PhD Studentship (Crispin Miller)
Application closing date
All tuition fees will be paid.
Deep Tissue Phenotyping and Explainable AI
As life sciences becomes increasingly data-centric, AI techniques including deep learning neural networks and classical machine learning algorithms are increasingly being used to characterise, classify, and make predictions from biological datasets. A challenge with many of these algorithms is that they can be both complex and difficult to interpret.
Explainable AI aims to improve the interpretability of machine learning approaches, with the potential both to increase confidence in the underlying basis of a prediction, and to uncover new patterns and relationships in the underlying data – therefore advancing our understanding of basic biology.
At the CRUK Scotland Institute we make extensive use of different technology platforms including spatial transcriptomics (Xenium, CosMX), single cell RNA-seq, MS-based proteomics and metabolomics, and whole exome and genome sequencing to capture a multimodal view of the tumour environment. We then use computational approaches to integrate and interrogate these datasets and generate a more holistic understanding of oncogenic transformation, tumour growth and maintenance. These analyses are performed on our dedicated HPC cluster.
The goal of this project is to develop Explainable AI techniques to analyse multimodal data arising from over 900 colorectal and pancreatic ductal adenoncarcinoma (PDAC) patients. These include, but are not limited to, extensive profiling using spatial transcriptomics, H&E images, high-plex immunofluorescence, genomics and transcriptomics data, and detailed clinical metadata. We will combine these datatypes with H&E images processed using AI computational pathology techniques to develop a better understanding of the molecular underpinnings of different tumour subtypes, to identify possible therapeutic targets, and to further advance our understanding of the changing landscape of tumour host interactions and tumour evolution.
The studentship will be embedded within a highly collaborative team comprising computer scientists, mathematicians, software engineers, bench-scientists and clinicians.
For informal enquires please contact Prof Crispin Miller ([email protected])
PhD Studentship (Crispin Miller)
Cancer Research UK
November 11, 2023
December 15, 2023
About the employer
Cancer Research UK is a cancer research and awareness charity in the United Kingdom and Isle of Man, formed on 4 February 2002 by the merger of The Cancer Research Campaign and the Imperial Cancer Research Fund. As the world's largest independent cancer research charity it conducts research by the charity's own staff and by its grant-funded researchers. It also provides information about cancer and runs campaigns aimed at raising awareness and influencing public policy.
Cancer Research UK is the world’s leading charity dedicated to beating cancer through research. They have discovered new ways to prevent, diagnose and treat cancer that together have saved millions of lives across the world. Cancer Research UK has been at the heart of the progress that has already seen survival rates double in the last thirty years. But one in three of us will still get cancer at some point. Our groundbreaking work, funded entirely by the public (It raises money through donations, legacies, community fundraising, events, retail and corporate partnerships. Over 40,000 people are regular volunteers), will help ensure that millions more people will survive. Cancer Research UK works in partnership with others to achieve the greatest impact in the global fight against cancer. They provide life-changing information to anyone affected by cancer, run awareness initiatives so that cancer can be detected early, and help people reduce their risk of the disease. Their campaigning and lobbying keeps cancer at the top of the political agenda. Cancer Research UK became full UICC member in 1986.