Materials Science

Accurate generation of crystal structures is the foundation to the discovery of high-performance materials for extreme-environment applications, such as aerospace, additive manufacturing, and fusion energy systems. Although generative modeling has emerged as a promising approach for crystal design, its performance remains limited by the complex crystal structures and diverse chemical compositions. In this work, we develop UFO-MGen, a universal flow-based generative model that learns topological features of Wyckoff representations and leverages this information to accurately generate crystals across vast structural and chemical spaces. Compared with state-of-the-art generative models, UFO-MGen achieves the highest crystal generation success rate under a rigorous multi-stability evaluation framework, the highest SUN (stable, unique, novel) rate, and a remarkable extrapolation capability that has not been reported by previous models. Furthermore, a fine-tuning module is implemented to UFO-MGen for property-constrained crystal generation, enabling the inverse materials design toward target properties. The UFO-MGen opens a new avenue for accelerated materials discovery and providing a foundation for universal materials intelligence.

The discovery of novel inorganic materials drives technological breakthroughs in critical fields such as computing and energy storage. Generative AI has promised to accelerate the materials discovery pipeline, but state-of-the-art flow and diffusion models remain bottlenecked by the cost of proposing candidate materials. To address this, we introduce OMatG-flash, an all-atom flow map for inorganic crystal structure prediction (CSP) and de novo generation (DNG). OMatG-flash is a Pareto-optimal inference engine for materials, sampling candidate materials with an order of magnitude fewer inference steps and less wall-clock time than existing flow and diffusion models while demonstrating benchmark performance on par with the state-of-the-art. To enable post-training fine-tuning we apply Reinforce Adjoint Matching to flow maps, further improving match rates and RMSE on the unconditional CSP task. OMatG-flash showcases the potential of flow maps to accelerate generation of high-quality candidate inorganic materials and demonstrates a step forward in sample throughput necessary for data-hungry materials discovery workflows.

Crystal structure refinement is a fundamental inverse problem in materials characterization, where structural parameters are optimized to reproduce experimental diffraction data. Conventional approaches, such as least-squares and likelihood-based optimization, rely on local search and often struggle with non-convex, noisy, and highly correlated parameter landscapes, particularly when integrating multiple diffraction modalities. Joint refinement of X-ray and neutron data is especially challenging due to their complementary but competing sensitivities, which are typically combined through scalarized objectives requiring manual weighting and leading to suboptimal solutions. We propose CrystalMO-TuRBO, a multi-objective trust region Bayesian optimization architecture for joint crystal structure refinement. The method models X-ray and neutron discrepancies as separate objectives and transforms the problem into a normalized maximization setting. A two-phase optimization strategy is introduced: Phase 1 performs global exploration using parallel trust-region Bayesian optimization across multiple scalarizations to identify promising regions of the parameter space, while Phase 2 conducts localized refinement within a shrinking region to achieve high-precision solutions. This design explicitly separates global search from fine-grained optimization, addressing the unique accuracy requirements of refinement tasks. We evaluate the proposed method on experimentally collected X-ray and neutron diffraction data from single-crystal Ho2Ti2O7. Results demonstrate improved convergence, robustness, and parameter precision compared to classical refinement methods and Bayesian optimization baselines on refinement of a single-crystal pyrochlore material system.

Reliable prediction of crystallographic texture in laser powder bed fusion is critical for linking process conditions with anisotropic response and for qualification. However, black-box models may fail under shift and cannot distinguish weak data support from loss of physical validity. This study develops a two-stage physics-based model for <001> || BD (build direction) texture in Inconel 718. Stage 1 maps process variables to melting mode and melt pool geometry. Stage 2 predicts texture by combining an empirical physics model with a random-forest residual model. A k-nearest-neighbor weight attenuates residual corrections for poorly supported queries, while a study-specific areal beam-power-density criterion withholds predictions outside the adopted conduction envelope. Conformal intervals are evaluated on the retained physics-valid set, and SHAP and Sobol analyses assess residual sensitivity. Under a controlled leave-one-defocus-out evaluation, the physics anchor achieved R^2 = 0.778, against -0.001 for the black-box model and 0.750 for the gated hybrid. Under leave-one-group-out cross-validation, the gated hybrid reached R^2 = 0.592 against 0.538 for the black-box model. Retained-set coverage was 92.9% at a mean full width of 3.65 multiples of a uniform distribution (MUD) under grouped cross-validation and 100% at a width of 3.21 MUD under transfer to a withheld +80 mm defocus regime. An illustrative mapping produced a retained BD elastic-modulus span of 127-187 GPa. On nine conditions from a separately built sample set, the framework withheld three, attenuated three, and matched the measured ordering for the rest. Separating data applicability, physics validity, and predictive uncertainty into distinct decisions lets the framework transfer where an unconstrained model does not, and withhold predictions where no model class performs adequately.

Self-driving laboratories can explore synthesis conditions autonomously, but their decision-making layer is typically a black-box optimizer, and the output is a set of optimized samples, with the measurements reduced to predefined scalar objectives and the reasons behind success left unarticulated. Here we present SynAgent, a framework in which large language model agents operate an automated experimental system and maintain an explicit, revisable understanding of the synthesis process as the campaign's primary output. Starting with no predefined analysis pipeline, SynAgent adaptively generates analysis skills for newly acquired data and evolves this understanding through multimodal reasoning over experimental data such as X-ray diffraction patterns and electron micrographs. The evolution is guided by a verify-falsify scheme, in which the agent deliberately challenges its own hypotheses by testing conditions predicted to fail as well as those predicted to succeed. In a single campaign of 18 autonomous experiments using LiCoO2 (001) thin-film deposition as a testbed, SynAgent synthesized highly crystalline films and evolved an understanding of how the substrate temperature governs crystallization, discovering an abrupt threshold and a narrow optimal growth window at 650-690 °C. These results extend autonomous experimentation beyond optimized samples to testable, human-readable understanding.

This thesis develops robust and efficient AI frameworks for accelerating crystalline materials discovery by addressing both major stages of the materials-design pipeline: crystal property prediction and crystal structure generation. Motivated by the high computational cost of Density Functional Theory (DFT) and the limited availability of labeled materials data, the thesis explores graph representation learning, pretraining, multimodal learning, and generative modeling for scalable materials design. For property prediction, the thesis first introduces CrysXPP, which learns transferable crystal representations through unsupervised graph autoencoding, reducing dependence on large property-labeled datasets. It then proposes CrysGNN, a large-scale self-supervised graph pretraining framework that captures atomic connectivity, chemical attributes, and global structural information and transfers this knowledge to downstream property predictors through knowledge distillation. CrysMMNet further enriches crystal representations by jointly modeling graph structure and textual descriptions, thereby incorporating both local chemical and global structural knowledge. For crystal generation, the thesis introduces TGDMat, a text-guided joint diffusion framework that jointly models lattice parameters, atomic types, and atomic coordinates while incorporating textual structural knowledge during denoising. This enables the generation of more valid and stable periodic materials while also supporting conditional generation from natural-language descriptions. Overall, the thesis establishes a unified AI-based framework for data-efficient property prediction and controllable crystal generation, demonstrating how graph learning, multimodal representations, and generative models can reduce computational cost and improve the scalability of materials

Understanding and inferring dislocation microstructures from diffraction patterns remains an open challenge in materials characterization, as diffraction measurements provide only indirect information about the underlying dislocation structure. In this work, a cross-modal learning framework is developed to enable the prediction of 3D dislocation structures directly from diffraction data. Dislocation density fields generated from discrete dislocation dynamics simulations are paired with corresponding virtual X-ray diffraction patterns and embedded into a shared 2D latent space using contrastive learning. The alignment between structural and diffraction representations of dislocation structures is evaluated directly in the learned latent space using correlations between corresponding latent features. To estimate the role of dataset size for this approach, farthest point sampling is employed to construct representative and diverse training subsets of varying sizes. The results show strong cross-modal alignment and that model performance improves rapidly with increasing dataset size. Near-saturation is achieved with approximately 500 representative observations from a dataset of 10,000 observations, enabling accurate prediction of dislocation density fields from previously unseen diffraction data of the same distribution. Qualitative comparisons confirm that the predicted structures capture the dominant spatial features of the underlying dislocation microstructures. These findings demonstrate an efficient approach for learning structure-diffraction relationships and highlight the potential for inferring structural characteristics of dislocation networks directly from diffraction patterns, providing a pathway toward diffraction-based structural analysis and future extension to experimental data.

