materials scientists

Abstract: Theoretical predictions of novel materials rely on a variety of techniques, from data-mining-based ion substitution methods to fully de novo generative models. Each approach imposes specific constraints and encounters unique challenges when extrapolating beyond the distribution of known materials to discover new ones. The foremost goal of materials generation is to produce stable, unique, and novel (S.U.N.) structures. Predicted structures that meet these criteria, however, typically result from novel chemical compositions mapped onto known structural prototypes or frameworks. We leverage this heuristic insight to present a new generative paradigm for the de novo prediction of inorganic crystalline materials constrained by their structural framework---i.e., the unit cell shapes and respective particle positions. Our method, termed OMatG-FC (Open Materials Framework-Conditional Generation), learns via a combination of discrete flow matching on the atomic species and stochastic interpolants for the volume scaling of the unit cell lattice, while fixing in-place the fractional coordinates and the unit-volume lattice vectors, dramatically reducing the dimensionality of the problem compared to unconstrained (framework-free) generation. Our method is more flexible than existing prototype-constrained methods, demonstrating capability for discovery of unseen, stable prototypes derived from known structural frameworks. We also investigate the number of unique frameworks in the MP-20 dataset, demonstrating the propensity of duplicate frameworks within the dataset and providing a framework-split version. We benchmark the performance of our model using the LeMat-GenBench suite using three ML interatomic potentials and achieve state-of-the-art S.U.N. rate below the convex hull, eschewing the need to learn atomic packings for materials discovery.

Abstract: Diffusion and flow matching models offer scalable approaches to generating crystalline materials, molecular conformers, and protein-ligand complexes. However, satisfying crystallographic symmetry, structural geometry, and accurate stereochemistry remains challenging. Satisfying these requirements calls for corrections that preserve the geometry already captured by the pretrained model. In this work, we propose AtomSteer, a test-time inference framework for steering pretrained atomistic generative models with structural constraints. During sampling, AtomSteer corrects intermediate structure predictions with bounded local projections, graph-rigid stereochemical transformations, and projections over periodic symmetries, accepting updates that improve constraint satisfaction while limiting changes to the rest of the structure. We demonstrate AtomSteer across three pretrained backbones, FlowMM, ET-Flow, and Boltz-2, spanning de novo crystal generation and crystal structure prediction, molecular conformer generation, and protein-ligand complex structure prediction. AtomSteer improves space-group distribution coverage in de novo crystal generation and improves target space-group recovery in crystal structure prediction. AtomSteer improves molecular validity and E/Z stereochemical accuracy while retaining conformer ensemble fidelity. For protein-ligand complexes, AtomSteer reduces ligand E/Z errors relative to experimental reference structures while achieving competitive docking success and PoseBusters validity. Our method provides a unified framework for adding chemical and crystallographic control to existing atomistic generative models without retraining or architectural changes.

Abstract: What is the intrinsic reason of emergence of macroscopic order parameter out of microscopic systems? In this article, we apply to physics the collective predictive coding (CPC), the theory of language/symbol emergence. As our language emerges out of our human communications, physical macroscopic order parameter emerges out of communications among atoms --- each atom is regarded as an agent who predicts each other's behavior through inference. We present three examples of classical spin systems: two-dimensional ferromagnetic and antiferromagnetic Ising models, a two-dimensional spin model with competing stripe orders, and the fully connected Sherrington--Kirkpatrick spin-glass model. In all of these examples, proper macroscopic order parameters including the replica overlap emerge automatically through communication informatics of CPC, only from observed spin configurations. We call the learned macroscopic coordinate the collective predictive order. Furthermore, for the ferromagnetic and antiferromagnetic Ising models, the equilibrium distribution of the collective predictive order yields an emergent potential with the symmetry and thermal evolution characteristic of a Landau potential. Notably, the emergence of the collective predictive order does not refer to any structure of microscopic Hamiltonians/Lagrangians. Thus our ``Atom-as-an-Agent" (AaaA) principle offers a completely data-driven method for the emergence of macroscopic order, that is, machine learning physics.

