Materials Science

Materials science data collection can be expensive, making the reuse and long-term utility of datasets critical important for future discovery campaigns. In practice, researchers prioritize a subset of properties due to research interests. However, ignoring a subset of outcomes in data collection campaigns potentially generate datasets poorly suited for future learning tasks. Here, we present a framework for dataset construction that maximizes informativeness for target properties of interest while preserving performance on untargeted ones. Our approach uses diversity-aware selection to ensure broad coverage of the materials space. In noisy experimental dataset construction, we find that without our diversity-aware framework, prediction performance on untargeted properties can degrade by up to 40% relative to random sampling, whereas applying our framework yields improvements of up to 10% . For targeted properties, performance can degrade with respect to random sampling by up to 12.5% without diversity, while our framework achieves gains of up to 25%. Incorporating diversity into dataset construction not only preserves informativeness for the targeted properties, but also improves materials coverage for potential future objectives. As a result, the constructed datasets remain broadly informative across considered and unconsidered outcomes, ensuring unbiased quality entries and mitigating cold-start limitations in subsequent modeling and discovery campaigns.

We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges posed by noise and artifacts that traditionally hinder this step. Our results demonstrate PhenixCraft's superior performance in TM-scores and sequence accuracy, significantly improving upon the limitations and inefficiencies of traditional model building using Phenix.

Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing databases that incorporate this data is a manual, time-consuming, and hard-to-scale process. Multimodal large language models have made it feasible to extract information from text and scientific figures with high speed and accuracy. This opens the possibility of an AI system that can create production-scale material databases. Material Database Agent (MDA) is a modular, multi-agent system architecture for converting research literature into structured databases. MDA accepts article PDFs as input, which are subsequently processed in parallel into markdown files and figures. Multiple sub-agents read these markdown files and figures in parallel to assemble sub-databases for each paper. These sub-databases are then compiled into a single tabular database by an agent. As opposed to using either a rule-based approach or a single-pass pipeline for extracting information, MDA is a specialized architecture for transforming the literature into a database in the field of materials science. More generally, this study provides a basis for positioning multimodal agentic information extraction as a viable means for constructing next-generation scientific databases from the primary literature.

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

We study the problem of denoising observations $Y_i=X_i+Z_i$, where the latent variables $X_i$ are sampled from a low-dimensional manifold in $\mathbb{R}^n$ and the noise variables $Z_i$ are isotropic Gaussian. We propose a convex-relaxation estimator that first reduces dimension by principal component analysis and then projects the observations onto the convex hull of the projected latent manifold. We construct a statistical oracle that estimates its supporting hyperplanes from empirical Gaussian tail probabilities of the noisy sample. Under a lower-mass condition on the latent distribution, we prove finite-sample guarantees for the oracle and derive error bounds for the resulting denoiser. The analysis combines risk bounds for least-squares projection under convex constraints with entropy bounds for convex hulls. We also verify the assumptions of the framework for a Cryo-Electron Microscopy observation model by establishing suitable covering number and Lipschitz estimates for the associated group action and imaging operators.

Autonomous science is transforming how we discover materials and chemical systems for advanced energy technologies. However, many initially promising systems never reach deployment. This "valley of death" stems from optimization that prioritizes laboratory metrics over industrial viability. We propose a new strategy: "born-qualified" autonomous development, which embeds manufacturability, cost, and durability constraints from the outset. This approach is enabled by four pillars, including the development of multi-objective metrics, causal models, a modular infrastructure, and embedding manufacturing in the discovery loop. Realizing this vision will require sustained, community-wide commitment, but the potential return on that investment is commensurate with the scale of the challenge.

The current structure-centric paradigm in artificial intelligence (AI)-driven materials discovery, despite delivering thousands of candidate structures, is stalling at a critical barrier: the synthesizability gap. We argue that closing this gap demands a pivot to a synthesis-first paradigm in which executable synthesis protocols, not just atomic configurations, are treated as primary design variables. We outline a roadmap built on three pillars: (i) representing synthesis procedures as machine-readable protocols, (ii) deploying generative and inverse-design models to propose actionable reaction pathways and recipes, and (iii) integrating closed-loop optimisation to refine protocols against experimental realities and sustainability constraints. Framed in terms of the causal backbone P->X->y from protocol P to structure X and properties y, this perspective sets out methodological building blocks, standards needs and self-driving laboratory (SDL) integration strategies to accelerate reproducible, data-first materials discovery.

