arXiv subjects

Jianjun Hu

Publications and source records attributed to Jianjun Hu.

At least 19 recordsLinked to original sources

arXiv2026

uFlowCSP: Crystal Structure Prediction using Mean flow generative models

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.

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arXiv2026

Foundation-Model Surrogates Enable Data-Efficient Active Learning for Materials Discovery

Active learning (AL) has emerged as a powerful paradigm for accelerating materials discovery by iteratively steering experiments toward promising candidates, reducing the number of costly synthesis-and-characterization cycles needed to identify optimal materials. However, current AL relies predominantly on Gaussian Process (GP) and Random Forest (RF) surrogates, which suffer from complementary limitations: GP underfits complex composition-property landscapes due to rigid kernel assumptions, while RF produces unreliable heuristic uncertainty estimates in small-data regimes. This small-data challenge is pervasive in materials science, making reliable surrogate modeling extremely difficult with models trained from scratch on each new dataset. Here we propose In-Context Active Learning (ICAL), which addresses this bottleneck by replacing conventional surrogates with TabPFN, a transformer-based foundation model (FM) pre-trained on millions of synthetic regression tasks to meta-learn a universal prior over tabular data, upon which TabPFN performs principled Bayesian inference in a single forward pass without dataset-specific retraining, delivering strong small-data regression performance and well-calibrated predictive uncertainty (required for effective AL). We benchmark ICAL against GP and RF across 10 materials datasets and TabPFN wins on 8 out of 10 datasets, achieving a mean saving of 52% in extra evaluations relative to GP and 29.77% relative to RF. Cross-validation analysis confirms that TabPFN's advantage stems from superior uncertainty calibration, achieving the lowest Negative Log-Likelihood and Area Under the Sparsification Error curve among all surrogates. These results demonstrate that pre-trained FMs can serve as effective surrogates for active learning, enabling data-efficient discovery across diverse materials systems and small-data experimental sciences.

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arXiv2025

In context learning Foundation models for Materials Property Prediction with Small datasets

Foundation models (FMs) have recently shown remarkable in-context learning (ICL) capabilities across diverse scientific domains. In this work, we introduce a unified in-context learning foundation model (ICL-FM) framework for materials property prediction that integrates both composition-based and structure-aware representations. The proposed approach couples the pretrained TabPFN transformer with graph neural network (GNN)-derived embeddings and our novel MagpieEX descriptors. MagpieEX augments traditional features with cation-anion interaction data to explicitly measure bond ionicity and charge-transfer asymmetry, capturing interatomic bonding characteristics that influence vibrational and thermal transport properties. Comprehensive experiments on the MatBench benchmark suite and a standalone lattice thermal conductivity (LTC) dataset demonstrate that ICL-FM achieves competitive or superior performance to state-of-the-art (SOTA) models with significantly reduced training costs. Remarkably, the training-free ICL-FM outperformed sophisticated SOTA GNN models in five out of six representative composition-based tasks, including a significant 9.93\% improvement in phonon frequency prediction. On the LTC dataset, the FM effectively models complex phenomena such as phonon-phonon scattering and atomic mass contrast. t-SNE analysis reveals that the FM acts as a physics-aware feature refiner, transforming raw, disjoint feature clusters into continuous manifolds with gradual property transitions. This restructured latent space enhances interpolative prediction accuracy while aligning learned representations with underlying physical laws. This study establishes ICL-FM as a generalizable, data-efficient paradigm for materials informatics.

