPT.org API), an open-access agentic AI platform that integrates more than eight open-source LLMs with over twenty materials-science API endpoints, unifying databases, simulation tools, and machine-learning models through a common orchestration framework. AGAPI employs an Agent-Planner-Executor-Summarizer architecture that autonomously constructs and executes multi-step workflows spanning materials data retrieval, graph neural network property prediction, machine-learning force-field optimization, tight-binding calculations, diffraction analysis, and inverse design. We demonstrate AGAPI through end-to-end workflows, including heterostructure construction, powder X-ray diffraction analysis, and semiconductor defect engineering requiring up to ten sequential operations. In addition, we evaluate AGAPI using 30+ example prompts as test cases and compare agentic predictions with and without tool access against experimental data. With more than 1,000 active users, AGAPI provides a scalable and transparent foundation for reproducible, AI-accelerated materials discovery. AGAPI-Agents codebase is available at https://github.com/atomgptlab/agapi.

Artificial intelligence and machine learning are reshaping how we approach scientific discovery, not by replacing established methods but by extending what researchers can probe, predict, and design. In this roadmap we provide a forward-looking view of AI-enabled science across biology, chemistry, climate science, mathematics, materials science, physics, self-driving laboratories and unconventional computing. Several shared themes emerge: the need for diverse and trustworthy data, transferable electronic-structure and interatomic models, AI systems integrated into end-to-end scientific workflows that connect simulations to experiments and generative systems grounded in synthesisability rather than purely idealised phases. Across domains, we highlight how large foundation models, active learning and self-driving laboratories can close loops between prediction and validation while maintaining reproducibility and physical interpretability. Taken together, these perspectives outline where AI-enabled science stands today, identify bottlenecks in data, methods and infrastructure, and chart concrete directions for building AI systems that are not only more powerful but also more transparent and capable of accelerating discovery in complex real-world environments.

We present Genie-CAT, a tool-augmented large-language-model (LLM) system designed to accelerate scientific hypothesis generation in protein design. Using metalloproteins (e.g., ferredoxins) as a case study, Genie-CAT integrates four capabilities -- literature-grounded reasoning through retrieval-augmented generation (RAG), structural parsing of Protein Data Bank files, electrostatic potential calculations, and machine-learning prediction of redox properties -- into a unified agentic workflow. By coupling natural-language reasoning with data-driven and physics-based computation, the system generates mechanistically interpretable, testable hypotheses linking sequence, structure, and function. In proof-of-concept demonstrations, Genie-CAT autonomously identifies residue-level modifications near [Fe--S] clusters that affect redox tuning, reproducing expert-derived hypotheses in a fraction of the time. The framework highlights how AI agents combining language models with domain-specific tools can bridge symbolic reasoning and numerical simulation, transforming LLMs from conversational assistants into partners for computational discovery.

Large-scale numerical simulations underpin modern scientific discovery but remain constrained by prohibitive computational costs. AI surrogates offer acceleration, yet adoption in mission-critical settings is limited by concerns over physical plausibility, trustworthiness, and the fusion of heterogeneous data. We introduce PHASE, a modular deep-learning framework for physics-integrated, heterogeneity-aware surrogates in scientific simulations. PHASE combines data-type-aware encoders for heterogeneous inputs with multi-level physics-based constraints that promote consistency from local dynamics to global system behavior. We validate PHASE on the biogeochemical (BGC) spin-up workflow of the U.S. Department of Energy's Energy Exascale Earth System Model (E3SM) Land Model (ELM), presenting-to our knowledge-the first scientifically validated AI-accelerated solution for this task. Using only the first 20 simulation years, PHASE infers a near-equilibrium state that otherwise requires more than 1,200 years of integration, yielding an effective reduction in required integration length by at least 60x. The framework is enabled by a pipeline for fusing heterogeneous scientific data and demonstrates strong generalization to higher spatial resolutions with minimal fine-tuning. These results indicate that PHASE captures governing physical regularities rather than surface correlations, enabling practical, physically consistent acceleration of land-surface modeling and other complex scientific workflows.

