Segmentation Loss Odyssey

Loss functions are one of the crucial ingredients in deep learning-based medical image segmentation methods. Many loss functions have been proposed in existing literature, but are studied separately or only investigated with few other losses. In this paper, we present a systematic taxonomy to sort existing loss functions into four meaningful categories. This helps to reveal links and fundamental similarities between them. Moreover, we explore the relationship between the traditional region-based and the more recent boundary-based loss functions. The PyTorch implementations of these loss functions are publicly available at \url{https://github.com/JunMa11/SegLoss}.Comment: Educational Materials (https://miccai-sb.github.io/materials/Ma2019.pdf

AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy

Methods: Our deep learning model, called AnatomyNet, segments OARs from head and neck CT images in an end-to-end fashion, receiving whole-volume HaN CT images as input and generating masks of all OARs of interest in one shot. AnatomyNet is built upon the popular 3D U-net architecture, but extends it in three important ways: 1) a new encoding scheme to allow auto-segmentation on whole-volume CT images instead of local patches or subsets of slices, 2) incorporating 3D squeeze-and-excitation residual blocks in encoding layers for better feature representation, and 3) a new loss function combining Dice scores and focal loss to facilitate the training of the neural model. These features are designed to address two main challenges in deep-learning-based HaN segmentation: a) segmenting small anatomies (i.e., optic chiasm and optic nerves) occupying only a few slices, and b) training with inconsistent data annotations with missing ground truth for some anatomical structures. Results: We collected 261 HaN CT images to train AnatomyNet, and used MICCAI Head and Neck Auto Segmentation Challenge 2015 as a benchmark dataset to evaluate the performance of AnatomyNet. The objective is to segment nine anatomies: brain stem, chiasm, mandible, optic nerve left, optic nerve right, parotid gland left, parotid gland right, submandibular gland left, and submandibular gland right. Compared to previous state-of-the-art results from the MICCAI 2015 competition, AnatomyNet increases Dice similarity coefficient by 3.3% on average. AnatomyNet takes about 0.12 seconds to fully segment a head and neck CT image of dimension 178 x 302 x 225, significantly faster than previous methods. In addition, the model is able to process whole-volume CT images and delineate all OARs in one pass, requiring little pre- or post-processing. https://github.com/wentaozhu/AnatomyNet-for-anatomical-segmentation.git.Comment: 6 figures, 4 videos in GitHub and YouTube. Accepted by Medical Physics. Code and videos are available on GitHub. Video: https://www.youtube.com/watch?v=_PpIUIm4XL

A Novel Focal Tversky loss function with improved Attention U-Net for lesion segmentation

We propose a generalized focal loss function based on the Tversky index to address the issue of data imbalance in medical image segmentation. Compared to the commonly used Dice loss, our loss function achieves a better trade off between precision and recall when training on small structures such as lesions. To evaluate our loss function, we improve the attention U-Net model by incorporating an image pyramid to preserve contextual features. We experiment on the BUS 2017 dataset and ISIC 2018 dataset where lesions occupy 4.84% and 21.4% of the images area and improve segmentation accuracy when compared to the standard U-Net by 25.7% and 3.6%, respectively.Comment: submitted to 2019 IEEE International Symposium on Biomedical Imaging (ISBI

Multiview and Multiclass Image Segmentation using Deep Learning in Fetal Echocardiography

Congenital heart disease (CHD) is the most common congenital abnormality associated with birth defects in the United States. Despite training efforts and substantial advancement in ultrasound technology over the past years, CHD remains an abnormality that is frequently missed during prenatal ultrasonography. Therefore, computer-aided detection of CHD can play a critical role in prenatal care by improving screening and diagnosis. Since many CHDs involve structural abnormalities, automatic segmentation of anatomical structures is an important step in the analysis of fetal echocardiograms. While existing methods mainly focus on the four-chamber view with a small number of structures, here we present a more comprehensive deep learning segmentation framework covering 14 anatomical structures in both three-vessel trachea and four-chamber views. Specifically, our framework enhances the V-Net with spatial dropout, group normalization, and deep supervision to train a segmentation model that can be applied on both views regardless of abnormalities. By identifying the pitfall of using the Dice loss when some labels are unavailable in some images, this framework integrates information from multiple views and is robust to missing structures due to anatomical anomalies, achieving an average Dice score of 79%.Comment: This paper was accepted by SPIE Medical Imaging 202

SemSegLoss: A python package of loss functions for semantic segmentation

Image Segmentation has been an active field of research as it has a wide range of applications, ranging from automated disease detection to self-driving cars. In recent years, various research papers proposed different loss functions used in case of biased data, sparse segmentation, and unbalanced dataset. In this paper, we introduce SemSegLoss, a python package consisting of some of the well-known loss functions widely used for image segmentation. It is developed with the intent to help researchers in the development of novel loss functions and perform an extensive set of experiments on model architectures for various applications. The ease-of-use and flexibility of the presented package have allowed reducing the development time and increased evaluation strategies of machine learning models for semantic segmentation. Furthermore, different applications that use image segmentation can use SemSegLoss because of the generality of its functions. This wide range of applications will lead to the development and growth of AI across all industries.Comment: 8 pages, 2 table