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arXiv2025

Facet: highly efficient E(3)-equivariant networks for interatomic potentials

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

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arXiv2025

Data-Driven Topological Analysis of Polymorphic Crystal Structures

Polymorphism, the ability of a compound to crystallize in multiple distinct structures, plays a vital role in determining the physical, chemical, and functional properties of materials. Accurate identification and prediction of polymorphic structures are critical for materials design, drug development, and device optimization, as unknown or overlooked polymorphs may lead to unexpected performance or stability issues. Despite its significance, predicting polymorphism directly from a chemical composition remains a challenging problem due to the complex interplay between molecular conformations, crystal packing, and symmetry constraints. In this study, we conduct a comprehensive data-driven analysis of polymorphic materials from the Materials Project database, uncovering key statistical patterns in their composition, space group distributions, and polyhedral building blocks. We discover that frequent polymorph pairs across space groups, such as (71, 225), display recurring topological motifs that persist across different compounds, highlighting topology not symmetry alone as a key factor in polymorphic recurrence. We reveal that many polymorphs exhibit consistent local polyhedral environments despite differences in their symmetry or packing. Additionally, by constructing polyhedron connectivity graphs and embedding their topology, we successfully cluster polymorphs and structurally similar materials even across different space groups, demonstrating that topological similarity serves as a powerful descriptor for polymorphic behavior. Our findings provide new insights into the structural characteristics of polymorphic materials and demonstrate the potential of data mining and machine learning for accelerating polymorph discovery and design.

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arXiv2025

Polymorphism Crystal Structure Prediction with Adaptive Space Group Diversity Control

Crystalline materials can form different structural arrangements (i.e. polymorphs) with the same chemical composition, exhibiting distinct physical properties depending on how they were synthesized or the conditions under which they operate. For example, carbon can exist as graphite (soft, conductive) or diamond (hard, insulating). Computational methods that can predict these polymorphs are vital in materials science, which help understand stability relationships, guide synthesis efforts, and discover new materials with desired properties without extensive trial-and-error experimentation. However, effective crystal structure prediction (CSP) algorithms for inorganic polymorph structures remain limited. We propose ParetoCSP2, a multi-objective genetic algorithm for polymorphism CSP that incorporates an adaptive space group diversity control technique, preventing over-representation of any single space group in the population guided by a neural network interatomic potential. Using an improved population initialization method and performing iterative structure relaxation, ParetoCSP2 not only alleviates premature convergence but also achieves improved convergence speed. Our results show that ParetoCSP2 achieves excellent performance in polymorphism prediction, including a nearly perfect space group and structural similarity accuracy for formulas with two polymorphs but with the same number of unit cell atoms. Evaluated on a benchmark dataset, it outperforms baseline algorithms by factors of 2.46-8.62 for these accuracies and improves by 44.8\%-87.04\% across key performance metrics for regular CSP. Our source code is freely available at https://github.com/usccolumbia/ParetoCSP2.

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arXiv2025

TCSP 2.0: Template Based Crystal Structure Prediction with Improved Oxidation State Prediction and Chemistry Heuristics

Crystal structure prediction remains a major challenge in materials science, directly impacting the discovery and development of next-generation materials. We introduce TCSP 2.0, a substantial evolution of our template-based crystal structure prediction framework that advances predictive capabilities through synergistic integration of several key techniques into its major components. Building upon TCSP 1.0's template-matching foundation, this enhanced version implements three critical innovations: (1) replacement of Pymatgen with deep learning-based BERTOS model for oxidation state prediction with superior performance, (2) implementation of sophisticated element embedding distance metrics for improved chemical similarity assessment, and (3) development of a robust majority voting mechanism for space group selection that reduces prediction uncertainty. TCSP 2.0 also expands its template base by incorporating template structures from Materials Cloud, C2DB, and GNoME databases alongside the original Materials Project repository, creating a more comprehensive structural foundation. Rigorous validation across 180 diverse test cases of the CSPBenchmark demonstrates TCSP 2.0's exceptional performance, achieving 83.89% space-group success rate and 78.33% structural similarity accuracy for top-5 predictions, substantially outperforming both its predecessor and the competing modern CSP algorithms including CSPML and EquiCSP.

