Biography

I am Assistant Professor (​Maître de Conférences) in Artificial Intelligence and Medical Imaging at Télécom Paris in the IMAGES group of the LTCI lab. I am also a research collaborator of the Ima-Brain research team at the Institute of Psychiatry and Neuroscience of Paris (IPNP) and of the research laboratory NeuroSpin at the CEA.

I did my academic training with Inria at the ARAMIS Lab in Paris where I worked with Stanley Durrleman (Inria Researcher), Olivier Colliot (CNRS Research Director) and Nicholas Ayache (Inria Research Director) and then at Neurospin (CEA) with Edouard Duchesnay (CEA Research Scientist), Josselin Houenou (M.D. APHP) and Jean-François Mangin (CEA Research Director). Previous to that, I obtained a MSc in Mathematical Modelling and Computation from the DTU in Copenhagen and a MSc in Biomedical Engineering from the University of Padova.

I participated to the development of the open source software suite deformetrica for statistical shape analysis and of the software platform Clinica for clinical neuroimaging studies.

My research interests lie primarily in the fields of machine learning, AI, medical imaging and computational anatomy.

Research Projects

Modeling, transferring and discovering anatomical knowledge using AI

Work on new learning methods (e.g., knowledge distillation, contrastive learning, image-to-image translation) for modeling prior anatomical knowledge, transferring relevant anatomical information between domains (e.g., from adult to pediatric data) and discovering new anatomical biomarkers.

Tractogram analysis

Explore new geometric representations, metrics and deformation models for fast, robust and reliable processing, comparison and visualization of tractograms from diffusion MRI (white matter, nerves, etc.).

Multi-modal Data Fusion: learning common and distinctive anatomical variations

Investigate new statistical methods to learn common and distinctive anatomical variations between different parts of a human organ (i.e. white and gray matter of the brain) or between two different populations (i.e. controls and patients).

Glioblastoma atlas estimation

Propose a method to estimate a 3D atlas of glioblastoma using a population of MR brain images. The resulting atlas should describe the average shape of glioblastoma and its variability, which will depend on its anatomical location, as well as the main variations of the surrounding tissues (mass effect).

Teaching

IMA205 - Machine learning for images and object recognition

Master's level course for 2nd year students of Télécom Paris about the main machine learning techniques used for image analysis.

IMA204 - Biomedical image registration and segmentation

Master's level course for 2nd year students of Télécom Paris about medical acquisition techniques, segmentation algorithms, deformation models and statistical shape analysis.

BIOMED - Medical image processing

Course of the Computer Science Master (IMA) at UPMC Sorbonne University and Télécom ParisTech about medical acquisition techniques and image processing.

Machine Learning for BioImaging

Course of the BioImaging Master (BIM) at Paris Descartes University and Télécom Paris about the main machine learning techniques used for medical image analysis.

Certificat d’Études Spécialisées (CES) Data Scientist

Formation Certifiante sur l'analyse et gestion de grandes masses de données.

MS Big Data

Mastère Spécialisé sur le Big Data

Supervision experience

PhD students

  • Ismaël Mounime (since 01/2023) , co-supervised with E. Angelini (Télécom Paris) and Chao Ma (Gordon Center, Harvard)
  • Edouard Pierre Baudoin (since 10/2022) , co-supervised with R. Colle, E. Duron (Bicêtre hospital) and I. Bloch (Sorbonne University)
  • Ali Mammadov (since 10/2022) , co-supervised with L. Le Folgoc (Télécom Paris), G. Hocquet and A. Buronfosse (Paris Saint-Joseph hospital)
  • Emma Sarfati (since 09/2022) , co-supervised with I. Bloch (Télécom Paris), Alexandre Bône (Guerbet) and Marc-Michel Rohe (Guerbet)
  • Rebeca Vetil (since 04/2021) , co-supervised with I. Bloch (Télécom Paris), Alexandre Bône (Guerbet) and Marc-Michel Rohe (Guerbet)
  • Robin Louiset (since 11/2020) , co-supervised with E. Duchesnay (NeuroSpin, CEA)