Predicting stable and metastable structures is central to molecular and materials discovery, but remains limited by the cost of searching high-dimensional energy landscapes. Deep generative models offer efficient structure sampling, yet their outputs remain shaped by training data and can underexplore minima that are rare but physically relevant. We introduce generative structure search (GSS), a unified framework that formulates diffusion-based generation and random structure search (RSS) as limiting regimes of a common sampling process driven by learned score fields and physical forces. Coupling these drivers lets GSS use data priors to accelerate sampling while retaining energy-guided exploration of local minima. Across molecular and crystalline systems, GSS recovers diverse metastable structures with more than tenfold lower sampling cost than RSS for broad coverage and remains effective for compositions outside the training distribution. The results establish a physically grounded generative search strategy for discovering structures beyond the reach of data-driven sampling alone.

Amorphous (disordered) materials are solids that have shown great potential in various domains, including energy storage, thermal management, and advanced materials. Unlike crystalline materials that can be described by unit cells containing a few to hundreds of atoms, amorphous materials require larger simulation cells with at least hundreds to thousands of atoms. To advance the design of amorphous materials with desired properties and facilitate the exploration of their vast design space, generative inverse design has emerged as a promising approach. It aims to directly output materials with properties closely aligned with the desired ones using probabilistic generative models conditioned on desired properties, which can be more resource efficient than the traditional trial-and-error approach. However, due to the inherent stochasticity of probabilistic generative models, when element assignments are unconstrained, a large portion of generated materials may be charge unbalanced, and no existing methods can effectively mitigate this limitation. In this work, we propose AMGenC, a new generative inverse design method for amorphous materials that can guarantee the generation of charge balanced samples, with minimal additional computational overhead and without sacrificing inverse design accuracy. AMGenC achieves this through an element noise that gives the generation process a starting point centered around charge balance, and the combination of a per-step soft projection and a final discrete projection for steering the elements toward exact charge balance throughout the generation. We perform extensive experiments on two amorphous materials datasets. Experimental results provide evidence that AMGenC achieves its design goal.

We introduce QERNEL, a foundational neural wavefunction that variationally solves families of parameterized many-electron Hamiltonians and captures their ground states throughout parameter space within a single model. QERNEL combines FiLM-based parameter conditioning with scale-efficient architectural elements -- mixture of experts and grouped-query attention, substantially improving expressivity at low computational cost. We apply QERNEL to interacting electrons in semiconductor moiré heterobilayers, training a single weight-shared model for systems of up to 150 electrons. By solving the many-electron Schrödinger equation conditioned on moiré potential depth, QERNEL captures both quantum liquid and crystal states and discovers the sharp phase transition between them, marked by abrupt changes in interaction energy and charge density. Our work establishes a foundation model for moiré quantum materials and a scalable architecture toward a Large Electron Model for solids.

Autonomous neutron spectroscopy must solve three distinct tasks: detection (where is the signal?), inference (which Hamiltonian governs it?), and refinement (what are the parameters?). No single controller solves all three equally well. We present TAS-AI, a hybrid agnostic-to-physics-informed framework for autonomous triple-axis spin-wave spectroscopy that separates these tasks explicitly. In blind reconstruction benchmarks, model-agnostic methods such as random sampling, coarse grids, and Gaussian-process mappers reach a global error threshold more reliably and with fewer measurements than physics-informed planning, supporting the claim that discovery and inference are distinct tasks requiring distinct controllers. Once signal structure is localized, the physics-informed stage performs in-loop Hamiltonian discrimination and parameter refinement: in a controlled square-lattice test between nearest-neighbor-only and J1-J2 Hamiltonians, TAS-AI reaches a decisive AIC-derived evidence ratio (>100) in fewer than 10 measurements, while motion-aware scheduling cuts wall-clock time by 32% at a fixed measurement budget. We also identify a failure mode of posterior-weighted design, algorithmic myopia, in which the planner over-refines the current leading model while under-sampling low-intensity falsification probes. A constrained falsification channel sharply reduces time spent committed to the wrong model and accelerates correct model selection without modifying the Bayesian inference engine. In controlled two-model ablations, both a deterministic top-two max-disagreement rule and an LLM-based audit committee achieve this gain under identical constraints. We demonstrate the full workflow in silico using a high-fidelity digital twin and provide an open-source Python implementation.

High-entropy alloys (HEAs) have attracted growing attention for their exceptional mechanical and thermal properties arising from complex atomic configurations. In this paper, we propose crystal fractional graph neural network for predicting the energy of high-entropy alloys by explicitly integrating both local atomic environments and global compositional information. The model consists of three components: a crystal graph neural network, which employs graph attention network layers to learn local interactions among 16 on-site atoms within the crystal lattice; fractional neural network, a fully connected network that embeds the global fraction of constituent elements; and feature fusion neural network, which fuses the outputs of the two submodels to predict the total crystal energy. We train the model on a dataset of 1,049 crystal structures and validate it on 198 quaternary structures, optimizing all hyperparameters via Optuna. Our results show that our model achieves an RMSE comparable to first-principles calculations and maintains high accuracy even for low-energy configurations. However, the model exhibits limitations in handling large crystal cells, which we aim to address in future work to extend its applicability to more complex systems.

