E-ABIN: an Explainable module for Anomaly detection in BIological Networks

TL;DR

E-ABIN is an explainable, versatile framework that combines machine learning and graph-based deep learning to detect and interpret anomalies in biological networks from gene expression data, aiding disease understanding.

Contribution

It introduces a unified, user-friendly platform integrating classical and deep learning methods for anomaly detection in biological networks, enhancing interpretability and applicability.

Findings

Successfully identified disease-relevant anomalies in case studies

Achieved high predictive accuracy with interpretable models

Demonstrated utility in bladder cancer and coeliac disease datasets

Abstract

The increasing availability of large-scale omics data calls for robust analytical frameworks capable of handling complex gene expression datasets while offering interpretable results. Recent advances in artificial intelligence have enabled the identification of aberrant molecular patterns distinguishing disease states from healthy controls. Coupled with improvements in model interpretability, these tools now support the identification of genes potentially driving disease phenotypes. However, current approaches to gene anomaly detection often remain limited to single datasets and lack accessible graphical interfaces. Here, we introduce E-ABIN, a general-purpose, explainable framework for Anomaly detection in Biological Networks. E-ABIN combines classical machine learning and graph-based deep learning techniques within a unified, user-friendly platform, enabling the detection and interpretation of anomalies from gene expression or methylation-derived networks. By integrating algorithms such as Support Vector Machines, Random Forests, Graph Autoencoders (GAEs), and Graph Adversarial Attributed Networks (GAANs), E-ABIN ensures a high predictive accuracy while maintaining interpretability. We demonstrate the utility of E-ABIN through case studies of bladder cancer and coeliac disease, where it effectively uncovers biologically relevant anomalies and offers insights into disease mechanisms.