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Common Limitations of Image Processing Metrics: A Picture Story


Apr 13, 2021
Annika Reinke, Matthias Eisenmann, Minu D. Tizabi, Carole H. Sudre, Tim Rädsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M. Jorge Cardoso, Veronika Cheplygina, Keyvan Farahani, Ben Glocker, Doreen Heckmann-Nötzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin Kurc, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus Maier-Hein, Bjoern Menze, Henning Müller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

* This is a dynamic paper on limitations of commonly used metrics. The current version discusses segmentation metrics only, while future versions will also include metrics for classification and detection. For missing use cases, comments or questions, please contact [email protected] or [email protected]. Substantial contributions to this document will be acknowledged with a co-authorship 

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How I failed machine learning in medical imaging -- shortcomings and recommendations


Mar 18, 2021
Gaël Varoquaux, Veronika Cheplygina


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Using uncertainty estimation to reduce false positives in liver lesion detection


Jan 26, 2021
Ishaan Bhat, Hugo J. Kuijf, Veronika Cheplygina, Josien P. W. Pluim

* Accepted at IEEE ISBI 2021 

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High-level Prior-based Loss Functions for Medical Image Segmentation: A Survey


Nov 22, 2020
Rosana El Jurdi, Caroline Petitjean, Paul Honeine, Veronika Cheplygina, Fahed Abdallah


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Crowdsourcing Airway Annotations in Chest Computed Tomography Images


Nov 20, 2020
Veronika Cheplygina, Adria Perez-Rovira, Wieying Kuo, Harm A. W. M. Tiddens, Marleen de Bruijne


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Primary Tumor Origin Classification of Lung Nodules in Spectral CT using Transfer Learning


Jun 30, 2020
Linde S. Hesse, Pim A. de Jong, Josien P. W. Pluim, Veronika Cheplygina

* MSc thesis Linde Hesse 

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Risk of Training Diagnostic Algorithms on Data with Demographic Bias


Jun 17, 2020
Samaneh Abbasi-Sureshjani, Ralf Raumanns, Britt E. J. Michels, Gerard Schouten, Veronika Cheplygina


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Predicting Scores of Medical Imaging Segmentation Methods with Meta-Learning


May 08, 2020
Tom van Sonsbeek, Veronika Cheplygina


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Multi-task Learning with Crowdsourced Features Improves Skin Lesion Diagnosis


Apr 28, 2020
Ralf Raumanns, Elif K Contar, Gerard Schouten, Veronika Cheplygina


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A Survey of Crowdsourcing in Medical Image Analysis


Feb 25, 2019
Silas Ørting, Andrew Doyle, Matthias Hirth Arno van Hilten, Oana Inel, Christopher R. Madan, Panagiotis Mavridis, Helen Spiers, Veronika Cheplygina

* While this paper is a preprint, we welcome feedback from other researchers, which we will aim to incorporate in the journal version. Interested researchers can submit comments via https://goo.gl/forms/Qzr2yAJQjOnRCAF23 

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Cats or CAT scans: transfer learning from natural or medical image source datasets?


Oct 12, 2018
Veronika Cheplygina


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Automatic Emphysema Detection using Weakly Labeled HRCT Lung Images


Oct 01, 2018
Isabel Pino Peña, Veronika Cheplygina, Sofia Paschaloudi, Morten Vuust, Jesper Carl, Ulla Møller Weinreich, Lasse Riis Østergaard, Marleen de Bruijne

* Accepted at PLoS ONE 

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Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis


Sep 14, 2018
Veronika Cheplygina, Marleen de Bruijne, Josien P. W. Pluim

* Submitted to Medical Image Analysis 

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Crowd disagreement about medical images is informative


Aug 17, 2018
Veronika Cheplygina, Josien P. W. Pluim

* Accepted for publication at MICCAI LABELS 2018 

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Characterizing multiple instance datasets


Jun 21, 2018
Veronika Cheplygina, David M. J. Tax

* Published at SIMBAD 2015 workshop 

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Feature learning based on visual similarity triplets in medical image analysis: A case study of emphysema in chest CT scans


Jun 19, 2018
Silas Nyboe Ørting, Jens Petersen, Veronika Cheplygina, Laura H. Thomsen, Mathilde M W Wille, Marleen de Bruijne

* 10 pages. Submitted to LABELS2018 - MICCAI Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis 

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Transfer learning for multi-center classification of chronic obstructive pulmonary disease


Nov 23, 2017
Veronika Cheplygina, Isabel Pino Peña, Jesper Holst Pedersen, David A. Lynch, Lauge Sørensen, Marleen de Bruijne

* Accepted at Journal of Biomedical and Health Informatics 

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Exploring the similarity of medical imaging classification problems


Jun 12, 2017
Veronika Cheplygina, Pim Moeskops, Mitko Veta, Behdad Dasht Bozorg, Josien Pluim


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Early Experiences with Crowdsourcing Airway Annotations in Chest CT


Jun 07, 2017
Veronika Cheplygina, Adria Perez-Rovira, Wieying Kuo, Harm A. W. M. Tiddens, Marleen de Bruijne

* LABELS 2016, DLMIA 2016: Deep Learning and Data Labeling for Medical Applications pp 209-218 

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Label Stability in Multiple Instance Learning


Mar 15, 2017
Veronika Cheplygina, Lauge Sørensen, David M. J. Tax, Marleen de Bruijne, Marco Loog

* Published at MICCAI 2015 

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Transfer Learning by Asymmetric Image Weighting for Segmentation across Scanners


Mar 15, 2017
Veronika Cheplygina, Annegreet van Opbroek, M. Arfan Ikram, Meike W. Vernooij, Marleen de Bruijne


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Classification of COPD with Multiple Instance Learning


Mar 15, 2017
Veronika Cheplygina, Lauge Sørensen, David M. J. Tax, Jesper Holst Pedersen, Marco Loog, Marleen de Bruijne

* Published at International Conference on Pattern Recognition (ICPR) 2014 

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Multiple Instance Learning: A Survey of Problem Characteristics and Applications


Dec 11, 2016
Marc-André Carbonneau, Veronika Cheplygina, Eric Granger, Ghyslain Gagnon


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On Classification with Bags, Groups and Sets


Oct 07, 2014
Veronika Cheplygina, David M. J. Tax, Marco Loog

* Pattern Recognition Letters Volume 59, 2015, Pages 11 - 17 

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Multiple Instance Learning with Bag Dissimilarities


Aug 12, 2014
Veronika Cheplygina, David M. J. Tax, Marco Loog

* Pattern Recognition 48.1 (2015): 264-275 
* Pattern Recognition, in press 

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Quantile Representation for Indirect Immunofluorescence Image Classification


Feb 06, 2014
David M. J. Tax, Veronika Cheplygina, Marco Loog


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