TABLE 3.
Result of the benchmark dataset of McPAS. APS stands for the average precision score.
| Model | Features in addition to peptides | ROC AUC | APS |
|---|---|---|---|
| Cross-TCR-interpreter (Ours) | CDR3s of α and β chains | 0.9154 | 0.6211 |
| NetTCR-2.0 | CDR3s of α- and β-chains | 0.9204 | 0.5808 |
| PanPep | CDR3 sequence of the β-chain with biochemical features | 0.8374 | 0.4519 |
| AttnTAP a | CDR3 sequence of the β-chain | 0.840 | - |
| DLpTCR a | CDR3 Sequence of the β-chain | 0.633 | - |
| ERGO-II, LSTM b | CDR3s of α- and β-chains | 0.855 | - |
| ERGO-II, LSTM b | CDR3s of α- and β-chains, VJ genes, and MHC type | 0.939 | - |
a
The numbers were derived from the AttnTAP paper because we observed that both DLpTCR and AttnTAP achieved only poor scores in our experiments. Hence, to avoid potential misinterpretation due to poor scores, we opted not to display the average precision score in this context. Regarding our experiments of AttnTAP, ROC AUC and APS on McPAS were 0.5934 and 0.3073, respectively. Those of VDJdb-without10x were 0.3951 and 0.1400, respectively. Those of our DLpTCR experiments on McPAS were 0.5346 and 0.1941, respectively, and those of DLpTCR on VDJdb-without10x were 0.5187 and 0.1914, respectively.
b
The numbers were derived from the ERGO-II paper.