Alumni

  • Carlo Alberto Barbano (10/2020 - 12/2023), co-supervised with M. Grangetto (University of Turin). Now post-doc at University of Turin.
  • Camille Ruppli (01/2021 - 12/2023) , PhD student co-supervised with I. Bloch and Roberto Ardon (Incepto). Now Data Scientist at Incepto.
  • Matthis Maillard (10/2019 - 06/2023) , Phd student co-supervised with I. Bloch. Now Data Scientist at Deemea.
  • Anton François (10/2019 - 05/2023) , Phd student co-supervised with J. Glaunès (MAP5). Now post-doc at ENS Paris-Saclay.
  • Florence Carton (09/2021 - 01/2023). Post-Doc. Now Research Engineer at Total.
  • Benoit Dufumier (10/2019 - 12/2022) , Phd student co-supervised with E. Duchesnay. Now post-doc at EPFL.
  • Giammarco La Barbera (10/2019 - 12/2022) , Phd student co-supervised with I. Bloch, L. Rouet and S. Sarnacki. Now Research Engineer at Necker hospital.
  • Mateus Riva (02/2019 - 12/2022) , Phd student co-supervised with I. Bloch and F. Yger. Now AI Data Engineer at Valeo.
  • Ariel Nora (04/2022 - 10/2022) , Master student IPParis, co-supervised with G. Hocquet. Now Phd candidate at Télécom Paris.
  • Robin Kips (01/2019 - 04/2022) , Phd student, co-supervised with I. Bloch (Télécom Paris) and M. Perrot (L'Oréal), Now Applied Research Scientist, Meta Reality Labs
  • Alessandro Hizdri (09/2021 - 02/2022) , Master student Politecnico of Torino
  • Corentin Mercier (10/2017 - 12/2020) , Phd student, co-supervised with I. Bloch, J.M. Thiery, D. Rohmer, T. Boubeker and M.P. Cani, Now Software engineer at Pixyz
  • Francesco Maso (09/2020 - 02/2021) , Master student Politecnico of Torino, Now Data Analyst at SDG (Padova)
  • Nemo Fournier (09/2020 - 02/2021) , Master student ENS de Lyon, Now Phd student at Aramis LAB (Paris)
  • Ilaria Battaglia (09/2020 - 02/2021) , Master student Politecnico of Torino, Now Junior Consultant & Engineer, Capgemini
  • Bruno Belucci Teixeira (05/2020 - 09/2020) , Master student ESPCI Paris, co-supervised with I. Bloch
  • Pierre Roussillon (09/2018 - 11/2019) , Postdoc , co-supervised with I. Bloch, J.M. Thiery , Now Prof. Prépa ECG at Lycée Louis Le Grand
  • Alessandro Di Girolamo (05/2019 - 10/2019) , Master student Politecnico of Torino , co-supervised with I. Bloch , Now Digital Business Integration Analyst at Accenture
  • Alessandro Delmonte (09/2017 - 02/2018) , Master student Politecnico of Torino , co-supervised with I. Bloch , Now Senior Artificial Intelligence Engineer at Clario
  • Ariane Fleury (02/2017 - 07/2017) , Master student Paris Descartes University , co-supervised with P. Roca
  • Raphaël Berdugo (05/2017 - 11/2017) , Master student Ensae ParisTech , Now CTO and Co-founder @alfred-eyes.ai

Publications

PhD Thesis

  • P. Gori
    Statistical models to learn the structural organisation of neural circuits from multimodal brain images - Application to Gilles de la Tourette syndrome
    PhD Thesis, UPMC, Paris, France  


Book chapters

  • N. Charon, B. Charlier, J. Glaunès, P. Gori, P. Roussillon
    Fidelity metrics between curves and surfaces: currents, varifolds, and normal cycles
    Book chapter in Riemannian Geometric Statistics in Medical Image Analysis, Elsevier, 2019  


Journal Articles

  • G. La Barbera, L. Rouet, H. Boussaid, A. Lubet, R. Kassir, S. Sarnacki, P. Gori, I. Bloch
    Tubular structures segmentation of pediatric abdominal-visceral ceCT images with renal tumors: assessment, comparison and improvement
    Medical Image Analysis, 2023  

  • R. Kips, R. Jiang, S. Ba, B. Duke, M. Perrot, P. Gori, I. Bloch
    Real-time Virtual-Try-On from a Single Example Image through Deep Inverse Graphics and Learned Differentiable Renderers
    Computer Graphics Forum (EuroGraphics), 2022  

