TABLE 3.

Results of the ablation study.

Excluded embedding	Gene/protein embedding by the LLM	Disease embedding by the LLM	Disease embedding by the KGE	Gene/protein embedding by the KGE
AUC	0.9653 ± 0.0002	0.9633 ± 0.0002	0.9520 ± 0.0005	0.8794 ± 0.0031
AUPR	0.9455 ± 0.0008	0.9404 ± 0.0004	0.9261 ± 0.0008	0.8236 ± 0.0052
F1 score	0.8774 ± 0.0026	0.8739 ± 0.0034	0.8552 ± 0.0018	0.7432 ± 0.0032
Accuracy	0.9051 ± 0.0032	0.9018 ± 0.0047	0.8903 ± 0.0016	0.8110 ± 0.0044
Recall	0.9096 ± 0.0115	0.9105 ± 0.0203	0.8672 ± 0.0098	0.7325 ± 0.0097
Precision	0.8477 ± 0.0139	0.8408 ± 0.0218	0.8437 ± 0.0088	0.7545 ± 0.0132
Specificity	0.9023 ± 0.0116	0.8966 ± 0.0190	0.9041 ± 0.0072	0.8577 ± 0.0119

Note: The results were reported as average ± standard deviation.

Abbreviations: AUC, area under the receiver operating characteristic curve; AUPR, area under the precision‐recall curve; GNN, graph neural network; LLM, large language model.