Publications

Leonardo V. Castorina, Christopher W. Wood, Kartic Subr (2025) From Atoms to Fragments: A Coarse Representation for Efficient and Functional Protein Design. BiorXiv. https://doi.org/10.1101/2025.03.19.644162 

James Broughton, Achille Fraisse, Meriem El Karoui (2025) Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli. BoiXriv. https://www.biorxiv.org/content/10.1101/2024.04.18.590101v1 

Hans-Christof Gasser; Diego A. Oyarzún; Javier Antonio Alfaro; Ajitha Rajan (2025) Tuning ProteinMPNN to reduce protein visibility via MHC Class I through direct preference optimization. PEDS. https://doi.org/10.1093/protein/gzaf003

Yongshuo Zong, Ondrej Bohdal, Timothy Hospedales (2025) VL-ICL Bench: The Devil in the Details of Multimodal In-Context Learning. The Thirteenth International Conference on Learning Representations (ICLR 2025). https://openreview.net/forum?id=cpGPPLLYYx 

(Preprint) Katharina Limbeck, Rayna Andreeva, Rik Sarkar, Bastian Rieck (2024) Metric Space Magnitude for Evaluating the Diversity of Latent Representations. arXiv:2311.16054. https://arxiv.org/abs/2311.16054

Leonardo V Castorina, Suleyman Mert Ünal, Kartic Subr, Christopher W Wood (2024) TIMED-Design: flexible and accessible protein sequence design with convolutional neural networks. Protein Engineering, Design and Selection, Volume 37, 2024, gzae002 https://academic.oup.com/peds/article-abstract/doi/10.1093/protein/gzae002/7591701

Filippo Corponi, Bryan M. Li, Gerard Anmella, Ariadna Mas, Isabella Pacchiarotti, Marc Valentí, Iria Grande, Antoni Benabarre,Marina Garriga, Eduard Vieta, Stephen M. Lawrie, Heather C. Whalley, Diego Hidalgo-Mazzei, Antonio Vergari (2024) Automated mood disorder symptoms monitoring from multivariate time-series sensory data: getting the full picture beyond a single number. Nature: Translational Psychiatry. https://www.nature.com/articles/s41398-024-02876-1

Jan K. Dabrowski, 1,2,11,  Emma J. Yang2,11,  Samuel J. C. Crofts 2,3, Robert F. Hillary 4, Daniel J. Simpson 2, Daniel L. McCartney 4, Riccardo E. Marioni 4, Kristina Kirschner 5,6,7,8,9,  Eric Latorre-Crespo 2,6,12  & Tamir Chandra 2,7,8,10,12 (2023) Probabilistic inference of epigenetic age acceleration from cellular dynamics. Nature Aging volume 4, pages 1493–1507 (2024). https://doi.org/10.1038/s43587-024-00700-5

Aryo Pradipta Gema, Dominik Grabarczyk, Wolf De Wulf, Piyush Borole, Javier Antonio Alfaro, Pasquale Minervini, Antonio Vergari, Ajitha Rajan (2024)  Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks.  Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae097, https://doi.org/10.1093/bioadv/vbae097

Polina Turishcheva, Paul G. Fahey, Michaela Vystrčilová, Laura Hansel, Rachel Froebe, Kayla Ponder, Yongrong Qiu, Konstantin F. Willeke, Mohammad Bashiri, Ruslan Baikulov, Yu Zhu, Lei Ma, Shan Yu, Tiejun Huang, Bryan M. Li, Wolf De Wulf, Nina Kudryashova, Matthias H. Hennig, Nathalie L. Rochefort, Arno Onken, Eric Wang, Zhiwei Ding, Andreas S. Tolias, Fabian H. Sinz, Alexander S Ecker (2024)  Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos.  arXiv https://arxiv.org/abs/2407.09100 

Raman Dutt, Linus Ericsson, Pedro Sanchez, Sotirios A. Tsaftaris, Timothy Hospedales (2024)  Parameter-Efficient Fine-Tuning for Medical Image Analysis: The Missed Opportunity. https://arxiv.org/abs/2305.08252

Raman Dutt, Ondrej Bohdal, Sotirios A. Tsaftaris, Timothy Hospedales (2024)  FairTune: Optimizing Parameter Efficient Fine Tuning for Fairness in Medical Image Analysis. International Conference on Learning Representations (ICLR 2024).  https://arxiv.org/abs/2310.05055

Hitoshi Tabuchi, Justin Engelmann, Fumiatsu Maeda, Ryo Nishikawa, Toshihiko Nagasawa, Tomofusa Yamauchi, Mao Tanabe, Masahiro Akada, Keita Kihara, Yasuyuki Nakae, Yoshiaki Kiuchi, Miguel O Bernabeu (2024) Using artificial intelligence to improve human performance: efficient retinal disease detection training with synthetic images. British Journal of Opthalmology. https://bjo.bmj.com/content/early/2024/03/14/bjo-2023-324923.abstract

Justin Engelmann, Diana Moukaddem, Lucas Gago, Niall Strang, Miguel O Bernabeu (2024) Applicability of oculomics for individual risk prediction: Repeatability and robustness of retinal Fractal Dimension using DART and AutoMorph. Arxiv pre-print. https://arxiv.org/abs/2403.06950