  • A. Routier, N. Burgos, M. Díaz, M. Bacci, S. Bottani, O. El-Rifai, S. Fontanella, P. Gori, ..., M.-O. Habert, S. Durrleman, O. Colliot
    Clinica: an open source software platform for reproducible clinical neuroscience studies
    Frontiers in Neuroinformatics, 2021  

  • M. Zanello, R. Carron, S. Peeters, P. Gori, A. Roux, I. Bloch, C. Oppenheim, J. Pallud
    Automated neurosurgical stereotactic planning for intraoperative use. A comprehensive review of the literature and perspectives
    Neurosurgical Review, 2020  

  • C. Mercier, S. Rousseau, P. Gori, I. Bloch, T. Boubekeur
    QFib: Fast and Efficient Brain Tractogram Compression
    Neuroinformatics, 2020  

  • A. Roux, P. Roca, M. Edjali-Goujon, K. Sato, M. Zanello, E. Dezamis, P. Gori, S. Lion, A. Fleury, F. Dhermain, J-F Meder, E. Lechapt-Zalcman, F. Chretien, P. Varlet, C. Oppenheim, J. Pallud
    MRI atlas of IDH-wildtype supratentorial glioblastoma: probabilistic maps of phenotype, management, and outcomes
    Radiology, 2019  

  • A. Virzi, C. Muller, J.B. Marret, E. Mille, L. Berteloot, D. Grévent, N. Boddaert, P. Gori, S. Sarnacki, I. Bloch
    Comprehensive Review of 3D Segmentation Software Tools for MRI Usable for Pelvic Surgery Planning
    Journal of Digital Imaging, 2019  

  • C. Muller, E. Mille, A. Virzi, J.B. Marret, Q. Peyrot, A. Delmonte, L. Berteloot, P. Gori, T. Blanc, D. Grevent, N. Boddaert, I. Bloch, S. Sarnacki
    Integrating tractography in pelvic surgery: a proof of concept
    Journal of Pediatric Surgery Case Reports, 2019  

  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, A. Routier, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    Double diffeomorphism: combining morphometry and structural connectivity analysis
    IEEE Transactions on Medical Imaging, 2018  

  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    A Bayesian Framework for Joint Morphometry of Surface and Curve meshes in Multi-Object Complexes
    Medical Image Analysis, 35, pp.458-474, 2017  

  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, F. De Vico Fallani, M. Chavez, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    Parsimonious Approximation of Streamline Trajectories in White Matter Fiber Bundles
    IEEE Transactions on Medical Imaging, 35(12), pp.2609-2619, 2016  


Conference Articles

  • R. Louiset, E. Duchesnay, A. Grigis, P. Gori
    Separating common from salient patterns with Contrastive Representation Learning
    ICLR, 2024  

  • F. Carton, R. Louiset, P. Gori
    Double InfoGAN for Contrastive Analysis
    AISTATS, 2024  

  • P. Auriau, A. Grigis, B. Dufumier, R. Louiset1, J. Chavas, P. Gori, JF Mangin, E. Duchesnay
    Supervised diagnosis prediction from cortical sulci: toward the discovery of neurodevelopmental biomarkers in mental disorders
    IEEE ISBI, 2024  

  • I. B.G. Mounime, W. Lee, T. Marin, P.K. Han, Y. Djebra, S.V. Eslahi, P. Gori, E. Angelini, G. El Fakhri, C. Ma
    Sparsity Constrained Linear Tangent Space Alignment Model (sLTSA) for 3D Cardiac Extracellular Volume Mapping
    IEEE ISBI, 2024  

  • E. Sarfati, A. Bône, M.-M. Rohé, P. Gori, I. Bloch
    Weakly-supervised positional contrastive learning: application to cirrhosis classification
    MICCAI, 2023  

  • C. Ruppli, P. Gori, R. Ardon, I. Bloch
    Decoupled conditional contrastive learning with variable metadata for prostate lesion detection
    MILLanD workshop (MICCAI), 2023 (Oral)  

  • R. Vétil, C. Abi-Nader, A. Bône, M.-P. Vullierme, M.-M. Rohé, P. Gori, I. Bloch
    Non-Redundant Combination of Hand-Crafted and Deep Learning Radiomics: Application to the Early Detection of Pancreatic Cancer
    CaPTion workshop (MICCAI), 2023  

