TABLE II.
Performance Metrics for the 3-Label (Normal vs. Luad vs. Lscc) Classification Task. Mean Performance Metrics Are Reported Along with the Corresponding Values of Standard Deviation in Parentheses
| (a) Precision, Recall/Sensitivity, find Specificity (Percentage (%) values are reported). | ||||||||||
|
| ||||||||||
| Method | Data | Precision | Recall/Sensitivity | Specificity | ||||||
| Normal | LUAD | LSCC | Normal | LUAD | LSCC | Normal | LUAD | LSCC | ||
|
| ||||||||||
| TransMIL [27] | CPTAC | 89.7(1.8) | 81.0(3.1) | 87.1(1.7) | 90.4(1.9) | 81.2(2.0) | 85.9(3.7) | 94.4(1.1) | 90.8(1.9) | 93.7(1.2) |
| TCGA | 76.6(5.1) | 64.3(4.1) | 80.4(1.7) | 87.3(3.6) | 75.8(5.3) | 55.6(7.7) | 90.6(2.9) | 73.0(5.6) | 92.4(1.9) | |
|
| ||||||||||
| TransMIL [27] | CPTAC | 89.7(1.8) | 81.0(3.1) | 87.1(1.7) | 90.4(1.9) | 81.2(2.0) | 85.9(3.7) | 94.4(1.1) | 90.8(1.9) | 93.7(1.2) |
| TCGA | 89.1(4.1) | 69.9(3.9) | 81.4(3.0) | 87.8(2.7) | 79.4(2.4) | 71.3(4.0) | 94.9(2.0) | 82.5(2.9) | 91.4(1.7) | |
|
| ||||||||||
| GTP* (only GCN) | CPTAC | 82.9(6.5) | 81.6(6.5) | 86.5(4.7) | 93.6(5.0) | 74.4(6.7) | 80.3(4.8) | 89.3(5.3) | 91.6(3.9) | 93.6(2.7) |
| TCGA | 72.5(9.0) | 69.1(3.2) | 82.0(9.8) | 90.7(8.3) | 57.7(9.7) | 69.9(9.5) | 82.4(9.9) | 85.7(8.4) | 90.7(6.1) | |
|
| ||||||||||
| GTP | CPTAC | 93.2(3.0) | 88.4(3.9) | 87.8(3.0) | 95.9(2.2) | 83.9(4.5) | 89.2(4.0) | 96.2(1.7) | 94.7(1.9) | 93.8(1.7) |
| TCGA | 89.2(2.8) | 74.4(2.7) | 84.4(0.7) | 92.6(2.7) | 79.8(1.9) | 75.2(1.6) | 94.7(1.6) | 86.0(2.3) | 92.7(0.4) | |
|
| ||||||||||
| (b) Accuracy and AUC (Percentage (%) values are reported). | ||||||||||
|
| ||||||||||
| Method | Data | Accuracy | AUC | |||||||
|
| ||||||||||
| TransMIL [27] | CPTAC | 85.9(0.7) | 96.1(0.3) | |||||||
| TCGA | 71.6(2.3) | 88.0(0.7) | ||||||||
|
| ||||||||||
| AttPool [15] | CPTAC | 81.9(2.1) | 92.5(1.6) | |||||||
| TCGA | 79.3(2.3) | 91.3(1.1) | ||||||||
|
| ||||||||||
| GTP* (only GCN) | CPTAC | 83.0(2.7) | 95.2(1.2) | |||||||
| TCGA | 72.4(4.9) | 86.6(3.8) | ||||||||
|
| ||||||||||
| GTP | CPTAC | 91.2(2.5) | 97.7(0.9) | |||||||
| TCGA | 82.3(1.0) | 92.8(0.3) | ||||||||
|
| ||||||||||
| (c) DeLong’s algorithm for comparing the AUC values between GTP and other methods. log10(0.05) = −1.301. | ||||||||||
|
| ||||||||||
| Method | Data | log10(p-value) | ||||||||
|
| ||||||||||
| TransMIL [27] | CPTAC | −1.578(0.853) | ||||||||
| TCGA | −5.627(2.263) | |||||||||
|
| ||||||||||
| AttPool [15] | CPTAC | −2.305(1.250) | ||||||||
| TCGA | −2.068(1.339) | |||||||||
|
| ||||||||||
| GTP* (only GCN) | CPTAC | −1.759(1.129) | ||||||||
| TCGA | −5.373(3.146) | |||||||||