Justin Engelmann, Stephanie Kearney, Alice McTrusty, Greta McKinlay, Miguel O. Bernabeu, Niall Strang (2024) Retinal Fractal Dimension Is a Potential Biomarker for Systemic Health—Evidence From a Mixed-Age, Primary-Care Population. tvst Volume 13, Issue 4. https://tvst.arvojournals.org/article.aspx?articleid=2793565

Matúš Falis, Aryo Pradipta Gema, Hang Dong, Luke Daines, Siddharth Basetti, Michael Holder, Rose S Penfold, Alexandra Birch, Beatrice Alex (2024) Can GPT-3.5 Generate and Code Discharge Summaries? ArXiv pre-print. 10.48550/arXiv.2401.13512

Aryo Pradipta Gema, Michał Kobiela, Achille Fraisse, Ajitha Rajan, Diego A. Oyarzún, Javier Antonio Alfaro (2024) Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2.  https://arxiv.org/abs/2305.11194

(Preprint) James Broughton, Achille Fraisse, Meriem El Karoui (2024)  Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli. BioRxiv https://www.biorxiv.org/content/10.1101/2024.04.18.590101v1

Hans-Christof Gasser; Diego A. Oyarzún; Ajitha Rajan; Javier Antonio Alfaro (2024)  Guiding a language-model based protein design method towards MHC Class-I immune-visibility targets in vaccines and therapeutics.  ImmunoInformatics Volume 14, June 2024, https://doi.org/10.1016/j.immuno.2024.100035 

(Preprint)  Hans-Christof Gasser; Diego A. Oyarzún; Ajitha Rajan; Javier Antonio Alfaro (2024)  Integrating MHC Class I visibility targets into the ProteinMPNN protein design process. doi: https://doi.org/10.1101/2024.06.04.597365

(Preprint) Aryo Pradipta Gema, Chen Jin, Ahmed Abdulaal, Tom Diethe, Philip Teare, Beatrice Alex, Pasquale Minervini, Amrutha Saseendran (2024)  DeCoRe: Decoding by Contrasting Retrieval Heads to Mitigate Hallucinations. arXiv https://arxiv.org/abs/2410.18860

(Preprint) Yu Zhao, Alessio Devoto, Giwon Hong, Xiaotang Du, Aryo Pradipta Gema, Hongru Wang, Kam-Fai Wong, Pasquale Minervini (2024)  Steering Knowledge Selection Behaviours in LLMs via SAE-Based Representation Engineering. arXiv https://arxiv.org/abs/2410.15999

(Preprint) Yu Zhao, Xiaotang Du, Giwon Hong, Aryo Pradipta Gema, Alessio Devoto, Hongru Wang, Xuanli He, Kam-Fai Wong, Pasquale Minervini (2024) Analysing the Residual Stream of Language Models Under Knowledge Conflicts. arXiv https://arxiv.org/abs/2410.16090

(Preprint) Joshua Ong Jun Leang, Aryo Pradipta Gema, Shay B Cohen (2024) CoMAT: Chain of Mathematically Annotated Thought Improves Mathematical Reasoning. arXiv https://arxiv.org/abs/2410.10336

Matúš Falis, Aryo Pradipta Gema, Hang Dong, Luke Daines, Siddharth Basetti, Michael Holder, Rose S Penfold, Alexandra Birch, Beatrice Alex (2024)  Can GPT-3.5 generate and code discharge summaries? Journal of the American Medical Informatics Association, Volume 31, Issue 10, October 2024 https://academic.oup.com/jamia/article/31/10/2284/7756747

Aryo Pradipta Gema, Joshua Ong Jun Leang, Giwon Hong, Alessio Devoto, Alberto Carlo Maria Mancino, Rohit Saxena, Xuanli He, Yu Zhao, Xiaotang Du, Mohammad Reza Ghasemi Madani, Claire Barale, Robert McHardy, Joshua Harris, Jean Kaddour, Emile van Krieken, Pasquale Minervini (2024) Are We Done with MMLU? arXiv https://arxiv.org/abs/2406.04127

Aryo Pradipta Gema, Chaeeun Lee, Pasquale Minervini, Luke Daines, T Ian Simpson, Beatrice Alex (2024) Edinburgh Clinical NLP at MEDIQA-CORR 2024: Guiding Large Language Models with Hints. Proceedings of the 6th Clinical Natural Language Processing Workshop pp 488–501 https://aclanthology.org/2024.clinicalnlp-1.49/ 

(Preprint) Giwon Hong, Aryo Pradipta Gema, Rohit Saxena, Xiaotang Du, Ping Nie, Yu Zhao, Laura Perez-Beltrachini, Max Ryabinin, Xuanli He, Clémentine Fourrier, Pasquale Minervini (2024) The Hallucinations Leaderboard -- An Open Effort to Measure Hallucinations in Large Language Models. arXiv https://arxiv.org/abs/2404.05904 

