Tianyu Liu

16 papers A* 3B 1Journal 10Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
Embeddings from language models are good learners for single-cell data analysis.
Patterns
Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo, Yiqun Chen, Hongyu Zhao
2025 J jnl
A perspective on developing foundation models for analyzing spatial transcriptomic data.
Quant. Biol.
Tianyu Liu, Minsheng Hao, Xinhao Liu, Hongyu Zhao
2025 J jnl
Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop.
CoRR
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 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
2025 J jnl
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.
Briefings Bioinform.
Tianyu Liu, Wenxin Long, Zhiyuan Cao, Yuge Wang, Chuan Hua He, Le Zhang, Stephen M. Strittmatter, Hongyu Zhao
2025 B conf
Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States.
RECOMB
Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Héctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg
2025 J jnl
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.
npj Digit. Medicine
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Rex Ying, Wengong Jin
2025 A* conf
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching.
ICML
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying
2025 J jnl
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching.
CoRR
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying
2025 J jnl
Towards Artificial Intelligence Research Assistant for Expert-Involved Learning.
CoRR
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
2024 — conf
Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
EMNLP (Findings)
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, Wenjin Jim Zheng, Hongyu Zhao
2024 J jnl
Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
CoRR
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, W. Jim Zheng, Hongyu Zhao
2024 A* conf
Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data.
NeurIPS
Fan Zhang, Tianyu Liu, Zihao Chen, Xiaojiang Peng, Chong Chen, Xian-Sheng Hua, Xiao Luo, Hongyu Zhao
2023 A* conf
MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data.
NeurIPS
Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao
2023 J jnl
MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data.
CoRR
Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao
2022 — conf
CVQVAE: A representation learning based method for multi-omics single cell data integration.
MLCB
Tianyu Liu, Grant Greenberg, Ilan Shomorony
2022 J jnl
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks.
Bioinform.
Yuge Wang, Tianyu Liu, Hongyu Zhao