The promise of data-driven materials discovery remains constrained by the scarcity of large, high-quality, and accessible experimental datasets. Here, we introduce a generalizable large language model (LLM)-powered pipeline for automated extraction and structuring of materials data from unstructured scientific literature, using concrete materials as a representative and particularly challenging example. The pipeline exhibits robust performance across a broad range of LLMs and achieves an $F_1$ score of up to 0.98 for diverse composition--process--property attributes. Within one hour, it extracts nearly 9,000 high-quality records with over 100 attributes from a corpus screened from more than 27,000 publications, enabling the construction of the largest open laboratory database for blended cement concrete. Machine learning analyses underscore the importance of large, diverse, and information-rich datasets for enhancing both in-distribution accuracy and out-of-distribution generalization to unseen materials. The proposed pipeline is readily adaptable to other materials domains and accelerates the development of scalable data infrastructures for materials informatics.

In spite of the utility of 3-D electron back-scattered diffraction (EBSD) microscopy, the data collection process can be time-consuming with serial-sectioning. Hence, it is natural to look at other modalities, such as polarized light (PL) data, to accelerate EBSD data collection, supplemented with shared information. Complementarily, features in chaotic PL data could even be enriched with a handful of EBSD measurements. To inherently learn the complex dynamics between EBSD and PL to solve these inverse problems, we use an unconditional multimodal diffusion model, motivated by progress in diffusion models for inverse problems. Although trained solely on synthetic data once, our model has strong generalizable capabilities on real data which can be low-resolution, noisy, corrupted, and misregistered. With inference-time scaling, we show gains in performance on a variety of objectives including grain boundary prediction, super-resolution, and denoising. With our model, we demonstrate that there is little difference from full resolution performance with only 25% (1/4 the resolution) of EBSD data and corrupted PL data.

Simulations of crystal growth are performed by using Convolutional Recurrent Neural Network surrogate models, trained on a dataset of time sequences computed by numerical integration of Allen-Cahn dynamics including faceting via kinetic anisotropy. Two network architectures are developed to take into account the effects of a variable supersaturation value. The first infers it implicitly by processing an input mini-sequence of a few evolution frames and then returns a consistent continuation of the evolution. The second takes the supersaturation parameter as an explicit input along with a single initial frame and predicts the entire sequence. The two models are systematically tested to establish strengths and weaknesses, comparing the prediction performance for models trained on datasets of different size and, in the first architecture, different lengths of input mini-sequence. The analysis of point-wise and mean absolute errors shows how the explicit parameter conditioning guarantees the best results, reproducing with high-fidelity the ground-truth profiles. Comparable results are achievable by the mini-sequence approach only when using larger training datasets. The trained models show strong conditioning by the supersaturation parameter, consistently reproducing its overall impact on growth rates as well as its local effect on the faceted morphology. Moreover, they are perfectly scalable even on 256 times larger domains and can be successfully extended to more than 10 times longer sequences with limited error accumulation. The analysis highlights the potential and limits of these approaches in view of their general exploitation for crystal growth simulations.

Glassy silica is a foundational material in optics and electronics, yet accurately predicting its medium-range order (MRO) remains a major challenge for machine-learning interatomic potentials (MLIPs). While local MLIPs reproduce the short-range SiO4 tetrahedral network well, it remains unclear whether locality alone is sufficient to recover the first sharp diffraction peak (FSDP), the principal experimental signature of MRO. Here, we combine neutron and X-ray diffraction measurements with large-scale molecular dynamics driven by two MACE-based models: a short-range (SR) potential and a long-range (LR) extension incorporating reciprocal-space gated attention. The SR model systematically over-structures the network, producing an overly intense FSDP in both the liquid and glassy states. Incorporating long-range interactions improves agreement with experiment for the liquid structure by reducing this excess ordering, but the LR model still fails to recover the experimental amorphous MRO after quenching. Ring-statistics and bond-angle analyses reveal that SR model exhibits an artificially narrow distribution dominated by six-membered rings, while the LR model produces a broader but still biased ring population. Despite preserving the correct tetrahedral geometry, both models show limited variability in Si-O-Si angles, indicating constrained network flexibility. These structural signatures demonstrate that both models retain excessive memory of the parent liquid network, leading to kinetically trapped and nonphysical medium-range configurations during vitrification. These results show that explicit long-range interactions are necessary but not sufficient for predictive modelling of disordered silica and suggest that accurate MRO further requires training data and sampling strategies that adequately represent the liquid-to-glass transition.

