Junhao Liu

I am a third-year PhD student in the Department of Computer Science at the University of California, Irvine, advised by Prof. Jing Zhang. Prior to this, I received my master’s degree from the University of Chinese Academy of Sciences (UCAS). During my time at UCAS, I was a member of SIAT-NLP and was advised by Prof. Min Yang. My bachelor’s degree was obtained from the South China University of Technology (SCUT).

Google Scholar | GitHub | Email

Recent News

• 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 Interests

I am interested in natural language processing, deep generative models, and their applications in computational biology. My current research focuses on:

• Deep Generative Models for Multi-Omics Data, including Single-Cell Sequencing and Spatial Transcriptomics

• Target-Driven Biological Representation and Interpretation Learning

Featured Publications

See also

* indicates equal contributions. My up-to-date publication list can be found on my Google Scholar profile.

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 | code

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.

Science, 2024

paper | cover

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

Preprints

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data

Junhao Liu, Siwei Xu, Lei Zhang, Jing Zhang

arXiv preprint, 2024

paper | code

Professional Services

• Reviewer for NeurIPS, ICML, ICLR, AISTATS, ACL Rolling Review, ACL, EMNLP, AAAI, COLING, IEEE Transactions on Cognitive and Developmental Systems, Neurocomputing

• Program Committee Member for IEEE AIMHC 2024

Honors and Awards

• UC Irvine CS Department Dean’s Award

• UC San Diego ECE Department Fellowship

• National Scholarship for Graduate Student

• AAAI 2020 Student Scholarship

Teaching Experiences

• Teaching Assistant, ICS 6D: Introduction to Discrete Mathematics, UC Irvine, Winter 2023

• Teaching Assistant, CS 178: Introduction of Machine Learning, UC Irvine, Fall 2022