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arXiv2024

Accelerating Discovery of Extreme Lattice Thermal Conductivity by Crystal Attention Graph Neural Network (CATGNN) Using Chemical Bonding Intuitive Descriptors

Designing materials with targeted lattice thermal conductivity (LTC) demands electronic-level insight into chemical bonding. We introduce two bonding descriptors, namely normalized negative integrated crystal orbital Hamilton populations (-ICOHP) and normalized integrated crystal orbital bond index (ICOBI), that strongly correlate with LTC and rattling (mean-squared displacement), surpassing empirical rules and the unnormalized -ICOHP across >4,500 inorganic crystals by first-principles. We train a Crystal Attention Graph Neural Network (CATGNN) to predict these descriptors and screen ~200,000 database structures for extreme LTCs. From 367 (533) candidates with low (high) normalized -ICOHP and normalized ICOBI, first-principles validation identifies 106 dynamically stable compounds with LTC <5 W/mK (68% <2 W/mK) and 13 stable compounds with LTC >100 W/mK. The descriptors' low cost and clear physical meaning provide a rapid, reliable route to high-throughput discovery and inverse design of crystalline materials with ultralow or ultrahigh LTC for applications in thermal insulation, thermoelectrics, and electronics cooling.

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arXiv2024

Out-of-distribution materials property prediction using adversarial learning based fine-tuning

The accurate prediction of material properties is crucial in a wide range of scientific and engineering disciplines. Machine learning (ML) has advanced the state of the art in this field, enabling scientists to discover novel materials and design materials with specific desired properties. However, one major challenge that persists in material property prediction is the generalization of models to out-of-distribution (OOD) samples,i.e., samples that differ significantly from those encountered during training. In this paper, we explore the application of advancements in OOD learning approaches to enhance the robustness and reliability of material property prediction models. We propose and apply the Crystal Adversarial Learning (CAL) algorithm for OOD materials property prediction,which generates synthetic data during training to bias the training towards those samples with high prediction uncertainty. We further propose an adversarial learning based targeting finetuning approach to make the model adapted to a particular OOD dataset, as an alternative to traditional fine-tuning. Our experiments demonstrate the success of our CAL algorithm with its high effectiveness in ML with limited samples which commonly occurs in materials science. Our work represents a promising direction toward better OOD learning and materials property prediction.

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arXiv2024

Physical Encoding Improves OOD Performance in Deep Learning Materials Property Prediction

Deep learning (DL) models have been widely used in materials property prediction with great success, especially for properties with large datasets. However, the out-of-distribution (OOD) performances of such models are questionable, especially when the training set is not large enough. Here we showed that using physical encoding rather than the widely used one-hot encoding can significantly improve the OOD performance by increasing the models' generalization performance, which is especially true for models trained with small datasets. Our benchmark results of both composition- and structure-based deep learning models over six datasets including formation energy, band gap, refractive index, and elastic properties predictions demonstrated the importance of physical encoding to OOD generalization for models trained on small datasets.

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arXiv2024

CSPBench: a benchmark and critical evaluation of Crystal Structure Prediction

Crystal structure prediction (CSP) is now increasingly used in discovering novel materials with applications in diverse industries. However, despite decades of developments and significant progress in this area, there lacks a set of well-defined benchmark dataset, quantitative performance metrics, and studies that evaluate the status of the field. We aim to fill this gap by introducing a CSP benchmark suite with 180 test structures along with our recently implemented CSP performance metric set. We benchmark a collection of 13 state-of-the-art (SOTA) CSP algorithms including template-based CSP algorithms, conventional CSP algorithms based on DFT calculations and global search such as CALYPSO, CSP algorithms based on machine learning (ML) potentials and global search, and distance matrix based CSP algorithms. Our results demonstrate that the performance of the current CSP algorithms is far from being satisfactory. Most algorithms cannot even identify the structures with the correct space groups except for the template-based algorithms when applied to test structures with similar templates. We also find that the ML potential based CSP algorithms are now able to achieve competitive performances compared to the DFT-based algorithms. These CSP algorithms' performance is strongly determined by the quality of the neural potentials as well as the global optimization algorithms. Our benchmark suite comes with a comprehensive open-source codebase and 180 well-selected benchmark crystal structures, making it convenient to evaluate the advantages and disadvantages of CSP algorithms from future studies. All the code and benchmark data are available at https://github.com/usccolumbia/cspbenchmark

