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Assessing eligibility for lung cancer screening using parsimonious ensemble machine learning models: A development and validation study.

Published version
Peer-reviewed

Repository DOI


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Authors

Cebere, Bogdan 
Pashayan, Nora 

Abstract

BACKGROUND: Risk-based screening for lung cancer is currently being considered in several countries; however, the optimal approach to determine eligibility remains unclear. Ensemble machine learning could support the development of highly parsimonious prediction models that maintain the performance of more complex models while maximising simplicity and generalisability, supporting the widespread adoption of personalised screening. In this work, we aimed to develop and validate ensemble machine learning models to determine eligibility for risk-based lung cancer screening. METHODS AND FINDINGS: For model development, we used data from 216,714 ever-smokers recruited between 2006 and 2010 to the UK Biobank prospective cohort and 26,616 high-risk ever-smokers recruited between 2002 and 2004 to the control arm of the US National Lung Screening (NLST) randomised controlled trial. The NLST trial randomised high-risk smokers from 33 US centres with at least a 30 pack-year smoking history and fewer than 15 quit-years to annual CT or chest radiography screening for lung cancer. We externally validated our models among 49,593 participants in the chest radiography arm and all 80,659 ever-smoking participants in the US Prostate, Lung, Colorectal and Ovarian (PLCO) Screening Trial. The PLCO trial, recruiting from 1993 to 2001, analysed the impact of chest radiography or no chest radiography for lung cancer screening. We primarily validated in the PLCO chest radiography arm such that we could benchmark against comparator models developed within the PLCO control arm. Models were developed to predict the risk of 2 outcomes within 5 years from baseline: diagnosis of lung cancer and death from lung cancer. We assessed model discrimination (area under the receiver operating curve, AUC), calibration (calibration curves and expected/observed ratio), overall performance (Brier scores), and net benefit with decision curve analysis. Models predicting lung cancer death (UCL-D) and incidence (UCL-I) using 3 variables-age, smoking duration, and pack-years-achieved or exceeded parity in discrimination, overall performance, and net benefit with comparators currently in use, despite requiring only one-quarter of the predictors. In external validation in the PLCO trial, UCL-D had an AUC of 0.803 (95% CI: 0.783, 0.824) and was well calibrated with an expected/observed (E/O) ratio of 1.05 (95% CI: 0.95, 1.19). UCL-I had an AUC of 0.787 (95% CI: 0.771, 0.802), an E/O ratio of 1.0 (95% CI: 0.92, 1.07). The sensitivity of UCL-D was 85.5% and UCL-I was 83.9%, at 5-year risk thresholds of 0.68% and 1.17%, respectively, 7.9% and 6.2% higher than the USPSTF-2021 criteria at the same specificity. The main limitation of this study is that the models have not been validated outside of UK and US cohorts. CONCLUSIONS: We present parsimonious ensemble machine learning models to predict the risk of lung cancer in ever-smokers, demonstrating a novel approach that could simplify the implementation of risk-based lung cancer screening in multiple settings.

Description

Acknowledgements: This research has been conducted using the UK Biobank Resource under application number 68073 and we wish to thank all participants in the included studies, as well as the National Cancer Institute for access to NCI’s data collected by the National Lung Screening Trial (NLST) and Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO). We also wish to thank Arjun Nair and Sujin Kang for their feedback on earlier versions of this project, as well as Stephen Duffy for his comments on this work. The statements contained herein are solely those of the authors and do not represent or imply concurrence or endorsement by NCI.

Keywords

Humans, Male, Early Detection of Cancer, Lung Neoplasms, Machine Learning, Mass Screening, Prospective Studies, Risk Assessment, Randomized Controlled Trials as Topic

Journal Title

PLoS Med

Conference Name

Journal ISSN

1549-1277
1549-1676

Volume Title

20

Publisher

Public Library of Science (PLoS)
Sponsorship
Wellcome Trust (222890/Z/21/Z)
National Science Foundation (1722516)
Medical Research Council (MR/T02481X/1)
Medical Research Council (MR/W025051/1)
Cancer Research UK (EDDCPGM\100002)