Abstract: Density functional theory (DFT) gives the electronic structure of materials, but its cost limits large-supercell calculations and materials screening. Machine-learned Hamiltonians bypass the self-consistent cycle but are usually system-specific; universal ones could cover new compositions and disordered solids. Such models must generalize across chemistry and keep downstream properties physical, while staying inexpensive for large cells. Here we introduce UniTB, a universal E(3) equivariant Hamiltonian representation framework that integrates physical priors rooted in density-functional tight-binding theory with deep learning. UniTB's network, which corrects a prior Hamiltonian, generalizes across chemistry through a mixture of experts routed by that prior and a charge-equilibration head as in self-consistent-charge tight binding. A projection bounds band shifts from the prior, suppressing spurious states and keeping downstream properties physical. We provide the fastest SO(2) tensor-product GPU kernels for the network. The variant UniTB-Flash assembles its prior from two-center tables at $O(N)$ cost for $N$ atoms, against $O(N\log N)$ on a grid. Trained on 29,242 crystals, UniTB reaches a 0.48 meV matrix-element error on nonmagnetic test crystals spanning 68 elements. Without amorphous training data, both models agree with DFT optics and conductivity of amorphous Ge-Sb-Te. UniTB-Flash ranks candidates with no significant difference from UniTB, whose property values are more accurate; together they screen 16,195 crystals for five application domains of industrial relevance.

Abstract: Deep graph generators (DGGs) largely lack interpretability, which is a significant limitation for one of their most crucial applications, drug discovery, where interpretable and transparent generation could provide greater control over the desirability of generated molecules, thereby reducing trial-and-error in candidate selection. Common approaches to interpretability, such as disentanglement, cannot guarantee that the learned representations are human-interpretable. To address this, we propose incorporating concept bottlenecks into DGGs, allowing users to interpret, debug, and steer the generation process. We show that this consistently improves distributional fidelity (lower FCD), with only modest, non-systematic effects on validity and uniqueness. We further explore Concept Controller, an optimization-based steering approach that has proven to be effective for steerable image generation. We evaluate our approach on a one-shot molecular graph generation framework, though the underlying ideas can be transferred to sequential graph generation as well.

Abstract: Graph Neural Networks are widely used to learn structural representations of relational data. Hierarchical graph pooling learns multi-level representations by progressively coarsening graphs; however, prior methods rely on predefined cluster numbers or fixed pooling ratios, limiting adaptability to individual graphs. We propose Graph-Dependent Pooling (GDPool), which dynamically determines pooling granularity for each graph. We analyze optimization conflicts among layer-wise objectives through gradient alignment, showing that independently supervised pooling levels can send conflicting gradients to shared parameters. GDPool uses self-attention to select graph-specific anchors representing structurally important nodes and constructs coarse graphs through soft node assignment. Experiments on metal-organic framework and molecular graph benchmarks show that GDPool consistently achieves the best predictive performance across all benchmarks. Evaluations using modularity and the effective number of clusters show that GDPool achieves consistently higher modularity than existing methods while the number of active clusters decreases monotonically with depth. Sensitivity analyses confirm stable behavior across hyperparameter and architectural choices.

Abstract: Predicting molecular magnetism often requires electronic-structure calculations with spin-orbit coupling (SOC), which are costly to repeat across many molecules. The underlying electronic states can transform as spinors, yet equivariant surrogates typically use only integer-rank features. Inspired by the spinor nature of these electronic states, we develop eSpinor, an SU(2)-equivariant graph neural network that propagates spinor features. We initialize spinor features from eigenvectors of an approximate SOC Hamiltonian and use gauge-covariant message passing with a gauge-invariant readout to make predictions independent of the arbitrary eigenbasis choice. On cobalt single-molecule magnet candidates, eSpinor improves zero-field-splitting predictions relative to NequIP, including for unseen ligands. For a dysprosium magnetic resonance imaging probe, eSpinor improves real electron-spin correlations over a Hamiltonian-informed baseline despite similar static crystal-field errors and fewer parameters, while accurately predicting low-field nuclear relaxation in water and after transfer to methanol without retraining. Overall, these results demonstrate that SU(2)-equivariant spinor message passing is a useful inductive bias for molecular magnetism. We also find that similar static tensor errors can yield different dynamical errors, motivating model selection based on accuracy for the intended physical observables.

