Daily Papers

Foundation machine-learned interatomic potentials (MLIPs) are trained on large quantum-mechanical datasets and generalise across broad regions of chemical and configurational space. Beyond their usual role in accelerating sampling-based simulations, their internal representations encode chemically rich local atomic environments. Here, we introduce Rem3Di, a representation-learning framework that repurposes latent features from atomistic foundation models as transferable molecular descriptors for property prediction and virtual screening. Rem3Di combines a potential's per-atom features into a single fixed-length descriptor of the whole molecule that varies smoothly with three-dimensional structure and is invariant to the ordering of the atoms. The descriptor can be used directly or fine-tuned for specific prediction tasks. To capture molecular handedness, Rem3Di constructs pseudoscalar features, which are unchanged by rotation but reverse sign under mirror reflection. This lets the descriptor distinguish enantiomers, which can differ in activity and toxicity. The transformer is pretrained on large molecular datasets by reconstructing corrupted atom features, so no experimental labels are required. Across public drug-property benchmarks, Rem3Di matches or exceeds published baselines without relying on classical 2D fingerprints. Additionally, the same descriptor yields chemically meaningful differentiation of transition-metal complexes without predefined bonding rules or handcrafted representations. Rem3Di therefore provides a route from simulation-trained atomistic representations to transferable, chirality-aware molecular representations for chemical machine learning.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

Machine-learned interatomic potentials are revolutionising atomistic materials simulations by providing accurate and scalable predictions within the scope covered by the training data. However, generation of an accurate and robust training data set remains a challenge, often requiring thousands of first-principles calculations to achieve high accuracy. Foundation models have started to emerge with the ambition to create universally applicable potentials across a wide range of materials. While foundation models can be robust and transferable, they do not yet achieve the accuracy required to predict reaction barriers, phase transitions, and material stability. This work demonstrates that foundation model potentials can reach chemical accuracy when fine-tuned using transfer learning with partially frozen weights and biases. For two challenging datasets on reactive chemistry at surfaces and stability and elastic properties of tertiary alloys, we show that frozen transfer learning with 10-20% of the data (hundreds of datapoints) achieves similar accuracies to models trained from scratch (on thousands of datapoints). Moreover, we show that an equally accurate, but significantly more efficient surrogate model can be built using the transfer learned potential as the ground truth. In combination, we present a simulation workflow for machine learning potentials that improves data efficiency and computational efficiency.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

We introduce Orb-v3, the next generation of the Orb family of universal interatomic potentials. Models in this family expand the performance-speed-memory Pareto frontier, offering near SoTA performance across a range of evaluations with a >10x reduction in latency and > 8x reduction in memory. Our experiments systematically traverse this frontier, charting the trade-off induced by roto-equivariance, conservatism and graph sparsity. Contrary to recent literature, we find that non-equivariant, non-conservative architectures can accurately model physical properties, including those which require higher-order derivatives of the potential energy surface. This model release is guided by the principle that the most valuable foundation models for atomic simulation will excel on all fronts: accuracy, latency and system size scalability. The reward for doing so is a new era of computational chemistry driven by high-throughput and mesoscale all-atom simulations.

Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model -- and its qualitative and at times quantitative accuracy -- on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, and chemical reactions. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.

Foundational machine learning interatomic potentials that can accurately and efficiently model a vast range of materials are critical for accelerating atomistic discovery. We introduce universal potentials based on the graph atomic cluster expansion (GRACE) framework, trained on several of the largest available materials datasets. Through comprehensive benchmarks, we demonstrate that the GRACE models establish a new Pareto front for accuracy versus efficiency among foundational interatomic potentials. We further showcase their exceptional versatility by adapting them to specialized tasks and simpler architectures via fine-tuning and knowledge distillation, achieving high accuracy while preventing catastrophic forgetting. This work establishes GRACE as a robust and adaptable foundation for the next generation of atomistic modeling, enabling high-fidelity simulations across the periodic table.

We introduce Orb, a family of universal interatomic potentials for atomistic modelling of materials. Orb models are 3-6 times faster than existing universal potentials, stable under simulation for a range of out of distribution materials and, upon release, represented a 31% reduction in error over other methods on the Matbench Discovery benchmark. We explore several aspects of foundation model development for materials, with a focus on diffusion pretraining. We evaluate Orb as a model for geometry optimization, Monte Carlo and molecular dynamics simulations.

Deep generative models have shown promise for modeling metal-organic frameworks (MOFs), but existing approaches (1) rely on coarse-grained representations that assume fixed bond lengths and angles, and (2) neglect the MOF-adsorbate interactions, which are critical for downstream applications. We introduce AtomMOF, a scalable flow-based model built on an all-atom Diffusion Transformer that maps 2D molecular graphs of building blocks and adsorbates directly to equilibrium 3D structures without imposing structural constraints. We further present scaling laws for porous crystal generation, indicating predictable performance gains with increased model capacity, and introduce Feynman-Kac steering guided by machine-learned interatomic potentials to improve geometric validity and sampling stability. On the (MOF-only) BW dataset, AtomMOF increases the match rate by 35.00% and reduces RMSD by 32.64%. On the ODAC25 dataset (MOF-adsorbate), AtomMOF is substantially more sample-efficient than grand canonical Monte Carlo in recovering adsorption configurations and can identify candidates with lower adsorption energies than the reference dataset. Code is available at https://github.com/nayoung10/AtomMOF.

Molecular dynamics simulation of plasma-surface interactions requires an interatomic potential that is simultaneously accurate, computationally efficient, and able to describe many elements and bonding types in reactive systems. In principle, a foundation model for machine-learned interatomic potential (MLIP) can meet these demands. We explore the use of the Universal Models for Atoms (UMA) model, developed by Meta FAIR, for the interactions of oxygen plasma species on a multilayer of WS_2, a promising 2D material. Starting from the pretrained uma-s-1p1 model under the Open Catalyst 2020 (OC20) task, we apply an iterative fine-tuning loop with maximally diverse configuration sampling using Smooth Overlap of Atomic Positions (SOAP) and Farthest Point Sampling (FPS); DFT labeling at the PBE+D3+U+spin level; and fine-tuning on energy, force, and stress labels. Even in the absence of fine-tuning, the pretrained model reproduces the production-scale observables of interest, namely, chemisorbed S and O coverage under 15eV O^+ and O_2^+ bombardment. These results were obtained without spin polarization and Hubbard U correction. Nonetheless, fine-tuning reduces the energy and force mean absolute error (MAE) to 4.5times10^{-3}eV/atom and 0.076eV/angstrom, respectively.

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own merit, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, from low-level libraries, training utilities, to interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

Traditional foundation models are pre-trained on broad datasets to reduce the training resources (e.g., time, energy, labeled samples) needed for fine-tuning a wide range of downstream tasks. However, traditional foundation models struggle with out-of-distribution prediction and can produce outputs that are unrealistic and physically infeasible. We propose the notation of physics-guided foundation models (PGFM), that is, foundation models integrated with broad or general domain (e.g., scientific) physical knowledge applicable to a wide range of downstream tasks.

We present FreeBird, an extensible Julia-based platform for computational studies of phase equilibria at generic interfaces. The package supports a range of system configurations, from atomistic solid surfaces to coarse-grained lattice-gas models, with energies evaluated using classical interatomic potentials or lattice Hamiltonians. Both atomistic and lattice systems accommodate single- or multi-component mixtures with flexibly definable surface and lattice geometries. Implemented sampling algorithms include nested sampling, Wang-Landau sampling, Metropolis Monte Carlo, and, for tractable lattice systems, exact enumeration. Leveraging Julia's type hierarchies and multiple dispatch, FreeBird provides a modular interface that allows seamless integration of system definitions, energy evaluators, and sampling schemes. Designed for flexibility, extensibility, and performance, FreeBird offers a versatile framework for exploring the thermodynamics of interfacial phenomena.

All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological scale. We present UBio-MolFM, a universal foundation model framework specifically engineered to bridge this gap. UBio-MolFM introduces three synergistic innovations: (1) UBio-Mol26, a large bio-specific dataset constructed via a multi-fidelity ``Two-Pronged Strategy'' that combines systematic bottom-up enumeration with top-down sampling of native protein environments (up to 1,200 atoms); (2) E2Former-V2, a linear-scaling equivariant transformer that integrates Equivariant Axis-Aligned Sparsification (EAAS) and Long-Short Range (LSR) modeling to capture non-local physics with up to ~4x higher inference throughput in our large-system benchmarks; and (3) a Three-Stage Curriculum Learning protocol that transitions from energy initialization to energy-force consistency, with force-focused supervision to mitigate energy offsets. Rigorous benchmarking across microscopic forces and macroscopic observables -- including liquid water structure, ionic solvation, and peptide folding -- demonstrates that UBio-MolFM achieves ab initio-level fidelity on large, out-of-distribution biomolecular systems (up to ~1,500 atoms) and realistic MD observables. By reconciling scalability with quantum precision, UBio-MolFM provides a robust, ready-to-use tool for the next generation of computational biology.

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

Universal machine learning force fields (UMLFFs) promise to revolutionize materials science by enabling rapid atomistic simulations across the periodic table. However, their evaluation has been limited to computational benchmarks that may not reflect real-world performance. Here, we present UniFFBench, a comprehensive framework for evaluating UMLFFs against experimental measurements of ~1,500 carefully curated mineral structures spanning diverse chemical environments, bonding types, structural complexity, and elastic properties. Our systematic evaluation of six state-of-the-art UMLFFs reveals a substantial reality gap: models achieving impressive performance on computational benchmarks often fail when confronted with experimental complexity. Even the best-performing models exhibit higher density prediction error than the threshold required for practical applications. Most strikingly, we observe disconnects between simulation stability and mechanical property accuracy, with prediction errors correlating with training data representation rather than the modeling method. These findings demonstrate that while current computational benchmarks provide valuable controlled comparisons, they may overestimate model reliability when extrapolated to experimentally complex chemical spaces. Altogether, UniFFBench establishes essential experimental validation standards and reveals systematic limitations that must be addressed to achieve truly universal force field capabilities.

With the development of foundation model (FM), agentic AI systems are getting more attention, yet their inherent issues like hallucination and poor reasoning, coupled with the frequent ad-hoc nature of system design, lead to unreliable and brittle applications. Existing efforts to characterise agentic design patterns often lack a rigorous systems-theoretic foundation, resulting in high-level or convenience-based taxonomies that are difficult to implement. This paper addresses this gap by introducing a principled methodology for engineering robust AI agents. We propose two primary contributions: first, a novel system-theoretic framework that deconstructs an agentic AI system into five core, interacting functional subsystems: Reasoning & World Model, Perception & Grounding, Action Execution, Learning & Adaptation, and Inter-Agent Communication. Second, derived from this architecture and directly mapped to a comprehensive taxonomy of agentic challenges, we present a collection of 12 agentic design patterns. These patterns - categorised as Foundational, Cognitive & Decisional, Execution & Interaction, and Adaptive & Learning - offer reusable, structural solutions to recurring problems in agent design. The utility of the framework is demonstrated by a case study on the ReAct framework, showing how the proposed patterns can rectify systemic architectural deficiencies. This work provides a foundational language and a structured methodology to standardise agentic design communication among researchers and engineers, leading to more modular, understandable, and reliable autonomous systems.

