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Register a new userRisk factor identification for incident heart failure using neural network distillation and variable selection
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Yikuan Li
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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Predicting the incidence of complex chronic conditions such as heart failure is challenging. Deep learning models applied to rich electronic health records may improve prediction but remain unexplainable hampering their wider use in medical practice. We developed a novel Transformer deep-learning model for more accurate and yet explainable prediction of incident heart failure involving 100,071 patients from longitudinal linked electronic health records across the UK. On internal 5-fold cross validation and held-out external validation, our model achieved 0.93 and 0.93 area under the receiver operator curve and 0.69 and 0.70 area under the precision-recall curve, respectively and outperformed existing deep learning models. Predictor groups included all community and hospital diagnoses and medications contextualised within the age and calendar year for each patients clinical encounter. The importance of contextualised medical information was revealed in a number of sensitivity analyses, and our perturbation method provided a way of identifying factors contributing to risk. Many of the identified risk factors were consistent with existing knowledge from clinical and epidemiological research but several new associations were revealed which had not been considered in expert-driven risk prediction models.
Most of the successful deep neural network architectures are structured, often consisting of elements like convolutional neural networks and gated recurrent neural networks. Recently, graph neural networks have been successfully applied to graph structured data such as point cloud and molecular data. These networks often only consider pairwise dependencies, as they operate on a graph structure. We generalize the graph neural network into a factor graph neural network (FGNN) in order to capture higher order dependencies. We show that FGNN is able to represent Max-Product Belief Propagation, an approximate inference algorithm on probabilistic graphical models; hence it is able to do well when Max-Product does well. Promising results on both synthetic and real datasets demonstrate the effectiveness of the proposed model.
Cardiovascular disease, especially heart failure is one of the major health hazard issues of our time and is a leading cause of death worldwide. Advancement in data mining techniques using machine learning (ML) models is paving promising prediction approaches. Data mining is the process of converting massive volumes of raw data created by the healthcare institutions into meaningful information that can aid in making predictions and crucial decisions. Collecting various follow-up data from patients who have had heart failures, analyzing those data, and utilizing several ML models to predict the survival possibility of cardiovascular patients is the key aim of this study. Due to the imbalance of the classes in the dataset, Synthetic Minority Oversampling Technique (SMOTE) has been implemented. Two unsupervised models (K-Means and Fuzzy C-Means clustering) and three supervised classifiers (Random Forest, XGBoost and Decision Tree) have been used in our study. After thorough investigation, our results demonstrate a superior performance of the supervised ML algorithms over unsupervised models. Moreover, we designed and propose a supervised stacked ensemble learning model that can achieve an accuracy, precision, recall and F1 score of 99.98%. Our study shows that only certain attributes collected from the patients are imperative to successfully predict the surviving possibility post heart failure, using supervised ML algorithms.
Bayesian neural networks (BNNs) allow us to reason about uncertainty in a principled way. Stochastic Gradient Langevin Dynamics (SGLD) enables efficient BNN learning by drawing samples from the BNN posterior using mini-batches. However, SGLD and its extensions require storage of many copies of the model parameters, a potentially prohibitive cost, especially for large neural networks. We propose a framework, Adversarial Posterior Distillation, to distill the SGLD samples using a Generative Adversarial Network (GAN). At test-time, samples are generated by the GAN. We show that this distillation framework incurs no loss in performance on recent BNN applications including anomaly detection, active learning, and defense against adversarial attacks. By construction, our framework not only distills the Bayesian predictive distribution, but the posterior itself. This allows one to compute quantities such as the approximate model variance, which is useful in downstream tasks. To our knowledge, these are the first results applying MCMC-based BNNs to the aforementioned downstream applications.
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Mistura Muibideen
, Rajesh Prasad (Department of Computer Sciencen African University of Science
, Technology
2020
Cardiovascular disease is the number one cause of death all over the world. Data mining can help to retrieve valuable knowledge from available data from the health sector. It helps to train a model to predict patients health which will be faster as compared to clinical experimentation. Various implementation of machine learning algorithms such as Logistic Regression, K-Nearest Neighbor, Naive Bayes (NB), Support Vector Machine, etc. have been applied on Cleveland heart datasets but there has been a limit to modeling using Bayesian Network (BN). This research applied BN modeling to discover the relationship between 14 relevant attributes of the Cleveland heart data collected from The UCI repository. The aim is to check how the dependency between attributes affects the performance of the classifier. The BN produces a reliable and transparent graphical representation between the attributes with the ability to predict new scenarios. The model has an accuracy of 85%. It was concluded that the model outperformed the NB classifier which has an accuracy of 80%.
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