ProtoGate: Prototype-Based Neural Networks with Local Feature Selection for Tabular Biomedical Data

Abstract

Tabular biomedical data poses challenges in machine learning because it is often high-dimensional and typically low-sample-size. Previous research has attempted to address these challenges via feature selection approaches, which can lead to unstable performance and insufficient interpretability on real-world data. This suggests that current methods lack appropriate inductive biases that capture informative patterns in different samples. In this paper, we propose ProtoGate, a local feature selection method that introduces an inductive bias by attending to the clustering characteristic of biomedical data. ProtoGate selects features in a global-to-local manner and leverages them to produce explainable predictions via an interpretable prototype-based model. We conduct comprehensive experiments to evaluate the performance of ProtoGate on synthetic and real-world datasets. Our results show that exploiting the homogeneous and heterogeneous patterns in the data can improve prediction accuracy while prototypes imbue interpretability.