Abstract: Reticular chemistry allows metal-organic frameworks (MOFs) to be designed from their building units, yet their synthesis remains constrained by sparse experimental data, noisy crystallization outcomes, and the absence of benchmarks for comparing active-learning strategies. While data-driven approaches such as Bayesian optimization (BO) can improve synthesis success rates, selecting appropriate optimizers beforehand for mapping MOF crystallization landscapes remains largely empirical. Here we present ActMOF, an experiment-grounded benchmark for comparing search strategies in aluminum-carboxylate MOF synthesis. ActMOF is emulated from experimentally measured microwave syntheses with each encoded condition assigned a crystallinity index calculated based on diffraction peak intensity and full width at half-maximum. By benchmarking policies guided by Gaussian processes (GP), tree ensembles and large language models (LLM), ActMOF placed the GP family among the leading policies for active learning in sparse synthesis landscapes. It then demonstrated transferability by guiding the microwave synthesis of six reticularly related aluminum MOFs. All six campaigns gave crystalline products within a fixed budget of 12 experiments each, and established a reusable testbed for AI-driven MOF synthesis.

Abstract: Microscopic simulations resolve spatial patterns but are feasible only over small domains and short timescales, whereas bulk descriptions erase those patterns through spatial averaging. Mesoscopic fields preserve this spatial organisation, but their effective equations are known only for selected microscopic systems and scaling limits. We introduce Deep Mesoscopic Dynamics (DeepMesoD), which uses neural networks to learn an effective mesoscopic field equation from microscopic trajectories at a prescribed coarse-graining scale. For the nonconserved dissipative dynamics studied here, DeepMesoD learns the free-energy functional with a spatial interaction kernel and a state-dependent dissipation operator constrained by the fluctuation-dissipation relation. We first validate the construction in the Ising-Kac model, where the learned mesoscopic equation recovers the known hydrodynamic limit and rollouts remain stable far beyond the training horizon. We then treat two systems without closed-form mesoscopic descriptions. For a two-dimensional Heisenberg ferromagnet governed by atomistic spin dynamics, DeepMesoD learns a mesoscopic model whose predictions match atomistic references up to 1 ns, and a rollout with an unseen initial condition remains bounded up to 25 ns. For layered CrBr$_3$, the learned kernel captures the suppression and sign reversal of interlayer coupling at a stacking fault whose location and strength are not supplied as inputs. Controlled changes to the learned interaction show how fault number and placement shape multistep magnetic responses, complementing our magneto-photoluminescence measurements. Across the two atomistic systems, DeepMesoD achieves a three-to-four-order-of-magnitude reduction in wall-clock time compared with atomistic spin dynamics.

Abstract: How can language models learn to optimize physical designs through experience? We introduce FracLearn, an experience-abstraction-generalization framework evaluated through a deliberately unfamiliar, Tetris-inspired fracture game. The model first proposes architectures and examines simulated fracture responses to accumulate experience. Abstraction organizes these observations into conditional principles linking reinforcement placement, crack evolution and load transfer, with supporting evidence and failure conditions. Generalization challenges the model to combine these principles in new architectures and surpass the earlier design record. Campaigns demonstrate progressive refinement and recovery through hypothesis revision, yielding a best composite score 11.0% above the experience-stage record. Fracture analyses connect improved performance to crack deflection and temporary trapping as toughening mechanisms, alongside greater residual load capacity. Learning occurs through external knowledge and decisions, without model-weight updates. This approach offers a route to scientific agents that turn computational experiments into reusable physical knowledge for materials discovery and engineering design.

