📝 Publications

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

Recent Preprints

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

  Junhao Liu, Siwei Xu, Yongxian Wu, Jing Zhang

  arXiv preprint, 2024 [paper] [code]

Featured Publications

• 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.

  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]