The probability of edge existence due to node degree: a baseline for network-based predictions.
Gigascience
; 132024 01 02.
Article
en En
| MEDLINE
| ID: mdl-38323677
ABSTRACT
Important tasks in biomedical discovery such as predicting gene functions, gene-disease associations, and drug repurposing opportunities are often framed as network edge prediction. The number of edges connecting to a node, termed degree, can vary greatly across nodes in real biomedical networks, and the distribution of degrees varies between networks. If degree strongly influences edge prediction, then imbalance or bias in the distribution of degrees could lead to nonspecific or misleading predictions. We introduce a network permutation framework to quantify the effects of node degree on edge prediction. Our framework decomposes performance into the proportions attributable to degree and the network's specific connections using network permutation to generate features that depend only on degree. We discover that performance attributable to factors other than degree is often only a small portion of overall performance. Researchers seeking to predict new or missing edges in biological networks should use our permutation approach to obtain a baseline for performance that may be nonspecific because of degree. We released our methods as an open-source Python package (https//github.com/hetio/xswap/).
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Algoritmos
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Gigascience
Año:
2024
Tipo del documento:
Article
País de afiliación:
Estados Unidos