Scope spectral clustering of 5610 prokaryotic metabolic networks to discover environmental phenotypes

Adèle Weber (UPMC)
Thursday, February 20, 2020 - 10:30 to 12:00
Room Aurigny
Talk abstract: 

The scope of metabolic networks, a method of analysis of metabolic graphs, is defined as all metabolites and reactions in an expanded network from a set of seed metabolites. We explore how the scope can be efficiently incorporated into state-of-the-art machine learning methods. In particular, we investigate how the scope can be used to perform dimensionality reduction, clustering, and real data exploration. We run our experiments on most prokaryotic species from KEGG database (5610). We perform the metabolic graph reconstruction using our pipeline, and we compute the metabolic scopes for all species. The spectral clustering applied to the reduced data set, represented by the metabolic scopes, leads to a partitioning of the species which can be linked to various biological, phylogenetic and environmental phenotypes. Furthermore, our method enables us to identify the underlying biological phenomenons characterising the different clusters.