CV

Education

• B.S./M.S. in Computer Science, Case Western Reserve University, 2020
• Ph.D in Computer Science, Case Western Reserve University, 2020-Present

Publications

DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution

Zhang, S., Plummer, D., Lu, L. et al. DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution. Nat Genet 54, 1013–1025 (2022). https://doi.org/10.1038/s41588-022-01116-w

Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A

Weng, C., Gu, A., Zhang, S. et al. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nat Commun 14, 5400 (2023). https://doi.org/10.1038/s41467-023-41228-3

Portfolio

Counting competitive jump rope events from video using computer vision

Software lead for winning entry in NASA Robotic Mining Competition

Jump Rope Tricktionary: Democratizing Jump Rope Knowledge Around the World

scloop: an embedding suite for single-cell Hi-C data

NextJump: running RepNet in realtime locally on iOS for jump rope training

Skills

• Machine learning
  • Representation learning and dimensionality reduction techniques
  • Deep generative models and probabilistic deep learning
  • Graph neural networks for embedding
  • Computer vision for video analysis
  • Toolkits and Libraries
    • PyTorch
    • TorchVision
    • Tensorflow/Keras
    • Gradio
    • Pandas, Numpy, and the whole Scipy suite
    • Scikit-learn
    • NetworkX
    • OpenCV
• Data visualization
  • High dimensional embedding visualization/interpretation
  • Graph/Network visualization
  • Genome tracks
  • Dynamic animated visualizations
  • Toolkits and Libraries
    • Matplotlib + Seaborn
    • Dash + Plotly
    • pyGenomeTracks
    • Blender
• Genomics and Single-Cell Epigenetics
  • Applications of representation learning and embedding methods to omics data
  • 3D genome architecture and Hi-C
  • Single-cell embedding and clustering
  • Diagonal integration of multi-modal single-cell data
  • Toolkits and Libraries
    • Cooler + Cooltools
    • Scanpy
    • AnnData
    • sc-vi-tools

Honors

• 2019-2020 Robert J. Herbold Endowment Fund Scholar
• 2020 CWRU Computer and Data Sciences Research Award
• 2020 Callahan Fellowship Recipient
• 2021-2022 Biometric Genetic Analysis of Cardiopulmonary Disease NIH T32 Training Fellowship
• 2022-2023 CWRU Computer and Data Sciences Outstanding Researcher Award
• 2023 CVPR Outstanding Demo Award

Teaching

Teaching Assistant: EECS 458: Intro to Bioinformatics

Teaching Assistant CSDS 364/464: Computational Perception

Course Design Collaborator for CSDS 364/464: Computational Perception

Teaching Assistant CSDS 391: Intro to Artificial Intelligence

Service and leadership

• CWRUBotix Software Lead (2017-2020)
  • Led the software team for CWRU’s entry in NASA’s Robotic Mining Competition with the goal of creating a fully autonomous robot capable of mining in a simulated lunar/martian environment.
    • Recruit and teach new team members about how the software system of our robot works
    • Hold workshops and lectures on various components of the software system
    • Train new undergraduate students to take over the role of software lead
  • Developed a real-time computer vision algorithm that utilizes an RGB-D sensor to sense obstacles in front of the robot and map their locations and sizes
  • Built a robot localization system that uses an extended Kalman filter to fuse sensor measurements from ultra-wideband radio signals, an inertial mass unit, and wheel odometry measurements.
• Jump Rope Instructor (2011-Present)
  • Started a jump rope club at Case for students to have fun learning new skills, meet new friends, and get active
  • Led the largest jump rope workshop in the world (JWTS in Ohio) along with other workshops and camps in the United States, Canada, Germany, the Czech Republic, Bermuda, and Portugal