Feature selection based on unsupervised clustering evaluation for predicting neoadjuvant chemoradiation response for patients with locally advanced rectal cancer

Accurate response prediction allows for personalized cancer treatment of locally advanced rectal cancer (LARC) with neoadjuvant chemoradiation. In this work, we designed a convolutional neural network (CNN) feature extractor with switchable 3D and 2D convolutional kernels to extract deep learning features for response prediction. Compared with radiomics features, convolutional kernels may adaptively extract local or global image features from multi-modal MR sequences without the need of feature predefinition. We then developed an unsupervised clustering based evaluation method to improve the feature selection operation in the feature space formed by the combination of CNN features and radiomics features. While normal process of feature selection generally includes the operations of classifier training and classification execution, the process needs to be repeated many times after new feature combinations were found to evaluate the model performance, which incurs a significant time cost. To address this issue, we proposed a cost effective process to use a constructed unsupervised clustering analysis indicator to replace the classifier training process by indirectly evaluating the quality of new found feature combinations in feature selection process. We evaluated the proposed method using 43 LARC patients underwent neoadjuvant chemoradiation. Our prediction model achieved accuracy, area-under-curve (AUC), sensitivity and specificity of 0.852, 0.871, 0.868, and 0.735 respectively. Compared with traditional radiomics methods, the prediction models (AUC = 0.846) based on deep learning-based feature sets are significantly better than traditional radiomics methods (AUC = 0.714). The experiments also showed following findings: (1) the features with higher predictive power are mainly from high-order abstract features extracted by CNN on ADC images and T2 images; (2) both ADC_Radiomics and ADC_CNN features are more advantageous for predicting treatment responses than the radiomics and CNN features extracted from T2 images; (3) 3D CNN features are more effective than 2D CNN features in the treatment response prediction. The proposed unsupervised clustering indicator is feasible with low computational cost, which facilitates the discovery of valuable solutions by highlighting the correlation and complementarity between different types of features.