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Rongzhi Dong

Publications and source records attributed to Rongzhi Dong.

At least 19 recordsLinked to original sources
arXiv2026

Deep Generative Crystal Structure Prediction: A Benchmark Study and a Controlled Test of Prototype Dependence

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.

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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

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

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

Improving realistic material property prediction using domain adaptation based machine learning

Materials property prediction models are usually evaluated using random splitting of datasets into training and test datasets, which not only leads to over-estimated performance due to inherent redundancy, typically existent in material datasets, but also deviate away from the common practice of materials scientists: they are usually interested in predicting properties for a known subset of related out-of-distribution (OOD) materials rather than a universally distributed samples. Feeding such target material formulas/structures to the machine learning models should improve the prediction performance while most current machine learning (ML) models neglect this information. Here we propose to use domain adaptation (DA) to enhance current ML models for property prediction and evaluate their performance improvements in a set of five realistic application scenarios. Our systematic benchmark studies show that there exist DA models that can significantly improve the OOD test set prediction performance while standard ML models and most of the other DAs cannot improve or even deteriorate the performance. Our benchmark datasets and DA code can be freely accessed at https://github.com/Little-Cheryl/MatDA.

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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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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

AlphaCrystal: Contact map based crystal structure prediction using deep learning

Crystal structure prediction is one of the major unsolved problems in materials science. Traditionally, this problem is formulated as a global optimization problem for which global search algorithms are combined with first principle free energy calculations to predict the ground-state crystal structure given only a material composition or a chemical system. These ab initio algorithms usually cannot exploit a large amount of implicit physicochemical rules or geometric constraints (deep knowledge) of atom configurations embodied in a large number of known crystal structures. Inspired by the deep learning enabled breakthrough in protein structure prediction, herein we propose AlphaCrystal, a crystal structure prediction algorithm that combines a deep residual neural network model that learns deep knowledge to guide predicting the atomic contact map of a target crystal material followed by reconstructing its 3D crystal structure using genetic algorithms. Based on the experiments of a selected set of benchmark crystal materials, we show that our AlphaCrystal algorithm can predict structures close to the ground truth structures. It can also speed up the crystal structure prediction process by predicting and exploiting the predicted contact map so that it has the potential to handle relatively large systems. We believe that our deep learning based ab initio crystal structure prediction method that learns from existing material structures can be used to scale up current crystal structure prediction practice. To our knowledge, AlphaCrystal is the first neural network based algorithm for crystal structure contact map prediction and the first method for directly reconstructing crystal structures from materials composition, which can be further optimized by DFT calculations.

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arXiv2023

Global mapping of structures and properties of crystal materials

Understanding material composition-structure-function relationships is of critical importance for the design and discovery of novel functional materials. While most such studies focus on individual materials, we conducted a global mapping study of all known materials deposited in the Material Project database to investigate their distributions in the space of a set of seven compositional, structural, physical, and neural latent descriptors. These two-dimensional materials maps along with their density maps allow us to illustrate the distribution of the patterns and clusters of different shapes, which indicates the propensity of these materials and the tinkering history of existing materials. We then overlap the material properties such as composition prototypes and piezoelectric properties over the background materials maps to study the relationships of how material compositions and structures affect their physical properties. We also use these maps to study the spatial distributions of properties of known inorganic materials, in particular those of local vicinities in structural space such as structural density and functional diversity. These maps provide a uniquely comprehensive overview of materials and space and thus reveal previously undescribed fundamental properties. Our methodology can be easily extended by other researchers to generate their own global material maps with different background maps and overlap properties for both distribution understanding and cluster-based new material discovery. The source code for feature generation and generated maps are available at https://github.com/usccolumbia/matglobalmapping

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arXiv2023

Discovery of 2D materials using Transformer Network based Generative Design

Two-dimensional (2D) materials have wide applications in superconductors, quantum, and topological materials. However, their rational design is not well established, and currently less than 6,000 experimentally synthesized 2D materials have been reported. Recently, deep learning, data-mining, and density functional theory (DFT)-based high-throughput calculations are widely performed to discover potential new materials for diverse applications. Here we propose a generative material design pipeline, namely material transformer generator(MTG), for large-scale discovery of hypothetical 2D materials. We train two 2D materials composition generators using self-learning neural language models based on Transformers with and without transfer learning. The models are then used to generate a large number of candidate 2D compositions, which are fed to known 2D materials templates for crystal structure prediction. Next, we performed DFT computations to study their thermodynamic stability based on energy-above-hull and formation energy. We report four new DFT-verified stable 2D materials with zero e-above-hull energies, including NiCl$_4$, IrSBr, CuBr$_3$, and CoBrCl. Our work thus demonstrates the potential of our MTG generative materials design pipeline in the discovery of novel 2D materials and other functional materials.

