Cross-cohort TB classification using clinical data gathered in Uganda and South Africa

Joshua M. Jansen van Vüren, Devendra S. Parihar, Daphne Naidoo, Marisa Klopper, Frank Cobelens +6

We present a first evaluation of machine learning applied to patient clinical and demographic data gathered in two different countries for the purpose of tuberculosis (TB) screening to identify people who would benefit from expensive molecular testing. Experiments are based on the recently-compiled CAGE-TB dataset, which includes sub-cohorts of people with presumptive TB presenting at community health care centres in South Africa and Uganda. Three neural network architectures (logistic regression (LR), multilayer perceptrons (MLP) and convolutional neural networks (CNN)) are considered in conjunction with greedy feature selection. For the convolutional neural network, a strategy that jointly optimises feature selection and feature ordering is proposed and shown to lead to consistent development and test set improvements. For all three models, development set area under the receiver operating characteristic (AUROC) curve is improved by 2-7% using feature selection. LR after feature selection achieves an AUROC of 0.8 [0.75,0.86] (95% CI) and 0.84 [0.78,0.9] when testing on the held-out Ugandan and South African data respectively. Although outperforming LR on the development cohort,…