Lei Huang

Short Biography [CV]

I’m a fourth-year Ph.D. student at the Department of Computer Science, City University of Hong Kong, advised by Prof. Ka-Chun Wong. Before that, I received my bachelor’s degree from Wuhan University (major in MIS and minor in CS). I was a joint visiting student with Prof. Manolis Kellis and Prof. Marinka Zitnik at MIT and Harvard. My research interests include AIDD (AI for drug design), Bioinformatics, and BioNLP. I am going to join Prof. Luca Pinello’s lab as a postdoc in MGH and Harvard University. I am also a big fan of Real Madrid ⚽️.

I am looking for the faculty position starting from 2024 Fall. Please do not hesitate to contact me (lhuang93-c@my.cityu.edu.hk; layne_huang@outlook.com) if you are interested in my research.

News

• [Oct 2024] I will join join Prof. Luca Pinello’s lab as a postdoc in MGH and Harvard University.
• [Sep 2024] Our paper “A versatile informative diffusion model for single-cell ATAC-seq data generation and analysis” is accepted to NeurIPS 2024.
• [Apr 2024] Our paper “A unified conditional diffusion framework for dual protein targets based bioactive molecule generation” is accepted to IEEE Transactions on Artificial Intelligence.
• [Mar 2024] Our paper “A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets” is accepted to Nature Communications.
• [Nov 2023] I also joined Prof. Marinka Zitnik’s lab at Harvard as a joint visiting student in November!
• [Jun 2023] I will join Prof. Manolis Kellis’s lab at MIT as a visiting student in September!
• [2023] I start my internship in Alibaba Damo Academy.
• [Nov 2022] Our paper “MDM: Molecular Diffusion Model for 3D Molecule Generation” is accepted to AAAI2023.
• [Nov 2022] Our paper “CoaDTI: Multi-modal co-attention based framework for drug-target interaction annotation” is accepted to Briefings in Bioinformatics
• [Mar 2022] I start my internship in Tencet AI Lab.

Publications

• A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets
  Lei Huang, Tingyang Xu, Yang Yu, Peilin Zhao, Ka-Chun Wong, Hengtong Zhang
  Nature Communications, Mar. 2024.
  [Paper] [Code]

• Enabling Single‐Cell Drug Response Annotations from Bulk RNA‐Seq Using SCAD
  Zetian Zheng, Junyi Chen, Xingjian Chen, Lei Huang, Weidun Xie, Qiuzhen Lin, Xiangtao Li, Ka-Chun Wong
  Advanced Science 2023, Jan. 2023.
  [Paper] [Code]

• MDM: Molecular Diffusion Model for 3D Molecule Generation
  Lei Huang, Hengtong Zhang, Tingyang Xu, Ka-Chun Wong
  AAAI 2023, Sep. 2022.
  [Paper] [Code]

• CoaDTI: Multi-modal co-attention based framework for drug-target interaction annotation
  Lei Huang, Jiecong Lin, Rui Liu, Zetian Zheng, Lingkuan Meng, Xingjian Chen, Xiangtao Li, Ka-Chun Wong
  Briefings in Bioinformatics, Sep. 2022.
  [Paper] [Code]

• Mini-review: Recent advances in post-translational modification site prediction based on deep learning
  Lingkuan Meng, Wai-Sum Chan, Lei Huang, Lingjing Liu, Xingjian Chen, Weitong Zhang, Fuzhou Wang, Ke Cheng, Hongyan Sun, Ka-Chun Wong
  Computational and Structural Biotechnology Journal, Jun. 2022.
  [Paper]

• Towards Better Understanding with Uniformity and Explicit Regularization of Embeddings in Embedding-based Neural Topic Models
  Wei Shao, Lei Huang, Shuqi Liu, Shihua Ma, Linqi Song
  International Joint Conference on Neural Networks, Apr. 2022.
  [Paper] [Code]

• SRG-vote: Predicting miRNA-gene relationships via embedding and LSTM ensemble
  Weidun Xie, Zetian Zheng, Weitong Zhang, Lei Huang, Qiuzhen Lin, Ka-Chun Wong
  IEEE Journal of Biomedical and Health Informatics, Apr. 2022.
  [Paper] [Code]

• Subclass-specific Prognosis and Treatment Efficacy Inference in Head and Neck Squamous Carcinoma
  Zetian Zheng, Weidun Xie, Xingjian Chen, Fuzhou Wang, Lei Huang, Xiangtao Li, Qiuzhen Lin, Ka-Chun Wong
  IEEE Journal of Biomedical and Health Informatics, Apr. 2022.
  [Paper] [Code]

• EGFI: drug–drug interaction extraction and generation with fusion of enriched entity and sentence information
  Lei Huang, Jiecong Lin, Xiangtao Li, Linqi Song, Zetian Zheng, Ka-Chun Wong
  Briefings in Bioinformatics, Nov. 2021.
  [Paper] [Code]

• High-throughput single-cell RNA-seq data imputation and characterization with surrogate-assisted automated deep learning
  Xiangtao Li, Shaochuan Li, Lei Huang, Shixiong Zhang, Ka-chun Wong
  Briefings in Bioinformatics, Sep. 2021.
  [Paper] [Code]

• DeepMotifSyn: a deep learning approach to synthesize heterodimeric DNA motifs
  Jiecong Lin, Lei Huang, Xingjian Chen, Shixiong Zhang, Ka-Chun Wong
  Briefings in Bioinformatics, Sep. 2021.
  [Paper] [Code]

• Metric Learning Based Vision Transformer for Product Matching
  Lei Huang, Wei Shao, Fuzhou Wang, Weidun Xie, Ka-Chun Wong
  International Conference on Neural Information Processing, Dec. 2021.
  [Paper] [Code]

• View analysis of personal information leakage and privacy protection in big data era—based on Q method
  Lei Huang, Jingyi Zhou, Jiecong Lin, Shengli Deng
  Aslib Journal of Information Management, Nov. 2021.
  [Paper] [Code]

Services

• Conference reviewer: ICA3PP, ACL.
• Journal reviewer: BioData Mining, Briefings in Bioinformatics.

Teaching

Department of Computer Science, CityU

• CS4465 Computational Biology and Bioinformatics
• CS5489 Machine Learning: Algorithms and Applications

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