Vision-language and language models increasingly interpret materials data, yet benchmarks report that they hallucinate invalid properties and violate physical law. Evaluation matches final answers to scarce human labels, while discovery agents verify final proposals or density functional theory (DFT) execution. Neither measures the physical consistency of a model's reasoning chain. Materials data carries its own physics, making a large class of materials reasoning verifiable without annotation. We introduce MatPCR, a label-free benchmark whose programmatic oracles check diffraction geometry through Bragg's law, scale bars, spectral peaks, and Materials Project-grounded checks of near-hull stability, computed band-gap class, and net magnetization. We define the Physical-Consistency Rate over image and structure inputs; introduce Constraint-Grounded Self-Verification, an agentic loop whose gain survives self-refinement and equal-compute re-prompting controls; release an open verifier useful in distribution but near chance on all six held-out constraint types; and derive an exact identity for how oracle error displaces the reported rate.

Atomic layer deposition (ALD) and atomic layer etching (ALE) are reported heterogeneously across experimental and simulation literature in materials science, hindering comparison and machine-actionable reuse. We present four domain-expert-reviewed JSON Schemas for ALD and ALE experimental and simulation processes. Curated with schema-miner and grounded in QUDT using schema-miner pro, the schemas structure materials, process conditions, configurations , and measured or predicted results. We compare their scope, structure, and semantic grounding, and demonstrate their use for schema-guided literature extraction and publication of structured records through ORKG templates.

Characterizing two-dimensional (2D) quantum materials by optical microscopy requires localizing exfoliated flakes and determining their layer thickness from subtle optical contrast and interference color to select suitable flakes for device fabrication. However, models face synthetic-to-real domain shifts and variation across materials, substrates, laboratories, and imaging conditions. We present QuPAINT, a physics-aware multimodal framework for transferable quantum flake characterization. The Synthetic Materials Framework (Synthia) generates diverse synthetic microscopy images while preserving layer-dependent optical behavior. Using these images, we construct QMat-Instruct, a multimodal instruction dataset with image-specific reasoning traces generated from verified annotations and constrained to observable optical cues. QuPAINT integrates these signals through Physics-Informed Attention (PIA), which injects substrate-relative optical priors into the visual representation to support grounded multimodal reasoning. For evaluation, we introduce QF-Bench, to our knowledge, the largest real-world benchmark for this problem, spanning diverse microscopy and substrate conditions. Using its verified annotations, we study counting, visual grounding, reasoning quality, confidence calibration, and transfer to an unseen material. QuPAINT-8B substantially outperforms prior methods and establishes state-of-the-art performance for both general and monolayer flake detection. Additional experiments show that image-grounded supervision improves strict spatial grounding and confidence calibration while preserving robust general flake detection on the unseen material.

Crystal-orientation maps are physical fields defined only up to crystal symmetry; electron backscatter diffraction (EBSD) resolves them experimentally, but acquisition-time constraints limit spatial resolution. Unlike conventional images, EBSD data lie on the quotient space $\mathrm{SO}(3)/G$, where $G$ is the crystal-symmetry group. Standard Euclidean interpolation can therefore mix symmetry-equivalent representations and blur grain boundaries. We introduce the Symmetry-Group-Aware Super-Resolution Attention Network (SG-SRAN), which incorporates crystal symmetry and boundary preservation by design. A frozen, locally isometric encoder maps equivalent orientations to a common latent representation in which Euclidean distance approximates misorientation. Super-resolution is performed in this space, with each high-resolution token restricted to a feature-consistent local support to prevent cross-boundary mixing. A dictionary-based decoder then recovers valid orientations. Across FCC and HCP benchmarks, SG-SRAN matches 15-16 million parameter backbones using only 27-49k trainable parameters, while achieving the lowest p68 errors, highest inverse-pole-figure fidelity, and zero-shot transfer to unseen alloys.

Crystal structure prediction (CSP) is fundamental to computational materials discovery. Generative models including CDVAE, DiffCSP, FlowMM, and CrystalFlow learn stable-crystal distributions directly, but diffusion and flow-matching inference requires tens to thousands of sequential network evaluations per candidate. We introduce uFlowCSP, a MeanFlow-based CSP model that learns the average, rather than instantaneous, probability-flow velocity. It generates a complete structure in one to five evaluations, delivering 5x-58x faster inference with equal or better performance. A chemistry- and symmetry-aware Transformer uses canonical atom ordering, global composition, and per-token chemistry embeddings. A coarse crystal-system token is used only during training; it provides additive gains, particularly improving space-group agreement despite being absent at inference, which remains formula-only. On MP-20 with 20 candidates per target, one step matches CrystalFlow (78.38% vs. 78.34%) with 100x fewer evaluations and about 10x lower wall-clock time. Five steps reach 83.64%, exceeding CrystalFlow (78.34% at 2,000 evaluations) and DiffCSP (77.93% at about 20,000), while using 20x fewer evaluations. uFlowCSP generates 10,000 structures in 0.39-1.31 minutes, versus 6.5 for CrystalFlow and 76.1 for DiffCSP. Under CSPBench's energy-ranked top-five structure-and-space-group criterion, five-step uFlowCSP reaches 72%/72%/65% structure, space-group, and consensus match rates. CrystalFlow reaches 78%/73%/68% at 100 steps but falls to 49%/32%/31% at five. Thus, uFlowCSP improves accuracy per network evaluation, not merely peak accuracy.

Automating filament tracing in Cryo-Electron Microscopy (Cryo-EM) is essential for 3D helical reconstruction but challenged by intersecting topologies and extremely low Signal-to-Noise Ratios ($\text{SNR} = σ_s^2/σ_n^2$ < 0.1 or -10 dB). Existing paradigms fail: pixel-wise segmenters suffer from severe topological fracturing, box-based detectors face ghost center drift, sequential trackers derail due to error accumulation, and traditional active contours collapse under artificial closed-curve constraints. To resolve these bottlenecks, we present FPicker, the first topology-guided framework reconciling these incompatibilities. It unifies perception via a center-endpoint representation and an open-curve evolution module to explicitly model non-cyclic connectivity. On simulated benchmarks, FPicker outperforms top baselines by over $40\%$ relative gain in mean spatio-angular precision (mSAP) and reduces topological gap rates by over $60\%$ under extreme noise ($-20\text{ dB}$). By learning intrinsic physical geometry rather than local texture, FPicker demonstrates strong potential as a resilient geometric backbone. Its zero-shot performance on the real-world EMPIAR dataset exhibits robust topological resistance, achieving a state-of-the-art 82.9% mSAP upon fine-tuning. Our results also suggest modeling physical priors is a highly robust path toward bridging the sim-to-real gap in signal-starved scientific imaging. The code is publicly available at: https://github.com/tomzhaosky/FPicker.

Crystal generators and tool-using agents propose structures faster than density functional theory (DFT) energy and phonon calculations or experiments can assess them. Deciding which candidates merit expensive assessment is therefore the bottleneck, yet most screens test little beyond atomic overlap and give no chemical reason for failure. Here, our agents generate, test and actively refute two million candidate laws, leaving eight Plausibility Rules for Inorganic Structures (PRIS). These laws encode five mechanisms: short-range repulsion, ionic contact and packing, electrostatic balance, bond-valence conservation and crystallographic site complexity. Experimental structures satisfy our law sets at 82--99%, but satisfy Pauling's rules 2--5 together at only 6.5%. The strictest set detects 87.9% of damaged crystal structures, whereas distance cutoffs detect only 1.6--3.2%. PRIS plausibility is linearly correlated with synthesizability, so the PRIS-derived synthesis score (PSS) explainably screens 83.7% of hard-to-synthesize structures while retaining 80.7% of experimental structures. In a property-conditioned inverse-design run, PRIS and PSS can reduce the DFT validation queue by up to 67.3% and keep 99.2% of the candidates whose DFT-validated bulk moduli reach the design target. Beyond screening, PRIS explains why GNoME remains enriched in rare low-symmetry structures and reveals how wrong-element assignments in falsified crystal reports hide behind plausible coordinates. PRIS moves screening from a pass-or-fail verdict to a chemical reason for failure, showing that autonomous agents can discover, by active refutation, physicochemical laws that guide calculations and experiments.

Crystal generators can now propose periodic structures, but their control interfaces remain poorly matched to the mixed descriptors used in materials design. Text provides a compact way to combine composition, symmetry, prototype and property cues, yet it has not been clear whether such information can steer flow-based crystal generation. Here we introduce TFMat, a text-conditioned flow-matching framework that uses structured materials language as a semantic prior for a CrystalFlow generator. Across Perov-5, Carbon-24 and MP-20 crystal structure prediction benchmarks, TFMat improves one-candidate match rates over CrystalFlow and reaches a 92.04% MP-20 match rate with 20 candidates; in de novo generation, it improves element-count and density distribution alignment while retaining coarse property consistency in composition-selected outputs. These results position structured text as an inspectable control layer for translating human-readable materials intent into candidate crystals for downstream simulation and validation.