The history of science is punctuated by serendipitous discoveries, where unexpected observations, rather than targeted hypotheses, opened new fields of inquiry. While modern autonomous laboratories excel at accelerating hypothesis testing, their optimization for efficiency risks overlooking these crucial, unplanned findings. To address this gap, we introduce SciLink, an open-source, multi-agent artificial intelligence framework designed to operationalize serendipity in materials research by creating a direct, automated link between experimental observation, novelty assessment, and theoretical simulations. The framework employs a hybrid AI strategy where specialized machine learning models perform quantitative analysis of experimental data, while large language models handle higher-level reasoning. These agents autonomously convert raw data from materials characterization techniques into falsifiable scientific claims, which are then quantitatively scored for novelty against the published literature. We demonstrate the framework's versatility across diverse research scenarios, showcasing its application to atomic-resolution and hyperspectral data, its capacity to integrate real-time human expert guidance, and its ability to close the research loop by proposing targeted follow-up experiments. By systematically analyzing all observations and contextualizing them, SciLink provides a practical framework for AI-driven materials research that not only enhances efficiency but also actively cultivates an environment ripe for serendipitous discoveries, thereby bridging the gap between automated experimentation and open-ended scientific exploration.

Large language models (LLMs) have moved far beyond their initial form as simple chatbots, now carrying out complex reasoning, planning, writing, coding, and research tasks. These skills overlap significantly with those that human scientists use day-to-day to solve complex problems that drive the cutting edge of research. Using LLMs in \quotes{agentic} AI has the potential to revolutionize modern science and remove bottlenecks to progress. In this work, we present URSA, a scientific agent ecosystem for accelerating research tasks. URSA consists of a set of modular agents and tools, including coupling to advanced physics simulation codes, that can be combined to address scientific problems of varied complexity and impact. This work highlights the architecture of URSA, as well as examples that highlight the potential of the system.

The AI for Nuclear Energy workshop at Oak Ridge National Laboratory evaluated the potential of Large Language Models (LLMs) to accelerate fusion and fission research. Fourteen interdisciplinary teams explored diverse nuclear science challenges using ChatGPT, Gemini, Claude, and other AI models over a single day. Applications ranged from developing foundation models for fusion reactor control to automating Monte Carlo simulations, predicting material degradation, and designing experimental programs for advanced reactors. Teams employed structured workflows combining prompt engineering, deep research capabilities, and iterative refinement to generate hypotheses, prototype code, and research strategies. Key findings demonstrate that LLMs excel at early-stage exploration, literature synthesis, and workflow design, successfully identifying research gaps and generating plausible experimental frameworks. However, significant limitations emerged, including difficulties with novel materials designs, advanced code generation for modeling and simulation, and domain-specific details requiring expert validation. The successful outcomes resulted from expert-driven prompt engineering and treating AI as a complementary tool rather than a replacement for physics-based methods. The workshop validated AI's potential to accelerate nuclear energy research through rapid iteration and cross-disciplinary synthesis while highlighting the need for curated nuclear-specific datasets, workflow automation, and specialized model development. These results provide a roadmap for integrating AI tools into nuclear science workflows, potentially reducing development cycles for safer, more efficient nuclear energy systems while maintaining rigorous scientific standards.

Recent advances in artificial intelligence (AI) and quantum computing are accelerating automation in scientific and engineering processes, fundamentally reshaping research methodologies. This perspective highlights parallels between scientific automation and established Computer-Aided Engineering (CAE) practices, introducing Quantum CAE as a framework that leverages quantum algorithms for simulation, optimization, and machine learning within engineering design. Practical implementations of Quantum CAE are illustrated through case studies for combinatorial optimization problems. Further discussions include advancements toward higher automation levels, highlighting the critical role of specialized AI agents proficient in quantum algorithm design. The integration of quantum computing with AI raises significant questions about the collaborative dynamics among human scientists and engineers, AI systems, and quantum computational resources, underscoring a transformative future for automated discovery and innovation.

Machine learning-based surrogate models have emerged as a powerful tool to accelerate simulation-driven scientific workflows. However, their widespread adoption is hindered by the lack of large-scale, diverse, and standardized datasets tailored to physics-based simulations. While existing initiatives provide valuable contributions, many are limited in scope-focusing on specific physics domains, relying on fragmented tooling, or adhering to overly simplistic datamodels that restrict generalization. To address these limitations, we introduce PLAID (Physics-Learning AI Datamodel), a flexible and extensible framework for representing and sharing datasets of physics simulations. PLAID defines a unified standard for describing simulation data and is accompanied by a library for creating, reading, and manipulating complex datasets across a wide range of physical use cases (gitlab.com/drti/plaid). We release six carefully crafted datasets under the PLAID standard, covering structural mechanics and computational fluid dynamics, and provide baseline benchmarks using representative learning methods. Benchmarking tools are made available on Hugging Face, enabling direct participation by the community and contribution to ongoing evaluation efforts (huggingface.co/PLAIDcompetitions).