Aryo Pradipta Gema, Giwon Hong, Pasquale Minervini, Luke Daines, Beatrice Alex (2024) Edinburgh Clinical NLP at SemEval-2024 Task 2: Fine-tune your model unless you have access to GPT-4. Proceedings of the 18th International Workshop on Semantic Evaluation (SemEval-2024) pp 1894–1904 https://aclanthology.org/2024.semeval-1.265/

(Preprint) Rohan Gorantla, Aryo Pradipta Gema, Ian Xi Yang, Álvaro Serrano-Morrás, Benjamin Suutari, Jordi Juárez Jiménez, Antonia SJS Mey (2024)  Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models. bioarXiv https://www.biorxiv.org/content/10.1101/2024.11.01.621495v1.abstract

Aryo Pradipta Gema, Dominik Grabarczyk, Wolf De Wulf, Piyush Borole, Javier Antonio Alfaro, Pasquale Minervini, Antonio Vergari, Ajitha Rajan (2024) Knowledge graph embeddings in the biomedical domain: are they useful? A look at link prediction, rule learning, and downstream polypharmacy tasks. Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae097 https://doi.org/10.1093/bioadv/vbae097

Rohan Gorantla, Alžbeta Kubincová, Benjamin Suutari, Benjamin P. Cossins, Antonia S. J. S. Mey (2024)  Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction.  ACS 2024. https://pubs.acs.org/doi/10.1021/acs.jcim.4c00220

Gerard Anmella, Ariadna Mas, Miriam Sanabra, Clàudia Valenzuela-Pascual, Marc Valentí, Isabella Pacchiarotti, Antoni Benabarre, Iria Grande, Michele De Prisco, Vincenzo Oliva, Giovanna Fico, Anna Giménez-Palomo, Anna Bastidas, Isabel Agasi, Allan H. Young, Marina Garriga, Filippo Corponi, Bryan M. Li, Peter de Looff, Eduard Vieta, Diego Hidalgo-Mazzei (2024)  Electrodermal activity in bipolar disorder: Differences between mood episodes and clinical remission using a wearable device in a real-world clinical setting.  Journal of Affective Disorders. https://www.sciencedirect.com/science/article/pii/S0165032723013149

Evgenii Lobzaev, Michael A. Herrera, Martyna Kasprzyk, Giovanni Stracquadanio (2024) Protein engineering using variational free energy approximation.  Nature Communications 15, Article number: 10447 (2024) https://doi.org/10.1038/s41467-024-54814-w

Evgenii Lobzaev, Giovanni Stracquadanio Evgenii Lobzaev, Giovanni Stracquadanio (2024)  Dirichlet latent modelling enables effective learning and sampling of the functional protein design space. Nature Communications https://doi.org/10.1038/s41467-024-53622-6 

Yongcheng Yao, Weitian Chen (2024) Quantifying Knee Cartilage Shape and Lesion: From Image to Metrics.  arXiv https://arxiv.org/abs/2409.07361 

(Preprint) Robin Williams, Stuart Anderson, Kathrin Cresswell, Mari Serine Kannelonning, Hajar Mozaffar, Xiao Yang (2024)  Domesticating AI in medical diagnosis. Technology in Society. https://www.sciencedirect.com/science/article/pii/S0160791X24000174?via%3Dihub 

Letian Zhang, Xiaotong Zhai, Zhongkai Zhao, Yongshuo Zong, Xin Wen, Bingchen Zhao (2024) What If the TV Was Off? Examining Counterfactual Reasoning Abilities of Multi-modal Language Models. Conference on Computer Vision and Pattern Recognition (CVPR). https://arxiv.org/abs/2310.06627

Yongshuo Zong, Oisin Mac Aodha, and Timothy Hospedales (2024)  Self-supervised multimodal learning: A survey. IEEE Transactions on Pattern Analysis and Machine Intelligence. arXiv https://arxiv.org/abs/2304.01008 

Yongshuo Zong, Ismail Elezi, Yongxin Yang, Jiankang Deng, Timothy Hospedales (2024) Long-Context Vision Large Language Models: Empirical Insights and A Baseline. Workshop on Long-Context Foundation Models  (ICML 2024) https://openreview.net/forum?id=NaldExCoyW 

Yongshuo Zong, Ondrej Bohdal, Tingyang Yu, Yongxin Yang, Timothy Hospedales (2024)  Safety Fine-Tuning at (Almost) No Cost: A Baseline for Vision Large Language Models.  International Conference on Machine Learning (ICML 2024) https://openreview.net/forum?id=bWZKvF0g7G

Yongshuo Zong, Tingyang Yu, Ruchika Chavhan, Bingchen Zhao, Timothy Hospedales (2024) Fool Your (Vision and) Language Model with Embarrassingly Simple Permutations. International Conference on Machine Learning (ICML 2024) https://openreview.net/forum?id=IUijgjJgWO 

Lauren Watson, Zeno Kujawa, Rayna Andreeva, Hao-Tsung Yang, Tariq Elahi, Rik Sarkar (2023)  Accelerated Shapley Value Approximation for Data Evaluation.  https://arxiv.org/pdf/2311.05346.pdf

Rayna Andreeva, Anwesha Sarkar, Rik Sarkar (2023)  Machine learning and Topological data analysis identify unique features of human papillae in 3D scans.  https://arxiv.org/abs/2307.06255

