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Bin Shao

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12 papers

2 author rows

ICML Conference 2025 Conference Paper

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

Erpai Luo
Xinran Wei
Lin Huang
Yunyang Li
Han Yang
Zaishuo Xia
Zun Wang
Chang Liu 0030

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost—driven by high-order tensor product (TP) operations—restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPH Net, an efficient and scalable equivariant network, that incorporates adaptive SP arsity into H amiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

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ICLR Conference 2025 Conference Paper

Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems

Yunyang Li
Zaishuo Xia
Lin Huang
Xinran Wei
Samuel Harshe
Han Yang
Erpai Luo
Zun Wang

Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18\%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

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TMLR Journal 2025 Journal Article

SE3Set: Harnessing Equivariant Hypergraph Neural Networks for Molecular Representation Learning

Hongfei Wu
Lijun Wu
Guoqing Liu
Zhirong Liu
Bin Shao
Zun Wang

In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning. Hypergraphs are not merely an extension of traditional graphs; they are pivotal for modeling high-order relationships, a capability that conventional equivariant graph-based methods lack due to their inherent limitations in representing intricate many-body interactions. To achieve this, we first construct hypergraphs by proposing a new fragmentation method that considers both chemical and three-dimensional spatial information of the molecular system. We then design SE3Set, which incorporates equivariance into the hypergraph neural network. This ensures that the learned molecular representations are invariant to spatial transformations, thereby providing robustness essential for the accurate prediction of molecular properties. SE3Set has shown performance on par with state-of-the-art (SOTA) models for small molecule datasets like QM9 and MD17. It demonstrates outstanding performance on the MD22 dataset, achieving a remarkable ~20\% improvement in accuracy across all molecules. Furthermore, on the OE62 dataset, SE3Set outperforms all short-range models. We also conducted a detailed analysis of OE62, highlighting the prevalence of complex many-body interactions in large molecules. This exceptional performance of SE3Set across diverse molecular structures underscores its transformative potential in computational chemistry, offering a route to more accurate and physically nuanced modeling. The code of this work is available at https://github.com/Navantock/SE3Set.

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NeurIPS Conference 2024 Conference Paper

Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models

Zun Wang
Chang Liu
Nianlong Zou
He Zhang
Xinran Wei
Lin Huang
Lijun Wu
Bin Shao

In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Models (DEQs) for predicting Density Functional Theory (DFT) Hamiltonians. The DEQH model inherently captures the self-consistency nature of Hamiltonian, a critical aspect often overlooked by traditional machine learning approaches for Hamiltonian prediction. By employing DEQ within our model architecture, we circumvent the need for DFT calculations during the training phase to introduce the Hamiltonian's self-consistency, thus addressing computational bottlenecks associated with large or complex systems. We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians. When benchmarked on the MD17 and QH9 datasets, DEQHNet, an instantiation of the DEQH framework, has demonstrated a significant improvement in prediction accuracy. Beyond a predictor, the DEQH model is a Hamiltonian solver, in the sense that it uses the fixed-point solving capability of the deep equilibrium model to iteratively solve for the Hamiltonian. Ablation studies of DEQHNet further elucidate the network's effectiveness, offering insights into the potential of DEQ-integrated networks for Hamiltonian learning. We open source our implementation at https: //github. com/Zun-Wang/DEQHNet.

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ICLR Conference 2024 Conference Paper

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

Yunyang Li
Yusong Wang
Lin Huang
Han Yang
Xinran Wei
Jia Zhang 0004
Tong Wang 0014
Zun Wang

Computational simulation of chemical and biological systems using *ab initio* molecular dynamics has been a challenge over decades. Researchers have attempted to address the problem with machine learning and fragmentation-based methods. However, the two approaches fail to give a satisfactory description of long-range and many-body interactions, respectively. Inspired by fragmentation-based methods, we propose the Long-Short-Range Message-Passing (LSR-MP) framework as a generalization of the existing equivariant graph neural networks (EGNNs) with the intent to incorporate long-range interactions efficiently and effectively. We apply the LSR-MP framework to the recently proposed ViSNet and demonstrate the state-of-the-art results with up to 40% MAE reduction for molecules in MD22 and Chignolin datasets. Consistent improvements to various EGNNs will also be discussed to illustrate the general applicability and robustness of our LSR-MP framework. The code for our experiments and trained model weights could be found at https://github.com/liyy2/LSR-MP.