Abstract: Determining crystal structures from powder X-ray diffraction (PXRD) would enable routine characterization of newly synthesized materials, including those absent from reference databases. Generative models offer a promising approach, but existing evaluations remain fragmented and largely assume single-phase samples with known composition. To fill this gap, we introduce PXRD-Bench, a unified benchmark that extends evaluation to unknown per-element atom counts and recovery of both structures in two-phase mixtures. It provides approximately 4.1 million training structures with simulated PXRD, tests generalization to unseen compositions and structural prototypes, and evaluates recovery from experimental PXRD after excluding structurally matching training entries. To provide a strong reference baseline, we also introduce Bragglite, a PXRD-to-structure model developed through a systematic study of PXRD modeling choices. It achieves a 44.2\% Top-1 match rate on experimental RRUFF patterns with known composition, 24.6\% above the strongest prior baseline. Further analysis yields several key findings: some models fail to benefit from experimental PXRD, while generalization to unseen structural prototypes and recovery from two-phase mixtures remain challenging. Together, our benchmark, systematic studies, and Bragglite clarify the capabilities and limitations of current PXRD-to-structure models.

Abstract: Large-scale self-supervised pretraining has reshaped modern machine learning, substantially advancing the ability of language and vision models to generalize across downstream tasks. While deep learning has driven considerable progress in modeling atomistic systems in recent years, self-supervised pretraining in this domain has not yet achieved comparable downstream generalization. To address this, we introduce Atom-JEPA, a self-supervised pretraining framework that learns latent representations from unlabeled 3D structures through complementary atom-level and substructure-level objectives inspired by joint-embedding predictive architectures. We pretrain Atom-JEPA on large-scale molecular and crystalline datasets and evaluate its transfer performance by fine-tuning on a diverse set of downstream property prediction tasks. Atom-JEPA achieves state-of-the-art performance on molecular ADMET and quantum-chemical property prediction tasks, and is highly competitive in predicting the physical properties of crystalline materials. These results demonstrate the potential of latent-space predictive pretraining to support broad downstream generalization from structural data alone. Code and pretrained model checkpoints are publicly available at https://github.com/khelverskovp/atom-jepa

Abstract: Classical force fields (FFs) remain the workhorse for large-scale simulations even as machine-learned interatomic potentials (MLIPs) approach ab initio accuracy. They decompose total configuration energies into simple effective interactions whose parameters are traditionally assigned based on atom or bond types, enabling efficient simulations but also limiting their ability to adapt across configurations. Recent machine learning approaches have improved the accuracy and transferability of bonded parameters in these FFs by inferring them as functions of local atomic environments, but still rely on empirical nonbonded parameters for practical simulations. In this work, we introduce a unified approach, \texttt{grappa-fullFF}, which learns both bonded and nonbonded parameters \emph{consistently} and simultaneously from ab initio reference data. By incorporating physically inspired regularization via supervision of the electrostatic potential and an architecture that facilitates charge equilibration, our model recovers accurate electric response properties, achieves state-of-the-art accuracy on geometry optimization benchmarks, and reproduces the conformational sampling of both classical and existing machine-learned FFs, without relying on externally assigned nonbonded parameters.

Abstract: Modern graph generative models typically operate directly in the discrete graph space, explicitly generating node and edge variables, which can become costly as graphs grow. In this paper, we perform generation explicitly on latent representations of entire graphs obtained from a pretrained Variational Autoencoder with high reconstruction fidelity. The generated representations, obtained through flow matching, are then decoded only at the final step. Across molecular benchmarks of increasing size, our approach achieves strong validity and FCD while offering a favorable quality-efficiency trade-off compared with state-of-the-art explicit graph generative models. One of the main advantages of this formulation is that the graph representation only needs to be learned once, after which the same one can be reused across multiple generative objectives without retraining. We demonstrate generation guided by molecular properties and further introduce validity-aware generation though a classifier learned directly in latent space. All code will be made available upon acceptance.