Rayna Andreeva, Katharina Limbeck, Bastian Rieck, Rik Sarkar (2023)  Metric Space Magnitude and Generalisation in Neural Networks.  Proceedings of 2nd Annual Workshop on Topology, Algebra, and Geometry in Machine Learning (TAG-ML), PMLR 221:242-253. https://proceedings.mlr.press/v221/andreeva23a/andreeva23a.pdf

Leonardo V Castorina, Filippo Grazioli, Pierre Machart, Anja Moesch, Federico Errica (2023) Assessing the Generalization Capabilities of TCR Binding Predictors via Peptide Distance Analysis. Biorxiv. https://www.biorxiv.org/content/10.1101/2023.07.29.551100.abstract

Filippo Grazioli, Pierre Machart, Anja Mösch, Kai Li, Leonardo V Castorina, Nico Pfeifer, Martin Renqiang Min (2023) Attentive Variational Information Bottleneck for TCR–peptide interaction prediction.  Bioinformatics, Volume 39, Issue 1, January 2023, btac820. https://academic.oup.com/bioinformatics/article-abstract/39/1/btac820/6960920

Leonardo V. Castorina, Rokas Petrenas, Kartic Subr, Christopher W Wood (2023) PDBench: Evaluating Computational Methods for Protein-Sequence Design. Bioinformatics https://doi.org/10.1093/bioinformatics/btad027

Gerard Anmella,   Filippo Corponi, Bryan M Li, Ariadna Mas, Miriam Sanabra, Isabella Pacchiarotti, Marc Valenti, Iria Grande, Antoni Benabarre , Anna Giménez-Palomo, Marina Garriga, Isabel Agasi, Anna Bastidas, Myriam Cavero, Tabatha Fernández-Plaza, Néstor Arbelo, Miquel Bioque, Clemente García-Rizo, Norma Verdolini, Santiago Madero, Andrea Murru, Silvia Amoretti, Anabel Martínez-Aran, Victoria Ruiz, Giovanna Fico, Michele De Prisco, Vincenzo Oliva, Aleix Solanes, Joaquim Radua, Ludovic Samalin, Allan H Young, Eduard Vieta, Antonio Vergari, Diego Hidalgo-Mazzei (2023) Exploring Digital Biomarkers of Illness Activity in Mood Episodes: Hypotheses Generating and Model Development Study.  JMIR Mhealth Uhealth 2023;11:e45405.  https://mhealth.jmir.org/2023/1/e45405

Filippo Corponi, Antoine Lefrere, Marion Leboyer, Frank Bellivier, Ophelia Godin, Josephine Loftus, Philippe Courtet, Caroline Dubertret, Emmanuel Haffen, Pierre Michel Llorca, Paul Roux, Mircea Polosan, Raymund Schwan, Ludovic Samalin, Emilie Olié, Bruno Etain, FACE-BD (FondaMental Academic Centers of Expertise for Bipolar Disorder) Groups, Peggy Seriès, Raoul Belzeaux (2023) Definition of early age at onset in bipolar disorder according to distinctive neurodevelopmental pathways: insights from the FACE-BD study. Psychological Medicine.  https://www.cambridge.org/core/journals/psychological-medicine/article/abs/definition-of-early-age-at-onset-in-bipolar-disorder-according-to-distinctive-neurodevelopmental-pathways-insights-from-the-facebd-study/DD12195A96AC2375D3B20EC5B19A93B1

Bryan M. Li, Filippo Corponi, Gerard Anmella, Ariadna Mas, Miriam Sanabra, Diego Hidalgo-Mazzei, Antonio Vergari (2023) Inferring mood disorder symptoms from multivariate time-series sensory data. NeurIPS.  https://openreview.net/forum?id=awjU8fCDZjS

Eleanor Davyson, Xueyi Shen, Danni A. Gadd, Elena Bernabeu, Robert F. Hillary, Daniel L. McCartney, Mark Adams, Riccardo Marioni, and Andrew M. McIntosh (2023)  Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids. Society of Biological Psychiatry.  https://www.biologicalpsychiatryjournal.com/article/S0006-3223(23)00055-0/fulltext#%20 and mental Elf blog https://www.nationalelfservice.net/mental-health/depression/does-what-you-eat-affect-how-you-feel/

Justin Engelmann, Amos Storkey, Miguel O. Bernabeu (2023); Deep learning (DL) identifies age as key axis of perceptual variation in fundus images – without training on fundus images. Invest. Ophthalmol. Vis. Sci. 2023;64(9):PB004.  https://iovs.arvojournals.org/article.aspx?articleid=2791219

Justin Engelmann, Amos Storkey, Miguel O. Bernabeu (2023); Exclusion of poor quality fundus images biases health research linking retinal traits and systemic health. Invest. Ophthalmol. Vis. Sci. 2023;64(8):2922. https://iovs.arvojournals.org/article.aspx?articleid=2789909

