Publications of year 2023

Thesis

Yann Fraboni. Reliability and robustness of federated learning in practical applications. Theses, Université Côte d'Azur, May 2023.

Keyword(s): Federated learning, Heterogeneous data, Privacy, Distributed optimization, Bias, Apprentissage fédéré, Données hétérogènes, Protection des données, Optimisation distribuée, Biais.

@phdthesis{fraboni:tel-04141520,
TITLE = {{Reliability and robustness of federated learning in practical applications}},
AUTHOR = {Fraboni, Yann},
url-hal= {https://theses.hal.science/tel-04141520},
NUMBER = {2023COAZ4033},
SCHOOL = {{Universit{\'e} C{\^o}te d'Azur}},
YEAR = {2023},
MONTH = May,
KEYWORDS = {Federated learning ; Heterogeneous data ; Privacy ; Distributed optimization ; Bias ; Apprentissage f{\'e}d{\'e}r{\'e} ; Donn{\'e}es h{\'e}t{\'e}rog{\`e}nes ; Protection des donn{\'e}es ; Optimisation distribu{\'e}e ; Biais},
TYPE = {Theses},
PDF = {https://theses.hal.science/tel-04141520/file/2023COAZ4033.pdf},
HAL_ID = {tel-04141520},
HAL_VERSION = {v1},

}

Dimitri Hamzaoui. AI-based diagnosis of prostate cancer from multiparametric MRI. Theses, Université Côte d'Azur, June 2023.

Keyword(s): Machine learning, Prostate-cancer, Inter-expert variability, Segmentation, Consensus, Medical imaging, Artificial intelligence, Apprentissage profond, Prostate-cancer, Variabilité inter-expert, Segmentation, Consensus, Imagerie médicale, Intelligence artificielle.

@phdthesis{hamzaoui:tel-04166332,
TITLE = {{AI-based diagnosis of prostate cancer from multiparametric MRI}},
AUTHOR = {Hamzaoui, Dimitri},
url-hal= {https://hal.science/tel-04166332},
NUMBER = {2023COAZ4044},
SCHOOL = {{Universit{\'e} C{\^o}te d'Azur}},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {Machine learning ; Prostate-cancer ; Inter-expert variability ; Segmentation ; Consensus ; Medical imaging ; Artificial intelligence ; Apprentissage profond ; Prostate-cancer ; Variabilit{\'e} inter-expert ; Segmentation ; Consensus ; Imagerie m{\'e}dicale ; Intelligence artificielle},
TYPE = {Theses},
PDF = {https://hal.science/tel-04166332v2/file/2023COAZ4044.pdf},
HAL_ID = {tel-04166332},
HAL_VERSION = {v2},

}

Victoriya Kashtanova. Learning cardiac electrophysiology dynamics with PDE-based physiological constraints for data-driven personalised predictions. Theses, Université Côte d'Azur, June 2023.

Keyword(s): Physics-based learning, Deep learning, Cardiac electrophysiology, Model personalisation, PDE, Simulations, Apprentissage basé sur la physique, Apprentissage profond, Electrophysiologie cardiaque, Personnalisation de modèle, EDP, Simulations.

@phdthesis{kashtanova:tel-04176798,
TITLE = {{Learning cardiac electrophysiology dynamics with PDE-based physiological constraints for data-driven personalised predictions}},
AUTHOR = {Kashtanova, Victoriya},
url-hal= {https://hal.science/tel-04176798},
NUMBER = {2023COAZ4043},
SCHOOL = {{Universit{\'e} C{\^o}te d'Azur}},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {Physics-based learning ; Deep learning ; Cardiac electrophysiology ; Model personalisation ; PDE ; Simulations ; Apprentissage bas{\'e} sur la physique ; Apprentissage profond ; Electrophysiologie cardiaque ; Personnalisation de mod{\`e}le ; EDP ; Simulations},
TYPE = {Theses},
PDF = {https://hal.science/tel-04176798v2/file/2023COAZ4043.pdf},
HAL_ID = {tel-04176798},
HAL_VERSION = {v2},

}

Paul Tourniaire. AI-based selection of imaging and biological markers predictive of therapy response in lung cancer. Theses, Université Côte d'Azur, June 2023.

Keyword(s): Digital pathology, Multiple instance learning, Mixed supervision, Deep learning, Survival analysis, Lung cancer, Immunotherapy, Histopathologie numérique, Apprentissage multi-instance, Supervision mélangée, Apprentissage profond, Analyse de survie, Cancer du poumon, Immunothérapie.

