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About CRUK Scotland Institute

Find out what we do, how we do it and why we do what we do.

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History

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Organisation Governance

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Scientific Advisory Board

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Sources of Funding

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Life in Glasgow

Find out about living and working in Glasgow and Scotland.

Our Research

Explore the science at CRUK Scotland Institute. Our research groups, the people who lead them, and how we work.

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Research Groups

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Vision and Strategy

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Research Integrity

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Grant Support

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Sustainability

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Use of Animals

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Annual Reports

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AI and Computational Biology

Advanced Technologies

State-of-the-art facilities and specialist expertise supporting research across the Institute.

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Technologies overview

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Beatson Advanced Imaging Resource

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Translational Molecular Imaging

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Flow Cytometry

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Mass Spectrometry

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Molecular Technology

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Deep Phenotyping

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Histology Service

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Transgenic Models of Cancer

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Transgenic Technology

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Data Science and Data Management

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Bioinformatics and Data Science

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Translational Research Collaborations Unit

Operations

The teams and services that keep the Institute running and support our research.

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Finance

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Information Services

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People and Culture

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Research Management

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Support Operations

Partners

The networks and organisations we work with to accelerate cancer research.

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Cancer Research UK Scotland Centre

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CRC Stars

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MRC National Mouse Genetics Network

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CRUK SI-UoG-Indonesia PhD Programme

Careers & Study

Jobs, studentships and opportunities for students at every stage at our world-renowned cancer research institute.

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Careers & Study Overview

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Current Vacancies

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Studentships

PhD opportunities at the Institute
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Studentship Vacancies

Open studentships to apply for
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CRUK SI-UoG-Indonesia PhD Programme

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John Paul Career Award

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Internships

For undergraduate and masters students
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High School Students

Events

The Institute hosts a range of seminars and meetings bringing international cancer researchers to Glasgow.

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All Events

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Glasgow Cancer Seminar Series

Dr Ke Yuan

AI for Cancer Research

Modern-day cancer research is generating an unprecedented amount of data, from high-resolution medical images to large-scale genomic and transcriptomic datasets. Harnessing this data through advanced AI, machine learning, and statistical models opens new avenues for discovery and translation into clinical practice. Our work focuses on developing state-of-the-art methods tailored to cancer research challenges, particularly in the analysis of imaging and sequencing data. By addressing critical questions, such as identifying predictive biomarkers and uncovering novel therapeutic targets, we aim to drive progress in precision oncology and improve patient outcomes.

Email

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Full research group pageRead more about the AI for Cancer Research research group
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Biography

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Recent Publications

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Biography

Education and qualifications

  • 2008–2012: PhD, Machine Learning, University of Southampton, UK
  • 2007–2008: MSc, Radio Frequency Communication Systems, University of Southampton, UK
  • 2003–2007: BEng, Telecommunication Engineering, Nanjing University of Posts and Telecommunications, China

Appointments

  • 2022–present: Senior Lecturer in Machine Learning and Computational Biology, School of Computing Science, University of Glasgow, UK
  • 2022–present: Secondment appointment, School of Cancer Sciences, University of Glasgow, UK
  • 2022–present: Secondment appointment, CRUK Scotland Institute, University of Glasgow, UK
  • 2016–present: Lecturer in Machine Learning and Computational Biology, School of Computing Science, University of Glasgow, UK
  • 2012–2016: Postdoctoral Research Associate, CRUK Cambridge Institute, University of Cambridge, UK

Current committee membership

  • Intelligent Systems for Molecular Biology (ISMB) 2024 Conference program committee

Recent Publications

2025

Coudray N, Occidental MA, Mantilla JG, Claudio Quiros A, Yuan K, Balko J, Tsirigos A, Jour G. Quantitative and Morphology-Based Deep Convolutional Neural Network Approaches for Osteosarcoma Survival Prediction in the Neoadjuvant and Metastatic Settings. Clin Cancer Res. 2025;31(2):365-375.

Coudray N, Juarez MC, Criscito MC, Quiros AC, Wilken R, Jackson Cullison SR, Stevenson ML, Doudican NA, Yuan K, Aquino JD, Klufas DM, North JP, Yu SS, Murad F, Ruiz E, Schmults CD, Cardona Machado CD, Cañueto J, Choudhary A, Hughes AN, Stockard A, Leibovit-Reiben Z, Mangold AR, Tsirigos A, Carucci JA. Self supervised artificial intelligence predicts poor outcome from primary cutaneous squamous cell carcinoma at diagnosis. NPJ Digit Med. 2025;8(1):105.

Fa’ak F, Coudray N, Jour G, Ibrahim M, Illa-Bochaca I, Qiu S, Claudio Quiros A, Yuan K, Johnson DB, Rimm DL, Weber JS, Tsirigos A, Osman I. Artificial Intelligence Algorithm Predicts Response to Immune Checkpoint Inhibitors. Clin Cancer Res. 2025.

