Graph Attention Based Prioritization of Disease Responsible Genes from Multimodal Alzheimer's Network

TL;DR

This paper introduces NETRA, a multimodal graph transformer framework that enhances gene prioritization in Alzheimer's disease by replacing static measures with attention-driven relevance scoring, integrating diverse biological data for improved accuracy.

Contribution

The paper presents a novel transformer-based approach for gene prioritization that effectively integrates multimodal biological networks and surpasses traditional centrality metrics.

Findings

NETRA achieves a normalized enrichment score of 3.9 for AD pathways.

Top-ranked genes recover known AD susceptibility loci.

Framework reveals conserved gene modules across diseases.

Abstract

Prioritizing disease-associated genes is central to understanding the molecular mechanisms of complex disorders such as Alzheimer's disease (AD). Traditional network-based approaches rely on static centrality measures and often fail to capture cross-modal biological heterogeneity. We propose NETRA (Node Evaluation through Transformer-based Representation and Attention), a multimodal graph transformer framework that replaces heuristic centrality metrics with attention-driven relevance scoring. Using AD as a case study, gene regulatory networks are independently constructed from microarray, single-cell RNA-seq, and single-nucleus RNA-seq data. Random-walk sequences derived from these networks are used to train a BERT-based model for learning global gene embeddings, while modality-specific gene expression profiles are compressed using variational autoencoders. These representations are integrated with auxiliary biological networks, including protein-protein interactions, Gene Ontology semantic similarity, and diffusion-based gene similarity, into a unified multimodal graph. A graph transformer assigns NETRA scores that quantify gene relevance in a disease-specific and context-aware manner. Gene set enrichment analysis shows that NETRA achieves a normalized enrichment score of about 3.9 for the Alzheimer's disease pathway, substantially outperforming classical centrality measures and diffusion models. Top-ranked genes enrich multiple neurodegenerative pathways, recover a known late-onset AD susceptibility locus at chr12q13, and reveal conserved cross-disease gene modules. The framework preserves biologically realistic heavy-tailed network topology and is readily extensible to other complex disorders.