Construction and Evaluation of Robust Interpretation Models for Breast Cancer Metastasis Prediction

Interpretability of machine learning (ML) models represents the extent to which a model’s decision-making process can be understood by model developers and/or end users. Transcriptomics-based cancer prognosis models, for example, while achieving good accuracy, are usually hard to interpret, due to the high-dimensional feature space and the complexity of models. As interpretability is critical for the transparency and fairness of ML models, several algorithms have been proposed to improve the interpretability of arbitrary classifiers. However, evaluation of these algorithms often requires substantial domain knowledge. Here, we propose a breast cancer metastasis prediction model using a very small number of biologically interpretable features, and a simple yet novel model interpretation approach that can provide personalized interpretations. In addition, we contributed, to the best of our knowledge, the first method to quantitatively compare different interpretation algorithms. Experimental results show that our model not only achieved competitive prediction accuracy, but also higher inter-classifier interpretation consistency than state-of-the-art interpretation methods. Importantly, our interpretation results can improve the generalizability of the prediction models. Overall, this work provides several novel ideas to construct and evaluate interpretable ML models that can be valuable to both the cancer machine learning community and related application domains.