First authorPreprint
Octave: Scale-Resolved Evaluation of Spatial Gene Expression Prediction from Histology
bioRxiv 2026.09.25.754484
Qing Wang
Ph.D. Student in Biomedical Informatics
Department of Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida
📧 wang.qing@ufl.edu · ☎️ (+1) 352-256-3237
About
I am a Ph.D. student in Biomedical Informatics at the University of Florida, co-mentored by Prof. Yijiang Chen and Prof. Qianqian Song in the UF College of Medicine's Emerging Research Scholars in AI (ERS-AI) Ph.D. Program. My research centers on AI for Science — building biomedical foundation models, large language models, and agent / RAG-based systems for drug discovery, single-cell analysis, electronic health records, and medical imaging. This research is currently supported by an NSF ACCESS "Discover" allocation that I lead as Principal Investigator — about 1.5 million ACCESS credits of national HPC/GPU resources, an NSF-estimated value of ≈$321,000.
Before joining UF, I received my B.S. in Internet of Things Engineering from Zhejiang Wanli University (2021), advised by Prof. Jiong Shi, and my M.S. in Computer Science from Zhejiang Normal University (2024) under Prof. Jia Zhu, where — as a member of the Zhejiang Key Laboratory of Intelligent Education Technology and Application — I was also guided by Prof. Changqin Huang and Prof. Ming Li. In summer 2023 I visited Prof. Daniel E. Acuna's lab in the Department of Computer Science at CU Boulder.
Since 2023 I have (co-)authored 22 peer-reviewed papers — including 12 first / co-first-author works — in venues such as Nature Communications, Advanced Science, Patterns, Briefings in Bioinformatics, Bioinformatics, and Findings of EMNLP, along with 2 preprints under review, and I hold one China patent. I serve as a reviewer for 35+ international journals and conferences (e.g., Medical Image Analysis, Patterns, Genome Biology, npj Precision Oncology, Neural Networks) and as a Program Committee member for ICIBM 2024–2026.
Research Interests
- AI4Science — AI4Health, AI4Biology, AI4Drug, AI4Pathology
- Biomedical Foundation Models
- Large Language Models, Agent-based and RAG / Knowledge-Graph Systems
News
- 2026.10First-author paper "CellPert" accepted at Patterns.
- 2026.10Co-first-author paper "MVCBench" accepted at Nature Communications.
- 2026.10Selected to receive $20,000 in Claude usage credits through the MIT–Anthropic AI for Science Study (MIT Sloan).
- 2026.08Two first-author papers — "DrugClaw and DrugAudit" and "UniD³" — accepted to Findings of EMNLP 2026.
- 2026.08Presented a poster at ICMST 2026 (International Conference on Movement Science and Technology), Purdue University, West Lafayette, IN — "DrugClaw and DrugAudit: A Primary-Source-Grounded Agent and Authority-Aware Benchmark for Drug-Information Question Answering."
- 2026.08Presented a poster at ICMST 2026 (International Conference on Movement Science and Technology), Purdue University, West Lafayette, IN — "UniD³: Open Knowledge Graphs and QA Benchmarks for Drug–Disease Discovery and Reasoning."
- 2026.08Teaching Assistant for CAI5720 Fundamentals of AI in Medicine I (Fall 2026), College of Medicine, University of Florida.
- 2026.06Awarded an NSF ACCESS "Discover" allocation as Principal Investigator (2026–2027) — about 1.5 million ACCESS credits (NSF-estimated value ≈$321,000) of national HPC/GPU resources for dissertation research on MKG4Drug; 750,000 credits in the first tranche.
- 2026.05Paper presentation at the 2026 FACCA Retreat (Florida Academic Cancer Center Alliance), Tampa, FL — "scDrugMap".
- 2026.02Invited talk at the Health Informatics & AI Learning Series (Spring 2026), Brown Center for Biomedical Informatics (BCBI), Brown University — "scDrugMap".
- 2026.02Guest Lecturer for GMS6804 Translational Bioinformatics (Spring 2026), HOBI, University of Florida — "AI-Driven Paradigm for Single-Cell Drug Resistance Prediction and Evaluation".
- 2025.12First-author paper "scDrugMap" accepted at Nature Communications.
- 2025.06First-author paper "HECLIP" accepted at Bioinformatics.
- 2024.10Co-first-author paper "DrugFormer" accepted at Advanced Science.
- 2024.09First-author paper "AntiFormer" accepted at Briefings in Bioinformatics.
Scroll inside the box for earlier news.
Selected Publications
My research builds multimodal AI that learns drug representations both machines can compute with and people can read, uses them to drive drug discovery, and integrates them into verifiable agent systems.
Representation
Multimodal representations of cells, tissues & patients
Discovery
Drug response, perturbation & binding prediction
First authorQ1 · IF 10.8In press
CellPert: Graph-Based Variational Learning with Biological Priors for Cross-Dataset Perturbation Prediction
Patterns (Cell Press)
Co-first authorQ1 · IF 18.1In press
MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes
Nature Communications
System
LLM agents, knowledge graphs & benchmarks
First author
UniD³: Open Knowledge Graphs and QA Benchmarks for Drug–Disease Discovery and Reasoning
Findings of the Association for Computational Linguistics: EMNLP 2026
Earlier Work
NLP & AI for education
First authorQ1 · IF 6.1
GUDN: A Novel Guide Network with Label Reinforcement Strategy for Extreme Multi-label Text Classification
Journal of King Saud University – Computer and Information Sciences
First author
Automatic Teaching Plan Grading with Distilled Multimodal Education Knowledge
International Conference on Computer Science and Educational Informatization (ICCSEI), Springer
Open Source
Founder & maintainer · 100+ GitHub stars
An agentic RAG system for drug intelligence — drug-target interactions, adverse drug reactions, drug-drug interactions, pharmacogenomics, and repurposing — built on LangGraph with evidence-grounded, source-attributed answers.
Education
University of Florida
Ph.D. in Biomedical Informatics (ERS-AI Program) · GPA 3.55/4
Aug 2025 – Present
Advisors: Yijiang Chen, Qianqian Song
University of Florida
M.S. program in Biomedical Informatics (transferred to Ph.D.)
Aug 2024 – May 2025
Advisor: Qianqian Song
University of Colorado Boulder
Visiting Student, Department of Computer Science
Jun 2023 – Sep 2023
Advisor: Daniel E. Acuna
Zhejiang Normal University
M.S. in Computer Science · GPA 3.79/4 (WES)
Sep 2021 – Jun 2024
Advisor: Jia Zhu
Zhejiang Wanli University
B.S. in Internet of Things Engineering · GPA 3.31/4 (WES)
Sep 2017 – Jun 2021
Advisor: Jiong Shi
Research Experience
Graduate Research Assistant — Chen Lab
Dept. of Medicine, College of Medicine, University of Florida
Aug 2026 – Present
Multimodal AI and computational pathology.
Graduate Research Assistant (external, remote) — Song Lab
School of Applied and Creative Computing, Purdue University
Aug 2026 – Present
AI for drug discovery, single-cell foundation models, and biomedical LLM / agent systems.
Graduate Research Assistant — Song Lab
Dept. of Health Outcomes & Biomedical Informatics, University of Florida
Aug 2024 – Jul 2026
AI for drug discovery, single-cell foundation models, and biomedical LLM / agent systems.
Visiting Student — Acuna Lab
Dept. of Computer Science, University of Colorado Boulder
Jun 2023 – Sep 2023
Research Assistant — Intelligent Education Technology Lab
Zhejiang Key Laboratory of Intelligent Education Technology and Application, Zhejiang Normal University · Advisor: Prof. Jia Zhu
Sep 2021 – Jun 2024
Natural language processing, knowledge graphs, and AI for Education (AI4EDU).
Undergraduate Research — Internet of Things
Zhejiang Wanli University · Advisor: Prof. Jiong Shi
Sep 2017 – Jun 2021
IoT systems for medical cold-chain transportation and logistics.
Teaching
Teaching Assistant — CAI5720: Fundamentals of AI in Medicine I
College of Medicine, University of Florida
Fall 2026
Guest Lecturer — GMS6804: Translational Bioinformatics
Dept. of Health Outcomes & Biomedical Informatics, University of Florida
Spring 2026
Topic: "AI-Driven Paradigm for Single-Cell Drug Resistance Prediction and Evaluation"
Teaching Assistant — Object-Oriented Analysis and Design
Zhejiang Normal University
Fall 2023
Professional Service
- Reviewer for 36 international journals, including Medical Image Analysis, Patterns, Genome Biology, npj Precision Oncology, CAAI Transactions on Intelligence Technology, Briefings in Bioinformatics, Neural Networks, Expert Systems with Applications, and Applied Soft Computing.
- Reviewer, ICLR 2027; Program Committee Member & Reviewer, ICIBM 2024 / 2025 / 2026; Reviewer, IEEE ICHI 2026.
- Student Member of IEEE and CCF.
Honors & Awards
- MIT–Anthropic AI for Science Study (MIT Sloan; PI: Nathan Wilmers) — selected to receive $20,000 in Claude usage credits, Oct 2026.
- NSF ACCESS "Discover" Allocation — Principal Investigator, 2026–2027. About 1.5 million ACCESS credits (NSF-estimated value ≈$321,000) of national HPC/GPU resources — 750,000 in the first tranche; Award No. CIS261195.
- NSF ACCESS Allocation — Allocation Manager (PI: Qianqian Song), 2026–2027. About 1.5 million ACCESS credits (NSF-estimated value ≈$321,000) of national HPC/GPU resources — 750,000 in the first tranche; Award No. CIS261339.
- ZJNU Graduate Study Abroad Exchange Scholarship, Dec 2023
- ZJNU First-Class Postgraduate Scholarship, Dec 2023
- Kaggle Featured Code Competition — Top 6% (59/1057, Bronze Medal), Mar 2023
- Kaggle Research Prediction Competition — Top 22% (201/936), Jan 2023
- ZJNU Best Academic Reporter Award, Dec 2022
- ZJNU Third-Class Postgraduate Scholarship, Dec 2022 & Dec 2021
- Bachelor's Degree with Honor, Zhejiang Wanli University, Jun 2021
- Third Prize, Physics Contest for College Students in Zhejiang Province, Dec 2018