Multimodal evaluations cannot say whether a vision-language model misread an image or misreasoned about it, because every existing method for separating the two places a second model in the loop. We introduce the render ceiling, a model-free reference for benchmarks built by rendering known objects: inverting the frozen cameras and re-solving cross-view correspondence recovers exactly the answer the images support. We prove the ceiling fails only through an enumerable set of projection coincidences and certify that set empty on 2,160 rendered crystal structures, so every point of a model's deficit belongs to the model. Across fourteen vision-language models, supplying exact geometry as text lifts every model yet closes under half the gap for thirteen, while a supervised vision model with no language component reads the same images at 0.8952, above every vision-language model. The instrument exposes extraction-stage fabrication that downstream accuracy would misattribute to reasoning, yields camera-placement rules for benchmark builders, and transfers to any benchmark with an invertible forward rendering.

Learning materials properties from scarce labels and unlabeled crystals is a central challenge for data-driven materials discovery. We present SemiMat, a controlled benchmark for semi-supervised materials property regression, and MatRank, a reliability-weighted objective for continuous pseudo-label uncertainty. SemiMat fixes labeled and unlabeled crystal inputs, graph-backbone interfaces, validation-only checkpoint selection, held-out test reporting, normalized MAE (NMAE), and method-rank summaries across six scarce-label tasks, four graph backbones, and five predefined split runs. MatRank builds pseudo-targets from labeled anchors, weights them by local reliability and weak-prediction agreement, trains weak and strong graph views consistently, and adds ranking signals so that unlabeled crystals shape both values and candidate order. Across the retained 24 backbone-task blocks, one fixed MatRank objective gives the lowest aggregate held-out test NMAE (0.896) and best average method rank (2.208). The component, OOD, and generated-pool diagnostics identify where the gain is reliable and where further screening evaluation remains necessary. Code is available at https://github.com/littlepeachs/SemiMat.

Crystal symmetry dictates whether a physical response tensor must vanish, establishing a direct test for machine learning predictions independent of property calculations. We derive the parity gap, a group-theoretic metric quantifying the piezoelectric tensor freedom permitted by a crystal's proper rotation subgroup $SO(3)$ but eliminated by inversion symmetry in $O(3)$. Across state-of-the-art equivariant neural network architectures, unconstrained $SO(3)$ models systematically predict forbidden non-zero responses matching the parity gap of each centrosymmetric crystal class, while polar distortion paths dynamically map output responses to the loss of inversion symmetry. Regression controls confirm that enforcing full $O(3)$ parity incurs no consistent accuracy cost across predictive tasks. Crucially, while training interventions using explicit zero labels reduce violation magnitudes, they leave residual forbidden outputs. Exact physical compliance instead requires structural enforcement through $O(3)$ representation design or explicit output antisymmetrization. The parity gap thus provides a unified framework to distinguish empirical error reduction from exact structural compliance with physical law.

Generating crystals has recently attracted significant interest due to their broad applications in materials science. However, existing generative models struggle to produce complete crystallographic specifications, limiting their ability to capture global symmetry and structural dependencies. In particular, current state-of-the-art approaches generate crystals only up to site symmetries and rely on sampling space groups from empirical distributions during generation. Inspired by \emph{spontaneous symmetry breaking} in physics, where crystals break symmetries under external conditions, we propose a novel diffusion-based framework that generates full structure specifications by reversing from the lowest-symmetry priors. Our method leverages a Markovian jump-diffusion process to model these symmetry-breaking dynamics, enabling it to traverse different space groups in a physically motivated manner. Our model, dubbed \emph{Symmetry-breaking Crystal Diffusion} (SbCD), introduces a principled approach to explicitly incorporate inter-space-group transitions into the generative process. In de novo generation experiments on MP20 and MPTS-52, SbCD outperforms its symmetry-preserving counterpart by a substantial margin, offering a promising perspective for generative modeling of crystalline materials.

Computation-ready metal-organic framework (MOF) databases are essential for high-throughput screening, yet many reported crystal structures remain chemically unreasonable or disordered, compromising simulation fidelity. Existing validation approaches can identify non-computation-ready structures, but they often rely on heuristic rules, license requirement, or offer limited interpretability. Here, we show that large language models (LLMs) can serve as interpretable validators of MOF structures when crystallographic information is transformed into chemically meaningful text. By benchmarking nine descriptors, we find that successful LLM-based validation depends not on the amount of structural information alone, but on whether local coordination, framework connectivity, and chemical context are organized into a linguistically learnable representation. Fine-tuned LLMs using specialized descriptors (mof2text) achieve performance comparable to graph-based models in identifying unreasonable MOFs. Importantly, these models extend beyond black-box classification by generating diagnostic rationales for likely error sources, including abnormal bonding, connectivity, and charge states, as well as error-category predictions for annotated datasets. This work establishes chemically informed textualization as the key step that transforms LLMs from generic text models into practical and explainable tools for curating MOF databases.

Double perovskites (DPs) offer broad compositional tunability, but predicting the space groups (SGs) of stable structures remains difficult because available datasets are often strongly imbalanced toward dominant SG classes. We refer to dominant SG classes as major SGs and underrepresented classes as minor SGs. We introduce Dynamic and Diversity-enhanced Few-shot Retrieval and Rule-Guided Inference for Space-Group Prediction (DyRIS), an LLM-agent-based framework that predicts ranked SG candidates from a given DP composition. DyRIS uses diversity-enhanced dynamic few-shot prompting to retrieve relevant in-context examples while limiting the dominance of frequently represented SGs. It further incorporates rule-guided inference based on B/B' cation ordering, quantitative indicators, and major-SG bias control to refine and rank the final Top-3 SG candidates. We evaluate DyRIS on 3,528 thermodynamically filtered DP entries and compare it with composition-based and descriptor-based baselines. At a training-data ratio of 0.5, DyRIS achieves competitive overall accuracy while obtaining the best Overall Top-1 macro-F1 score and the best performance across all Minor-SG metrics. DyRIS improves Minor-SG Top-1 accuracy by 3.26 percentage points relative to CrabNet and achieves higher Minor-SG Top-3 accuracy than the strongest PyCaret-based baseline. Ablation studies show that diversity-enhanced retrieval, quantitative indicators, major-SG bias control, and B/B' ordering information each contribute to prediction performance. Additional experiments show that the final rule-guided inference step is not easily replaced by conventional classifier- or ranker-based models. These findings demonstrate the potential of combining retrieval-based LLM reasoning with crystallographic domain knowledge for SG prediction in imbalanced materials datasets.

Scanning probe microscopy provides nanoscale access to structural, electrical, electromechanical, magnetic, and mechanical properties of materials. Its increasing use for wafer-scale characterization and combinatorial materials exploration creates a need to distribute measurements efficiently across large spatial domains. This is particularly important when available modalities differ in acquisition time and potential for tip and sample damage, making exhaustive multimodal mapping over spatial grids impractical. Here, we demonstrate multitask scanning probe microscopy, a live, closed-loop workflow in which a multitask Gaussian process learns spatial and cross-modal relationships and autonomously selects both the next measurement location and the next experimental protocol. The approach is implemented on an automated large-sample atomic force microscope and demonstrated on a composition-spread AlScN wafer using tapping-mode and Dual AC Resonance Tracking (DART) measurements. Paired initial measurements establish the relation between the tasks, after which noncoincident measurements are used to update both response landscapes. The resulting workflow extends active learning in scanning probe microscopy from spatial sampling to autonomous allocation of measurement modalities and provides a basis for combining rapid, weakly perturbative imaging with slower contact, electrical, electromechanical, magnetic, or spectroscopic measurements.

The search for new crystalline materials spans an enormous compositional and structural space. Generating candidates in this space requires jointly modeling discrete crystallographic symmetry, elemental composition, and continuous geometry. We introduce DynaCrys, a generative model for crystals in which the space group co-evolves with Wyckoff occupations and elements through a coupled symbolic diffusion process. The structured space-group transitions follow crystallographic group-subgroup relations. As the space group changes, a shared, pretrained symmetry codebook provides both the legality-constrained stochastic decoder and the symmetry-constrained crystal-geometry model with a common representation of the corresponding Wyckoff vocabulary. Across large-scale evaluations using two independent relaxation-and-evaluation engines, DynaCrys achieves best-in-class performance in symmetry-aware discovery of stable, unique, and novel crystals, both overall and under the additional requirement of nontrivial post-relaxation symmetry. It also enables fast sampling while generating structures with consistently low relaxation-induced structural displacements.