Abstract: Recovering complete phase sets from powder X-ray diffraction (PXRD) is challenging when weak-phase peaks overlap stronger signals. A natural strategy is to identify phases iteratively, removing the contribution of each identified phase from the observed pattern before predicting the next. However, even after a phase is correctly identified, misestimating its contribution can distort the residual and cause subsequent errors. We introduce PhaseMatcher, an autoregressive framework for complete phase-set identification with physics-guided spectral decomposition. After each phase prediction, PhaseMatcher re-estimates the contributions of all selected phases and the residual from the original observation and all selected reference patterns, accounting for physically plausible variation between reference patterns and the corresponding phase contributions in the observation. The resulting residual guides subsequent phase identification, while a separate stopping module determines when the phase set is complete. On synthetic mixtures and controlled mixtures constructed from measured single-phase patterns, PhaseMatcher improves complete-set identification over the evaluated baselines. On PhaseMix-135K, it also estimates contributions and residuals more accurately than scalar subtraction.

Abstract: In this paper, we unravel the effect of different decoder architectures on the interpretability of the latent space of the Physically Recurrent Neural Network. Particular emphasis is given to a new weight normalization constraint, which acts as a regularization technique and enables robust training in the low-data regime. A brief visual exploration illustrates how these changes impact the latent space and how the fictitious stress can align with the true state of the RVE without explicit training. Reaping the benefits of a meaningful latent space, a case study illustrates how information from the microscopic level can be retrieved and incorporated into a multi-task approach that does not require extra parameters or larger training sets. Another key contribution shows that a specific architectural choice can naturally lead to a thermodynamically consistent formulation. By enforcing an adjoint encoder-decoder structure with positive scalar contributions, this modification ensures energy consistency across scales and non-negative dissipation, leading to even lower training requirements. This alternative completes the study on interpretability, inductive bias, and thermodynamic consistency, and demonstrates that data efficiency can be improved with careful architectural choices rooted in the underlying physics.

Abstract: Yield point phenomena in metals, anticracks in soils and snows, or planewise collapses in lattice metamaterials, are different manifestations of plastic instabilities characterized by stress softening and strain localization. Several independent constitutive descriptions exist and suffer from similar challenges: experimental difficulties to link local events to global measurements, and computational lack of convergence, spurious localization and mesh sensitivity. This work proposes a minimal field-agnostic constitutive framework where plastic softening is represented by a damage-like internal variable which explicitly separates stable hardening behavior from unstable softening. The resulting formulation admits a variational structure and can leverage regularization tools originally developed by the ductile fracture community. The framework aims at emphasizing similarities within plastic instability phenomena and establishing a bridge with continuum damage mechanics, to open a path towards regularized variational formulations of localized plastic flows.

Abstract: Equivariant machine learning interatomic potentials (MLIPs) have revolutionized atomistic modeling, but accurate treatment of complex materials and molecular systems demands expensive models. This limits simulation length- and time-scales, with tensor products a key computational bottleneck. The recent emergence of foundation-scale MLIPs further exacerbates this challenge. We present Branch Interatomic Potential (BranchIP), a single-model framework for learned adaptive tensor product computation, trained with a novel distillation loss. In our experiments on two systems of physical interest, a heterogeneous catalysis system and a proton-conducting solid acid electrolyte, BranchIP accelerates MLIPs across model sizes by up to $2.4\times$ while reducing memory usage by up to $2.6\times$. This is achieved while maintaining physical fidelity. Furthermore, the learned adaptive computation provides model interpretability by revealing which interactions demand deeper computation and showing how computational depth relates to chemical complexity and dynamics.

Abstract: Simulating microstructure evolution requires quantum-mechanical accuracy and mesoscopic reach in length and time scales, a combination that no current method achieves. Classical phase-field models provide this reach, but their accuracy is limited by phenomenological free energies and mobilities. Here we develop a framework for learning ab initio phase-field models, where the mesoscopic equation is not postulated but derived from a Mori-Zwanzig projection of molecular dynamics onto species-density fields under explicit assumptions. The nonlocal free energy and mobility left unspecified by this equation are parametrized by neural networks and learned from short molecular dynamics trajectories generated with machine-learning interatomic potentials of ab initio accuracy. We demonstrate the framework on an iron-boron melt and on hydrogen-helium mixtures under planetary conditions. For iron-boron, the model shows that the melt at the FeB$_4$ composition is spinodally unstable at ambient pressure but stabilized at 10 GPa, offering a thermodynamic rationale for why FeB$_4$ has been synthesized only under high pressure. For hydrogen-helium, the model predicts the immiscibility boundary and captures droplet nucleation and growth in helium-rain simulations of a column corresponding to 2.2 million atoms, far beyond the scale of atomistic modeling at comparable accuracy. Trained across compositions and conditions, such models could provide a mesoscopic counterpart to ab initio molecular dynamics.