Justin Engelmann, Jamie Burke, Charlene Hamid, Megan Reid-Schachter, Dan Pugh, Neeraj Dhaun, Diana Moukaddem, Lyle Gray, Niall Strang, Paul McGraw, Amos Storkey, Paul J Steptoe, Stuart King, Tom MacGillivray, Miguel O Bernabeu, Ian JC MacCormick (2023) Choroidalyzer: An open-source, end-to-end pipeline for choroidal analysis in optical coherence tomography. Arxiv pre-print. https://arxiv.org/abs/2312.02956v1

Jamie Burke, Justin Engelmann, Charlene Hamid, Megan Reid-Schachter, Tom Pearson, Dan Pugh, Neeraj Dhaun, Amos Storkey, Stuart King, Tom J MacGillivray, Miguel O Bernabeu, Ian JC MacCormick (2023) An Open-Source Deep Learning Algorithm for Efficient and Fully Automatic Analysis of the Choroid in Optical Coherence Tomography. Translational Vision Science & Technology. https://tvst.arvojournals.org/article.aspx?articleid=2793042

Justin Engelmann, Amos Storkey, Miguel O Bernabeu (2023) QuickQual: Lightweight, convenient retinal image quality scoring with off-the-shelf pretrained models. International Workshop on Ophthalmic Medical Image Analysis, Lecture Notes in Computer Science pp 32–41. https://link.springer.com/chapter/10.1007/978-3-031-44013-7_4

Alessandro Fontanella, A Antoniou, W Li, J Wardlaw, G Mair, E Truco, A Storkey (2023)  ACAT: Adversarial Counterfactual Attention for Classification and Detection in Medical Imaging. To appear at the International Conference on Machine Learning (ICML).  https://arxiv.org/abs/2303.15421

Wenwen Li, Grant Mair, Alessandro Fontanella, Antreas Antoniou, Eleanor Platt , Chloe Martin, Paul Armitage , Emanuele Trucco, Amos Storkey, Joanna Wardlaw (2023) Challenges of building medical image datasets for development of deep learning software in stroke. https://arxiv.org/abs/2309.15081

Alessandro Fontanella, Grant Mair, Joanna Wardlaw, Emanuele Trucco, Amos Storkey (2023) Diffusion models for counterfactual generation and anomaly detection in brain images. arXiv preprint. https://arxiv.org/abs/2308.02062

Alessandro Fontanella *, Wenwen Li*, Grant Mair*, Anreas Antoniou, Eleanor Platt, Paul Armitage, Emanuele Trucco, Joanna Wardlaw, Amos Storkey *Equal contribution (2023) Development of A Deep Learning Method to Identify Acute Ischemic Stroke Lesions on Brain CT. arXiv preprint. https://arxiv.org/abs/2309.17320

Georges Bedran, Hans-Christof Gasser, Kenneth Weke, Tongjie Wang, Dominika Bedran, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Catia Pesquita, Håkan Axelson, Ajitha Rajan, David J. Harrison, Aleksander Palkowski, Maciej Pawlik, Maciej Parys, J. Robert O'Neill, Paul M. Brennan, Stefan N. Symeonides, David R. Goodlett, Kevin Litchfield, Robin Fahraeus, Ted R. Hupp, Sachin Kote, Javier A. Alfaro (2023)  The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res (2023) 11 (6): 747–762. https://doi.org/10.1158/2326-6066.CIR-22-0621

Hans-Christof Gasser, Diego Oyarzun, Ajitha Rajan, Javier Alfaro (2023)  Comparing a language model and a physics-based approach to modify MHC Class-I immune-visibility for the design of vaccines and therapeutics. bioRxiv 2023. https://www.biorxiv.org/content/10.1101/2023.07.10.548300v3

(Preprint) Aryo Pradipta Gema, Michał Kobiela, Achille Fraisse, Ajitha Rajan, Diego A Oyarzún, Javier Antonio Alfaro, (2023).  Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2. ArXiv.  https://arxiv.org/pdf/2305.11194.pdf

(Preprint) Aryo Pradipta Gema, Dominik Grabarczyk, Wolf De Wulf, and Piyush Borole, Javier Antonio Alfaro, Pasquale Minervini, Antonio Vergari, Ajitha Rajan, (2023) .  Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks.   ArXiv. https://arxiv.org/abs/2305.19979

(Preprint) Aryo Pradipta Gema, Luke Daines, Pasquale Minervini, Beatrice Alex (2023).  Parameter-Efficient Fine-Tuning of LLaMA for the Clinical Domain. ArXiv. https://arxiv.org/pdf/2307.03042.pdf

(Preprint) Bryan M. Li, Isabel M. Cornacchia, Nathalie L. Rochefort, Arno Onken (2023)  V1T: large-scale mouse V1 response prediction using a Vision Transformer.  https://arxiv.org/abs/2302.03023

(Preprint) Filippo Corponi, Bryan M. Li, Gerard Anmella, Clàudia Valenzuela-Pascual, Ariadna Mas, Isabella Pacchiarotti, Marc Valentí, Iria Grande, Antonio Benabarre, Marina Garriga, Eduard Vieta, Allan H Young, Stephen M. Lawrie, Heather C. Whalley, Diego Hidalgo-Mazzei, Antonio Vergari (2023)  Wearable data from subjects playing Super Mario, sitting university exams, or performing physical exercise help detect acute mood episodes via self-supervised learning. https://arxiv.org/abs/2311.04215