Test-time scaling can correct difficult text-to-SQL queries, but the extra computation is normally discarded after each answer. Systems increasingly retain verified repair episodes, yet evaluations still report one end-to-end score. It cannot distinguish replay on recurring questions from help on unseen questions, or identify the responsible memory choice. We call measuring this future value the crystallization problem. Our controlled evaluation holds the single-shot solver fixed and varies one memory choice at a time. We separately measure replay, cross-question retention, and held-out same-database transfer. On BIRD, storing verified corrected queries improves held-out first-attempt accuracy by 4.34 percentage points. This gain captures 44.4% of the accuracy headroom provided by on-demand repair on the same questions. Controlled interventions identify database-specific content as the main operating ingredient. Reliable verification and broader retrieval coverage yield supported gains; richer formats and elaborate retrievers do not. Open-source code, evaluation artifacts, and reproduction instructions are available at https://github.com/ai-jiaqian/text-to-sql-memory-crystallization.

Recovering a periodic 3D crystal structure from sparse, unindexed electron diffraction (ED) observations is a challenging generative inverse problem. Existing ED-based learning methods mainly predict crystallographic labels, reconstruct structures from indexed reflections, or retrieve candidates from finite structure libraries. Here, we introduce ED-CSP, a machine learning framework that predicts crystal structures from chemical composition, atom count, and multiple detector-plane ED spot sets. ED-CSP combines a relational set encoder, permutation-invariant multi-view aggregation, and a periodic flow generator to jointly predict lattice parameters and fractional atomic coordinates. To train the model, we construct ED-CS, a dataset of 4.85 million simulated multi-view ED crystal structures, deduplicated across seven materials repositories and filtered to exclude CHILI-100K overlaps. On 2,075 held-out CHILI-100K materials, ED-CSP trained only on CHILI achieves a structural match rate of 57.49% MR@5, outperforming PXRDGen (52.92%), a state-of-the-art crystal structure prediction model conditioned on powder X-ray diffraction. Scaling training data further improves performance: initializing from a one-million-structure precursor raises MR@5 to 66.27%. On 1,024 compositions absent from the training retrieval library, the model still achieves 53.52% MR@5, demonstrating true generative capability beyond exact-formula retrieval. Replacing target ED observations with diffraction from non-isomorphic structures of identical composition decreases MR@5 by 22.09 percentage points, confirming that predictions depend on the input diffraction patterns rather than composition alone. ED-CSP and ED-CS establish a benchmark for generative crystal structure prediction from sparse ED observations and provide a foundation for future transfer to experimental data.

Advanced materials discovery increasingly relies on machine learning and Bayesian optimization to explore large discrete design spaces under limited evaluation budgets. However, conventional Bayesian optimization (BO) can become inefficient as candidate spaces grow, often evaluating low-value regions before reaching informative areas. We propose an active-learning (AL)-guided adaptive search-space refinement framework combined with multi-objective BO to accelerate materials optimization while preserving Pareto-relevant regions. We evaluate the approach on CH4/N2 separation in covalent-organic frameworks and pressure-vessel design with material-direction stress components and thickness objectives. Results show that the AL-guided refinement reduces the candidate space by approximately half while preserving more than 99 percent of the original hypervolume. The reduced-space strategy improves early convergence and cumulative Pareto-front discovery from the BO, demonstrating efficient large-scale materials optimization across constrained autonomous materials discovery settings.

Pretraining has shown strong potential for learning transferable representations, yet it remains underexplored for electron-density-based molecular learning. Electron density provides a continuous three-dimensional description of molecular electronic structure, capturing both local spatial patterns and global physical quantities. This raises a key question: can electron-density fields be used for self-supervised pretraining to learn a shared representation that transfers across diverse electronic-structure-related tasks? We propose ED-DiT, a physics-guided Diffusion Transformer for self-supervised pretraining on electron-density point clouds. ED-DiT learns reusable representations by reconstructing corrupted and partially masked log-density fields across diffusion noise levels. An electron-number consistency constraint is further introduced to preserve the total electronic mass. The pretrained encoder can be adapted to property prediction, open-/closed-shell classification, molecule-electron-density retrieval, and molecule-conditioned electron-density prediction. Experiments on six EDBench tasks show that ED-DiT consistently outperforms the same architecture trained from scratch, especially under limited supervision. For molecule-conditioned electron-density prediction, it reduces RMSE from 2.2474 to 1.3753 and surpasses the available baseline. With only 10% labels, it improves orbital energy prediction RMSE from 0.0293 to 0.0138. These results demonstrate the effectiveness of physics-guided electron-density pretraining for learning transferable molecular representations.

Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance. Here we present a systematic, compute-aware study of BO that evaluates surrogate models along two axes: optimization quality and computational frugality. Across eight benchmark functions and nine real-world datasets spanning materials science, mechanics, robotics, chemistry, and machine learning, we benchmark four surrogate models: Gaussian Processes, Random Forests, NGBoost, and Bayesian Adaptive Spline Surfaces. We show that Gaussian Process-based BO consistently incurs the highest time and memory overhead without delivering superior optimization or sample efficiency. In contrast, scalable alternatives achieve equal or better performance at a fraction of the computational cost. Motivated by these findings, we introduce a surrogate-recommendation framework that predicts the most suitable BO surrogate from inexpensive dataset characteristics. Together, these results establish FruBO as a reproducible, compute-aware baseline for Bayesian Optimization and provide practical guidance for surrogate selection under limited computational and experimental budgets.

Data augmentations define the invariances learned by self-supervised learning (SSL). Standard augmentation pipelines were designed for natural images, yet scientific imaging modalities are governed by physical measurement processes with distinct symmetry and acquisition constraints. Enforcing invariances that contradict these constraints can distort learned representations and limit downstream performance, but practitioners moving from machine learning into a new scientific modality currently have little guidance beyond transferring natural-image pipelines unexamined. We address this gap with a principled, reproducible procedure for augmentation design in scientific SSL: we formalise the physics-aligned augmentation set as a union of measurement-consistent symmetries and acquisition-driven perturbations, and we give a concrete, largely label-free workflow---enumerate candidates, label each by the measurement operator, validate with representation-geometry diagnostics, and confirm by single-factor ablation---for selecting them. We instantiate the procedure for real-space electron microscopy and reciprocal-space 4D-STEM diffraction, and evaluate it across five SSL paradigms (DINOv2, SimCLR, MAE, VICRegL, I-JEPA) on classification and crystal-orientation regression. Physics-aligned augmentations substantially improve downstream performance for objectives relying on cross-view consistency, reduce geodesic error and improve robustness under realistic acquisition variability (detector gain, resolution loss), and systematically reshape representation geometry. While our experiments use electron microscopy, the procedure is modality-agnostic and applies to other measurement-driven domains such as medical and remote-sensing imaging. These results position augmentation design as a primary, and controllable, source of inductive bias in scientific self-supervised learning.

Generative machine learning is increasingly used for inorganic crystal structure generation. Most models and the corresponding evaluation approaches rely on simple forms of crystal structure representation. In this paper, we showcase the power of atom-averaged features from pretrained Machine-Learning Interatomic Potentials (MLIPs), such as MACE, for such tasks. We first introduce a distance measure that assesses the output of material generative models by capturing both quality and novelty in a single distribution-based evaluation framework. In particular, we introduce the Coarse-Fine Transport Distance (CFTD) using two different featurizers, where the quality component is based on coarse MACE features. We showcase CFTD's versatility in capturing crystal-structure quality while also detecting memorization, and compare it with the recently introduced continuous SUN metrics. We further show that coarse MACE features can be used as guidance for a material generative model.

Inverse design of three-dimensional porous media is central to applications in filtration, catalysis, energy storage, fuel cells, thermal management, and biomedical scaffolds, but remains challenging because many distinct pore geometries can share similar porosity or permeability while small structural changes can strongly affect transport behaviour. This paper proposes a physics-guided generative AI framework for property-targeted porous media design, combining a property-aware variational autoencoder, a conditional latent diffusion model, and an independently trained differentiable structure-to-property surrogate. The framework learns a compact, physically informative latent design space, generates porous structures conditioned on target porosity and directional permeability, and refines generated samples using property-level feedback during denoising and decoding. Experiments on procedurally generated structures and real micro-CT porous-media datasets show improved target-property matching, directional permeability control, and property correlation compared with representative property-aware variational-autoencoder and latent-diffusion baselines. The results demonstrate a scalable route towards controllable inverse design of complex porous geometries and establish a foundation for simulation-informed generative AI tools in engineering and advanced materials discovery.

