1. Machine Learning-Assisted Recurrence Prediction for Early-Stage Non-Small-Cell Lung Cancer Patients
- Author
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Janik, Adrianna, Torrente, Maria, Costabello, Luca, Calvo, Virginia, Walsh, Brian, Camps, Carlos, Mohamed, Sameh K., Ortega, Ana L., Nováček, Vít, Massutí, Bartomeu, Minervini, Pasquale, Campelo, M. Rosario Garcia, del Barco, Edel, Bosch-Barrera, Joaquim, Menasalvas, Ernestina, Timilsina, Mohan, and Provencio, Mariano
- Subjects
Computer Science - Machine Learning ,Quantitative Biology - Quantitative Methods - Abstract
Background: Stratifying cancer patients according to risk of relapse can personalize their care. In this work, we provide an answer to the following research question: How to utilize machine learning to estimate probability of relapse in early-stage non-small-cell lung cancer patients? Methods: For predicting relapse in 1,387 early-stage (I-II), non-small-cell lung cancer (NSCLC) patients from the Spanish Lung Cancer Group data (65.7 average age, 24.8% females, 75.2% males) we train tabular and graph machine learning models. We generate automatic explanations for the predictions of such models. For models trained on tabular data, we adopt SHAP local explanations to gauge how each patient feature contributes to the predicted outcome. We explain graph machine learning predictions with an example-based method that highlights influential past patients. Results: Machine learning models trained on tabular data exhibit a 76% accuracy for the Random Forest model at predicting relapse evaluated with a 10-fold cross-validation (model was trained 10 times with different independent sets of patients in test, train and validation sets, the reported metrics are averaged over these 10 test sets). Graph machine learning reaches 68% accuracy over a 200-patient, held-out test set, calibrated on a held-out set of 100 patients. Conclusions: Our results show that machine learning models trained on tabular and graph data can enable objective, personalised and reproducible prediction of relapse and therefore, disease outcome in patients with early-stage NSCLC. With further prospective and multisite validation, and additional radiological and molecular data, this prognostic model could potentially serve as a predictive decision support tool for deciding the use of adjuvant treatments in early-stage lung cancer. Keywords: Non-Small-Cell Lung Cancer, Tumor Recurrence Prediction, Machine Learning
- Published
- 2022