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Loss functions for image segmentation

A collection of loss functions for medical image segmentation

@article{LossOdyssey,
title = {Loss Odyssey in Medical Image Segmentation},
journal = {Medical Image Analysis},
volume = {71},
pages = {102035},
year = {2021},
author = {Jun Ma and Jianan Chen and Matthew Ng and Rui Huang and Yu Li and Chen Li and Xiaoping Yang and Anne L. Martel}
doi = {https://doi.org/10.1016/j.media.2021.102035},
url = {https://www.sciencedirect.com/science/article/pii/S1361841521000815}
}

Take-home message: compound loss functions are the most robust losses, especially for the highly imbalanced segmentation tasks.

Some recent side evidence: the winner in MICCAI 2020 HECKTOR Challenge used DiceFocal loss; the winner and runner-up in MICCAI 2020 ADAM Challenge used DiceTopK loss.

DateFirst AuthorTitleConference/Journal
20231101Bingyuan LiuDo we really need dice? The hidden region-size biases of segmentation losses (pytorch)MedIA
2023 MICCAIAlvaro Gonzalez-JimenezRobust T-Loss for Medical Image Segmentation (pytorch)MICCAI23
2023 MICCAIZifu WangDice Semimetric Losses: Optimizing the Dice Score with Soft Labels (pytorch)MICCAI23
2023 MICCAIFan SunBoundary Difference Over Union Loss For Medical Image Segmentation (pytorch)MICCAI23
20220517Florian Koflerblob loss: instance imbalance aware loss functions for semantic segmentation (pytorch)IPMI23
20220426Zhaoqi LenPolyLoss: A Polynomial Expansion Perspective of Classification Loss Functions (pytorch)ICLR
20211109Litao YuDistribution-Aware Margin Calibration for Semantic Segmentation in Images (pytorch)IJCV
20211013Pei WangRelax and Focus on Brain Tumor SegmentationMedIA
20210418Bingyuan LiuThe hidden label-marginal biases of segmentation losses (pytorch)arxiv
20210330Suprosanna Shit and Johannes C. PaetzoldclDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation (keras and pytorch)CVPR 2021
20210325Attila Szabo, Hadi Jamali-RadTilted Cross Entropy (TCE): Promoting Fairness in Semantic SegmentationCVPR21 Workshop
20210318Xiaoling HuTopology-Aware Segmentation Using Discrete Morse Theory arxivICLR 2021
20210211Hoel KervadecBeyond pixel-wise supervision: semantic segmentation with higher-order shape descriptorsSubmitted to MIDL 2021
20210210Rosana EL JurdiA Surprisingly Effective Perimeter-based Loss for Medical Image SegmentationSubmitted to MIDL 2021
20201222Zeju LiAnalyzing Overfitting Under Class Imbalance in Neural Networks for Image SegmentationTMI
20210129Nick ByrneA Persistent Homology-Based Topological Loss Function for Multi-class CNN Segmentation of Cardiac MRI arxivSTACOM 2020
20201019Hyunseok SeoClosing the Gap Between Deep Neural Network Modeling and Biomedical Decision-Making Metrics in Segmentation via Adaptive Loss FunctionsTMI
20200929Stefan GerlA Distance-Based Loss for Smooth and Continuous Skin Layer Segmentation in Optoacoustic ImagesMICCAI 2020
20200821Nick ByrneA persistent homology-based topological loss function for multi-class CNN segmentation of cardiac MRI arxivSTACOM
20200720Boris ShirokikhUniversal Loss Reweighting to Balance Lesion Size Inequality in 3D Medical Image Segmentation arxiv (pytorch)MICCAI 2020
20200708Gonglei ShiMarginal loss and exclusion loss for partially supervised multi-organ segmentation (arXiv)MedIA
20200706Yuan LanAn Elastic Interaction-Based Loss Function for Medical Image Segmentation (pytorch) (arXiv)MICCAI 2020
20200615Tom EelbodeOptimization for Medical Image Segmentation: Theory and Practice when evaluating with Dice Score or Jaccard IndexTMI
20200605Guotai WangNoise-robust Dice loss: A Noise-robust Framework for Automatic Segmentation of COVID-19 Pneumonia Lesions from CT Images (pytorch)TMI
202004J. H. MoltzContour Dice coefficient (CDC) Loss: Learning a Loss Function for Segmentation: A Feasibility StudyISBI
201912Yuan XueShape-Aware Organ Segmentation by Predicting Signed Distance Maps (arxiv) (pytorch)AAAI 2020