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NeurIPS Conference 2024 Conference Paper

Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs

Yusong Wang
Chaoran Cheng
Shaoning Li
Yuxuan Ren
Bin Shao
Ge Liu
Pheng-Ann Heng
Nanning Zheng

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce **Neural P$^3$M**, a versatile enhancer of geometric GNNs to expand the scope of their capabilities by incorporating mesh points alongside atoms and reimaging traditional mathematical operations in a trainable manner. Neural P$^3$M exhibits flexibility across a wide range of molecular systems and demonstrates remarkable accuracy in predicting energies and forces, outperforming on benchmarks such as the MD22 dataset. It also achieves an average improvement of 22% on the OE62 dataset while integrating with various architectures. Codes are available at https: //github. com/OnlyLoveKFC/Neural_P3M.

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ICML Conference 2024 Conference Paper

Self-Consistency Training for Density-Functional-Theory Hamiltonian Prediction

He Zhang
Chang Liu 0030
Zun Wang
Xinran Wei
Siyuan Liu 0005
Nanning Zheng 0001
Bin Shao
Tie-Yan Liu

Predicting the mean-field Hamiltonian matrix in density functional theory is a fundamental formulation to leverage machine learning for solving molecular science problems. Yet, its applicability is limited by insufficient labeled data for training. In this work, we highlight that Hamiltonian prediction possesses a self-consistency principle, based on which we propose self-consistency training, an exact training method that does not require labeled data. It distinguishes the task from predicting other molecular properties by the following benefits: (1) it enables the model to be trained on a large amount of unlabeled data, hence addresses the data scarcity challenge and enhances generalization; (2) it is more efficient than running DFT to generate labels for supervised training, since it amortizes DFT calculation over a set of queries. We empirically demonstrate the better generalization in data-scarce and out-of-distribution scenarios, and the better efficiency over DFT labeling. These benefits push forward the applicability of Hamiltonian prediction to an ever-larger scale.

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NeurIPS Conference 2024 Conference Paper

UltraPixel: Advancing Ultra High-Resolution Image Synthesis to New Peaks

Jingjing Ren
Wenbo Li
Haoyu Chen
Renjing Pei
Bin Shao
Yong Guo
Long Peng
Fenglong Song

Ultra-high-resolution image generation poses great challenges, such as increased semantic planning complexity and detail synthesis difficulties, alongside substantial training resource demands. We present UltraPixel, a novel architecture utilizing cascade diffusion models to generate high-quality images at multiple resolutions (\textit{e. g. }, 1K, 2K, and 4K) within a single model, while maintaining computational efficiency. UltraPixel leverages semantics-rich representations of lower-resolution images in a later denoising stage to guide the whole generation of highly detailed high-resolution images, significantly reducing complexity. Specifically, we introduce implicit neural representations for continuous upsampling and scale-aware normalization layers adaptable to various resolutions. Notably, both low- and high-resolution processes are performed in the most compact space, sharing the majority of parameters with less than 3$\%$ additional parameters for high-resolution outputs, largely enhancing training and inference efficiency. Our model achieves fast training with reduced data requirements, producing photo-realistic high-resolution images and demonstrating state-of-the-art performance in extensive experiments.

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NeurIPS Conference 2023 Conference Paper

Efficiently incorporating quintuple interactions into geometric deep learning force fields

Zun Wang
Guoqing Liu
Yichi Zhou
Tong Wang
Bin Shao

Machine learning force fields (MLFFs) have instigated a groundbreaking shift in molecular dynamics (MD) simulations across a wide range of fields, such as physics, chemistry, biology, and materials science. Incorporating higher order many-body interactions can enhance the expressiveness and accuracy of models. Recent models have achieved this by explicitly including up to four-body interactions. However, five-body interactions, which have relevance in various fields, are still challenging to incorporate efficiently into MLFFs. In this work, we propose the quintuple network (QuinNet), an end-to-end graph neural network that efficiently expresses many-body interactions up to five-body interactions with \emph{ab initio} accuracy. By analyzing the topology of diverse many-body interactions, we design the model architecture to efficiently and explicitly represent these interactions. We evaluate QuinNet on public datasets of small molecules, such as MD17 and its revised version, and show that it is compatible with other state-of-the-art models on these benchmarks. Moreover, QuinNet surpasses many leading models on larger and more complex molecular systems, such as MD22 and Chignolin, without increasing the computational complexity. We also use QuinNet as a force field for molecular dynamics (MD) simulations to demonstrate its accuracy and stability, and conduct an ablation study to elucidate the significance of five-body interactions. We open source our implementation at https: //github. com/Zun-Wang/QuinNet.