@phdthesis{tourniaire:tel-04189450,
TITLE = {{AI-based selection of imaging and biological markers predictive of therapy response in lung cancer}},
AUTHOR = {Tourniaire, Paul},
url-hal= {https://theses.hal.science/tel-04189450},
NUMBER = {2023COAZ4041},
SCHOOL = {{Universit{\'e} C{\^o}te d'Azur}},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {Digital pathology ; Multiple instance learning ; Mixed supervision ; Deep learning ; Survival analysis ; Lung cancer ; Immunotherapy ; Histopathologie num{\'e}rique ; Apprentissage multi-instance ; Supervision m{\'e}lang{\'e}e ; Apprentissage profond ; Analyse de survie ; Cancer du poumon ; Immunoth{\'e}rapie},
TYPE = {Theses},
PDF = {https://theses.hal.science/tel-04189450v2/file/2023COAZ4041.pdf},
HAL_ID = {tel-04189450},
HAL_VERSION = {v2},

}

Articles in journal, book chapters

Arnaud Berenbaum, Hervé Delingette, Aurélien Maire, Cécile Poret, Claire Hassen-Khodja, Stéphane Bréant, Christel Daniel, Patricia Martel, Lamiae Grimaldi, Marie Frank, Emmanuel Durand, and Florent Besson. Performance of AI-Based Automated Classifications of Whole-Body FDG PET in Clinical Practice: The CLARITI Project. Applied Sciences, 13(9):5281, May 2023.

Keyword(s): FDG PET, artificial intelligence, deep learning, convolutional neural network.

@article{berenbaum:hal-04081046,
TITLE = {{Performance of AI-Based Automated Classifications of Whole-Body FDG PET in Clinical Practice: The CLARITI Project}},
AUTHOR = {Berenbaum, Arnaud and Delingette, Herv{\'e} and Maire, Aur{\'e}lien and Poret, C{\'e}cile and Hassen-Khodja, Claire and Br{\'e}ant, St{\'e}phane and Daniel, Christel and Martel, Patricia and Grimaldi, Lamiae and Frank, Marie and Durand, Emmanuel and Besson, Florent},
url-hal= {https://inria.hal.science/hal-04081046},
JOURNAL = {{Applied Sciences}},
PUBLISHER = {{Multidisciplinary digital publishing institute (MDPI)}},
VOLUME = {13},
NUMBER = {9},
PAGES = {5281},
YEAR = {2023},
MONTH = May,
DOI = {10.3390/app13095281},
KEYWORDS = {FDG PET ; artificial intelligence ; deep learning ; convolutional neural network},
HAL_ID = {hal-04081046},
HAL_VERSION = {v1},

}

Nina Brillat-Savarin, Carine Wu, Laurène Aupin, Camille Thoumin, Dimitri Hamzaoui, and Raphaële Renard-Penna. 3.0 T prostate MRI: Visual assessment of 2D and 3D T2-weighted imaging sequences using PI-QUAL score. European Journal of Radiology, 166:110974, September 2023.

@article{brillatsavarin:hal-04162794,
TITLE = {{3.0 T prostate MRI: Visual assessment of 2D and 3D T2-weighted imaging sequences using PI-QUAL score}},
AUTHOR = {Brillat-Savarin, Nina and Wu, Carine and Aupin, Laur{\`e}ne and Thoumin, Camille and Hamzaoui, Dimitri and Renard-Penna, Rapha{\"e}le},
url-hal= {https://hal.science/hal-04162794},
JOURNAL = {{European Journal of Radiology}},
PUBLISHER = {{Elsevier}},
VOLUME = {166},
PAGES = {110974},
YEAR = {2023},
MONTH = Sep,
DOI = {10.1016/j.ejrad.2023.110974},
HAL_ID = {hal-04162794},
HAL_VERSION = {v1},

}

Hind Dadoun, Hervé Delingette, Anne-Laure Rousseau, Eric de Kerviler, and Nicholas Ayache. Deep Clustering for Abdominal Organ Classification in US imaging. Journal of Medical Imaging, 2023.

Keyword(s): ultrasound imaging, representation learning, deep clustering, semi-supervised learning.

@article{dadoun:hal-03773082,
TITLE = {{Deep Clustering for Abdominal Organ Classification in US imaging}},
AUTHOR = {Dadoun, Hind and Delingette, Herv{\'e} and Rousseau, Anne-Laure and de Kerviler, Eric and Ayache, Nicholas},
url-hal= {https://inria.hal.science/hal-03773082},
JOURNAL = {{Journal of Medical Imaging}},
PUBLISHER = {{SPIE Digital Library}},
YEAR = {2023},
KEYWORDS = {ultrasound imaging ; representation learning ; deep clustering ; semi-supervised learning},
PDF = {https://inria.hal.science/hal-03773082v3/file/soumission_jmi_dadoun_vf.pdf},
HAL_ID = {hal-03773082},
HAL_VERSION = {v3},

}

Nicolas Guigui, Nina Miolane, and Xavier Pennec. Introduction to Riemannian Geometry and Geometric Statistics: from basic theory to implementation with Geomstats. Foundations and Trends in Machine Learning, 16(3):329-493, February 2023.

Keyword(s): Riemannian Geometry, Geometric Statistics, Python Library.

