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Publications of year 2020

Books and proceedings

  1. Xavier Pennec, Stephan Sommer, and Tom Fletcher. Riemannian Geometric Statistics in Medical Image Analysis. Elsevier, 2020.
    @book{pennec:hal-02341896,
    TITLE = {{Riemannian Geometric Statistics in Medical Image Analysis}},
    AUTHOR = {Pennec, Xavier and Sommer, Stephan and Fletcher, Tom},
    url-hal= {https://hal.inria.fr/hal-02341896},
    PUBLISHER = {{Elsevier}},
    YEAR = {2020},
    DOI = {10.1016/C2017-0-01561-6},
    HAL_ID = {hal-02341896},
    HAL_VERSION = {v1},
    
    }
    


Thesis

  1. Wen Wei. Learning Brain Alterations in Multiple Sclerosis from Multimodal Neuroimaging Data. Theses, Université Côte d'Azur ; INRIA Sophia Antipolis - Méditerranée, June 2020. Keyword(s): Multiple Sclerosis, PET Imaging, MR Imaging, Brain Alterations, Deep Learning, Convolutional Neural Networks (CNN), Generative Adversarial Network (GAN), Image Synthesis, Missing MRI Sequences, Missing Modalities, Sclérose en Plaques, IRM, TEP, Apprentissage en Profondeur, Altérations Cérébrales, Modalités Manquantes, Séquences IRM Manquantes, Réseau de Neurones Convolutifs (CNN), Réseaux Antagonistes Génératifs (GAN), Synthèse d'images.
    @phdthesis{wei:tel-02862395,
    TITLE = {{Learning Brain Alterations in Multiple Sclerosis from Multimodal Neuroimaging Data}},
    AUTHOR = {Wei, Wen},
    url-hal= {https://hal.inria.fr/tel-02862395},
    SCHOOL = {{Universit{\'e} C{\^o}te d'Azur ; INRIA Sophia Antipolis - M{\'e}diterran{\'e}e}},
    YEAR = {2020},
    MONTH = Jun,
    KEYWORDS = {Multiple Sclerosis ; PET Imaging ; MR Imaging ; Brain Alterations ; Deep Learning ; Convolutional Neural Networks (CNN) ; Generative Adversarial Network (GAN) ; Image Synthesis ; Missing MRI Sequences ; Missing Modalities ; Scl{\'e}rose en Plaques ; IRM ; TEP ; Apprentissage en Profondeur ; Alt{\'e}rations C{\'e}r{\'e}brales ; Modalit{\'e}s Manquantes ; S{\'e}quences IRM Manquantes ; R{\'e}seau de Neurones Convolutifs (CNN) ; R{\'e}seaux Antagonistes G{\'e}n{\'e}ratifs (GAN) ; Synth{\`e}se d'images},
    TYPE = {Theses},
    PDF = {https://hal.inria.fr/tel-02862395/file/thesis-wen-2020-06-09_fr.pdf},
    HAL_ID = {tel-02862395},
    HAL_VERSION = {v1},
    
    }
    


Articles in journal, book chapters

  1. Emmanuel Chevallier and Nicolas Guigui. A Bi-Invariant Statistical Model Parametrized by Mean and Covariance on Rigid Motions. Entropy, 22(4):432, 2020. Keyword(s): differential of the exponential, Euclidean groups, rigid motions, wrapped distributions, sampling, density estimation, moment-matching estimator.
    @article{chevallier:hal-02568245,
    TITLE = {{A Bi-Invariant Statistical Model Parametrized by Mean and Covariance on Rigid Motions}},
    AUTHOR = {Chevallier, Emmanuel and Guigui, Nicolas},
    url-hal= {https://hal.archives-ouvertes.fr/hal-02568245},
    JOURNAL = {{Entropy}},
    PUBLISHER = {{MDPI}},
    VOLUME = {22},
    NUMBER = {4},
    PAGES = {432},
    YEAR = {2020},
    DOI = {10.3390/e22040432},
    KEYWORDS = {differential of the exponential ; Euclidean groups ; rigid motions ; wrapped distributions ; sampling ; density estimation ; moment-matching estimator},
    PDF = {https://hal.archives-ouvertes.fr/hal-02568245/file/SEnHAL_Chevallier_Guigui.pdf},
    HAL_ID = {hal-02568245},
    HAL_VERSION = {v1},
    