We present MOFA, an open-source generative AI (GenAI) plus simulation workflow for high-throughput generation of metal-organic frameworks (MOFs) on large-scale high-performance computing (HPC) systems. MOFA addresses key challenges in integrating GPU-accelerated computing for GPU-intensive GenAI tasks, including distributed training and inference, alongside CPU- and GPU-optimized tasks for screening and filtering AI-generated MOFs using molecular dynamics, density functional theory, and Monte Carlo simulations. These heterogeneous tasks are unified within an online learning framework that optimizes the utilization of available CPU and GPU resources across HPC systems. Performance metrics from a 450-node (14,400 AMD Zen 3 CPUs + 1800 NVIDIA A100 GPUs) supercomputer run demonstrate that MOFA achieves high-throughput generation of novel MOF structures, with CO$_2$ adsorption capacities ranking among the top 10 in the hypothetical MOF (hMOF) dataset. Furthermore, the production of high-quality MOFs exhibits a linear relationship with the number of nodes utilized. The modular architecture of MOFA will facilitate its integration into other scientific applications that dynamically combine GenAI with large-scale simulations.

Ocean forecasting is crucial for both scientific research and societal benefits. Currently, the most accurate forecasting systems are global ocean forecasting systems (GOFSs), which represent the ocean state variables (OSVs) as discrete grids and solve partial differential equations (PDEs) governing the transitions of oceanic state variables using numerical methods. However, GOFSs processes are computationally expensive and prone to cumulative errors. Recently, large artificial intelligence (AI)-based models significantly boosted forecasting speed and accuracy. Unfortunately, building a large AI ocean forecasting system that can be considered cross-spatiotemporal and air-sea coupled forecasts remains a significant challenge. Here, we introduce LangYa, a cross-spatiotemporal and air-sea coupled ocean forecasting system. Results demonstrate that the time embedding module in LangYa enables a single model to make forecasts with lead times ranging from 1 to 7 days. The air-sea coupled module effectively simulates air-sea interactions. The ocean self-attention module improves network stability and accelerates convergence during training, and the adaptive thermocline loss function improves the accuracy of thermocline forecasting. Compared to existing numerical and AI-based ocean forecasting systems, LangYa uses 27 years of global ocean data from the Global Ocean Reanalysis and Simulation version 12 (GLORYS12) for training and achieves more reliable deterministic forecasting results for OSVs. LangYa forecasting system provides global ocean researchers with access to a powerful software tool for accurate ocean forecasting and opens a new paradigm for ocean science.

In recent years, Artificial intelligence (AI) has become ubiquitous, empowering various fields, especially integrating artificial intelligence and traditional science (AI for Science: Artificial intelligence for science), which has attracted widespread attention. In AI for Science, using artificial intelligence algorithms to solve partial differential equations (AI for PDEs: Artificial intelligence for partial differential equations) has become a focal point in computational mechanics. The core of AI for PDEs is the fusion of data and partial differential equations (PDEs), which can solve almost any PDEs. Therefore, this article provides a comprehensive review of the research on AI for PDEs, summarizing the existing algorithms and theories. The article discusses the applications of AI for PDEs in computational mechanics, including solid mechanics, fluid mechanics, and biomechanics. The existing AI for PDEs algorithms include those based on Physics-Informed Neural Networks (PINNs), Deep Energy Methods (DEM), Operator Learning, and Physics-Informed Neural Operator (PINO). AI for PDEs represents a new method of scientific simulation that provides approximate solutions to specific problems using large amounts of data, then fine-tuning according to specific physical laws, avoiding the need to compute from scratch like traditional algorithms. Thus, AI for PDEs is the prototype for future foundation models in computational mechanics, capable of significantly accelerating traditional numerical algorithms.

We study a discrete denoising diffusion framework that integrates a sample-efficient estimator of single-site conditionals with round-robin noising and denoising dynamics for generative modeling over discrete state spaces. Rather than approximating a discrete analog of a score function, our formulation treats single-site conditional probabilities as the fundamental objects that parameterize the reverse diffusion process. We employ a sample-efficient method known as Neural Interaction Screening Estimator (NeurISE) to estimate these conditionals in the diffusion dynamics. Controlled experiments on synthetic Ising models, MNIST, and scientific data sets produced by a D-Wave quantum annealer, synthetic Potts model and one-dimensional quantum systems demonstrate the proposed approach. On the binary data sets, these experiments demonstrate that the proposed approach outperforms popular existing methods including ratio-based approaches, achieving improved performance in total variation, cross-correlations, and kernel density estimation metrics.

