Multi-Modal Classification for Human Breast Cancer Prognosis Prediction: Proposal of Deep-Learning Based Stacked Ensemble Model

Breast Cancer is a highly aggressive type of cancer generally formed in the cells of the breast. Despite significant advances in the treatment of primary breast cancer in the last decade, there is a dire need to attempt of an accurate predictive model for breast cancer prognosis prediction. Researchers from various disciplines are working together to develop methods to save people from this fatal disease. A good predictive model can help in correct prognosis prediction of breast cancer. This accurate prediction can have several benefits like detection of cancer in the early stage, spare patients from getting unnecessary treatment and medical expenses related to it. Previous works rely mostly on uni-modal data (selected gene expression)for predictive model design. In recent years, however, multi-modal cancer data sets have become available (gene expression, copy number alteration and clinical). Motivated by the enhancement of deep-learning based models, in the current study, we propose to use some deep-learning based predictive models in a stacked ensemble framework to improve the prognosis prediction of breast cancer from available multi-modal data sets. One of the unique advantages of the proposed approach lies in the architecture of the model. It is a two-stage model. Stage one uses a convolutional neural network for feature extraction, while stage two uses the extracted features as input to the stack-based ensemble model. The predictive performance evaluated using different performance measures shows that this model produces better result than already existing approaches. This model results in AUC value of 0.93 and accuracy of 90.2 percent at medium stringency level (Specificity = 95 percent and threshold = 0.45). Keras 2.2.1, along with Tensorflow 1.12, is used for implementing the source code of the model. The source code can be downloaded from Github:
https://github.com/nikhilaryan92/BreastCancer
.