Autonomous laboratories automate experimental execution, but a campaign must also decide which recovery pathway merits optimization. We formulate this as a sequential decision problem with a discrete pathway-identification stage and a continuous within-pathway optimization stage under heterogeneous experimental costs. Our implementation, Coactive learning, combines a cost-sensitive Bayesian hypothesis-discrimination policy motivated by EC2 (Golovin et al., 2010) with Gaussian-process Bayesian optimization (Srinivas et al., 2010). Under explicitly stated assumptions, the expected spend of one fixed-budget campaign attempt is bounded by the expected pathway-identification cost plus the capped within-pathway optimization budget. We evaluate the method on synthetic benchmarks constrained by selected results reported for PNNL's CICERO selective-precipitation study (Ritchhart et al., 2026). The method performs comparably to an oracle-pathway Bayesian-optimization reference and to a strong split-plate baseline that discriminates pathways with its first plate, without receiving an oracle label for the correct pathway. It is given a candidate hypothesis space and a diagnostic likelihood model. On an NdFeB-inspired instance, it avoids the simulated penalty of a commit-first baseline that initially selects a plausible but inferior hydroxide pathway. This hypothetical wrong-first-commitment scenario is motivated by the hydroxide-oxalate performance contrast reported by CICERO. We characterize the sensitivity of these conclusions to the assumed cost model. The code and benchmark are open source.

Machine learning interatomic potentials (MLIPs) approximate quantum-mechanical energies and forces---conventionally computed by density functional theory (DFT) or wave-function methods---at a fraction of the cost. The field encompasses a growing ecosystem of algorithms, training datasets, hyperparameters, and target materials, yet the metadata needed to systematically compare, reproduce, and build upon MLIP studies remains scattered across papers, scripts, and ad-hoc file formats. We present the MLIPs ontology, an OWL 2 DL ontology that captures the concepts needed to describe MLIP methods, their hyperparameters, training datasets with DFT provenance, and published benchmarks. The ontology is organized into three modules---Method, Training Data, and Benchmark---and connects existing ontologies in materials science (MDO, CMSO/ASMO) and machine learning (ML-Schema), complementing dataset-side schemas such as Croissant. It declares 27 formal axioms enforcing data completeness and consistency, including property chains that link trained models to their methods and training data. We demonstrate the ontology through a running example based on Moment Tensor Potentials and evaluate it through competency-question execution on a 20-paper seeded knowledge graph, OWL reasoning, and comparison with existing ontologies.

Materials research advances through accumulated experience - scripts that work, protocols that are trusted, warnings attached to failed calculations or experiments, and judgement that links a new question to an old result. This experience is essential for reproducibility and knowledge transfer, yet it is usually fragmented across notebooks, repositories, job logs and individual memory, and it is rarely portable across artificial-intelligence agents. Here we argue that a lifelong AI partner for materials science can be designed around persistent memory rather than around a particular agent implementation. We introduce a self-evolving memory framework that stores scientific experience as inspectable facts and executable skills, so that observations, failure boundaries, protocols and validation checks can be retrieved, revised and migrated across models. We evaluate the idea in three computational settings that expose different layers of materials-research competence. In 49 real-world materials-tool-use questions comprising 138 executable subtasks, memory nearly doubles GPT-5.2 task success without model-parameter updates. In elemental-solid equation-of-state calculations, memory converts a wavefunction-initialization failure into a pre-execution guardrail, improving outcomes from 22/1/4 to 25/2/0 Correct/Partial/Error and avoiding 92% of repeated errors. In 13 practical material simulation workflows, remembered skills and failure facts halve the aggregate trace burden (tokens) and reduce tool calls by over a factor of two by the third round, while preserving physically meaningful outputs in band-gap, phonon, vacancy and work-function analyses. These results show that agent memory can serve as a durable scientific asset; a portable, self-improving record of materials-research experience that outlives any single model or agent stack.

Chemists and materials scientists increasingly use machine learning models, such as graph neural networks (GNNs), to predict properties of molecules and the outcomes of their reactions. Beyond predictive performance, understanding how these models organize chemical information internally in their latent spaces, i.e., the embeddings of the molecules, is critical. Analyzing latent spaces helps diagnose model behavior and assess whether the learned embeddings are organized in ways that reflect meaningful chemical relationships. Unfortunately, existing methods provide limited support for analyzing latent spaces across layers and across different model states (e.g., training epochs, model configurations, and input data), making it difficult to understand how these latent spaces evolve throughout a model or relate to chemical concepts. We present LatentFlow, a visual analytics system developed in collaboration with a domain expert for analyzing latent spaces in molecular GNNs. LatentFlow groups embeddings into clusters and supports exploration of latent spaces by tracking how these clusters change across layers and model states using a modified Sankey diagram. To support interpretation, LatentFlow links these clusters to representative molecules and their shared substructures, and it allows scientists to introduce their own domain knowledge and compare it with the patterns found in the latent spaces. We evaluate LatentFlow through two case studies. The results show that LatentFlow helps scientists understand how latent spaces evolve, identify meaningful molecular patterns, and better interpret model behavior.

Artificial intelligence (AI) is accelerating materials prediction and design by enabling efficient exploration of chemical and structural spaces, with particular promise for novel materials discovery. However, novelty in materials discovery encompasses chemical plausibility, structural distinctiveness, property relevance and experimental realisability, making AI-driven novelty claims difficult to substantiate. We introduce a materials property hierarchy, from intrinsic, composition-determined properties to extrinsic, processing-dependent performance, to clarify deployment constraints and distinguish structural, physical and deployment novelty. This framework motivates an evidence-based view of multimodal materials data spanning chemical composition, microstructure, processing, and testing and characterisation, showing that current evidence remains concentrated in composition and idealised structure while heterogeneous, under-represented and weakly integrated modalities limit support for physical and deployment novelty. It also highlights the limitations of benchmarks based mainly on computational labels and proxy novelty criteria. Community-wide standards for data collection, modality alignment and evidence synthesis are needed to support multimodal data construction, process-aware multimodal modelling, feasibility-first generative modelling and deployment-aware benchmarking, so that generative and multimodal AI can design experimentally realisable materials with defensible scientific and practical novelty.

Large language models can answer scientific questions, yet a correct output does not reveal whether the model represents or uses the governing physics. Here, using three open-weight Gemma 4 models (google/gemma-4-E4B-it, google/gemma-4-12B-it, google/gemma-4-31B-it) we identify three experimentally separable signatures of materials-science mechanism information: selective concept readability, relational encoding of qualitative constitutive orientation, and causal, context-dependent control of constrained engineering answers. We combine matched direct and Jacobian vocabulary readouts, option-free state geometry, a 60-law counterfactual benchmark and causal interventions. In 50 held-out materials descriptions, three independently fitted Jacobian lenses reproduced concept ranks, and target-free word sets from both readouts enabled blinded identification of 9 of 10 mechanism families. A separate 72-prompt benchmark produced mechanism-specific hidden-state neighborhoods, but an exact graph audit showed that this apparent physical organization was equally explained by numerical comparison. We therefore compared otherwise identical prompts in which only the direction of the physical input was reversed, asking whether the resulting hidden-state movement followed the supplied constitutive law. These state transformations ordered direct, physically neutral and inverse laws across 60 frozen relations and correctly oriented 39 of 40 directional laws, whereas lexical controls were near chance. Bidirectional interventions shifted answer probabilities toward or away from the physically appropriate outcome across all 12 matched cases, while counterfactual state patches transferred opposing decision signals across mechanisms and answer formats. Physical relationships were therefore more visible in controlled state changes than in absolute states alone.

Large metal-organic framework (MOF) databases support simulation, screening, and machine learning through crystallographic information files (CIFs). Subtle chemical and structural errors in these inputs can compromise downstream results and hinder manual inspection. LLM advances in computational chemistry offer paths beyond predictive screening toward fine-grained diagnosis with evidence-grounded explanations. However, two challenges remain: (i) limited fine-grained attribution: MOF-specific validators and machine-learning models scale detection but provide fixed checks, readiness scores, or coarse labels rather than evidence-grounded explanations; and (ii) unreliable CIF reasoning: direct LLM auditing is costly and unreliable because chemical evidence is implicit across atom-site records and requires geometric, connectivity, occupancy, and charge calculations. Both stem from weak coupling between chemical evidence and language-model explanation. We introduce MOF-Sleuth, a reinforcement-guided CIF auditing agent with two modules: a deterministic Forensic Lab and a Sleuth reasoning engine. The Lab derives composition, geometry, connectivity, occupancy, coordination, and charge evidence, and Sleuth uses this evidence to produce an evidence-grounded explanation, error types, and a binary decision. Reward-guided reinforcement learning (RL) turns tool measurements into chemical explanation-level supervision, rewarding not only the final answer but also cited chemical evidence and evidence-supported diagnoses. We introduce Chemically Grounded Diagnosis (Chem-GD), a metric that assesses whether a correct diagnosis is explained by factual, relevant CIF-derived evidence. Across four benchmarks, MOF-Sleuth establishes state-of-the-art performance among LLM-based approaches and MOF-specific machine-learning methods, demonstrating gains in detection, attribution, and grounded explanation quality.

