Lucian Beer

Jeanny Pan, Philipp Seeböck, Christoph Fürböck et al.

Identifying new disease-related patterns in medical imaging data with the help of machine learning enlarges the vocabulary of recognizable findings. This supports diagnostic and prognostic assessment. However, image appearance varies not only due to biological differences, but also due to imaging technology linked to vendors, scanning- or re- construction parameters. The resulting domain shifts impedes data representation learning strategies and the discovery of biologically meaningful cluster appearances. To address these challenges, we introduce an approach to actively learn the domain shift via post-hoc rotation of the data latent space, enabling disentanglement of biological and technical factors. Results on real-world heterogeneous clinical data showcase that the learned disentangled representation leads to stable clusters representing tissue-types across different acquisition settings. Cluster consistency is improved by +19.01% (ARI), +16.85% (NMI), and +12.39% (Dice) compared to the entangled representation, outperforming four state-of-the-art harmonization methods. When using the clusters to quantify tissue composition on idiopathic pulmonary fibrosis patients, the learned profiles enhance Cox survival prediction. This indicates that the proposed label-free framework facilitates biomarker discovery in multi-center routine imaging data. Code is available on GitHub https://github.com/cirmuw/latent-space-rotation-disentanglement.

Daniel Sobotka, Alexander Herold, Matthias Perkonigg et al.

Liver vessel segmentation in magnetic resonance imaging data is important for the computational analysis of vascular remodelling, associated with a wide spectrum of diffuse liver diseases. Existing approaches rely on contrast enhanced imaging data, but the necessary dedicated imaging sequences are not uniformly acquired. Images without contrast enhancement are acquired more frequently, but vessel segmentation is challenging, and requires large-scale annotated data. We propose a multi-task learning framework to segment vessels in liver MRI without contrast. It exploits auxiliary contrast enhanced MRI data available only during training to reduce the need for annotated training examples. Our approach draws on paired native and contrast enhanced data with and without vessel annotations for model training. Results show that auxiliary data improves the accuracy of vessel segmentation, even if they are not available during inference. The advantage is most pronounced if only few annotations are available for training, since the feature representation benefits from the shared task structure. A validation of this approach to augment a model for brain tumor segmentation confirms its benefits across different domains. An auxiliary informative imaging modality can augment expert annotations even if it is only available during training.

Alexander Herold, Daniel Sobotka, Lucian Beer et al.

Background: We aimed to quantify hepatic vessel volumes across chronic liver disease stages and healthy controls using deep learning-based magnetic resonance imaging (MRI) analysis, and assess correlations with biomarkers for liver (dys)function and fibrosis/portal hypertension. Methods: We assessed retrospectively healthy controls, non-advanced and advanced chronic liver disease (ACLD) patients using a 3D U-Net model for hepatic vessel segmentation on portal venous phase gadoxetic acid-enhanced 3-T MRI. Total (TVVR), hepatic (HVVR), and intrahepatic portal vein-to-volume ratios (PVVR) were compared between groups and correlated with: albumin-bilirubin (ALBI) and model for end-stage liver disease-sodium (MELD-Na) score, and fibrosis/portal hypertension (Fibrosis-4 [FIB-4] score, liver stiffness measurement [LSM], hepatic venous pressure gradient [HVPG], platelet count [PLT], and spleen volume). Results: We included 197 subjects, aged 54.9 $\pm$ 13.8 years (mean $\pm$ standard deviation), 111 males (56.3\%): 35 healthy controls, 44 non-ACLD, and 118 ACLD patients. TVVR and HVVR were highest in controls (3.9; 2.1), intermediate in non-ACLD (2.8; 1.7), and lowest in ACLD patients (2.3; 1.0) ($p \leq 0.001$). PVVR was reduced in both non-ACLD and ACLD patients (both 1.2) compared to controls (1.7) ($p \leq 0.001$), but showed no difference between CLD groups ($p = 0.999$). HVVR significantly correlated indirectly with FIB-4, ALBI, MELD-Na, LSM, and spleen volume ($ρ$ ranging from -0.27 to -0.40), and directly with PLT ($ρ= 0.36$). TVVR and PVVR showed similar but weaker correlations. Conclusions: Deep learning-based hepatic vessel volumetry demonstrated differences between healthy liver and chronic liver disease stages and shows correlations with established markers of disease severity.

Xiang Bai, Hanchen Wang, Liya Ma et al.

Artificial intelligence (AI) provides a promising substitution for streamlining COVID-19 diagnoses. However, concerns surrounding security and trustworthiness impede the collection of large-scale representative medical data, posing a considerable challenge for training a well-generalised model in clinical practices. To address this, we launch the Unified CT-COVID AI Diagnostic Initiative (UCADI), where the AI model can be distributedly trained and independently executed at each host institution under a federated learning framework (FL) without data sharing. Here we show that our FL model outperformed all the local models by a large yield (test sensitivity /specificity in China: 0.973/0.951, in the UK: 0.730/0.942), achieving comparable performance with a panel of professional radiologists. We further evaluated the model on the hold-out (collected from another two hospitals leaving out the FL) and heterogeneous (acquired with contrast materials) data, provided visual explanations for decisions made by the model, and analysed the trade-offs between the model performance and the communication costs in the federated training process. Our study is based on 9,573 chest computed tomography scans (CTs) from 3,336 patients collected from 23 hospitals located in China and the UK. Collectively, our work advanced the prospects of utilising federated learning for privacy-preserving AI in digital health.

Michael Roberts, Derek Driggs, Matthew Thorpe et al.

Machine learning methods offer great promise for fast and accurate detection and prognostication of COVID-19 from standard-of-care chest radiographs (CXR) and computed tomography (CT) images. Many articles have been published in 2020 describing new machine learning-based models for both of these tasks, but it is unclear which are of potential clinical utility. In this systematic review, we search EMBASE via OVID, MEDLINE via PubMed, bioRxiv, medRxiv and arXiv for published papers and preprints uploaded from January 1, 2020 to October 3, 2020 which describe new machine learning models for the diagnosis or prognosis of COVID-19 from CXR or CT images. Our search identified 2,212 studies, of which 415 were included after initial screening and, after quality screening, 61 studies were included in this systematic review. Our review finds that none of the models identified are of potential clinical use due to methodological flaws and/or underlying biases. This is a major weakness, given the urgency with which validated COVID-19 models are needed. To address this, we give many recommendations which, if followed, will solve these issues and lead to higher quality model development and well documented manuscripts.