Yiming Gao

Yiming Gao

PhD Student in Electrical & Computer Engineering at Texas A&M.
Bioinformatics • LLM Agents • Machine Learning

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Research Experience

Research Assistant

Prof. Yang Shen Lab, Texas A&M University (ECE)

Sep 2025 – Present
  • Leading development of the Virtual Cell Challenge project.
  • Utilizing State models and Correlational Lagrangian Schrodinger Bridge to predict genetic perturbation effects in perturb-seq datasets.

Research Intern (AI Scientist)

Prof. Zhiting Hu Lab, UCSD Halıcıoğlu Data Science Institute

Nov 2023 – June 2025
  • Spearheaded AI Scientist project: a multi-LLM agent-based AI tool for scientific discovery.
  • Addressed complex tasks like scRNA-seq cell type annotation and small molecule optimization.
  • Developed CellMaster: an interpretable cell type annotation tool with human-in-the-loop feedback.
  • Created scPilot: the first framework enabling LLMs to analyze scRNA-seq data with interpretable reasoning.

Research Assistant

Feng Lab of Pathology, UCSD Medical School

Apr 2022 – June 2025
  • Primary dry lab analyst focusing on liver cancer mechanisms in aged models.
  • Performed comprehensive bioinformatics analyses (bulk/single-cell RNA, ATAC-seq, spatial transcriptomics).
  • Key contributor to discovering TNF-alpha gene upregulation in neutrophils of aged mice.
  • Managed and optimized lab servers for high-performance computing.

Selected Publications

scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery

Y. Gao, et al. — NeurIPS 2025

CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis

Z. Wang, Y. Gao*, et al. — Arxiv 2025

A TNF-producing neutrophil subset drives age-dependent hepatotoxicity

J. Lee, Y. Gao, et al. — In review, Nature Immunology 2025

Education

Texas A&M University

PhD in Electrical & Computer Engineering

2025 – Present

Advisor: Yang Shen

University of California, San Diego (UCSD)

B.S. Bioinformatics & B.S. Computer Engineering

2021 – 2025

Advisors: Zhiting Hu & Gen-Sheng Feng

Skills

Bioinformatics

scRNA-seq Analysis ATAC-seq Spatial Transcriptomics Cross-omics

Computer Science

LLM Agents Machine Learning Python Parallel Computing Linux/Shell