Performance evaluation of DeCEP compared with existing methods on simulated data sets. (A) Accuracy of gene program characterization using DeCEP (discrete mode) and existing methods across three simulation tests. (B) F1 score of DeCEP (discrete mode) and existing methods for each cell cluster in simulation tests 1–3. (C) ROC curves and corresponding AUC values of DeCEP (discrete mode) for each cell cluster in simulation tests 1–3. (D) Mean values of the silhouette coefficients (SCs) obtained in simulated tests 1–3 using DeCEP (discrete mode) and existing methods. (E) Correlation strength between gene program activity scores and simulated cell steps in DeCEP (continuous mode) and existing methods.