Amorphous materials exhibit exceptional mechanical and functional properties, yet their rugged energy landscapes are notoriously difficult to sample. Below the glass-transition temperature, conventional molecular dynamics and Monte Carlo become inefficient because equilibration relies on rare barrier-crossing events, while data-driven generative models are constrained by scarce and biased reference ensembles. Here, we introduce ATLAS, an efficient sampler that learns a diffusion process to generate Boltzmann-distributed amorphous structures directly from a target energy function. Parameterized by an equivariant graph neural network, ATLAS generalizes across system size, temperature, and composition. By exploiting the time reversal of the diffusion process, it enables efficient estimation of thermodynamic quantities and steering toward target observables. In two-dimensional Kob-Andersen systems, ATLAS reproduces parallel tempering Markov chain Monte Carlo structural distributions, free energies and entropies, achieving below 0.2% free energy error in the low-temperature glass regime with over 500-fold fewer energy evaluations. In Cu-Zr and Cr-Co-Ni metallic glasses, ATLAS recovers experimentally observed short-range-order trends and steers structures toward prescribed order parameters and optimized bulk moduli. Moreover, composition-amortized pretraining outperforms composition-specific training from scratch, reduces inverse-design costs by several hundred-fold, and enables sampling with expensive universal machine learning interatomic potentials. Coupled to a large language model agent, ATLAS searches an eight-element space for high-entropy metallic glasses balancing stiffness and ductility, identifying a converged Pareto frontier within 480 oracle evaluations. Together, these results establish ATLAS as a foundation model for sampling, steering and designing amorphous materials.

Organic mixed ionic electronic conductors (OMIECs) are a promising class of polymer materials for applications spanning neuromorphic computation to energy efficient electronics and bioelectronics. Despite being highly tunable, the relationship between structural features and key performance properties such as charge carrier mobility is poorly understood. Scanning nanodiffraction in the transmission electron microscope (TEM) is a powerful probe for elucidating this structure-property relationship, but produces large, noisy datasets that are difficult to interpret because polymer reflections exhibit several distinct morphologies. To address the complexity, we trained a machine learning (ML) model to detect these polymer diffraction peaks and their intensities from synthetic data. Compared to correlative peak detection algorithms, the conventional method for analyzing nanobeam 4D scanning transmission electron microscopy (4DSTEM) data, we show that the ML model is significantly faster and outperforms correlative algorithms in almost all cases, opening up the possibility of near-live visualization of 4DSTEM experiments.

Accurate prediction of crystal properties remains a key challenge in computational materials science. While graph neural networks (GNNs) such as CGCNN, MEGNet, ALIGNN, and SchNet have shown strong performance, they primarily represent crystals at the atomic level and implicitly learn local chemical environments through message passing. However, many material properties are governed by coordination polyhedra, the fundamental structural units formed by atoms and their neighboring atoms. To address this limitation, we propose the Coordination Polyhedron Graph Network (CPGN), a multi-scale GNN that jointly learns atomic, bond, and coordination-polyhedron representations. CPGN constructs three coupled graphs: an atom graph encoding elemental and bonding information, a line graph capturing angular interactions, and a coordination polyhedron graph describing Voronoi-derived local environments through corner-, edge-, and face-sharing relationships. Physically meaningful geometric descriptors are incorporated for each polyhedron, while an interleaved message-passing mechanism with bidirectional cross-attention enables effective information exchange across structural levels. Extensive evaluations on the Materials Project, JARVIS-DFT, and QM9 benchmark datasets demonstrate that CPGN outperforms existing state-of-the-art GNN models. It achieves a formation-energy MAE of 0.060 eV/atom and a band-gap MAE of 0.292 eV on the Materials Project, while providing competitive multi-property prediction on JARVIS-DFT and superior HOMO prediction on QM9. The results highlight that explicit modeling of coordination polyhedra improves crystal representation learning and enables accurate, physically interpretable prediction of material properties.

Disordered metamaterials feature microstructures with inherent randomness and irregularity, enabling them to achieve broader property coverage and superior performance unavailable in their regular counterparts. Despite their promise, designing disordered microstructures is substantially harder than designing regular ones. Their design remains trapped between manual parameterizations with limited expressiveness, and generative AI that is data-hungry and struggles to generalize. To address these limitations, we propose a generative design framework based on Neural Cellular Automata that dynamically grows complex microstructures through learned local interaction rules, inspired by the self-organizing processes in natural materials. This framework requires only a single training template, yet accommodates diverse disordered microstructures and adapts to irregular domains and arbitrary discretizations. By manipulating the learned local rules, we can steer the growth process to generate microstructures unseen during training, providing control over orientation, anisotropy, and directional thickness without retraining. As a dynamic, local growth process, it naturally produces spatially varying microstructures that transition smoothly to enable location-specific mechanical properties. We demonstrate this in a multiscale mechanical cloaking design, where microstructures vary across the space to meet an optimized heterogeneous property distribution. Our design enables excellent cloaking performance without complicated post-processing and incompatible assembly common in existing methods. This data-efficient, generalizable approach opens access to previously intractable disordered materials for biomedical implants and soft robotics.

Procedural material creation underpins applications in digital content creation, visual effects, and 3D asset design. Achieving high-quality results requires more than reproducing node graphs -- it demands understanding the process by which experts construct materials. We formulate procedural material generation as retrieval-time process reasoning over expert demonstrations, elevating process to a first-class representation beyond graph-only synthesis. Concretely, we represent expert workflows as process traces: textual records of construction steps, parameters, and design intent. To instantiate this idea, we use a pretrained LLM-based ProcessSynthesizer to synthesize a process trace aligned with a user's intent and a pretrained LLM-based Compiler to ground the process trace into an executable Blender material graph. Because procedural expertise is most naturally conveyed through demonstrations, we leverage tutorial videos as a source of process knowledge and extract textual, LLM-compatible traces using automated video analysis tools. In an expert study with five Blender artists (avg. 7.5 years of experience), materials generated by reflecting expert demonstrations were found to produce workflows requiring fewer edits, and more closely match professional design strategies than methods operating solely on static artifacts. A user study with 150 participants further shows that our approach achieves superior generation and editing performance compared to prior procedural systems. All code, models, and data will be available at https://materialapprentice.github.io

The experimental reconstruction of the 3D two-photon momentum density (TPMD) via angular correlation of electron-positron annihilation radiation (ACAR) is a particularly useful method for studying material Fermi surfaces. It does not rely on low temperatures, UHV conditions, or strong magnetic fields, and enables the study of the spin-resolved electronic structure of materials. Yet, it remains a challenging inverse problem. Typically, 10^8 positron annihilation events are measured for 3--6 projections of the TPMD at different angles. The standard reconstruction approach is an ACAR adaptation of Cormack's method (the MCM) that leverages the inherent symmetry in the crystal's structure. However, the poor signal-to-noise ratio means collecting data of sufficient quality for Fermi surface studies can take months per sample. We present DeepCormack, a family of data-driven model-based reconstruction algorithms that augments the MCM by integrating supervised deep-learning models (CNN, MLP, and UNet) at various stages. To overcome the lack of large experimental training sets, we propose a method which leverages singular value decomposition with dynamic mode decomposition to generate realistic synthetic TPMD volumes, requiring only a single reference momentum density computed via density functional theory. On test data, DeepCormack improves reconstruction quality over MCM by about 8.5 dB PSNR at 200M counts and remains stable at reduced counts, enabling significantly faster acquisition times. Generalisation to experimental data depends strongly on how well the training distribution from the reference momentum density matches the sample. We therefore recommend pairing DeepCormack with a DFT calculation of the target material to create sample-specific training data. Our proposed method offers either much higher quality reconstructions, or enables significantly faster ones, on the order of weeks.

Material property prediction (MPP) infers key properties from chemical composition and structure, accelerating the discovery and optimization of novel materials. In the realm of MPP, MatBench is a widely accepted benchmarking tool that defines over ten significant problems and provides the paradigm of performance evaluation for AI prediction models. Even though MatBench works well in benchmarking the performances of prediction models on in-distribution (ID) tasks and datasets, it lacks the ability to reflect their performances on out-of-distribution (OOD) material data, resulting failure in new material discovery. By combining the pipelines of MatBench and the existing researches on OOD performance evaluation, this study enables a huge space of benchmarking configurations, comprehensively reflecting the performances, abilities, and disadvantages of various AI prediction models. This work reports that the discrepancy of performances at different configuration values is huge and can be illustrated with prior knowledge and novel insights, therefore consideration of causal effect of configurations on performance results is necessary. In case of the impossibility of enumerative benchmarking at every configuration, this work further proposes AutoMatBench, an automatic toolkit with Bayesian optimization. Experiments with AutoMatBench reports that, within twelve steps of optimization, the similar results with MatBench and former OOD research can be accessed while more than half of the cost are saved. Besides, this tool also yields more essential findings on MPP benchmarking, positively contributing to the cost and efficiency of new material discovery.

