Timo Loehr

Chinmay Prabhakar, Hongwei Bran Li, Johannes C. Paetzold et al.

Multiple Sclerosis (MS) is a severe neurological disease characterized by inflammatory lesions in the central nervous system. Hence, predicting inflammatory disease activity is crucial for disease assessment and treatment. However, MS lesions can occur throughout the brain and vary in shape, size and total count among patients. The high variance in lesion load and locations makes it challenging for machine learning methods to learn a globally effective representation of whole-brain MRI scans to assess and predict disease. Technically it is non-trivial to incorporate essential biomarkers such as lesion load or spatial proximity. Our work represents the first attempt to utilize graph neural networks (GNN) to aggregate these biomarkers for a novel global representation. We propose a two-stage MS inflammatory disease activity prediction approach. First, a 3D segmentation network detects lesions, and a self-supervised algorithm extracts their image features. Second, the detected lesions are used to build a patient graph. The lesions act as nodes in the graph and are initialized with image features extracted in the first stage. Finally, the lesions are connected based on their spatial proximity and the inflammatory disease activity prediction is formulated as a graph classification task. Furthermore, we propose a self-pruning strategy to auto-select the most critical lesions for prediction. Our proposed method outperforms the existing baseline by a large margin (AUCs of 0.67 vs. 0.61 and 0.66 vs. 0.60 for one-year and two-year inflammatory disease activity, respectively). Finally, our proposed method enjoys inherent explainability by assigning an importance score to each lesion for the overall prediction. Code is available at https://github.com/chinmay5/ms_ida.git

Florian Kofler, Suprosanna Shit, Ivan Ezhov et al.

Deep convolutional neural networks (CNN) have proven to be remarkably effective in semantic segmentation tasks. Most popular loss functions were introduced targeting improved volumetric scores, such as the Dice coefficient (DSC). By design, DSC can tackle class imbalance, however, it does not recognize instance imbalance within a class. As a result, a large foreground instance can dominate minor instances and still produce a satisfactory DSC. Nevertheless, detecting tiny instances is crucial for many applications, such as disease monitoring. For example, it is imperative to locate and surveil small-scale lesions in the follow-up of multiple sclerosis patients. We propose a novel family of loss functions, \emph{blob loss}, primarily aimed at maximizing instance-level detection metrics, such as F1 score and sensitivity. \emph{Blob loss} is designed for semantic segmentation problems where detecting multiple instances matters. We extensively evaluate a DSC-based \emph{blob loss} in five complex 3D semantic segmentation tasks featuring pronounced instance heterogeneity in terms of texture and morphology. Compared to soft Dice loss, we achieve 5% improvement for MS lesions, 3% improvement for liver tumor, and an average 2% improvement for microscopy segmentation tasks considering F1 score.

Leon Mächler, Ivan Ezhov, Florian Kofler et al.

We propose a simple new aggregation strategy for federated learning that won the MICCAI Federated Tumor Segmentation Challenge 2021 (FETS), the first ever challenge on Federated Learning in the Machine Learning community. Our method addresses the problem of how to aggregate multiple models that were trained on different data sets. Conceptually, we propose a new way to choose the weights when averaging the different models, thereby extending the current state of the art (FedAvg). Empirical validation demonstrates that our approach reaches a notable improvement in segmentation performance compared to FedAvg.

Hongwei Li, Timo Loehr, Anjany Sekuboyina et al.

In medical imaging, the heterogeneity of multi-centre data impedes the applicability of deep learning-based methods and results in significant performance degradation when applying models in an unseen data domain, e.g. a new centreor a new scanner. In this paper, we propose an unsupervised domain adaptation framework for boosting image segmentation performance across multiple domains without using any manual annotations from the new target domains, but by re-calibrating the networks on few images from the target domain. To achieve this, we enforce architectures to be adaptive to new data by rejecting improbable segmentation patterns and implicitly learning through semantic and boundary information, thus to capture disease-specific spatial patterns in an adversarial optimization. The adaptation process needs continuous monitoring, however, as we cannot assume the presence of ground-truth masks for the target domain, we propose two new metrics to monitor the adaptation process, and strategies to train the segmentation algorithm in a stable fashion. We build upon well-established 2D and 3D architectures and perform extensive experiments on three cross-centre brain lesion segmentation tasks, involving multicentre public and in-house datasets. We demonstrate that recalibrating the deep networks on a few unlabeled images from the target domain improves the segmentation accuracy significantly.