Abstract: Bayesian Optimisation (BO) is a powerful framework for the optimisation of expensive black-box functions, but typically requires refitting a surrogate and maximising an acquisition function at every evaluation step. In-context approaches based on Prior-data Fitted Networks (PFNs) amortise part of this cost by pre-training transformers on functions drawn from synthetic priors. PFNs4BO amortises the surrogate but still relies on a numerically maximised acquisition function, while FIBO performs BO fully in-context by sampling optimiser locations from a learned density, which fixes the decision rule and admits no surrogate. Learned acquisition functions score a finite candidate set with a trained network, but, lacking a label for the query, learn the score by reinforcement learning on previously solved tasks. We propose IQS-BO, a PFN that learns the query decision by supervised learning on synthetic priors. In a single forward pass, IQS-BO predicts the probability that each candidate maximises the objective over the set, and we show that the minimiser of its objective is the posterior probability of this event. The model can be pre-trained without a surrogate for fully in-context BO, or take the predictions of a fixed probabilistic surrogate as additional input, amortising only the decision step. Our method proposes queries at a fraction of the cost of acquisition-based methods, while either matching or outperforming standard BO with Gaussian processes (GPs) and available in-context methods on synthetic and real-world benchmarks. Finally, we propose a mixture prior for pre-training PFNs which combines samples from GPs with functions exhibiting warped inputs, isolated narrow optima, or plateaus that are poorly modeled by stationary kernels common in GP surrogates. We show that pre-training on this prior can lead to improved optimisation performance.

Abstract: Final predictive accuracy is the standard basis for comparing graph neural networks (GNNs) in materials-property prediction, but it does not show how strongly performance depends on access to trainable parameter-space directions. Here, we introduce trainable-degree dependence as a complementary characterization of materials GNN learning. Using random-subspace intrinsic-dimension analysis, we train CGCNN, ALIGNN, and DimeNet++ in randomly oriented parameter subspaces across six prediction tasks and measure how performance recovers as independent trainable degrees of freedom are restored. The resulting recovery curves separate endpoint accuracy from the trainable-dimensional demand required to recover it. They reveal distinctions that final errors alone miss: metallic classification and log-bulk-modulus regression recover near-reference performance from small fractional subspaces, formation-energy and band-gap prediction show stronger architecture dependence, and phonon prediction is most sensitive to dimensional restriction. Dataset-size sweeps show that band-gap models require larger fractional subspaces as training data grows, whereas formation-energy and bulk-modulus responses are more stable. A width sweep shows that fractional thresholds can remain stable while absolute threshold dimensions increase with model size. Random-subspace analysis therefore provides a targeted stress test for how materials GNNs use their optimization space.

Abstract: In materials machine learning, closely related retained structures can sustain accurate property predictions even after removing a specific record, rendering post-deletion prediction error an ambiguous metric for machine unlearning. To resolve this ambiguity, we define the deletion floor as the expected target loss under a specified retraining procedure at the deleted request. Standard indistinguishability constraints yield a sharp interval bounding an update's target loss around this baseline reference. Theoretically, a conditional neighbor bound links a low deletion floor directly to retained fit, prediction regularity, and local label agreement, while an exact ridge identity isolates residual fit from the prediction change induced by record deletion. Empirically, controlled redundancy sweeps show an $\approx 8\times$ drop in median normalized retraining loss when one retained relative remains after deletion. Across two distinct fitting regimes in a paired Materials Project study, the lower-floor regime also exhibits a larger prediction change on more than 50% of the shared requests. Systematic comparisons against approximate updates and the original model decouple deliberate target suppression from preserved overall model utility. Consequently, request-level unlearning evaluations should report reference loss, prediction change, and retained utility together, interpreting post-deletion accuracy against what retraining itself leaves behind.