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NeurIPS Conference 2023 Conference Paper

Geometric Transformer with Interatomic Positional Encoding

Yusong Wang
Shaoning Li
Tong Wang
Bin Shao
Nanning Zheng
Tie-Yan Liu

The widespread adoption of Transformer architectures in various data modalities has opened new avenues for the applications in molecular modeling. Nevertheless, it remains elusive that whether the Transformer-based architecture can do molecular modeling as good as equivariant GNNs. In this paper, by designing Interatomic Positional Encoding (IPE) thatparameterizes atomic environments as Transformer's positional encodings, we propose Geoformer, a novel geometric Transformer to effectively model molecular structures for various molecular property prediction. We evaluate Geoformer on several benchmarks, including the QM9 dataset and the recently proposed Molecule3D dataset. Compared with both Transformers and equivariant GNN models, Geoformer outperforms the state-of-the-art (SoTA) algorithms on QM9, and achieves the best performance on Molecule3D for both random and scaffold splits. By introducing IPE, Geoformer paves the way for molecular geometric modeling based on Transformer architecture. Codes are available at https: //github. com/microsoft/AI2BMD/tree/Geoformer.

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ICML Conference 2022 Conference Paper

SE(3) Equivariant Graph Neural Networks with Complete Local Frames

Weitao Du
He Zhang
Yuanqi Du
Qi Meng
Wei Chen 0034
Nanning Zheng 0001
Bin Shao
Tie-Yan Liu

Group equivariance (e. g. SE(3) equivariance) is a critical physical symmetry in science, from classical and quantum physics to computational biology. It enables robust and accurate prediction under arbitrary reference transformations. In light of this, great efforts have been put on encoding this symmetry into deep neural networks, which has been shown to improve the generalization performance and data efficiency for downstream tasks. Constructing an equivariant neural network generally brings high computational costs to ensure expressiveness. Therefore, how to better trade-off the expressiveness and computational efficiency plays a core role in the design of the equivariant deep learning models. In this paper, we propose a framework to construct SE(3) equivariant graph neural networks that can approximate the geometric quantities efficiently. Inspired by differential geometry and physics, we introduce equivariant local complete frames to graph neural networks, such that tensor information at given orders can be projected onto the frames. The local frame is constructed to form an orthonormal basis that avoids direction degeneration and ensure completeness. Since the frames are built only by cross product operations, our method is computationally efficient. We evaluate our method on two tasks: Newton mechanics modeling and equilibrium molecule conformation generation. Extensive experimental results demonstrate that our model achieves the best or competitive performance in two types of datasets.

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NeurIPS Conference 2021 Conference Paper

Co-evolution Transformer for Protein Contact Prediction

He Zhang
Fusong Ju
Jianwei Zhu
Liang He
Bin Shao
Nanning Zheng
Tie-Yan Liu

Proteins are the main machinery of life and protein functions are largely determined by their 3D structures. The measurement of the pairwise proximity between amino acids of a protein, known as inter-residue contact map, well characterizes the structural information of a protein. Protein contact prediction (PCP) is an essential building block of many protein structure related applications. The prevalent approach to contact prediction is based on estimating the inter-residue contacts using hand-crafted coevolutionary features derived from multiple sequence alignments (MSAs). To mitigate the information loss caused by hand-crafted features, some recently proposed methods try to learn residue co-evolutions directly from MSAs. These methods generally derive coevolutionary features by aggregating the learned residue representations from individual sequences with equal weights, which is inconsistent with the premise that residue co-evolutions are a reflection of collective covariation patterns of numerous homologous proteins. Moreover, non-homologous residues and gaps commonly exist in MSAs. By aggregating features from all homologs equally, the non-homologous information may cause misestimation of the residue co-evolutions. To overcome these issues, we propose an attention-based architecture, Co-evolution Transformer (CoT), for PCP. CoT jointly considers the information from all homologous sequences in the MSA to better capture global coevolutionary patterns. To mitigate the influence of the non-homologous information, CoT selectively aggregates the features from different homologs by assigning smaller weights to non-homologous sequences or residue pairs. Extensive experiments on two rigorous benchmark datasets demonstrate the effectiveness of CoT. In particular, CoT achieves a $51. 6\%$ top-L long-range precision score for the Free Modeling (FM) domains on the CASP14 benchmark, which outperforms the winner group of CASP14 contact prediction challenge by $9. 8\%$.

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