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University of East Anglia
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1 week ago
PhD Studentship: From Explanation to Experiment: Agentic AI for Interpreting Nucleotide Foundation Models University of East Anglia in United Kingdom
Degree Level
PhD
Field of study
Computer Science
Funding
Full funding availableDeadline
Jul 30, 2026
Country
United Kingdom
University
University of East Anglia
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About this position
PhD Studentship at the University of East Anglia in collaboration with the Earlham Institute.
This project, From Explanation to Experiment: Agentic AI for Interpreting Nucleotide Foundation Models, sits at the intersection of artificial intelligence, genomics, and explainable machine learning. The research will investigate how to interpret foundation models trained on DNA and RNA sequences, with the goal of turning model explanations into biologically grounded, testable hypotheses.
The successful PhD researcher will develop agentic explainable AI methods for nucleotide sequence models. Key research themes include selecting and evaluating explanation methods, measuring explanation quality through faithfulness, robustness, and biological plausibility, and building knowledge-grounded reasoning approaches that connect salient nucleotides, motifs, genes, and regulatory elements to biological annotations, ontologies, knowledge graphs, and literature evidence.
The project is designed to support the development of an AI research assistant that can help scientists understand why a model made a prediction, what biological mechanisms may underlie it, and which experiments or sequence perturbations should be prioritised next. Possible application areas include regulatory sequence interpretation, RNA motif analysis, gene expression modelling, and other sequence-to-function prediction tasks relevant to bioscience.
Students will benefit from existing code, datasets, and expertise in foundation models, AI agentic frameworks, XAI, optimisation, and knowledge graphs. Training will be provided across frontier AI model training, explainable AI, genomics, and open-source scientific software. Applicants should have strong AI and/or computational skills and an interest in transparent, trustworthy AI systems. No prior biology background is required, although interdisciplinary enthusiasm is essential.
Funding: The PhD is funded for four years by the Earlham Institute. It includes tuition fees at Home-fee or International-fee rate, a UKRI-rate annual stipend of £21,805 (2026/7), and £5,000 per year to support research training.
Eligibility: Minimum UK equivalent 2:1 Bachelors (Honours) degree or a UK equivalent Masters degree. English language requirement: IELTS 6.5 overall and 6.0 in each component.
Deadline: 30 July 2026. Start date: 1 October 2026.
Funding details
Full funding including tuition fees and living expenses is available for this position. The scholarship covers all educational costs and provides a monthly stipend.
How to apply
Please submit your application including a cover letter, CV, academic transcripts, and contact information for two references. Applications should be sent via the online portal before the deadline.
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