Feature graphs for interpretable unsupervised tree ensembles: centrality, interaction, and application in disease subtyping

TL;DR

This paper introduces novel feature graph methods for unsupervised random forests to improve interpretability and feature selection in clustering, with applications in biomedical disease subtyping.

Contribution

It develops new techniques to construct feature graphs from unsupervised random forests and uses graph centrality for feature selection, addressing a gap in unsupervised interpretability methods.

Findings

Feature graphs effectively identify important features for clustering.

Graph-based feature selection improves clustering performance.

Application to biomedical data reveals meaningful disease subtypes.

Abstract

Interpretable machine learning has emerged as central in leveraging artificial intelligence within high-stakes domains such as healthcare, where understanding the rationale behind model predictions is as critical as achieving high predictive accuracy. In this context, feature selection assumes a pivotal role in enhancing model interpretability by identifying the most important input features in black-box models. While random forests are frequently used in biomedicine for their remarkable performance on tabular datasets, the accuracy gained from aggregating decision trees comes at the expense of interpretability. Consequently, feature selection for enhancing interpretability in random forests has been extensively explored in supervised settings. However, its investigation in the unsupervised regime remains notably limited. To address this gap, the study introduces novel methods to construct feature graphs from unsupervised random forests and feature selection strategies to derive effective feature combinations from these graphs. Feature graphs are constructed for the entire dataset as well as individual clusters leveraging the parent-child node splits within the trees, such that feature centrality captures their relevance to the clustering task, while edge weights reflect the discriminating power of feature pairs. Graph-based feature selection methods are extensively evaluated on synthetic and benchmark datasets both in terms of their ability to reduce dimensionality while improving clustering performance, as well as to enhance model interpretability. An application on omics data for disease subtyping identifies the top features for each cluster, showcasing the potential of the proposed approach to enhance interpretability in clustering analyses and its utility in a real-world biomedical application.