    }
    


  2. James S Duncan, Michel F Insana, and Nicholas Ayache. Biomedical Imaging and Analysis In the Age of Big Data and Deep Learning. Proceedings of the IEEE, 14:3-10, January 2020.
    @article{duncan:hal-02395429,
    TITLE = {{Biomedical Imaging and Analysis In the Age of Big Data and Deep Learning}},
    AUTHOR = {Duncan, James S and Insana, Michel F and Ayache, Nicholas},
    url-hal= {https://hal.archives-ouvertes.fr/hal-02395429},
    JOURNAL = {{Proceedings of the IEEE}},
    PUBLISHER = {{Institute of Electrical and Electronics Engineers}},
    VOLUME = {14},
    PAGES = {3-10},
    YEAR = {2020},
    MONTH = Jan,
    PDF = {https://hal.archives-ouvertes.fr/hal-02395429/file/Proceedings_of_IEEE_Editors_Overview_Article-10.pdf},
    HAL_ID = {hal-02395429},
    HAL_VERSION = {v2},
    
    }
    


  3. Pawel Mlynarski, Hervé Delingette, Hamza A Alghamdi, Pierre-Yves Bondiau, and Nicholas Ayache. Anatomically consistent CNN-based segmentation of organs-at-risk in cranial radiotherapy. Journal of Medical Imaging, 7(1):1-21, February 2020. Keyword(s): segmentation, organs at risk, Convolutional Neural Networks, radiotherapy, MRI.
    @article{mlynarski:hal-02181181,
    TITLE = {{Anatomically consistent CNN-based segmentation of organs-at-risk in cranial radiotherapy}},
    AUTHOR = {Mlynarski, Pawel and Delingette, Herv{\'e} and Alghamdi, Hamza A and Bondiau, Pierre-Yves and Ayache, Nicholas},
    url-hal= {https://hal.inria.fr/hal-02181181},
    JOURNAL = {{Journal of Medical Imaging}},
    PUBLISHER = {{SPIE Digital Library}},
    VOLUME = {7},
    NUMBER = {1},
    PAGES = {1--21},
    YEAR = {2020},
    MONTH = Feb,
    DOI = {10.1117/1.JMI.7.1.014502},
    KEYWORDS = {segmentation ; organs at risk ; Convolutional Neural Networks ; radiotherapy ; MRI},
    PDF = {https://hal.inria.fr/hal-02181181/file/article.pdf},
    HAL_ID = {hal-02181181},
    HAL_VERSION = {v2},
    
    }
    


  4. Raphaël Sivera, Nicolas Capet, Valeria Manera, Roxane Fabre, Marco Lorenzi, Hervé Delingette, Xavier Pennec, Nicholas Ayache, and Philippe Robert. Voxel-based assessments of treatment effects on longitudinal brain changes in the Multidomain Alzheimer Preventive Trial cohort. Neurobiology of Aging, 94:50-59, October 2020. Keyword(s): Multidomain intervention, Clinical trial, Subjective memory complaint, Deformation-based morphometry.
    @article{sivera:hal-02166357,
    TITLE = {{Voxel-based assessments of treatment effects on longitudinal brain changes in the Multidomain Alzheimer Preventive Trial cohort}},
    AUTHOR = {Sivera, Rapha{\"e}l and Capet, Nicolas and Manera, Valeria and Fabre, Roxane and Lorenzi, Marco and Delingette, Herv{\'e} and Pennec, Xavier and Ayache, Nicholas and Robert, Philippe},
    url-hal= {https://hal.inria.fr/hal-02166357},
    JOURNAL = {{Neurobiology of Aging}},
    PUBLISHER = {{Elsevier}},
    VOLUME = {94},
    PAGES = {50-59},
    YEAR = {2020},
    MONTH = Oct,
    DOI = {10.1016/j.neurobiolaging.2019.11.020},
    KEYWORDS = {Multidomain intervention ; Clinical trial ; Subjective memory complaint ; Deformation-based morphometry},
    PDF = {https://hal.inria.fr/hal-02166357/file/paper-mapt-final.pdf},
    HAL_ID = {hal-02166357},
    HAL_VERSION = {v2},
    
    }
    


  5. Nicholas Ayache. Medical Imaging in the Age of Artificial Intelligence. In Nordlinger B., Villani C., and Rus D., editors, Healthcare and Artificial Intelligence, pages 89-91. Springer International Publishing, March 2020.
    @incollection{ayache:hal-02522507,
    TITLE = {{Medical Imaging in the Age of Artificial Intelligence}},
    AUTHOR = {Ayache, Nicholas},
    url-hal= {https://hal.inria.fr/hal-02522507},
    BOOKTITLE = {{Healthcare and Artificial Intelligence}},
    EDITOR = {Nordlinger B. and Villani C. and Rus D.},
    PUBLISHER = {{Springer International Publishing}},
    PAGES = {89-91},
    YEAR = {2020},
    MONTH = Mar,
    DOI = {10.1007/978-3-030-32161-1\_13},
    PDF = {https://hal.inria.fr/hal-02522507/file/Ayache-Nordlinger2020-AuthorVersion.pdf},
    HAL_ID = {hal-02522507},
    HAL_VERSION = {v1},
    