(Preprint) Filippo Corponi*, Bryan M. Li*, Gerard Anmella, Ariadna Mas, Miriam Sanabra, Eduard Vieta, INTREPIBD Group, Stephen M. Lawrie, Heather C. Whalley, Diego Hidalgo-Mazzei, Antonio Vergari (2023)  Automated mood disorder symptoms monitoring from multivariate time-series sensory data: Getting the full picture beyond a single number. https://www.medrxiv.org/content/10.1101/2023.03.25.23287744v1

Gerard Anmella*, Filippo Corponi*, Bryan M. Li*, Ariadna Mas, Miriam Sanabra, Isabella Pacchiarotti, Marc Valentí, Iria Grande, Antoni Benabarre, Anna Giménez-Palomo, Marina Garriga, Isabel Agasi, Anna Bastidas, Myriam Cavero, Tabatha Fernández-Plaza, Néstor Arbelo, Miquel Bioque, Clemente García-Rizo, Norma Verdolini, Santiago Madero, Andrea Murru, Silvia Amoretti, Anabel Martínez-Aran, Victoria Ruiz, Giovanna Fico, Michele De Prisco, Vincenzo Oliva, Aleix Solanes, Joaquim Radua, Ludovic Samalin, Allan H. Young, Eduard Vieta, Antonio Vergari, Diego Hidalgo-Mazzei (2023) Exploring digital biomarkers of illness activity in mood episodes: hypotheses generating and model development study. Journal of Medical Internet Research (JMIR) mHealth and uHealth. https://www.medrxiv.org/content/10.1101/2023.03.25.23287744v1

Weimin Zhang, Luciana Lazar-Stefanita, Hitoyoshi Yamashita, Michael J. Shen, Leslie A. Mitchell, Hikaru Kurasawa, Evgenii Lobzaev, Viola Fanfani, Max A.B. Haase, Xiaoji Sun, Qingwen Jiang, Gregory W. Goldberg, David M. Ichikawa, Stephanie L. Lauer, Laura H. McCulloch, Nicole Easo, S. Jiaming Lin, Brendan R. Camellato, Yinan Zhu, Jitong Cai …Jef D. Boeke (2023)  Manipulating the 3D organization of the largest synthetic yeast chromosome. Molecular Cell Volume 83, Issue 23, 7 December 2023, Pages 4424-4437.e5. https://doi.org/10.1016/j.molcel.2023.10.015    

Benjamin A. Blount, Xinyu Lu, Maureen R.M. Driessen, Dejana Jovicevic, Mateo I. Sanchez, Klaudia Ciurkot, Yu Zhao, Stephanie Lauer, Robert M. McKiernan, Glen-Oliver F. Gowers, Fiachra Sweeney, Viola Fanfani, Evgenii Lobzaev, Kim Palacios-Flores, Roy S.K. Walker, Andy Hesketh, Jitong Cai, Stephen G. Oliver, Yizhi Cai, Giovanni Stracquadanio, Tom Ellis (2023)  Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.  Cell Genomics Volume 3, Issue 11, 8 November 2023, 100418. https://doi.org/10.1016/j.xgen.2023.100418

Stephanie Lauer,  Jingchuan Luo,  Luciana Lazar-Stefanita,  Weimin Zhang,  Laura H. McCulloch, Viola Fanfani,  Evgenii Lobzaev, Max A.B. Haase, Nicole Easo, Yu Zhao, Fangzhou Yu, Jitong Cai (2023) Context-dependent neocentromere activity in synthetic yeast chromosome VIII. Cell Genomics Volume 3, Issue 11, 8 November 2023, 100437, 100437. https://doi.org/10.1016/j.xgen.2023.100437

Laura H. McCulloch, Vijayan Sambasivam, Amanda L. Hughes, Narayana Annaluru, Sivaprakash Ramalingam, Viola Fanfani, Evgenii Lobzaev, Leslie A. Mitchell, Jitong Cai (2023)  Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains.  Cell Genomics Volume 3, Issue 11, 8 November 2023, 100419. https://doi.org/10.1016/j.xgen.2023.100419

Charlotte Merzbacher, Diego Oyarzun (2023) Applications of artificial intelligence and machine learning in dynamic pathway engineering. Biochemical Society Transactions. https://pubmed.ncbi.nlm.nih.gov/37656433/

Charlotte Merzbacher , Barry Ryan , Thibaut Goldsborough, Robert F Hillary , Archie Campbell , Lee Murphy , Andrew M McIntosh, David Liewald, Sarah E Harris, Allan F McRae , Simon R Cox , Timothy I Cannings , Catalina A Vallejos, Daniel L McCartney, Riccardo E Marioni (2023) Integration of DNA methylation datasets for individual prediction of DNA methylation-based biomarkers. Genome Biology. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03114-5

Charlotte Merzbacher, Oisin Mac Aodha, Diego Oyarzun (2023) Bayesian optimization for design of multiscale biological circuits. ACS Synthetic Biology. ACS Synthetic Biology. https://pubs.acs.org/doi/10.1021/acssynbio.3c00120

