Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks.

ABSTRACT:

Motivation

Spatial Analysis of Functional Enrichment (SAFE) is a popular tool for biologists to investigate the functional organization of biological networks via highly intuitive 2D functional maps. To create these maps, SAFE uses Spring embedding to project a given network into a 2D space in which nodes connected in the network are near each other in space. However, many biological networks are scale-free, containing highly connected hub nodes. Because Spring embedding fails to separate hub nodes, it provides uninformative embeddings that resemble a 'hairball'. In addition, Spring embedding only captures direct node connectivity in the network and does not consider higher-order node wiring patterns, which are best captured by graphlets, small, connected, nonisomorphic, induced su

SUBMITTER: Windels SFL 

PROVIDER: S-EPMC11568109 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature