About me

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My research focuses on elucidating complex biological interactions using and developing computational techniques such as machine learning, deep neural networks, graph neural networks, causal discovery and inference, large language models, multimodal language models, and network analysis, as well as building mobile and web applications for biological, clinical, and computational related research.

Beyond this research, I am passionate about leveraging and advancing computer vision to detect complex biological structures and activities in large-scale clinical and biomedical imaging datasets. I also explore computational methods for analyzing biological systems (Next-Generation Sequencing (NGS) data (bulk RNA-seq, single-cell RNA-seq, multiomics (e.g., genomics, transcriptomics, proteomics), and spatial transcriptomics), including multimodal language models. Additionally, I am interested in developing simulation tools for biological dynamics—such as multi-scale molecular and cellular interactions—using open-source frameworks like MuJoCo.

I've been working on various research topics, such as uncovering genetic regulatory mechanisms and interactions, identifying genetic functionalities and roles in certain biological activities, discovering nuanced cell types, identifying cell-type–specific activities and events, learning cell-to-cell communications, finding critical biomarkers to accurately predict disease outcomes from clinical data, inferring causal relationships from complex biological and clinical environments, and so on.

What i'm doing

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People

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Resume

Training

  1. Postdoctoral Researcher

    Stanford Medicine

    2024 — 2025
    • Implement research projects using programming languages.
    • Develop and extend technical methods.
    • Develop website tools for research projects.
    • Perform computational and statistical analyses on research project data.
    • Draft manuscripts for research projects.
    • Collaborate with other group members and other research groups.

Education

  1. Ph.D. in Computer Science

    University of Pittsburgh

    2015 — 2023
    Dissertation: Elucidating complex biological interactions using computational techniques.

  2. B.S in Computer Science

    Tianjin University of Technology

    2007 — 2011

Academic Service

  1. International Journal of Medical Informatics

    2023 - present
  2. Briefings in Bioinformatics

    2024 - present
  3. Nature Portfolio’s npj Digital Medicine

    2025 - present
  4. Nature’s npj Precision Oncology

    2025 - present

Academic Conferences

  1. Session Presentation at JSM 2025 Conference in Nashville

    Aug 2025

    Session: Causal Inference and Generative AI: Discovering Causal Relations Using Large Language Models
    Presentation Title: A Causal Estimation Language Model for Tabular Data in Complex Biological Systems with Local Scores, Conditional Independence Tests, and Relation Attributes.

Research Monitoring

  1. Sponsor for An Undergraduate Research Course Project (CS/CompBio Capstone)

    Spring 2023

    Department of Computer Science, University of Pittsburgh
    • Project Name: Cell Clustering Using Graph Neural Networks.
    • Undergraduate Students: Kareem Zein and Siddharth Mahesh.

Teaching Experience

  1. Teaching Assistant, Department of Computer Science, University of Pittsburgh

    2015 - 2023

    • Course: CS 1550 Introduction to Operating System Fall 2022
    • Course: CS 0447 Computer Organization and Assembly Language Fall 2021
    • Course: CS 0449 Introduction to Systems Software Spring 2019, Spring 2020
    • Course: CS 1501 Algorithm Implementation Fall 2018, Fall 2019
    • Course: CS 0445 Algorithms and Data Structures Fall 2017
    • Course: CS 0401 Intermediate Programming Summer 2016, Summer 2017, Summer 2019
    • Course: CS 0441 Discrete Structures Fall 2015

Industry Work Experience

  1. Human Frontier Collective Specialist (part-time)

    Scale AI, Inc., 2025 — Present

    • Conducted research to identify limitations of large language models and developed solutions to enhance their reasoning and capabilities.
    • Collaborated with a team to implement innovative strategies for improving large language models' performance.

  2. Android Project Development

    Beijing Adwo Mobile Media Technology, Ltd, 2013-2015

    • Coordinated a 5-member team on 7 projects for clients such as Disney China.

  3. Server-side Engineer and Android SDK Engineer

    Wooboo International Media, Ltd, 2011-2013

    • Developed a server-side advertising engine.
    • Led the development of a server-side advertising engine for China Telecom.
    • Subsequently assisted in the creation of the company's Android App marketplace.
    • Provided pivotal support in the development of an Online Mobile Application Market for China Telecom.
    • Coordinated development of platform architecture, services and protocol between server and client SDKs.
    • Completed system architecture for Android applications, including File Manager, Task Manager and the Wooboo Application Market for Android and deployed core system server, on behalf of Samsung China.

Refereed Abstract and Posters

  1. Poster Presentation at Pitt Public Health's Annual Showcase of Student Research

    Mar 2018

    • Fan Z, Kim S, Bai Y, Diergaarde B, Park HJ. 3 -UTR Shortening Contributes to Subtype-Specific Cancer Growth by Breaking Stable ceRNA Crosstalk of Housekeeping Genes.

Awards and Honors

  1. Dietrich School of Arts and Sciences Graduate Fellowship, University of Pittsburgh

    Spring 2016
  2. School of Public Health Graduate Fellowship

    Spring 2021
  3. School of Public Health Graduate Student Researcher, University of Pittsburgh

    Summer 2022
  4. Elected and served as the Vice President of the Graduate Student Organization, Department of Computer Science, Kenneth P. Dietrich School of Arts and Sciences

    2018 - 2020
  5. Granted Google Cloud Research Credits from GCP Education Programs

    July - 2024
  6. • AMD’s High Performance Compute Fund

    January - 2025

My skills

  • Programming Languages (Expert):
    Java, Python, C/C++, JavaScript
  • Programming Languages (Adept):
    R, MATLAB, HTML, CSS.
  • Technical Skills:
    Next-Generation Sequencing (NGS) Data Analysis (Bulk RNA-Seq, Single-Cell RNA-Seq, Multiomics (e.g., Genomics, Transcriptomics, Proteomics), and Spatial Transcriptomics), Language Models, Multimodal Language Models, Machine Learning, Feature Selection, Graph Neural Network, Causal Discovery and Inference, Computational Biology, Network Analysis, Artificial Neural Networks, Android Application Development, Server-Side Program Development, and Dynamic Web Application Development.

CV

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Portfolio

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