Lun Ai

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I am a Marie Skłodowska-Curie Fellow at EMBL’s European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK, working with Julio Saez-Rodriguez. I received my PhD from Imperial College London, supervised by Stephen Muggleton.

I study how to monitor and control LLM agents, using scientific discovery in biology as the testbed. My research focuses on: (1) evaluating and controlling LLM agents in knowledge-intensive workflows, including when they game their evaluations and how external judges can govern them, and (2) whether model explanations faithfully convey what a model knows to a human overseer.

Where I have worked:

  • EMBL’s European Bioinformatics Institute (EMBL-EBI), Marie Skłodowska-Curie Fellow (2026 -) and Postdoctoral Research Fellow (2025 - 2026)
  • Imperial College London, Department of Life Sciences, Research Associate (2024 - 2025)
  • Imperial College London, Department of Computing, PhD and Research Assistant (2019 - 2024)

Working with agents: I use coding agents every day in my research, and I keep experimenting with how to work with them better. When a way of working holds up, I package it as an open skill that anyone can drop into Claude Code, Codex or Gemini CLI. Two I use most:

  • Want to learn a technical concept without the hassle? Mental gym lets you learn it by building it from scratch. The agent coaches you through a checklist one item at a time without writing the solution for you: it scaffolds a skeleton with hints, you fill the blanks, it critiques your attempt, then asks a depth question to check you really understood.
  • Juggling many open research questions across many sessions? Research dashboard keeps them in one place. The agent groups questions into areas, keeps one dashboard plus a plan file per area with effort estimates, and writes every result back into both, so findings outlive the chat.

The rest are in lun-ai/skills. Feedback and ideas are welcome.

News

Jun 01, 2026 I started my Marie Skłodowska-Curie Fellowship at EMBL-EBI, where I will focus on using DREAM challenges, computational biology tasks that build predictive models, as a testbed to evaluate LLM agents and develop mechanisms to monitor and control them.
Mar 08, 2026 I presented at face-to-face meeting of Kidney Precision Medicine Project on organising community-driven challenges as driver of treatment development for chronic kidney diseases.
Jan 26, 2026 My work “Adaptive Data–Knowledge Alignment in Genetic Perturbation Prediction” with my student Yuanfang Xiang has been accepted to ICLR 2026.
Oct 19, 2025 Our work on “Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models” is published in Machine Learning Journal.
Sep 11, 2025 I presented my sole-author work on “Boolean Matrix Logic Programming on the GPU” at the 5th International Joint Conference on Learning & Reasoning in Surrey UK.
May 01, 2025 I am joining European Molecular Biology Laboratory (EMBL-EBI) to work with Julio Saez-Rodriguez on the Kidney Precision Medicine Project for discovering new molecular mechanisms that can inform novel treatment of chronic kidney diseases.
Nov 08, 2024 I presented “Active Abductive Learning of Multigenic Interactions from High-Throughput Repression Screening Data” at AAAI Fall Symposium on Integrated Approaches to Computational Scientific Discovery (Online).
Sep 22, 2024 I presented “Active learning of digenic functions with boolean matrix logic programming” at the 4th International Joint Conference of Learning and Reasoning (Nanjing, China).
May 01, 2024 I received my PhD degree in Computing Research. Here is my thesis on “Effects of Machine-Learned Logic Theories on Human Comprehension in Machine-Human Teaching”. I truly appreciate Prof. Stephen Muggleton for the amazing support and examiners (Prof. Francesca Toni and Prof. Nick Chater) for their insightful feedback.
Nov 15, 2023 I presented “A Comprehensible Framework to Active Learning Genome-Scale Metabolic Networks” at AAAI Fall Symposium on Artificial Intelligence for Synthetic Biology (Online).