Signal Processing & Computational Biology
The Signal Processing and Computational Biology Group is an interdisciplinary research group in the Department of Electronic and Computer Engineering at The Hong Kong University of Science and Technology (HKUST). We focus on developing high dimensional statistical and machine learning methods, and applying them to problems in signal processing and computational biology. Our group also works on the theory and applications of random matrices
Important group update
Prof. Matthew McKay will be joining University of Melbourne (UoM) as a Professor in the Department of Electrical and Electronic Engineering (EEE), and as an Honorary Professorial Fellow within the Department of Microbiology and Immunology, located within the Doherty Institute. He will retain an Adjunct Professor position at HKUST. The SPCB group will continue to operate at HKUST under Prof. Ahmed Abdul Quadeer. Prof. McKay will continue to work closely with the group at HKUST, while developing a new team at UoM. Research Assistant Professor (RAP) and postdoctoral fellow (PDF) positions are available (see below).
Our first monkeypox virus related research “Vaccinia-Virus-Based Vaccines Are Expected to Elicit Highly Cross-Reactive Immunity to the 2022 Monkeypox Virus” has been published in Viruses.
Related bioRxiv preprint: “Vaccinia virus vaccination is expected to elicit highly cross-reactive immunity to the 2022 monkeypox virus“.
- Plenary talk at The 11th IEEE International Conference on CYBER Technology in Automation, Control, and Intelligent Systems
(IEEE-CYBER 2021), Jiaxing, China, July 27-21, 2021.
Title: Computational Approaches for Guiding Rational Vaccine Design: Case Studies of HIV, HCV and COVID-19
Speaker: Matthew R. McKay
- Talk at Structured Random Matrices in Down Under: New Developments and Applications, Creswick, Victoria, Australia, July 26-August 7, 2021.
Title: Guiding rational vaccine design with random matrix theory
Speaker: Matthew R. McKay
A Theme-Based project “Virological, Immunological and Epidemiological Characterization of COVID-19” on COVID-19 involving our group has been funded by the Hong Kong Research Grants Council. The awarded funding is 60 million HKD.
Matthew is a Co-PI on this project, together with 8 Co-PIs from Hong Kong University (HKU), and 1 Co-PI from the Chinese University of Hong Kong (CUHK). The Project Coordinator is Prof. Leo Poon (HKU).
Related media article: SCMP
Congratulations to Ahmed Abdul Quadeer for his first funded Hong Kong Research Grant Council’s General Research Fund (GRF) project as a principal investigator! Ahmed has been funded 838K HKD and the project is entitled “Identifying targets for a cross-coronavirus vaccine using intelligent computational techniques”. Further details here.
Matthew will be joining 2021 World Laureates Forum as a young scientist.
Ahmed and Faraz’s paper “Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform” has been published in Cell Reports Medicine. As a part of this work, we have developed a web-dashboard that provides an up-to-date information of the emerging data of SARS-CoV-2 T cell epitopes targeted in convalescent patients.
Related bioRxiv preprint: “Epitopes targeted by T cells in convalescent COVID-19 patients“.
Neelkanth’s paper “Large Intelligent Surfaces with Channel Estimation Overhead: Achievable Rate and Optimal Configuration” has been published in IEEE Wireless Communications Letters.
Congratulations to Syed Muhammad Umer Abdullah for completing his MPhil! Umer’s thesis was entitled “Methods for Inferring Selection from Short-read Time-series Genomic Data“. Umer will be joining Prof. Kelvin Kai Wing To’s lab at The University of Hong Kong to work on COVID-19 research.
Neelkanth’s paper “Channel Estimation for Reconfigurable Intelligent Surface Aided MISO Communications: From LMMSE to Deep Learning Solutions” has been published in IEEE Open Journal of the Communications Society.
Neelkanth’s paper “A Deep Learning-Based Channel Estimation Approach for MISO Communications with Large Intelligent Surfaces” has been published in IEEE 31st Annual International Symposium on Personal, Indoor and Mobile Radio Communications.
- Identification of SARS-derived B-cell and T-cell epitopes that provide vaccine target recommendations for SARS-CoV-2;
- For T cell epitopes, it reports estimated population coverage using HLA/MHC statistical information;
- Intuitive graphical interface with flexible parameter setting;
- Up-to-date reporting based on latest sequence data available (from GISAID).
An article related to the platform “COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2” has been published in Nature Protocols.
Highlighted on the cover page of Nature Protocols (July issue).
Related bioRxiv preprint: “COVIDep platform for real-time reporting of vaccine target recommendations for SARS-CoV-2: Description and connections with COVID-19 immune responses and preclinical vaccine trials“.
Neelkanth’s paper “Signal Design for Frequency-Phase Keying” has been published in IEEE Transactions on Wireless Communications.
Saqib and Ahmed’s paper, “How genetic sequence data can guide vaccine design“, has been published in IEEE Potentials Magazine.
Neelkanth, Faraz, and Awais shared their experience as international PhD students at HKUST in a Study International article.
February – March 2020
Faraz’s paper “Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies” has been published in Viruses on 25th Feb. 2020.
Cover article of Viruses (March 2020 issue).
Coverage in World Economic Forum article (by Prof. Wei Shyy, President of HKUST).
Coverage in the cover story (on COVID-19 vaccines) of New Scientist.
Congratulations to Muhammad Saqib Sohail for successfully defending his Ph.D.! Saqib’s thesis was entitled “A Stochastic Framework for Inference of Population Genetics Parameters from Time-series Genomic Data”. Saqib is going to continue his research as a post-doctoral fellow in our group.
- “RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins”. Joint with David Morales-Jimenez (Queens University, Belfast).
- “MPF-BML: A standalone GUI-based package for maximum entropy model inference”. Joint with Ray Louie (Kirby Institute, UNSW) and John Barton (University of California-Riverside).
Talk at 2018 Artificial Intelligence (AI) in Healthcare Summit, The Ritz Carlton, International Commerce Center, Hong Kong
Title: Inferring the fitness landscape of HIV by unsupervised learning
Speaker: Raymond Louie
Title: Using data science to find weak spots of Hepatitis C virus: Implications for rational vaccine design
Speaker: Matthew R. McKay
Local, mainland China, and general media
- South China Morning Post – Breakthrough HKUST-led research on mapping of HIV weak spots paves way for vaccine
- RTHK – Hong Kong Today (Big data analysis helping in development of HIV vaccine)
- World News – HKUST Researchers Discover Fitness Landscape of HIV Envelope Protein That May Help Vaccine Development
- Public Now
- Brinkwire – Big data methods learn the fitness landscape of the HIV Envelope protein
- Yahoo – 推算結果 實驗驗證 科大大數據分析病毒 助研發抗愛滋疫苗
- Eurekalert – Big data methods learn the fitness landscape of the HIV envelope protein
- Healthcare Analytics News – Big Data and Machine Learning Take on HIV
- Science Daily – Big data methods learn the fitness landscape of the HIV Envelope protein
- Medical Express – Big data methods applied to the fitness landscape of the HIV envelope protein
— Banner photo taken by HKUST alumnus Terence Pang