Author name cluster

Hang Zheng

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5 papers

2 author rows

TMLR Journal 2024 Journal Article

3D Molecular Generation via Virtual Dynamics

Shuqi Lu
Lin Yao
Xi Chen
Hang Zheng
Di He
Guolin Ke

Structure-based drug design, a critical aspect of drug discovery, aims to identify high-affinity molecules for target protein pockets. Traditional virtual screening methods, which involve exhaustive searches within large molecular databases, are inefficient and limited in discovering novel molecules. The pocket-based 3D molecular generation model offers a promising alternative by directly generating molecules with 3D structures and binding positions in the pocket. In this paper, we present VD-Gen, a novel pocket-based 3D molecular generation pipeline. VD-Gen features a series of carefully designed stages to generate fine-grained 3D molecules with binding positions in the pocket cavity end-to-end. Rather than directly generating or sampling atoms with 3D positions in the pocket, VD-Gen randomly initializes multiple virtual particles within the pocket and learns to iteratively move them to approximate the distribution of molecular atoms in 3D space. After the iterative movement, a 3D molecule is extracted and further refined through additional iterative movement, yielding a high-quality 3D molecule with a confidence score. Comprehensive experimental results on pocket-based molecular generation demonstrate that VD-Gen can generate novel 3D molecules that fill the target pocket cavity with high binding affinities, significantly outperforming previous baselines.

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NeurIPS Conference 2024 Conference Paper

Exploring Molecular Pretraining Model at Scale

Xiaohong Ji
Zhen Wang
Zhifeng Gao
Hang Zheng
Linfeng Zhang
Guolin Ke
Weinan E

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining model remains unexplored. In this work, we present an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, examining the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale the model to 1. 1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show the consistent improvement on the downstream tasks as the model size grows up. The model with 1. 1 billion parameters also outperform over existing methods, achieving an average 27\% improvement on the QM9 and 14\% on COMPAS-1D dataset.

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AAAI Conference 2024 Conference Paper

SENCR: A Span Enhanced Two-Stage Network with Counterfactual Rethinking for Chinese NER

Hang Zheng
Qingsong Li
Shen Chen
Yuxuan Liang
Li Liu

Recently, lots of works that incorporate external lexicon information into character-level Chinese named entity recognition(NER) to overcome the lackness of natural delimiters of words, have achieved many advanced performance. However, obtaining and maintaining high-quality lexicons is costly, especially in special domains. In addition, the entity boundary bias caused by high mention coverage in some boundary characters poses a significant challenge to the generalization of NER models but receives little attention in the existing literature. To address these issues, we propose SENCR, a Span Enhanced Two-stage Network with Counterfactual Rethinking for Chinese NER, that contains a boundary detector for boundary supervision, a convolution-based type classifier for better span representation and a counterfactual rethinking(CR) strategy for debiased boundary detection in inference. The proposed boundary detector and type classifier are jointly trained with the same contextual encoder and then the trained boundary detector is debiased by our proposed CR strategy without modifying any model parameters in the inference stage. Extensive experiments on four Chinese NER datasets show the effectiveness of our proposed approach.

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ICLR Conference 2023 Conference Paper

Uni-Mol: A Universal 3D Molecular Representation Learning Framework

Gengmo Zhou
Zhifeng Gao
Qiankun Ding
Hang Zheng
Hongteng Xu
Zhewei Wei
Linfeng Zhang 0002
Guolin Ke

Molecular representation learning (MRL) has gained tremendous attention due to its critical role in learning from limited supervised data for applications like drug design. In most MRL methods, molecules are treated as 1D sequential tokens or 2D topology graphs, limiting their ability to incorporate 3D information for downstream tasks and, in particular, making it almost impossible for 3D geometry prediction/generation. In this paper, we propose a universal 3D MRL framework, called Uni-Mol, that significantly enlarges the representation ability and application scope of MRL schemes. Uni-Mol contains two pretrained models with the same SE(3) Transformer architecture: a molecular model pretrained by 209M molecular conformations; a pocket model pretrained by 3M candidate protein pocket data. Besides, Uni-Mol contains several finetuning strategies to apply the pretrained models to various downstream tasks. By properly incorporating 3D information, Uni-Mol outperforms SOTA in 14/15 molecular property prediction tasks. Moreover, Uni-Mol achieves superior performance in 3D spatial tasks, including protein-ligand binding pose prediction, molecular conformation generation, etc. The code, model, and data are made publicly available at https://github.com/dptech-corp/Uni-Mol.

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AAAI Conference 2016 Conference Paper

Optimizing Trading Assignments in Water Right Markets

Yicheng Liu
Pingzhong Tang
Tingting Xu
Hang Zheng

Over the past two decades, water markets have been successfully ﬁelded in countries such as Australia, the United states, Chile, China, etc. Water users, mainly irrigators, have beneﬁted immensely from water markets. However, the current water market design also faces certain serious barriers. It has been pointed out that transaction costs, which exists in most markets, induce great welfare loss. For example, for water markets in western China discussed in this paper, the inﬂuence of transaction costs is signiﬁcant. Another important barrier is the locality of trades due to geographical constraints. Based on the water market at Xiying Irrigation, one of the most successful water market in western China, we model the water market as a graph with minimum transaction thresholds on edges. Our goal is to maximize the transaction volume or welfare. We prove that the existence of transaction costs results in no polynomial time approximation scheme (PTAS) to maximize social welfare (MAX SNP-hard). The complexities on special graphs are also presented. From a practical point of view, however, optimal social welfare can be obtained via a well-designed mixed integer linear program and can be approximated near optimally at a large scale via a heuristic algorithm. Both algorithms are tested on data sets generated from real historical trading data. Our study also suggests the importance of reducing transaction costs, for example, institutional costs in water market design. Our work opens a potentially important avenue of market design within the agenda of computational sustainability.

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