A collection of loss functions for medical image segmentation

Related tags

Deep LearningSegLoss
Overview

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.

Date First Author Title Conference/Journal
20210330 Suprosanna Shit and Johannes C. Paetzold clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation (keras and pytorch) CVPR 2021
20210318 Xiaoling Hu Topology-Aware Segmentation Using Discrete Morse Theory arxiv ICLR 2021
20210211 Hoel Kervadec Beyond pixel-wise supervision: semantic segmentation with higher-order shape descriptors Submitted to MIDL 2021
20210210 Rosana EL Jurdi A Surprisingly Effective Perimeter-based Loss for Medical Image Segmentation Submitted to MIDL 2021
20201222 Zeju Li Analyzing Overfitting Under Class Imbalance in Neural Networks for Image Segmentation TMI
20210129 Nick Byrne A Persistent Homology-Based Topological Loss Function for Multi-class CNN Segmentation of Cardiac MRI arxiv STACOM 2020
20201019 Hyunseok Seo Closing the Gap Between Deep Neural Network Modeling and Biomedical Decision-Making Metrics in Segmentation via Adaptive Loss Functions TMI
20200929 Stefan Gerl A Distance-Based Loss for Smooth and Continuous Skin Layer Segmentation in Optoacoustic Images MICCAI 2020
20200821 Nick Byrne A persistent homology-based topological loss function for multi-class CNN segmentation of cardiac MRI arxiv STACOM
20200720 Boris Shirokikh Universal Loss Reweighting to Balance Lesion Size Inequality in 3D Medical Image Segmentation arxiv (pytorch) MICCAI 2020
20200708 Gonglei Shi Marginal loss and exclusion loss for partially supervised multi-organ segmentation (arXiv) MedIA
20200706 Yuan Lan An Elastic Interaction-Based Loss Function for Medical Image Segmentation (pytorch) (arXiv) MICCAI 2020
20200615 Tom Eelbode Optimization for Medical Image Segmentation: Theory and Practice when evaluating with Dice Score or Jaccard Index TMI
20200605 Guotai Wang Noise-robust Dice loss: A Noise-robust Framework for Automatic Segmentation of COVID-19 Pneumonia Lesions from CT Images (pytorch) TMI
202004 J. H. Moltz Contour Dice coefficient (CDC) Loss: Learning a Loss Function for Segmentation: A Feasibility Study ISBI
201912 Yuan Xue Shape-Aware Organ Segmentation by Predicting Signed Distance Maps (arxiv) (pytorch) AAAI 2020
201912 Xiaoling Hu Topology-Preserving Deep Image Segmentation (paper) (pytorch) NeurIPS
201910 Shuai Zhao Region Mutual Information Loss for Semantic Segmentation (paper) (pytorch) NeurIPS 2019
201910 Shuai Zhao Correlation Maximized Structural Similarity Loss for Semantic Segmentation (paper) arxiv
201908 Pierre-AntoineGanaye Removing Segmentation Inconsistencies with Semi-Supervised Non-Adjacency Constraint (paper) (official pytorch) Medical Image Analysis
201906 Xu Chen Learning Active Contour Models for Medical Image Segmentation (paper) (official-keras) CVPR 2019
20190422 Davood Karimi Reducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks (paper) (pytorch) TMI 201907
20190417 Francesco Caliva Distance Map Loss Penalty Term for Semantic Segmentation (paper) MIDL 2019
20190411 Su Yang Major Vessel Segmentation on X-ray Coronary Angiography using Deep Networks with a Novel Penalty Loss Function (paper) MIDL 2019
20190405 Boah Kim Multiphase Level-Set Loss for Semi-Supervised and Unsupervised Segmentation with Deep Learning (paper) arxiv
201901 Seyed Raein Hashemi Asymmetric Loss Functions and Deep Densely Connected Networks for Highly Imbalanced Medical Image Segmentation: Application to Multiple Sclerosis Lesion Detection (paper) IEEE Access
201812 Hoel Kervadec Boundary loss for highly unbalanced segmentation (paper), (pytorch 1.0) MIDL 2019
201810 Nabila Abraham A Novel Focal Tversky loss function with improved Attention U-Net for lesion segmentation (paper) (keras) ISBI 2019
201809 Fabian Isensee CE+Dice: nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation (paper) arxiv
20180831 Ken C. L. Wong 3D Segmentation with Exponential Logarithmic Loss for Highly Unbalanced Object Sizes (paper) MICCAI 2018
20180815 Wentao Zhu Dice+Focal: AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy (arxiv) (pytorch) Medical Physics
201806 Javier Ribera Weighted Hausdorff Distance: Locating Objects Without Bounding Boxes (paper), (pytorch) CVPR 2019
201805 Saeid Asgari Taghanaki Combo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation (arxiv) (keras) Computerized Medical Imaging and Graphics
201709 S M Masudur Rahman AL ARIF Shape-aware deep convolutional neural network for vertebrae segmentation (paper) MICCAI 2017 Workshop
201708 Tsung-Yi Lin Focal Loss for Dense Object Detection (paper), (code) ICCV, TPAMI
20170711 Carole Sudre Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations (paper) DLMIA 2017
20170703 Lucas Fidon Generalised Wasserstein Dice Score for Imbalanced Multi-class Segmentation using Holistic Convolutional Networks (paper) MICCAI 2017 BrainLes
201705 Maxim Berman The Lovász-Softmax loss: A tractable surrogate for the optimization of the intersection-over-union measure in neural networks (paper), (code) CVPR 2018
201701 Seyed Sadegh Mohseni Salehi Tversky loss function for image segmentation using 3D fully convolutional deep networks (paper) MICCAI 2017 MLMI
201612 Md Atiqur Rahman Optimizing Intersection-Over-Union in Deep Neural Networks for Image Segmentation (paper) 2016 International Symposium on Visual Computing
201608 Michal Drozdzal "Dice Loss (without square)" The Importance of Skip Connections in Biomedical Image Segmentation (arxiv) DLMIA 2016
201606 Fausto Milletari "Dice Loss (with square)" V-net: Fully convolutional neural networks for volumetric medical image segmentation (arxiv), (caffe code) International Conference on 3D Vision
201605 Zifeng Wu TopK loss Bridging Category-level and Instance-level Semantic Image Segmentation (paper) arxiv
201511 Tom Brosch "Sensitivity-Specifity loss" Deep Convolutional Encoder Networks for Multiple Sclerosis Lesion Segmentation (paper) (code) MICCAI 2015
201505 Olaf Ronneberger "Weighted cross entropy" U-Net: Convolutional Networks for Biomedical Image Segmentation (paper) MICCAI 2015
201309 Gabriela Csurka What is a good evaluation measure for semantic segmentation? (paper) BMVA 2013