Artificial intelligence (AI) is transforming electron microscopy by enabling quantitative analysis of increasingly large and complex datasets for nanoparticle characterization. Recent advances in machine learning (ML) and deep learning (DL) have expanded microscopy from a descriptive imaging technique into a data-driven platform for structural interpretation, dynamic analysis, and scientific inference. This review examines AI methodologies for nanoparticle electron microscopy, focusing on transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), scanning transmission electron microscopy (STEM), and in situ TEM. The discussion is organized around the principal challenges in nanoparticle characterization, including particle detection, segmentation, morphology quantification, atomic-resolution restoration, defect identification, two-dimensional-to-three-dimensional structural inference, and analysis of dynamic processes in situ. We review computational approaches from conventional ML and convolutional neural networks to transformer architectures, self-supervised learning, foundation models, multimodal AI, and physics-informed learning. We further discuss integrating microscopy data with simulations, metadata, and autonomous experimentation to relate nanoparticle structure, dynamics, synthesis conditions, and functional properties. The advantages, limitations, benchmarking, and data requirements of current methodologies are critically assessed. Finally, emerging opportunities for foundation models, AI-guided microscopy, closed-loop experimentation, and autonomous materials discovery are discussed. By integrating advances across computer vision, materials informatics, and electron microscopy, this review highlights the role of AI in next-generation nanoparticle characterization and accelerated materials discovery.

Artificial intelligence (AI) is transforming scientific discovery, but its effectiveness is fundamentally limited by the availability of structured scientific knowledge. Although existing databases have accelerated data-driven materials research, much of the knowledge needed for predictive modeling and inverse design remains embedded in unstructured scientific literature. We present an Autonomous Scientific Knowledge Generation Framework that transforms scientific publications into a Unified AI-Ready Scientific Knowledge Base. The framework integrates ontology-guided literature acquisition, hybrid scientific knowledge extraction, semantic harmonization, knowledge fusion, and validation within a unified workflow. Rather than treating literature retrieval, information extraction, and database construction as separate tasks, the framework progressively converts scientific publications into structured, semantically consistent, and provenance-preserving knowledge suitable for AI-driven reasoning. As a proof of concept, the framework was applied to electro-optic materials. Autonomous literature acquisition retrieved and validated about 1,000 publications from multiple scholarly repositories. A representative subset of eight publications was processed through the complete workflow, generating 29 structured scientific records that were harmonized into 7 canonical scientific records. The results demonstrate the complete transformation from scientific literature to an AI-ready scientific knowledge base while preserving quantitative measurements, operating conditions, provenance, and scientific context. The proposed framework provides a scalable, domain-independent foundation for predictive AI, generative AI, and closed-loop AI-driven scientific discovery.

Fully characterizing a crystalline material requires integrating heterogeneous data sources -- atomic structures, diffraction patterns, electronic density of states, and natural language -- each of which captures a different facet of the same physical object. In practice, however, these modalities are stored and analyzed in isolation, making it difficult to relate or query materials across representational boundaries. We present MatBind, a contrastive learning framework that aligns four materials modalities -- crystal structure, powder X-ray diffraction (pXRD) simulated from structures, density of states (DOS), and text -- into a unified embedding space using crystal structure as the central physical anchor. The framework induces alignment between modalities never explicitly paired during training, enabling emergent zero-shot cross-modal retrieval as a direct consequence of the shared representation. The learned embedding space organizes materials according to physically meaningful properties without explicit supervision, and retrieval performance improves systematically when modalities are combined at query time. These results demonstrate that treating heterogeneous materials data as complementary projections of a single physical reality, rather than as isolated data sources, is not a practical choice but is consistent with the underlying physics.

This paper studies the problem of learning a joint distribution from marginal observations, which is inherently ill-posed due to the ambiguity of feasible couplings. We propose LUD-MSR, a latent-variable probabilistic framework that models the joint distribution via auxiliary representations and optimizes evidence lower bounds using only marginal data. Under mild assumptions, we establish an upper bound on the distribution approximation error. This analysis reveals a trade-off in representation learning between domain consistency and information preservation. To address this trade-off, we introduce a Multi-Scale image Representation (MSR) mapping that exploits structural similarity at coarse scales while suppressing domain-specific variations. We show that MSR achieves a more favorable balance of this trade-off compared to existing approaches. Experiments on real-world denoising benchmarks, including cryo-electron microscopy (cryo-EM), demonstrate the effectiveness of the proposed framework.

Catalysts are essential for sustainable chemical manufacturing, yet discovering novel architectures remains a bottleneck dominated by trial-and-error experimentation and computationally intensive screening. In complex reactions such as electrochemical carbon dioxide reduction, product selectivity is governed by dynamic interfacial, electrolyte, and potential factors as well as kinetic pathway competition. Conventional descriptor-based machine learning and computational potentials struggle to resolve these mechanistic branch points, primarily relying on static ground-state descriptors or bulk structural correlations rather than end-to-end topological pathway analysis. Here, we show that frontier language models, when strictly constrained to reason over explicit reaction networks, can discover novel catalysts by identifying the physical levers that govern pathway competition. We developed a human-AI co-thinking framework that enforces network invariance to extract testable hypotheses from complex chemical graphs. Applied to CO2 electroreduction, the framework identified ketene desorption and hydroxide capture as the acetate-forming pathway, and predicted a distinct adsorbed CO and CH2 coupling route to ketene. By isolating actionable control levers, specifically local alkalinity, controlled iron incorporation, and restricted interfacial proton-donor accessibility, the framework guided the prospective synthesis of a copper-iron oxide catalyst demonstrating a threefold increase in acetate selectivity over matched Cu-rich baselines. This mechanism-guided reasoning architecture shifts the computational paradigm from retrospective statistical prediction to forward-looking hypothesis generation, providing a broadly applicable blueprint for mechanism-guided materials discovery.

This study presents a multi-fidelity framework for the systematic optimization of genetic algorithm (GA) hyperparameters. The framework integrates three fidelity levels: high-fidelity Fast Fourier Transform (FFT) homogenization for validation, a medium-fidelity 3D convolutional neural network surrogate for rapid property evaluation, and a low-fidelity Gaussian process (GP) surrogate within a Bayesian optimization (BO) framework to guide the hyperparameter search. Various acquisition functions are evaluated, with logNEI achieving the best performance by effectively accounting for the noise inherent in GA evaluations. The proposed framework identifies hyperparameter configurations that enable a 25-generation GA run to achieve elastic modulus values comparable to those obtained in a full 75-generation optimization. Furthermore, introducing a penalized BO objective significantly reduces the number of required lattices with only minor decreases in absolute achieved elastic modulus, revealing a practical trade-off between performance and the number of structures that must be evaluated. High-fidelity FFT validation verifies the effectiveness of the surrogate-driven optimization strategy. The optimized hyperparameters allow for rapid convergence, eliminate the need for lattice mutation, and reduce the overall computational cost by 24% (from 225 to 171 hours) while preserving mechanical performance. These results demonstrate the potential of multi-fidelity optimization as an efficient and practical approach for GA hyperparameter tuning and future experimental lattice design studies.

The precise pixel-level localization of 2D material flakes is crucial for high-throughput screening. However, traditional fully supervised methods rely on dense annotations, which are costly and time-consuming, severely limiting the practical deployment of segmentation models. This paper proposes TACoS, a specialized scribble segmentation framework tailored for 2D materials. First, we design a unified framework that integrates semi-supervised consistency learning with structured tree energy constraints. This framework comprises two core components: an unlabeled weak-strong distribution alignment module and a tree energy regularization module. The former employs cosine consistency constraints to enhance prediction alignment across views. Meanwhile, the latter utilizes minimum spanning trees to establish pixel affinity relationships and generate structure-aware soft pseudo labels for online semantic guidance. Next, we introduce asymmetric regional contrast learning. This approach fuses high-confidence predictions from the weak augmentation branch with scribbles to form augmented labels, and construct category prototypes in the representation space. Simultaneously, we prioritize contrastive constraints on challenging pixels in boundary-unlabeled regions. This strategy enhances intra-class cohesion and inter-class separation at the representation level, effectively reducing category confusion in low-contrast edges and complex backgrounds. Experiments conducted on the constructed graphene and MoS2 datasets demonstrate that our method TACoS achieves over 96% of fully supervised performance using less than 0.6% annotated data. Furthermore, it exhibits superior structural coherence and boundary stability in scenarios with weakly contrasting edges and complex backgrounds, providing an efficient and scalable solution for automated high-throughput screening of 2D material flakes.

