Automatic segmentation methods are an important advancement in medical image analysis. Machine learning techniques, and deep neural networks in particular, are the state-of-the-art for most medical image segmentation tasks. Issues with class imbalance pose a significant challenge in medical datasets, with lesions often occupying a considerably smaller volume relative to the background. Loss functions used in the training of deep learning algorithms differ in their robustness to class imbalance, with direct consequences for model convergence. The most commonly used loss functions for segmentation are based on either the cross entropy loss, Dice loss or a combination of the two. We propose the Unified Focal loss, a new hierarchical framework that generalises Dice and cross entropy-based losses for handling class imbalance. We evaluate our proposed loss function on five publicly available, class imbalanced medical imaging datasets: CVC-ClinicDB, Digital Retinal Images for Vessel Extraction (DRIVE), Breast Ultrasound 2017 (BUS2017), Brain Tumour Segmentation 2020 (BraTS20) and Kidney Tumour Segmentation 2019 (KiTS19). We compare our loss function performance against six Dice or cross entropy-based loss functions, across 2D binary, 3D binary and 3D multiclass segmentation tasks, demonstrating that our proposed loss function is robust to class imbalance and consistently outperforms the other loss functions. Source code is available at: https://github.com/mlyg/unified-focal-loss
Do We Really Need Dice? The Hidden Region-Size Biases of Segmentation Losses
ÉTS Montréal（蒙特利尔工程学院）；MILA（蒙特利尔学习算法研究所）；CNRS（法国国家科学研究中心）；Université Paris-Saclay（巴黎萨克雷大学）；CentraleSupélec（中央理工-高等电力学院）；Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM)（蒙特利尔大学医院研究中心）；Universitat Pompeu Fabra（庞培法布拉大学）；Diagnos Inc.（诊断公司）
UMIT – Private University for Health Sciences, Medical Informatics and Technology（UMIT——健康科学、医学信息学与技术私立大学）
The segmentation of organs at risk (OAR) is a required precondition for the cancer treatment with image guided radiation therapy. The automation of the segmentation task is therefore of high clinical relevance. Deep Learning (DL) based medical image segmentation is currently the most successful approach, but suffers from the over-presence of the background class and the anatomically given organ size difference, which is most severe in the head and neck (HAN) area. To tackle the HAN area specific class imbalance problem we first optimize the patch-size of the currently best performing general p…
The Institute of Cancer Research（癌症研究所）；University College London Cancer Institute（伦敦大学学院癌症研究所）
Automated analysis of tissue sections allows a better understanding of disease biology and may reveal biomarkers that could guide prognosis or treatment selection. In digital pathology, less abundant cell types can be of biological significance, but their scarcity can result in biased and sub-optimal cell detection model. To minimize the effect of cell imbalance on cell detection, we proposed a deep learning pipeline that considers the abundance of cell types during model training. Cell weight images were generated, which assign larger weights to less abundant cells and used the weights to reg…
Automatic segmentation of the heart cavity is an essential task for the diagnosis of cardiac diseases. In this paper, we propose a semi-supervised segmentation setup for leveraging unlabeled data to segment Left-ventricle, Right-ventricle, and Myocardium. We utilize an enhanced version of residual U-Net architecture on a large-scale cardiac MRI dataset. Handling the class imbalanced data issue using dice loss, the enhanced supervised model is able to achieve better dice scores in comparison with a vanilla U-Net model. We applied several augmentation techniques including histogram matching to i…
VRVis Center for Virtual Reality and Visualization（VRVis虚拟现实与可视化中心）
The success of deep convolutional neural networks on image classification and recognition tasks has led to new applications in very diversified contexts, including the field of medical imaging. In this paper we investigate and propose neural network architectures for automated multi-class segmentation of anatomical organs in chest radiographs, namely for lungs, clavicles and heart. We address several open challenges including model overfitting, reducing number of parameters and handling of severely imbalanced data in CXR by fusing recent concepts in convolutional networks and adapting them to …
University of Arkansas（阿肯色大学）；Carnegie Mellon University（卡内基梅隆大学）
Medical image segmentation has played an important role in medical analysis and widely developed for many clinical applications. Deep learning-based approaches have achieved high performance in semantic segmentation but they are limited to pixel-wise setting and imbalanced classes data problem. In this paper, we tackle those limitations by developing a new deep learning-based model which takes into account both higher feature level i.e. region inside contour, intermediate feature level i.e. offset curves around the contour and lower feature level i.e. contour. Our proposed Offset Curves (OsC) …
Beyond scalar losses: calibrating segmentation models via gradient vector field surgery
School of Computation, Information and Technology, TUM（慕尼黑工业大学计算、信息与技术学院）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Department of Radiology, Weill Cornell Medicine（威尔康乃尔医学院放射科）；School of Medicine and Health, TUM University Hospital（慕尼黑工业大学医院医学与健康学院）；Cornell Tech（康奈尔科技学院）；Department of Computing, Imperial College London（伦敦帝国理工学院计算系）
University of Delaware（特拉华大学）；University of Guilan（吉兰大学）；Eindhoven University of Technology（埃因霍温理工大学）；Iran University of Science and Technology（伊朗科学技术大学）
Automated 3-D breast ultrasound (ABUS) is a newfound system for breast screening that has been proposed as a supplementary modality to mammography for breast cancer detection. While ABUS has better performance in dense breasts, reading ABUS images is exhausting and time-consuming. So, a computer-aided detection system is necessary for interpretation of these images. Mass segmentation plays a vital role in the computer-aided detection systems and it affects the overall performance. Mass segmentation is a challenging task because of the large variety in size, shape, and texture of masses. Moreov…
Generative deep learning for foundational video translation in ultrasound
Department of Medicine, Division of Cardiology（医学系，心脏病科）；Bakar Computational Health Sciences Institute（Bakar计算健康科学研究所）；University of California, San Francisco（加州大学旧金山分校）；UCSF-UC Berkeley Joint Program in Computational Precision Health（UCSF-伯克利计算精准健康联合项目）；Department of Radiology, Center for Intelligent Imaging（放射科，智能成像中心）
Disentangling Sampling from Training Budget in Class-Imbalanced CT Body Composition Segmentation
Amsterdam University Medical Center（阿姆斯特丹大学医学中心）；University of Amsterdam（阿姆斯特丹大学）；Informatics Institute, Faculty of Science（信息学院，科学学院）；Department of Radiology（放射科）；Mayo Clinic Rochester（罗切斯特梅奥诊所）
Friedrich-Alexander University Erlangen-Nürnberg（埃尔朗根-纽伦堡大学）
The vast majority of the outlet glaciers and ice streams of the polar ice sheets end in the ocean. Ice mass loss via calving of the glaciers into the ocean has increased over the last few decades. Information on the temporal variability of the calving front position provides fundamental information on the state of the glacier and ice stream, which can be exploited as calibration and validation data to enhance ice dynamics modeling. To identify the calving front position automatically, deep neural network-based semantic segmentation pipelines can be used to delineate the acquired SAR imagery. H…
University of Cambridge（剑桥大学）；Cancer Research UK Cambridge Centre（英国癌症研究中心剑桥中心）
Background: Colonoscopy remains the gold-standard screening for colorectal cancer. However, significant miss rates for polyps have been reported, particularly when there are multiple small adenomas. This presents an opportunity to leverage computer-aided systems to support clinicians and reduce the number of polyps missed. Method: In this work we introduce the Focus U-Net, a novel dual attention-gated deep neural network, which combines efficient spatial and channel-based attention into a single Focus Gate module to encourage selective learning of polyp features. The Focus U-Net further incorp…
