About Myself

Michele Allegra


I am a physicist and data analyst with a broad interest for biology and neuroscience. Upon completing a Ph.D in quantum physics at University of Turin, I switched my research interest to data analysis for the biological sciences and I joined the Statistical and Biological Physics sector of the International School for Advanced Studies (SISSA), Trieste, where I worked in Prof.~Alessandro Laio's group from 2015 to 2018. My research activity within Prof.~Laio's grup has focused on advanced clustering techniques to the analysis of biological data.

In particular, I worked on the application of density peak clustering to brain imaging data (Allegra et al., Hum. Brain Mapp., 2017; Allegra et al., biorXiv 2018). More recently, I developed a Bayesian approach to cluster data according to the local intrinsic dimension (Allegra et al., arXiv 2019), with broad applicability to biological as well as social data.

My current research at the Timone Institute for Neuroscience in Marseille, together with the BraiNets group led by Andrea Brovelli, focuses on applying unsupervised learning, statistics and information theory to brain imaging data to to provide new insights in medical research.




  • Advanced : Italian (mother tongue), English, French, German
  • Intermediate : Spanish
  • Programming

  • Advanced : Python, Matlab, LateX, C/C++
  • Intermediate : R
  • Notions : HTML/CSS, Bash
  • Neuroscience

  • Advanced : functional connectivity analysis
  • Intermediate : fMRI preprocessing, fMRI analysis
  • Notions : EEG, MEG, spike analysis
  • Statistics

  • Clustering analysis
  • Bayesian Statistics
  • Information theory
  • Physics

  • Quantum Physics
  • Quantum Information Science
  • Statistical Physics
  • Dynamical Systems
  • Complex Networks
  • Publications

    • M. Allegra, C. Favretto, N. Metcalf, M. Corbetta, A. Brovelli, Stroke-related alterations in inter-areal communication revealed via Granger causality analysis, bioRxiv 2021.01.04.425190 (2021) PDF
    • D. Mouillot, N. Loiseau, M. Grenié, A. C. Algar, M. Allegra, M. W. Cadotte, N. Casajus, P. Denelle, M. Guéguen, A. Maire, B. Maitner, B. McGill, M. McLean, N. Mouquet, F. Munoz, W. Thuiller, S. Villéger, C. Violle, Arnaud Auber, The dimensionality and structure of species trait spaces, submitted (2020)
    • M. Allegra, E. Facco, F. Denti, A. Laio, A. Mira, Data segmentation based on the local intrinsic dimension, Scientific Reports 10,16449 (2020) PDF
    • M. Allegra, S. Seyed-Allaei, N.W. Schuck, D. Amati, A. Laio, C. Reverberi, Brain network dynamics during spontaneous strategy shifts and incremental task optimization, NeuroImage, 116854 (2020) PDF
    • N. I. Ilieva, N. Galvanetto, M. Allegra, M. Brucale, and A. Laio, Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples, Bioinformatics, btaa626 (2020) PDF
    • M. Allegra, S. Seyed‐Allaei, F. Pizzagalli, F. Baftizadeh, M. Maieron, Carlo Reverberi, Alessandro Laio, Daniele Amati, fMRI single trial discovery of spatio‐temporal brain activity patterns, Human brain mapping 38 (3), 1421-1437 (2017) PDF
    • P. Giorda, M. Allegra, Coherence in quantum estimation, Journal of Physics A: Mathematical and Theoretical 51 (2), 025302 (2017) PDF
    • P. Giorda, M. Allegra, Two-qubit correlations revisited: average mutual information, relevant (and useful) observables and an application to remote state preparation, Journal of Physics A: Mathematical and Theoretical 50 (29), 295302 (2017) PDF
    • M. Allegra, P. Giorda, S. Lloyd, Global coherence of quantum evolutions based on decoherent histories: theory and application to photosynthetic quantum energy transport, Physical Review A 93 (4), 042312 (2016) PDF
    • X. Wang, M. Allegra, K. Jacobs, S. Lloyd, C. Lupo, M. Mohseni, Quantum brachistochrone curves as geodesics: Obtaining accurate minimum-time protocols for the control of quantum systems, Physical Review Letters 114 (17), 170501(2015) PDF
    • C.D. Aiello, M. Allegra, B. Hemmerling, X. Wan, P. Cappellaro, Algebraic synthesis of time-optimal unitaries in SU (2) with alternating controls, Quantum Information Processing 14 (9), 3233-3256 (2015) PDF
    • M. Allegra, Gain and loss of information by decoherence, PhD thesis, University of Turin (2014) PDF
    • M. Allegra, P. Giorda, M.G.A. Paris, Quantum discord for Gaussian states with non-Gaussian measurements, Physical Review A 86 (5), 052328 (2012) PDF
    • M. Allegra, P. Giorda, Topology and energy transport in networks of interacting photosynthetic complexes, Physical Review E 85 (5), 051917 (2012) PDF
    • M. Allegra, P. Giorda, A. Montorsi, Quantum discord and classical correlations in the bond-charge Hubbard model: Quantum phase transitions, off-diagonal long-range order, and violation of the monogamy property, Physical Review B 84 (24), 245133 (2011) PDF
    • M. Allegra, P. Giorda, M.G.A. Paris, Role of initial entanglement and non-Gaussianity in the decoherence of photon-number entangled states evolving in a noisy channel, Physical Review Letters 105 (10), 100503 (2010) PDF


    Coherence Density Peak Clustering


    Heterogeneous Intrinsic Dimension Estimation


    Single Molecule Force Spectroscopy Clustering


    covariance-based Granger causality fMRi for



    • 25/01/2018: invited talk at the Monthly Neuroimaging Meeting, Aix-Marseille Université, Marseille (France) PDF ODP
    • 04/17/2018: invited talk at the Institute for Computational Science, Università della Svizzera Italiana, Lugano (Switzerland) PDF ODP
    • 06/08/2018 invited talk at the CECAM Workshop on Machine Learning at Interfaces, CECAM-HQ-EPFL, Lausanne (Switzerland) PDF ODP
    • 06/22/2018: invited talk at the 49. Meeting of the Italian Statistical Society, Palermo (Italy) PDF ODP
    • 09/04/2019: invited talk at the Theoretical Neuroscience group meeting, Institut de Neurosciences de Systèmes, Marseille, France PDF
    • 05/09/2019: invited talk at the Young Researcher’s Workshop on Machine Learning for Materials Science 2019, Helsinki (Finland) PDF ODP Video
    • 06/11/2019: invited talk at the CINaM, Aix-Marseille Université, Marseille, France ODP
    • 16/05/2020: invited talk at Department of Physics, Università di Padova, (Italy) PDF ODP



    Phone: (+33) 7-67-42-39-68
    Skype: michele.allegra