Signal Processing & Computational Biology

Research Focus

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

News

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.  PhD positions are available (see below).

Fully funded Ph.D. positions available

One/two Ph.D. positions in machine learning and computational biology at ECE, HKUST [Start date: September 2022]

One/two Ph.D. positions in data science and infectious diseases at EEE, University of Melbourne [Start date: 2022]

October 2021

Our research on COVID-19 was highlighted at Advance.org.

September 2021

Matthew contributed to the 2021 World Laureates Forum as a young scientist. He presented in a session entitled: “Biology, Medicine and Clinical Sciences”.  He also served as a moderator of this session.

July 2021

Upcoming talks:

  1. 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
  2. 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.  

June 2021

Congratulations to Syed Faraz Ahmed for defending his PhD! Faraz’s thesis was entitled “Genetic Sequence Analysis to Inform Design of Universal Vaccines against Infectious Diseases“. Faraz is going to continue his research as a post-doctoral fellow in our group.

 

May 2021

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. 

Selected media coverage: MedScape, Reuters; The Medical News; The Tyee;

Related bioRxiv preprint: “Epitopes targeted by T cells in convalescent COVID-19 patients“. 

April 2021

Nicolas’s paper “Large-Dimensional Characterization of Robust Linear Discriminant Analysis” has been accepted for publication in IEEE Transactions on Signal Processing.

Congratulations to Faraz who was shortlisted as a finalist for the SENG PhD Research Excellence Award.  

March 2021

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 accepted for publication in IEEE Open Journal of the Communications Society.

February 2021

Preprint of Hang’s Hepatitis C virus related work “Evolutionary modelling of HCV subtypes provides rationale for their different disease outcomes” has been posted on bioRxiv. 


January 2021

Phoom’s paper “Detection of Diabetic Retinopathy from Ultra-Wide Field Scanning Laser Ophthalmoscope Images: A Multi-Center Deep-Learning Analysis” has been published in Ophthalmology Retina. This is a joint work with Fangyao Tang, An Ran Ran, and Carol Y. Cheung (The Chinese University of Hong Kong) and collaborators from Hong Kong Eye Hospital, Sankara Nethralaya and Giridhar Eye Institute (India), Moorfields Eye Hospital (UK), Tel Aviv Medical Center (Israel), and University of Buenos Aires (Argentina).

Our review paper “In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives” has been published in Advanced Drug Delivery Reviews.

Matthew was elevated to IEEE Fellow “for contributions to random matrix theory in statistical signal processing”. 

Congratulations to Neelkanth for being selected as one of the three winners of the video contest at the 2021 Global Young Scientists Summit. The summit included recipients of the Nobel Prize, Fields Medal, Millennium Technology Prize, and Turing Award. Neelkanth’s submission “Signal Processing for 6G: From Classical to Quantum Communications” was selected from around 110 entries, all from young scientists who had been selected for the forum.

Neelkanth’s paper “Large Intelligent Surfaces with Channel Estimation Overhead: Achievable Rate and Optimal Configuration” has been accepted for publication in IEEE Wireless Communications Letters.

December 2020

Saqib’s paper “MPL resolves genetic linkage in fitness inference from complex evolutionary histories“ has been published in Nature Biotechnology. This is a joint work with Raymond Louie (University of New South Wales) and John Barton (University of California-Riverside).

Media coverage: UCR Release, Eurekalert.

November 2020

Congratulations to Neel for being selected to participate in the 2021 Global Young Scientists Summit.

October 2020

Matthew contributed to the 2020 World Laureates Forum as a young scientist.  He gave a presentation in a session entitled: “Learn from the Pandemic: Public Health and Economy”.   The session involved 2 Nobel Laureates:  Dr. Harvey Alter (2020 Nobel Prize in Physiology and Medicine), and Dr. Ada Yonath (2009 Nobel Prize in Chemistry).

Faraz’s paper “Cross-serotypically conserved epitope recommendations for a universal T cell-based dengue vaccine” has been published in PLOS Neglected Tropical Diseases. This is a joint work with John Barton (University of California-Riverside).
June 2020

We have developed a web-based platform, “COVIDep“, for real-time reporting of vaccine target recommendations for the COVID-19 coronavirus (SARS-CoV-2). 

Main features:
  • 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“.

May 2020

Saqib and Ahmed’s paper, “How genetic sequence data can guide vaccine design“, has been published in IEEE Potentials Magazine.

Neil, 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 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.

Selected press coverage (more on News page): The Standard, Study International, Science Daily, Pharmaceutical Technologies, UST release.

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.

