Topic: MedGIFT - HES SO Valais Publications

Vincent Andrearczyk, Mara Graziani, Henning Müller and Adrien Depeursinge, Consistency of Scale Covariance in Internal Representations of CNNs, in: Irish Machine Vision and Image Processing Conference, 2020

Gwenaelle Creff, Anne Devillers, Adrien Depeursinge, Xavier Palard-Novello, Oscar Acosta, Franck Jegoux and Joel Castelli, Evaluation of the Prognostic Value of FDG PET/CT Parameters for Patients with Surgically Treated Head and Neck Cancer: A Systematic Review (2020), in: JAMA Otolaryngology - Head and Neck Surgery, 146:5(471-479)

[]: IF 2019 = 3.295

[DOI]

Anjani Dhrangadhariya, Oscar Jimenez del Toro, Vincent Andrearczyk, Manfredo Atzori and Henning Müller, Exploiting the PubMed Central repository to mine out a large multimodal dataset of rare cancer studies, in: SPIE Medical Imaging, Houston, TX, USA, 2020

Roberto Gatta, Adrien Depeursinge, Osman Ratib, Olivier Michielin and Antoine Leimgruber, Integrating radiomics into holomics for personalised oncology: from algorithms to bedside (2020), in: European Radiology Experimental, 4(11)

Mara Graziani, Thomas Lompech, Henning Müller, Adrien Depeursinge and Vincent Andrearczyk, Interpretable CNN Pruning for Preserving Scale-Covariant Features in Medical Imaging, in: Workshop on Interpretability of Machine Intelligence in Medical Image Computing at MICCAI 2020, 2020

Vincent Andrearczyk, Julien Fageot, Valentin Oreiller, Xavier Montet and Adrien Depeursinge, Local Rotation Invariance in 3D CNNs (2020), in: Medical Image Analysis, 65(101756)

[]: IF 2018 = 8.79

[DOI]
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Vincent Andrearczyk, Valentin Oreiller and Adrien Depeursinge, Oropharynx Detection in PET-CT for Tumor Segmentation, in: Irish Machine Vision and Image Processing Conference, 2020, 2020

Sylvie Belleville, Marc Cuesta, Mélanie Bieler-Aeschlimann, Katia Giacomino, Antoine Widmer, Anne-Gabrielle {Mittaz Hager}, Daniel Perez-Marcos, Sylvain Cardin, Benjamin Boller, Nathalie Bier, Mylène Aubertin-Leheudr and Jean-François Démonet, Rationale and protocol of the StayFitLonger study: a multicentre trial to measure efficacy and adherence of a home-based computerised multidomain intervention in healthy older adults. (2020), in: BMC Geriatrics

Adrien Depeursinge, Vincent Andrearczyk, Philip Whybra, Joost van Griethuysen, Henning Müller, Roger Schaer, Martin Vallìères and Alex Zwanenburg, Standardised convolutional filtering for radiomics, 2020

[URL]

Alex Zwanenburg, Mahmoud A. Abdalah, Hugo Aerts, Vincent Andrearczyk, Aditya Apte, Saeed Ashrafinia, Roelof J. Beukinga, Ronald Boellaard, Marta Bogowicz, Luca Boldrini, Adrien Depeursinge, Marie-Charlotte Desseroit, Nicola Dinapoli, Cuong Viet Dinh, Sebastian Echegaray, Issam El Naqa, Andriy Y. Fedorov, Roberto Gatta, Robert J. Gillies, Matthias Guckenberger, Nils Gählert, Michael Götz, Mathieu Hatt, Fabian Isensee, Philippe Lambin, Stefan Leger, Ralph T. H. Leijenaar, Jacopo Lenkowicz, Fiona Lippert, Are Losnegård, Klaus H. Maier-Hein, Olivier Morin, Henning Müller, Sandy Napel, Arman Rahmim, Arvind U. K. Rao, Nanna M. Sijtsema, Jairo Socarras Fernandez, Emiliano Spezi, Roel J. H. M Steenbakkers, Stephanie Tanadini-Lang, Daniela Thorwarth, Esther G. C. Troost, Taman Upadhaya, Vincenzo Valentini, Martin Vallìères, Uulke A. van der Heide, Lisanne V. van Dijk, Joost van Griethuysen, Floris H. P. van Velden, Philip Whybra, Christian Richter and Steffen Löck, Standardized quantitative radiomics for high-throughput image-based phenotyping (2020), in: Radiology, 295:2(328-338)

