Publications

Selected Publications

Underline means these authors contribute equally to this work.

^*: To whom the correspondence should be addressed.

• Liu Tianyu, Chu Tinyi, Luo Xiao, Zhao Hongyu^*. BAITSAO: Building A Foundation Model for Drug Synergy Analysis Powered by Language Models. Preprint, 2025. (in press, Nature Communications)
• Liu Tianyu, Zhang Xiangyu, Ying Rex, Zhao Hongyu^*. Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics. Preprint, 2024. (Under review by Cell Press Multi-Journals)
• Liu Tianyu, Huang Tinglin, Lin Yingxin, Ying Rex, Zhao Hongyu^*. UNICORN: Towards Universal Cellular Expression Prediction with an Explainable Multi-Task Learning Framework. Preprint, 2024. (Under review by Nature Communications)
• Liu Tianyu, Huang Tinglin, Ying Rex, Zhao Hongyu^*. spEMO: Exploring the Capacity of Foundation Models for Analyzing Spatial Multi-Omic Data. Preprint, 2024. (Under review by Nature Biotechnology)
• Liu, Tianyu and De Brouwer, Edward and Kuo, Tony and Diamant, Nathaniel and Missarova, Alsu and Wang, Hanchen and Hao, Minsheng and Bravo, Hector Corrada and Scalia, Gabriele^* and Regev, Aviv^* and Heimberg Graham^* . Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states. Research in Computational Molecular Biology (RECOMB), 2025. (oral, under review by Cell Systems)
• Liu Tianyu, Xiao Yijia, Luo Xiao, Xu Hua, Zheng Jim Wenjin, Zhao Hongyu^*. Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. The 2024 Conference on Empirical Methods in Natural Language Processing. ACL, 2024. (poster)
• Liu Tianyu, Lin Yingxin, Luo Xiao, Sun Yizhou, Zhao Hongyu^*. VISTA Uncovers Missing Gene Expression and Spatial-induced Information for Spatial Transcriptomic Data Analysis. Preprint, 2024. (Under review by Cell Genomics)
• Liu Tianyu, Chen Tianqi, Zheng Wangjie, Luo Xiao, Zhao Hongyu^*. scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis. Preprint, 2023. (Under review by Nature Methods)
• Liu Tianyu, Wang Yuge, Ying Rex, Zhao Hongyu^* . MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data. Thirty-seventh Conference on Neural Information Processing Systems. PMLR, 2023. (poster)
• Liu Tianyu, Li Kexing, Wang Yuge, Li Hongyu, Zhao Hongyu^*. Evaluating the Utilities of Foundation Models in Single-cell Data Analysis. Preprint, 2023. (Under review by Molecular Systems Biology)
• Liu Tianyu^*, Greenberg Grant, Shomorony Ilan. CVQVAE: A Representation Learning based Method for Multi-omics Single Cell Data Integration. Machine Learning in Computational Biology. PMLR, 2022. (Spotlight, top 12%)

Talk

• Second Annual Yale Single Cell Symposium
• 2nd Open Problems in Single-cell Competition during NeurIPS 2022
• Novo Nordisk, Oct 2023
• Emory University, Oct 2023
• Chan Zuckerberg Initiative, Mar 2024

Services

As (Associate) Editors or (Area) Chairs:

• NENLP 2025
• ARR

As reviewers:

• Journals: PLOS Comp Bio, BMC Bioinformatics, TNNLS, TALLIP, Communication Biology, Genome Biology, BMC Genomics
• Conferences: NeurIPS, ML4H, MLCB, CVPR, ICLR, ICML, AAAI, AISTATS, ARR
• Competitions: 3rd Open Problems in Single-cell Competition

As organizers:

• AI+Music social activity: NeurIPS 2023.
• LLMs for biomedical research meeting: EMNLP 2024.

As contributors:

• open-source softwares including scGLUE, guidance, Deeprobust, and scVI.

Mentees

• Wenxin Long (BS @ NKU -> PhD @ PSU)
• Zhiyuan Cao (BS @ SJTU, MS @ Yale -> PhD @ Yale)
• Kexing Li (BS @ THU -> PhD @ Yale)
• Bizhe Bai (ML4H mentee, BS @ UoT, MS @ UQ)
• Maira Elahi (ML4H mentee, Riverside Secondary School)