CV

Education

• M.Phil. in Bioengineering (BIEN), The Hong Kong University of Science and Technology, 2019
  • Thesis: ‘Deep Learning Enables Instance Edge Detection of Vertebral Bodies on X-ray Images’
• B.Eng. in Computer Engineering (CPEG), The Hong Kong University of Science and Technology, 2017
  • Minor in Mathematics

Work experience

• Nov 2019 to present: Bioinformatician
  • Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
  • Develop machine learning methods to analyze biomedical data.
  • Design website to share and visualize data resources to the general public.
  • Teaching assistant of ‘Machine Learning for Biomedical Data Science’ (Spring I 2020 & 2021).
  • Supervisor: Prof. Gaurav Pandey.
• Aug 2019 to Oct 2019: Consultant
  • Department of Industrial Engineering & Decison Analytics,The Hong Kong University of Science and Technology
  • Develop Smart Fever Screening System with ZED stereo camera & FLIR thermal camera
  • Supervisor: Prof. Richard H.Y. So
• Jun 2015 to Aug 2015: Summer Intern
  • Hong Kong Telecom (HKT) Limited
• Feb 2015 to May 2015: Part-time Tutor
  • Pigeon City Creative Computing Training Centre
• Jun 2013 to Aug 2013: Technical Support
  • SkyWare Communication Limited

Publications

eipy: An Open-Source Python Package for Multi-modal Data Integration using Heterogeneous Ensembles

eipy: An Open-Source Python Package for Multi-modal Data Integration using Heterogeneous Ensembles. Bennett, Jamie J.R.; Li, Yan Chak; Pandey, Gaurav; arXiv, 2023.

KinAce: a web portal for exploring kinase-substrate interactions

KinAce: a web portal for exploring kinase-substrate interactions. Sekar, John A P.; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; bioRxiv, 2023.

Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures

Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures. Herrington, Noah B.; Stein, David; Li, Yan Chak; Pandey, Gaurav; Schlessinger, Avner; bioRxiv, 2023.

Facilitating youth diabetes studies with the most comprehensive epidemiological dataset available through a public web portal

Facilitating youth diabetes studies with the most comprehensive epidemiological dataset available through a public web portal. McDonough, Catherine; Li, Yan Chak; Vangeepuram, Nita; Liu, Bian; Pandey Gaurav. medRxiv, 2023.

Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge

Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. Sieberts, Solveig K; Borzymowski, Henryk; Guan, Yuanfang; Huang, Yidi; Matzner, Ayala; Page, Alex; … ; Li, Yan-Chak; … ; Stanescu, Ana; … ; Pandey, Gaurav; Shawen, Nicholas; Synder, Phil; Omberg, Larsson. PLOS Digital Health 2 (3), e0000208. 2023.

Integrating multimodal data through interpretable heterogeneous ensembles

Integrating multimodal data through interpretable heterogeneous ensembles, Li, Yan Chak; Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. Bioinformtics Advances, Volume 2, Issue 1, 2022, vbac065

Machine learning–driven identification of early-life air toxic combinations associated with childhood asthma outcomes

Li, Yan-Chak; Hsu, Hsiao-Hsien Leon; Chun, Yoojin; Chiu, Po-Hsiang; Arditi, Zoe; Claudio, Luz; Pandey, Gaurav; Bunyavanich, Supinda. The Journal of Clinical Investigation. 2021. 131(22).

Clinical features of COVID-19 mortality: development and validation of a clinical prediction model

Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. The Lancet Digital Health. 2020. 2(10).

Automatic instance-edge detection network (AID-Net)-vertebral edge detection by deep learning

Yan Li, Jing Chin, Yixiang Wang, Richard So, "Automatic instance-edge detection network (AID-Net)-vertebral edge detection by deep learning." European Journal of Clinical Investigation, 2019.

Talks/Conference Presentations

Integrating multimodal data through interpretable heterogeneous ensembles

July 11, 2022

Conference & Poster Presentation at Intelligent Systems for Molecular Biology (ISMB) 2022, Madison, Wisconsin

Predicting biomedical characteristics and outcomes using Ensemble Integration

March 10, 2021

Work In Progress(WIP) talk at Icahn School of Medicine at Mount Sinai, New York, US

Automatic Instance-edge Detection Network (AID-Net) - vertebral edge detection by deep learning

May 21, 2019

Conference Presentation at European Society for Clinical Investigation(ESCI) Congress, Coimbra, Portugal

Fast similarity measure of SWATH-MS by Cosine Similarity of Random Pairs(CS-RP)

December 13, 2017

Conference Presentation at Asia Oceania Mass Spectrometry Conference (AOMSC) 2017, Biopolis, Singapore

Teaching

• Spring I 2020 & 2021: Teaching Assistant
  • Icahn School of Medicine at Mount Sinai
  • BMI3002 Machine Learning for Biomedical Data Science
• Spring I 2018 & 2019: Teaching Assistant
  • Department of Industrial Engineering & Decison Analytics, The Hong Kong University of Science and Technology
  • IELM/IEDA2100E Computing and Industrial Applications

Skills

• Machine learning model development
• Programming Languages:
  • Python: Numpy, OpenCV, Pytorch, Scikit-learn, Pandas etc.
  • R, R Markdown
  • Javascript, Vue.js
  • MATLAB, C, C++, CUDA C
• Others:
  • High Performance Computing, Oracle Cloud, Google Cloud
  • Firebase, Basic SQL
  • Google Analytics

Academic Services

• Conference Reviewer:
  • IEEE Big Data 2020, 2022
  • ACM-BCB 2021-2023
  • ISMB 2022, 2023
  • ACM-SIGKDD 2022

Voluntary Services/Part-time Job Experiences

• SUG mentor of Hall II (Vertex), HKUST, 2016-2017
• Student Helper, Computer Science System Office, HKUST, 2016-2017
• Student Helper, Institute of Emerging Market Studies, HKUST, 2015-2017
• President, Nature Club, HKUSTSU, 2014-2015

CV in PDF