Rui Jiao

Rui Jiao, Jiaqi Han, Wenbing Huang et al.

Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of characterizing 3D geometry and thus defective for downstream 3D tasks. In this work, we tackle 3D molecular pretraining in a complete and novel sense. In particular, we first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merits of fulfilling the symmetry of 3D space. Then we develop a node-level pretraining loss for force prediction, where we further exploit the Riemann-Gaussian distribution to ensure the loss to be E(3)-invariant, enabling more robustness. Moreover, a graph-level noise scale prediction task is also leveraged to further promote the eventual performance. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9. Experimental results demonstrate the efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component.

Rui Jiao, Wenbing Huang, Peijia Lin et al.

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

Peijia Lin, Pin Chen, Rui Jiao et al.

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

Zhixun Li, Bin Cao, Rui Jiao et al.

Materials are the foundation of modern society, underpinning advancements in energy, electronics, healthcare, transportation, and infrastructure. The ability to discover and design new materials with tailored properties is critical to solving some of the most pressing global challenges. In recent years, the growing availability of high-quality materials data combined with rapid advances in Artificial Intelligence (AI) has opened new opportunities for accelerating materials discovery. Data-driven generative models provide a powerful tool for materials design by directly create novel materials that satisfy predefined property requirements. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. To fill this gap, this paper provides a comprehensive overview of recent progress in AI-driven materials generation. We first organize various types of materials and illustrate multiple representations of crystalline materials. We then provide a detailed summary and taxonomy of current AI-driven materials generation approaches. Furthermore, we discuss the common evaluation metrics and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future directions and challenges in this fast-growing field. The related sources can be found at https://github.com/ZhixunLEE/Awesome-AI-for-Materials-Generation.

Liming Wu, Rui Jiao, Qi Li et al.

The design of materials with tailored properties is crucial for technological progress. However, most deep generative models focus exclusively on perfectly ordered crystals, neglecting the important class of disordered materials. To address this gap, we introduce DMFlow, a generative framework specifically designed for disordered crystals. Our approach introduces a unified representation for ordered, Substitutionally Disordered (SD), and Positionally Disordered (PD) crystals, and employs a flow matching model to jointly generate all structural components. A key innovation is a Riemannian flow matching framework with spherical reparameterization, which ensures physically valid disorder weights on the probability simplex. The vector field is learned by a novel Graph Neural Network (GNN) that incorporates physical symmetries and a specialized message-passing scheme. Finally, a two-stage discretization procedure converts the continuous weights into multi-hot atomic assignments. To support research in this area, we release a benchmark containing SD, PD, and mixed structures curated from the Crystallography Open Database. Experiments on Crystal Structure Prediction (CSP) and De Novo Generation (DNG) tasks demonstrate that DMFlow significantly outperforms state-of-the-art baselines adapted from ordered crystal generation. We hope our work provides a foundation for the AI-driven discovery of disordered materials.

Xixian Liu, Rui Jiao, Zhiyuan Liu et al.

Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising methods rely on oversimplied molecular dynamics that assume atomic motions to be isotropic and homoscedastic. To address these limitations, we propose a novel denoising framework AniDS: Anisotropic Variational Autoencoder for 3D Molecular Denoising. AniDS introduces a structure-aware anisotropic noise generator that can produce atom-specific, full covariance matrices for Gaussian noise distributions to better reflect directional and structural variability in molecular systems. These covariances are derived from pairwise atomic interactions as anisotropic corrections to an isotropic base. Our design ensures that the resulting covariance matrices are symmetric, positive semi-definite, and SO(3)-equivariant, while providing greater capacity to model complex molecular dynamics. Extensive experiments show that AniDS outperforms prior isotropic and homoscedastic denoising models and other leading methods on the MD17 and OC22 benchmarks, achieving average relative improvements of 8.9% and 6.2% in force prediction accuracy. Our case study on a crystal and molecule structure shows that AniDS adaptively suppresses noise along the bonding direction, consistent with physicochemical principles. Our code is available at https://github.com/ZeroKnighting/AniDS.

Rui Jiao, Wenbing Huang, Yu Liu et al.

Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods seldom consider the space group constraint which is crucial in describing the geometry of crystals and closely relevant to many desirable properties. However, considering space group constraint is challenging owing to its diverse and nontrivial forms. In this paper, we reduce the space group constraint into an equivalent formulation that is more tractable to be handcrafted into the generation process. In particular, we translate the space group constraint into two parts: the basis constraint of the invariant logarithmic space of the lattice matrix and the Wyckoff position constraint of the fractional coordinates. Upon the derived constraints, we then propose DiffCSP++, a novel diffusion model that has enhanced a previous work DiffCSP by further taking space group constraint into account. Experiments on several popular datasets verify the benefit of the involvement of the space group constraint, and show that our DiffCSP++ achieves promising performance on crystal structure prediction, ab initio crystal generation and controllable generation with customized space groups.

Jiaqi Han, Jiacheng Cen, Liming Wu et al.

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Mingze Li, Yu Rong, Songyou Li et al.

The discovery of novel materials is critical for global energy and quantum technology transitions. While deep learning has fundamentally reshaped this landscape, existing predictive or generative models typically operate in isolation, lacking the autonomous orchestration required to execute the full discovery process. Here we present ElementsClaw, an agentic framework for materials discovery that synergizes Large Atomic Models (LAMs) with Large Language Models (LLMs). In response to varied human requirements, ElementsClaw dynamically orchestrates a suite of LAM tools finetuned from our proposed model Elements for atomic-scale numerical computation, while leveraging LLMs for high-level semantic reasoning. This shift moves AI-driven materials science from isolated processes toward integrated and human interactive discovery. In the demanding domain of superconductors, our agentic system guides the experimental synthesis of four new superconductors, including Zr3ScRe8 with a transition temperature of 6.8 K and HfZrRe4 at 6.7 K. At scale, ElementsClaw screens more than 2.4 million stable crystals within only 28 GPU hours, identifying 68,000 high-confidence superconducting candidates and vastly expanding the known superconducting space. These results demonstrate how our agent accelerates materials discovery with high physical fidelity.

Liming Wu, Wenbing Huang, Rui Jiao et al.

Crystal Structure Prediction (CSP), which aims to generate stable crystal structures from compositions, represents a critical pathway for discovering novel materials. While structure prediction tasks in other domains, such as proteins, have seen remarkable progress, CSP remains a relatively underexplored area due to the more complex geometries inherent in crystal structures. In this paper, we propose Siamese foundation models specifically designed to address CSP. Our pretrain-finetune framework, named DAO, comprises two complementary foundation models: DAO-G for structure generation and DAO-P for energy prediction. Experiments on CSP benchmarks (MP-20 and MPTS-52) demonstrate that our DAO-G significantly surpasses state-of-the-art (SOTA) methods across all metrics. Extensive ablation studies further confirm that DAO-G excels in generating diverse polymorphic structures, and the dataset relaxation and energy guidance provided by DAO-P are essential for enhancing DAO-G's performance. When applied to three real-world superconductors ($\text{CsV}_3\text{Sb}_5$, $ \text{Zr}_{16}\text{Rh}_8\text{O}_4$ and $\text{Zr}_{16}\text{Pd}_8\text{O}_4$) that are known to be challenging to analyze, our foundation models achieve accurate critical temperature predictions and structure generations. For instance, on $\text{CsV}_3\text{Sb}_5$, DAO-G generates a structure close to the experimental one with an RMSE of 0.0085; DAO-P predicts the $T_c$ value with high accuracy (2.26 K vs. the ground-truth value of 2.30 K). In contrast, conventional DFT calculators like Quantum Espresso only successfully derive the structure of the first superconductor within an acceptable time, while the RMSE is nearly 8 times larger, and the computation speed is more than 1000 times slower. These compelling results collectively highlight the potential of our approach for advancing materials science research and development.

Xiangzhe Kong, Zishen Zhang, Ziting Zhang et al.

The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability to enhance model performance. In this paper, we introduce Unified generative Modeling of 3D Molecules (UniMoMo), the first framework capable of designing binders of multiple molecular domains using a single model. In particular, UniMoMo unifies the representations of different molecules as graphs of blocks, where each block corresponds to either a standard amino acid or a molecular fragment. Subsequently, UniMoMo utilizes a geometric latent diffusion model for 3D molecular generation, featuring an iterative full-atom autoencoder to compress blocks into latent space points, followed by an E(3)-equivariant diffusion process. Extensive benchmarks across peptides, antibodies, and small molecules demonstrate the superiority of our unified framework over existing domain-specific models, highlighting the benefits of multi-domain training.