    }
    


  6. Nina Miolane, Loïc Devilliers, and Xavier Pennec. Bias on estimation in quotient space and correction methods: Applications to statistics on organ shapes. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 9, pages 343-376. Elsevier, 2020.
    @incollection{miolane:hal-02342155,
    TITLE = {{Bias on estimation in quotient space and correction methods: Applications to statistics on organ shapes}},
    AUTHOR = {Miolane, Nina and Devilliers, Lo{\"i}c and Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02342155},
    BOOKTITLE = {{Riemannian Geometric Statistics in Medical Image Analysis}},
    PUBLISHER = {{Elsevier}},
    NUMBER = {Chap. 9},
    PAGES = {343-376},
    YEAR = {2020},
    DOI = {10.1016/B978-0-12-814725-2.00017-0},
    PDF = {https://hal.inria.fr/hal-02342155/file/chapterQuotient.pdf},
    HAL_ID = {hal-02342155},
    HAL_VERSION = {v1},
    
    }
    


  7. Xavier Pennec. Advances in Geometric Statistics for Manifold Dimension Reduction. In Handbook of Variational Methods for Nonlinear Geometric Data, pages 339-359. Springer International Publishing, April 2020.
    @incollection{pennec:hal-02560938,
    TITLE = {{Advances in Geometric Statistics for Manifold Dimension Reduction}},
    AUTHOR = {Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02560938},
    BOOKTITLE = {{Handbook of Variational Methods for Nonlinear Geometric Data}},
    PUBLISHER = {{Springer International Publishing}},
    PAGES = {339-359},
    YEAR = {2020},
    MONTH = Apr,
    DOI = {10.1007/978-3-030-31351-7\_11},
    PDF = {https://hal.inria.fr/hal-02560938/file/XP_GeomStats_ManifoldReductionPCA.pdf},
    HAL_ID = {hal-02560938},
    HAL_VERSION = {v1},
    
    }
    


  8. Xavier Pennec. Manifold-valued image processing with SPD matrices. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 3, pages 75-134. Elsevier, 2020.
    @incollection{pennec:hal-02341958,
    TITLE = {{Manifold-valued image processing with SPD matrices}},
    AUTHOR = {Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02341958},
    BOOKTITLE = {{Riemannian Geometric Statistics in Medical Image Analysis}},
    PUBLISHER = {{Elsevier}},
    NUMBER = {Chap. 3},
    PAGES = {75-134},
    YEAR = {2020},
    DOI = {10.1016/B978-0-12-814725-2.00010-8},
    PDF = {https://hal.inria.fr/hal-02341958/file/chapter3.pdf},
    HAL_ID = {hal-02341958},
    HAL_VERSION = {v1},
    
    }
    


  9. Xavier Pennec and Marco Lorenzi. Beyond Riemannian geometry: The affine connection setting for transformation groups. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 5, pages 169-229. Elsevier, 2020.
    @incollection{pennec:hal-02342137,
    TITLE = {{Beyond Riemannian geometry: The affine connection setting for transformation groups}},
    AUTHOR = {Pennec, Xavier and Lorenzi, Marco},
    url-hal= {https://hal.inria.fr/hal-02342137},
    BOOKTITLE = {{Riemannian Geometric Statistics in Medical Image Analysis}},
    PUBLISHER = {{Elsevier}},
    NUMBER = {Chap. 5},
    PAGES = {169-229},
    YEAR = {2020},
    DOI = {10.1016/B978-0-12-814725-2.00012-1},
    PDF = {https://hal.inria.fr/hal-02342137/file/chapter5.pdf},
    HAL_ID = {hal-02342137},
    HAL_VERSION = {v1},
    
    }
    


  10. Stefan Sommer, Tom Fletcher, and Xavier Pennec. Introduction to differential and Riemannian geometry. In Riemannian Geometric Statistics in Medical Image Analysis, number Chap. 1, pages 3-37. Elsevier, 2020.
    @incollection{sommer:hal-02341901,
    TITLE = {{Introduction to differential and Riemannian geometry}},
    AUTHOR = {Sommer, Stefan and Fletcher, Tom and Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02341901},
    BOOKTITLE = {{Riemannian Geometric Statistics in Medical Image Analysis}},
    PUBLISHER = {{Elsevier}},
    NUMBER = {Chap. 1},
    PAGES = {3-37},
    YEAR = {2020},
    DOI = {10.1016/b978-0-12-814725-2.00008-x},
    PDF = {https://hal.inria.fr/hal-02341901/file/chapter1.pdf},
    HAL_ID = {hal-02341901},
    HAL_VERSION = {v1},
    
