Interpreting tree ensemble machine learning models with endoR
Fig 5
endoR recapitulates previous findings on differences in gut microbiomes between healthy individuals and patients diagnosed with cirrhosis.
A: Feature importance aggregated across each level of discretized variables and influence per-level as determined by endoR. Levels correspond to discrete variable categories, and here represent relative abundance groups created by endoR (i.e., whether samples had ‘Low’, ‘Medium’ or ‘High’ relative abundances of each taxon). ‘closely related’ designates taxa that are the direct parent or child taxonomic classification of a taxon originally associated with disease status in Qin et al. [41]. White boxes in the influence plot signify that the level was not used in any stable decision; thus, the influence could not be calculated. B: Decision network extracted from the stable decision ensembles. See Fig 2 for the description of the network; the boxed legend is shared for A and B.