Rui Jiao, Xiangzhe Kong, Li Zhang et al.

Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models in a specific domain, either proteins or small molecules, missing the opportunity to leverage cross-domain knowledge. To mitigate this gap, we introduce Equivariant Pretrained Transformer (EPT), an all-atom foundation model that can be pretrained from multiple domain 3D molecules. Built upon an E(3)-equivariant transformer, EPT is able to not only process atom-level information but also incorporate block-level features (e.g. residuals in proteins). Additionally, we employ a block-level denoising task, rather than the conventional atom-level denoising, as the pretraining objective. To pretrain EPT, we construct a large-scale dataset of 5.89M entries, comprising small molecules, proteins, protein-protein complexes, and protein-molecule complexes. Experimental evaluations on downstream tasks including ligand binding affinity prediction, protein property prediction, and molecular property prediction, show that EPT significantly outperforms previous state-of-the-art methods in the first task and achieves competitively superior performance for the remaining two tasks. Furthermore, we demonstrate the potential of EPT in identifying small molecule drug candidates targeting 3CL protease, a critical target in the replication of SARS-CoV-2. Among 1,978 FDA-approved drugs, EPT ranks 7 out of 8 known anti-COVID-19 drugs in the top 200, indicating the high recall of EPT. By using Molecular Dynamics (MD) simulations, EPT further discoveries 7 novel compounds whose binding affinities are higher than that of the top-ranked known anti-COVID-19 drug, showcasing its powerful capabilities in drug discovery.

Rui Jiao, Yue Zhang, Jinku Li

We present a novel framework addressing a critical vulnerability in Large Language Models (LLMs): the prevalence of factual inaccuracies within intermediate reasoning steps despite correct final answers. This phenomenon poses substantial risks in high-stakes domains including healthcare, legal analysis, and scientific research, where erroneous yet confidently presented reasoning can mislead users into dangerous decisions. Our framework integrates three core components: (1) a specialized fact-checking classifier trained on counterfactually augmented data to detect subtle factual inconsistencies within reasoning chains; (2) an enhanced Group Relative Policy Optimization (GRPO) reinforcement learning approach that balances factuality, coherence, and structural correctness through multi-dimensional rewards; and (3) a mechanistic interpretability method examining how factuality improvements manifest in model activations during reasoning processes. Extensive evaluation across multi state-of-the-art models reveals concerning patterns: even leading models like Claude-3.7 and GPT-o1 demonstrate reasoning factual accuracy of only 81.93% and 82.57% respectively. Our approach significantly enhances factual robustness (up to 49.90% improvement) while maintaining or improving performance on challenging benchmarks including Math-500, AIME-2024, and GPQA. Furthermore, our neural activation-level analysis provides actionable insights into how factual enhancements reshape reasoning trajectories within model architectures, establishing foundations for future training methodologies that explicitly target factual robustness through activation-guided optimization.

Dapeng Jiang, Xiangzhe Kong, Jiaqi Han et al.

Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the gap, we propose CP-Composer, a novel generative framework that enables zero-shot cyclic peptide generation via composable geometric constraints. Our approach decomposes complex cyclization patterns into unit constraints, which are incorporated into a diffusion model through geometric conditioning on nodes and edges. During training, the model learns from unit constraints and their random combinations in linear peptides, while at inference, novel constraint combinations required for cyclization are imposed as input. Experiments show that our model, despite trained with linear peptides, is capable of generating diverse target-binding cyclic peptides, reaching success rates from 38% to 84% on different cyclization strategies.

Rui Jiao, Zonghan Yang, Maosong Sun et al.

While synthetic bilingual corpora have demonstrated their effectiveness in low-resource neural machine translation (NMT), adding more synthetic data often deteriorates translation performance. In this work, we propose alternated training with synthetic and authentic data for NMT. The basic idea is to alternate synthetic and authentic corpora iteratively during training. Compared with previous work, we introduce authentic data as guidance to prevent the training of NMT models from being disturbed by noisy synthetic data. Experiments on Chinese-English and German-English translation tasks show that our approach improves the performance over several strong baselines. We visualize the BLEU landscape to further investigate the role of authentic and synthetic data during alternated training. From the visualization, we find that authentic data helps to direct the NMT model parameters towards points with higher BLEU scores and leads to consistent translation performance improvement.