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Department
  • Psychiatry
  • Research Focus

    Keywords

  • Deep Learning
  • Deep Neural Networks
  • Machine Learning
  • Artificial Intelligence
  • Uncertainty
  • Brain Image Processing
  • Brain Mapping
  • Brain Segmentation
  • Brain Tumours
  • Brain Development
  • Human Computer Interaction
  • Clinical Conditions

  • Bipolar disorder
  • Schizophrenia
  • Brain cancer
  • Alzheimer's disease
  • Equipment & Techniques

  • Magnetic resonance imaging (MRI)
  • Statistical analysis
  • Computational modelling
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    Dr Michail (Mike) Mamalakis

    (he/him/his)
    University Position
    Senior Research Associate
    Dr Michail (Mike) Mamalakis is pleased to consider applications from prospective PhD students.

    Interests

    My research expertise spans both applied and theoretical AI, including Deep Learning, Multi-Modal AI, and eXplainable AI. Throughout my career, I have collaborated with interdisciplinary teams to tackle challenges in biomedical applications, and healthcare. At the University of Cambridge, I am working on foundational AI models for medical imaging, leveraging deep learning and explainability for diagnostic and prognostic predictions.   Over the past several years, my research has focused on leveraging state-of-the-art AI techniques to solve complex biomedical problems and neuroscience. My work has encompassed developing XAI models for clinical imaging and genomics that directly inform diagnostic and therapeutic decisions. For example, in collaboration with multi-disciplinary teams from Oxford, Glasgow, Lincoln, Brighton, and Sheffield, I have contributed to biomarker discovery in COVID-19 by integrating phenotyping, blood, and imaging datasets. My collaborative projects at the University of Cambridge have further honed my expertise. Working with Professor Richard Clayton’s group (University of Sheffield, till 2022), I developed robust computer vision AI applications for cardiac arrhythmias, while my engagements with Professor Andriew Shift’s group i(University of Sheffield, till 2022) involved pulmonary hypertension research focusing on uncertainty estimation and explainability. Additionally, I have collaborated with Professor George Panoutsos (University of Sheffield, till 2022) on metastatic mutation cell detection and the explanation of potential biomarkers, as well as with Professor Pietro Lio, Murray Graham and John Suckling (University of Cambridge, till 2025) in neuroscience, focusing on secondary sulci region identification, phenotyping, and genetic correlations in psychotic patients and brain tumors.  Currently, I am actively involved in several cutting edge projects that align closely with the mission of the University of Cambridge and its School of Clinical Medicine. I am developing predictive models for neuroscience by integrating multimodal data including text, imaging, phenotyping, and genomics, using explainable AI on large scale datasets. Notably, I am also engaged in research involving pre and post surgery datasets from brain tumour patients, applying gradient based explainability methods to uncover novel connectomic patterns in high grade glioblastoma. Additionally, I serve as a Senior Research Associate at the University of Cambridge School of Clinical Medicine and the Cancer Research UK (CRUK) Cambridge Centre, where I focus on childhood brain cancer.

    3D eXplainability Artificial Intelligence

    The 3D explainable framework that provides both local and global interpretations and explanations of our deep learning 3D classification network's results. The ratio of the aithfulness and complexity metrics are compute in that stage. In this example we include only the GradCam explainability method just for simplicity.

    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

    MA-SOCRATIS: An automatic pipeline for robust segmentation of the left ventricle and scar.

    DOI: http://doi.org/10.1016/j.compmedimag.2021.101982
    Journal: Comput Med Imaging Graph
    E-pub date: 1 Oct 2021
    Authors: M Mamalakis, P Garg, T Nelson, J Lee, JM Wild, RH Clayton

    Publications

    Reassessing Asymmetry Reduction in Psychosis: Cingulate Folding and Gyrification Covariance in Patients with Auditory Hallucinations

    DOI: http://doi.org/10.1093/schbul/sbaf086
    Journal: Schizophr Bull
    E-pub date: 7 Mar 2026
    Authors: S-CJ Wu, H de Vareilles, SC Mitchell, A Al-Manea, J Garrison, M Mamalakis, JS Simons, A Cachia, J-F Mangin, S Nerland, L Mørch-Johnsen, I Agartz, J Suckling, GK Murray

    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

    A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

    DOI: http://doi.org/10.1109/bibm62325.2024.10821894
    Journal:
    E-pub date: 6 Dec 2024
    Authors: Y Shen, Z Chen, M Mamalakis, L He, H Xia, T Li, Y Su, J He, YG Wang

    Reassessing Asymmetry Reduction in Psychosis: Cingulate Folding and Gyrification Covariance in Patients with Auditory Hallucinations