December 2019
Matthew delivered an invited talk at the Random Matrices and Complex Data Analysis Workshop, held at the Shanghai University of Finance and Economics (SUFE).
November 2019
Ahmed’s paper “Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape” has been accepted to Nature Communications. This is joint work with Arup Chakraborty (MIT) and John Barton (University of California-Riverside).
 
Ahmed’s following 2 papers have been accepted to Bioinformatics:
  • “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).
October 2019
We welcome back Faraz and Umer after both spent 3 months visiting John Barton at the University of California (Riverside).
September 2019
Matthew contributed an invited talk at the Physical Concepts and Computational Models in Immunology workshop at MIT and the Ragon Institute of MGH, MIT, and Harvard.
 
Congratulations to Liusha Yang (our group alumni, now at the Shenzhen Big Data Research Institute) for being selected to represent HKUST as a “Rising Star” at the Asia Dean’s Forum Rising Stars Workshop to be held in Seoul, Korea. 
 
Laureano’s paper entitled “Extreme eigenvalue distributions of Jacobi ensembles: New exact representations, asymptotics and finite size corrections” has been accepted to Nuclear Physics B. This is joint work with David Morales (Queens University Belfast).
August 2019
Congratulations to Nicolas Auguin for successfully defending his Ph.D.!  Nicolas’ thesis was entitled Random Matrix Analysis of Gram Matrices and Large Robust Covariance Estimators with Applications.  We wish Nicolas all the best as he takes up his new position in the finance world, joining Qube Research and Technologies in HK.
 
Congrats to Ahmed for receiving the Best Poster Prize for his work on HCV data analysis at the 24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) held at Hong Kong U. 
July 2019
A pre-print of Saqib’s work entitled “Resolving genetic linkage reveals patterns of selection in HIV-1 evolution” has been posted on bioRxiv. This is joint work with Ray Louie (UNSW) and John Barton (University of California, Riverside). 
 
Faraz and Ahmed’s paper “Sub-dominant principal components inform new vaccine targets for HIV Gag” has been accepted for publication in Bioinformatics.  This was joint work with David Morales (Queens University Belfast).
June 2019
Our paper “Asymptotics of eigenstructure of sample correlation matrices for high-dimensional spiked models” has been accepted for publication in Statistica Sinica.  This is joint work with David Morales (Queens University Belfast), Iain Johnstone and Jeha Yang (Stanford).
May 2019
Ahmed’s paper “Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them” has appeared in Nature Communications.  This is joint work with Ray Louie (UNSW).
 
Congrats to our group’s Final Year Project student, Phoomraphee Leunam, whose project was selected as the Best Final Year Project in the ECE Department. He also received the Silver Award for the industry demo competition.  Phoom’s work developed deep learning solutions to detect eye diseases from images extracted from diabetic patients in Hong Kong.  It was a collaboration with the HK Eye Hospital.
January – March 2019
November 2018 
An article related to our group’s research, titled “Fighting disease with data and hope”, is published in The Standard ​newspaper.
September 2018
Matthew was invited to present an “IdeasLab” talk on the use of Big Data Methods to Guide Rational Vaccine Design at the World Economic Forum.  Here is the YouTube link.
 
Matthew was also selected as a Young Scientist of the World Economic Forum.
 
Welcome to Hang Zhang (from Shanghai Jiaotong), Awais Wahab Shah (from KFUPM), and Neel Kanth (from IIT-Delhi) to our group as new Ph.D. students.  Congrats also to Awais and Neel for being selected as recipients of the prestigious Hong Kong Ph.D. Fellowship.
August 2018
Liusha Yang successfully defended her Ph.D. thesis entitled Random-Matrix-Based High-Dimensional Covariance Estimation and Signal Processing Applications. Congratulations to Dr. Yang!  We wish her all the best as she starts her new job at the Shenzhen Big Data Research Institute.
June 2018
We bid farewell to Raymond Louie who had been with our group for five years. He was a core  member of our group’s work related to computational biology. We wish Raymond the best of luck as he moves to the medical school at UNSW, Australia.

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

May 2018
Talk at 2018 Hospital Authority Convention, Hong Kong Convention and Exhibition Center, Hong Kong
Title: Using data science to find weak spots of Hepatitis C virus: Implications for rational vaccine design
Speaker: Matthew R. McKay
McKay_HAC2
McKay_HAC3
February 2018
Our work, published in PNAS, has received media attention.  Here are some examples (more complete list on News page):

Local, mainland China, and general media

Science channels

January 2018
Matthew is now Area Editor (Feature Articles) of the IEEE Signal Processing Magazine.  

Videos of HKUST

Useful Links

— Banner photo taken by HKUST alumnus Terence Pang