friends.test: rank-based method for feature selection in interaction matrices

TL;DR

friends.test is a rank-based method designed to identify specific interactions within heterogeneous interaction matrices, effectively distinguishing meaningful signals from background noise across diverse datasets.

Contribution

The paper introduces friends.test, a novel rank-based approach for detecting structural breaks in interaction matrices, accommodating data heterogeneity and integrating multiple sources.

Findings

Successfully applied to head and neck cancer data

Efficient R implementation available

Effective in distinguishing specific interactions from background

Abstract

The analysis of the interaction matrix between two distinct sets is essential across diverse fields, from pharmacovigilance to transcriptomics. Not all interactions are equally informative: a marker gene associated with a few specific biological processes is more informative than a highly expressed non-specific gene associated with most observed processes. Identifying these interactions is challenging due to background connections. Furthermore, data heterogeneity across sources precludes universal identification criteria. To address this challenge, we introduce \textsf{friends.test}, a method for identifying specificity by detecting structural breaks in entity interactions. Rank-based representation of the interaction matrix ensures invariance to heterogeneous data and allows for integrating data from diverse sources. To automatically locate the boundary between specific interactions and background activity, we employ model fitting. We demonstrate the applicability of \textsf{friends.test} on the GSE112026 -- transnational data from head and neck cancer. A computationally efficient \textsf{R} implementation is available at https://github.com/favorov/friends.test.