cv

Basics

Name Ke Xu
Label PhD Student
Email k.xu@yale.edu
Phone (608) 867-6776
Url https://scottxuke-gif.github.io/
Summary PhD student in Computer Science at Yale University, working on machine learning for sequential and dynamical data with applications in computational biology.

Education

  • 2024 - Present

    New Haven, CT

    PhD
    Yale University
    Computer Science
    • Advisors: Mark Gerstein & Smita Krishnaswamy
  • 2022 - 2024

    New Haven, CT

    Master of Public Health
    Yale University
    Biostatistics
  • 2020 - 2022

    Madison, WI

    Bachelor of Science
    University of Wisconsin--Madison
    Mathematics
  • 2017 - 2020

    Hong Kong

    Undergraduate Coursework
    Hong Kong Baptist University
    Mathematics & Statistics

Work

  • 2024.04 - Present
    Graduate Research Assistant
    Krishnaswamy Lab, Yale University
    Advisor: Prof. Smita Krishnaswamy
    • ImageFlowNet: Neural ODE/SDE-based model for forecasting disease progression trajectories from longitudinal medical images (ICASSP 2025, co-first author)
    • STAGED: Multi-agent neural network for modeling cellular interaction dynamics via message passing on learned communication graphs (MLCB 2025, co-first author)
  • 2022.06 - Present
    Graduate Research Assistant
    Gerstein Lab, Yale University
    Advisor: Prof. Mark Gerstein
    • ChronODE: ODE-based framework for modeling multi-omic time series across species and developmental stages (Nature Communications 2025)
    • WasteWatcher: Unsupervised temporal clustering of longitudinal wastewater microbiome data using EM with B-spline basis functions
    • transferQTL: Computational toolkit for tissue-specific eQTL regulatory mechanisms using GTEx data
  • 2022.01 - 2022.04
    Undergraduate Research Assistant
    McArdle Laboratory for Cancer Research, UW--Madison
    Advisor: Prof. Huy Dinh
    • Bioinformatics analysis of somatic mutations in kidney cancer; inferred cell-type-specific GRNs from single-cell and bulk DNA methylation data

Awards

Skills

Programming
Python (PyTorch, JAX)
R
Java
SAS
Bioinformatics
Seurat
GATK
Samtools
Picard
scanpy
Languages
Chinese (native)
English (proficient)

Volunteer