Discovering materials that must simultaneously satisfy multiple competing constraints remains a central challenge in computational materials design, particularly in data-scarce regimes where conventional data-driven approaches are least effective. Magnetic insulators represent a stringent example: the electronic conditions that favor magnetic order often also promote metallicity, while insulating behavior suppresses the interactions that stabilize magnetism. As a result, experimentally viable magnetic insulators are rare and difficult to identify through conventional screening. Here, we introduce MagMatLLM, a constraint-guided generative discovery framework that integrates language-model-based crystal generation with evolutionary selection, surrogate screening, and first-principles validation to target simultaneous stability, magnetism, and insulating behavior. Unlike stability-first approaches, the framework enforces functional constraints during generation and selection, steering the search toward sparsely populated regions of materials space defined by competing physical requirements. Using this workflow, we identify twelve previously unreported candidate magnetic insulators, including Tm$_4$Co$_2$Cr$_2$O$_{12}$ and Cr$_4$Nb$_2$O$_{12}$. Of these, ten are dynamically stable by phonon analysis and exhibit finite band gaps and nonzero magnetic moments in spin-polarized density functional theory calculations. Beyond the specific compounds identified here, this work establishes a general constraint-guided paradigm for multi-objective materials discovery in sparse chemical spaces and provides a transferable strategy for the design of quantum materials under competing physical constraints.

The most technologically consequential materials are often the rarest: they occupy narrow regions of chemical space, obey competing physical constraints, and appear only sparsely in existing databases. High-kappa dielectrics, high-Tc superconductors, and ferromagnetic insulators are to name a few. This scarcity fundamentally limits today's data-driven materials discovery, where machine-learning models excel at interpolation but struggle to generate genuinely new candidates. Here, we introduce DielecMIND, an artificial intelligence framework that reframes materials discovery as a reasoning-driven exploration instead of a database-screening problem. Using high-kappa dielectrics as a data-scarce and technologically stringent test case, DielecMIND combines large-language-model hypothesis generation for the first time with physics validated first-principles calculation to navigate chemical space beyond known compounds. Prior to our work, only 14 experimentally or computationally validated materials with kappa > 150 were known. Our framework discovers and validates 5 new such compounds, expanding this rare-materials class by a remarkable = 35% in a single study. Among them, we find that Ba2TiHfO6 exhibits a dielectric constant of 637, minimal loss at low optical frequencies, and stability up to 800 K. Beyond dielectrics, this work demonstrates a new paradigm for artificial-intelligence-guided discovery: one that generates a small number of physically grounded, experimentally plausible candidates yet measurably expands sparsely populated functional materials spaces. Thus, DielecMIND points toward a general strategy for discovering rare, high-impact functional materials where data scarcity has long constrained progress.

Metal-organic frameworks (MOFs) are a major target of machine-learning-based property prediction, yet most models assume that a single framework representation maps to a single property value. This assumption becomes problematic for experimental MOFs, where samples reported as the same framework can exhibit different properties because of differences in crystallinity, phase purity, defects, and other sample-dependent factors. Here we introduce Experimental X-ray Diffraction Integrated Transformer (EXIT), a multimodal transformer for sample-aware prediction of MOF properties that combines MOFid with X-ray diffraction (XRD). In EXIT, MOFid encodes MOF identity, whereas XRD provides complementary information about the experimentally realized sample state. EXIT is pre-trained on one million hypothetical MOFs with simulated XRD to learn transferable representations, leading to improved downstream performance relative to existing approaches. EXIT is fine-tuned on literature-derived experimental datasets for surface area and pore volume prediction. Incorporating experimental XRD improves predictive performance relative to models without experimental XRD, and attention analysis and sample-level case studies further show that EXIT assigns different predictions to samples sharing the same MOF identity when their XRD patterns differ. These results establish a practical step from framework-aware to sample-aware MOF property prediction and highlight the value of incorporating experimental characterization into porous materials informatics.

A major challenge for niche scientific and technical domains in leveraging coding agents is the lack of access to up-to-date, domain- specific knowledge. Foundational models often demonstrate limited reasoning capabilities in specialized fields and cannot inherently incorporate knowledge that evolves through ongoing research and experimentation. Materials scientists exploring novel compounds, communication engineers designing and evaluating new protocols, and bioengineering researchers conducting iterative experiments all face this limitation. These experts typically lack the resources to fine-tune large models or continuously embed new findings, creating a barrier to adopting AI-driven coding agents. To address this, we introduce a framework that gives coding agents instanta- neous access to research repositories and technical documentation, enabling real-time, context-aware operation. Our open-source im- plementation allows users to upload documents via doc-search.dev and includes zed-fork, which enforces domain-specific rules and workflows. Together, these tools accelerate the integration of coding agents into specialized scientific and technical workflows