    DOI: http://doi.org/10.1101/2024.11.07.24316889
    Journal:
    E-pub date: 17 Nov 2024
    Authors: S-CJ Wu, H de Vareilles, SC Mitchell, A Al-Manea, J Garrison, M Mamalakis, JS Simons, A Cachia, J-F Mangin, S Nerland, L Mørch-Johnsen, I Agartz, J Suckling, GK Murray

    P11.05.B LONGITUDINAL MODIFICATIONS OF GRADIENTS AND GRAPH-THEORY MEASURES OF FUNCTIONAL MRI CONNECTIVITY IN GLIOMA PATIENTS AS POTENTIAL MARKERS OF POST-SURGICAL LONG-TERM COGNITIVE OUTCOME

    DOI: http://doi.org/10.1093/neuonc/noae144.207
    Journal: Neuro-Oncology
    E-pub date: 17 Oct 2024
    Authors: G Sansone, A Poologaindran, R Romero-Garcia, M Mamalakis, R Bethlehem, M Hart, T Santarius, Y Wan, C Li, M Corbetta, Y Erez, SJ Price, J Suckling

    Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge.

    DOI: http://doi.org/10.1016/j.media.2024.103253
    Journal: Med Image Anal
    E-pub date: 1 Oct 2024
    Authors: Y Nan, X Xing, ShiyiWang, Z Tang, FN Felder, S Zhang, RE Ledda, X Ding, R Yu, W Liu, F Shi, T Sun, Z Cao, M Zhang, Y Gu, H Zhang, J Gao, P Wang, W Tang, P Yu, H Kang, J Chen, X Lu, B Zhang, M Mamalakis, F Prinzi, G Carlini, L Cuneo, A Banerjee, Z Xing, L Zhu, Z Mesbah, D Jain, T Mayet, H Yuan, Q Lyu, A Qayyum, M Mazher, A Wells, SL Walsh, G Yang

    Deep multi-metric training: the need of multi-metric curve evaluation to avoid weak learning

    DOI: http://doi.org/10.1007/s00521-024-10182-6
    Journal: Neural Computing and Applications
    E-pub date: 1 Oct 2024
    Authors: M Mamalakis, A Banerjee, S Ray, C Wilkie, RH Clayton, AJ Swift, G Panoutsos, B Vorselaars

    A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

    DOI: http://doi.org/10.48550/arxiv.2406.05540
    Journal:
    E-pub date: 8 Jul 2024
    Authors: Y Shen, Z Chen, M Mamalakis, L He, H Xia, T Li, Y Su, J He, YG Wang

    Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

    DOI: http://doi.org/10.48550/arxiv.2312.13752
    Journal:
    E-pub date: 16 Apr 2024
    Authors: Y Nan, X Xing, S Wang, Z Tang, FN Felder, S Zhang, RE Ledda, X Ding, R Yu, W Liu, F Shi, T Sun, Z Cao, M Zhang, Y Gu, H Zhang, J Gao, P Wang, W Tang, P Yu, H Kang, J Chen, X Lu, B Zhang, M Mamalakis, F Prinzi, G Carlini, L Cuneo, A Banerjee, Z Xing, L Zhu, Z Mesbah, D Jain, T Mayet, H Yuan, Q Lyu, A Qayyum, M Mazher, A Wells, SL Walsh, G Yang

    Improving Prognostication in Pulmonary Hypertension Using AI-quantified Fibrosis and Radiologic Severity Scoring at Baseline CT.

    DOI: http://doi.org/10.1148/radiol.231718
    Journal: Radiology
    E-pub date: 1 Feb 2024
    Authors: K Dwivedi, M Sharkey, L Delaney, S Alabed, S Rajaram, C Hill, C Johns, A Rothman, M Mamalakis, AAR Thompson, J Wild, R Condliffe, DG Kiely, AJ Swift

    Intra-operative applications of augmented reality in glioma surgery: a systematic review.

    DOI: http://doi.org/10.3389/fsurg.2023.1245851
    Journal: Front Surg
    E-pub date: 1 Aug 2023
    Authors: A Ragnhildstveit, C Li, MH Zimmerman, M Mamalakis, VN Curry, W Holle, N Baig, AK Uğuralp, L Alkhani, Z Oğuz-Uğuralp, R Romero-Garcia, J Suckling

    A transparent artificial intelligence framework to assess lung disease in pulmonary hypertension.

    DOI: http://doi.org/10.1038/s41598-023-30503-4
    Journal: Sci Rep
    E-pub date: 7 Mar 2023
    Authors: M Mamalakis, K Dwivedi, M Sharkey, S Alabed, D Kiely, AJ Swift

    Artificial Intelligence as a Diagnostic Tool in Non-Invasive Imaging in the Assessment of Coronary Artery Disease.