Jonathan Feldstein, Dominic Phillips, Efthymia Tsamoura (2023)  Principled and Efficient Motif Finding for Structure Learning of Lifted Graphical Models.  Proceedings of the AAAI Conference on Artificial Intelligence, 37. 10 edn, vol. 37. https://arxiv.org/abs/2302.04599

Dominic Phillips, Charles Matthews, Benedict Leimkuhler (2023)  Numerical Methods with Coordinate Transforms for Efficient Brownian Dynamics Simulations. https://arxiv.org/abs/2307.02913

Yongshuo Zong, Yongxin Yang, Timothy Hospedales (2023) MEDFAIR: Benchmarking Fairness for Medical Imaging.  International Conference on Learning Representations (ICLR). https://openreview.net/forum?id=6ve2CkeQe5S

Ondrej Bohdal, Yinbing Tian, Yongshuo Zong, Ruchika Chavhan, Da Li, Henry Gouk, Li Guo, Timothy Hospedales (2023)   Meta Omnium: A Benchmark for General-Purpose Learning-to-Learn.  IEEE/CVF Conference on Computer Vision and Pattern Recognition 2023. https://openaccess.thecvf.com/content/CVPR2023/html/Bohdal_Meta_Omnium_A_Benchmark_for_General-Purpose_Learning-To-Learn_CVPR_2023_paper.html

Laura Watson, Rayna Andreeva, Hao-Tsung Yang, Rik Sarkar (2022) Differentially Private Shapley Values for Data Evaluation. https://arxiv.org/abs/2206.00511

Leonardo V. Castorina, Kartic Subr, Christopher W. Wood (2022) TIMED-Design: Efficient Protein Sequence Design with Deep Learning. Zenodo https://doi.org/10.5281/zenodo.6997495 

Justin Engelmann, Alice D. McTrusty, Ian J. C. MacCormick, Emma Pead, Amos Storkey & Miguel O. Bernabeu (2022) Detecting multiple retinal diseases in ultra-widefield fundus imaging and data-driven identification of informative regions with deep learning. Nature machine intelligence. https://www.nature.com/articles/s42256-022-00566-5

Justin Engelmann, Ana Villaplana-Velasco, Amos Storkey & Miguel O. Bernabeu (2022) Robust and Efficient Computation of Retinal Fractal Dimension Through Deep Approximation. Ophthalmic Medical Image Analysis. OMIA 2022. Lecture Notes in Computer Science, vol 13576. https://link.springer.com/chapter/10.1007/978-3-031-16525-2_9

Matúš Falis, Hang Dong, Alexandra Birch, Beatrice Alex (2022) Horses to Zebras: Ontology-Guided Data Augmentation and Synthesis for ICD-9 Coding. Proceedings of the 21st Workshop on Biomedical Language Processing.  10.18653/v1/2022.bionlp-1.39

Dominic Phillips, Hans-Christof Gasser, Sebestyén Kamp, Aleksander Pałkowski, Lukasz Rabalski, Diego A. Oyarzún, Ajitha Rajan, Javier Antonio Alfaro (2022)  Generating Immune-aware SARS-CoV-2 Spike Proteins for Universal Vaccine Design.  Proceedings of the 1st Workshop on Healthcare AI and COVID-19, ICML 2022, PMLR 184:100-116, 2022. https://proceedings.mlr.press/v184/phillips22a.html 

(Preprint)  Olivier Labayle Pabet, Kelsey Tetley-Campbell, Mark Van Der Laan, Chris P. Ponting, Sjoerd Viktor Beentjes, Ava Khamseh (2022) Dispensing with unnecessary assumptions in population genetics analysis  https://www.biorxiv.org/content/10.1101/2022.09.12.507656v1

Bryan M. Li, Leonardo V. Castorina, Maria del C. Valdés-Hernández, Una Clancy, Stewart J. Wiseman, Eleni Sakka, Amos J. Storkey, Daniela Jaime Garcia, Yajun Cheng, Fergus Doubal, Michael T. Thrippleton, Michael Stringer, Joanna M. Wardlaw (2022)  Deep attention super-resolution of brain magnetic resonance images acquired under clinical protocols. Frontiers in Computational Neuroscience. https://www.frontiersin.org/articles/10.3389/fncom.2022.887633/full

Bryan M. Li*, Filippo Corponi*, Gerard Anmella, Ariadna Mas, Miriam Sanabra, Diego Hidalgo-Mazzei, Antonio Vergari (2022)  Inferring mood disorder symptoms from multivariate time-series sensory data. NeurIPS Workshop on Learning from Time Series for Health. https://openreview.net/forum?id=awjU8fCDZjS

Beltramo, G., Skraba, P., Andreeva, Rayna, Sarkar, R., Giarratano, Y. and Bernabeu, M., (2021). Euler characteristic surfaces. Foundations of Data Sciences http://dx.doi.org/10.3934/fods.2021027

Saadat-Yazdi A., Andreeva Rayna, Sarkar R. (2021) Topological Detection of Alzheimer’s Disease Using Betti Curves. In: Reyes M. et al. (eds) Interpretability of Machine Intelligence in Medical Image Computing, and Topological Data Analysis and Its Applications for Medical Data. IMIMIC 2021, TDA4MedicalData 2021. Lecture Notes in Computer Science, vol 12929. Springer, Cham. https://doi.org/10.1007/978-3-030-87444-5_12