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arXiv2024

AlphaCrystal-II: Distance matrix based crystal structure prediction using deep learning

Computational prediction of stable crystal structures has a profound impact on the large-scale discovery of novel functional materials. However, predicting the crystal structure solely from a material's composition or formula is a promising yet challenging task, as traditional ab initio crystal structure prediction (CSP) methods rely on time-consuming global searches and first-principles free energy calculations. Inspired by the recent success of deep learning approaches in protein structure prediction, which utilize pairwise amino acid interactions to describe 3D structures, we present AlphaCrystal-II, a novel knowledge-based solution that exploits the abundant inter-atomic interaction patterns found in existing known crystal structures. AlphaCrystal-II predicts the atomic distance matrix of a target crystal material and employs this matrix to reconstruct its 3D crystal structure. By leveraging the wealth of inter-atomic relationships of known crystal structures, our approach demonstrates remarkable effectiveness and reliability in structure prediction through comprehensive experiments. This work highlights the potential of data-driven methods in accelerating the discovery and design of new materials with tailored properties.

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arXiv2024

Structure-based out-of-distribution (OOD) materials property prediction: a benchmark study

In real-world material research, machine learning (ML) models are usually expected to predict and discover novel exceptional materials that deviate from the known materials. It is thus a pressing question to provide an objective evaluation of ML model performances in property prediction of out-of-distribution (OOD) materials that are different from the training set distribution. Traditional performance evaluation of materials property prediction models through random splitting of the dataset frequently results in artificially high performance assessments due to the inherent redundancy of typical material datasets. Here we present a comprehensive benchmark study of structure-based graph neural networks (GNNs) for extrapolative OOD materials property prediction. We formulate five different categories of OOD ML problems for three benchmark datasets from the MatBench study. Our extensive experiments show that current state-of-the-art GNN algorithms significantly underperform for the OOD property prediction tasks on average compared to their baselines in the MatBench study, demonstrating a crucial generalization gap in realistic material prediction tasks. We further examine the latent physical spaces of these GNN models and identify the sources of CGCNN, ALIGNN, and DeeperGATGNN's significantly more robust OOD performance than those of the current best models in the MatBench study (coGN and coNGN), and provide insights to improve their performance.

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arXiv2024

Physics guided dual Self-supervised learning for structure-based materials property prediction

Deep learning (DL) models have now been widely used for high-performance material property prediction for properties such as formation energy and band gap. However, training such DL models usually requires a large amount of labeled data, which is usually not available for most materials properties such as exfoliation energy and elastic properties. Self-supervised learning (SSL) methods have been proposed to address this data scarcity issue by learning inherent representations from unlabeled data in various research fields. Herein, we present DSSL, a physics-guided Dual SSL framework, for graph neural networks (GNNs) based material property prediction. This hybrid framework combines node-masking based predictive SSL with atomic coordinate perturbation based contrastive SSL strategies, allowing it to learn structural embeddings that capture both local and global information of input crystals. Especially, we propose to use predicting the macroproperty (e.g. elasticity) related microproperty such as atomic stiffness as an additional pretext task to achieve physics-guided pretraining process. We pretrain our DSSL model on the Materials Project database with unlabeled data and finetune it with ten extra datasets with different material properties. The experimental results demonstrate that teaching neural networks some physics using the SSL strategy can bring up to 26.89\% performance improvement compared to the baseline GNN models. Our source code is now freely available at https://github.com/usccolumbia/DSSL

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arXiv2023

Deep Learning-Based Classification of Gamma Photon Interactions in Room-Temperature Semiconductor Radiation Detectors