  • B. Dufumier, C. A. Barbano, R. Louiset, E. Duchesnay, P. Gori
    Integrating Prior Knowledge in Contrastive Learning with Kernel
    ICML, 2023  

  • R. Louiset, E. Duchesnay, A. Grigis, B. Dufumier, P. Gori
    SepVAE: a contrastive VAE to separate pathological patterns from healthy ones
    IMLH workshop (ICML), 2023  

  • C. A. Barbano, B. Dufumier, E. Tartaglione, M. Grangetto, P. Gori
    Unbiased Supervised Contrastive Learning
    ICLR, 2023  

  • C. A. Barbano, B. Dufumier, E. Duchesnay, M. Grangetto, P. Gori
    Contrastive learning for regression in multi-site brain age prediction
    IEEE ISBI, 2023  

  • E. Sarfati, A. Bône, M.-M. Rohé, P. Gori, I. Bloch
    Learning to diagnose cirrhosis from radiological and histological labels with joint self and weakly-supervised pretraining strategies
    IEEE ISBI, 2023 (Oral)  

  • G. La Barbera, H. Boussaid, F. Maso, S. Sarnacki, L. Rouet, P. Gori, I. Bloch
    Anatomically constrained CT image translation for heterogeneous blood vessel segmentation
    BMVC, 2022  

  • M. Riva, P. Gori, F. Yger, I. Bloch
    Is the U-Net Directional-Relationship Aware?
    ICIP, 2022  

  • C. Ruppli, P. Gori, R. Ardon, I. Bloch
    Optimizing transformations for contrastive learning in a differentiable framework
    MILLanD workshop (MICCAI), 2022  

  • R. Vétil, C. Abi-Nader, A. Bône, M.P. Vullierme, M.M. Rohé, P. Gori, I. Bloch
    Learning shape distributions from large databases of healthy organs: applications to zero-shot and few-shot abnormal pancreas detection
    MICCAI, 2022 (Student Travel Award)  

  • A. François, M. Maillard, C. Oppenheim, J. Pallud, I. Bloch, P. Gori, J. Glaunès
    Weighted Metamorphosis for registration of images with different topologies
    WBIR, 2022 (Best Paper Award)  

  • M. Maillard, A. François, J. Glaunès, I. Bloch, P. Gori
    A Deep Residual Learning Implementation of Metamorphosis
    IEEE ISBI, 2022  

  • R. Vétil, A. Bône, M.P. Vullierme, M.M. Rohé, P. Gori, I. Bloch
    Improving The Automatic Segmentation Of Elongated Organs Using Geometrical Priors
    IEEE ISBI, 2022  

  • R. Kips, P.-A. Bokaris, M. Perrot, P. Gori, I. Bloch
    Hair Color Digitization through Imaging and Deep Inverse Graphics
    Electronic Imaging (EI), 2022  

  • B. Dufumier, P. Gori, J. Victor, A. Grigis, E. Duchesnay
    Conditional Alignment and Uniformity for Contrastive Learning with Continuous Proxy Labels
    MedNeurIPS, 2021 (Oral)  

  • R. Louiset, P. Gori, B. Dufumier, J. Houenou, A. Grigis, E. Duchesnay
    UCSL : A Machine Learning Expectation-Maximization framework for Unsupervised Clustering driven by Supervised Learning
    ECML/PKDD, 2021  

  • B. Dufumier, P. Gori, J. Victor, A. Grigis, E. Duchesnay
    Contrastive Learning with Continuous Proxy Meta-Data for 3D MRI Classification
    MICCAI, 2021  

  • R. Kips, R. Jiang, S. Ba, E. Phung, P. Aarabi, P. Gori, M. Perrot, I. Bloch
    Deep Graphics Encoder for Real-Time Video Makeup Synthesis from Example
    CVPR Workshop AI for Content Creation, 2021  

  • A. François, P. Gori, J. Glaunès
    Metamorphic image registration using a semi-Lagrangian scheme
    SEE GSI, 2021  

  • G. Barbera, P. Gori, H. Boussaid, B. Belucci, A. Delmonte, J. Goulin, S. Sarnacki, L. Rouet, I. Bloch
    Automatic size and pose homogenization with Spatial Transformer Network to improve and accelerate pediatric segmentation
    IEEE ISBI, 2021  