Assessing whether two datasets are distributionally consistent is central to modern scientific analysis, particularly as generative artificial intelligence produces synthetic data whose fidelity must be validated against real observations in increasingly high-dimensional settings. Existing approaches are typically relative: they determine whether one dataset is more consistent with a reference than another, but do not provide a physically grounded absolute standard for fidelity. We propose an information-theoretic approach in which lossless compression via arithmetic coding provides an operational measure of dataset fidelity under a physics-informed probabilistic representation. Datasets sharing the same underlying physical correlations admit comparable optimal descriptions, while discrepancies-arising from miscalibration, mismodeling, or bias-manifest as an irreducible excess in codelength relative to the Shannon-optimal limit defined by the physics itself. This excess codelength defines an absolute fidelity metric, quantified directly in bits. Unlike conventional measures, which lack an intrinsic scale, zero excess provides a well-defined and physically meaningful target corresponding to consistency with the underlying distribution. We show that this metric is global, interpretable, additive across components, and asymptotically optimal, with differences in codelength corresponding to differences in expected negative log-likelihood under a common reference model. As a byproduct, our approach achieves improved compression relative to standard general-purpose algorithms such as gzip. These results establish arithmetic coding not merely as a compression tool, but as a measurement instrument for absolute, physics-grounded assessment of distributional fidelity.

We present a generative modeling framework for synthesizing physically feasible two-dimensional incompressible flows under arbitrary obstacle geometries and boundary conditions. Whereas existing diffusion-based flow generators either ignore physical constraints, impose soft penalties that do not guarantee feasibility, or specialize to fixed geometries, our approach integrates three complementary components: (1) a boundary-conditioned diffusion model operating on velocity fields; (2) a physics-informed training objective incorporating a divergence penalty; and (3) a projection-constrained reverse diffusion process that enforces exact incompressibility through a geometry-aware Helmholtz-Hodge operator. We derive the method as a discrete approximation to constrained Langevin sampling on the manifold of divergence-free vector fields, providing a connection between modern diffusion models and geometric constraint enforcement in incompressible flow spaces. Experiments on analytic Navier-Stokes data and obstacle-bounded flow configurations demonstrate significantly improved divergence, spectral accuracy, vorticity statistics, and boundary consistency relative to unconstrained, projection-only, and penalty-only baselines. Our formulation unifies soft and hard physical structure within diffusion models and provides a foundation for generative modeling of incompressible fields in robotics, graphics, and scientific computing.

Generating samples from limited information is a fundamental problem across scientific domains. Classical maximum entropy methods provide principled uncertainty quantification from moment constraints but require sampling via MCMC or Langevin dynamics, which typically exhibit exponential slowdown in high dimensions. In contrast, generative models based on diffusion and flow matching efficiently transport noise to data but offer limited theoretical guarantees and can overfit when data is scarce. We introduce Moment Guided Diffusion (MGD), which combines elements of both approaches. Building on the stochastic interpolant framework, MGD samples maximum entropy distributions by solving a stochastic differential equation that guides moments toward prescribed values in finite time, thereby avoiding slow mixing in equilibrium-based methods. We formally obtain, in the large-volatility limit, convergence of MGD to the maximum entropy distribution and derive a tractable estimator of the resulting entropy computed directly from the dynamics. Applications to financial time series, turbulent flows, and cosmological fields using wavelet scattering moments yield estimates of negentropy for high-dimensional multiscale processes.

In dynamical systems reconstruction (DSR) we aim to recover the dynamical system (DS) underlying observed time series. Specifically, we aim to learn a generative surrogate model which approximates the underlying, data-generating DS, and recreates its long-term properties (`climate statistics'). In scientific and medical areas, in particular, these models need to be mechanistically tractable -- through their mathematical analysis we would like to obtain insight into the recovered system's workings. Piecewise-linear (PL), ReLU-based RNNs (PLRNNs) have a strong track-record in this regard, representing SOTA DSR models while allowing mathematical insight by virtue of their PL design. However, all current PLRNN variants are discrete-time maps. This is in disaccord with the assumed continuous-time nature of most physical and biological processes, and makes it hard to accommodate data arriving at irregular temporal intervals. Neural ODEs are one solution, but they do not reach the DSR performance of PLRNNs and often lack their tractability. Here we develop theory for continuous-time PLRNNs (cPLRNNs): We present a novel algorithm for training and simulating such models, bypassing numerical integration by efficiently exploiting their PL structure. We further demonstrate how important topological objects like equilibria or limit cycles can be determined semi-analytically in trained models. We compare cPLRNNs to both their discrete-time cousins as well as Neural ODEs on DSR benchmarks, including systems with discontinuities which come with hard thresholds.