Photon counting radiation detectors have become an integral part of medical imaging modalities such as Positron Emission Tomography or Computed Tomography. One of the most promising detectors is the wide bandgap room temperature semiconductor detectors, which depends on the interaction gamma/x-ray photons with the detector material involves Compton scattering which leads to multiple interaction photon events (MIPEs) of a single photon. For semiconductor detectors like CdZnTeSe (CZTS), which have a high overlap of detected energies between Compton and photoelectric events, it is nearly impossible to distinguish between Compton scattered events from photoelectric events using conventional readout electronics or signal processing algorithms. Herein, we report a deep learning classifier CoPhNet that distinguishes between Compton scattering and photoelectric interactions of gamma/x-ray photons with CdZnTeSe (CZTS) semiconductor detectors. Our CoPhNet model was trained using simulated data to resemble actual CZTS detector pulses and validated using both simulated and experimental data. These results demonstrated that our CoPhNet model can achieve high classification accuracy over the simulated test set. It also holds its performance robustness under operating parameter shifts such as Signal-Noise-Ratio (SNR) and incident energy. Our work thus laid solid foundation for developing next-generation high energy gamma-rays detectors for better biomedical imaging.

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arXiv2023

Generative Design of inorganic compounds using deep diffusion language models

Due to the vast chemical space, discovering materials with a specific function is challenging. Chemical formulas are obligated to conform to a set of exacting criteria such as charge neutrality, balanced electronegativity, synthesizability, and mechanical stability. In response to this formidable task, we introduce a deep learning-based generative model for material composition and structure design by learning and exploiting explicit and implicit chemical knowledge. Our pipeline first uses deep diffusion language models as the generator of compositions and then applies a template-based crystal structure prediction algorithm to predict their corresponding structures, which is then followed by structure relaxation using a universal graph neural network-based potential. The density functional theory (DFT) calculations of the formation energies and energy-above-the-hull analysis are used to validate new structures generated through our pipeline. Based on the DFT calculation results, six new materials, including Ti2HfO5, TaNbP, YMoN2, TaReO4, HfTiO2, and HfMnO2, with formation energy less than zero have been found. Remarkably, among these, four materials, namely Ti2$HfO5, TaNbP, YMoN2, and TaReO4, exhibit an e-above-hull energy of less than 0.3 eV. These findings have proved the effectiveness of our approach.

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arXiv2023

Crystal structure prediction using neural network potential and age-fitness Pareto genetic algorithm

While crystal structure prediction (CSP) remains a longstanding challenge, we introduce ParetoCSP, a novel algorithm for CSP, which combines a multi-objective genetic algorithm (MOGA) with a neural network inter-atomic potential (IAP) model to find energetically optimal crystal structures given chemical compositions. We enhance the NSGA-III algorithm by incorporating the genotypic age as an independent optimization criterion and employ the M3GNet universal IAP to guide the GA search. Compared to GN-OA, a state-of-the-art neural potential based CSP algorithm, ParetoCSP demonstrated significantly better predictive capabilities, outperforming by a factor of $2.562$ across $55$ diverse benchmark structures, as evaluated by seven performance metrics. Trajectory analysis of the traversed structures of all algorithms shows that ParetoCSP generated more valid structures than other algorithms, which helped guide the GA to search more effectively for the optimal structures

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arXiv2023

Towards Quantitative Evaluation of Crystal Structure Prediction Performance

Crystal structure prediction (CSP) is now increasingly used in the discovery of novel materials with applications in diverse industries. However, despite decades of developments, the problem is far from being solved. With the progress of deep learning, search algorithms, and surrogate energy models, there is a great opportunity for breakthroughs in this area. However, the evaluation of CSP algorithms primarily relies on manual structural and formation energy comparisons. The lack of a set of well-defined quantitative performance metrics for CSP algorithms make it difficult to evaluate the status of the field and identify the strengths and weaknesses of different CSP algorithms. Here, we analyze the quality evaluation issue in CSP and propose a set of quantitative structure similarity metrics, which when combined can be used to automatically determine the quality of the predicted crystal structures compared to the ground truths. Our CSP performance metrics can be then utilized to evaluate the large set of existing and emerging CSP algorithms, thereby alleviating the burden of manual inspection on a case-by-case basis. The related open-source code can be accessed freely at https://github.com/usccolumbia/CSPBenchMetrics

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