Predicting IDH Mutation in Glioma Patients Using Deep Learning Algorithms with Conformal Prediction

The World Health Organization glioma classification highlights genetic profiles, such as isocitrate dehydrogenase (IDH) mutation. This study developed an uncertainty-aware deep learning model to predict IDH mutations in glioma patients, employing conformal prediction (CP) for uncertainty quantification (UQ). The UCSF dataset split into training (70%) and validation (30%) sets, and the UPENN dataset divided into calibration (30%) and external test (70%) sets. We developed various 3D convolutional neural network models and selected the best based on the validation set area under the precision-recall curve (AUPRC). Also, we trained a logistic regression (LR) ensemble classifier on the training set and selected the best ensemble model based on the validation set AUPRC. Finally, we employed CP, with nonconformity thresholds set at the error rate of 0.01. The conformal model was calibrated on the calibration set and was evaluated on the external test set using the AUPRC and the area under the receiver operating characteristic (AUROC). 3D convolutional models achieved a mean AUROC and AUPRC of 0.9004 and 0.8102 on the validation set, and a mean AUROC and AUPRC of 0.7340 and 0.2139 on the external test set, respectively. Using the LR ensemble model, the model achieved an AUROC and AUPRC of 0.79820 and 0.2583 on the external test set, respectively. CP with a 0.01 nonconformity threshold with 0.9917 coverage reached an AUROC and AUPRC of 0.8592 and 0.5217, respectively. Integrating CP for UQ improves the performance of deep learning models for predicting IDH mutation in glioma patients.