[]: IF 2018 = 7.608

Pierre Fontaine, Oscar Acosta, Joel Castelli, R. De Crevoisier, Henning Müller and Adrien Depeursinge, The Importance of Feature Aggregation in Radiomics: A Head and Neck Cancer Study (2020), in: Nature Scientific Reports, 10:19679

[]: IF 2019 = 3.998

Guillaume Vanoost, Yashin Dicente Cid, Daniel L. Rubin and Adrien Depeursinge, A lung graph model for the classification of interstitial lung disease on CT images, in: SPIE Medical Imaging 2019: Computer-Aided Diagnosis, International Society for Optics and Photonics, pages 869-876, SPIE, 2019

Roger Schaer, Sebastian Otalora, Oscar Jimenez del Toro, Manfredo Atzori and Henning Müller, Deep learning based retrieval system for gigapixel histopathology cases and open access literature (2019), in: Pathology Informatics

[DOI]

Vincent Andrearczyk, Julien Fageot, Valentin Oreiller, Xavier Montet and Adrien Depeursinge, Exploring local rotation invariance in 3D CNNs with steerable filters, in: Medical Imaging with Deep Learning, pages 15-26, Proceedings of Machine Learning Research, 2019

[]: Won the overall best paper award of MIDL 2019 !

[URL]

Ranveer Joyseeree, Sebastian Otalora, Henning Müller and Adrien Depeursinge, Fusing Learned Representations from Riesz and Deep CNNs for Lung Tissue Classification (2019), in: Medical Image Analysis, 56(172-183)

[]: IF 2017 = 5.356

[URL]

Vincent Andrearczyk, Adrien Depeursinge and Henning Müller, Learning Cross-Protocol Radiomics and Deep Feature Standardization from CT Images of Texture Phantoms, in: SPIE Medical Imaging 2019, International Society for Optics and Photonics, pages 109-116, SPIE, 2019

Vincent Andrearczyk, Adrien Depeursinge and Henning Müller, Neural Network Training for Cross-Protocol Radiomic Feature Standardization in Computed Tomography (2019), in: Journal of Medical Imaging, 6:3(024008)

[URL]

Joel Castelli, Adrien Depeursinge, Anne Devillers, B. Campillo-Gimenez, Yashin Dicente Cid, John O. Prior, Enrique Chajon, Franck Jegoux, C. Sire, Oscar Acosta, X. Sun, B. De Bari, J. Bourhis and R. De Crevoisier, PET-based predictive survival model after radiotherapy for head and neck cancer (2019), in: European Journal of Nuclear Medicine and Molecular Imaging, 46:3(638-649)

[]: IF 2016 = 7.277

[URL]

Julien Fageot, Virginie Uhlmann, Adrien Depeursinge, Zsuzsanna Püspöki, Daniel Sage and Michael Unser, Radial B-Splines for Optimal Detection in Images, in: ISBI Special Session on Spline Models in Biomedical Imaging, 2019

Dmitry Chezerov, Dmitry Goldgof, Lawrence Hall, Robert Gillies, Matther Schabath, Henning Müller and Adrien Depeursinge, Revealing Tumor Habitats from Texture Heterogeneity Analysis for Classification of Lung Cancer Malignancy and Aggressiveness (2019), in: Nature Scientific Reports, 9:1(4500)

[]: IF 2016 = 4.259

Vincent Andrearczyk, Valentin Oreiller, Julien Fageot, Xavier Montet and Adrien Depeursinge, Solid Spherical Energy (SSE) CNNs for Efficient 3D Medical Image Analysis, in: Irish Machine Vision and Image Processing Conference, pages 37-44, 2019

Anaïs Badoual, Michael Unser and Adrien Depeursinge, Texture-Driven Parametric Snakes for Semi-Automatic Image Segmentation (2019), in: Computer Vision and Image Understanding, 188(102793)

[]: IF 2018 = 2.645
[]: Icy plugin and source code: https://bigwww.epfl.ch/demo/texture-snake/

Sebastian Otalora, Roger Schaer, Manfredo Atzori, Oscar Jimenez del Toro and Henning Müller, Deep learning based retrieval system for gigapixel histopathology cases and open access literature (2018), in: BioArXiv