Many scientific and engineering systems exhibit intrinsically multimodal behavior arising from latent regime switching and non-unique physical mechanisms. In such settings, learning the full conditional distribution of admissible outcomes in a physically consistent and interpretable manner remains a challenge. While recent advances in machine learning have enabled powerful multimodal generative modeling, their integration with physics-constrained scientific modeling remains nontrivial, particularly when physical structure must be preserved or data are limited. This work develops a physics-informed multimodal conditional modeling framework based on mixture density representations. Mixture density networks (MDNs) provide an explicit and interpretable parameterization of multimodal conditional distributions. Physical knowledge is embedded through component-specific regularization terms that penalize violations of governing equations or physical laws. This formulation naturally accommodates non-uniqueness and stochasticity while remaining computationally efficient and amenable to conditioning on contextual inputs. The proposed framework is evaluated across a range of scientific problems in which multimodality arises from intrinsic physical mechanisms rather than observational noise, including bifurcation phenomena in nonlinear dynamical systems, stochastic partial differential equations, and atomistic-scale shock dynamics. In addition, the proposed method is compared with a conditional flow matching (CFM) model, a representative state-of-the-art generative modeling approach, demonstrating that MDNs can achieve competitive performance while offering a simpler and more interpretable formulation.

Discrete diffusion models have recently emerged as a powerful class of generative models for chemistry and biology data. In these fields, the goal is to generate various samples with high rewards (e.g., drug-likeness in molecules), making reward-based guidance crucial. Most existing methods are based on guiding the diffusion model using intermediate rewards but tend to underperform since intermediate rewards are noisy due to the non-smooth nature of reward functions used in scientific domains. To address this, we propose Clean-Sample Markov Chain (CSMC) Sampler, a method that performs effective test-time reward-guided sampling for discrete diffusion models, enabling local search without relying on intermediate rewards. CSMC constructs a Markov chain of clean samples using the Metropolis-Hastings algorithm such that its stationary distribution is the target distribution. We design a proposal distribution by sequentially applying the forward and backward diffusion processes, making the acceptance probability tractable. Experiments on molecule and biological sequence generation with various reward functions demonstrate that our method consistently outperforms prior approaches that rely on intermediate rewards.

Modeling time series with long- or short-memory characteristics is a fundamental challenge in many scientific and engineering domains. While fractional Brownian motion has been widely used as a noise source to capture such memory effects, its incompatibility with It\^o calculus limits its applicability in neural stochastic differential equation~(SDE) frameworks. In this paper, we propose a novel class of noise, termed Neural Network-kernel ARMA-type noise~(NA-noise), which is an It\^o-process-based alternative capable of capturing both long- and short-memory behaviors. The kernel function defining the noise structure is parameterized via neural networks and decomposed into a product form to preserve the Markov property. Based on this noise process, we develop NANSDE-Net, a generative model that extends Neural SDEs by incorporating NA-noise. We prove the theoretical existence and uniqueness of the solution under mild conditions and derive an efficient backpropagation scheme for training. Empirical results on both synthetic and real-world datasets demonstrate that NANSDE-Net matches or outperforms existing models, including fractional SDE-Net, in reproducing long- and short-memory features of the data, while maintaining computational tractability within the It\^o calculus framework.

Physiologically Based Pharmacokinetic (PBPK) modeling is a cornerstone of model-informed drug development (MIDD), providing a mechanistic framework to predict drug absorption, distribution, metabolism, and excretion (ADME). Despite its utility, adoption is hindered by high computational costs for large-scale simulations, difficulty in parameter identification for complex biological systems, and uncertainty in interspecies extrapolation. In this work, we propose a unified Scientific Machine Learning (SciML) framework that bridges mechanistic rigor and data-driven flexibility. We introduce three contributions: (1) Foundation PBPK Transformers, which treat pharmacokinetic forecasting as a sequence modeling task; (2) Physiologically Constrained Diffusion Models (PCDM), a generative approach that uses a physics-informed loss to synthesize biologically compliant virtual patient populations; and (3) Neural Allometry, a hybrid architecture combining Graph Neural Networks (GNNs) with Neural ODEs to learn continuous cross-species scaling laws. Experiments on synthetic datasets show that the framework reduces physiological violation rates from 2.00% to 0.50% under constraints while offering a path to faster simulation.

