Gholamreza Salimi Khorshidi

Yikuan Li, Mohammad Mamouei, Gholamreza Salimi-Khorshidi et al.

Electronic health records represent a holistic overview of patients' trajectories. Their increasing availability has fueled new hopes to leverage them and develop accurate risk prediction models for a wide range of diseases. Given the complex interrelationships of medical records and patient outcomes, deep learning models have shown clear merits in achieving this goal. However, a key limitation of these models remains their capacity in processing long sequences. Capturing the whole history of medical encounters is expected to lead to more accurate predictions, but the inclusion of records collected for decades and from multiple resources can inevitably exceed the receptive field of the existing deep learning architectures. This can result in missing crucial, long-term dependencies. To address this gap, we present Hi-BEHRT, a hierarchical Transformer-based model that can significantly expand the receptive field of Transformers and extract associations from much longer sequences. Using a multimodal large-scale linked longitudinal electronic health records, the Hi-BEHRT exceeds the state-of-the-art BEHRT 1% to 5% for area under the receiver operating characteristic (AUROC) curve and 3% to 6% for area under the precision recall (AUPRC) curve on average, and 3% to 6% (AUROC) and 3% to 11% (AUPRC) for patients with long medical history for 5-year heart failure, diabetes, chronic kidney disease, and stroke risk prediction. Additionally, because pretraining for hierarchical Transformer is not well-established, we provide an effective end-to-end contrastive pre-training strategy for Hi-BEHRT using EHR, improving its transferability on predicting clinical events with relatively small training dataset.

Yikuan Li, Shishir Rao, Mohammad Mamouei et al.

Recent evidence shows that deep learning models trained on electronic health records from millions of patients can deliver substantially more accurate predictions of risk compared to their statistical counterparts. While this provides an important opportunity for improving clinical decision-making, the lack of interpretability is a major barrier to the incorporation of these black-box models in routine care, limiting their trustworthiness and preventing further hypothesis-testing investigations. In this study, we propose two methods, namely, model distillation and variable selection, to untangle hidden patterns learned by an established deep learning model (BEHRT) for risk association identification. Due to the clinical importance and diversity of heart failure as a phenotype, it was used to showcase the merits of the proposed methods. A cohort with 788,880 (8.3% incident heart failure) patients was considered for the study. Model distillation identified 598 and 379 diseases that were associated and dissociated with heart failure at the population level, respectively. While the associations were broadly consistent with prior knowledge, our method also highlighted several less appreciated links that are worth further investigation. In addition to these important population-level insights, we developed an approach to individual-level interpretation to take account of varying manifestation of heart failure in clinical practice. This was achieved through variable selection by detecting a minimal set of encounters that can maximally preserve the accuracy of prediction for individuals. Our proposed work provides a discovery-enabling tool to identify risk factors in both population and individual levels from a data-driven perspective. This helps to generate new hypotheses and guides further investigations on causal links.

Vincent Moens, Simiao Yu, Gholamreza Salimi-Khorshidi

Convolutional neural networks have had a great success in numerous tasks, including image classification, object detection, sequence modelling, and many more. It is generally assumed that such neural networks are translation invariant, meaning that they can detect a given feature independent of its location in the input image. While this is true for simple cases, where networks are composed of a restricted number of layer classes and where images are fairly simple, complex images with common state-of-the-art networks do not usually enjoy this property as one might hope. This paper shows that most of the existing convolutional architectures define, at initialisation, a specific feature importance landscape that conditions their capacity to attend to different locations of the images later during training or even at test time. We demonstrate how this phenomenon occurs under specific conditions and how it can be adjusted under some assumptions. We derive the P-objective, or PILCRO for Pixel-wise Importance Landscape Curvature Regularised Objective, a simple regularisation technique that favours weight configurations that produce smooth, low-curvature importance landscapes that are conditioned on the data and not on the chosen architecture. Through extensive experiments, we further show that P-regularised versions of popular computer vision networks have a flat importance landscape, train faster, result in a better accuracy and are more robust to noise at test time, when compared to their original counterparts in common computer-vision classification settings.