Cryo-electron microscopy (cryo-EM) enables single-particle analysis of biological macromolecules under strict low-dose imaging conditions, but the resulting micrographs often exhibit extremely low signal-to-noise ratios and weak particle visibility. Image denoising is therefore an important preprocessing step for downstream cryo-EM analysis, including particle picking, 2D classification, and 3D reconstruction. Existing cryo-EM denoising methods are commonly trained with pixel-wise or Noise2Noise-style objectives, which can improve visual quality but do not explicitly account for structural consistency required by downstream analysis. In this work, we propose a score-based denoising framework for cryo-EM that learns the clean-data score to recover particle signals while better preserving structural information. Building on this formulation, we further introduce a target-guided variant that incorporates reference-density guidance to stabilize score learning under weak and ambiguous signal conditions. Rather than simply amplifying particle-like responses, our framework better suppresses structured low-frequency background, which improves particle--background separability for downstream analysis. Experiments on multiple cryo-EM datasets show that our score-based methods consistently improve downstream particle picking and produce more structure-consistent 3D reconstructions. Experiments on multiple cryo-EM datasets show that our methods improve downstream particle picking and produce more structure-consistent reconstructions.

This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron microscopy (cryo-EM). In the first part, we present ViDa, a biophysics-informed framework leveraging variational autoencoders (VAEs) and geometric scattering transforms to generate biophysically-plausible embeddings of DNA reaction kinetics simulations. These embeddings are reduced to a two-dimensional space to visualize DNA hybridization and toehold-mediated strand displacement reactions. ViDa preserves structure and clusters trajectory ensembles into reaction pathways, making simulation results more interpretable and revealing new mechanistic insights. In the second part, we address key challenges in cryo-EM density map interpretation and protein structure modeling. We provide a comprehensive review and benchmarking of deep learning methods for atomic model building, with improved evaluation metrics and practical guidance. We then present Struc2mapGAN, a generative adversarial network that synthesizes high-fidelity experimental-like cryo-EM density maps from protein structures. Finally, we present CryoSAMU, a structure-aware multimodal U-Net that enhances intermediate-resolution cryo-EM maps by integrating density features with structural embeddings from protein language models via cross-attention. Overall, these contributions demonstrate the potential of deep generative models to interpret DNA reaction mechanisms and advance cryo-EM density map analysis and protein structure modeling.

Generative diffusion models have emerged as powerful tools for the discovery of inorganic crystal structures, yet steering their sampling process toward user-defined physical and chemical objectives remains challenging. We present a computational framework that integrates adaptive constraint guidance into a pre-trained crystal diffusion model, enabling the generation of candidate structures that satisfy targeted structural and chemical requirements without model retraining. The approach incorporates differentiable constraint functions directly during sampling, providing an interpretable mechanism for expert-driven exploration of the crystal structure space. To assess the reliability of generated candidates, we introduce a multi-stage validation workflow combining descriptor-based analysis, duplicate removal, comparison with reference crystal databases, graph neural network energy prediction, and thermodynamic stability evaluation through convex-hull analysis. The framework is applied to several classes of inorganic compounds and to constraints involving atomic volume, local coordination environments, and near-neighbor structural motifs. Results demonstrate that adaptive guidance effectively redirects the sampling distribution toward structures exhibiting the desired characteristics while preserving chemical plausibility. Subsequent validation reveals which generated candidates remain viable after energetic and thermodynamic screening. The proposed methodology provides a practical and transparent strategy for incorporating expert knowledge into crystal generative models and establishes a general computational framework for constrained materials discovery.

Generative models for crystalline materials often rely on equivariant graph neural networks, which capture geometric structure well but are costly to train and slow to sample. We present Crystalite, a lightweight diffusion Transformer for crystal modeling built around two simple inductive biases. The first is Subatomic Tokenization, a compact chemically structured atom representation that replaces high-dimensional one-hot encodings and is better suited to continuous diffusion. The second is the Geometry Enhancement Module (GEM), which injects periodic minimum-image pair geometry directly into attention through additive geometric biases. Together, these components preserve the simplicity and efficiency of a standard Transformer while making it better matched to the structure of crystalline materials. Crystalite achieves state-of-the-art results on crystal structure prediction benchmarks, and de novo generation performance, attaining the best S.U.N. discovery score among the evaluated baselines while sampling substantially faster than geometry-heavy alternatives.

