Publications
Publications
Pre-Prints
- BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse, Divyang Deep Tiwari, Nils Hoffmann, Kieran Didi, Sumukh Deshpande, Sucheta Ghosh, Tung V. N. Nguyen, Karthik Raman, Henning Hermjakob, Rahuman S Malik Sheriff, biorxviv, 05/2023
Under review
- Structure-based Drug Design with Equivariant Diffusion Models, Arne Schneuing, Yuanqi Du, Charles Harris, Kieran Didi, Arian Jamasb, Ilia Igashov, weitao Du, Tom Blundell, Pietro Liò, Carla Gomes, Max Welling, Michael Bronstein, Bruno Correia
Science Journals
- AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for hit selection, humanisation, and engineering, Aubin Ramon, Montader Ali, Misha Atkinson, Alessio Saturnino, Kieran Didi, Cristina Visentin, Stefano Ricagno, Xing Xu, Matthew Greenig, Pietro Sormanni, Nature Machine Intelligence, 04/2023
- Biomolecular condensate phase diagrams with a combinatorial microdroplet platform, William E. Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Kieran Didi, Timothy J. Welsh, Julia Acker, Jonathan Nixon-Abell, Seema Qamar, Jordina Guillén-Boixet, Titus M. Franzmann, David Kuster, Anthony A. Hyman, Alexander Borodavka, Peter St George-Hyslop, Simon Alberti & Tuomas P. J. Knowles, Nature Communications, 12/2022
ML Conferences
- Dynamics-Informed Protein Design with Structure Conditioning, Urszula Julia Komorowska, Simon V Mathis, Kieran Didi, Francisco Vargas, Pietro Lio, Mateja Jamnik , ICLR,01/2024
- Evaluating Representation Learning on the Protein Structure Universe, Arian Rokkum Jamasb, Alex Morehead, Zuobai Zhang, Chaitanya Joshi, Kieran Didi, Simon Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Liò, Tom Blundell, ICLR,01/2024
- A framework for conditional diffusion modelling with applications in motif scaffolding for protein design, Kieran Didi, Francisco Vargas, Simon Mathis, Vincent Dutordoir, Emile Mathieu, Urszula Julia Komorowska, Pietro Lio, NeurIPS AI4D3 2023 (Oral Presentation), 11/2023
- Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?, Charles Harris, Kieran Didi, Arian Jamasb, Chaitanya Joshi, Simon Mathis, Pietro Lio, Tom Blundell, NeurIPS MLSB 2023 (Oral Presentation), 11/2023
- Modelling biology in novel ways - an AI-first course in Structural Bioinformatics, Kieran Didi, Charles Harris, Pietro Liò, Rainer Beck, NeurIPS AI4Science 2023, 10/2023
- Flexible Small-Molecule Design and Optimization with Equivariant Diffusion Models, Charles Harris, Kieran Didi, Arne Schneuing, Yuanqi Du, Arian Jamasb, Michael Bronstein, Bruno Correia, Pietro Liò, Tom Blundell, ICLR MLDD 2023, 03/2023
Book Chapters
- Generative Models in Bioinformatics, invited book chapter in Encyclopedia of Bioinformatics and Computational Biology, under review, 01/2023
- The Art of Molecular Programming, textbook editor
Conference Presentations
- Conditioning generative models for proteins, images and more (oral presentation), AI and Biology Conference, EMBL Heidelberg (Germany), 01/2024
- Where do we stand in protein and ligand design? (oral presentation), Computational Structural Biology Conference, EMBL Heidelberg (Germany), 12/2023
- Conditional Diffusion Models for Protein Design via Doob’s h-transform (poster), MoML Conference, MIT (US), 11/2023
- Reality Check - Evaluating Generative Models for Protein and Ligand Design (poster), Machine Learning in Drug Discovery Symposium, Broad Institute (US), 10/2023
- Accessible AMR-detection tools for clinicians via cloud-based bioinformatics (oral presentation), Clinical Informatics Symposium, Melbourne (Australia), 12/2022
- sINSIDER: a cloud-native modular platform for kmer-based genomic analysis (oral presentation), ABACBS Conference, Melbourne (Australia), 11/2022
- Moving bioinformatics to the cloud (keynote presentation), eSCAMPS Symposium, Cambridge (UK), 09/2022
- Detecting DNA integration via HPC bioinformatics pipeline (poster),R&I Conference, Sydney (Australia), 08/2022
Reviewing
ICML CompBio 2023, NeurIPS AI4Science 2023, NeurIPS GenBio 2023, MoML@MIT 2023, ICLR GEM 2024
Teaching
- SDEs and Diffusion Processes, lecture, Cambridge University (MPhil Advanced Computer Science), 01/2024
- Structural Bioinformatics, lecture, Heidelberg University (BSc Biochemistry), 10/2023
- Advanced Python for Scientists, lecture, Heidelberg University, 06/2023
- Algorithms II, supervising course on data structures and graph algorithms, Cambridge University, 03-05/2023
- Algorithms I, Cambridge University, 01-03/2023
- MLOps with PyTorch Lightning and W&B, conceptualised and lecture workshop, ML Forum CSIRO Australia, 01/2023
- Python for Scientists, lecture, Heidelberg University, 11/2022
- Python Best Practices, workshop (co-host), Scientific Software Center Heidelberg, 11/2022
- Deep Learning with PyTorch, Lunch Time Python workshop, Scientific Software Center Heidelberg, 10/2022
- Python for Biochemists, lecture, Heidelberg University, 03/2022