    DOI: http://doi.org/10.3390/medsci11010020
    Journal: Med Sci (Basel)
    E-pub date: 24 Feb 2023
    Authors: G Doolub, M Mamalakis, S Alabed, RJ Van der Geest, AJ Swift, JCL Rodrigues, P Garg, NV Joshi, A Dastidar

    Automatic development of 3D anatomical models of border zone and core scar regions in the left ventricle.

    DOI: http://doi.org/10.1016/j.compmedimag.2022.102152
    Journal: Comput Med Imaging Graph
    E-pub date: 1 Jan 2023
    Authors: M Mamalakis, P Garg, T Nelson, J Lee, AJ Swift, JM Wild, RH Clayton

    P41 CT lung parenchymal appearances in chronic thromboembolic pulmonary hypertension (CTEPH)

    DOI: http://doi.org/10.1136/thorax-2022-btsabstracts.177
    Journal:
    E-pub date: 1 Nov 2022
    Authors: L Abdulaal, K Dwivedi, MJ Sharkey, S Alabed, M Mamalakis, D Alkhanfar, R Condliffe, DG Kiely, AJ Swift

    A robust COVID-19 mortality prediction calculator based on Lymphocyte count, Urea, C-Reactive Protein, Age and Sex (LUCAS) with chest X-rays.

    DOI: http://doi.org/10.1038/s41598-022-21803-2
    Journal: Sci Rep
    E-pub date: 29 Oct 2022
    Authors: S Ray, A Banerjee, A Swift, JW Fanstone, M Mamalakis, B Vorselaars, C Wilkie, J Cole, LS Mackenzie, S Weeks

    Validation of Artificial Intelligence Cardiac MRI Measurements: Relationship to Heart Catheterization and Mortality Prediction.

    DOI: http://doi.org/10.1148/radiol.212929
    Journal: Radiology
    E-pub date: 1 Oct 2022
    Authors: S Alabed, F Alandejani, K Dwivedi, K Karunasaagarar, M Sharkey, P Garg, PJH de Koning, A Tóth, Y Shahin, C Johns, M Mamalakis, S Stott, D Capener, S Wood, P Metherall, AMK Rothman, R Condliffe, N Hamilton, JM Wild, DP O'Regan, H Lu, DG Kiely, RJ van der Geest, AJ Swift

    Fully automatic deep learning pulmonary hypertension diagnosis using CT pulmonary angiography

    DOI: http://doi.org/10.1183/13993003.congress-2022.3655
    Journal:
    E-pub date: 4 Sep 2022
    Authors: M Sharkey, K Karunasaagarar, CS Johns, S Rajaram, K Dwivedi, P Garg, D Alkhanfar, S Alabed, P Metherall, J Taylor, RJ Van Der Geest, R Condliffe, M Mamalakis, DG Kiely, AJ Swift, K Dwivedi

    Prognostic importance of centrilobular ground glass changes in patients with Idiopathic Pulmonary Arterial Hypertension

    DOI: http://doi.org/10.1183/13993003.congress-2022.261
    Journal:
    E-pub date: 4 Sep 2022
    Authors: K Dwivedi, M Sharkey, R Lewis, M Mamalakis, S Alabed, S Rajaram, C Hill, D Kiely, J Wild, A Swift, R Condliffe

    Validation of Artificial Intelligence Cardiac MRI Measurements: Relationship to Heart Catheterization and Mortality Prediction.

    DOI: http://doi.org/10.1148/radiol.229014
    Journal: Radiology
    E-pub date: 1 Sep 2022
    Authors: S Alabed, F Alandejani, K Dwivedi, K Karunasaagarar, M Sharkey, P Garg, PJH de Koning, A Tóth, Y Shahin, C Johns, M Mamalakis, S Stott, D Capener, S Wood, P Metherall, AMK Rothman, R Condliffe, N Hamilton, JM Wild, DP O'Regan, H Lu, DG Kiely, RJ van der Geest, AJ Swift

    The quality of reporting in cardiac MRI artificial intelligence segmentation studies – a systematic review

    DOI: http://doi.org/10.1093/ehjci/jeac141.002
    Journal: European Heart Journal - Cardiovascular Imaging
    E-pub date: 23 Aug 2022
    Authors: S Alabed, A Maiter, A Mahmood, S Daniel, M Salehi, S Jenkins, M Sharkey, V Rakocevic, K Dwivedi, H Asaadi, M Mamalakis, DP O'regan, P Garg, R Van Der Geest, AJ Swift

    Fully automatic cardiac four chamber and great vessel segmentation on CT pulmonary angiography using deep learning.

    DOI: http://doi.org/10.3389/fcvm.2022.983859
    Journal: Front Cardiovasc Med
    E-pub date: 1 Aug 2022
    Authors: MJ Sharkey, JC Taylor, S Alabed, K Dwivedi, K Karunasaagarar, CS Johns, S Rajaram, P Garg, D Alkhanfar, P Metherall, DP O'Regan, RJ van der Geest, R Condliffe, DG Kiely, M Mamalakis, AJ Swift

    Development of a Mortality Prediction Model in Hospitalised SARS-CoV-2 Positive Patients Based on Routine Kidney Biomarkers.