Foundation models have revolutionized natural language processing through a ``train once, deploy anywhere'' paradigm, where a single pre-trained model adapts to countless downstream tasks without retraining. Access to a Physics Foundation Model (PFM) would be transformative -- democratizing access to high-fidelity simulations, accelerating scientific discovery, and eliminating the need for specialized solver development. Yet current physics-aware machine learning approaches remain fundamentally limited to single, narrow domains and require retraining for each new system. We present the General Physics Transformer (GPhyT), trained on 1.8 TB of diverse simulation data, that demonstrates foundation model capabilities are achievable for physics. Our key insight is that transformers can learn to infer governing dynamics from context, enabling a single model to simulate fluid-solid interactions, shock waves, thermal convection, and multi-phase dynamics without being told the underlying equations. GPhyT achieves three critical breakthroughs: (1) superior performance across multiple physics domains, outperforming specialized architectures by up to 29x, (2) zero-shot generalization to entirely unseen physical systems through in-context learning, and (3) stable long-term predictions through 50-timestep rollouts. By establishing that a single model can learn generalizable physical principles from data alone, this work opens the path toward a universal PFM that could transform computational science and engineering.

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD by providing inexpensive predictions of the forces, but they remain constrained to minuscule time integration steps, which are required by the fast time scale of atomic motion. In this work, we propose FlashMD, a method to predict the evolution of positions and momenta over strides that are between one and two orders of magnitude longer than typical MD time steps. We incorporate considerations on the mathematical and physical properties of Hamiltonian dynamics in the architecture, generalize the approach to allow the simulation of any thermodynamic ensemble, and carefully assess the possible failure modes of such a long-stride MD approach. We validate FlashMD's accuracy in reproducing equilibrium and time-dependent properties, using both system-specific and general-purpose models, extending the ability of MD simulation to reach the long time scales needed to model microscopic processes of high scientific and technological relevance.

Classical force fields (FF) based on machine learning (ML) methods show great potential for large scale simulations of materials. MLFFs have hitherto largely been designed and fitted for specific systems and are not usually transferable to chemistries beyond the specific training set. We develop a unified atomisitic line graph neural network-based FF (ALIGNN-FF) that can model both structurally and chemically diverse materials with any combination of 89 elements from the periodic table. To train the ALIGNN-FF model, we use the JARVIS-DFT dataset which contains around 75000 materials and 4 million energy-force entries, out of which 307113 are used in the training. We demonstrate the applicability of this method for fast optimization of atomic structures in the crystallography open database and by predicting accurate crystal structures using genetic algorithm for alloys.

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

Foundation models (FMs) for the Earth system learn statistical relationships between physical variables across massive datasets to enable versatile downstream applications through finetuning, separating them from task-specific weather models. Here, we introduce Earth System Foundation Model (ESFM), a fully open model building on the 3D Swin UNet backbone of the pioneering Aurora model. ESFM introduces extensions that increase functionality and foster adoption in climate sciences. First, the encoding scheme and training protocols have been extended to handle diverse datasets, including those containing missing values across all spatio-temporal dimensions such as satellite data, as well as station data, all under one backbone. Axial attention is introduced to capture inter-variable dependencies. As a result ESFM skillfully predicts variables in regions or on pressure levels where no data is present at the initial time, while preserving inter-variable relationships, for example between temperature, pressure, and humidity. Individual variable tokenization enables different sets of variables to be shuffled during training and simplifies the process of building extensions for new downstream tasks. Adaptive layer norm-based ensembles allow for a simple yet effective way to transform deterministic ESFM to a probabilistic FM. We present findings using dense gridded data (ERA5, CMIP6), regionally masked dense data, sparse gridded MODIS satellite data, and station data. Results demonstrate competitive or superior performance relative to state-of-the-art benchmarks. Case studies of Super Typhoon Doksuri (2023) and 2024 sudden stratospheric warming events show accurate positional and magnitude estimations of extreme weather. ESFM retains the strengths of previous foundation models, such as long-term stability, but facilitates application to a variety of downstream tasks.

Foundation Models are neural networks that are capable of simultaneously solving many problems. Large Language Foundation Models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new Foundation Model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet Foundation Models beyond proof-of-principle studies and into the toolkit of practitioners.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

Foundation models for predictive machine learning on tabular data have recently gained significant traction in academia and industry. Research communities across disciplines are increasingly evaluating tabular foundation models on diverse datasets and tasks. However, these task- and discipline-specific evaluations remain largely inaccessible to model researchers because benchmark software and evaluation protocols are fragmented. As a result, model researchers rely on standard benchmarks, which are mostly defined for tasks where tabular foundation models already excel. The most challenging scenarios are excluded, limiting meaningful progress in the field by focusing on marginal improvements on IID data rather than on broader, more demanding challenges. To overcome this, we introduce BeyondArena, the first unified holistic benchmark for tabular data that supports diverse task types (IID, temporal, grouped), across sample size and feature dimensionality scales, with diverse feature types (with text, with high cardinality) from a broad range of disciplines. To enable unified benchmarking beyond standard benchmarks, we introduce Data Foundry, a Python framework and metadata schema for curating tabular datasets for predictive machine learning. Our results across 11 models and 142 curated datasets show that existing tabular foundation models excel on tiny- to medium-sized IID data, while traditional tree-based and deep learning models still dominate on non-IID, large, and high-dimensional datasets. BeyondArena guides model research for the most demanding challenges in tabular data, enabling progress towards truly foundational tabular models.

Large language models (LLMs) have shown promising potential in scientific research, enabling tasks ranging from knowledge retrieval to property prediction. Existing science benchmarks mainly focus on perceptual or knowledge-based tasks, largely ignoring the modelling tasks, a fundamental starting point for any real scientific research. For materials science, constructing and manipulating atomic structures is one of the most creative and least automated steps. In this work, we introduce AtomWorld, a benchmark designed to evaluate the abilities of LLMs on structure modifications. The benchmark includes ten fundamental actions under four widely used modelling categories, enabling verifiable evaluation metrics. We find that Claude Opus 4.6 generally performs the best. While the success rate decreases markedly with increasing modelling complexity, with particularly low success rates (below 12\% for rotation) for operations involving complex spatial relations. Our results suggest that contemporary LLMs are better suited as copilots for materials structure modelling rather than fully unsupervised autonomous scientific agents. Beyond evaluation, AtomWorld also serves as a testbed and playground for developing future structure-aware models, including reinforcement learning and agentic approaches.

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

Accurate and fast prediction of materials properties is central to the digital transformation of materials design. However, the vast design space and diverse operating conditions pose significant challenges for accurately modeling arbitrary material candidates and forecasting their properties. We present MatterSim, a deep learning model actively learned from large-scale first-principles computations, for efficient atomistic simulations at first-principles level and accurate prediction of broad material properties across the periodic table, spanning temperatures from 0 to 5000 K and pressures up to 1000 GPa. Out-of-the-box, the model serves as a machine learning force field, and shows remarkable capabilities not only in predicting ground-state material structures and energetics, but also in simulating their behavior under realistic temperatures and pressures, signifying an up to ten-fold enhancement in precision compared to the prior best-in-class. This enables MatterSim to compute materials' lattice dynamics, mechanical and thermodynamic properties, and beyond, to an accuracy comparable with first-principles methods. Specifically, MatterSim predicts Gibbs free energies for a wide range of inorganic solids with near-first-principles accuracy and achieves a 15 meV/atom resolution for temperatures up to 1000K compared with experiments. This opens an opportunity to predict experimental phase diagrams of materials at minimal computational cost. Moreover, MatterSim also serves as a platform for continuous learning and customization by integrating domain-specific data. The model can be fine-tuned for atomistic simulations at a desired level of theory or for direct structure-to-property predictions, achieving high data efficiency with a reduction in data requirements by up to 97%.

Recent advances in large language models (LLMs) and multi-agent systems have demonstrated remarkable capabilities in complex problem-solving tasks such as deep research, vibe coding, and mathematical reasoning. However, most existing multi-agent systems are built upon manual prompt/workflow engineering with sophisticated agent frameworks, making them computationally inefficient, less capable, and can not benefit from data-centric learning. In this work, we introduce Chain-of-Agents (CoA), a novel paradigm of LLM reasoning that enables native end-to-end complex problem-solving in the same way as a multi-agent system (i.e., multi-turn problem solving with multiple tools and multiple agents) within one model. In chain-of-agents problem-solving, the model dynamically activates different tool agents and role-playing agents to simulate multi-agent collaboration in an end-to-end fashion. To elicit end-to-end chain-of-agents problem-solving abilities in LLMs, we introduce a multi-agent distillation framework to distill state-of-the-art multi-agent systems into chain-of-agents trajectories for agentic supervised fine-tuning. We then use agentic reinforcement learning on verifiable agentic tasks to further improve the models' capabilities on chain-of-agents problem solving. We call the resulting models Agent Foundation Models (AFMs). Our empirical studies demonstrate that AFM establishes new state-of-the-art performance across diverse benchmarks in both web agent and code agent settings. We make the entire research, including the model weights, code for training and evaluation, and the training data, fully open-sourced, which offers a solid starting point for future research on agent models and agentic RL.

Adapting machine-learned interatomic potential (MLIP) foundation models to specialised tasks through fine-tuning is an increasingly important practice, yet systematic guidance on when and how to fine-tune is currently limited. We evaluate seven fine-tuning strategies -- naive full-parameter updates, two layer-freezing variants, Low-Rank Adaptation (LoRA), multihead replay, pseudolabelled replay, and replay combined with LoRA -- across five chemically diverse benchmarks (aqueous NaCl, ice polymorphs, S_N2 reactions, SPICE biomolecules, and lithium electrolytes), three generations of foundation models, and training sets spanning five orders of magnitude. To support this evaluation we implement three capabilities in the MACE codebase: LoRA adapted for equivariant message-passing architectures, including both scalar and equivariant linear layers; pseudolabelled replay, which decouples the replay data source from the original pretraining corpus; and model-aware atomic reference energy (E0) reestimation for fine-tuning workflows. We find that foundation model quality, correct E0 initialisation, and well-chosen hyperparameters are prerequisites whose impact routinely exceeds that of the fine-tuning strategy itself. Once these prerequisites are met, most strategies achieve strong target-task accuracy, consistently surpassing models trained from scratch. The practical distinction depends on deployment scope: naive fine-tuning offers the best convergence for single-system applications, while multihead replay -- with either original or pseudolabelled data -- is the only approach tested that consistently preserves out-of-distribution robustness, maintaining both pretraining-distribution accuracy for broader deployment and many-body short-range repulsion.

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research.

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Machine-learned coarse-grained (CG) models often suffer from noisy training data, limiting their accuracy and transferability. We propose a method to generate low-noise training data based on the potential of mean force by constraining CG beads during atomistic simulations and accumulating time-averaged forces. Implemented within the neuroevolution potential (NEP) framework, our approach achieves training accuracy comparable to atomistic models trained on density functional theory data. For liquid water, the NEP-CG model accurately reproduces densities from 1 bar to 1 GPa, successfully extrapolating beyond the 0.5 GPa training limit, with a virial correction essential for the correct equation of state. For an anisotropic C_{60} monolayer, distinguishing crystallographically distinct bead types reduces stress errors by an order of magnitude and captures directional thermal conductivity. We further introduce a multiscale NEP-AACG model integrating all-atom (AA) and CG degrees of freedom, demonstrated for gold nanowire fracture at an experimentally relevant strain rate. Computational speeds for NEP-CG models reach hundreds to thousands of ns/day using a single consumer-grade GPU. This work provides a robust framework for constructing accurate, transferable, and efficient CG models across diverse systems.