201912Xiaoling HuTopology-Preserving Deep Image Segmentation (paper) (pytorch)NeurIPS
201910Shuai ZhaoRegion Mutual Information Loss for Semantic Segmentation (paper) (pytorch)NeurIPS 2019
201910Shuai ZhaoCorrelation Maximized Structural Similarity Loss for Semantic Segmentation (paper)arxiv
201908Pierre-AntoineGanayeRemoving Segmentation Inconsistencies with Semi-Supervised Non-Adjacency Constraint (paper) (official pytorch)Medical Image Analysis
201906Xu ChenLearning Active Contour Models for Medical Image Segmentation (paper) (official-keras)CVPR 2019
20190422Davood KarimiReducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks (pytorch)TMI 201907
20190417Francesco CalivaDistance Map Loss Penalty Term for Semantic Segmentation (paper)MIDL 2019
20190411Su YangMajor Vessel Segmentation on X-ray Coronary Angiography using Deep Networks with a Novel Penalty Loss Function (paper)MIDL 2019
20190405Boah KimMumford–Shah Loss Functional for Image Segmentation With Deep LearningTIP
201901Seyed Raein HashemiAsymmetric Loss Functions and Deep Densely Connected Networks for Highly Imbalanced Medical Image Segmentation: Application to Multiple Sclerosis Lesion Detection (paper)IEEE Access
201812Hoel KervadecBoundary loss for highly unbalanced segmentation (paper), (pytorch 1.0)MIDL 2019
201810Nabila AbrahamA Novel Focal Tversky loss function with improved Attention U-Net for lesion segmentation (paper) (keras)ISBI 2019
201809Fabian IsenseeCE+Dice: nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation (paper)Nautre Methods
20180831Ken C. L. Wong3D Segmentation with Exponential Logarithmic Loss for Highly Unbalanced Object Sizes (paper)MICCAI 2018
20180815Wentao ZhuDice+Focal: AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy (arxiv) (pytorch)Medical Physics
201806Javier RiberaWeighted Hausdorff Distance: Locating Objects Without Bounding Boxes (paper), (pytorch)CVPR 2019
201805Saeid Asgari TaghanakiCombo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation (arxiv) (keras)Computerized Medical Imaging and Graphics
201709S M Masudur Rahman AL ARIFShape-aware deep convolutional neural network for vertebrae segmentation (paper)MICCAI 2017 Workshop
201708Tsung-Yi LinFocal Loss for Dense Object Detection (paper), (code)ICCV, TPAMI
20170711Carole SudreGeneralised Dice overlap as a deep learning loss function for highly unbalanced segmentations (paper)DLMIA 2017
20170703Lucas FidonGeneralised Wasserstein Dice Score for Imbalanced Multi-class Segmentation using Holistic Convolutional Networks (paper)MICCAI 2017 BrainLes
201705Maxim BermanThe Lovász-Softmax loss: A tractable surrogate for the optimization of the intersection-over-union measure in neural networks (paper), (code)CVPR 2018
201701Seyed Sadegh Mohseni SalehiTversky loss function for image segmentation using 3D fully convolutional deep networks (paper)MICCAI 2017 MLMI
201612Md Atiqur RahmanOptimizing Intersection-Over-Union in Deep Neural Networks for Image Segmentation (paper)2016 International Symposium on Visual Computing
201608Michal Drozdzal"Dice Loss (without square)" The Importance of Skip Connections in Biomedical Image Segmentation (arxiv)DLMIA 2016
201606Fausto Milletari"Dice Loss (with square)" V-net: Fully convolutional neural networks for volumetric medical image segmentation (arxiv), (caffe code)International Conference on 3D Vision
201605Zifeng WuTopK loss Bridging Category-level and Instance-level Semantic Image Segmentation (paper)arxiv
201511Tom Brosch"Sensitivity-Specifity loss" Deep Convolutional Encoder Networks for Multiple Sclerosis Lesion Segmentation (code)MICCAI 2015
201505Olaf Ronneberger"Weighted cross entropy" U-Net: Convolutional Networks for Biomedical Image Segmentation (paper)MICCAI 2015
201309Gabriela CsurkaWhat is a good evaluation measure for semantic segmentation? (paper)BMVA 2013

Most of the corresponding tensorflow code can be found here.