    DOI: http://doi.org/10.3390/ijms23137260
    Journal: Int J Mol Sci
    E-pub date: 30 Jun 2022
    Authors: AN Boss, A Banerjee, M Mamalakis, S Ray, AJ Swift, C Wilkie, JW Fanstone, B Vorselaars, J Cole, S Weeks, LS Mackenzie

    Deep Learning Approaches to Classify Lung Parenchymal Disease on CT Images

    DOI: http://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5431
    Journal: American Journal of Respiratory and Critical Care Medicine
    E-pub date: 1 May 2022
    Authors: M Mamalakis, K Dwivedi, M Sharkey, S Alabed, P Metherall, D Kiely, A Swift

    Computed Tomography (CT) Features Are of Diagnostic Utility in Pre Diagnosis Idiopathic Pulmonary Arterial Hypertension (IPAH): A Case Controlled Study

    DOI: http://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3605
    Journal: American Journal of Respiratory and Critical Care Medicine
    E-pub date: 1 May 2022
    Authors: K Dwivedi, R Lewis, R Condliffe, MJ Sharkey, M Mamalakis, S Alabed, JM Wild, AJ Swift, D Kiely

    Fully Automatic Cardiac and Great Vessel Segmentation on CT Pulmonary Angiography (CTPA) Using Deep Learning

    DOI: http://doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5437
    Journal: American Journal of Respiratory and Critical Care Medicine
    E-pub date: 1 May 2022
    Authors: MJ Sharkey, K Karunasaagarar, C Johns, S Rajaram, D Alkhanfar, K Dwivedi, S Alabed, P Metherall, R Van Der Geest, M Mamalakis, D Kiely, AJ Swift

    Training and clinical testing of artificial intelligence derived right atrial cardiovascular magnetic resonance measurements.

    DOI: http://doi.org/10.1186/s12968-022-00855-3
    Journal: J Cardiovasc Magn Reson
    E-pub date: 7 Apr 2022
    Authors: F Alandejani, S Alabed, P Garg, ZM Goh, K Karunasaagarar, M Sharkey, M Salehi, Z Aldabbagh, K Dwivedi, M Mamalakis, P Metherall, J Uthoff, C Johns, A Rothman, R Condliffe, A Hameed, A Charalampoplous, H Lu, S Plein, JP Greenwood, A Lawrie, JM Wild, PJH de Koning, DG Kiely, R Van Der Geest, AJ Swift

    DenResCov-19: A deep transfer learning network for robust automatic classification of COVID-19, pneumonia, and tuberculosis from X-rays.

    DOI: http://doi.org/10.1016/j.compmedimag.2021.102008
    Journal: Comput Med Imaging Graph
    E-pub date: 1 Dec 2021
    Authors: M Mamalakis, AJ Swift, B Vorselaars, S Ray, S Weeks, W Ding, RH Clayton, LS Mackenzie, A Banerjee

    LUCAS: A highly accurate yet simple risk calculator that predicts survival of COVID-19 patients using rapid routine tests

    DOI: http://doi.org/10.1101/2021.04.27.21256196
    Journal:
    E-pub date: 2 May 2021
    Authors: S Ray, A Swift, JW Fanstone, A Banerjee, M Mamalakis, B Vorselaars, LS Mackenzie, S Weeks

    Use of Machine Learning and Artificial Intelligence to predict SARS-CoV-2 infection from Full Blood Counts in a population

    DOI: http://doi.org/10.48550/arxiv.2007.06971
    Journal:
    E-pub date: 12 Apr 2021
    Authors: A Banerjee, S Ray, B Vorselaars, J Kitson, M Mamalakis, S Weeks, M Baker, LS Mackenzie

    DenResCov-19: A deep transfer learning network for robust automatic classification of COVID-19, pneumonia, and tuberculosis from X-rays

    DOI: http://doi.org/10.48550/arxiv.2104.04006
    Journal:
    E-pub date: 8 Apr 2021
    Authors: M Mamalakis, AJ Swift, B Vorselaars, S Ray, S Weeks, W Ding, RH Clayton, LS Mackenzie, A Banerjee

    Use of Machine Learning and Artificial Intelligence to predict SARS-CoV-2 infection from Full Blood Counts in a population.

    DOI: http://doi.org/10.1016/j.intimp.2020.106705
    Journal: Int Immunopharmacol
    E-pub date: 1 Sep 2020
    Authors: A Banerjee, S Ray, B Vorselaars, J Kitson, M Mamalakis, S Weeks, M Baker, LS Mackenzie