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ZENODO
Software . 2024
Data sources: ZENODO
ZENODO
Software . 2024
Data sources: Datacite
ZENODO
Software . 2024
Data sources: Datacite
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GA2Vec: Optimizing Global Network Alignment with a Genetic Algorithm

Authors: DJEDDI, Warith Eddine; BEN YAHIA, sadok; DIALLO, Gayo;

GA2Vec: Optimizing Global Network Alignment with a Genetic Algorithm

Abstract

GA2Vec is a novel method for the global alignment of multiple PPI networks in a many-to-many framework, utilizing genetic algorithms. It reconstructs weighted PPI networks by incorporating protein sequence embeddings from ProtBERT, ESM-2, and ProtT5-XL-UniRef50 and functional similarity from Gene Ontology (GO) embeddings via Anc2vec. To generate candidate clusters as initial alignment solutions, GA2Vec applies four community detection algorithms on the weighted graph. The genetic algorithm then iteratively refines these clusters, optimizing network alignment through a fitness function that combines similarity scores from both sequence embeddings and GO terms, achieving robust global alignment across PPI networks.

Keywords

protein network alignment, Proteins

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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average