@article{guigui:hal-03766900,
TITLE = {{Introduction to Riemannian Geometry and Geometric Statistics: from basic theory to implementation with Geomstats}},
AUTHOR = {Guigui, Nicolas and Miolane, Nina and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-03766900},
JOURNAL = {{Foundations and Trends in Machine Learning}},
PUBLISHER = {{Now Publishers}},
VOLUME = {16},
NUMBER = {3},
PAGES = {329-493},
YEAR = {2023},
MONTH = Feb,
DOI = {10.1561/2200000098},
KEYWORDS = {Riemannian Geometry ; Geometric Statistics ; Python Library},
PDF = {https://inria.hal.science/hal-03766900v2/file/main-now.pdf},
HAL_ID = {hal-03766900},
HAL_VERSION = {v2},

}

Dimitri Hamzaoui, Sarah Montagne, Raphaële Renard-Penna, Nicholas Ayache, and Hervé Delingette. Morphologically-Aware Consensus Computation via Heuristics-based IterATive Optimization (MACCHIatO). Journal of Machine Learning for Biomedical Imaging, 2(UNSURE 2022 Special Issue):361-389, September 2023.

Keyword(s): Consensus, Distance, Heuristic, Optimization, STAPLE.

@article{hamzaoui:hal-04208018,
TITLE = {{Morphologically-Aware Consensus Computation via Heuristics-based IterATive Optimization (MACCHIatO)}},
AUTHOR = {Hamzaoui, Dimitri and Montagne, Sarah and Renard-Penna, Rapha{\"e}le and Ayache, Nicholas and Delingette, Herv{\'e}},
url-hal= {https://hal.science/hal-04208018},
JOURNAL = {{Journal of Machine Learning for Biomedical Imaging}},
PUBLISHER = {{Melba editors}},
VOLUME = {2},
NUMBER = {UNSURE 2022 Special Issue},
PAGES = {361-389},
YEAR = {2023},
MONTH = Sep,
DOI = {10.59275/j.melba.2023-219c},
KEYWORDS = {Consensus ; Distance ; Heuristic ; Optimization ; STAPLE},
PDF = {https://hal.science/hal-04208018/file/MOJITO_MELBA.pdf},
HAL_ID = {hal-04208018},
HAL_VERSION = {v1},

}

Philipp Harms, Peter W. Michor, Xavier Pennec, and Stefan Sommer. Geometry of Sample Spaces. Differential Geometry and its Applications, 90:102029, October 2023. Note: 29 pages, 1 figure.

@article{harms:hal-02972385,
TITLE = {{Geometry of Sample Spaces}},
AUTHOR = {Harms, Philipp and Michor, Peter W. and Pennec, Xavier and Sommer, Stefan},
url-hal= {https://inria.hal.science/hal-02972385},
NOTE = {29 pages, 1 figure},
JOURNAL = {{Differential Geometry and its Applications}},
PUBLISHER = {{Elsevier}},
VOLUME = {90},
PAGES = {102029},
YEAR = {2023},
MONTH = Oct,
DOI = {10.1016/j.difgeo.2023.102029},
HAL_ID = {hal-02972385},
HAL_VERSION = {v1},

}

Sébastien Molière, Dimitri Hamzaoui, Anna Luzurier, Benjamin Granger, Sarah Montagne, Alexandre Allera, Malek Ezziane, Raphaële Quint, Mehdi Kalai, Nicholas Ayache, Hervé Delingette, and Raphaële Renard-Penna. Reference standard for the evaluation of automatic segmentation algorithms: Quantification of inter observer variability of manual delineation of prostate contour on MRI. Diagnostic and Interventional Imaging, August 2023.

Keyword(s): Artificial intelligence Inter-reader variability Magnetic resonance imaging Prostate Segmentation.

@article{moliere:hal-04185065,
TITLE = {{Reference standard for the evaluation of automatic segmentation algorithms: Quantification of inter observer variability of manual delineation of prostate contour on MRI}},
AUTHOR = {Moli{\`e}re, S{\'e}bastien and Hamzaoui, Dimitri and Luzurier, Anna and Granger, Benjamin and Montagne, Sarah and Allera, Alexandre and Ezziane, Malek and Quint, Rapha{\"e}le and Kalai, Mehdi and Ayache, Nicholas and Delingette, Herv{\'e} and Renard-Penna, Rapha{\"e}le},
url-hal= {https://hal.science/hal-04185065},
JOURNAL = {{Diagnostic and Interventional Imaging}},
PUBLISHER = {{Elsevier}},
YEAR = {2023},
MONTH = Aug,
DOI = {10.1016/j.diii.2023.08.001},
KEYWORDS = {Artificial intelligence Inter-reader variability Magnetic resonance imaging Prostate Segmentation},
HAL_ID = {hal-04185065},
HAL_VERSION = {v1},

}

Yann Thanwerdas and Xavier Pennec. O(n)-invariant Riemannian metrics on SPD matrices. Linear Algebra and its Applications, 661:163-201, March 2023.

Keyword(s): 53B20, Symmetric Positive Definite matrices, Riemannian geometry, Invariance under orthogonal transformations, Families of metrics, Log-Euclidean metric, Affine-invariant metric, Bures-Wasserstein metric, Kernel metrics.

