Publications

A focused selection of papers that best represent my work in AI for drug design, biomedical machine learning, and computational biology.

Selected publications

Cell2025

Single-cell multiregion epigenomic rewiring in Alzheimer's disease progression and cognitive resilience

Zunpeng Liu, Shanshan Zhang, ..., Lei Huang, ..., Manolis Kellis

Overview of the Alzheimer's disease single-cell epigenomics study — Figure 1 from Liu et al., *Cell* (2025), CC BY-NC-ND 4.0.

Paper

NeurIPS2024

A versatile informative diffusion model for single-cell ATAC-seq data generation and analysis

Lei Huang, Lei Xiong, Na Sun, Zunpeng Liu, Ka-Chun Wong, Manolis Kellis

Overview of the ATAC-Diff framework — Figure 1 from Huang et al., NeurIPS (2024).

Paper

Nature Communications2024

A dual diffusion model enables 3D binding bioactive molecule generation and lead optimization given target pockets

Lei Huang, Tingyang Xu, Yang Yu, Peilin Zhao, Ka-Chun Wong, Hengtong Zhang

Overview of the PMDM target-conditioned molecular generation framework — Figure 1 from Huang et al., *Nature Communications* (2024), CC BY 4.0.

Paper Code

IEEE Transactions on Artificial Intelligence2024

DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins

Lei Huang, Zheng Yuan, Huihui Yan, Rong Sheng, Linjing Liu, Fuzhou Wang, Weidun Xie, Nanjun Chen, Fei Huang, Songfang Huang, Ka-Chun Wong, Yaoyun Zhang

Overview of the DiffDTM conditional dual-protein molecular generation framework — Figure 1 from Huang et al., *IEEE Transactions on Artificial Intelligence* (2024).

Paper

Preprint2025

ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals

Shania Mitra, Lei Huang (co-first author), Manolis Kellis

Overview of the ProteinRPN framework for graph-based protein function prediction — Figure 1 from Mitra, Huang, and Kellis, preprint (2025).

Paper

Advanced Science2023

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

Architecture of the SCAD single-cell drug response annotation model — Figure 1 from Zheng et al., *Advanced Science* (2023), CC BY.

Paper

AAAI2023

MDM: Molecular Diffusion Model for 3D Molecule Generation

Lei Huang, Hengtong Zhang, Tingyang Xu, Ka-Chun Wong

Paper Code

Briefings in Bioinformatics2022

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

Overview of the CoaDTI multimodal co-attention framework — Figure 1 from Huang et al., *Briefings in Bioinformatics* (2022).

Paper

Briefings in Bioinformatics2021

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

Overview of the EGFI extraction and generation framework for drug-drug interactions — Figure 1 from Huang et al., *Briefings in Bioinformatics* (2021).

Paper