Dr Pietro Lio'

University Position

Professor

Interests

I am a Reader in Computational Biology in the Computer Laboratory which is the department of Computer Science of the University of Cambridge and I am a member of the Artificial Intelligence group of the Computer Laboratory. I hold a PhD in Complex Systems and Non Linear Dynamics (School of Informatics, dept of Engineering of the University of Firenze, Italy) and a PhD in (Theoretical) Genetics (University of Pavia, Italy). My research interests are: Bioinformatics algorithms, Predictive models in Personalised medicine, Modeling comorbidity and aging, Methods for combining Multi scale biological processes, Statistics of Multi omics and Multi physics modelling of molecules-cell-tissue-organ interactions.

Key Publications

Solving the enigma: Enhancing faithfulness and comprehensibility in explanations of deep networks

DOI: http://doi.org/10.1016/j.aiopen.2025.02.001
Journal: AI Open
E-pub date: 1 Aug 2025
Authors: M Mamalakis, A Mamalakis, I Agartz, LE Mørch-Johnsen, GK Murray, J Suckling, P Lio

The Explanation Necessity for Healthcare AI

DOI: http://doi.org/10.1109/citrexcompanion65208.2025.10981502
Journal:
E-pub date: 20 Mar 2025
Authors: M Mamalakis, H de Vareilles, GK Murray, P Lio, J Suckling

Identifying healthy individuals with Alzheimer’s disease neuroimaging phenotypes in the UK Biobank.

DOI: http://doi.org/10.1038/s43856-023-00313-w
Journal: Commun Med (Lond)
E-pub date: 20 Jul 2023
Authors: T Azevedo, RAI Bethlehem, DJ Whiteside, N Swaddiwudhipong, JB Rowe, P Lió, T Rittman, Alzheimer’s Disease Neuroimaging Initiative

A deep graph neural network architecture for modelling spatio-temporal dynamics in resting-state functional MRI data.

DOI: http://doi.org/10.1016/j.media.2022.102471
Journal: Med Image Anal
E-pub date: 1 Jul 2022
Authors: T Azevedo, A Campbell, R Romero-Garcia, L Passamonti, RAI Bethlehem, P Liò, N Toschi

A Deep Graph Neural Network Architecture for Modelling Spatio-temporal Dynamics in resting-state functional MRI Data

DOI: http://doi.org/10.1101/2020.11.08.370288
Journal:
E-pub date: 9 Nov 2020
Authors: T Azevedo, A Campbell, R Romero-Garcia, L Passamonti, RAI Bethlehem, P Liò, N Toschi

Publications

Uncertainty-Aware Tau Detection in Progressive Supranuclear Palsy Using Object Detection Models

DOI: http://doi.org/10.1109/ispa66905.2025.11259454
Journal:
E-pub date: 31 Oct 2025
Authors: G Zhou, T Azevedo, A Quaegebeur, T Pansuwan, T Rittman, P Lió

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

DOI: http://doi.org/10.1109/bibm62325.2024.10822695
Journal:
E-pub date: 6 Dec 2024
Authors: Y Shen, Z Chen, M Mamalakis, Y Liu, T Li, Y Su, J He, P Liò, YG Wang

ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology.

DOI: http://doi.org/10.1038/s41592-023-01815-0
Journal: Nat Methods
E-pub date: 1 Apr 2023
Authors: M Lu, CN Christensen, JM Weber, T Konno, NF Läubli, KM Scherer, E Avezov, P Lio, AA Lapkin, GS Kaminski Schierle, CF Kaminski

ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology for video-rate super-resolution imaging

DOI: http://doi.org/10.1101/2022.05.17.492189
Journal:
E-pub date: 21 May 2022
Authors: M Lu, C Christensen, J Weber, T Konno, N Läubli, K Scherer, E Avezov, P Lio, A Lapkin, G Kaminski Schierle, C Kaminski

A class-contrastive human-interpretable machine learning approach to predict mortality in severe mental illness.

DOI: http://doi.org/10.1038/s41537-021-00191-y
Journal: NPJ Schizophr
E-pub date: 8 Dec 2021
Authors: S Banerjee, P Lio, PB Jones, RN Cardinal

Mapping the human genetic architecture of COVID-19.

DOI: http://doi.org/10.1038/s41586-021-03767-x
Journal: Nature
E-pub date: 1 Dec 2021
Authors: COVID-19 Host Genetics Initiative

Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits.

DOI: http://doi.org/10.1038/s41540-021-00186-6
Journal: NPJ Syst Biol Appl
E-pub date: 27 May 2021
Authors: T Azevedo, GM Dimitri, P Lió, ER Gamazon

A human-interpretable machine learning approach to predict mortality in severe mental illness

DOI: http://doi.org/10.1101/2021.04.05.21254684
Journal:
E-pub date: 11 Apr 2021
Authors: S Banerjee, P Liò, P Jones, R Cardinal

Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans

DOI: http://doi.org/10.1038/s42256-021-00307-0
Journal: Nature Machine Intelligence
E-pub date: 1 Mar 2021
Authors: M Roberts, D Driggs, M Thorpe, J Gilbey, M Yeung, S Ursprung, AI Aviles-Rivero, C Etmann, C McCague, L Beer, JR Weir-McCall, Z Teng, E Gkrania-Klotsas, A Ruggiero, A Korhonen, E Jefferson, E Ako, G Langs, G Gozaliasl, G Yang, H Prosch, J Preller, J Stanczuk, J Tang, J Hofmanninger, J Babar, LE Sánchez, M Thillai, PM Gonzalez, P Teare, X Zhu, M Patel, C Cafolla, H Azadbakht, J Jacob, J Lowe, K Zhang, K Bradley, M Wassin, M Holzer, K Ji, MD Ortet, T Ai, N Walton, P Lio, S Stranks, T Shadbahr, W Lin, Y Zha, Z Niu, JHF Rudd, E Sala, CB Schönlieb

A Human-Interpretable Machine Learning Approach to Predict Mortality in Severe Mental Illness

DOI: http://doi.org/10.2139/ssrn.3824766
Journal:
E-pub date: 1 Jan 2021
Authors: S Banerjee, P Lio, PB Jones, RN Cardinal

Evidence in cortical folding patterns for prenatal predispositions to hallucinations in schizophrenia.

DOI: http://doi.org/10.1038/s41398-020-01075-y
Journal: Transl Psychiatry
E-pub date: 6 Nov 2020
Authors: CPE Rollins, JR Garrison, M Arribas, A Seyedsalehi, Z Li, RCK Chan, J Yang, D Wang, P Liò, C Yan, Z-H Yi, A Cachia, R Upthegrove, B Deakin, JS Simons, GK Murray, J Suckling

The neurodevelopment of anomalous perception: Evidence in cortical folding patterns for prenatal predispositions to hallucinations in schizophrenia

DOI: http://doi.org/10.1101/2020.06.04.20122424
Journal:
E-pub date: 5 Jun 2020
Authors: CPE Rollins, J Garrison, M Arribas, A Seyedsalehi, Z Li, RCK Chan, J Yang, D Wang, P Lio, C Yan, Z-H Yi, A Cachia, R Upthegrove, B Deakin, J Simons, G Murray, J Suckling

Neural network fusion: a novel CT-MR Aortic Aneurysm image segmentation method.

DOI: http://doi.org/10.1117/12.2293371
Journal: Proc SPIE Int Soc Opt Eng
E-pub date: 2 Mar 2018
Authors: D Wang, R Zhang, J Zhu, Z Teng, Y Huang, F Spiga, M Hong-Fei Du, JH Gillard, Q Lu, P Liò