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We introduce Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), an active learning framework where large language models autonomously design, execute, and interpret atomistic simulations. In MASTER, a multimodal system translates natural language into density functional theory workflows, while higher-level reasoning agents guide discovery through a hierarchy of strategies, including a single agent baseline and three multi-agent approaches: peer review, triage-ranking, and triage-forms. Across two chemical applications, CO adsorption on Cu-surface transition metal (M) adatoms and on M-N-C catalysts, reasoning-driven exploration reduces required atomistic simulations by up to 90% relative to trial-and-error selection. Reasoning trajectories reveal chemically grounded decisions that cannot be explained by stochastic sampling or semantic bias. Altogether, multi-agent collaboration accelerates materials discovery and marks a new paradigm for autonomous scientific exploration.

Foundation models (FMs) have shown transformative potential in radiology by performing diverse, complex tasks across imaging modalities. Here, we developed CT-FM, a large-scale 3D image-based pre-trained model designed explicitly for various radiological tasks. CT-FM was pre-trained using 148,000 computed tomography (CT) scans from the Imaging Data Commons through label-agnostic contrastive learning. We evaluated CT-FM across four categories of tasks, namely, whole-body and tumor segmentation, head CT triage, medical image retrieval, and semantic understanding, showing superior performance against state-of-the-art models. Beyond quantitative success, CT-FM demonstrated the ability to cluster regions anatomically and identify similar anatomical and structural concepts across scans. Furthermore, it remained robust across test-retest settings and indicated reasonable salient regions attached to its embeddings. This study demonstrates the value of large-scale medical imaging foundation models and by open-sourcing the model weights, code, and data, aims to support more adaptable, reliable, and interpretable AI solutions in radiology.

Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently complex and interconnected processes and are further constrained by limited observational data in many environmental applications. Foundation models, which leverages large-scale pre-training and universal representations of complex and heterogeneous data, offer transformative opportunities for capturing spatiotemporal dynamics and dependencies in environmental processes, and facilitate adaptation to a broad range of applications. This survey presents a comprehensive overview of foundation model applications in environmental science, highlighting advancements in common environmental use cases including forward prediction, data generation, data assimilation, downscaling, inverse modeling, model ensembling, and decision-making across domains. We also detail the process of developing these models, covering data collection, architecture design, training, tuning, and evaluation. Through discussions on these emerging methods as well as their future opportunities, we aim to promote interdisciplinary collaboration that accelerates advancements in machine learning for driving scientific discovery in addressing critical environmental challenges.

6G networks will introduce unprecedented complexity, which calls for a paradigm shift in network optimization and management. Artificial intelligence (AI)-based solutions, especially those enabled by the recently developed foundation models, have been recognized as promising candidates. Foundation models are large-scale AI models with general-purpose feature extraction capabilities, and once trained on massive amounts of data, they can be adapted to solve a wide range of downstream tasks, either in a zero-shot manner or with few-shot fine-tuning. This article provides a comprehensive overview of how foundation models are reshaping physical-layer processing and wireless resource management across three progressive paradigms. First, we examine the adaptation of off-the-shelf pre-trained foundation models to various wireless tasks. Second, we explore wireless-native foundation models, built from scratch on wireless data to bridge cross-domain modality gaps and capture universal wireless-domain physical characteristics. Third, we highlight agentic foundation models, which elevate static data processing into autonomous, reasoning-driven network orchestration. Furthermore, we discuss the impact of applying foundation models to emerging 6G frontiers, including integrated sensing and communications (ISAC), new multiple-input multiple-output (MIMO) architectures, semantic communications, and system-level network autonomy. Finally, we identify critical open challenges and opportunities, charting a promising path toward fully intelligent and adaptive wireless networks.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

Foundation models are a strong trend in deep learning and computer vision. These models serve as a base for applications as they require minor or no further fine-tuning by developers to integrate into their applications. Foundation models for zero-shot object segmentation such as Segment Anything (SAM) output segmentation masks from images without any further object information. When they are followed in a pipeline by an object identification model, they can perform object detection without training. Here, we focus on training such an object identification model. A crucial practical aspect for an object identification model is to be flexible in input size. As object identification is an image retrieval problem, a suitable method should handle multi-query multi-gallery situations without constraining the number of input images (e.g. by having fixed-size aggregation layers). The key solution to train such a model is the centroid triplet loss (CTL), which aggregates image features to their centroids. CTL yields high accuracy, avoids misleading training signals and keeps the model input size flexible. In our experiments, we establish a new state of the art on the ArmBench object identification task, which shows general applicability of our model. We furthermore demonstrate an integrated unseen object detection pipeline on the challenging HOPE dataset, which requires fine-grained detection. There, our pipeline matches and surpasses related methods which have been trained on dataset-specific data.

Tabular foundation models such as TabPFN have revolutionized predictive machine learning for tabular data. At the same time, the driving factors of this revolution are hard to understand. Existing open-source tabular foundation models are implemented in complicated pipelines boasting over 10,000 lines of code, lack architecture documentation or code quality. In short, the implementations are hard to understand, not beginner-friendly, and complicated to adapt for new experiments. We introduce nanoTabPFN, a simplified and lightweight implementation of the TabPFN v2 architecture and a corresponding training loop that uses pre-generated training data. nanoTabPFN makes tabular foundation models more accessible to students and researchers alike. For example, restricted to a small data setting it achieves a performance comparable to traditional machine learning baselines within one minute of pre-training on a single GPU (160,000x faster than TabPFN v2 pretraining). This eliminated requirement of large computational resources makes pre-training tabular foundation models accessible for educational purposes. Our code is available at https://github.com/automl/nanoTabPFN.

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

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

Large Language Models (LLMs) promise to accelerate discovery by reasoning across the expanding scientific landscape. Yet, the challenge is no longer access to information but connecting it in meaningful, domain-spanning ways. In materials science, where innovation demands integrating concepts from molecular chemistry to mechanical performance, this is especially acute. Neither humans nor single-agent LLMs can fully contend with this torrent of information, with the latter often prone to hallucinations. To address this bottleneck, we introduce a multi-agent framework guided by large-scale knowledge graphs to find sustainable substitutes for per- and polyfluoroalkyl substances (PFAS)-chemicals currently under intense regulatory scrutiny. Agents in the framework specialize in problem decomposition, evidence retrieval, design parameter extraction, and graph traversal, uncovering latent connections across distinct knowledge pockets to support hypothesis generation. Ablation studies show that the full multi-agent pipeline outperforms single-shot prompting, underscoring the value of distributed specialization and relational reasoning. We demonstrate that by tailoring graph traversal strategies, the system alternates between exploitative searches focusing on domain-critical outcomes and exploratory searches surfacing emergent cross-connections. Illustrated through the exemplar of biomedical tubing, the framework generates sustainable PFAS-free alternatives that balance tribological performance, thermal stability, chemical resistance, and biocompatibility. This work establishes a framework combining knowledge graphs with multi-agent reasoning to expand the materials design space, showcasing several initial design candidates to demonstrate the approach.

Foundation models are vital tools in various Computer Vision applications. They take as input a single RGB image and output a deep feature representation that is useful for various applications. However, in case we have multiple views of the same 3D scene, they operate on each image independently and do not always produce consistent features for the same 3D point. We propose a way to convert a Foundation Model into a Multi-View Foundation Model. Such a model takes as input a set of images and outputs a feature map for each image such that the features of corresponding points are as consistent as possible. This approach bypasses the need to build a consistent 3D model of the features and allows direct manipulation in the image space. Specifically, we show how to augment Transformers-based foundation models (i.e., DINO, SAM, CLIP) with intermediate 3D-aware attention layers that help match features across different views. As leading examples, we show surface normal estimation and multi-view segmentation tasks. Quantitative experiments show that our method improves feature matching considerably compared to current foundation models.

The demand for safe, high-energy-density batteries has spotlighted halide solid-state electrolytes, which offer the potential for enhanced ionic mobility, electrochemical stability, and interfacial deformability. Accelerating their discovery requires extensive molecular dynamics, which has been increasingly enabled by universal machine learning interatomic potentials trained on foundational datasets. However, the dynamic softness of halides poses a stringent test of whether general-purpose models can reliably replace first-principles calculations under the highly distorted, elevated-temperature regimes necessary to probe ion transport. Here, we present AQVolt26, a dataset of 322,656 r^2SCAN single-point calculations for lithium halides, generated via high-temperature configurational sampling across sim5K structures. We demonstrate that foundational datasets provide a strong baseline for stable halide chemistries and transfer local forces well, however absolute energy predictions degrade in distorted higher-temperature regimes. Co-training with AQVolt26 resolves this blind spot. Furthermore, incorporating Materials Project relaxation data improves near-equilibrium performance but degrades extreme-strain robustness without enhancing high-temperature force accuracy. These results demonstrate that domain-specific configurational sampling is essential for the reliable dynamic screening of halide electrolytes. Furthermore, our findings suggest that while foundational models provide a robust base, they are most effective for dynamically soft solid-state chemistries when augmented with targeted, high-temperature data. Finally, we show that near-equilibrium relaxation data serves as a task-specific complement rather than a universally beneficial addition.

Recent physics foundation models claim general spatiotemporal forecasting ability, yet their evaluations often collapse performance into a single average score under a fixed training distribution. This makes it difficult to determine whether a model has learned generalizable physical dynamics or only performs well under particular settings. We construct a benchmark with 8 physical dynamics, 3 training-data mixtures, and 25 test regimes induced by dynamic-scale and initial-condition complexity shifts, covering in-distribution, distribution-shift, and out-of-distribution settings. We evaluate five physics foundation model architectures and four model variants per architecture (scratch and three pretrained sizes), resulting in 60,000 measurements. Our results show that current physics foundation models behave as conditional rather than universal generalists: their generality depends on the physical regime, temporal scale, initial-condition setting, pretraining, model size, and architecture. Improving the training data distribution only partially mitigates this limitation. Pretraining and scaling are also unable to reliably remove their ability biases. We argue that improving physics foundation models requires moving beyond scaling models or expanding data, toward learning mechanisms that better capture transferable physical knowledge across regimes, temporal scales, and distribution shifts.