@article{thanwerdas:hal-03338601,
TITLE = {{O(n)-invariant Riemannian metrics on SPD matrices}},
AUTHOR = {Thanwerdas, Yann and Pennec, Xavier},
url-hal= {https://hal.science/hal-03338601},
JOURNAL = {{Linear Algebra and its Applications}},
PUBLISHER = {{Elsevier}},
VOLUME = {661},
PAGES = {163-201},
YEAR = {2023},
MONTH = Mar,
DOI = {10.1016/j.laa.2022.12.009},
KEYWORDS = {53B20 ; Symmetric Positive Definite matrices ; Riemannian geometry ; Invariance under orthogonal transformations ; Families of metrics ; Log-Euclidean metric ; Affine-invariant metric ; Bures-Wasserstein metric ; Kernel metrics},
PDF = {https://hal.science/hal-03338601v3/file/LAA_YT_XP_O_n_invariant_metrics_v3%20%282%29.pdf},
HAL_ID = {hal-03338601},
HAL_VERSION = {v3},

}

Paul Tourniaire, Marius Ilie, Paul Hofman, Nicholas Ayache, and Hervé Delingette. MS-CLAM: Mixed Supervision for the classification and localization of tumors in Whole Slide Images. Medical Image Analysis, 85:102763, 2023.

Keyword(s): Digital Pathology, Mixed Supervision, Deep Learning, Camelyon16, DigestPath2019.

@article{tourniaire:hal-03972289,
TITLE = {{MS-CLAM: Mixed Supervision for the classification and localization of tumors in Whole Slide Images}},
AUTHOR = {Tourniaire, Paul and Ilie, Marius and Hofman, Paul and Ayache, Nicholas and Delingette, Herv{\'e}},
url-hal= {https://inria.hal.science/hal-03972289},
JOURNAL = {{Medical Image Analysis}},
PUBLISHER = {{Elsevier}},
VOLUME = {85},
PAGES = {102763},
YEAR = {2023},
DOI = {10.1016/j.media.2023.102763},
KEYWORDS = {Digital Pathology ; Mixed Supervision ; Deep Learning ; Camelyon16 ; DigestPath2019},
PDF = {https://inria.hal.science/hal-03972289/file/article_MedIA_hal_version.pdf},
HAL_ID = {hal-03972289},
HAL_VERSION = {v1},

}

Zihao Wang, Zhifei Xu, Jiayi He, Herve Delingette, and Jun Fan. Long Short-Term Memory Neural Equalizer. IEEE Transactions on Signal and Power Integrity, 2:13-22, 2023.

@article{wang:hal-04042921,
TITLE = {{Long Short-Term Memory Neural Equalizer}},
AUTHOR = {Wang, Zihao and Xu, Zhifei and He, Jiayi and Delingette, Herve and Fan, Jun},
url-hal= {https://inria.hal.science/hal-04042921},
JOURNAL = {{IEEE Transactions on Signal and Power Integrity}},
VOLUME = {2},
PAGES = {13-22},
YEAR = {2023},
DOI = {10.1109/TSIPI.2023.3242855},
HAL_ID = {hal-04042921},
HAL_VERSION = {v1},

}

Buntheng Ly, Mihaela Pop, Hubert Cochet, Nicolas Duchateau, Declan O'regan, and Maxime Sermesant. Outcome Prediction. In AI and Big Data in Cardiology : A Practical Guide, pages 105-133. Springer International Publishing, May 2023.

@incollection{ly:hal-04212068,
TITLE = {{Outcome Prediction}},
AUTHOR = {Ly, Buntheng and Pop, Mihaela and Cochet, Hubert and Duchateau, Nicolas and O'regan, Declan and Sermesant, Maxime},
url-hal= {https://hal.science/hal-04212068},
BOOKTITLE = {{AI and Big Data in Cardiology : A Practical Guide}},
PUBLISHER = {{Springer International Publishing}},
PAGES = {105-133},
YEAR = {2023},
MONTH = May,
DOI = {10.1007/978-3-031-05071-8\_6},
HAL_ID = {hal-04212068},
HAL_VERSION = {v1},

}

Conference articles

Morten Akhoj, Xavier Pennec, and Stefan Sommer. Tangent phylogenetic PCA. In Scandinavian Conference on Image Analysis 2023, Levi Ski Resort (Lapland), Finland, April 2023.

@inproceedings{akhoj:hal-03842847,
TITLE = {{Tangent phylogenetic PCA}},
AUTHOR = {Akh{{\o}}j, Morten and Pennec, Xavier and Sommer, Stefan},
url-hal= {https://inria.hal.science/hal-03842847},
BOOKTITLE = {{Scandinavian Conference on Image Analysis 2023}},
ADDRESS = {Levi Ski Resort (Lapland), Finland},
YEAR = {2023},
MONTH = Apr,
PDF = {https://inria.hal.science/hal-03842847/file/2208.12730.pdf},
HAL_ID = {hal-03842847},
HAL_VERSION = {v1},

}

Nicolas Cedilnik and Jean-Marc Peyrat. Weighted tissue thickness. In FIMH 2023 - 12th International Conference On Functional Imaging And Modeling Of The Heart, Lecture Notes in Computer Science, Lyon, France, June 2023. Springer.

Keyword(s): Thickness, Thickness measurements, Medical image analysis.

