đź—¨ About Me
I am currently a research intern at the Representation Learning Lab at the Westlake University working with Prof. Fajie Yuan and collaborating with Dr. Zitong Jerry Wang.
Previously, I received my Master’s degree in Computer Science from Johns Hopkins University and Bachelor’s degree in Computer Science from Wenzhou-Kean University. I did my master thesis advised by Prof. Kimia Ghobadi at Johns Hopkins University on multi-agent simulation. I was fortunate to work with Prof. Aloysius Wong’s Group at Wenzhou-Kean University during my undergraduate where I first stepped into the field of bioinformatics. After graduation, I worked as a lab specialist at Prof. Chongzhi Zang’s Lab at the University of Virginia Medical School exploring epigenomics-related topics.
In addition, I developed a deep learning model for RNA-ligand interaction prediction with Prof. Yanjun Li at University of Florida and later participated in developing a single-cell foundation model in Prof. Xiaojie Qiu’s Lab at Stanford University. I am also working with Prof. Han Xiao’s Group at Rice University Chemistry for developing a robust platform for machine learning guided protein evolution.
I mainly work on the intersection of machine learning and biology in a broad scope. I am interested in foundation models and LLMs for life sciences around the central dogma and how to use them to interpret and discover the biological mechanism.
Research Interests:
- Genomics and Epigenomics
- Deep learning for Cancer Biology and Chemical Biology
- AI for Drug Discovery
đź“– Educations
- 2022 - 2024, Master of Science in Engineering, Computer Science. Johns Hopkins University. Baltimore, MD
- 2018 - 2022, Bachelor of Science, Computer Science. Wenzhou-Kean University. Wenzhou, China
đź“° News
đź“ť Publications
Integrating Metal–Phenolic Networks-Mediated Separation and Machine Learning-Aided Surface-Enhanced Raman Spectroscopy for Accurate Nanoplastics Quantification and Classification Haoxin Ye, Shiyu Jiang, Yan Yan, Bin Zhao, Edward R Grant, David D Kitts, Rickey Y Yada, Anubhav Pratap-Singh, Alberto Baldelli, Tianxi Yang. ACS Nano, 2024. Featured on Cover
Simulating Disease Spread During Disaster Scenarios Shiyu Jiang, Heejoong Kim, Fabio Henrique Tanaka, Claus Aranha, Anna Bogdanova, Kimia Ghobadi, Anton Dahbura. The International Conference on Artificial Life, 2023. Code
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence Shiyu Jiang, Hemn Barzan Abdalla, Chuyun Bi, Yi Zhu, Xuechen Tian, Yixin Yang, Aloysius Wong. Bioinformatics, 2022 Website | Code
Deblur-yolo: Real-time object detection with efficient blind motion deblurring
Shen Zheng, Yuxiong Wu, Shiyu Jiang, Changjie Lu, Gaurav Gupta. International Joint Conference on Neural Networks, 2021
🧑‍💻 Professional Experience
- 2024.08 - Present, Research Intern, Representation Learning Lab, Westlake University, Hangzhou, China.
- 2024.01 - 2024.07, Lab Specialist, Chongzhi Zang Lab, University of Virginia School of Medicine, Charlottesville, VA.
- 2022.06 - 2022.08, Software Engineer Intern, Alibaba Cloud - PolarDB, Hangzhou, China.
- 2021.09 - 2022.03, Applied Research Intern, Institute of Automation, Chinese Academy of Sciences, Beijing, China.
🔨 Tools
Model
- Koudou: an agent-based model that simulates the infectious disease spread under college town scenario.
Web server
- HNOXPred (Prediction of Heme-Nitric oxide/OXygen domains): a web server that predicts gas-sensing H-NOX proteins from amino acid sequences.
Python Package
- SICER 2.0 (Spatial-clustering Identification of ChIP-Enriched Regions): a ChIP-Seq broad peak calling data analysis method.
🌎 Miscellaneous
Soccer (Visca Barça), Gym, Table tennis, Piano, Travel, etc.
