Table 4.
Performance scores and validation scheme of some methods involved in this review
| Study | Algorithms | Validation scheme | Classification performance | Regression performance | Remarks | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AUROC | AUPR | ACC | F1 | MCC | Recall | Pre | Kappa | MSE | RMSE | SCC | PCC | R 2 | ||||
| Chen et al. [98] | RF | 0.880 | 0.915 | |||||||||||||
| Sun et al. [90] | One-class SVM | 10-fold CV | 0.684 | 0.670 | ||||||||||||
| Huang et al. [132] | LR | 10-fold CV | 0.92 | 0.86 | ||||||||||||
| Li et al. [159] | PEA | 10-fold CV | 0.90 | |||||||||||||
| Sun et al. [38] | RACS | 0.85 | ||||||||||||||
| Wildenhain et al. [97] | SONAR | LOOCV | 0.91 | 0.56 | ||||||||||||
| Chen et al. [39] | NLLSS | LOOCV | 0.905 | |||||||||||||
| Gayvert et al. [81] | RF | 10-fold CV | 0.866 | 0.821 | ||||||||||||
| Li et al. [100] | RF | 0.89 | ||||||||||||||
| Xu et al. [82] | SGB | 10-fold CV | 0.952 | 0.898 | 0.805 | 0.869 | 0.929 | |||||||||
| Shi et al. [108] | TLMCS | 10-fold CV | 0.824 | 0.372 | ||||||||||||
| Shi et al. [133] | LR, Ensemble learning | 10-fold CV | 0.954 | 0.821 | ||||||||||||
| Preuer et al. [20] | DeepSynergy | 5-fold CV | 0.90 | 0.59 | 0.92 | 0.56 | 0.51 | 255.5 | 15.91 | 0.73 | ||||||
| Janizek et al. [80] | TreeCombo | 5-fold CV | 0.519 | 0.70 | ||||||||||||
| Chen et al. [116] | DBN | LOOCV | 0.654 | 0.602 | 0.715 | |||||||||||
| Cheng et al. [129] | Proximity | 0.589 | ||||||||||||||
| Liu et al. [136] | GTB | 10-fold CV | 0.949 | 0.884 | 0.772 | 0.872 | 0.897 | |||||||||
| Sidorov et al. [36] | RF, XGBoost | Leave-one-drug-out CV | 35.6–45.0 | 0.39–0.81 | 0.43–0.86 | 0.17–0.74 | Performance in different cell line | |||||||||
| Andrew et al. [103] | RF | 5 or 10-fold CV | 0.81 | |||||||||||||
| Lanevski et al. [18] | DECREASE | 5-fold CV | 0.82–0.91 | Dose–response matrix prediction | ||||||||||||
| Zhang et al. [137] | FFM | 5-fold CV | 0.925 | 0.934 | 0.761 | |||||||||||
| Julkunen et al. [94] | comboFM | 10 × 5 nested CV |
9.86–13.04 | 0.88–0.91 | 0.95–0.97 | Dose–response matrix prediction | ||||||||||
| Jiang et al. [121] | GCN | 10-fold CV | 0.892 | 0.794 | 0.919 | 0.584 | ||||||||||
| Kuru et al. [113] | MatchMaker | Leave-drug combination-out CV | 0.97 | 0.85 | 267.9 | 0.69 | 0.69 | |||||||||
| Zhang et al. [117] | AuDNNsynergy | 5-fold CV | 0.91 | 0.63 | 0.93 | 0.72 | 0.51 | |||||||||
CV: Cross validation. LOOCV: Leave-one-out cross validation.