    }
    


Conference articles

  1. Nina Miolane, Nicolas Guigui, Hadi Zaatiti, Christian Shewmake, Hatem Hajri, Daniel Brooks, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Yann Cabanes, Thomas Gerald, Paul Chauchat, Bernhard Kainz, Claire Donnat, Susan Holmes, and Xavier Pennec. Introduction to Geometric Learning in Python with Geomstats. In Meghann Agarwal, Chris Calloway, Dillon Niederhut, and David Shupe, editors, SciPy 2020 - 19th Python in Science Conference, Austin, Texas, United States, pages 48-57, July 2020. Keyword(s): Index Terms-differential geometry, statistics, manifold, machine learning.
    @inproceedings{miolane:hal-02908006,
    TITLE = {{Introduction to Geometric Learning in Python with Geomstats}},
    AUTHOR = {Miolane, Nina and Guigui, Nicolas and Zaatiti, Hadi and Shewmake, Christian and Hajri, Hatem and Brooks, Daniel and Le Brigant, Alice and Mathe, Johan and Hou, Benjamin and Thanwerdas, Yann and Heyder, Stefan and Peltre, Olivier and Koep, Niklas and Cabanes, Yann and Gerald, Thomas and Chauchat, Paul and Kainz, Bernhard and Donnat, Claire and Holmes, Susan and Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02908006},
    BOOKTITLE = {{SciPy 2020 - 19th Python in Science Conference}},
    ADDRESS = {Austin, Texas, United States},
    EDITOR = {Meghann Agarwal and Chris Calloway and Dillon Niederhut and David Shupe},
    PAGES = {48-57},
    YEAR = {2020},
    MONTH = Jul,
    DOI = {10.25080/Majora-342d178e-007},
    KEYWORDS = {Index Terms-differential geometry ; statistics ; manifold ; machine learning},
    PDF = {https://hal.inria.fr/hal-02908006/file/geomstats.pdf},
    HAL_ID = {hal-02908006},
    HAL_VERSION = {v1},
    
    }
    


  2. Pamela Moceri, Nicolas Duchateau, N Dursent, Xavier Iriart, Sébastien Hascoet, D Baudouy, Emile Ferrari, and Maxime Sermesant. Right ventricular remodelling in CHD-PAH patients using 3D speckle tracking. In JESFC 2020 - 30es Journées Européennes de la Société Française de Cardiologie, volume 12 of Archives of Cardiovascular Diseases Supplements, Paris, France, pages 163-4, January 2020.
    @inproceedings{moceri:hal-02445303,
    TITLE = {{Right ventricular remodelling in CHD-PAH patients using 3D speckle tracking}},
    AUTHOR = {Moceri, Pamela and Duchateau, Nicolas and Dursent, N and Iriart, Xavier and Hascoet, S{\'e}bastien and Baudouy, D and Ferrari, Emile and Sermesant, Maxime},
    url-hal= {https://hal.archives-ouvertes.fr/hal-02445303},
    BOOKTITLE = {{JESFC 2020 - 30es Journ{\'e}es Europ{\'e}ennes de la Soci{\'e}t{\'e} Fran{\c c}aise de Cardiologie}},
    ADDRESS = {Paris, France},
    SERIES = {Archives of Cardiovascular Diseases Supplements},
    VOLUME = {12},
    PAGES = {163-4},
    YEAR = {2020},
    MONTH = Jan,
    HAL_ID = {hal-02445303},
    HAL_VERSION = {v1},
    
    }
    


  3. Zihao Wang, Clair Vandersteen, Thomas Demarcy, Dan Gnansia, Charles Raffaelli, Nicolas Guevara, and Hervé Delingette. A Deep Learning based Fast Signed Distance Map Generation. In Medical Imaging with Deep Learning, Montréal, Canada, July 2020.
    @inproceedings{wang:hal-02570026,
    TITLE = {{A Deep Learning based Fast Signed Distance Map Generation}},
    AUTHOR = {Wang, Zihao and Vandersteen, Clair and Demarcy, Thomas and Gnansia, Dan and Raffaelli, Charles and Guevara, Nicolas and Delingette, Herv{\'e}},
    url-hal= {https://hal.inria.fr/hal-02570026},
    BOOKTITLE = {{Medical Imaging with Deep Learning}},
    ADDRESS = {Montr{\'e}al, Canada},
    YEAR = {2020},
    MONTH = Jul,
    PDF = {https://hal.inria.fr/hal-02570026/file/MIDL2020__A_Deep_Learning_based_Fast_Signed_Distance_MapGeneration%20%281%29.pdf},
    HAL_ID = {hal-02570026},
    HAL_VERSION = {v1},
    