Most of the corresponding tensorflow code can be found here.

A heterogeneous entity-augmented academic language model based on Open Academic Graph (OAG)

Library | Paper | Slack We released two versions of OAG-BERT in CogDL package. OAG-BERT is a heterogeneous entity-augmented academic language model wh

THUDM 58 Dec 17, 2022
"Neural Turing Machine" in Tensorflow

Neural Turing Machine in Tensorflow Tensorflow implementation of Neural Turing Machine. This implementation uses an LSTM controller. NTM models with m

Taehoon Kim 1k Dec 06, 2022
Simulate genealogical trees and genomic sequence data using population genetic models

msprime msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consis

Tskit developers 150 Dec 14, 2022
Code repository for "Free View Synthesis", ECCV 2020.

Free View Synthesis Code repository for "Free View Synthesis", ECCV 2020. Setup Install the following Python packages in your Python environment - num

Intelligent Systems Lab Org 253 Dec 07, 2022
Learn other languages ​​using artificial intelligence with python.

The main idea of ​​the project is to facilitate the learning of other languages. We created a simple AI that will interact with you. Just ask questions that if she knows, she will answer.

Pedro Rodrigues 2 Jun 07, 2022
Use AI to generate a optimized stock portfolio

Use AI, Modern Portfolio Theory, and Monte Carlo simulation's to generate a optimized stock portfolio that minimizes risk while maximizing returns. Ho

Greg James 30 Dec 22, 2022
Official implementation of Densely connected normalizing flows

Densely connected normalizing flows This repository is the official implementation of NeurIPS 2021 paper Densely connected normalizing flows. Poster a

Matej Grcić 31 Dec 12, 2022
The Rich Get Richer: Disparate Impact of Semi-Supervised Learning

The Rich Get Richer: Disparate Impact of Semi-Supervised Learning Preprocess file of the dataset used in implicit sub-populations: (Demographic groups

<a href=[email protected]"> 4 Oct 14, 2022
Bottom-up Human Pose Estimation

Introduction This is the official code of Rethinking the Heatmap Regression for Bottom-up Human Pose Estimation. This paper has been accepted to CVPR2

108 Dec 01, 2022
An LSTM for time-series classification

Update 10-April-2017 And now it works with Python3 and Tensorflow 1.1.0 Update 02-Jan-2017 I updated this repo. Now it works with Tensorflow 0.12. In

Rob Romijnders 391 Dec 27, 2022
Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic

Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic [Paper] [Colab is coming soon] Approach Example Usage To r

170 Jan 03, 2023
RL algorithm PPO and IRL algorithm AIRL written with Tensorflow.

RL algorithm PPO and IRL algorithm AIRL written with Tensorflow. They have a parallel sampling feature in order to increase computation speed (especially in high-performance computing (HPC)).

Fangjian Li 3 Dec 28, 2021
What can linearized neural networks actually say about generalization?

What can linearized neural networks actually say about generalization? This is the source code to reproduce the experiments of the NeurIPS 2021 paper

gortizji 11 Dec 09, 2022
The Wearables Development Toolkit - a development environment for activity recognition applications with sensor signals

Wearables Development Toolkit (WDK) The Wearables Development Toolkit (WDK) is a framework and set of tools to facilitate the iterative development of

Juan Haladjian 114 Nov 27, 2022
FCOS: Fully Convolutional One-Stage Object Detection (ICCV'19)

FCOS: Fully Convolutional One-Stage Object Detection This project hosts the code for implementing the FCOS algorithm for object detection, as presente

Tian Zhi 3.1k Jan 05, 2023
Implementation of various Vision Transformers I found interesting

Implementation of various Vision Transformers I found interesting

Kim Seonghyeon 78 Dec 06, 2022
PRIME: A Few Primitives Can Boost Robustness to Common Corruptions

PRIME: A Few Primitives Can Boost Robustness to Common Corruptions This is the official repository of PRIME, the data agumentation method introduced i

Apostolos Modas 34 Oct 30, 2022
Semi-Autoregressive Transformer for Image Captioning

Semi-Autoregressive Transformer for Image Captioning Requirements Python 3.6 Pytorch 1.6 Prepare data Please use git clone --recurse-submodules to clo

YE Zhou 23 Dec 09, 2022
Categorizing comments on YouTube into different categories.

Youtube Comments Categorization This repo is for categorizing comments on a youtube video into different categories. negative (grievances, complaints,

Rhitik 5 Nov 26, 2022
Explainable Zero-Shot Topic Extraction

Zero-Shot Topic Extraction with Common-Sense Knowledge Graph This repository contains the code for reproducing the results reported in the paper "Expl

D2K Lab 56 Dec 14, 2022