Angeletos Chrysaitis Nikitas, Jardri R, Denève S, Seriès P (2021) No increased circular inference in adults with high levels of autistic traits or autism. PLOS Computational Biology 17(9): e1009006. https://doi.org/10.1371/journal.pcbi.1009006

Leonardo V. Castorina, Bryan M. Li, Amos Storkey, Maria. Valdés Hernández (2021) Metrics for quality control of results from super-resolution machine-learning algorithms – Data extracted from publications in the period 2017- May 2021. University of Edinburgh. Centre for Clinical Brain Sciences and School of Informatics. https://doi.org/10.7488/ds/3062

Filippo Corponi, Zorkina, Y., Stahl, D., Murru, A., Vieta, E., Serretti, A., Morozova, А., Reznik, A., Kostyuk, G. and Chekhonin, V.P. (2021). Frontal lobes dysfunction across clinical clusters of acute schizophrenia. Revista de Psiquiatría y Salud Mental. https://doi.org/10.1016/j.rpsm.2021.12.002

Matúš Falis, Dong, H., Birch, A., & Alex, B. (Accepted/In press). CoPHE: A Count-Preserving Hierarchical Evaluation Metric in Large-Scale Multi-Label Text Classification. In Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP 2021)

Bryan M. Li, Theoklitos Amvrosiadis, Nathalie Rochefort, Arno Onken (2021)  Neuronal Learning Analysis using Cycle-Consistent Adversarial Networks (Preprint). https://arxiv.org/abs/2111.13073

(Preprint) Super-Resolution of Magnetic Resonance Images Acquired Under Clinical Protocols using Deep Attention-based Method. Bryan Li, Leonardo Castorina, Maria del C. Valdés-Hernández, Una Clancy, Stewart J. Wiseman, Eleni Sakka, Amos J. Storkey, Daniela Jaime Garcia, Yajun Cheng, Fergus Doubal, Michael T. Thrippleton, Michael Stringer, Joanna M. Wardlaw medRxiv 2022.01.24.22269144; doi: https://doi.org/10.1101/2022.01.24.22269144

(Preprint) Designing human Sphingosine-1-phosphate lyases using a temporal Dirichlet variational autoencoder. Evgenii Lobzaev, Michael A. Herrera, Dominic J. Campopiano, Giovanni Stracquadanio bioRxiv 2022.02.14.480330; doi: https://doi.org/10.1101/2022.02.14.480330

Michael Stam, Wood C W, DE-STRESS: a user-friendly web application for the evaluation of protein designs, Protein Engineering, Design and Selection, Volume 34, 2021, gzab029, https://doi.org/10.1093/protein/gzab029

(Preprint) DNA Methylation scores augment 10-year risk prediction of diabetes. Yipeng Cheng, Danni A Gadd, Christian Gieger, Karla Monterrubio-Gómez, Yufei Zhang, Imrich Berta, Michael Stam, Natalia Szlachetka, Evgenii Lobzaev, Archie Campbell, Cliff Nangle, Rosie M Walker, Chloe Fawns-Ritchie, Annette Peters, Wolfgang Rathmann, David J Porteous, Kathryn L Evans, Andrew M McIntosh, Timothy I Cannings, Melanie Waldenberger, Andrea Ganna, Daniel L McCartney, Catalina A Vallejos, Riccardo E Marioni medRxiv 2021.11.19.21266469; doi: https://doi.org/10.1101/2021.11.19.21266469

Andreeva, Rayna, Fontanella, Alessandro, Giarratano Y., Bernabeu M.O. (2020) DR Detection Using Optical Coherence Tomography Angiography (OCTA): A Transfer Learning Approach with Robustness Analysis. In: Fu H., Garvin M.K., MacGillivray T., Xu Y., Zheng Y. (eds) Ophthalmic Medical Image Analysis. OMIA 2020. Lecture Notes in Computer Science, vol 12069. Springer, Cham. https://doi.org/10.1007/978-3-030-63419-3_2

Giarratano, Y., Pavel, A., Lian, J., Andreeva, Rayna, Fontanella, Alessandro, Sarkar, R., Reid, L., Forbes, S., Pugh, D., Farrah, T., Dhaun, N., Dhillon, B., MacGillivray, T. and Bernabeu, M., 2020. A Framework for the Discovery of Retinal Biomarkers in Optical Coherence Tomography Angiography (OCTA). Ophthalmic Medical Image Analysis, pp.155-164.OMIA 2020. Lecture Notes in Computer Science, vol 12069. Springer, Cham. https://doi.org/10.1007/978-3-030-63419-3_16

Fontanella, Alessandro, Pead, E.,Macgillivray, T., Bernabeu, M., & Storkey, A. (2020). Classification with a domain shift in medical imaging. Med-NeurIPS 2020: Medical Imaging meets NeurIPS Workshop http://www.cse.cuhk.edu.hk/~qdou/public/medneurips2020/43_Classification_with_a_domain_shift_in_medical_imaging.pdf