@inproceedings{cedilnik:hal-04111276,
TITLE = {{Weighted tissue thickness}},
AUTHOR = {Cedilnik, Nicolas and Peyrat, Jean-Marc},
url-hal= {https://inria.hal.science/hal-04111276},
BOOKTITLE = {{FIMH 2023 - 12th International Conference On Functional Imaging And Modeling Of The Heart}},
ADDRESS = {Lyon, France},
PUBLISHER = {{Springer}},
SERIES = {Lecture Notes in Computer Science},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {Thickness ; Thickness measurements ; Medical image analysis},
PDF = {https://inria.hal.science/hal-04111276/file/article.pdf},
HAL_ID = {hal-04111276},
HAL_VERSION = {v1},

}

Hind Dadoun, Hervé Delingette, Anne-Laure Rousseau, Eric de Kerviler, and Nicholas Ayache. Joint representation learning from french radiological reports and ultrasound images. In IEEE ISBI 2023 - International Symposium on Biomedical Imaging, Cartagena de Indias, Colombia, April 2023. IEEE.

Keyword(s): multimodal learning deep clustering natural language processing ultrasound examinations kidneys, multimodal learning, deep clustering, natural language processing, ultrasound examinations, kidneys.

@inproceedings{dadoun:hal-03984528,
TITLE = {{Joint representation learning from french radiological reports and ultrasound images}},
AUTHOR = {Dadoun, Hind and Delingette, Herv{\'e} and Rousseau, Anne-Laure and de Kerviler, Eric and Ayache, Nicholas},
url-hal= {https://inria.hal.science/hal-03984528},
BOOKTITLE = {{IEEE ISBI 2023 - International Symposium on Biomedical Imaging}},
ADDRESS = {Cartagena de Indias, Colombia},
ORGANIZATION = {{IEEE}},
YEAR = {2023},
MONTH = Apr,
KEYWORDS = {multimodal learning deep clustering natural language processing ultrasound examinations kidneys ; multimodal learning ; deep clustering ; natural language processing ; ultrasound examinations ; kidneys},
PDF = {https://inria.hal.science/hal-03984528/file/HIND_DADOUN_ISBI_2023.pdf},
HAL_ID = {hal-03984528},
HAL_VERSION = {v1},

}

Zhijie Fang, Hervé Delingette, and Nicholas Ayache. Anatomical Landmark Detection for Initializing US and MR Image Registration. In MICCAI ASMUS 2023 - 4th International Workshop of Advances in Simplifying Medical UltraSound - a workshop held in conjunction with MICCAI 2023, the 26th International Conference on Medical Image Computing and Computer Assisted Intervention, Vancouver, Canada, October 2023.

Keyword(s): Landmark detection, Image-guided intervention, Convolutional neural network and Prostate cancer.

@inproceedings{fang:hal-04189905,
TITLE = {{Anatomical Landmark Detection for Initializing US and MR Image Registration}},
AUTHOR = {Fang, Zhijie and Delingette, Herv{\'e} and Ayache, Nicholas},
url-hal= {https://hal.science/hal-04189905},
BOOKTITLE = {{MICCAI ASMUS 2023 - 4th International Workshop of Advances in Simplifying Medical UltraSound - a workshop held in conjunction with MICCAI 2023, the 26th International Conference on Medical Image Computing and Computer Assisted Intervention}},
ADDRESS = {Vancouver, Canada},
YEAR = {2023},
MONTH = Oct,
KEYWORDS = {Landmark detection ; Image-guided intervention ; Convolutional neural network and Prostate cancer},
PDF = {https://hal.science/hal-04189905/file/Fang-ASMUS-camera-ready-version-18Aug2023.pdf},
HAL_ID = {hal-04189905},
HAL_VERSION = {v1},

}

Hari Sreedhar, Guillaume P R Lajoinie, Charles Raffaelli, and Hervé Delingette. Active Learning Strategies on a Real-World Thyroid Ultrasound Dataset. In DALI 2023 - Data Augmentation, Labelling, and Imperfections / MICCAI Workshop 2023, MICCAI Workshop on Data Augmentation, Labelling, and Imperfections, DALI 2023, held in conjunction with MICCAI 2023 Proceedings, Vancouver, Canada, October 2023.

Keyword(s): Thyroid cancer, Active learning, Ultrasound imaging.

@inproceedings{sreedhar:hal-04209622,
TITLE = {{Active Learning Strategies on a Real-World Thyroid Ultrasound Dataset}},
AUTHOR = {Sreedhar, Hari and Lajoinie, Guillaume P R and Raffaelli, Charles and Delingette, Herv{\'e}},
url-hal= {https://inria.hal.science/hal-04209622},
BOOKTITLE = {{DALI 2023 - Data Augmentation, Labelling, and Imperfections / MICCAI Workshop 2023}},
ADDRESS = {Vancouver, Canada},
SERIES = {MICCAI Workshop on Data Augmentation, Labelling, and Imperfections, DALI 2023, held in conjunction with MICCAI 2023 Proceedings},
YEAR = {2023},
MONTH = Oct,
KEYWORDS = {Thyroid cancer ; Active learning ; Ultrasound imaging},
PDF = {https://inria.hal.science/hal-04209622/file/manuscript.pdf},
HAL_ID = {hal-04209622},
HAL_VERSION = {v1},

}

Yingyu Yang and Maxime Sermesant. Unsupervised Polyaffine Transformation Learning for Echocardiography Motion Estimation. In FIMH 2023 - The 12th International Conference on Functional Imaging and Modeling of The Heart, Lyon, France, June 2023.

