Simulation results.

Performance is evaluated through the AUC of the precision-recall curve generated by applying different thresholds to the maximal connection of molecular features to each other. For this simulation, 20 replications are the AUC median and interquartile range in parenthesis of is reported. “Best” AUC for SmCCNet and DIABLO denotes that in each replication, 9 SmCCNet/DIABLO models are run and only the highest AUC score is recorded. The first table is the simulation study for setting 1, which uses latent factors simulated from multivariate normal distribution; the second panel is the simulation study for setting 2, where latent factors are simulated with a highly right-skewed distribution; the third panel is the simulation study for setting 3, where latent factors are simulated with a multivariate normal distribution (same as case 1), but strong random noise is enforced on omics data. Each simulation study contains 3 cases: Case 1 means that the signal molecular features are defined as all 4-way, 3-way, and pairwise phenotype-specific correlation structure; case 2 removes the phenotype-specific 4-way correlation structure; case 3 removes the phenotype-specific 3-way and pairwise correlation structure. In each case, the data is simulated with 100 or 200 subjects.