Hongyu Zhao

Nov 21, 2024 | biorxiv.org | Tianyu Liu |Xiao Luo |Yijia Xiao |Hongyu Zhao

AbstractComputational methods should be accurate and robust for tasks in biology and medicine, especially when facing different types of attacks, defined as perturbations of benign data that can cause a significant drop in method performance. Therefore, there is a need for robust models that can defend attacks. In this manuscript, we propose a novel framework named RobustCell to analyze attack-defense methods in single-cell and spatial transcriptomic data analysis.

Nov 21, 2024 | biorxiv.org | Tianyu Liu |Jia Zhao |Hongyu Zhao

AbstractSingle-cell Multi-modal Data Integration has been an area of active research in recent years. However, it is difficult to unify the integration process of different omics in a pipeline, and evaluate the contributions of data integration.

Nov 17, 2024 | biorxiv.org | Tianyu Liu |Tinyi Chu |Xiao Luo |Hongyu Zhao

AbstractDrug synergy prediction is a challenging and important task in the treatment of complex diseases including cancer. In this manuscript, we present a novel Foundation Model, known as BAITSAO, for tasks related to drug synergy prediction with a unified pipeline to handle different datasets. We construct the training datasets for BAITSAO based on the context-enriched embeddings from Large Language Models for the initial representation of drugs and cell lines.

Nov 11, 2024 | biorxiv.org | Xinning Shan |Hongyu Zhao

AbstractCell-type-specific gene co-expression networks are widely used to characterize gene relationships.

Nov 11, 2024 | dx.doi.org | Mengyue Wang |Wentao Dong |Xi Lu |Hongyu Zhao