@inbook{899098f19a9c4feaaf5ce34bc5e82fb3,
title = "Label-Set Loss Functions for Partial Supervision: Application to Fetal Brain 3D MRI Parcellation",
abstract = "Deep neural networks have increased the accuracy of automatic segmentation, however their accuracy depends on the availability of a large number of fully segmented images. Methods to train deep neural networks using images for which some, but not all, regions of interest are segmented are necessary to make better use of partially annotated datasets. In this paper, we propose the first axiomatic definition of label-set loss functions that are the loss functions that can handle partially segmented images. We prove that there is one and only one method to convert a classical loss function for fully segmented images into a proper label-set loss function. Our theory also allows us to define the leaf-Dice loss, a label-set generalisation of the Dice loss particularly suited for partial supervision with only missing labels. Using the leaf-Dice loss, we set a new state of the art in partially supervised learning for fetal brain 3D MRI segmentation. We achieve a deep neural network able to segment white matter, ventricles, cerebellum, extra-ventricular CSF, cortical gray matter, deep gray matter, brainstem, and corpus callosum based on fetal brain 3D MRI of anatomically normal fetuses or with open spina bifida. Our implementation of the proposed label-set loss functions is available at https://github.com/LucasFidon/label-set-loss-functions.",
author = "Lucas Fidon and Michael Aertsen and Doaa Emam and Nada Mufti and Frederic Guffens and Thomas Deprest and Philippe Demaerel and David, {Anna L.} and Andrew Melbourne and Sebastien Ourselin and Jan Deprest and Tom Vercauteren",
note = "Funding Information: Acknowledgments. This project has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation program under the Marie Sk lodowska-Curie grant agreement TRABIT No 765148. This work was supported by core and project funding from the Wellcome [203148/Z/16/Z; 203145Z/16/Z; WT101957], and EPSRC [NS/A000049/1; NS/A000050/1; NS/A000027/1]. TV is supported by a Medtronic / RAEng Research Chair [RCSRF1819\7\34]. Publisher Copyright: {\textcopyright} 2021, Springer Nature Switzerland AG.",
year = "2021",
doi = "10.1007/978-3-030-87196-3_60",
language = "English",
isbn = "978-3-030-87195-6",
volume = "12902",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "647--657",
editor = "{de Bruijne}, Marleen and Cattin, {Philippe C.} and St{\'e}phane Cotin and Nicolas Padoy and Stefanie Speidel and Yefeng Zheng and Caroline Essert",
booktitle = "Medical Image Computing and Computer Assisted Intervention – MICCAI 2021 - 24th International Conference, Proceedings",
}