To investigate the performance of DeepMO on binary classification, we compared the results by using single omics data and combining three omics data based on DeepMO to classify any two subtypes of breast cancer, including (1) luminal A versus luminal B, (2) luminal A versus HER2(+), (3) luminal A versus TNBC, (4) luminal A versus unclear, (5) luminal B versus HER2(+), (6) luminal B versus TNBC, (7) luminal B versus unclear, (8) HER2(+) versus TNBC, (9) HER2(+) versus unclear, and (10) TNBC versus unclear. Here, ERBB2 is linked to breast carcinoma.