Abstract: Soft electroactive composites can exhibit strongly architecture-dependent mechanical and electrical responses, but explicitly resolving dense fiber networks in three dimensions is computationally expensive. We develop a mixed-dimensional finite-element formulation in which electroactive fibers are represented by geometrically exact beams embedded in a deformable dielectric matrix. Unlike existing electroactive beam formulations in which the electric potential is defined directly on the beam, the embedded fibers here are driven by the three-dimensional electric field of the surrounding matrix. The matrix field is sampled along the beam centerlines and enters the beam dielectric enthalpy directly, providing two-way electromechanical coupling without introducing independent electric-potential degrees of freedom on the beams. Beam and matrix mechanics are coupled through projected mortar constraints, and the electromechanical problem is solved monolithically. We use the formulation as the microscale model in a periodic homogenization framework to compute effective stress and electric displacement. Verification studies quantify discretization and field-sampling sensitivity, followed by structured and irregular network examples that demonstrate architecture-dependent mechanical and electrical responses without body-fitted three-dimensional fiber meshes.

Abstract: De novo 3D molecular generation jointly models molecular size, topology, and geometry. Most methods pre-sample molecular size and generate Cartesian coordinates, limiting variable-size conditional tasks such as fragment completion and scaffold decoration while often relying on equivariant architectures. Internal-coordinate methods avoid rigid-body redundancy but typically require a known molecular graph or autoregressive construction, which may accumulate errors. We propose TreeRef, a tree-based molecular representation that assigns molecular topology and topology-dependent local 3D geometry to a naturally variable-size tree. RingRef nodes encode ring closures while preserving the tree structure, while Null nodes allow molecular size to emerge directly from node occupancy. Based on TreeRef, we develop TreeRef-BFN, a Bayesian Flow Network with a standard Transformer backbone that globally couples these locally defined variables and jointly generates discrete molecular variables and continuous local geometry. A single pretrained TreeRef-BFN supports unconditional generation and variable-size structure-conditioned 3D generation through masking alone, without retraining. Empirical studies demonstrate strong chemical validity, molecular stability, and diversity, accurate local geometric distributions, fast sampling, and competitive property-conditioned generation, establishing TreeRef-BFN as an efficient and flexible framework for 3D molecular generation.

Abstract: Vibrational spectral prediction can become inaccurate when localized stereoelectronic environments perturb intermediate response states and high-risk response units dominate characteristic spectral fingerprints, making prediction across external chemical space difficult. SO(3) Equivariant Neural Kalman Networks (SENK) form a response-state cascade that combines an equivariant transformer backbone for Hessian, dipole-derivative and polarizability-derivative learning, an Equivariant Neural Kalman bridge for state-dependent refinement and reliability sensing, and an NBO-informed electronic-prior pathway coupling consistency regularization with bounded, branch-specific guided spectral calibration. SENK outperforms DetaNet on QM9S and QMe14S while preserving full-spectrum IR and Raman fidelity from small molecules to drug-like systems. SENK remains stable and selectively improves spectrally sensitive features in biomolecular systems with complex stereoelectronic effects. It therefore integrates tensor prediction, reliability diagnosis and physics-informed calibration, supporting transferable vibrational spectroscopy from molecular systems to functional molecular materials.

Abstract: Deep generative models are widely reported to enable de novo crystal structure prediction (CSP), but their capability has not been measured consistently against template-based methods. We evaluate 12 representative generative CSP models, spanning latent-variable, diffusion, flow-matching, autoregressive, and manifold random-walk architectures, against TCSP 2.0 on 180 test structures and a leakage-controlled subset of 46. All methods use identical structure-matching, symmetry, and consensus criteria. Template retrieval is the strongest single method, reaching 68.3% top-1 success; symmetry-aware EquiCSP (66.4%) and Uni-3DAR (62.9%) form the next tier. However, comparison with TCSP 2.0 shows that most structures correctly predicted by generative models are also correctly predicted by template substitution. Thus, the set of structures uniquely reachable by generation is small, limiting its practical advantage for discovering structures outside existing prototype libraries. To test the source of this performance, we removed entire stoichiometric prototype families from the training set and retrained the strongest generative model. Accuracy declined by 50-78% across four families, establishing that performance is substantially prototype-dependent. A small minority of structures survived removal of their prototype family, demonstrating a real but limited retrieval-independent predictive capacity. Present generative CSP models therefore function largely as implicit, softer-edged prototype libraries rather than genuinely de novo predictors. Enlarging this residual capacity, rather than aggregate match rate alone, is the central open problem.

