Tianyu Liu

According to our database, Tianyu Liu authored at least 17 papers between 2022 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

A Versatile AI Agent for Rare Disease Diagnosis and Risk Gene Prioritization.

Tianyu Liu, Wangjie Zheng, Rui Yang, Benny Kai Guo Loo, Hui Zhang, Jeffries Lauran, Jianlei Gu, Botao Yu, Weihao Xuan, Kexin Huang, Nan Liu, James Y. Zou, Yonghui Jiang, Hua Xu, Hongyu Zhao

CoRR, May, 2026

DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery.

Tianyu Liu, Sihan Jiang, Fan Zhang, Kunyang Sun, Teresa Head-Gordon, Hongyu Zhao

CoRR, April, 2026

Embeddings from language models are good learners for single-cell data analysis.

Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo, Yiqun Chen, Hongyu Zhao

Patterns, 2026

2025

Accelerating Scientific Discovery with Autonomous Goal-evolving Agents.

Yuanqi Du, Botao Yu, Tianyu Liu, Tony Shen, Junwu Chen, Jan G. Rittig, Kunyang Sun, Yikun Zhang, Zhangde Song, Bo Zhou, Cassandra Masschelein, Yingze Wang, Haorui Wang, Haojun Jia, Chao Zhang, Hongyu Zhao, Martin Ester, Teresa Head-Gordon, Carla P. Gomes, Huan Sun, Chenru Duan, Philippe Schwaller, Wengong Jin

CoRR, December, 2025

TeamPath: Building MultiModal Pathology Experts with Reasoning AI Copilots.

Tianyu Liu, Weihao Xuan, Hao Wu, Peter Humphrey, Marcello DiStasio, Heli Qi, Rui Yang, Simeng Han, Tinglin Huang, Fang Wu, Nan Liu, Irene Li, Hua Xu, Hongyu Zhao

CoRR, November, 2025

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop.

Elizabeth Fahsbender, Alma Andersson, Jeremy Ash, Polina Binder, Daniel Burkhardt, Benjamin Chang, Georg K. Gerber, Anthony Gitter, Patrick Godau, Ankit Gupta, Genevieve Haliburton, Siyu He, Trey Ideker, Ivana Jelic, Aly Khan, Yang-Joon Kim, Aditi S. Krishnapriyan, Jon M. Laurent, Tianyu Liu, Emma Lundberg, Shalin B. Mehta, Rob Moccia, Angela Oliveira Pisco, Katherine S. Pollard, Suresh Ramani, Julio Saez-Rodriguez, Yasin Senbabaoglu, Elana Simon, Srinivasan Sivanandan, Gustavo Stolovitzky, Marc Valer, Bo Wang, Xikun Zhang, James Zou, Katrina Kalantar

CoRR, July, 2025

Towards Artificial Intelligence Research Assistant for Expert-Involved Learning.

Tianyu Liu, Simeng Han, Xiao Luo, Hanchen Wang, Pan Lu, Biqing Zhu, Yuge Wang, Keyi Li, Jiapeng Chen, Rihao Qu, Yufeng Liu, Xinyue Cui, Aviv Yaish, Yuhang Chen, Minsheng Hao, Chuhan Li, Kexing Li, Arman Cohan, Hua Xu, Mark Gerstein, James Zou, Hongyu Zhao

CoRR, May, 2025

CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.

Tianyu Liu, Wenxin Long, Zhiyuan Cao, Yuge Wang, Chuan Hua He, Le Zhang, Stephen M. Strittmatter, Hongyu Zhao

Briefings Bioinform., January, 2025

A perspective on developing foundation models for analyzing spatial transcriptomic data.

Tianyu Liu, Minsheng Hao, Xinhao Liu, Hongyu Zhao

Quant. Biol., 2025

STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.

Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Rex Ying, Wengong Jin

npj Digit. Medicine, 2025

Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States.

Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Héctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg

Proceedings of the Research in Computational Molecular Biology, 2025

Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching.

Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying

Proceedings of the Forty-second International Conference on Machine Learning, 2025

2024

Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data.

Fan Zhang, Tianyu Liu, Zihao Chen, Xiaojiang Peng, Chong Chen, Xian-Sheng Hua, Xiao Luo, Hongyu Zhao

Proceedings of the Advances in Neural Information Processing Systems 37: Annual Conference on Neural Information Processing Systems 2024, 2024

Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.

Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, Wenjin Jim Zheng, Hongyu Zhao

Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2024, 2024

2023

MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data.

Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks.

Yuge Wang, Tianyu Liu, Hongyu Zhao

Bioinform., 2022

CVQVAE: A representation learning based method for multi-omics single cell data integration.

Tianyu Liu, Grant Greenberg, Ilan Shomorony

Proceedings of the Machine Learning in Computational Biology, 21-22 November 2022, Online, 2022