The discovery of novel materials is critical for global energy and quantum technology transitions. While deep learning has fundamentally reshaped this landscape, existing predictive or generative models typically operate in isolation, lacking the autonomous orchestration required to execute the full discovery process. Here we present ElementsClaw, an agentic framework for materials discovery that synergizes Large Atomic Models (LAMs) with Large Language Models (LLMs). In response to varied human queries, ElementsClaw orchestrates a suite of LAM tools finetuned from our proposed 1-billion-parameter model Elements for atomic-scale numerical computation, while leveraging LLMs for high-level semantic reasoning. This shift moves AI-driven materials science from isolated processes toward integrated and human interactive discovery. Applied to superconductors, ElementsClaw screens 2.4 million crystals in just 28 GPU hours to identify 68,000 high-confidence candidates (The complete dataset of screened superconductors is available at https://developer.damo-academy.com/material), expanding known superconducting space by orders of magnitude compared to datasets curated over decades. Critically, ElementsClaw achieves a high success rate in identifying superconductors hidden in literature and discovers four novel experimentally verified superconductors, exemplified by Zr3ScRe8 with a transition temperature of 6.8 K and HfZrRe4 at 6.7 K. Together, our results establish a knowledge integrated, autonomously orchestrated, and experimentally grounded paradigm for materials discovery.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

Atomistic structure and natural language have long been modeled separately, with language models either calling atomistic models as tools or being fine-tuned on lossy textual encodings that discard atomistic information. We introduce Atomistic Language Models (ALMs) to pursue native multimodality, in which a single language backbone understands atomistic structures, generates materials from natural language, and optimizes crystal structures as instructed by text. By unifying a pretrained atomistic encoder, large language model, and denoising diffusion model through purely continuous projectors and staged training, ALMs achieve state-of-the-art results on crystal structure prediction and de novo generation. ALMs are enabled by a continuous bridge that maps language model embeddings directly into the steering space of atomistic diffusion, and are assisted by Text-to-Crystal Feynman-Kac (T2C-FK), a particle-based sampler that scores partial denoising trajectories to enforce stoichiometric targets at inference time. To evaluate the ability of ALMs to optimize and generate materials from natural-language prompts and 3D atom-coordinate inputs, we introduce ALM Bench, the first benchmark for text-conditioned crystal generation and optimization. Code, training data, and model weights will be released soon.

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

Foundation models (FMs) are increasingly used to bridge language and action in embodied agents, yet the operational characteristics of different FM integration strategies remain under-explored -- particularly for complex instruction following and versatile action generation in changing environments. This paper examines three paradigms for building robotic systems: end-to-end vision-language-action (VLA) models that implicitly integrate perception and planning, and modular pipelines incorporating either vision-language models (VLMs) or multimodal large language models (LLMs). We evaluate these paradigms through two focused case studies: a complex instruction grounding task assessing fine-grained instruction understanding and cross-modal disambiguation, and an object manipulation task targeting skill transfer via VLA finetuning. Our experiments in zero-shot and few-shot settings reveal trade-offs in generalization and data efficiency. By exploring performance limits, we distill design implications for developing language-driven physical agents and outline emerging challenges and opportunities for FM-powered robotics in real-world conditions.

Foundation Models (FMs) are models trained on large corpora of data that, at very large scale, can generalize to new tasks without any task-specific finetuning. As these models continue to grow in size, innovations continue to push the boundaries of what these models can do on language and image tasks. This paper aims to understand an underexplored area of FMs: classical data tasks like cleaning and integration. As a proof-of-concept, we cast five data cleaning and integration tasks as prompting tasks and evaluate the performance of FMs on these tasks. We find that large FMs generalize and achieve SoTA performance on data cleaning and integration tasks, even though they are not trained for these data tasks. We identify specific research challenges and opportunities that these models present, including challenges with private and domain specific data, and opportunities to make data management systems more accessible to non-experts. We make our code and experiments publicly available at: https://github.com/HazyResearch/fm_data_tasks.

Traditional AI methods often rely on task-specific model designs and training, which constrain both the scalability of model size and generalization across different tasks. Here, we introduce ChemFM, a large foundation model specifically developed for chemicals. By conducting a series of scaling experiments, we identify UniChem as the informative molecular database for pre-training the foundation model. ChemFM comprises 3 billion parameters and is pre-trained on 178 million molecules using self-supervised causal language modeling to extract generalizable molecular representations. This model can be adapted to diverse downstream chemical applications using either full-parameter or parameter-efficient fine-tuning methods. ChemFM consistently outperforms state-of-the-art task-specific AI models across all tested tasks. Notably, it achieves up to 67.48% performance improvement across 34 property prediction benchmarks, up to 33.80% reduction in mean average deviation between conditioned and actual properties of generated molecules in conditional molecular generation tasks, and up to 3.7% top-1 accuracy improvement across 4 reaction prediction datasets. Moreover, ChemFM demonstrates its superior performance in predicting antibiotic activity and cytotoxicity, highlighting its potential to advance the discovery of novel antibiotics. Furthermore, we demonstrate that, as a foundation model, ChemFM exhibits strong data efficiency, requiring significantly fewer labeled training samples to achieve state-of-the-art performance. We anticipate that ChemFM will significantly advance chemistry research by providing a foundation model capable of effectively generalizing across a broad range of tasks with minimal additional training.

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

The rapid progress of foundation models has led to the prosperity of autonomous agents, which leverage the universal capabilities of foundation models to conduct reasoning, decision-making, and environmental interaction. However, the efficacy of agents remains limited when operating in intricate, realistic environments. In this work, we introduce the principles of Unified Alignment for Agents (UA^2), which advocate for the simultaneous alignment of agents with human intentions, environmental dynamics, and self-constraints such as the limitation of monetary budgets. From the perspective of UA^2, we review the current agent research and highlight the neglected factors in existing agent benchmarks and method candidates. We also conduct proof-of-concept studies by introducing realistic features to WebShop, including user profiles to demonstrate intentions, personalized reranking for complex environmental dynamics, and runtime cost statistics to reflect self-constraints. We then follow the principles of UA^2 to propose an initial design of our agent, and benchmark its performance with several candidate baselines in the retrofitted WebShop. The extensive experimental results further prove the importance of the principles of UA^2. Our research sheds light on the next steps of autonomous agent research with improved general problem-solving abilities.

The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density functional theory (DFT) calculations are often resource-intensive, limiting their scalability. Machine learning (ML) models offer a promising alternative by learning complex structure-property relationships from data, enabling faster predictions. Yet, existing ML models often rely on labeled data, adopt representations that poorly capture essential structural characteristics, and lack integration with physical principles--factors that limit their generalizability and interpretability. Here, we introduce CLOUD (Crystal Language mOdel for Unified and Differentiable materials modeling), a transformer-based framework trained on a novel Symmetry-Consistent Ordered Parameter Encoding (SCOPE) that encodes crystal symmetry, Wyckoff positions, and composition in a compact, coordinate-free string representation. Pre-trained on over six million crystal structures, CLOUD is fine-tuned on multiple downstream tasks and achieves competitive performance in predicting a wide range of material properties, demonstrating strong scaling performance. Furthermore, as proof of concept of differentiable materials modeling, CLOUD is applied to predict the phonon internal energy and heat capacity, which integrates the Debye model to preserve thermodynamic consistency. The CLOUD-DEBYE framework enforces thermodynamic consistency and enables temperature-dependent property prediction without requiring additional data. These results demonstrate the potential of CLOUD as a scalable and physics-informed foundation model for crystalline materials, unifying symmetry-consistent representations with physically grounded learning for property prediction and materials discovery.

Foundation models, such as large language models (LLMs), have been widely recognised as transformative AI technologies due to their capabilities to understand and generate content, including plans with reasoning capabilities. Foundation model based agents derive their autonomy from the capabilities of foundation models, which enable them to autonomously break down a given goal into a set of manageable tasks and orchestrate task execution to meet the goal. Despite the huge efforts put into building foundation model based agents, the architecture design of the agents has not yet been systematically explored. Also, while there are significant benefits of using agents for planning and execution, there are serious considerations regarding responsible AI related software quality attributes, such as security and accountability. Therefore, this paper presents a pattern-oriented reference architecture that serves as guidance when designing foundation model based agents. We evaluate the completeness and utility of the proposed reference architecture by mapping it to the architecture of two real-world agents.

Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range electrostatic effects. We present a new electrostatic foundation model for molecular chemistry that extends the MACE architecture with explicit treatment of long-range interactions and electrostatic induction. Our approach combines local many-body geometric features with a non-self-consistent field formalism that updates learnable charge and spin densities through polarisable iterations to model induction, followed by global charge equilibration via learnable Fukui functions to control total charge and total spin. This design enables an accurate and physical description of systems with varying charge and spin states while maintaining computational efficiency. Trained on the OMol25 dataset of 100 million hybrid DFT calculations, our models achieve chemical accuracy across diverse benchmarks, with accuracy competitive with hybrid DFT on thermochemistry, reaction barriers, conformational energies, and transition metal complexes. Notably, we demonstrate that the inclusion of long-range electrostatics leads to a large improvement in the description of non-covalent interactions and supramolecular complexes over non-electrostatic models, including sub-kcal/mol prediction of molecular crystal formation energy in the X23-DMC dataset and a fourfold improvement over short-ranged models on protein-ligand interactions. The model's ability to handle variable charge and spin states, respond to external fields, provide interpretable spin-resolved charge densities, and maintain accuracy from small molecules to protein-ligand complexes positions it as a versatile tool for computational molecular chemistry and drug discovery.

Foundation models (FMs) are pre-trained on large-scale datasets and then fine-tuned on a downstream task for a specific application. The most successful and most commonly used fine-tuning method is to update the pre-trained weights via a low-rank adaptation (LoRA). LoRA introduces new weight matrices that are usually initialized at random with a uniform rank distribution across model weights. Recent works focus on weight-driven initialization or learning of adaptive ranks during training. Both approaches have only been investigated in isolation, resulting in slow convergence or a uniform rank distribution, in turn leading to sub-optimal performance. We propose to enhance LoRA by initializing the new weights in a data-driven manner by computing singular value decomposition on minibatches of activation vectors. Then, we initialize the LoRA matrices with the obtained right-singular vectors and re-distribute ranks among all weight matrices to explain the maximal amount of variance and continue the standard LoRA fine-tuning procedure. This results in our new method Explained Variance Adaptation (EVA). We apply EVA to a variety of fine-tuning tasks ranging from language generation and understanding to image classification and reinforcement learning. EVA exhibits faster convergence than competitors and attains the highest average score across a multitude of tasks per domain.

Building models that generalize across physical systems without retraining remains a central challenge in computational science. Here we introduce In-Context Modeling (ICM), a retrain-free paradigm that infers physical relationships directly from observational fields. Rather than encoding system-specific behavior in fixed parameters, ICM assimilates measurements as physical context and performs inference through a single forward pass. Trained in a physics-informed, label-free manner using governing equations, a single model generalizes across unseen materials, geometries, and loading conditions. Demonstrated on hyperelasticity, ICM integrates with finite-element simulations and is validated using experimental full-field measurements. Moreover, performance improves with increasing data diversity and computational budget, exhibiting favorable scaling behavior analogous to foundation models. By recasting physical modeling as in-context inference, this work establishes a transferable paradigm for retrain-free scientific learning and a foundation for scalable modeling across computational science.

Deep learning foundation models are revolutionizing many facets of science by leveraging vast amounts of data to learn general-purpose representations that can be adapted to tackle diverse downstream tasks. Foundation models hold the promise to also transform our ability to model our planet and its subsystems by exploiting the vast expanse of Earth system data. Here we introduce Aurora, a large-scale foundation model of the atmosphere trained on over a million hours of diverse weather and climate data. Aurora leverages the strengths of the foundation modelling approach to produce operational forecasts for a wide variety of atmospheric prediction problems, including those with limited training data, heterogeneous variables, and extreme events. In under a minute, Aurora produces 5-day global air pollution predictions and 10-day high-resolution weather forecasts that outperform state-of-the-art classical simulation tools and the best specialized deep learning models. Taken together, these results indicate that foundation models can transform environmental forecasting.