AI agents deployed for IT operations are typically permanent cost centers because every execution requires full LLM inference, even for previously solved problems. This paper introduces progressive crystallization, a lifecycle that treats agent exploration as a discovery mechanism rather than a permanent execution model. It defines a three-stage execution taxonomy, from fully agent-orchestrated to hybrid to fully deterministic workflows, together with an evidence-based promotion mechanism that converts repeatedly validated agent behaviors into cheaper and more reproducible deterministic workflows, while automatically demoting workflows that regress. Evaluated on a production cloud networking AIOps system processing tens of thousands of incidents per month, the approach increased deterministic execution from 0% to 45% over eight months, reduced per-incident agent costs by more than 70% despite doubling incident volume, and improved safety through greater reproducibility and auditability. The paper also presents the execution taxonomy, promotion and demotion criteria, trace extraction methodology, economic model, safety considerations, and discusses limitations and threats to validity.

Accelerating materials discovery requires AI systems that can generate scientifically valid hypotheses through multi-step, domain-grounded reasoning. Standard large language models often produce fluent but weakly traceable responses to open-ended materials design problems, making it difficult to determine whether final answers are supported by coherent intermediate reasoning. We develop Graph-PRefLexOR, a family of graph-native reasoning models fine-tuned with Group Relative Policy Optimization (GRPO) to organize reasoning into explicit phases for mechanism exploration, graph construction, pattern extraction, and hypothesis synthesis. This design links neural language generation with symbolic relational structure, enabling causal connections to be constructed, inspected, and reused. On 100 open-ended questions from materials science and mechanics literature, Graph-PRefLexOR achieves 40-65% improvements over corresponding base models, with the largest gains in reasoning traceability. Embedding analyses show broader semantic exploration and approximately 2-3 times greater semantic diversity than baselines. Semantic backtracking and layer-wise hidden-state analyses further show stronger alignment between structured reasoning and final answers. Finally, test-time graph expansion reveals that additional compute primarily increases long-range conceptual recombination within a bounded semantic space, rather than simply expanding semantic coverage. These results establish graph-native reinforcement learning as a pathway toward interpretable AI systems for scientific hypothesis generation in materials design and other scientific applications.

Driven by high-throughput experimentation, computational modeling, and artificial intelligence (AI), materials data has expanded at an unprecedented rate. Conventional materials databases function only as passive repositories, archiving raw experimental records indiscriminately including both successful and failed data, without systematic value filtering or asset management. This creates a critical gap between massive data accumulation and actionable innovation, hindering the identification of high-potential materials and industrial translation. To address this bottleneck, we propose an industrialization-oriented Materials Bank, a dedicated valuefiltering and assetization layer that operates beyond traditional databases. It does not merely curate high-quality data but systematically elevates qualified candidates into standardized, upgradable materials assets via a multi-dimensional BankCard framework covering scientific validity, synthesis feasibility, application readiness, and industrial value. By unifying databases, AI models, automated experimentation, and multi-criteria assessment into a cohesive closed-loop ecosystem, the Materials Bank establishes a clear trajectory from data to knowledge, candidate, asset, and product. It serves not as an enhanced database or screening tool, but as a decision infrastructure bridging academic discovery and industrial demand, offering a scalable paradigm to accelerate AI-driven materials innovation and deliver tangible real-world impact.

Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity. Current solvers are often limited to static predictions or require computationally intensive heuristic searches. We present CryoACE, an end-to-end framework that reconstructs precise atomic graphs for both homogeneous and heterogeneous structures. Our method features two key innovations: an atom-centric reconstruction paradigm, where density features are sampled directly at atomic coordinates and iteratively recycled to refine structures, replacing expensive voxel convolutions for efficient multimodal fusion; and a training-free guidance mechanism that leverages predicted local resolution priors to resolve dynamic ambiguity. Validated on a newly constructed high-quality dataset, CryoACE significantly outperforms existing baselines on static benchmarks and, for the first time, unveils atomic-level dynamic conformations on complex real-world datasets like EMPIAR-10345 without relying on pre-built static structures.

Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets. This combination yields strong benchmark metrics but limits transferability to domains structurally distinct from drug discovery. To overcome this limitation and drive discovery toward real, scientifically grounded targets, we introduce the Nanotechnology Molecular Optimization (NMO) Benchmark, which bridges machine learning (ML) and quantum materials science. NMO acts simultaneously as a rigorous testbed for the ML community and a discovery engine for nanotechnology research. The suite replaces proxy oracles with quantum simulations and introduces strict protocols that prioritize scientific utility over leaderboard-oriented overfitting. The physics-based NMO tasks impose hard structural constraints and rugged fitness landscapes, posing fundamentally new requirements on generative models. Notably, advanced molecular optimization methods underperform much simpler approaches on the NMO tasks. We develop a new baseline method identifying the critical components to solve the NMO tasks, including a novel representation for modeling structural constraints and a domain-agnostic pretraining strategy to eliminate pharmaceutical dataset bias. Our results surpass state-of-the-art physical properties and reveal previously unknown structural motifs, offering new insights for the nanotechnology community and demonstrating that ML can drive genuine scientific discovery.

The alignment of language models is typically studied through the lens of capability benchmarks, but the dynamics of how models change during post-training remain poorly understood. We argue that the physical sciences, and thermodynamic phase-transition theory in particular, offer a principled and underexplored vocabulary for reasoning about these dynamics. As a case study, we instantiate this position through the lens of material Crystallization, which is a well-studied thermodynamic phase transition. For tasks like random number generation, this breaks into 3 phases: (1) the high entropy liquid phase in the pretrained model, with many distinct sampling distributions promptable from the model; (2) the nucleation phase caused by supervised finetuning, in which behavior collapses onto a single seed distribution present in the pretrained LLM; and (3) a settling phase in which reinforcement learning techniques redistribute probability of the collapsed distribution, but largely keep it concentrated on the same options as the seed distribution. We propose intuitive metrics to verify the transitions between these phases, and validate the idea across a range of random tasks. Crystallization is one instance of a broader class of physical frameworks we believe alignment research should import to answer questions about where alignment-induced structure comes from, why it converges where it does, and what it fundamentally cannot change.

This project introduces the CRISTAL Method (Coherent Reliable Intentional Synthesis of Truthful Analysis Logic), a neurosymbolic framework for automating complex analysis workflows, with fundamental investment analysis as a primary use case. This domain poses major challenges: high structural uncertainty, noisy and subjective data, tight attention budgets, and the need for justified, reproducible decisions. Human analysts often struggle in this domain due to cognitive biases and limitations, suggesting significant value in automation. But while LLM-based agents have been proposed as analytical aids, their limitations -- poor numerical reasoning, unawareness of uncertainty, and lack of reproducibility -- hinder their effectiveness in this context. CRISTAL addresses these gaps through a principled blend of statistical model synthesis, continuous learning, and active learning. Starting from a natural-language prior knowledge curriculum, CRISTAL builds a dynamic, interpretable probabilistic program that enables full Bayesian inference, including uncertainty quantification and budget-aware data acquisition. CRISTAL continually refines its world model during analysis, leveraging LLMs for code synthesis and learning. We validate CRISTAL on a novel benchmark of synthetic equities with rich financial and textual data. On a company classification task, CRISTAL achieves Bayes-optimal accuracy with just 5 examples and a 5-second budget, outperforming state-of-the-art LLMs that plateau around 40% accuracy even with order-of-magnitude more input data and compute.

Predicting a material's properties from its structure is a central, fast-advancing problem in computational materials science. A decade of work has produced standard public benchmarks and many published machine-learning models for the task (Dunn et al., 2020). The task's fixed metric and these baselines make it a natural setting for autonomous agent research (Karpathy, 2026). On the MatBench band-gap benchmark ($>$100k crystals), a general-purpose coding agent autonomously built the most accurate model trained without external pretraining, ahead of all seventeen expert-designed models reported for the task. A closer analysis shows it reached this by implementing known methods: either already standard in crystal neural-network models, or borrowed from other areas of machine learning. The contributing implementations include element-pair features on each message-passing edge and a crystal space-group embedding. The work not only demonstrates that LLM-agent autonomous research can optimize an expert-designed machine learning model for material property prediction, but also investigates the limitations of such autonomous research.