Biography

Professor Li, Ph.D. supervisor and professor at the College of Artificial Intelligence, Jilin University, is a recipient of national-level young talent awards, Jilin Province Excellent Young Scientist Award, and Jilin Province Innovative Leading Talent Award. He has been consecutively listed in Stanford University's Global Top 2% Scientists from 2020 to 2024. Dr. Li has led over ten research projects, including the National Natural Science Foundation of China (General and Youth Programs) and Jilin Province's youth and general projects.

His team focuses on developing artificial intelligence algorithms to uncover the biological principles embedded in data, addressing biological questions across multiple levels, from genomics to proteomics. Their work advances the integration of biology with computational intelligence, laying a foundation for combining multi-omics data, including genomics, transcriptomics, and proteomics, to better understand the mechanisms of disease development.

In recent years, He has published approximately 110 papers as the first or corresponding author in high-impact journals and top conferences, including Nature Communications (2 papers), Advanced Science (6 papers), Nucleic Acids Research (1 paper), Bioinformatics, PLoS Computational Biology, Briefings in Bioinformatics, Communications Biology, and AAAI. He serves as an Area Chair for NeurIPS 2024 and is an editorial board member for journals such as BMC Biology (Q1 in the Chinese Academy of Sciences ranking) and BMC Bioinformatics.

Education

2012-2015    Ph.D., School of Information Science and Technology, Northeast Normal University

2009-2012    M.S., School of Information Science and Technology, Northeast Normal University

2005-2009    B.S., School of Information Science and Technology, Northeast Normal University

Positions

2020-Present    Professor, School of Artificial Intelligence, Jilin University

2017-2019    Research Fellow, Department of Computer Science, City University of Hong Kong

2015-2016    Academic Scholar, Department of Computer Science, University of Surrey

2015-2020    Associate Professor, School of Information Science and Technology, Northeast Normal University

Awards/Academic Honors
2024    Chinese Innovator in Intelligent Computing （MIT Technology Review）

2023    National-level Young Talent

2023    Outstanding Youth of Jilin Province

2022    Top Innovative Talent of Jilin Province

2020-2024    Stanford's list World Top 2% scientists

2018    Natural Science Academic Achievement Award Second Prize, Jilin Province

2013    Natural Science Academic Achievement Award Second Prize, Jilin Province

2013    Science and Technology Award Second Prize, Jilin Province

Professional Service

2024                 Area Chair, NeurIPS 2024

2023-Present    Associate Editor, BMC Biology

2022-Present    Associate Editor, BMC Bioinformatics

2022-Present    Associate Editor, BMC Genomics

2021-Present    Section Editor, Current Bioinformatics

2021-Present    Section Editor, Current Gene Therapy

2021-Present    Editor Board Member, PeerJ Computer Science

2019-Present    Editor Board Member, Mini-Reviews in Medicinal Chemistry

2017-Present    Academic Editor, Scientific Report

2017-Present    Academic Editor, Plos one

2017-Present    Academic Editor, IEEE Access

Research Directions:
1. Demystifying Mechanisms of Regulation Through Interpretable Deep Learning Models for Single-cell Transcriptomics Data;

2. Deep Sequence Language Deciphers the Life Semantics of Proteins

Selected Publications：
Coauthored over 110 papers in international journals, including Nature Communications (2 articles)，Advanced Science（6 articles），Nucleic Acids Research (1 articles), etc.

Total citations: > 4000 - H-index = 35.

1. Z. Yu, Y. Su, Y. Lu, F. Wang, S. Zhang, Y. Chang, K. Wong*, X. Li*. Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA[J]. Nature Communications, 2023, 14(1): 400.

2. H. Zhu, Y. Yang, Y. Wang, F. Wang, Y. Huang, Y. Chang, K. Wong*, X. Li*. Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet[J]. Nature Communications, 2023, 14(1): 6824.

3. Y. Su, Z. Yu, Y. Yang, K. Wong, Li X*. Distribution-agnostic Deep Learning Enables Accurate Single Cell Data Recovery and Transcriptional Regulation Interpretation[J]. Advanced Science, 2024, 2307280.

4. Y. Fan, Y. Wang, F. Wang, L. Huang, Y. Yang, K. Wong, X. Li*. Reliable Identification and Interpretation of Single‐Cell Molecular Heterogeneity and Transcriptional Regulation using Dynamic Ensemble Pruning[J]. Advanced Science, 2023, 10(22): 2205442.

5. Y. Yang, G. Li, K. Pan, W. Cao, Z. Zhang*, X. Li*, Deciphering 3’ UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning, Advanced Science, 2024.

6. Z. Yu, Y. Yang, X. Chen, K. Wong, Z. Zhang, Y. Zhao*, X. Li*, Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning, Advanced Science, 2024.

7. Z. Zheng, J. Chen, X. Chen, L. Huang, W. Xie, Q. Lin, X. Li*, K. Wong*. A Lightweight Framework for Chromatin Loop Detection at the Single-Cell Level[J]. Advanced Science, 2023, 10(33): 2303502.

8. F. Wang, H. Alinejad-Rokny, J. Lin, T. Gao, X. Chen, L. Meng, X. Li*, K. Wong*. Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD[J]. Advanced Science, 2023: 2204113.

9. N. Chen, J. Yu, Z. Liu, L. Meng, X. Li*, K. Wong*, Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation, Nucleic Acids Research, 2024, gkae210.

Patents
1. A multi-objective heuristic single-cell deep clustering method, X.T.Li, Y.Fan, W.J.Ma, Chinese Patent No. CN118136116A, 2024 2.

2. A method and system for annotating single cell data based on Pareto integrated pruning. X.Li, Q.Qi, Y.Yin, Y.Fan, Chinese Patent.

Projects

2025.1-2028.12   Characterization and interpretation of single-Cell ATAC-seq data using deep learning, General Program of NSFC, 0.6 million (RMB)

2023.1-2025.12   Research on Deep Learning Methods for Single-cell Spatial Transcriptome Data, Jilin Provincial        Excellent Young Science and Technology Talent Program, 0.25 million (RMB)

2021.1-2024.12   Research on Evolutionary Deep Clustering in High-Dimensional Sparse Data, General Program of NSFC, 0.59 million (RMB)

2017.1-2019.12   Research on multi-objective bi-level programming problems based on surrogate models and hierarchical evolutionary algorithms, Youth Project of NSFC, 0.21 million (RMB)

2017.1-2019.12   Research on hybrid scheduling problems based on multi-objective swarm intelligence algorithms, Jilin Provincial Science and Technology Department Youth Fund Project, 0.1 million (RMB)