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Register a new userInterpretable Machine Learning for COVID-19: An Empirical Study on Severity Prediction Task
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The black-box nature of machine learning models hinders the deployment of some high-accuracy models in medical diagnosis. It is risky to put ones life in the hands of models that medical researchers do not fully understand. However, through model interpretation, black-box models can promptly reveal significant biomarkers that medical practitioners may have overlooked due to the surge of infected patients in the COVID-19 pandemic. This research leverages a database of 92 patients with confirmed SARS-CoV-2 laboratory tests between 18th Jan. 2020 and 5th Mar. 2020, in Zhuhai, China, to identify biomarkers indicative of severity prediction. Through the interpretation of four machine learning models, decision tree, random forests, gradient boosted trees, and neural networks using permutation feature importance, Partial Dependence Plot (PDP), Individual Conditional Expectation (ICE), Accumulated Local Effects (ALE), Local Interpretable Model-agnostic Explanations (LIME), and Shapley Additive Explanation (SHAP), we identify an increase in N-Terminal pro-Brain Natriuretic Peptide (NTproBNP), C-Reaction Protein (CRP), and lactic dehydrogenase (LDH), a decrease in lymphocyte (LYM) is associated with severe infection and an increased risk of death, which is consistent with recent medical research on COVID-19 and other research using dedicated models. We further validate our methods on a large open dataset with 5644 confirmed patients from the Hospital Israelita Albert Einstein, at S~ao Paulo, Brazil from Kaggle, and unveil leukocytes, eosinophils, and platelets as three indicative biomarkers for COVID-19.
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With a mortality rate of 5.4 million lives worldwide every year and a healthcare cost of more than 16 billion dollars in the USA alone, sepsis is one of the leading causes of hospital mortality and an increasing concern in the ageing western world. Recently, medical and technological advances have helped re-define the illness criteria of this disease, which is otherwise poorly understood by the medical society. Together with the rise of widely accessible Electronic Health Records, the advances in data mining and complex nonlinear algorithms are a promising avenue for the early detection of sepsis. This work contributes to the research effort in the field of automated sepsis detection with an open-access labelling of the medical MIMIC-III data set. Moreover, we propose MGP-AttTCN: a joint multitask Gaussian Process and attention-based deep learning model to early predict the occurrence of sepsis in an interpretable manner. We show that our model outperforms the current state-of-the-art and present evidence that different labelling heuristics lead to discrepancies in task difficulty. For instance, when predicting sepsis five hours prior to onset on our new realistic labels, our proposed model achieves an area under the ROC curve of 0.660 and an area under the PR curve of 0.483, whereas the (less interpretable) previous state-of-the-art model (MGP-TCN) achieves 0.635 AUROC and 0.460 AUPR and the popular commercial InSight model achieves 0.490 AUROC and 0.359 AUPR.
Kearns et al. [2018] recently proposed a notion of rich subgroup fairness intended to bridge the gap between statistical and individual notions of fairness. Rich subgroup fairness picks a statistical fairness constraint (say, equalizing false positive rates across protected groups), but then asks that this constraint hold over an exponentially or infinitely large collection of subgroups defined by a class of functions with bounded VC dimension. They give an algorithm guaranteed to learn subject to this constraint, under the condition that it has access to oracles for perfectly learning absent a fairness constraint. In this paper, we undertake an extensive empirical evaluation of the algorithm of Kearns et al. On four real datasets for which fairness is a concern, we investigate the basic convergence of the algorithm when instantiated with fast heuristics in place of learning oracles, measure the tradeoffs between fairness and accuracy, and compare this approach with the recent algorithm of Agarwal et al. [2018], which implements weaker and more traditional marginal fairness constraints defined by individual protected attributes. We find that in general, the Kearns et al. algorithm converges quickly, large gains in fairness can be obtained with mild costs to accuracy, and that optimizing accuracy subject only to marginal fairness leads to classifiers with substantial subgroup unfairness. We also provide a number of analyses and visualizations of the dynamics and behavior of the Kearns et al. algorithm. Overall we find this algorithm to be effective on real data, and rich subgroup fairness to be a viable notion in practice.
We present a novel methodology to jointly perform multi-task learning and infer intrinsic relationship among tasks by an interpretable and sparse graph. Unlike existing multi-task learning methodologies, the graph structure is not assumed to be known a priori or estimated separately in a preprocessing step. Instead, our graph is learned simultaneously with model parameters of each task, thus it reflects the critical relationship among tasks in the specific prediction problem. We characterize graph structure with its weighted adjacency matrix and show that the overall objective can be optimized alternatively until convergence. We also show that our methodology can be simply extended to a nonlinear form by being embedded into a multi-head radial basis function network (RBFN). Extensive experiments, against six state-of-the-art methodologies, on both synthetic data and real-world applications suggest that our methodology is able to reduce generalization error, and, at the same time, reveal a sparse graph over tasks that is much easier to interpret.
As the second wave in India mitigates, COVID-19 has now infected about 29 million patients countrywide, leading to more than 350 thousand people dead. As the infections surged, the strain on the medical infrastructure in the country became apparent. While the country vaccinates its population, opening up the economy may lead to an increase in infection rates. In this scenario, it is essential to effectively utilize the limited hospital resources by an informed patient triaging system based on clinical parameters. Here, we present two interpretable machine learning models predicting the clinical outcomes, severity, and mortality, of the patients based on routine non-invasive surveillance of blood parameters from one of the largest cohorts of Indian patients at the day of admission. Patient severity and mortality prediction models achieved 86.3% and 88.06% accuracy, respectively, with an AUC-ROC of 0.91 and 0.92. We have integrated both the models in a user-friendly web app calculator, https://triage-COVID-19.herokuapp.com/, to showcase the potential deployment of such efforts at scale.
The COVID-19 pandemic has created an urgent need for robust, scalable monitoring tools supporting stratification of high-risk patients. This research aims to develop and validate prediction models, using the UK Biobank, to estimate COVID-19 mortality risk in confirmed cases. From the 11,245 participants testing positive for COVID-19, we develop a data-driven random forest classification model with excellent performance (AUC: 0.91), using baseline characteristics, pre-existing conditions, symptoms, and vital signs, such that the score could dynamically assess mortality risk with disease deterioration. We also identify several significant novel predictors of COVID-19 mortality with equivalent or greater predictive value than established high-risk comorbidities, such as detailed anthropometrics and prior acute kidney failure, urinary tract infection, and pneumonias. The model design and feature selection enables utility in outpatient settings. Possible applications include supporting individual-level risk profiling and monitoring disease progression across patients with COVID-19 at-scale, especially in hospital-at-home settings.
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