BackgroundThis study proposes machine learning-driven data preparation (MLDP) for optimal data preparation (DP) prior to building prediction models for cancer cohorts.MethodsA collection of well-established DP methods were incorporated for building the DP pipelines for various clinical cohorts prior to machine learning. Evolutionary algorithm principles combined with hyperparameter optimization were employed to iteratively select the best fitting subset of data preparation algorithms for the given dataset. The proposed method was validated for glioma and prostate single center cohorts by 100-fold Monte Carlo (MC) cross-validation scheme with 80-20% training-validation split ratio. In addition, a dual-center diffuse large B-cell lymphoma (DLBCL) cohort was utilized with Center 1 as training and Center 2 as independent validation datasets to predict cohort-specific clinical endpoints. Five machine learning (ML) classifiers were employed for building prediction models across all analyzed cohorts. Predictive performance was estimated by confusion matrix analytics over the validation sets of each cohort. The performance of each model with and without MLDP, as well as with manually-defined DP were compared in each of the four cohorts.ResultsSixteen of twenty established predictive models demonstrated area under the receiver operator characteristics curve (AUC) performance increase utilizing the MLDP. The MLDP resulted in the highest performance increase for random forest (RF) (+0.16 AUC) and support vector machine (SVM) (+0.13 AUC) model schemes for predicting 36-months survival in the glioma cohort. Single center cohorts resulted in complex (6-7 DP steps) DP pipelines, with a high occurrence of outlier detection, feature selection and synthetic majority oversampling technique (SMOTE). In contrast, the optimal DP pipeline for the dual-center DLBCL cohort only included outlier detection and SMOTE DP steps.ConclusionsThis study demonstrates that data preparation prior to ML prediction model building in cancer cohorts shall be ML-driven itself, yielding optimal prediction models in both single and multi-centric settings.