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

Foundation model development attracts a rapidly expanding body of contributors, scientists, and applications. To help shape responsible development practices, we introduce the Foundation Model Development Cheatsheet: a growing collection of 250+ tools and resources spanning text, vision, and speech modalities. We draw on a large body of prior work to survey resources (e.g. software, documentation, frameworks, guides, and practical tools) that support informed data selection, processing, and understanding, precise and limitation-aware artifact documentation, efficient model training, advance awareness of the environmental impact from training, careful model evaluation of capabilities, risks, and claims, as well as responsible model release, licensing and deployment practices. We hope this curated collection of resources helps guide more responsible development. The process of curating this list, enabled us to review the AI development ecosystem, revealing what tools are critically missing, misused, or over-used in existing practices. We find that (i) tools for data sourcing, model evaluation, and monitoring are critically under-serving ethical and real-world needs, (ii) evaluations for model safety, capabilities, and environmental impact all lack reproducibility and transparency, (iii) text and particularly English-centric analyses continue to dominate over multilingual and multi-modal analyses, and (iv) evaluation of systems, rather than just models, is needed so that capabilities and impact are assessed in context.

Recent advances in AI weather forecasting have led to the emergence of so-called "foundation models", typically defined by expensive pretraining and minimal fine-tuning for downstream tasks. However, in the natural sciences, a desirable foundation model should also encode meaningful statistical relationships between the underlying physical variables. This study evaluates the performance of the state-of-the-art Aurora foundation model in predicting hydrological variables, which were not considered during pretraining. We introduce a lightweight approach using shallow decoders trained on the latent representations of the pretrained model to predict these new variables. As a baseline, we compare this to fine-tuning the full model, which allows further optimization of the latent space while incorporating new variables into both inputs and outputs. The decoder-based approach requires 50% less training time and 35% less memory, while achieving strong accuracy across various hydrological variables and preserving desirable properties of the foundation model, such as autoregressive stability. Notably, decoder accuracy depends on the physical correlation between the new variables and those used during pretraining, indicating that Aurora's latent space captures meaningful physical relationships. In this sense, we argue that an important quality metric for foundation models in Earth sciences is their ability to be extended to new variables without a full fine-tuning. This provides a new perspective for making foundation models more accessible to communities with limited computational resources, while supporting broader adoption in Earth sciences.

Given the remarkable ability of 2D foundation image models to generate high-fidelity outputs, we investigate a fundamental question: do 2D foundation image models inherently possess 3D world model capabilities? To answer this, we systematically evaluate multiple state-of-the-art image generation models and Vision-Language Models (VLMs) on the task of 3D world synthesis. To harness and benchmark their potential implicit 3D capability, we propose an agentic framing to facilitate 3D world generation. Our approach employs a multi-agent architecture: a VLM-based director that formulates prompts to guide image synthesis, a generator that synthesizes new image views, and a VLM-backed two-step verifier that evaluates and selectively curates generated frames from both 2D image and 3D reconstruction space. Crucially, we demonstrate that our agentic approach provides coherent and robust 3D reconstruction, producing output scenes that can be explored by rendering novel views. Through extensive experiments across various foundation models, we demonstrate that 2D models do indeed encapsulate a grasp of 3D worlds. By exploiting this understanding, our method successfully synthesizes expansive, realistic, and 3D-consistent worlds.

We introduce PHYSICS, a comprehensive benchmark for university-level physics problem solving. It contains 1297 expert-annotated problems covering six core areas: classical mechanics, quantum mechanics, thermodynamics and statistical mechanics, electromagnetism, atomic physics, and optics. Each problem requires advanced physics knowledge and mathematical reasoning. We develop a robust automated evaluation system for precise and reliable validation. Our evaluation of leading foundation models reveals substantial limitations. Even the most advanced model, o3-mini, achieves only 59.9% accuracy, highlighting significant challenges in solving high-level scientific problems. Through comprehensive error analysis, exploration of diverse prompting strategies, and Retrieval-Augmented Generation (RAG)-based knowledge augmentation, we identify key areas for improvement, laying the foundation for future advancements.

Foundation models have transformed machine learning for language and vision, but achieving comparable impact in physical simulation remains a challenge. Data heterogeneity and unstable long-term dynamics inhibit learning from sufficiently diverse dynamics, while varying resolutions and dimensionalities challenge efficient training on modern hardware. Through empirical and theoretical analysis, we incorporate new approaches to mitigate these obstacles, including a harmonic-analysis-based stabilization method, load-balanced distributed 2D and 3D training strategies, and compute-adaptive tokenization. Using these tools, we develop Walrus, a transformer-based foundation model developed primarily for fluid-like continuum dynamics. Walrus is pretrained on nineteen diverse scenarios spanning astrophysics, geoscience, rheology, plasma physics, acoustics, and classical fluids. Experiments show that Walrus outperforms prior foundation models on both short and long term prediction horizons on downstream tasks and across the breadth of pretraining data, while ablation studies confirm the value of our contributions to forecast stability, training throughput, and transfer performance over conventional approaches. Code and weights are released for community use.

Foundation models (FMs) are transforming computational pathology by offering new ways to analyze histopathology images. However, FMs typically require weeks of training on large databases, making their creation a resource-intensive process. In this paper, we present a training for foundation models from whole slide images using supervised, end-to-end, multitask learning on slide-level labels. Notably, it is the first model to incorporate cancer subtyping, risk estimation, and genetic mutation prediction into one model. The presented model outperforms self-supervised models on seven benchmark tasks while the training only required 5% of the computational resources. The results not only show that supervised training can outperform self-supervision with less data, but also offer a solution to annotation problems, as patient-based labels are widely available through routine clinical processes. Furthermore, an attention module provides a layer of explainability across different tasks and serves as a tumor detector for unseen cancer types. To address the issue of closed-source datasets, the model was fully trained on openly available data. The code and model weights are made available under https://github.com/FraunhoferMEVIS/MedicalMultitaskModeling.

Large language model (LLM)-based agentic frameworks increasingly adopt the paradigm of dynamically generating task-specific agents. We suggest that not only agents but also specialized software modules for scientific and engineering tasks can be generated on demand. We demonstrate this concept in the field of solid mechanics. There, so-called constitutive models are required to describe the relationship between mechanical stress and body deformation. Constitutive models are essential for both the scientific understanding and industrial application of materials. However, even recent data-driven methods of constitutive modeling, such as constitutive artificial neural networks (CANNs), still require substantial expert knowledge and human labor. We present a framework in which an LLM generates a CANN on demand, tailored to a given material class and dataset provided by the user. The framework covers LLM-based architecture selection, integration of physical constraints, and complete code generation. Evaluation on three benchmark problems demonstrates that LLM-generated CANNs achieve accuracy comparable to or greater than manually engineered counterparts, while also exhibiting reliable generalization to unseen loading scenarios and extrapolation to large deformations. These findings indicate that LLM-based generation of physics-constrained neural networks can substantially reduce the expertise required for constitutive modeling and represent a step toward practical end-to-end automation.

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.

Toward recursive self-improvement, we investigate LLM agents autonomously designing foundation models beyond standard Transformers. We introduce a dual-framework approach: AIRA-Compose for high-level architecture search, and AIRA-Design for low-level mechanistic implementation. AIRA-Compose uses 11 agents to explore fundamental computational primitives under a 24-hour budget. Agents evaluate million-parameter candidates, extrapolating top designs to 350M, 1B, and 3B scales. This yields 14 architectures across two families: AIRAformers (Transformer-based) and AIRAhybrids (Transformer-Mamba). Pre-trained at 1B scale, these consistently outperform Llama 3.2 and Composer-found baselines. On downstream tasks, AIRAformer-D and AIRAhybrid-D improve accuracy by 2.4% and 3.8% over Llama 3.2. Furthermore, AIRA-Compose finds models with highly efficient scaling frontiers: AIRAformer-C scales 54% and 71% faster than Llama 3.2 and Composer's best Transformer, while AIRAhybrid-C outscales Nemotron-2 by 23% and Composer's best hybrid by 37%. AIRA-Design tasks 20 agents with writing novel attention mechanisms for long-range dependencies and high-performing training scripts. On the Long Range Arena benchmark, agent-designed architectures reach within 2.3% and 2.6% of human state-of-the-art on document matching and text classification. On the Autoresearch benchmark, Greedy Opus 4.5 achieves 0.968 validation bits-per-byte under a fixed time budget, surpassing the published minimum. Together, these frameworks show AI agents can autonomously discover architectures and algorithmic optimizations matching or surpassing hand-designed baselines. This establishes a powerful paradigm for discovering next-generation foundation models, marking a clear step toward recursive self-improvement.

The groundbreaking advance in materials and chemical research has been driven by the development of atomistic simulations. However, the broader applicability of the atomistic simulations remains restricted, as they inherently depend on energy models that are either inaccurate or computationally prohibitive. Machine learning interatomic potentials (MLIPs) have recently emerged as a promising class of energy models, but their deployment remains challenging due to the lack of systematic protocols for generating diverse training data. Here we automate the construction of training datasets to enable the development of general-purpose MLIPs, by introducing GAIA, an end-to-end framework to build a wide range of atomic arrangements. By employing systematic evaluation of metadynamics for effective structural exploration, GAIA overcomes the heuristic nature of conventional dataset generation. Using GAIA, we constructed Titan25, a benchmark-scale dataset, and trained MLIPs that closely match both static and dynamic density functional theory results. The models further reproduce experimental observations across reactive regimes, including detonation, coalescence, and catalytic activity. GAIA narrows the gap between experiment and simulation, and paves the way for the development of universal MLIPs that can reliably describe a wide spectrum of materials and chemical processes.

