Comparison of Loss Functions for Robust Deep Learning-based Echocardiography Segmentation when Learning with Partially Labelled Data from Multiple Domains

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.

Detecting and refurbishing ground truth errors during training of deep learning-based echocardiography segmentation models

Deep learning-based medical image segmentation typically relies on ground truth (GT) labels obtained through manual annotation, but these can be prone to random errors or systematic biases. This study examines the robustness of deep learning models to such errors in echocardiography (echo) segmentation and evaluates a novel strategy for detecting and refurbishing erroneous labels during model training. Using the CAMUS dataset, we simulate three error types, then compare a loss-based GT label error detection method with one based on Variance of Gradients (VOG). We also propose a pseudo-labelling approach to refurbish suspected erroneous GT labels. We assess the performance of our proposed approach under varying error levels. Results show that VOG proved highly effective in flagging erroneous GT labels during training. However, a standard U-Net maintained strong performance under random label errors and moderate levels of systematic errors (up to 50%). The detection and refurbishment approach improved performance, particularly under high-error conditions.

Label Dropout: Improved Deep Learning Echocardiography Segmentation Using Multiple Datasets With Domain Shift and Partial Labelling

Echocardiography (echo) is the first imaging modality used when assessing cardiac function. The measurement of functional biomarkers from echo relies upon the segmentation of cardiac structures and deep learning models have been proposed to automate the segmentation process. However, in order to translate these tools to widespread clinical use it is important that the segmentation models are robust to a wide variety of images (e.g. acquired from different scanners, by operators with different levels of expertise etc.). To achieve this level of robustness it is necessary that the models are trained with multiple diverse datasets. A significant challenge faced when training with multiple diverse datasets is the variation in label presence, i.e. the combined data are often partially-labelled. Adaptations of the cross entropy loss function have been proposed to deal with partially labelled data. In this paper we show that training naively with such a loss function and multiple diverse datasets can lead to a form of shortcut learning, where the model associates label presence with domain characteristics, leading to a drop in performance. To address this problem, we propose a novel label dropout scheme to break the link between domain characteristics and the presence or absence of labels. We demonstrate that label dropout improves echo segmentation Dice score by 62% and 25% on two cardiac structures when training using multiple diverse partially labelled datasets.