The lack of explainability of deep learning models limits the adoption of such models in clinical practice. Prototype-based models can provide inherent explainable predictions, but these have predominantly been designed for classification tasks, despite many important tasks in medical imaging being continuous regression problems. Therefore, in this work, we present ExPeRT: an explainable prototype-based model specifically designed for regression tasks. Our proposed model makes a sample prediction from the distances to a set of learned prototypes in latent space, using a weighted mean of prototype labels. The distances in latent space are regularized to be relative to label differences, and each of the prototypes can be visualized as a sample from the training set. The image-level distances are further constructed from patch-level distances, in which the patches of both images are structurally matched using optimal transport. This thus provides an example-based explanation with patch-level detail at inference time. We demonstrate our proposed model for brain age prediction on two imaging datasets: adult MR and fetal ultrasound. Our approach achieved state-of-the-art prediction performance while providing insight into the model’s reasoning process.

Since the rise of deep learning, new medical segmentation methods have rapidly been proposed with extremely promising results, often reporting marginal improvements on the previous state-of-the-art (SOTA) method. However, on visual inspection errors are often revealed, such as topological mistakes (e.g. holes or folds), that are not detected using traditional evaluation metrics. Incorrect topology can often lead to errors in clinically required downstream image processing tasks. Therefore, there is a need for new methods to focus on ensuring segmentations are topologically correct. In this work, we present TEDS-Net: a segmentation network that preserves anatomical topology whilst maintaining segmentation performance that is competitive with SOTA baselines. Further, we show how current SOTA segmentation methods can introduce problematic topological errors. TEDS-Net achieves anatomically plausible segmentation by using learnt topology-preserving fields to deform a prior. Traditionally, topology-preserving fields are described in the continuous domain and begin to break down when working in the discrete domain. Here, we introduce additional modifications that more strictly enforce topology preservation. We illustrate our method on an open-source medical heart dataset, performing both single and multi-structure segmentation, and show that the generated fields contain no folding voxels, which corresponds to full topology preservation on individual structures whilst vastly outperforming the other baselines on overall scene topology. The code is available at: https://github.com/mwyburd/TEDS-Net.

To represent the biological variability of clinical neuroimaging populations, it is vital to be able to combine data across scanners and studies. However, different MRI scanners produce images with different characteristics, resulting in a domain shift known as the ‘harmonisation problem’. Additionally, neuroimaging data is inherently personal in nature, leading to data privacy concerns when sharing the data. To overcome these barriers, we propose an Unsupervised Source-Free Domain Adaptation (SFDA) method, SFHarmony. Through modelling the imaging features as a Gaussian Mixture Model and minimising an adapted Bhattacharyya distance between the source and target features, we can create a model that performs well for the target data whilst having a shared feature representation across the data domains, without needing access to the source data for adaptation or target labels. We demonstrate the performance of our method on simulated and real domain shifts, showing that the approach is applicable to classification, segmentation and regression tasks, requiring no changes to the algorithm. Our method outperforms existing SFDA approaches across a range of realistic data scenarios, demonstrating the potential utility of our approach for MRI harmonisation and general SFDA problems. Our code is available at https://github.com/nkdinsdale/SFHarmony.

Acquisition of high quality manual annotations is vital for the development of segmentation algorithms. However, to create them we require a substantial amount of expert time and knowledge. Large numbers of labels are required to train convolutional neural networks due to the vast number of parameters that must be learned in the optimisation process. Here, we develop the STAMP algorithm to allow the simultaneous training and pruning of a UNet architecture for medical image segmentation with targeted channelwise dropout to make the network robust to the pruning. We demonstrate the technique across segmentation tasks and imaging modalities. It is then shown that, through online pruning, we are able to train networks to have much higher performance than the equivalent standard UNet models while reducing their size by more than 85% in terms of parameters. This has the potential to allow networks to be directly trained on datasets where very low numbers of labels are available.

Robust automated segmentation of white matter hyperintensities (WMHs) in different datasets (domains) is highly challenging due to differences in acquisition (scanner, sequence), population (WMH amount and location) and limited availability of manual segmentations to train supervised algorithms. In this work we explore various domain adaptation techniques such as transfer learning and domain adversarial learning methods, including domain adversarial neural networks and domain unlearning, to improve the generalisability of our recently proposed triplanar ensemble network, which is our baseline model. We used datasets with variations in intensity profile, lesion characteristics and acquired using different scanners. For the source domain, we considered a dataset consisting of data acquired from 3 different scanners, while the target domain consisted of 2 datasets. We evaluated the domain adaptation techniques on the target domain datasets, and additionally evaluated the performance on the source domain test dataset for the adversarial techniques. For transfer learning, we also studied various training options such as minimal number of unfrozen layers and subjects required for fine-tuning in the target domain. On comparing the performance of different techniques on the target dataset, domain adversarial training of neural network gave the best performance, making the technique promising for robust WMH segmentation.