Ivan Eggel, Roger Schaer and Henning Müller, Distributed container-based evaluation platform for private/large datasets, in: ISPDC 2018, Geneva, Switzerland, 2018

Michael T. McCann, Vincent Andrearczyk, Michael Unser and Adrien Depeursinge, Fast Rotational Sparse Coding (2018)(arXiv:1806.04374)

[URL]

Adrien Depeursinge, Tunde Szilágyi, Yan Liu, Kazmer Kovacs, Reena Thomas, Kristen Yeom, Nancy Fischbein, Daniel L. Rubin, Michael Iv and Olivier Gevaert, Locoregional radiogenomic models to capture gene expression heterogeneity in glioblastoma (2018), in: biorXiv

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Adrien Depeursinge, Julien Fageot, Vincent Andrearczyk, John-Paul Ward and Michael Unser, Rotation Invariance and Directional Sensitivity: Spherical Harmonics versus Radiomics Features, in: Machine Learning in Medical Imaging (MLMI), pages 107--115, Springer International Publishing, 2018

[URL]

Ranveer Joyseeree, Henning Müller and Adrien Depeursinge, Rotation-Covariant Tissue Analysis for Interstitial Lung Diseases Using Learned Steerable Filters: Performance Evaluation and Relevance for Diagnostic Aid (2018), in: Computerized Medical Imaging and Graphics, 64(1-11)

[DOI]

Vincent Andrearczyk and Adrien Depeursinge, Rotational 3D Texture Classification Using Group Equivariant CNNs (2018), in: ArXiv

[URL]

Pierre Starkov, Todd A. Aguilera, Daniel Golden, David B. Shultz, Nicholas Trakul, Peter G. Maxim, Quynh-Thu Le, Billy W. Loo Jr., Maximilian Diehn, Adrien Depeursinge and Daniel L. Rubin, The Use of Texture Based Radiomics CT Analysis to Predict Outcomes in Early-Stage Non-Small Cell Lung Cancer Treated with Stereotactic Ablative Radiotherapy (2018), in: The British Journal of Radiology, 92:1094(20180228)

[]: IF 2016 = 2.05

Yashin Dicente Cid, Henning Müller, Alexandra Platon, Pierre-Alexandre Poletti and Adrien Depeursinge, 3-D Solid Texture Classification Using Locally-Oriented Wavelet Transforms (2017), in: IEEE Transactions on Image Processing, 26:4(1899-1910)

[]: IF 2015 = 3.735
[]: Matlab code available! click on this entry to download the library.

[DOI]

Joel Castelli, Adrien Depeursinge, Vanessa Ndoh, John O. Prior, Esat Ozsahin, Anne Devillers, Hanan Bouchaab, Enrique Chajon, R. De Crevoisier, Nathaniel Scher, Franck Jegoux, B. Laguerre, B. De Bari and J. Bourhis, A PET-based nomogram for oropharyngeal cancers (2017), in: European Journal of Cancer, 75(222-230)

[]: IF 2015 = 6.16

Adrien Depeursinge, Omar S. Al-Kadi and J Ross Mitchell, Biomedical Texture Analysis: Fundamentals, Applications and Tools, Elsevier, Elsevier-MICCAI Society Book series, 2017

[URL]

Adrien Depeursinge and Julien Fageot, Biomedical Texture Operators and Aggregation Functions: A Methodological Review and User’s Guide, in: Biomedical Texture Analysis: Fundamentals, Applications and Tools, pages 55-94, Elsevier, 2017

[DOI]
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Oscar Jimenez del Toro, Pol Cirujeda and Henning Müller, Combining Radiology Images and Meta-data for Multimodal Medical Case-Based Retrieval, Springer, 2017

Oscar Jimenez del Toro, Manfredo Atzori, Sebastian Otalora, Mats Andersson, Kristian Euren, Martin Hedlund, Peter Rönnquist and Henning Müller, Convolutional neural networks for an automatic classification of prostate tissue slides with high-grade Gleason score, in: SPIE Medical Imaging, pages 101400O-101400O-9, 2017

[DOI]
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Oscar Jimenez del Toro, Sebastian Otalora, Mats Andersson, Kristian Euren, Martin Hedlund, Mikael Rousson, Henning Müller and Manfredo Atzori, Elsevier book on Texture Analysis, chapter Analysis of Histopathology Images: From Traditional Machine Learning to Deep Learning, 2017