Foundation models (FM) have unlocked powerful zero-shot capabilities in vision and language, yet their reliance on internet pretraining data leaves them brittle in unstructured, real-world settings. The messy, real-world data encountered during deployment (e.g. occluded or multilingual text) remains massively underrepresented in existing corpora. Robots, as embodied agents, are uniquely positioned to close this gap: they can act in physical environments to collect large-scale, real-world data that enriches FM training with precisely the examples current models lack. We introduce the Robot-Powered Data Flywheel, a framework that transforms robots from FM consumers into data generators. By deploying robots equipped with FMs in the wild, we enable a virtuous cycle: robots perform useful tasks while collecting real-world data that improves both domain-specific adaptation and domain-adjacent generalization. We instantiate this framework with Scanford, a mobile manipulator deployed in the East Asia Library for 2 weeks. Scanford autonomously scans shelves, identifies books using a vision-language model (VLM), and leverages the library catalog to label images without human annotation. This deployment both aids librarians and produces a dataset to finetune the underlying VLM, improving performance on the domain-specific in-the-wild library setting and on domain-adjacent multilingual OCR benchmarks. Using data collected from 2103 shelves, Scanford improves VLM performance on book identification from 32.0% to 71.8% and boosts domain-adjacent multilingual OCR from 24.8% to 46.6% (English) and 30.8% to 38.0% (Chinese), while saving an ~18.7 hrs of human time. These results highlight how robot-powered data flywheels can both reduce human effort in real deployments and unlock new pathways for continually adapting FMs to the messiness of reality. More details are at: https://scanford-robot.github.io

Self-supervised pretraining from static structures of drug-like compounds and proteins enable powerful learned feature representations. Learned features demonstrate state of the art performance on a range of predictive tasks including molecular properties, structure generation, and protein-ligand interactions. The majority of approaches are limited by their use of static structures and it remains an open question, how best to use atomistic molecular dynamics (MD) simulations to develop more generalized models to improve prediction accuracy for novel molecular structures. We present SURrogate mmGBSA (SurGBSA) as a new modeling approach for MD-based representation learning, which learns a surrogate function of the Molecular Mechanics Generalized Born Surface Area (MMGBSA). We show for the first time the benefits of physics-informed pre-training to train a surrogate MMGBSA model on a collection of over 1.4 million 3D trajectories collected from MD simulations of the CASF-2016 benchmark. SurGBSA demonstrates a dramatic 27,927x speedup versus a traditional physics-based single-point MMGBSA calculation while nearly matching single-point MMGBSA accuracy on the challenging pose ranking problem for identification of the correct top pose (-0.4% difference). Our work advances the development of molecular foundation models by showing model improvements when training on MD simulations. Models, code and training data are made publicly available.

The rapid advancement of AI technology has led to widespread applications of agent systems across various domains. However, the need for detailed architecture design poses significant challenges in designing and operating these systems. This paper introduces a taxonomy focused on the architectures of foundation-model-based agents, addressing critical aspects such as functional capabilities and non-functional qualities. We also discuss the operations involved in both design-time and run-time phases, providing a comprehensive view of architectural design and operational characteristics. By unifying and detailing these classifications, our taxonomy aims to improve the design of foundation-model-based agents. Additionally, the paper establishes a decision model that guides critical design and runtime decisions, offering a structured approach to enhance the development of foundation-model-based agents. Our contributions include providing a structured architecture design option and guiding the development process of foundation-model-based agents, thereby addressing current fragmentation in the field.

Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.

Artificial intelligence (AI) has become a fundamental tool for assisting clinicians in analyzing ophthalmic images, such as optical coherence tomography (OCT). However, developing AI models often requires extensive annotation, and existing models tend to underperform on independent, unseen data. Foundation models (FMs), large AI models trained on vast unlabeled datasets, have shown promise in overcoming these challenges. Nonetheless, available FMs for ophthalmology lack extensive validation, especially for segmentation tasks, and focus on a single imaging modality. In this context, we propose MIRAGE, a novel multimodal FM for the analysis of OCT and scanning laser ophthalmoscopy (SLO) images. Additionally, we propose a new evaluation benchmark with OCT/SLO classification and segmentation tasks. The comparison with general and specialized FMs and segmentation methods shows the superiority of MIRAGE in both types of tasks, highlighting its suitability as a basis for the development of robust AI systems for retinal OCT image analysis. Both MIRAGE and the evaluation benchmark are publicly available: https://github.com/j-morano/MIRAGE.

We explore adapting foundation models (FMs) from the computer vision domain to geoscience. FMs, large neural networks trained on massive datasets, excel in diverse tasks with remarkable adaptability and generality. However, geoscience faces challenges like lacking curated training datasets and high computational costs for developing specialized FMs. This study considers adapting FMs from computer vision to geoscience, analyzing their scale, adaptability, and generality for geoscientific data analysis. We introduce a workflow that leverages existing computer vision FMs, fine-tuning them for geoscientific tasks, reducing development costs while enhancing accuracy. Through experiments, we demonstrate this workflow's effectiveness in broad applications to process and interpret geoscientific data of lunar images, seismic data, DAS arrays and so on. Our findings introduce advanced ML techniques to geoscience, proving the feasibility and advantages of cross-domain FMs adaptation, driving further advancements in geoscientific data analysis and offering valuable insights for FMs applications in other scientific domains.

Tabular foundation models represent a growing paradigm in structured data learning, extending the benefits of large-scale pretraining to tabular domains. However, their adoption remains limited due to heterogeneous preprocessing pipelines, fragmented APIs, inconsistent fine-tuning procedures, and the absence of standardized evaluation for deployment-oriented metrics such as calibration and fairness. We present TabTune, a unified library that standardizes the complete workflow for tabular foundation models through a single interface. TabTune provides consistent access to seven state-of-the-art models supporting multiple adaptation strategies, including zero-shot inference, meta-learning, supervised fine-tuning (SFT), and parameter-efficient fine-tuning (PEFT). The framework automates model-aware preprocessing, manages architectural heterogeneity internally, and integrates evaluation modules for performance, calibration, and fairness. Designed for extensibility and reproducibility, TabTune enables consistent benchmarking of adaptation strategies of tabular foundation models. The library is open source and available at https://github.com/Lexsi-Labs/TabTune .

3D foundation models (3DFMs) have recently transformed 3D vision, enabling joint prediction of depths, poses, and point maps directly from images. Yet their ability to reason under extreme, non-overlapping views remains largely unexplored. In this work, we study their internal representations and find that 3DFMs exhibit an emergent understanding of extreme-view geometry, despite never being trained for such conditions. To further enhance these capabilities, we introduce a lightweight alignment scheme that refines their internal 3D representation by tuning only a small subset of backbone bias terms, leaving all decoder heads frozen. This targeted adaptation substantially improves relative pose estimation under extreme viewpoints without degrading per-image depth or point quality. Additionally, we contribute MegaUnScene, a new benchmark of Internet scenes unseen by existing 3DFMs, with dedicated test splits for both relative pose estimation and dense 3D reconstruction. All code and data will be released.

Deep learning-based methods have been widely researched in the areas of language and vision, demonstrating their capacity to understand long sequences of data and their usefulness in numerous helio-physics applications. Foundation models (FMs), which are pre-trained on a large-scale datasets, form the basis for a variety of downstream tasks. These models, especially those based on transformers in vision and language, show exceptional potential for adapting to a wide range of downstream applications. In this paper, we provide our perspective on the criteria for designing an FM for heliophysics and associated challenges and applications using the Solar Dynamics Observatory (SDO) dataset. We believe that this is the first study to design an FM in the domain of heliophysics.

We propose PROSE-FD, a zero-shot multimodal PDE foundational model for simultaneous prediction of heterogeneous two-dimensional physical systems related to distinct fluid dynamics settings. These systems include shallow water equations and the Navier-Stokes equations with incompressible and compressible flow, regular and complex geometries, and different buoyancy settings. This work presents a new transformer-based multi-operator learning approach that fuses symbolic information to perform operator-based data prediction, i.e. non-autoregressive. By incorporating multiple modalities in the inputs, the PDE foundation model builds in a pathway for including mathematical descriptions of the physical behavior. We pre-train our foundation model on 6 parametric families of equations collected from 13 datasets, including over 60K trajectories. Our model outperforms popular operator learning, computer vision, and multi-physics models, in benchmark forward prediction tasks. We test our architecture choices with ablation studies.

We survey applications of pretrained foundation models in robotics. Traditional deep learning models in robotics are trained on small datasets tailored for specific tasks, which limits their adaptability across diverse applications. In contrast, foundation models pretrained on internet-scale data appear to have superior generalization capabilities, and in some instances display an emergent ability to find zero-shot solutions to problems that are not present in the training data. Foundation models may hold the potential to enhance various components of the robot autonomy stack, from perception to decision-making and control. For example, large language models can generate code or provide common sense reasoning, while vision-language models enable open-vocabulary visual recognition. However, significant open research challenges remain, particularly around the scarcity of robot-relevant training data, safety guarantees and uncertainty quantification, and real-time execution. In this survey, we study recent papers that have used or built foundation models to solve robotics problems. We explore how foundation models contribute to improving robot capabilities in the domains of perception, decision-making, and control. We discuss the challenges hindering the adoption of foundation models in robot autonomy and provide opportunities and potential pathways for future advancements. The GitHub project corresponding to this paper (Preliminary release. We are committed to further enhancing and updating this work to ensure its quality and relevance) can be found here: https://github.com/robotics-survey/Awesome-Robotics-Foundation-Models

Whether physics foundation models can be usefully deployed on laboratory experiments remains an open question for scientific machine learning (ML). We test this question on the Rayleigh-Taylor instability (RTI), a ubiquitous and demanding fluid instability seen from tabletop flows to supernova explosions, in which small perturbations at a density interface grow into chaotic, multiscale mixing as a lighter fluid accelerates into a heavier one. Standard ML models struggle with RTI, and despite over a century of theoretical, numerical, and experimental work, it carries an unresolved discrepancy between simulation and experiment: the late-time mixing growth rate, α, measured in most laboratory experiments (sim 0.06-0.07), is roughly three times the value from idealized direct numerical simulations (DNS, sim 0.02). The gap's origin remains debated. These properties make RTI a stringent test for a question that matters well beyond RTI: can foundation models trained only on simulations generalise to sparse, messy, and noisy laboratory settings? We finetune Walrus, a foundation model for continuum dynamics, on three or fewer DNS realizations and recover key RTI physics over long rollouts. Applied zero-shot to sliding-barrier laboratory data, the finetuned model leaves the DNS-like regime and enters the observed growth band, having never seen a single experimental sample. These results provide independent, data-driven evidence that initial conditions play a crucial role in the longstanding sim-experiment gap in α. The model also generalises zero-shot to stable stratification, a buoyancy regime absent from training, correctly slowing mixing-layer growth. Together, our results show that foundation models can generalise well beyond their training data, predicting laboratory behavior and unseen physical regimes, opening new ways to probe longstanding simulation-experiment gaps.

AI-assisted radiological interpretation is based on predominantly narrow, single-task models. This approach is impractical for covering the vast spectrum of imaging modalities, diseases, and radiological findings. Foundation models (FMs) hold the promise of broad generalization across modalities and in low-data settings. However, this potential has remained largely unrealized in radiology. We introduce Curia, a foundation model trained on the entire cross-sectional imaging output of a major hospital over several years, which to our knowledge is the largest such corpus of real-world data-encompassing 150,000 exams (130 TB). On a newly curated 19-task external validation benchmark, Curia accurately identifies organs, detects conditions like brain hemorrhages and myocardial infarctions, and predicts outcomes in tumor staging. Curia meets or surpasses the performance of radiologists and recent foundation models, and exhibits clinically significant emergent properties in cross-modality, and low-data regimes. To accelerate progress, we release our base model's weights at https://huggingface.co/raidium/curia.

