journal article·2022-02-12Open access

Explainable Machine Learning for Lung Cancer Screening Models

Katarzyna Kobylińska, Tadeusz Orłowski, Mariusz Adamek, Przemysław Biecek

Applied Sciences· Volume 12· Issue 4

Abstract

Modern medicine is supported by increasingly sophisticated algorithms. In diagnostics or screening, statistical models are commonly used to assess the risk of disease development, the severity of its course, and expected treatment outcome. The growing availability of very detailed data and increased interest in personalized medicine are leading to the development of effective but complex machine learning models. For these models to be trusted, their predictions must be understandable to both the physician and the patient, hence the growing interest in the area of Explainable Artificial Intelligence (XAI). In this paper, we present selected methods from the XAI field in the example of models applied to assess lung cancer risk in lung cancer screening through low-dose computed tomography. The use of these techniques provides a better understanding of the similarities and differences between three commonly used models in lung cancer screening, i.e., BACH, PLCOm2012, and LCART. For the presentation of the results, we used data from the Domestic Lung Cancer Database. The XAI techniques help to better understand (1) which variables are most important in which model, (2) how they are transformed into model predictions, and facilitate (3) the explanation of model predictions for a particular screenee.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Radiomics and Machine Learning in Medical Imaging · Lung Cancer Diagnosis and Treatment · AI in cancer detection

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 00-927 Warsaw, Poland

National Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland

Faculty of Medicine and Dentistry, Medical University of Silesia, 40-055 Katowice, Poland

Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-661 Warsaw, Poland

Funding

Polish National Centre For Research and Development · NCN Opus Grant

References (42)

