omicverse.micro.MMvec.cooccurrence

MMvec.cooccurrence()

Raw log-odds co-occurrence matrix U · Vᵀ (microbes × metabolites).

Symmetric scoring before per-microbe softmax normalisation: positive entries indicate microbes and metabolites that appear together in the same samples; negative entries the opposite. Useful when you want signed scores and don’t need them to sum to 1 per microbe — for example, downstream co-occurrence heatmaps and top_pairs(n). Use conditional_probabilities() instead when you want proper P(metabolite | microbe) probabilities.