We present AutoGLM, a new series in the ChatGLM family, designed to serve as foundation agents for autonomous control of digital devices through Graphical User Interfaces (GUIs). While foundation models excel at acquiring human knowledge, they often struggle with decision-making in dynamic real-world environments, limiting their progress toward artificial general intelligence. This limitation underscores the importance of developing foundation agents capable of learning through autonomous environmental interactions by reinforcing existing models. Focusing on Web Browser and Phone as representative GUI scenarios, we have developed AutoGLM as a practical foundation agent system for real-world GUI interactions. Our approach integrates a comprehensive suite of techniques and infrastructures to create deployable agent systems suitable for user delivery. Through this development, we have derived two key insights: First, the design of an appropriate "intermediate interface" for GUI control is crucial, enabling the separation of planning and grounding behaviors, which require distinct optimization for flexibility and accuracy respectively. Second, we have developed a novel progressive training framework that enables self-evolving online curriculum reinforcement learning for AutoGLM. Our evaluations demonstrate AutoGLM's effectiveness across multiple domains. For web browsing, AutoGLM achieves a 55.2% success rate on VAB-WebArena-Lite (improving to 59.1% with a second attempt) and 96.2% on OpenTable evaluation tasks. In Android device control, AutoGLM attains a 36.2% success rate on AndroidLab (VAB-Mobile) and 89.7% on common tasks in popular Chinese APPs.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled scientific discovery.

We develop a framework for on-the-fly machine learned force field molecular dynamics simulations based on the multipole featurization scheme that overcomes the bottleneck with the number of chemical elements. Considering bulk systems with up to 6 elements, we demonstrate that the number of density functional theory calls remains approximately independent of the number of chemical elements, in contrast to the increase in the smooth overlap of atomic positions scheme.

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Merging first-principles calculations with machine learning (ML), we aim to accelerate the exploration of catalytic behaviour in novel materials. We focus on two-dimensional (2D) Ti_2CT_y MXenes, whose versatile surface chemistry makes them particularly compelling candidates for catalysis. Resolving their composition and structure under realistic conditions exceeds the reach of standard density functional theory (DFT) due to computational cost. To address this challenge, we generate a comprehensive dataset of 50,000 DFT calculations for training and 10,000 for testing, encompassing both Ti_2CT_y MXene configurations and molecular systems, along with an additional test dataset with 1000 genuinely new, larger systems to investigate how well models generalise. We train and validate widely used and competitive machine learning interatomic potential (MLIP) models, including EquiformerV2, MACE, MatRIS, and UPET, that accurately predict atomic forces and formation energies -- quantities that DFT must repeatedly compute for structural and catalytic investigations -- for these 2D materials. This combined DFT-ML framework achieves computational acceleration on the order of approximately 1-4 cdot 10^3 (on a CPU) while maintaining desired-level accuracy (approximately +/- 10 meV/A for forces and approximately +/- 1 meV for per-atom energies), paving the way for more efficient investigations of MXene catalytic behaviour. Moreover, we perform an extensive qualitative evaluation of the trained models, showcasing the importance of comprehensive simulation-based comparison beyond benchmark metrics. The dataset and the trained models with the code are available at https://huggingface.co/datasets/CatalystAnonymous/catalyst_mxenes.

Realistic simulation of dynamic scenes requires accurately capturing diverse material properties and modeling complex object interactions grounded in physical principles. However, existing methods are constrained to basic material types with limited predictable parameters, making them insufficient to represent the complexity of real-world materials. We introduce a novel approach that leverages multi-modal foundation models and video diffusion to achieve enhanced 4D dynamic scene simulation. Our method utilizes multi-modal models to identify material types and initialize material parameters through image queries, while simultaneously inferring 3D Gaussian splats for detailed scene representation. We further refine these material parameters using video diffusion with a differentiable Material Point Method (MPM) and optical flow guidance rather than render loss or Score Distillation Sampling (SDS) loss. This integrated framework enables accurate prediction and realistic simulation of dynamic interactions in real-world scenarios, advancing both accuracy and flexibility in physics-based simulations.

Foundation models pretrained on diverse data at scale have demonstrated extraordinary capabilities in a wide range of vision and language tasks. When such models are deployed in real world environments, they inevitably interface with other entities and agents. For example, language models are often used to interact with human beings through dialogue, and visual perception models are used to autonomously navigate neighborhood streets. In response to these developments, new paradigms are emerging for training foundation models to interact with other agents and perform long-term reasoning. These paradigms leverage the existence of ever-larger datasets curated for multimodal, multitask, and generalist interaction. Research at the intersection of foundation models and decision making holds tremendous promise for creating powerful new systems that can interact effectively across a diverse range of applications such as dialogue, autonomous driving, healthcare, education, and robotics. In this manuscript, we examine the scope of foundation models for decision making, and provide conceptual tools and technical background for understanding the problem space and exploring new research directions. We review recent approaches that ground foundation models in practical decision making applications through a variety of methods such as prompting, conditional generative modeling, planning, optimal control, and reinforcement learning, and discuss common challenges and open problems in the field.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

Although Foundation Models (FMs), such as GPT-4, are increasingly used in domains like finance and software engineering, reliance on textual interfaces limits these models' real-world interaction. To address this, FM providers introduced tool calling-triggering a proliferation of frameworks with distinct tool interfaces. In late 2024, Anthropic introduced the Model Context Protocol (MCP) to standardize this tool ecosystem, which has become the de facto standard with over eight million weekly SDK downloads. Despite its adoption, MCP's AI-driven, non-deterministic control flow introduces new risks to sustainability, security, and maintainability, warranting closer examination. Towards this end, we present the first large-scale empirical study of MCP servers. Using state-of-the-art health metrics and a hybrid analysis pipeline, combining a general-purpose static analysis tool with an MCP-specific scanner, we evaluate 1,899 open-source MCP servers to assess their health, security, and maintainability. Despite MCP servers demonstrating strong health metrics, we identify eight distinct vulnerabilities - only three overlapping with traditional software vulnerabilities. Additionally, 7.2% of servers contain general vulnerabilities and 5.5% exhibit MCP-specific tool poisoning. Regarding maintainability, while 66% exhibit code smells, 14.4% contain nine bug patterns overlapping with traditional open-source software projects. These findings highlight the need for MCP-specific vulnerability detection techniques while reaffirming the value of traditional analysis and refactoring practices.

We investigate how to make small tabular foundation models effective for High-Dimensional, Low-Sample Size (HDLSS) tabular prediction without retraining large backbones. We introduce Graph-guided Ordering with Local Refinement (GO-LR), show its equivalence to weighted Minimum Linear Arrangement, and interpret the practical solver as a TSP-path-style surrogate. We propose GOTabPFN,which builds on GO-LR, and a Neuro-Inspired Subunit Compression (NSC) unit to pool locally adjacent ordered features into meta-features, yielding a compact representation that makes TabPFN-style prediction practical in HDLSS regimes. Across tabular benchmarks, GOTabPFN improves stability and accuracy under tight token budgets.

Foundation vision or vision-language models are trained on large unlabeled or noisy data and learn robust representations that can achieve impressive zero- or few-shot performance on diverse tasks. Given these properties, they are a natural fit for active learning (AL), which aims to maximize labeling efficiency. However, the full potential of foundation models has not been explored in the context of AL, specifically in the low-budget regime. In this work, we evaluate how foundation models influence three critical components of effective AL, namely, 1) initial labeled pool selection, 2) ensuring diverse sampling, and 3) the trade-off between representative and uncertainty sampling. We systematically study how the robust representations of foundation models (DINOv2, OpenCLIP) challenge existing findings in active learning. Our observations inform the principled construction of a new simple and elegant AL strategy that balances uncertainty estimated via dropout with sample diversity. We extensively test our strategy on many challenging image classification benchmarks, including natural images as well as out-of-domain biomedical images that are relatively understudied in the AL literature. We also provide a highly performant and efficient implementation of modern AL strategies (including our method) at https://github.com/sanketx/AL-foundation-models.

Large foundation models, including large language models (LLMs), vision transformers (ViTs), diffusion, and LLM-based multimodal models, are revolutionizing the entire machine learning lifecycle, from training to deployment. However, the substantial advancements in versatility and performance these models offer come at a significant cost in terms of hardware resources. To support the growth of these large models in a scalable and environmentally sustainable way, there has been a considerable focus on developing resource-efficient strategies. This survey delves into the critical importance of such research, examining both algorithmic and systemic aspects. It offers a comprehensive analysis and valuable insights gleaned from existing literature, encompassing a broad array of topics from cutting-edge model architectures and training/serving algorithms to practical system designs and implementations. The goal of this survey is to provide an overarching understanding of how current approaches are tackling the resource challenges posed by large foundation models and to potentially inspire future breakthroughs in this field.

Foundation model-enabled generative artificial intelligence facilitates the development and implementation of agents, which can leverage distinguished reasoning and language processing capabilities to takes a proactive, autonomous role to pursue users' goals. Nevertheless, there is a lack of systematic knowledge to guide practitioners in designing the agents considering challenges of goal-seeking (including generating instrumental goals and plans), such as hallucinations inherent in foundation models, explainability of reasoning process, complex accountability, etc. To address this issue, we have performed a systematic literature review to understand the state-of-the-art foundation model-based agents and the broader ecosystem. In this paper, we present a pattern catalogue consisting of 18 architectural patterns with analyses of the context, forces, and trade-offs as the outcomes from the previous literature review. We propose a decision model for selecting the patterns. The proposed catalogue can provide holistic guidance for the effective use of patterns, and support the architecture design of foundation model-based agents by facilitating goal-seeking and plan generation.

While computer science has seen remarkable advancements in foundation models, which remain underexplored in geoscience. Addressing this gap, we introduce a workflow to develop geophysical foundation models, including data preparation, model pre-training, and adaption to downstream tasks. From 192 globally collected 3-D seismic volumes, we create a carefully curated dataset of 2,286,422 2-D seismic images. Fully using these unlabeled images, we employ the self-supervised learning to pre-train a Transformer-based Seismic Foundation Model (SFM) for producing all-purpose seismic features that work across various tasks and surveys. Through experiments on seismic facies classification, geobody identification, interpolation, denoising, and inversion, our pre-trained model demonstrates versatility, generalization, scalability, and superior performance over baseline models. Conclusively, we provide a foundation model and vast dataset to advance AI in geophysics, addressing challenges (poor generalization, lacking labels, and repetitive training for task-specified models) of applying AI in geophysics and paving the way for future innovations in geoscience.

Foundation models (FMs), large deep learning models pre-trained on vast, unlabeled datasets, exhibit powerful capabilities in understanding complex patterns and generating sophisticated outputs. However, they often struggle to adapt to specific tasks. Reinforcement learning (RL), which allows agents to learn through interaction and feedback, offers a compelling solution. Integrating RL with FMs enables these models to achieve desired outcomes and excel at particular tasks. Additionally, RL can be enhanced by leveraging the reasoning and generalization capabilities of FMs. This synergy is revolutionizing various fields, including robotics. FMs, rich in knowledge and generalization, provide robots with valuable information, while RL facilitates learning and adaptation through real-world interactions. This survey paper comprehensively explores this exciting intersection, examining how these paradigms can be integrated to advance robotic intelligence. We analyze the use of foundation models as action planners, the development of robotics-specific foundation models, and the mutual benefits of combining FMs with RL. Furthermore, we present a taxonomy of integration approaches, including large language models, vision-language models, diffusion models, and transformer-based RL models. We also explore how RL can utilize world representations learned from FMs to enhance robotic task execution. Our survey aims to synthesize current research and highlight key challenges in robotic reasoning and control, particularly in the context of integrating FMs and RL--two rapidly evolving technologies. By doing so, we seek to spark future research and emphasize critical areas that require further investigation to enhance robotics. We provide an updated collection of papers based on our taxonomy, accessible on our open-source project website at: https://github.com/clmoro/Robotics-RL-FMs-Integration.