Autonomous experimental systems are increasingly used in materials research to accelerate scientific discovery, but their performance is often limited by low-quality, noisy data. This issue is especially problematic in data-intensive structure-property learning tasks such as Image-to-Spectrum (Im2Spec) and Spectrum-to-Image (Spec2Im) translations, where standard active learning strategies can mistakenly prioritize poor-quality measurements. We introduce a gated active learning framework that combines curiosity-driven sampling with a physics-informed quality control filter based on the Simple Harmonic Oscillator model fits, allowing the system to automatically exclude low-fidelity data during acquisition. Evaluations on a pre-acquired dataset of band-excitation piezoresponse spectroscopy (BEPS) data from PbTiO3 thin films with spatially localized noise show that the proposed method outperforms random sampling, standard active learning, and multitask learning strategies. The gated approach enhances both Im2Spec and Spec2Im by handling noise during training and acquisition, leading to more reliable forward and inverse predictions. In contrast, standard active learners often misinterpret noise as uncertainty and end up acquiring bad samples that hurt performance. Given its promising applicability, we further deployed the framework in real-time experiments on BiFeO3 thin films, demonstrating its effectiveness in real autonomous microscopy experiments. Overall, this work supports a shift toward hybrid autonomy in self-driving labs, where physics-informed quality assessment and active decision-making work hand-in-hand for more reliable discovery.

Volume denoising is a foundational problem in computational imaging, as many 3D imaging inverse problems face high levels of measurement noise. Inspired by the strong 2D image denoising properties of Field of Junctions (ICCV 2021), we propose a novel, fully volumetric 3D Field of Junctions (3D FoJ) representation that optimizes a junction of 3D wedges that best explain each 3D patch of a full volume, while encouraging consistency between overlapping patches. In addition to direct volume denoising, we leverage our 3D FoJ representation as a structural prior that: (i) requires no training data, and thus precludes the risk of hallucination, (ii) preserves and enhances sharp edge and corner structures in 3D, even under low signal to noise ratio (SNR), and (iii) can be used as a drop-in denoising representation via projected or proximal gradient descent for any volumetric inverse problem with low SNR. We demonstrate successful volume reconstruction and denoising with 3D FoJ across three diverse 3D imaging tasks with low-SNR measurements: low-dose X-ray computed tomography (CT), cryogenic electron tomography (cryo-ET), and denoising point clouds such as those from lidar in adverse weather. Across these challenging low-SNR volumetric imaging problems, 3D FoJ outperforms the evaluated classical denoisers, untrained neural denoisers, and denoisers trained only on noisy examples. Code is available at https://github.com/voilalab/3D-Field-of-Junctions.

The discovery of catalysts for electrochemical applications such as the oxygen reduction reaction (ORR), nitrogen reduction reaction (NRR), and CO2 reduction reaction (CO2RR) remains a central challenge in chemistry and materials science. Machine-learning interatomic potentials (MLIPs) and graph neural network models now accelerate individual adsorption-energy calculations by orders of magnitude relative to density functional theory. However, true large-scale screening is still blocked by human decisions: selecting candidates, constructing slabs, enumerating adsorption sites, interpreting descriptor failures, and choosing follow-up modifications. Here, we introduce Catalyst-Agent, a Model Context Protocol (MCP) server-based, LLM-powered agent that autonomously coordinates closed-loop catalyst screening. Catalyst-Agent searches materials databases through OPTIMADE, constructs slabs, computes adsorption energies using Meta FAIRchem's UMA MLIP within AdsorbML, evaluates reaction-specific descriptors, and applies structural modifications to refine near-miss candidates. In ORR, NRR, and CO2RR campaigns, Catalyst-Agent demonstrates high performance and converges in 1.40-3.41 trials per successful material on average. It identified Sn3Sc, Sn3Y, Tl3La, Pb3Y and In3Y as CO2RR candidates for further validation that were not previously reported in the literature. DFT single-point checks confirmed screening outcomes for representative NRR and CO2RR candidates. Ablations show these gains arise from chemically informed candidate selection and feedback-directed modification rather than brute-force evaluation: fully randomized screening dropped to 13.3%, 16.7%, and 0% success for ORR, NRR, and CO2RR, respectively. These results show that tool-grounded LLM agents can shift catalyst screening from manual trial-and-error toward more autonomous, reproducible and adaptive workflows.

Crystal structure prediction (CSP), which aims to predict the 3D atomic arrangement of a crystal from its composition, is central to materials discovery and mechanistic understanding. Crystal symmetry plays a crucial role in CSP, but given the composition in a unit cell, existing methods either struggle with the NP-hard combinatorial challenge of enforcing symmetry rigorously or rely on retrieving known templates, inherently limiting both physical fidelity and the discovery of genuinely new materials. To address this challenge, we introduce NextCrystal, a symmetry-driven generative framework that employs large language models to encode chemical semantics and directly generate fine-grained Wyckoff site patterns from atomic stoichiometry, eliminating reliance on database lookups. To overcome the combinatorial complexity of site assignments, we incorporate domain knowledge via an efficient, linear-complexity heuristic beam search, rigorously enforcing algebraic consistency between site multiplicities and atomic stoichiometry. By integrating this symmetry-consistent template into a diffusion backbone, the framework constrains the stochastic generative trajectory to a physically plausible geometric manifold. NextCrystal achieves state-of-the-art performance on stability, uniqueness, and novelty (SUN) benchmarks, as well as superior structural matching, establishing a rigorous paradigm for exploring previously unexplored crystallographic space without relying on prior structural templates. As a representative application, first-principles screening of HfO2 candidates generated by NextCrystal identifies a previously unreported dynamically stable Pnma phase, 0.056~eV/atom lower in energy than the conventional high-pressure Pnma phase.