Abstract: Four-dimensional scanning transmission electron microscopy (4D-STEM) records a two-dimensional diffraction pattern at each electron-probe position, yielding spatially resolved reciprocal-space information but large, heterogeneous data volumes. Here we describe 4D-ImageNet, a collection of 174,000 diffraction patterns comprising 145,000 experimental patterns selected from 29 acquisitions and 29,000 multislice simulations. The experimental data cover acquisition-level labels for Ag, Au, mixed Au-Ag, CoO, Pd and ZnO specimens across multiple fields of view, scan dimensions, camera lengths and exposure times. Each acquisition contributes 5,000 quality-ranked patterns with source scan coordinates and acquisition metadata. A set-prediction detector provides model-derived pseudo-labels for the direct-beam position and Bragg-disk centres, with a confidence score for each disk. The simulation data cover 13 crystal structures and include Euler rotations, reciprocal-space sampling and approximate low-index beam directions. A grouped mixed-domain masked-reconstruction benchmark is provided to assess leakage-resistant loading and evaluation across experimental and simulated data. The dataset is intended for representation learning, disk detection, diffraction-pattern retrieval, orientation analysis and simulation-to-experiment studies.

Abstract: The Hohenberg-Kohn theorem establishes that, in principle, the ground state (GS) charge density contains all GS information of a many-electron system, such that all GS observables can be expressed as functionals of the GS charge density. Conventional Kohn-Sham density functional theory requires iterative solution of the self-consistent-field equations at substantial computational cost, motivating the development of deep learning surrogates for electronic structure calculations and, in turn, accelerating computer-aided materials design. Here, we propose \textbf{AIDEN}, an \underline{A}tomic-\underline{I}nteraction \underline{D}ensity \underline{E}quivariant \underline{N}etwork for solving real-space charge density. AIDEN separates the element-dependent one-center density from environment-induced density redistribution and represents the latter through complementary atom- and edge-centered tensor correlations. A continuous low-rank Gaussian decoder then reconstructs the density at arbitrary spatial coordinates while reusing atomic encodings independently of the evaluation grid. AIDEN achieves state-of-the-art accuracy on periodic crystal benchmarks while remaining competitive for molecular systems, and further demonstrates zero-shot transferability across several structurally distinct out-of-distribution case studies. Furthermore, AIDEN provides substantially faster inference than both baseline models and full SCF calculations, enabling efficient charge density reconstruction for large-scale electronic structure calculations.

Abstract: Quantum reservoir computing (QRC) uses quantum dynamics to represent input histories for prediction through a trained classical readout. Discrete time crystals (DTCs) exhibit robust subharmonic responses under periodic driving, and previous work has used their dynamics to construct DTC-QRC. Here we construct a DTC-based reservoir architecture to predict molecular properties from structural and dynamical observations. Coherent Floquet evolution processes local molecular graph events and surface-hopping frames, while controlled reset regulates the contribution of earlier inputs. Measurements at the end of each input sequence yield a feature vector of fixed dimension. Trained classical decoders use this vector for inhibitor-activity and blood--brain-barrier permeability classification and electronic-gap forecasting, while the reservoir parameters remain fixed during training. With matched input lengths and output widths, DTC-QRC outperforms echo-state networks on long-prefix graph classification and the studied ethene gap forecasting tasks. Dephasing lowers performance in both applications, consistent with a role for coherent propagation. Experiments on the Quafu superconducting quantum cloud platform show that pair observables retain task information under device noise. The architecture provides a common framework for molecular screening and time-resolved property prediction using quantum reservoir computing.