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present a novel foundation model, VISION-MAE, specifically designed for medical imaging. Specifically, VISION-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET, X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VISION-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications, and achieves high performance even with reduced availability of labeled data. This model represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload.

The Materials Genome Initiative catalyzed the proliferation of centralized platforms--SaaS, PaaS, and IaaS--that aggregate computational and experimental resources for accelerated materials discovery. In parallel, breakthroughs in large language models (LLMs) and autonomous agents have created powerful new reasoning capabilities for scientific research. Yet a critical "last mile" problem remains: while we possess world-class models and vast repositories of materials data, we lack the organizational infrastructure to compose these capabilities securely across institutional boundaries. The development of structural and functional materials for harsh service environments--high-temperature alloys, radiation resistant steels, corrosion-resistant coatings--remains characterized by long-term iteration, mechanistic complexity, and high domain expertise--demands that exceed both monolithic agent systems and traditional centralized platforms. To address this gap we propose OpenAaaS, an open-source hierarchical and distributed Agent-as-a-Service framework that enables organized multi-agent collaboration for intelligent materials design. OpenAaaS is built on a single foundational principle: code flows, data stays still. A Master Agent plans and decomposes complex research tasks without requiring direct access to subordinate agents' managed data and computational resources. Sub-agents, deployed as near-data execution nodes, retain full sovereignty over local datasets, proprietary algorithms, and specialized hardware. This architecture guarantees that raw data never leaves its domain of origin while enabling cross-scale, cross-domain secure integration of previously isolated materials intelligence silos. We validate the framework through two representative case studies: (i) AlphaAgent, an evidence-grounded materials literature analysis executor that achieves 4.66/5.0 on deep analytical questions against single-pass RAG baselines; and (ii) an ultra-large-scale hexa-high-entropy alloy descriptor database service that demonstrates secure near-data execution and domain-specific scientific workflows under strict data-sovereignty constraints. OpenAaaS establishes a principled pathway toward "organized research" via agent collectives, offering a scalable foundation for next-generation materials intelligent design platforms. All source code is available at https://github.com/Wolido/OpenAaaS.

Foundation models (FM), such as large language models (LLMs), which are large-scale machine learning (ML) models, have demonstrated remarkable adaptability in various downstream software engineering (SE) tasks, such as code completion, code understanding, and software development. As a result, FM leaderboards, especially those hosted on cloud platforms, have become essential tools for SE teams to compare and select the best third-party FMs for their specific products and purposes. However, the lack of standardized guidelines for FM evaluation and comparison threatens the transparency of FM leaderboards and limits stakeholders' ability to perform effective FM selection. As a first step towards addressing this challenge, our research focuses on understanding how these FM leaderboards operate in real-world scenarios ("leaderboard operations") and identifying potential leaderboard pitfalls and areas for improvement ("leaderboard smells"). In this regard, we perform a multivocal literature review to collect up to 721 FM leaderboards, after which we examine their documentation and engage in direct communication with leaderboard operators to understand their workflow patterns. Using card sorting and negotiated agreement, we identify 5 unique workflow patterns and develop a domain model that outlines the essential components and their interaction within FM leaderboards. We then identify 8 unique types of leaderboard smells in LBOps. By mitigating these smells, SE teams can improve transparency, accountability, and collaboration in current LBOps practices, fostering a more robust and responsible ecosystem for FM comparison and selection.

Molecular dynamics (MD) simulations play a crucial role in scientific research. Yet their computational cost often limits the timescales and system sizes that can be explored. Most data-driven efforts have been focused on reducing the computational cost of accurate interatomic forces required for solving the equations of motion. Despite their success, however, these machine learning interatomic potentials (MLIPs) are still bound to small time-steps. In this work, we introduce TrajCast, a transferable and data-efficient framework based on autoregressive equivariant message passing networks that directly updates atomic positions and velocities lifting the constraints imposed by traditional numerical integration. We benchmark our framework across various systems, including a small molecule, crystalline material, and bulk liquid, demonstrating excellent agreement with reference MD simulations for structural, dynamical, and energetic properties. Depending on the system, TrajCast allows for forecast intervals up to 30times larger than traditional MD time-steps, generating over 15 ns of trajectory data per day for a solid with more than 4,000 atoms. By enabling efficient large-scale simulations over extended timescales, TrajCast can accelerate materials discovery and explore physical phenomena beyond the reach of traditional simulations and experiments. An open-source implementation of TrajCast is accessible under https://github.com/IBM/trajcast.

High-pressure crystal structure prediction (CSP) underpins advances in condensed matter physics, planetary science, and materials discovery. Yet, most large atomistic models are trained on near-ambient, equilibrium data, leading to degraded stress accuracy at tens to hundreds of gigapascals and sparse coverage of pressure-stabilized stoichiometries and dense coordination motifs. Here, we introduce OpenCSP, a machine learning framework for CSP tasks spanning ambient to high-pressure conditions. This framework comprises an open-source pressure-resolved dataset alongside a suite of publicly available atomistic models that are jointly optimized for accuracy in energy, force, and stress predictions. The dataset is constructed via randomized high-pressure sampling and iteratively refined through an uncertainty-guided concurrent learning strategy, which enriches underrepresented compression regimes while suppressing redundant DFT labeling. Despite employing a training corpus one to two orders of magnitude smaller than those of leading large models, OpenCSP achieves comparable or superior performance in high-pressure enthalpy ranking and stability prediction. Across benchmark CSP tasks spanning a wide pressure window, our models match or surpass MACE-MPA-0, MatterSim v1 5M, and GRACE-2L-OAM, with the largest gains observed at elevated pressures. These results demonstrate that targeted, pressure-aware data acquisition coupled with scalable architectures enables data-efficient, high-fidelity CSP, paving the way for autonomous materials discovery under ambient and extreme conditions.

Modern materials science has historically been founded on combining restricted subsets of the periodic table, favoring high-purity, few-element systems. However, the demands of an emerging circular economy, together with the need to understand materials behavior under planetary and industrial extremes, increasingly require mastering Mendeleev materials - chemically and structurally complex systems that span large portions of the periodic table. In these regimes, current universal machine-learning interatomic potentials often fail, largely due to systematic gaps in traditional training datasets that heavily emphasize low-energy, near-equilibrium structures. We address this limitation by introducing a chemistry-agnostic, information-entropy-maximization protocol for data generation. By decoupling structural sampling from thermodynamic bias, our approach provides a robust physical prior for atomic interactions across the entire periodic table, including regimes far from equilibrium and under extreme conditions. Training a Graph Atomic Cluster Expansion (GRACE) model on the resulting statistically maximized entropy (SMAX) dataset yields markedly improved robustness across a range of stringent benchmarks. These include large-strain phase transformations in tin, defect evolution in tungsten-based alloys, and catalytic reaction barrier prediction. More broadly, our approach establishes a scalable and principled methodology for navigating the vast chemical and configurational space relevant to future materials design. It enables a paradigm of discovery by simulation in which unbiased sampling protocols autonomously resolve emergent structures in multi-elemental mixtures-such as systems containing the nine most abundant elements in the Earth's crust-without reliance on a priori chemical assumptions.

Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches that can autonomously propose and synthesize in the laboratory new porous reticular structures on demand. We outline the progress of employing deep learning models, such as variational autoencoders, diffusion models, and large language model-based agents, that are fueled by the growing amount of available data from the MOF community and suggest novel crystalline materials designs. These generative tools can be combined with high-throughput computational screening and even automated experiments to form accelerated, closed-loop discovery pipelines. The result is a new paradigm for reticular chemistry in which AI algorithms more efficiently direct the search for high-performance MOF materials for clean air and energy applications. Finally, we highlight remaining challenges such as synthetic feasibility, dataset diversity, and the need for further integration of domain knowledge.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

3D medical image classification is essential for modern clinical workflows. Medical foundation models (FMs) have emerged as a promising approach for scaling to new tasks, yet current research suffers from three critical pitfalls: data-regime bias, suboptimal adaptation, and insufficient task coverage. In this paper, we address these pitfalls and introduce AnyMC3D, a scalable 3D classifier adapted from 2D FMs. Our method scales efficiently to new tasks by adding only lightweight plugins (about 1M parameters per task) on top of a single frozen backbone. This versatile framework also supports multi-view inputs, auxiliary pixel-level supervision, and interpretable heatmap generation. We establish a comprehensive benchmark of 12 tasks covering diverse pathologies, anatomies, and modalities, and systematically analyze state-of-the-art 3D classification techniques. Our analysis reveals key insights: (1) effective adaptation is essential to unlock FM potential, (2) general-purpose FMs can match medical-specific FMs if properly adapted, and (3) 2D-based methods surpass 3D architectures for 3D classification. For the first time, we demonstrate the feasibility of achieving state-of-the-art performance across diverse applications using a single scalable framework (including 1st place in the VLM3D challenge), eliminating the need for separate task-specific models.

Foundation models for Earth systems have so far been trained primarily on physical climate and weather data, with limited representation of the human systems that both drive and respond to environmental change. The lack of a unified global training resource that combines climate, land, ocean, cryosphere, infrastructure, hazards, and socioeconomic data on a common grid hinders progress toward truly multimodal Earth system foundation models. We present WorldTensor, a harmonised global dataset that aligns hundreds of environmental and socioeconomic variables to a standardised 0.25^circ spatial grid and annual temporal framework. WorldTensor integrates reanalysis products, remote sensing, emissions inventories, land use reconstructions, hydrological observations, infrastructure and hazard datasets, and socioeconomic indicators within a single representation designed for machine learning workflows. To build the dataset, we regridded inputs across heterogeneous native resolutions and projections, rasterised point and vector datasets into spatially meaningful gridded fields, and reconciled temporal coverages ranging from daily observations to sparse multiyear socioeconomic snapshots. All outputs are distributed as NetCDF files with standardised coordinates, variable metadata, and a common CF metadata convention. WorldTensor provides a reproducible resource for training and evaluating foundation models that learn coupled dynamics across environmental and human systems at planetary scale.

We present PhysInOne, a large-scale synthetic dataset addressing the critical scarcity of physically-grounded training data for AI systems. Unlike existing datasets limited to merely hundreds or thousands of examples, PhysInOne provides 2 million videos across 153,810 dynamic 3D scenes, covering 71 basic physical phenomena in mechanics, optics, fluid dynamics, and magnetism. Distinct from previous works, our scenes feature multiobject interactions against complex backgrounds, with comprehensive ground-truth annotations including 3D geometry, semantics, dynamic motion, physical properties, and text descriptions. We demonstrate PhysInOne's efficacy across four emerging applications: physics-aware video generation, long-/short-term future frame prediction, physical property estimation, and motion transfer. Experiments show that fine-tuning foundation models on PhysInOne significantly enhances physical plausibility, while also exposing critical gaps in modeling complex physical dynamics and estimating intrinsic properties. As the largest dataset of its kind, orders of magnitude beyond prior works, PhysInOne establishes a new benchmark for advancing physics-grounded world models in generation, simulation, and embodied AI.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.