As a pioneer of the third-generation photovoltaic revolution, Perovskite Solar Cells (PSCs) are renowned for their superior optoelectronic performance and cost potential. The development process of PSCs is precise and complex, involving a series of closed-loop workflows such as literature retrieval, data integration, experimental design, and synthesis. However, existing AI perovskite approaches focus predominantly on discrete models, including material design, process optimization,and property prediction. These models fail to propagate physical constraints across the workflow, hindering end-to-end optimization. In this paper, we propose a multi-agent system for perovskite material discovery, named PeroMAS. We first encapsulated a series of perovskite-specific tools into Model Context Protocols (MCPs). By planning and invoking these tools, PeroMAS can design perovskite materials under multi-objective constraints, covering the entire process from literature retrieval and data extraction to property prediction and mechanism analysis. Furthermore, we construct an evaluation benchmark by perovskite human experts to assess this multi-agent system. Results demonstrate that, compared to single Large Language Model (LLM) or traditional search strategies, our system significantly enhances discovery efficiency. It successfully identified candidate materials satisfying multi-objective constraints. Notably, we verify PeroMAS's effectiveness in the physical world through real synthesis experiments.

Agentic AI systems increasingly connect large language models (LLMs) to external scientific tools, yet whether and when tool access improves prediction accuracy remains uncharacterized. We present AGAPI (AtomGPT.org API), an open access platform integrating eight open-source LLMs with 18 REST endpoints (28 agent tools, 50 web apps) spanning materials databases, force fields, tight-binding band structures, X-ray diffraction, and protein structure. A three-evaluation residual decomposition on JARVIS-Leaderboard electronic-structure test sets separates agent pipeline fidelity from inherited density functional theory (DFT) functional bias. For bulk modulus and bandgap the agent reproduces JARVIS-DFT entries to numerical precision, so the experimental-reference degradation is functional bias, not agentic malfunction. On memorization-resistant test sets (57 defective supercells, 60 hypothetical compositions), tool-augmented mean absolute error (MAE) is below 0.005 eV versus 1.25 to 1.86 eV tool-free, confirming tools are indispensable where parametric knowledge is unavailable. We further demonstrate autonomous multi-step workflows including 10-operation defect-engineering pipelines. AGAPI is available at https://github.com/atomgptlab/agapi.

Predicting which hypothetical inorganic crystals can be experimentally realized remains a central challenge in accelerating materials discovery. SyntheFormer is a positive-unlabeled framework that learns synthesizability directly from crystal structure, combining Fourier-transformed crystal properties (FTCP) representation with structure-aware feature extraction, Random-Forest feature selection, and a compact deep MLP classifier. The model is trained on historical data from 2011 through 2018 and evaluated prospectively on future years from 2019 to 2025, where the positive class constitutes only 1.02 percent of samples. Under this temporally separated evaluation, SyntheFormer achieves a test AUC of 0.735, AUPRC of 0.099 and 97.6 percent recall at 94.2 percent coverage with dual-threshold calibration. Direct prospective validation supports this result as two materials that were unlabeled at the time of data curation, Y6Fe(SiS7)2 and BaYb2F8, were assigned high SyntheFormer scores (0.961 and 0.753, respectively) and were subsequently reported experimentally. Crucially, the model recovers experimentally confirmed metastable compounds that lie far from the convex hull and simultaneously assigns low scores to many thermodynamically stable yet unsynthesized candidates, demonstrating that stability alone is insufficient to predict experimental attainability.