Adrien Depeursinge, Julien Fageot and Omar S. Al-Kadi, Fundamentals of Texture Processing for Biomedical Image Analysis: A General Definition and Problem Formulation, in: Biomedical Texture Analysis: Fundamentals, Applications and Tools, pages 1-27, Elsevier, 2017

[DOI]
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Joel Castelli, Adrien Depeursinge, B. De Bari, Anne Devillers, R. De Crevoisier, J. Bourhis and John O. Prior, Metabolic Tumor Volume and Total Lesion Glycolysis in Oropharyngeal Cancer treated with definitive radiotherapy: Which threshold is the best predictor of local control ? (2017), in: Clinical Nuclear Medicine, 42:6(e281–e285)

[]: IF 2015 = 4.27

Adrien Depeursinge, Multi-Scale and Multi-Directional Biomedical Texture Analysis: Finding the Needle in the Haystack, in: Biomedical Texture Analysis: Fundamentals, Applications and Tools, pages 29-53, Elsevier, 2017

[DOI]
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Yashin Dicente Cid, Joel Castelli, Roger Schaer, Nathaniel Scher, Anastasia Pomoni, John O. Prior and Adrien Depeursinge, QuantImage: An Online Tool for High-Throughput 3D Radiomics Feature Extraction in PET-CT, in: Biomedical Texture Analysis: Fundamentals, Applications and Tools, pages 349-377, Elsevier, 2017

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Oscar Jimenez del Toro, Henning Müller, Antonio Foncubierta-Rodríguez, Georg Langs and Allan Hanbury, Retrieval of Medical Cases for Diagnostic Decisions: VISCERAL Retrieval Benchmark, chapter Retrieval of Medical Cases for Diagnostic Decisions: VISCERAL Retrieval Benchmark, Springer, 2017

Paul Blanc-Durand, Axel Van der Gucht, Mario Jreige, Marie Nicod-Lalonde, Marina Silva-Monteiro, John O. Prior, Alban Denys, Adrien Depeursinge and Niklaus Schaefer, Signature of Survival: A 18F-FDG PET Based Whole-Liver Radiomics Analysis Predicts Survival After 90Y-TARE for Hepatocellular Carcinoma (2017), in: OncoTarget, 9:4(4549-4558)

[]: IF 2016 = 5.168

Adrien Depeursinge, Zsuzsanna Püspöki, John-Paul Ward and Michael Unser, Steerable Wavelet Machines (SWM): Learning Moving Frames for Texture Classification (2017), in: IEEE Transactions on Image Processing, 26:4(1626-1636)

[]: IF 2015 = 3.735
[]: Matlab code available! click on this entry to download the library.

Fan Zhang, Yang Song, Weidong Cai, Adrien Depeursinge and Henning Müller, Text- and content-based medical image retrievals in the VISCERAL retrieval benchmark, Springer, 2017

Allan Hanbury, Henning Müller and Georg Langs, VISCERAL book, Springer, 2017

Allan Hanbury and Henning Müller, VISCERAL: Evaluation-as-a-Service for Medical Imaging, VISCERAL book, Springer, 2017

Pol Cirujeda, Yashin Dicente Cid, Henning Müller, Daniel L. Rubin, Todd A. Aguilera, Billy W. Loo Jr., Maximilian Diehn, Xavier Binefa and Adrien Depeursinge, A 3-D Riesz-Covariance Texture Model for Prediction of Nodule Recurrence in Lung CT (2016), in: IEEE Transactions on Medical Imaging, 35:12(2620-2630)

[]: IF 2015 = 3.76
[]: video presentation of the paper: https://portal.klewel.com/watch/webcast/valaiswallis-ai-workshop-reproducibility-in-research/talk/9

Ranveer Joyseeree, Roger Schaer and Henning Müller, A Demo of Multimodal Medical Retrieval, in: Workshop on Content-based Multimedia Indexing (CBMI), Bucharest, Romania, 2016

Yashin Dicente Cid, Henning Müller, Alexandra Platon, Jean-Paul Janssens, Lador Frédéric, Pierre-Alexandre Poletti and Adrien Depeursinge, A Lung Graph-Model for Pulmonary Hypertension and Pulmonary Embolism Detection on DECT images, in: MICCAI Workshop on Medical Computer Vision: Algorithms for Big Data, pages 58-68, 2016