Comparison of Loss Functions for Robust Deep Learning-based Echocardiography Segmentation when Learning with Partially Labelled Data from Multiple Domains
School of Biomedical Engineering & Imaging Sciences, King’s College London, UK（英国伦敦国王学院生物医学工程与影像科学学院）
Iman Islam, Esther Puyol-Antón, Bram Ruijsink, Andrew J. Reader, Andrew P. King
Echocardiography is the first imaging modality used for assessing cardiac function, and accurate segmentation of cardiac structures is essential for deriving biomarkers. However, the development of effective automated segmentation models for multiple cardiac structures is challenged by the difficulty of training on datasets from different sources that are often partially-labelled. This study aims to address this challenge by evaluating the performance of three loss functions - adaptive categorical cross entropy (aCCE) loss, marginal loss, and the adaptive binary cross entropy (aBCE) loss - in handling partially-labelled data. We conduct a comprehensive comparison of these loss functions across multiple scenarios and network architectures: intra-domain and inter-domain tasks, with both single and multiple partial-labels, and varying proportions of fully-labelled to partially-labelled data.
Our experiments reveal that all three loss functions exhibit strong performance in intra-domain segmentation tasks, effectively handling label variations within the same domain. For inter-domain tasks, where models are trained on datasets with a domain shift, the aBCE and marginal losses show superior performance when dealing with the case of one label being missing from some training examples. In scenarios involving more than one label being missing, marginal loss outperforms the other methods, demonstrating its robustness in such complex conditions. These results highlight the strengths of each loss function depending on the labelling scenario, emphasizing the importance of selecting the appropriate loss function to optimize model performance. This study represents the first investigation of techniques for handling partially-labelled data from multiple different domains in echocardiography segmentation and provides a comprehensive comparison of loss-based solutions.
Comparative evaluation of training strategies using partially labelled datasets for segmentation of white matter hyperintensities and stroke lesions in FLAIR MRI
Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Contrastive learning has proven useful in many applications where access to labelled data is limited. The lack of annotated data is particularly problematic in medical image segmentation as it is difficult to have clinical experts manually annotate large volumes of data such as cardiac structures in ultrasound images of the heart. In this paper, We propose a self supervised contrastive learning method to segment the left ventricle from echocardiography when limited annotated images exist. Furthermore, we study the effect of contrastive pretraining on two well-known segmentation networks, UNet …
In the object detection task, merging various datasets from similar contexts but with different sets of Objects of Interest (OoI) is an inexpensive way (in terms of labor cost) for crafting a large-scale dataset covering a wide range of objects. Moreover, merging datasets allows us to train one integrated object detector, instead of training several ones, which in turn resulting in the reduction of computational and time costs. However, merging the datasets from similar contexts causes samples with partial labeling as each constituent dataset is originally annotated for its own set of OoI and …
In this work we present a novel end-to-end framework for tracking and classifying a robot's surroundings in complex, dynamic and only partially observable real-world environments. The approach deploys a recurrent neural network to filter an input stream of raw laser measurements in order to directly infer object locations, along with their identity in both visible and occluded areas. To achieve this we first train the network using unsupervised Deep Tracking, a recently proposed theoretical framework for end-to-end space occupancy prediction. We show that by learning to track on a large amount…
Center for Machine Vision and Signal Analysis (CMVS)（机器视觉与信号分析中心）；University of Oulu（奥卢大学）；Department of Eye and Vision Science（眼科学与视觉科学系）；University of Liverpool（利物浦大学）；Center for Medical Data Science（医学数据科学中心）；Medical University of Vienna（维也纳医学大学）
CITIC；Universidade da Coruña（拉科鲁尼亚大学）；CiTIUS；Universidade de Santiago de Compostela（圣地亚哥-德孔波斯特拉大学）
Deep Learning approaches have brought solutions, with impressive performance, to general classification problems where wealthy of annotated data are provided for training. In contrast, less progress has been made in continual learning of a set of non-stationary classes, mainly when applied to unsupervised problems with streaming data. Here, we propose a novel incremental learning approach which combines a deep features encoder with an Open-Set Dynamic Ensembles of SVM, to tackle the problem of identifying individuals of interest (IoI) from streaming face data. From a simple weak classifier tra…
Despite the recent advances in multi-task learning of dense prediction problems, most methods rely on expensive labelled datasets. In this paper, we present a label efficient approach and look at jointly learning of multiple dense prediction tasks on partially annotated data (i.e. not all the task labels are available for each image), which we call multi-task partially-supervised learning. We propose a multi-task training procedure that successfully leverages task relations to supervise its multi-task learning when data is partially annotated. In particular, we learn to map each task pair to a…
Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a…
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）
Due to the intensive cost of labor and expertise in annotating 3D medical images at a voxel level, most benchmark datasets are equipped with the annotations of only one type of organs and/or tumors, resulting in the so-called partially labeling issue. To address this, we propose a dynamic on-demand network (DoDNet) that learns to segment multiple organs and tumors on partially labeled datasets. DoDNet consists of a shared encoder-decoder architecture, a task encoding module, a controller for generating dynamic convolution filters, and a single but dynamic segmentation head. The information of …
University of Cambridge（剑桥大学）；Shanghai General Hospital（上海市第一人民医院）；Shanghai Jiao Tong University（上海交通大学）；Southern University of Science and Technology（南方科技大学）；University of Bath（巴斯大学）
We present an Expectation-Maximization (EM) Regularized Deep Learning (EMReDL) model for weakly supervised tumor segmentation. The proposed framework is tailored to glioblastoma, a type of malignant tumor characterized by its diffuse infiltration into the surrounding brain tissue, which poses significant challenge to treatment target and tumor burden estimation using conventional structural MRI. Although physiological MRI provides more specific information regarding tumor infiltration, the relatively low resolution hinders a precise full annotation. This has motivated us to develop a weakly su…
Samsung AI Center Cambridge（三星人工智能中心剑桥）；The University of Edinburgh（爱丁堡大学）
Domain adaptation (DA) is the topical problem of adapting models from labelled source datasets so that they perform well on target datasets where only unlabelled or partially labelled data is available. Many methods have been proposed to address this problem through different ways to minimise the domain shift between source and target datasets. In this paper we take an orthogonal perspective and propose a framework to further enhance performance by meta-learning the initial conditions of existing DA algorithms. This is challenging compared to the more widely considered setting of few-shot meta…
Monash University（莫纳什大学）；University of Adelaide（阿德莱德大学）
We present LAVA, a simple yet effective method for multi-domain visual transfer learning with limited data. LAVA builds on a few recent innovations to enable adapting to partially labelled datasets with class and domain shifts. First, LAVA learns self-supervised visual representations on the source dataset and ground them using class label semantics to overcome transfer collapse problems associated with supervised pretraining. Secondly, LAVA maximises the gains from unlabelled target data via a novel method which uses multi-crop augmentations to obtain highly robust pseudo-labels. By combining…
Semi-supervised learning (SSL) can reduce the need for large labelled datasets by incorporating unlabelled data into the training. This is particularly interesting for semantic segmentation, where labelling data is very costly and time-consuming. Current SSL approaches use an initially supervised trained model to generate predictions for unlabelled images, called pseudo-labels, which are subsequently used for training a new model from scratch. Since the predictions usually do not come from an error-free neural network, they are naturally full of errors. However, training with partially incorre…
