Dr Kevin Bryson
- Senior Lecturer (School of Computing Science)
https://orcid.org/0000-0002-1163-6368Biography
I joined the School in 2021 as a Senior Lecturer in Bioinformatics and Machine Learning.
I received a BSc honours degree (1st class) in Mathematics and Computer Science from Heriot-Watt University in 1991 and a DPhil in Physics from the University of York in 1996, and then spent 3 years in industry working at Oxford Molecular Ltd. developing bioinformatics software before taking up a BBSRC Fellowship at University of Warwick, studying the application of multi-agent systems to bioinformatics.
After my postdoc position at Warwick, I got an EU Individual Marie Curie Fellowship at INRA in Paris where we developed another cooperative distributed system for annotating the genomes of fermented sausage, cheese and yogurt bacteria.
I then moved to the Department of Computer Science at UCL to take up a Fellowship position analyzing gene expression profiles of stem cells; leading onto a lectureship position, senior lecturer and associate professor in in bioinformatics and systems biology where we applied machine learning techniques to protein structure, biological networks, -omics data and histopathology images, collaborating with bioscience groups mostly in the area of cancer.
Research interests
We use machine learning, and in particular deep learning, to tackle challenges in the area of bioscience. A lot of our research has been in the area of cancer and we are grateful to the clinical research groups that have allowed us to work with them on these problems.
We work with -omics data including gene expression, genomic methylation, proteomics and metabolics data. We employ supervised and unsupervised machine learning approaches to make predictions and reveal patterns in the data. We use biological network information to integrate data and gain holistic understanding of biological mechanisms. We also analyze image data including fluorescent labelled images of E. coli and H&E microscope slide images of cancer tissues sections. The long-term goal is to integrate molecular information, imaging data and clinical data to gain holistic understanding of diseases, particularly targeted at cancer.
- Breast cancer subtypes.
- Psychiatric conditions such as depression and autism.
We have also developed a number of machine learning tools to:
- Find patterns within large heterogeneous gene expression data collections (MCbiclust based on R).
- Create realistic synthetic gene expression datasets (GANs using TensorFlow).
We have recently started projects doing traditional image analysis (scikit-image) and CNN image prediction (PyTorch/Tensorflow) including:
- Phenotype analysis of fluorescent C. elegans worms.
- Nucleus image analysis using PCA, t-SNE and TensorFlow.
- Classification between liposarcoma and lipoma using H&E whole slide images.
- Classification between synovial sarcoma and singular fibrous tumour using H&E images.
We also analyze protein sequences using machine learning approaches to predict both structural and functional aspects of proteins including:
- Secondary structure.
- Protein disorder.
- Amyloid propensity.
- B-cell epitopes.
Teaching
Currently I'm the Director of the MSc in Data Science and also the MSc in Computer Science.
I currently teach the following courses:
- COMPSCI5103 Deep Learning for MSc
- COMPSCI4084 Programming and Development
Previously I have taught at Glasgow:
- COMPSCI4039 Programming (IT)
Previously, at UCL, I was the Undergraduate Programme Director and also the Director of the MSc in Computer Science. I have taught in the past the following subjects:
- BIOC0016 (3rd year Computational and Systems Biology within the Department of Structural and Molecular Biology, UCL)
- COMP0008 (2nd year Computer Architecture and Concurrency)
- COMP0082 (Bioinformatics module as part of the MSc in Machine Learning)
- COMP1001 (1st year Computer Architecture) using assembly language programming to explain the underlying working of the MIPS processor (and processors in general).
- COMP2007 (2nd year Networking and Concurrency) teaching Java Concurrent Programming and introduces the concepts of computer networking by developing concurrent Java simulators demonstrating the key principles.
- COMP3006 (Advanced Mathematics) where I taught advanced linear algebra and vector calculus.
- CPLXG001 (MRes Advanced Biological Modelling and Bioinformatics within CoMPLEX) teaching bioinformatics.
- CPLXG003 (MRes Transferrable Skills Module within CoMPLEX) teaching the application of SQL relational databases within bioinformatics.
- INFN3004 (MSc and Intercalating Medical BSc in Immunology and Cell Pathology and Infection) taught introductory bioinformatics to medical students.
- WIBRG001 (MSc Drug Design within the Wolfson Institute of Medical Research) teaching introductory bioinformatics.
I was also an Honorary Teaching Fellow at Birkbeck College where I taught:
- Birkbeck MSc in Bioinformatics and Systems Biology teaching biological networks and mathematical modelling.