Multi Scale Supervised 3D U-Net for Kidney and Tumor Segmentation

U-Net has achieved huge success in various medical image segmentation challenges. Kinds of new architectures with bells and whistles might succeed in certain dataset when employed with optimal hyper-parameter, but their generalization always can't be guaranteed. Here, we focused on the basic U-Net architecture and proposed a multi scale supervised 3D U-Net for the segmentation task in KiTS19 challenge. To enhance the performance, our work can be summarized as three folds: first, we used multi scale supervision in the decoder pathway, which could encourage the network to predict right results from the deep layers; second, with the aim to alleviate the bad effect from the sample imbalance of kidney and tumor, we adopted exponential logarithmic loss; third, a connected-component based post processing method was designed to remove the obviously wrong voxels. In the published KiTS19 training dataset (totally 210 patients), we divided 42 patients to be test dataset and finally obtained DICE scores of 0.969 and 0.805 for the kidney and tumor respectively. In the challenge, we finally achieved the 7th place among 106 teams with the Composite Dice of 0.8961, namely 0.9741 for kidney and 0.8181 for tumor.Comment: 7 pages, 5 figure

Universal Loss Reweighting to Balance Lesion Size Inequality in 3D Medical Image Segmentation

Target imbalance affects the performance of recent deep learning methods in many medical image segmentation tasks. It is a twofold problem: class imbalance - positive class (lesion) size compared to negative class (non-lesion) size; lesion size imbalance - large lesions overshadows small ones (in the case of multiple lesions per image). While the former was addressed in multiple works, the latter lacks investigation. We propose a loss reweighting approach to increase the ability of the network to detect small lesions. During the learning process, we assign a weight to every image voxel. The assigned weights are inversely proportional to the lesion volume, thus smaller lesions get larger weights. We report the benefit from our method for well-known loss functions, including Dice Loss, Focal Loss, and Asymmetric Similarity Loss. Additionally, we compare our results with other reweighting techniques: Weighted Cross-Entropy and Generalized Dice Loss. Our experiments show that inverse weighting considerably increases the detection quality, while preserves the delineation quality on a state-of-the-art level. We publish a complete experimental pipeline for two publicly available datasets of CT images: LiTS and LUNA16 (https://github.com/neuro-ml/inverse_weighting). We also show results on a private database of MR images for the task of multiple brain metastases delineation.Comment: Accepted to MICCAI 202

Segmentation overlapping wear particles with few labelled data and imbalance sample

Ferrograph image segmentation is of significance for obtaining features of wear particles. However, wear particles are usually overlapped in the form of debris chains, which makes challenges to segment wear debris. An overlapping wear particle segmentation network (OWPSNet) is proposed in this study to segment the overlapped debris chains. The proposed deep learning model includes three parts: a region segmentation network, an edge detection network and a feature refine module. The region segmentation network is an improved U shape network, and it is applied to separate the wear debris form background of ferrograph image. The edge detection network is used to detect the edges of wear particles. Then, the feature refine module combines low-level features and high-level semantic features to obtain the final results. In order to solve the problem of sample imbalance, we proposed a square dice loss function to optimize the model. Finally, extensive experiments have been carried out on a ferrograph image dataset. Results show that the proposed model is capable of separating overlapping wear particles. Moreover, the proposed square dice loss function can improve the segmentation results, especially for the segmentation results of wear particle edge

Boundary loss for highly unbalanced segmentation

Widely used loss functions for convolutional neural network (CNN) segmentation, e.g., Dice or cross-entropy, are based on integrals (summations) over the segmentation regions. Unfortunately, it is quite common in medical image analysis to have highly unbalanced segmentations, where standard losses contain regional terms with values that differ considerably --typically of several orders of magnitude-- across segmentation classes, which may affect training performance and stability. The purpose of this study is to build a boundary loss, which takes the form of a distance metric on the space of contours, not regions. We argue that a boundary loss can mitigate the difficulties of regional losses in the context of highly unbalanced segmentation problems because it uses integrals over the boundary between regions instead of unbalanced integrals over regions. Furthermore, a boundary loss provides information that is complementary to regional losses. Unfortunately, it is not straightforward to represent the boundary points corresponding to the regional softmax outputs of a CNN. Our boundary loss is inspired by discrete (graph-based) optimization techniques for computing gradient flows of curve evolution. Following an integral approach for computing boundary variations, we express a non-symmetric L2 distance on the space of shapes as a regional integral, which avoids completely local differential computations involving contour points. Our boundary loss is the sum of linear functions of the regional softmax probability outputs of the network. Therefore, it can easily be combined with standard regional losses and implemented with any existing deep network architecture for N-D segmentation. Our boundary loss has been validated on two benchmark datasets corresponding to difficult, highly unbalanced segmentation problems: the ischemic stroke lesion (ISLES) and white matter hyperintensities (WMH).Comment: Talk at MIDL 2019 [arXiv:1907.08612

Improved Inference via Deep Input Transfer

Although numerous improvements have been made in the field of image segmentation using convolutional neural networks, the majority of these improvements rely on training with larger datasets, model architecture modifications, novel loss functions, and better optimizers. In this paper, we propose a new segmentation performance boosting paradigm that relies on optimally modifying the network's input instead of the network itself. In particular, we leverage the gradients of a trained segmentation network with respect to the input to transfer it to a space where the segmentation accuracy improves. We test the proposed method on three publicly available medical image segmentation datasets: the ISIC 2017 Skin Lesion Segmentation dataset, the Shenzhen Chest X-Ray dataset, and the CVC-ColonDB dataset, for which our method achieves improvements of 5.8%, 0.5%, and 4.8% in the average Dice scores, respectively.Comment: Accepted to MICCAI 201