BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data
Fig 2
Benchmarking performance for network structure and edge directionality.
Note that CCREPE has two versions with Pearson and Spearman correlations (CCREPE.P and CCREPE.S), while SPIEC-EASI using “mb” and “glasso” algorithms is represented as SE.mb and SE.glasso, respectively. (A) ROC curves for different correlation based methods, the regression method using true biomass values and BEEM-Static for one simulated dataset with 30 species and 500 samples. (B) Boxplots showing precision and recall for directionality/sign of interactions for 30 different simulated communities with 30 species and 500 samples each. (C) True interaction network for a synthetic community based on all-pair co-culture data (Ground truth), inferred correlation network by BAnOCC and inferred interaction network by BEEM-Static (numbers on edges represent gLVM parameter values or correlation coefficients). PC: Prevotella copri, BV: Bacteroides vulgatus, BU: Bacteroides uniformis, BO: Bacteroides ovatus, BT: Bacteroides thetaiotaomicron, FP: Faecalibacterium prausnitzii, BH: Blautia hydrogenotrophica, ER: Eubacterium rectale, CA: Collinsella aerofaciens, EL: Eggerthella lenta, DP: Desulfovibrio piger, CH: Clostridium hiranonis.