A key question in benchmarking generative crystal reconstruction models is how the amount and type of crystallographic information provided to a generative model affects its ability to reconstruct atomic structures. Yet such comparisons often overlook the fact that models receive unequal information about the target during reconstruction, thereby confounding architectural conclusions. We present AtomBench, an extensible, model-agnostic framework for comparing generative models on a well-defined crystal reconstruction task (rather than \textit{de novo} generation), which we here apply to conventional superconductors. We train and evaluate four models, AtomGPT, CDVAE, FlowMM, and MatterGen, on the JARVIS Supercon-3D and Alexandria DS-A/B datasets, grouping them by the information each accesses at inference. Reconstruction fidelity is measured by the Kullback-Leibler divergence (KLD) and mean absolute error (MAE) of lattice parameters and the root-mean-squared displacement (RMSD) of atomic coordinates. We further introduce the continuous corrected RMSD (ccRMSD), a continuous measure of local geometric fidelity defined for every structure in the test set. MatterGen achieves the best atomic-coordinate reconstruction, followed by AtomGPT, while CDVAE reconstructs lattices most accurately, and FlowMM is the least accurate but fastest overall. We find that conditioning on critical temperature T$_c$ does not consistently improve fidelity. We also release AtomBench as an open-source Python package that reproduces all reported reconstruction metrics, figures, and tables from one or more benchmark files and supports direct submission to the JARVIS-Leaderboard. Any inverse model emitting crystal reconstructions can be benchmarked with \texttt{atombench}, and we encourage community use. https://github.com/atomgptlab/atombench

Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics. However, CSP remains challenging and computationally intensive due to the need to explore a large search space with sub-kJ/mol accuracy to distinguish between competing polymorphs. While dispersion-inclusive density functional theory (DFT) offers the necessary precision, its computational cost is impractical for a large number of putative structures. Here, we present FastCSP, an open-source, end-to-end CSP workflow driven entirely by a single pretrained universal machine learning interatomic potential (MLIP), the Universal Model for Atoms (UMA), without any system-specific fine-tuning or DFT calculations. FastCSP integrates conformer generation, random structure generation via Genarris 3, geometry optimization, free energy evaluation, and conformer energy corrections, all powered by UMA. Benchmarked on 28 semi-rigid and 10 flexible molecules spanning 74 experimental polymorphs, FastCSP reliably recovers all known structures, ranking them within 9 kJ/mol of the global minimum. UMA reproduces dispersion-inclusive DFT results with high fidelity across chemically diverse compounds. Conformer corrections are particularly beneficial for flexible compounds with conformational polymorphism, such as ROY. UMA's accuracy, transferability, and computational cost thus eliminate the need for classical force fields in early-stage screening and DFT-based re-ranking in CSP workflows. The open-source release of the entire FastCSP workflow lowers the barrier to accessing CSP, enabling both pharmaceutical-grade and high-throughput polymorph screening within practical computational reach.

Novelty search (NS) aims to uncover diverse system behaviors through simulation or experiment without requiring a pre-specified scalar objective. This capability is especially relevant to modern discovery problems in chemistry, materials science, and molecular design, where researchers often seek broad coverage of attainable property space rather than a single optimum and where each evaluation may require a costly computation or experiment. For such expensive black-box settings, we propose BEACON, a sample-efficient NS strategy inspired by Bayesian optimization principles. BEACON models the input-to-outcome mapping using multi-output Gaussian processes and selects new inputs by scoring how far plausible posterior outcomes lie from a denoised archive of previously observed outcomes. This gives a distance-based novelty acquisition that accounts for predictive uncertainty and observational noise while operating directly in continuous outcome space, rather than requiring direct optimization over a discretized partition of behaviors. By leveraging efficient posterior sampling together with scalable high-dimensional Gaussian process models, the proposed framework can be extended to settings with large data sets and high-dimensional design variables. We demonstrate BEACON on established benchmark problems together with real-world case studies in materials and molecular discovery. Across these settings, BEACON consistently discovers broader sets of distinct behaviors than several competing baselines under limited evaluation budgets.

This study investigates how automated and interoperable research infrastructures can accelerate experimental materials research, using battery formation as a case study. We introduce a methodological framework that integrates the FINALES and Kadi Research Data Management ecosystems, enabling coordinated experiment execution, data management, and analysis across distributed research infrastructures. The FINALES framework orchestrates experiment planning and execution on the POLiS Materials Acceleration Platform, while Kadi handles data management, visualization, experiment selection, and persistent storage. This interoperability enables reproducible, coordinated, end-to-end experimental workflows that connect automated systems and human-operated processes across multiple research sites. To showcase the framework's capabilities, we investigate the formation process of sodium-ion coin cells, a critical step that influences cell lifetime. Using a dataset generated through the proposed infrastructure, we analyze the relationships between formation parameters and electrochemical performance. A Gaussian process model is employed to identify regions associated with favorable performance within the investigated parameter domain while quantifying predictive uncertainty, highlighting where additional experimental evidence would be most informative. The presented workflow demonstrates that interoperable, automated infrastructures can support experimental campaigns, enhance data consistency and traceability, and support reproducible, data-driven analysis. While demonstrated through a battery application, the framework provides a general methodology for integrating distributed experimental platforms with RDM systems, transferable across materials science and engineering domains.