Show source-provided references
1. O’Neil, C. (2016). Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy, Crown Publishing Group.
2. European Commission (2020). On Artificial Intelligence—A European Approach to Excellence and Trust, European Commission.
3. EU Expert Group (2019). Ethics Guidelines for Trustworthy AI, EU Expert Group.
4. Dickson, B. (2019). Inside DARPA’s Effort to Create Explainable Artificial Intelligence, DARPA.
5. Guyon, I., Luxburg, U.V., Bengio, S., Wallach, H., Fergus, R., Vishwanathan, S., and Garnett, R. (2017). A Unified Approach to Interpreting Model Predictions. Advances in Neural Information Processing Systems 30, Curran Associates, Inc.
6. Ribeiro, M.T., Singh, S., and Guestrin, C. (2016, January 13–17). “Why Should I Trust You?”: Explaining the Predictions of Any Classifier. Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Francisco, CA, USA.10.1145/2939672.2939778 ↗
7. Gosiewska, A., and Biecek, P. (2019). Do Not Trust Additive Explanations. arXiv.
8. DALEX: Explainers for Complex Predictive Models in R
9. Wexler, J., Pushkarna, M., Bolukbasi, T., Wattenberg, M., Viégas, F., and Wilson, J. (2019). The What-If Tool: Interactive Probing of Machine Learning Models, Institute of Electrical and Electronics Engineers (IEEE).10.1109/TVCG.2019.2934619 ↗
10. Nori, H., Jenkins, S., Koch, P., and Caruana, R. (2019). InterpretML: A Unified Framework for Machine Learning Interpretability. arXiv.
11. Dynamic and explainable machine learning prediction of mortality in patients in the intensive care unit: A retrospective study of high-frequency data in electronic patient records10.1016/S2589-7500(20)30018-2 ↗
12. From local explanations to global understanding with explainable AI for trees10.1038/s42256-019-0138-9 ↗
13. Early Prediction of Circulatory Failure in the Intensive Care Unit Using Machine Learning10.1038/s41591-020-0789-4 ↗
14. Explainable machine-learning predictions for the prevention of hypoxaemia during surgery10.1038/s41551-018-0304-0 ↗
15. Singh, A., Sengupta, S., and Lakshminarayanan, V. (2020). Explainable Deep Learning Models in Medical Image Analysis. J. Imaging, 6.10.3390/jimaging6060052 ↗
16. Holzinger, A., Biemann, C., Pattichis, C.S., and Kell, D.B. (2017). What do we need to build explainable AI systems for the medical domain?. arXiv.
17. Xie, Y., Chen, M., Kao, D., Gao, G., and Chen, X. (2020, January 25–30). CheXplain: Enabling Physicians to Explore and Understand Data-Driven, AI-Enabled Medical Imaging Analysis. Proceedings of the CHI’20: CHI Conference on Human Factors in Computing Systems, Honolulu, HI, USA.10.1145/3313831.3376807 ↗
18. Lauritsen, S.M., Kristensen, M.R.B., Olsen, M.V., Larsen, M.S., Lauritsen, K.M., Jørgensen, M.J., Lange, J., and Thiesson, B. (2019). Explainable artificial intelligence model to predict acute critical illness from electronic health records. arXiv.10.1038/s41467-020-17431-x ↗
19. Convolutional Neural Network ensembles for accurate lung nodule malignancy prediction 2 years in the future10.1016/j.compbiomed.2020.103882 ↗
20. Multi-resolution classification of exhaled aerosol images to detect obstructive lung diseases in small airways10.1016/j.compbiomed.2017.05.019 ↗
21. Recognizing lung cancer using a homemade e-nose: A comprehensive study10.1016/j.compbiomed.2020.103706 ↗
22. National Lung Screening Trial Research Team (2011). Reduced Lung-Cancer Mortality with Low-Dose Computed Tomographic Screening. N. Engl. J. Med., 365, 395–409.10.1056/NEJMoa1102873 ↗
23. Reduced Lung-Cancer Mortality with Volume CT Screening in a Randomized Trial10.1056/NEJMoa1911793 ↗
24. Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models10.1136/thoraxjnl-2018-212638 ↗
25. Selecting lung cancer screenees using risk prediction models—Where do we go from here10.21037/tlcr.2018.06.03 ↗
26. Variations in Lung Cancer Risk Among Smokers10.1093/jnci/95.6.470 ↗
27. Selection Criteria for Lung-Cancer Screening10.1056/NEJMoa1211776 ↗
28. Development and Validation of Risk Models to Select Ever-Smokers for CT Lung Cancer Screening10.1001/jama.2016.6255 ↗
29. R Core Team (2020). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing.
30. Cheung, L.C., Kovalchik, S.A., and Katki, H.A. (2021, November 06). lcmodels: Predictions from Lung Cancer Models. R Package Version 4.0.0, Available online: https://dceg.cancer.gov/tools/risk-assessment/lcmodels/lcmodels-manual.pdf.
31. Implications of nine risk prediction models for selecting ever-smokers for computed tomography lung cancer screening10.7326/M17-2701 ↗
32. Miller, T. (2018). Explanation in Artificial Intelligence: Insights from the Social Sciences. arXiv.10.1016/j.artint.2018.07.007 ↗
33. Biecek, P., and Burzykowski, T. (2021). Explanatory Model Analysis, Chapman and Hall/CRC.10.1201/9780429027192 ↗
34. Pękala, K., and Biecek, P. (2021, November 06). triplot: Explaining Correlated Features in Machine Learning Models. Available online: https://cran.r-project.org/web/packages/triplot/triplot.pdf.10.32614/CRAN.package.triplot ↗
35. Apley, D. (2021, November 06). ALEPlot: Accumulated Local Effects (ALE) Plots and Partial Dependence (PD) Plots. R Package. Available online: https://cran.r-project.org/web/packages/ALEPlot/ALEPlot.pdf.
36. All Models are Wrong, but Many are Useful: Learning a Variable’s Importance by Studying an Entire Class of Prediction Models Simultaneously
37. Hastie, T., Tibshirani, R., and Friedman, J. (2009). The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Springer. [2nd ed.].10.1007/978-0-387-84858-7 ↗
38. Molnar, C. (2018). Interpretable Machine Learning. A Guide for Making Black Box Models Explainable, Leanpub.
39. Explanations of Model Predictions with live and breakDown Packages10.32614/RJ-2018-072 ↗
40. Explanatory Artificial Intelligence (XAI) in the prediction of post-operative life expectancy in lung cancer patients
41. Marcos, M., Juarez, J.M., Lenz, R., Nalepa, G.J., Nowaczyk, S., Peleg, M., Stefanowski, J., and Stiglic, G. (2019). Explainable Machine Learning for Modeling of Early Postoperative Mortality in Lung Cancer. Artificial Intelligence in Medicine: Knowledge Representation and Transparent and Explainable Systems, Springer International Publishing.10.1007/978-3-030-37446-4 ↗
42. Greedy Function Approximation: A Gradient Boosting Machine