Keyword(s): Motion Estimation Echocardiography Polyaffine Transformation, Motion Estimation, Echocardiography, Polyaffine Transformation.

@inproceedings{yang:hal-04109721,
TITLE = {{Unsupervised Polyaffine Transformation Learning for Echocardiography Motion Estimation}},
AUTHOR = {Yang, Yingyu and Sermesant, Maxime},
url-hal= {https://inria.hal.science/hal-04109721},
BOOKTITLE = {{FIMH 2023 - The 12th International Conference on Functional Imaging and Modeling of The Heart}},
ADDRESS = {Lyon, France},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {Motion Estimation Echocardiography Polyaffine Transformation ; Motion Estimation ; Echocardiography ; Polyaffine Transformation},
PDF = {https://inria.hal.science/hal-04109721/file/Unsupervised_Polyaffine_Motion_Model_for_Echocardiography_Analysis__final_-2.pdf},
HAL_ID = {hal-04109721},
HAL_VERSION = {v1},

}

Internal reports

Frédéric Blanqui, Anne Canteaut, Hidde De Jong, Sébastien Imperiale, Nathalie Mitton, Guillaume Pallez, Xavier Pennec, Xavier Rival, and Bertrand Thirion. Recommendations on ''Grey-Zone Publishers''. Technical report, Inria, January 2023.

@techreport{blanqui:hal-04201298,
TITLE = {{Recommendations on ''Grey-Zone Publishers''}},
AUTHOR = {Blanqui, Fr{\'e}d{\'e}ric and Canteaut, Anne and Jong, Hidde De and Imperiale, S{\'e}bastien and Mitton, Nathalie and Pallez, Guillaume and Pennec, Xavier and Rival, Xavier and Thirion, Bertrand},
url-hal= {https://inria.hal.science/hal-04201298},
PAGES = {1-3},
INSTITUTION = {{Inria}},
YEAR = {2023},
MONTH = Jan,
PDF = {https://inria.hal.science/hal-04201298/file/CE_note-editeurs-douteux-EN.pdf},
HAL_ID = {hal-04201298},
HAL_VERSION = {v1},

}

Frédéric Blanqui, Anne Canteaut, Hidde de Jong, Sébastien Imperiale, Nathalie Mitton, Guillaume Pallez, Xavier Pennec, Xavier Rival, and Bertrand Thirion. Recommandations sur les `` éditeurs de la zone grise ''. Technical report, Inria, January 2023.

@techreport{blanqui:hal-04001505,
TITLE = {{Recommandations sur les `` {\'e}diteurs de la zone grise ''}},
AUTHOR = {Blanqui, Fr{\'e}d{\'e}ric and Canteaut, Anne and de Jong, Hidde and Imperiale, S{\'e}bastien and Mitton, Nathalie and Pallez, Guillaume and Pennec, Xavier and Rival, Xavier and Thirion, Bertrand},
url-hal= {https://inria.hal.science/hal-04001505},
PAGES = {1-3},
INSTITUTION = {{Inria}},
YEAR = {2023},
MONTH = Jan,
PDF = {https://inria.hal.science/hal-04001505/file/CE_note-editeurs-douteux.pdf},
HAL_ID = {hal-04001505},
HAL_VERSION = {v1},

}

Miscellaneous

Yanis Aeschlimann, Anna Calissano, Samuel Deslauriers-Gauthier, Théodore Papadopoulo, and Andreas Hansen. Preliminary results on the graph matching of structural and functional brain networks. Neuromod Yearly Meeting 2023, June 2023. Note: Poster.

Keyword(s): brain networks, structural connectivity, functional connectivity, brain atlas, network alignment.

@misc{aeschlimann:hal-04165209,
TITLE = {{Preliminary results on the graph matching of structural and functional brain networks}},
AUTHOR = {Aeschlimann, Yanis and Calissano, Anna and Deslauriers-Gauthier, Samuel and Papadopoulo, Th{\'e}odore and Hansen, Andreas},
url-hal= {https://inria.hal.science/hal-04165209},
NOTE = {Poster},
HOWPUBLISHED = {{Neuromod Yearly Meeting 2023}},
YEAR = {2023},
MONTH = Jun,
KEYWORDS = {brain networks ; structural connectivity ; functional connectivity ; brain atlas ; network alignment},
PDF = {https://inria.hal.science/hal-04165209/file/Neuromod_2023_poster_Yanis_AESCHLIMANN.pdf},
HAL_ID = {hal-04165209},
HAL_VERSION = {v1},

}

Morten Akhoj, James Benn, Erlend Grong, Stefan Sommer, and Xavier Pennec. Principal subbundles for dimension reduction. Note: Working paper or preprint, July 2023.