Farndale L, Insall R, Yuan K. TriDeNT: Triple deep network training for privileged knowledge distillation in histopathology. Med Image Anal. 2025;102:103479.

Ji Y, Cutiongco MFA, Jensen BS, Yuan K. Generating realistic single-cell images from CellProfiler representations. Med Image Anal. 2025;103:103574.

Liu D, Young F, Lamb KD, Claudio Quiros A, Pancheva A, Miller CJ, Macdonald C, Robertson DL, Yuan K. PLM-interact: extending protein language models to predict protein-protein interactions. Nat Commun. 2025;16(1):9012.

Lytras S, Lamb KD, Ito J, Grove J, Yuan K, Sato K, Hughes J, Robertson DL. Pathogen genomic surveillance and the AI revolution. J Virol. 2025:e0160124.

Seyedshahi F, Rakovic K, Poulain N, Claudio Quiros A, Powley IR, Richards C, Uraiby H, Klebe S, Moore DA, Nakas A, Wilson CR, Sereno M, Officer-Jones L, Ficken C, Teodosio A, Ballantyne F, Murphy D, Yuan K, Le Quesne J. A histomorphological atlas of resected mesothelioma discovered by self-supervised learning from 3446 whole-slide images. Nat Commun. 2025;16(1):8891.

2024

Claudio Quiros A, Coudray N, Yeaton A, Yang X, Liu B, Le H, Chiriboga L, Karimkhan A, Narula N, Moore DA, Park CY, Pass H, Moreira AL, Le Quesne J, Tsirigos A, Yuan K. Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unannotated pathology slides. Nat Commun. 2024;15(1):4596.

Farndale L, Walsh C, Insall R, Yuan K. Synthetic Privileged Information Enhances Medical Image Representation Learning. 2024; arXiv:2403.05220.

Lamb K, Luka M, Saathoff M, Orton R, Phan M, Cotten M, Yuan K, Robertson DL. Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules. PLOS Computational Biology. 2024;20(1), e1011795.

Lamb KD, Hughes J, Lytras S, Koci O, Young F, Grove J, Yuan K, Robertson DL. From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. 2024; bioRxiv 2024.07.05.602129.

Liu D, Young F, Lamb KD, Claudio Quiros A, Pancheva A, Miller C, Macdonald C, Robertson DL, Yuan K. PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv. 2024:2024.2011.2005.622169.

Liu B, Polack M, Coudray N, Claudio Quiros A, Sakellaropoulos T, Crobach A, van Krieken J, Yuan K, Tollenaar R, Mesker WE, Tsirigos A. Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer. bioRxiv 2024.02.26.582106.

Seyedshahi F, Rakovic K, Poulain N, Quiros AC, Powley IR, Richards C, Uraiby H, Klebe S, Nakas A, Wilson C, Sereno M, Officer-Jones L, Ficken C, Teodosio A, Ballantyne F, Murphy D, Yuan K, Le Quesne J. A histomorphological atlas of resected mesothelioma from 3446 whole-slide images discovered by self-supervised learning. bioRxiv. 2024:2024.2011.2018.624103.

2023

Coudray N, Juarez MC, Criscito MC, Quiros AC, Wilken R, Cullison SRJ, Stevenson ML, Doudican NA, Yuan K, Aquino JD, Klufas DM, North JP, Yu SS, Murad F, Ruiz E, Schmults CD, Tsirigos A, Carucci JA. Self-supervised artificial intelligence predicts recurrence, metastasis and disease specific death from primary cutaneous squamous cell carcinoma at diagnosis. Res Sq [Preprint]. 2023 Dec 13:rs.3.rs-3607399.

Farndale L, Insall R, Yuan K. TriDeNT: Triple Deep Network Training for Privileged Knowledge Distillation in Histopathology. 2023; arXiv:2312.02111.

Liu D, Young F, Robertson D, Yuan K. Prediction of virus-host association using protein language models and multiple instance learning. (2023) bioRxiv 2023.04.07.536023.

Yang X, Liu W, Macintyre G, Van Loo P, Markowetz F, Bailey P, Yuan K. Pan-cancer evolution signatures link clonal expansion to dynamic changes in the tumour immune microenvironment. (2023) bioRxiv 2023.10.12.560630.

2021

Dentro SC, Leshchiner I, Hasse K, Tarabichi M, et al., Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P, PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021;184(8):2239-2254.e39. (Glasgow & Cambridge Working Group lead)

Macintyre G, Piskorz AM, Berman A, Ross E, Morse DB, Yuan K, Ennis D, Pike JA, Goranova T, McNeish IA, Brenton JD, Markowetz F. FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections. JCO Clin Cancer Inform. 2021 Feb;5:176-186.