  • M. Hu, M. Maillard, Y. Zhang, T. Ciceri, G. Barbera, I. Bloch, P. Gori
    Knowledge distillation from multi-modal to mono-modal segmentation networks
    MICCAI, 2020  

  • R. Kips, P. Gori, M. Perrot, I. Bloch
    CA-GAN: Weakly Supervised Color Aware GAN for Controllable Makeup Transfer
    AIM (ECCV Workshop), 2020  

  • M. Riva, F. Yger, P. Gori, R. Cesar, I. Bloch
    Template-Based Graph Clustering
    GEM (ECML-PKDD 2020 Workshop), 2020   (Oral)  

  • E. Olivetti, P. Gori, P. Astolfi, G. Bertò, P. Avesani
    Nonlinear Alignment of Whole Tractograms with the Linear Assignment Problem
    WBIR, 2020  

  • J. Feydy, P. Roussillon, A. Trouvé, P. Gori
    Fast and Scalable Optimal Transport for Brain Tractograms
    MICCAI, 2019   (Poster)  

  • P. Roussillon, J.M. Thiery, I. Bloch, P. Gori
    Appariement difféomorphique robuste de faisceaux neuronaux
    GRETSI, 2019   (Poster)  

  • A. Delmonte, C. Mercier, J. Pallud, I. Bloch, P. Gori
    White matter multi-resolution segmentation using fuzzy set theory
    IEEE ISBI, 2019   (Poster)  

  • C. Mercier, P. Gori, D. Rohmer, M-P. Cani, T. Boubekeur, J-M. Thiery, I. Bloch
    Progressive and Efficient Multi-Resolution Representations for Brain Tractograms
    EG VCBM, Eurographics Workshop, 2018   (Oral)  

  • A. Virzi, P. Gori, C. Muller, E. Mille, Q. Peyrot, L. Berteloot, N. Boddaert, S. Sarnacki, I. Bloch
    Segmentation of pelvic vessels in pediatric MRI using a patch-based deep learning approach
    PIPPI MICCAI Workshop, Springer (LNCS), 2018   (Oral)  

  • K. Kumar, P. Gori, B. Charlier, S. Durrleman, O. Colliot, C. Desrosiers
    White matter fiber segmentation using functional varifolds
    MICCAI Workshop, Springer (LNCS), 2017   (Oral)  

  • E. Olivetti, G. Berto, P. Gori, N. Sharmin, P. Avesani
    Comparison of distances for supervised segmentation of white matter tractography
    PRNI, IEEE, 2017   (Oral)  

  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, A. Routier, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    Joint Morphometry of Fiber Tracts and Gray Matter Structures Using Double Diffeomorphisms
    IPMI, Springer (LNCS), 2015   (Oral - Acceptance rate: ~5%)  

  • P. Gori, O. Colliot, L. Marrakchi-Kacem, Y. Worbe, F.D.V. Fallani, M. Chavez, S. Lecomte, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    A Prototype Representation to Approximate White Matter Bundles with Weighted Currents
    MICCAI, Springer (LNCS), 2014   (Poster - Acceptance rate: ~30%)  

  • A. Routier, P. Gori, A.B. Graciano Fouquier, S. Lecomte, O. Colliot, S. Durrleman
    Evaluation of morphometric descriptors of deep brain structures for the automatic classification of patients with Alzheimer’s disease...
    MICCAI Challenge CADDementia, 2014   (Oral)  

  • P. Gori, O. Colliot, Y. Worbe, L. Marrakchi-Kacem, S. Lecomte, C. Poupon, A. Hartmann, N. Ayache, S. Durrleman
    Bayesian Atlas Estimation for the Variability Analysis of Shape Complexes
    MICCAI, Springer (LNCS), 2013   (Poster - Acceptance rate: ~32%)  

  • T. Ingeman-Nielsen, S. Tomaskovicova, S. H. Larsen, S. F. Aparicio, P. Gori
    Surface geophysical measurements for locating and mapping ice-wedges
    Cold Regions Engineering, 2012   (Poster)  

  • T. Ingeman-Nielsen, P. Gori, S. Tomaskovicova
    An Optimization Algorithm For Interpreting Thermal Parameters For Frozen Soils With Significant Unfrozen Water Content
    Conference on Permafrost, 2012   (Poster)