@unpublished{akhoj:hal-04156036,
TITLE = {{Principal subbundles for dimension reduction}},
AUTHOR = {Akh{{\o}}j, Morten and Benn, James and Grong, Erlend and Sommer, Stefan and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04156036},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = Jul,
HAL_ID = {hal-04156036},
HAL_VERSION = {v1},

}

Safaa Al-Ali, Jordi Llopis-Lorente, Maria Teresa Mora, Maxime Sermesant, Beatriz Trénor, and Irene Balelli. A causal discovery approach for streamline ion channels selection to improve drug-induced TdP risk assessment. Note: Working paper or preprint, 2023.

Keyword(s): Causal discovery, Drug safety, Ions channel, TdP risk.

@unpublished{alali:hal-04105144,
TITLE = {{A causal discovery approach for streamline ion channels selection to improve drug-induced TdP risk assessment}},
AUTHOR = {Al-Ali, Safaa and Llopis-Lorente, Jordi and Mora, Maria Teresa and Sermesant, Maxime and Tr{\'e}nor, Beatriz and Balelli, Irene},
url-hal= {https://hal.science/hal-04105144},
NOTE = {working paper or preprint},
YEAR = {2023},
KEYWORDS = {Causal discovery ; Drug safety ; Ions channel ; TdP risk},
PDF = {https://hal.science/hal-04105144/file/Draft_CMSB_Sept_2023-2.pdf},
HAL_ID = {hal-04105144},
HAL_VERSION = {v1},

}

Irene Balelli, Aude Sportisse, Francesco Cremonesi, Pierre-Alexandre Mattei, and Marco Lorenzi. Fed-MIWAE: Federated Imputation of Incomplete Data via Deep Generative Models. Note: Working paper or preprint, 2023.

Keyword(s): Missing data, Federated learning, Federated pre-processing, Variational autoencoders, Deep Learning.

@unpublished{balelli:hal-04069795,
TITLE = {{Fed-MIWAE: Federated Imputation of Incomplete Data via Deep Generative Models}},
AUTHOR = {Balelli, Irene and Sportisse, Aude and Cremonesi, Francesco and Mattei, Pierre-Alexandre and Lorenzi, Marco},
url-hal= {https://hal.science/hal-04069795},
NOTE = {working paper or preprint},
YEAR = {2023},
KEYWORDS = {Missing data ; Federated learning ; Federated pre-processing ; Variational autoencoders ; Deep Learning},
PDF = {https://hal.science/hal-04069795/file/main_MICCAI.pdf},
HAL_ID = {hal-04069795},
HAL_VERSION = {v1},

}

Blanche Buet and Xavier Pennec. Flagfolds. Note: Working paper or preprint, 2023.

@unpublished{buet:hal-04112465,
TITLE = {{Flagfolds}},
AUTHOR = {Buet, Blanche and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04112465},
NOTE = {working paper or preprint},
YEAR = {2023},
HAL_ID = {hal-04112465},
HAL_VERSION = {v1},

}

Anna Calissano, Elodie Maignant, and Xavier Pennec. Towards Quotient Barycentric Subspaces. Note: Working paper or preprint, May 2023.

Keyword(s): Discrete Group, Quotient Space, Barycentric Subspace Analysis, Graph Space, Object Oriented Data Analysis.

@unpublished{calissano:hal-04162647,
TITLE = {{Towards Quotient Barycentric Subspaces}},
AUTHOR = {Calissano, Anna and Maignant, Elodie and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04162647},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = May,
KEYWORDS = {Discrete Group ; Quotient Space ; Barycentric Subspace Analysis ; Graph Space ; Object Oriented Data Analysis},
PDF = {https://inria.hal.science/hal-04162647/file/Towards_Quotient_Barycentric_Subspaces.pdf},
HAL_ID = {hal-04162647},
HAL_VERSION = {v1},

}

Quentin Clairon, Chloé Pasin, Irene Balelli, Rodolphe Thiébaut, and Mélanie Prague. Parameter estimation in nonlinear mixed effect models based on ordinary differential equations: An optimal control approach. Note: Working paper or preprint, January 2023.

Keyword(s): Dynamic population models, Ordinary differential equations, Optimal control theory, Mechanistic models, Nonlinear mixed effects models, Clinical trial analysis.

@unpublished{clairon:hal-03335826,
TITLE = {{Parameter estimation in nonlinear mixed effect models based on ordinary differential equations: An optimal control approach}},
AUTHOR = {Clairon, Quentin and Pasin, Chlo{\'e} and Balelli, Irene and Thi{\'e}baut, Rodolphe and Prague, M{\'e}lanie},
url-hal= {https://hal.science/hal-03335826},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = Jan,
KEYWORDS = {Dynamic population models ; Ordinary differential equations ; Optimal control theory ; Mechanistic models ; Nonlinear mixed effects models ; Clinical trial analysis},
PDF = {https://hal.science/hal-03335826v2/file/Manuscript_Estimation_NLMEODE_via_OCA_CompStat%20%281%29.pdf},
HAL_ID = {hal-03335826},
HAL_VERSION = {v2},

}

Francesco Cremonesi, Marc Vesin, Sergen Cansiz, Yannick Bouillard, Irene Balelli, Lucia Innocenti, Santiago Silva, Samy-Safwan Ayed, Riccardo Taiello, Laetita Kameni, Richard Vidal, Fanny Orlhac, Christophe Nioche, Nathan Lapel, Bastien Houis, Romain Modzelewski, Olivier Humbert, Melek Önen, and Marco Lorenzi. Fed-BioMed: Open, Transparent and Trusted Federated Learning for Real-world Healthcare Applications. Note: Working paper or preprint, April 2023.