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arXiv2022

Materials Property Prediction with Uncertainty Quantification: A Benchmark Study

Uncertainty quantification (UQ) has increasing importance in building robust high-performance and generalizable materials property prediction models. It can also be used in active learning to train better models by focusing on getting new training data from uncertain regions. There are several categories of UQ methods each considering different types of uncertainty sources. Here we conduct a comprehensive evaluation on the UQ methods for graph neural network based materials property prediction and evaluate how they truly reflect the uncertainty that we want in error bound estimation or active learning. Our experimental results over four crystal materials datasets (including formation energy, adsorption energy, total energy, and band gap properties) show that the popular ensemble methods for uncertainty estimation is NOT the best choice for UQ in materials property prediction. For the convenience of the community, all the source code and data sets can be accessed freely at \url{https://github.com/usccolumbia/materialsUQ}.

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arXiv2022

Materials Transformers Language Models for Generative Materials Design: a benchmark study

Pre-trained transformer language models on large unlabeled corpus have produced state-of-the-art results in natural language processing, organic molecule design, and protein sequence generation. However, no such models have been applied to learn the composition patterns of inorganic materials. Here we train a series of seven modern transformer language models (GPT, GPT-2, GPT-Neo, GPT-J, BLMM, BART, and RoBERTa) using the expanded formulas from material deposited in the ICSD, OQMD, and Materials Projects databases. Six different datasets with/out non-charge-neutral or balanced electronegativity samples are used to benchmark the performances and uncover the generation biases of modern transformer models for the generative design of materials compositions. Our extensive experiments showed that the causal language models based materials transformers can generate chemically valid materials compositions with as high as 97.54\% to be charge neutral and 91.40\% to be electronegativity balanced, which has more than 6 times higher enrichment compared to a baseline pseudo-random sampling algorithm. These models also demonstrate high novelty and their potential in new materials discovery has been proved by their capability to recover the leave-out materials. We also find that the properties of the generated samples can be tailored by training the models with selected training sets such as high-bandgap materials. Our experiments also showed that different models each have their own preference in terms of the properties of the generated samples and their running time complexity varies a lot. We have applied our materials transformer models to discover a set of new materials as validated using DFT calculations.

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arXiv2022

DeepXRD, a Deep Learning Model for Predicting of XRD spectrum from Materials Composition

One of the long-standing problems in materials science is how to predict a material's structure and then its properties given only its composition. Experimental characterization of crystal structures has been widely used for structure determination, which is however too expensive for high-throughput screening. At the same time, directly predicting crystal structures from compositions remains a challenging unsolved problem. Herein we propose a deep learning algorithm for predicting the XRD spectrum given only the composition of a material, which can then be used to infer key structural features for downstream structural analysis such as crystal system or space group classification or crystal lattice parameter determination or materials property predictions. Benchmark studies on two datasets show that our DeepXRD algorithm can achieve good performance for XRD prediction as evaluated over our test sets. It can thus be used in high-throughput screening in the huge materials composition space for new materials discovery.

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arXiv2021

TCSP: a Template based crystal structure prediction algorithm and web server for materials discovery

Fast and accurate crystal structure prediction (CSP) algorithms and web servers are highly desirable for exploring and discovering new materials out of the infinite design space. However, currently, the computationally expensive first principle calculation based crystal structure prediction algorithms are applicable to relatively small systems and are out of reach of most materials researchers due to the requirement of high computing resources or the software cost related to ab initio code such as VASP. Several computational teams have used an element substitution approach for generating or predicting new structures, but usually in an ad hoc way. Here we develop a template based crystal structure prediction algorithm (TCSP) and its companion web server, which makes this tool to be accessible to all materials researchers. Our algorithm uses elemental/chemical similarity and oxidation states to guide the selection of template structures and then rank them based on the substitution compatibility and can return multiple predictions with ranking scores in a few minutes. Benchmark study on the ~98,290 formulas of the Materials Project database using leave-one-out evaluation shows that our algorithm can achieve high accuracy (for 13,145 target structures, TCSP predicted their structures with RMSD < 0.1) for a large portion of the formulas. We have also used TCSP to discover new materials of the Ga-B-N system showing its potential for high-throughput materials discovery. Our user-friendly web app TCSP can be accessed freely at \url{www.materialsatlas.org/crystalstructure} on our MaterialsAtlas.org web app platform.

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