    }
    


Patents, standards

  1. Julian Krebs and Tommaso Mansi. Method and System for Deep Motion Model Learning in Medical Images. US20200090345A1, United States, March 2020.
    @patent{krebs:hal-02536459,
    TITLE = {{Method and System for Deep Motion Model Learning in Medical Images}},
    AUTHOR = {Krebs, Julian and Mansi, Tommaso},
    url-hal= {https://hal.archives-ouvertes.fr/hal-02536459},
    NUMBER = {US20200090345A1},
    ADDRESS = {United States},
    YEAR = {2020},
    MONTH = Mar,
    HAL_ID = {hal-02536459},
    HAL_VERSION = {v1},
    
    }
    


Miscellaneous

  1. Nicolas Guigui and Xavier Pennec. Numerical Accuracy of Ladder Schemes for Parallel Transport on Manifolds. Note: Working paper or preprint, July 2020. Keyword(s): Parallel Transport, Riemannian Geometry, Numerical Methods.
    @unpublished{guigui:hal-02894783,
    TITLE = {{Numerical Accuracy of Ladder Schemes for Parallel Transport on Manifolds}},
    AUTHOR = {Guigui, Nicolas and Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02894783},
    NOTE = {working paper or preprint},
    YEAR = {2020},
    MONTH = Jul,
    KEYWORDS = {Parallel Transport ; Riemannian Geometry ; Numerical Methods},
    PDF = {https://hal.inria.fr/hal-02894783/file/main.pdf},
    HAL_ID = {hal-02894783},
    HAL_VERSION = {v1},
    
    }
    


  2. Alice Le Brigant, Nicolas Guigui, Sana Rebbah, and Stéphane Puechmorel. Classifying histograms of medical data using information geometry of beta distributions. Note: Working paper or preprint, June 2020. Keyword(s): histogram analysis, clustering, medical imaging, Information geometry, classification.
    @unpublished{lebrigant:hal-02671122,
    TITLE = {{Classifying histograms of medical data using information geometry of beta distributions}},
    AUTHOR = {Le Brigant, Alice and Guigui, Nicolas and Rebbah, Sana and Puechmorel, St{\'e}phane},
    url-hal= {https://hal.archives-ouvertes.fr/hal-02671122},
    NOTE = {working paper or preprint},
    YEAR = {2020},
    MONTH = Jun,
    KEYWORDS = {histogram analysis ; clustering ; medical imaging ; Information geometry ; classification},
    PDF = {https://hal.archives-ouvertes.fr/hal-02671122/file/info_geom_beta.pdf},
    HAL_ID = {hal-02671122},
    HAL_VERSION = {v1},
    
    }
    


  3. Nina Miolane, Alice Le Brigant, Johan Mathe, Benjamin Hou, Nicolas Guigui, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Hadi Zaatiti, Hatem Hajri, Yann Cabanes, Thomas Gerald, Paul Chauchat, Christian Shewmake, Bernhard Kainz, Claire Donnat, Susan Holmes, and Xavier Pennec. Geomstats: A Python Package for Riemannian Geometry in Machine Learning. Note: Working paper or preprint, April 2020.
    @unpublished{miolane:hal-02536154,
    TITLE = {{Geomstats: A Python Package for Riemannian Geometry in Machine Learning}},
    AUTHOR = {Miolane, Nina and Le Brigant, Alice and Mathe, Johan and Hou, Benjamin and Guigui, Nicolas and Thanwerdas, Yann and Heyder, Stefan and Peltre, Olivier and Koep, Niklas and Zaatiti, Hadi and Hajri, Hatem and Cabanes, Yann and Gerald, Thomas and Chauchat, Paul and Shewmake, Christian and Kainz, Bernhard and Donnat, Claire and Holmes, Susan and Pennec, Xavier},
    url-hal= {https://hal.inria.fr/hal-02536154},
    NOTE = {working paper or preprint},
    YEAR = {2020},
    MONTH = Apr,
    PDF = {https://hal.inria.fr/hal-02536154/file/main.pdf},
    HAL_ID = {hal-02536154},
    HAL_VERSION = {v1},
    
    }
    



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Last modified: Fri Aug 7 12:30:04 2020
Author: epione-publi.

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