Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

OBJECTIVE: We aim to reduce overfitting and model overconfidence by distilling the knowledge of an ensemble of deep learning models into a single model for the classification of cancer pathology reports. MATERIALS AND METHODS: We consider the text classification problem that involves 5 individual tasks. The baseline model consists of a multitask convolutional neural network (MtCNN), and the implemented ensemble (teacher) consists of 1000 MtCNNs. We performed knowledge transfer by training a single model (student) with soft labels derived through the aggregation of ensemble predictions. We evaluate performance based on accuracy and abstention rates by using softmax thresholding. RESULTS: The student model outperforms the baseline MtCNN in terms of abstention rates and accuracy, thereby allowing the model to be used with a larger volume of documents when deployed. The highest boost was observed for subsite and histology, for which the student model classified an additional 1.81% reports for subsite and 3.33% reports for histology. DISCUSSION: Ensemble predictions provide a useful strategy for quantifying the uncertainty inherent in labeled data and thereby enable the construction of soft labels with estimated probabilities for multiple classes for a given document. Training models with the derived soft labels reduce model confidence in difficult-to-classify documents, thereby leading to a reduction in the number of highly confident wrong predictions. CONCLUSIONS: Ensemble model distillation is a simple tool to reduce model overconfidence in problems with extreme class imbalance and noisy datasets. These methods can facilitate the deployment of deep learning models in high-risk domains with low computational resources where minimizing inference time is required.