Although diffusion models have successfully extended to function-valued data, stochastic interpolants -- which offer a flexible way to bridge arbitrary distributions -- remain limited to finite-dimensional settings. This work bridges this gap by establishing a rigorous framework for stochastic interpolants in infinite-dimensional Hilbert spaces. We provide comprehensive theoretical foundations, including proofs of well-posedness and explicit error bounds. We demonstrate the effectiveness of the proposed framework for conditional generation, focusing particularly on complex PDE-based benchmarks. By enabling generative bridges between arbitrary functional distributions, our approach achieves state-of-the-art results, offering a powerful, general-purpose tool for scientific discovery.

Scientific machine learning (SciML) increasingly requires models that capture multimodal conditional uncertainty arising from ill-posed inverse problems, multistability, and chaotic dynamics. While recent work has favored highly expressive implicit generative models such as diffusion and flow-based methods, these approaches are often data-hungry, computationally costly, and misaligned with the structured solution spaces frequently found in scientific problems. We demonstrate that Mixture Density Networks (MDNs) provide a principled yet largely overlooked alternative for multimodal uncertainty quantification in SciML. As explicit parametric density estimators, MDNs impose an inductive bias tailored to low-dimensional, multimodal physics, enabling direct global allocation of probability mass across distinct solution branches. This structure delivers strong data efficiency, allowing reliable recovery of separated modes in regimes where scientific data is scarce. We formalize these insights through a unified probabilistic framework contrasting explicit and implicit distribution networks, and demonstrate empirically that MDNs achieve superior generalization, interpretability, and sample efficiency across a range of inverse, multistable, and chaotic scientific regression tasks.

Generative models have enjoyed widespread success in a variety of applications. However, they encounter inherent mathematical limitations in modeling distributions where samples are constrained by equalities, as is frequently the setting in scientific domains. In this work, we develop a computationally cheap, mathematically justified, and highly flexible distributional modification for combating known pitfalls in equality-constrained generative models. We propose perturbing the data distribution in a constraint-aware way such that the new distribution has support matching the ambient space dimension while still implicitly incorporating underlying manifold geometry. Through theoretical analyses and empirical evidence on several representative tasks, we illustrate that our approach consistently enables data distribution recovery and stable sampling with both diffusion models and normalizing flows.

Diffusion models have emerged as powerful generative tools for modeling complex data distributions, yet their purely data-driven nature limits applicability in practical engineering and scientific problems where physical laws need to be followed. This paper proposes Physics-Informed Learning via Diffusion (PILD), a framework that unifies diffusion modeling and first-principles physical constraints by introducing a virtual residual observation sampled from a Laplace distribution to supervise generation during training. To further integrate physical laws, a conditional embedding module is incorporated to inject physical information into the denoising network at multiple layers, ensuring consistent guidance throughout the diffusion process. The proposed PILD framework is concise, modular, and broadly applicable to problems governed by ordinary differential equations, partial differential equations, as well as algebraic equations or inequality constraints. Extensive experiments across engineering and scientific tasks including estimating vehicle trajectories, tire forces, Darcy flow and plasma dynamics, demonstrate that our PILD substantially improves accuracy, stability, and generalization over existing physics-informed and diffusion-based baselines.

Modern generative modeling methods have demonstrated strong performance in learning complex data distributions from clean samples. In many scientific and imaging applications, however, clean samples are unavailable, and only noisy or linearly corrupted measurements can be observed. Moreover, latent structures, such as manifold geometries, present in the data are important to extract for further downstream scientific analysis. In this work, we introduce Riemannian AmbientFlow, a framework for simultaneously learning a probabilistic generative model and the underlying, nonlinear data manifold directly from corrupted observations. Building on the variational inference framework of AmbientFlow, our approach incorporates data-driven Riemannian geometry induced by normalizing flows, enabling the extraction of manifold structure through pullback metrics and Riemannian Autoencoders. We establish theoretical guarantees showing that, under appropriate geometric regularization and measurement conditions, the learned model recovers the underlying data distribution up to a controllable error and yields a smooth, bi-Lipschitz manifold parametrization. We further show that the resulting smooth decoder can serve as a principled generative prior for inverse problems with recovery guarantees. We empirically validate our approach on low-dimensional synthetic manifolds and on MNIST.