Keyword(s): Machine learning, Biomedical Application, Healthcare, Federated Learning Framework.

@unpublished{cremonesi:hal-04081557,
TITLE = {{Fed-BioMed: Open, Transparent and Trusted Federated Learning for Real-world Healthcare Applications}},
AUTHOR = {Cremonesi, Francesco and Vesin, Marc and Cansiz, Sergen and Bouillard, Yannick and Balelli, Irene and Innocenti, Lucia and Silva, Santiago and Ayed, Samy-Safwan and Taiello, Riccardo and Kameni, Laetita and Vidal, Richard and Orlhac, Fanny and Nioche, Christophe and Lapel, Nathan and Houis, Bastien and Modzelewski, Romain and Humbert, Olivier and {\"O}nen, Melek and Lorenzi, Marco},
url-hal= {https://inria.hal.science/hal-04081557},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = Apr,
KEYWORDS = {Machine learning ; Biomedical Application ; Healthcare ; Federated Learning Framework},
PDF = {https://inria.hal.science/hal-04081557/file/fedbiomed_paper-5.pdf},
HAL_ID = {hal-04081557},
HAL_VERSION = {v1},

}

Etrit Haxholli and Marco Lorenzi. Faster Training and Improved Performance of Diffusion Models via Parallel Score Matching. Note: Working paper or preprint, March 2023.

@unpublished{haxholli:hal-04032669,
TITLE = {{Faster Training and Improved Performance of Diffusion Models via Parallel Score Matching}},
AUTHOR = {Haxholli, Etrit and Lorenzi, Marco},
url-hal= {https://inria.hal.science/hal-04032669},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = Mar,
HAL_ID = {hal-04032669},
HAL_VERSION = {v1},

}

Elodie Maignant, Alain Trouvé, and Xavier Pennec. Riemannian Locally Linear Embedding with Application to Kendall Shape Spaces. Note: Working paper or preprint, May 2023.

Keyword(s): Locally Linear Embedding, Optimisation on Quotient Manifolds, Shape Spaces.

@unpublished{maignant:hal-04122754,
TITLE = {{Riemannian Locally Linear Embedding with Application to Kendall Shape Spaces}},
AUTHOR = {Maignant, Elodie and Trouv{\'e}, Alain and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04122754},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = May,
KEYWORDS = {Locally Linear Embedding ; Optimisation on Quotient Manifolds ; Shape Spaces},
PDF = {https://inria.hal.science/hal-04122754/file/Riemannian_Locally_Linear_Embedding_with_Application_to_Kendall_Shape_Spaces.pdf},
HAL_ID = {hal-04122754},
HAL_VERSION = {v1},

}

Tom Szwagier and Xavier Pennec. Rethinking the Riemannian Logarithm on Flag Manifolds as an Orthogonal Alignment Problem. Note: Working paper or preprint, May 2023.

Keyword(s): Flag manifolds, Riemannian logarithm, Orthogonal alignment, Procrustes analysis, Flag manifolds Riemannian logarithm Orthogonal alignment Procrustes analysis, Flag manifolds.

@unpublished{szwagier:hal-04100534,
TITLE = {{Rethinking the Riemannian Logarithm on Flag Manifolds as an Orthogonal Alignment Problem}},
AUTHOR = {Szwagier, Tom and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04100534},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = May,
KEYWORDS = {Flag manifolds ; Riemannian logarithm ; Orthogonal alignment ; Procrustes analysis ; Flag manifolds Riemannian logarithm Orthogonal alignment Procrustes analysis ; Flag manifolds},
PDF = {https://inria.hal.science/hal-04100534/file/GSI-119.pdf},
HAL_ID = {hal-04100534},
HAL_VERSION = {v1},

}

Tom Szwagier and Xavier Pennec. Stratified Principal Component Analysis. Note: Working paper or preprint, July 2023.

Keyword(s): Probabilistic principal component analysis, Parsimony, Eigenvalue multiplicity, Flag manifolds, Stratified space.

@unpublished{szwagier:hal-04171853,
TITLE = {{Stratified Principal Component Analysis}},
AUTHOR = {Szwagier, Tom and Pennec, Xavier},
url-hal= {https://inria.hal.science/hal-04171853},
NOTE = {working paper or preprint},
YEAR = {2023},
MONTH = Jul,
KEYWORDS = {Probabilistic principal component analysis ; Parsimony ; Eigenvalue multiplicity ; Flag manifolds ; Stratified space},
PDF = {https://inria.hal.science/hal-04171853/file/Stratified-PCA.pdf},
HAL_ID = {hal-04171853},
HAL_VERSION = {v1},

}

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