Junhao Liu¶
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My name is Junhao Liu (刘俊浩). I am a fourth-year PhD candidate in Computer Science at the University of California, Irvine, advised by Prof. Jing Zhang. Previously, I earned my master’s degree from the University of Chinese Academy of Sciences; during that time, I was a member of SIAT-NLP under the supervision of Prof. Min Yang. I completed my undergraduate studies at the South China University of Technology.
Nov 2025 - Single-Cell Omics Arena is accepted by Briefings in Bioinformatics! 🎉
May 2025 - One position paper on multimodal DNA generative models accepted by ICIP 2025!
May 2025 - One paper accepted by KDD 2025 (acceptance rate 18.4%)!
Dec 2024 - Our ACML paper has been selected as the Best Student Paper!!!
Dec 2024 - One paper accepted by AAAI 2025! Thanks to all coauthors!
Sep 2024 - One paper accepted by ACML 2024 (acceptance rate 26%)!
July 2024 - One paper accepted by CIKM 2024!
Research¶
My research interests lie in natural language processing (NLP), large language models (LLMs), and deep generative models, with a particular emphasis on their applications in computational biology. Recently, I have focused on the following directions:
🧬 Genomics Language Models: Foundation Models for DNA and Cell Biology
⚗️ AI for Science: Deep Generative and Agentic Models for Biological Data Processing and Scientific Discovery
🧐 Interpretable Learning for Biological Problem: Feature Explanation and Visualization for Single-Cell Data
Selected Publications¶
A complete list of my publications is available on Google Scholar. (* denotes equal contribution)
Single-Cell Omics Arena: Evaluation of Large Language Models for Automatic Cell Type Annotations on Single-Cell Omics Data via RNA-seq Bridging
Junhao Liu, Siwei Xu, Yongxian Wu, Jing Zhang
Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations
Junhao Liu, Pengpeng Zhang, Martin Renqiang Min, Jing Zhang
The 31st SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2025 [paper] [code]
Multimodal Cell Context Instruction Tuning for Conditional DNA Regulatory Sequence Generation with Large Language Models
Junhao Liu*, Pengpeng Zhang*, Siwei Xu, Shushrruth Sai Srinivasan, Yongxian Wu, Jing Zhang
2025 IEEE International Conference on Image Processing (ICIP), 2025 [paper] [code]
Understanding Transcriptional Regulatory Redundancy by Learnable Global Subset Perturbations
Junhao Liu*, Siwei Xu*, Dylan Riffle, Ziheng Duan, Martin Renqiang Min, Jing Zhang
Asian Conference on Machine Learning (ACML), 2024 (Best Student Paper Award) [paper] [code]
Learnable Subset Perturbations for Understanding Transcriptional Regulatory Redundancy
Junhao Liu, Siwei Xu, Dylan Riffle, Ziheng Duan, Jing Zhang
NeurIPS 2024 Workshop on Data-driven and Differentiable Simulations, Surrogates, and Solvers [paper] [code]
Hierarchical Context Pruning: Optimizing Real-World Code Completion with Repository-Level Pretrained Code LLMs
Lei Zhang, Yunshui Li, Jiaming Li, Xiaobo Xia, Jiaxi Yang, Run Luo, Minzheng Wang, Longze Chen, Junhao Liu, Min Yang
The 39th Annual AAAI Conference on Artificial Intelligence (AAAI), 2025 [paper]
scACT: Accurate Cross-modality Translation via Cycle-consistent Training from Unpaired Single-cell Data
Siwei Xu*, Junhao Liu*, Jing Zhang
The Conference on Information and Knowledge Management (CIKM), 2024 [paper] [code]
Single-Cell Genomics and Regulatory Networks for 388 Human Brains
Prashant S. Emani et al.
Multi-perspective Coherent Reasoning for Helpfulness Prediction of Multimodal Reviews
Junhao Liu, Zhen Hai, Min Yang, Lidong Bing
Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics (ACL), 2021 [paper] [code]
Honors and Awards¶
UC Irvine CS Department Dean’s Award
National Scholarship for Graduate Student
AAAI 2020 Student Scholarship
Third Prize of Byte Cup 2018 IML Contest (Awarded by CAAI and ByteDance)
Professional Service¶
Conference Reviewer: NeurIPS, ICML, ICLR, KDD, ICCV, AISTATS, ACL Rolling Review, ACL, EMNLP, AAAI, COLING
Journal Reviewer: IEEE Transactions on Cybernetics, IEEE Transactions on Circuits and Systems for Video Technology, IEEE Transactions on Cognitive and Developmental Systems, Pattern Recognition, Knowledge-Based Systems, Neurocomputing
Teaching Experience¶
Teaching Assistant, ICS 6D: Introduction to Discrete Mathematics, UC Irvine, Winter 2023
Teaching Assistant, CS 178: Introduction of Machine Learning, UC Irvine, Fall 2022