Performance of Predictive Models and Input Variables Selected at Different Timepoints for LR, RF, and GBDT
| Performance of Predictive Models for LR, RF, and GBDT at Different Timepoints* . | . | . | . | . | . |
|---|---|---|---|---|---|
| . | Baseline . | Week 1 . | Week 2 . | Week 3 . | Week 6 . |
| LR | AUC, 0.74 ± 0.14 | AUC, 0.79 ± 0.17 | AUC, 0.77 ± 0.15 | AUC, 0.77 ± 0.15 | AUC, 0.83 ± 0.14 |
| Se, 76.5% | Se, 74% | Se, 71% | Se, 71% | Se, 79% | |
| Sp, 61% | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 71% | |
| PPV, 54.5% | PPV, 61.1% | PPV, 60.1% | PPV, 60.1% | PPV, 62.6% | |
| NPV, 80.5% | NPV, 81.6% | NPV, 79.9% | NPV, 79.9% | NPV, 84.6% | |
| Nagelkerke R2, 0.43 | Nagelkerke R2, 0.59 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.46 | |
| Number input, 6 | Number input, 9 | Number input, 6 | Number input, 6 | Number input, 2 | |
| RF | AUC, 0.77 ± 0.13 | AUC, 0.84 ± 0.14 | AUC, 0.84 ± 0.16 | AUC, 0.86 ± 0.14 | AUC, 0.9 ± 0.12 |
| Se, 78 % | Se, 81% | Se, 81% | Se, 87% | Se, 89% | |
| Sp, 62 % | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 75% | |
| PPV, 55.8% | PPV, 63.2% | PPV, 63.2% | PPV, 64.9% | PPV, 68.7% | |
| NPV, 82.1% | NPV, 85.9% | NPV, 85.9% | NPV, 89.9% | NPV, 91.7% | |
| Number input, 7 | Number input, 2 | Number input, 4 | Number input, 5 | Number input, 3 | |
| GBDT | AUC, 0.74 ± 0.16 | AUC, 0.81 ± 0.14 | AUC, 0.81 ± 0.14 | AUC, 0.83 ± 0.15 | AUC, 0.88 ± 0.1 |
| Se, 72 % | Se, 78% | Se, 79% | Se, 87% | Se, 86% | |
| Sp, 70 % | Sp, 74% | Sp, 72% | Sp, 62% | Sp, 75% | |
| PPV, 59.6% | PPV, 64.9% | PPV, 63.5% | PPV, 58.5% | PPV, 67.9% | |
| NPV, 80.2% | NPV, 84.5% | NPV, 84.8% | NPV, 88.5% | NPV, 89.7% | |
| Number input, 2 | Number input, 2 | Number input, 2 | Number input, 3 | Number input, 3 | |
| Input Variables Selected at Different Timepoints for LR, RF, and GBDT | |||||
| Baseline | Week 1 | Week 2 | Week 3 | Week 6 | |
| LR | Use of IMM | Eosinophil count at baseline | CRP level at week 1 | CRP level at week 1 | Neutrophil count at week 1 |
| Eosinophil count | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 | IFX trough level at week 6† | |
| Lymphocyte count | CRP level at week 1 | Monocyte count at week 1 | Monocyte count at week 1 | ||
| Monocyte count | Neutrophil count at week 1 | Eosinophil count at week 1 | Eosinophil count at week 1 | ||
| Albumin level | Leukocyte count at week 1 | Leukocyte count at week 1 | Leukocyte count at week 1 | ||
| Height | Eosinophil count at week 1 | Albumin level at baseline | Albumin level at baseline | ||
| Monocyte count at week 1 | |||||
| Albumin level at baseline | |||||
| Height | |||||
| RF | Neutrophil count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Lymphocyte count | Lymphocyte count at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| Eosinophil count | Platelet count at week 2 | FC level at week 2 | IFX trough level at week 6† | ||
| Albumin level | Age at diagnosis | Eosinophil count at week 1 | |||
| Age at diagnosis | IFX level at week 3† | ||||
| Age at IFX start | |||||
| GBDT | Lymphocyte count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Albumin level | Lymphocyte at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| FC level at week 2 | IFX trough level at week 6† |
| Performance of Predictive Models for LR, RF, and GBDT at Different Timepoints* . | . | . | . | . | . |
|---|---|---|---|---|---|
| . | Baseline . | Week 1 . | Week 2 . | Week 3 . | Week 6 . |
| LR | AUC, 0.74 ± 0.14 | AUC, 0.79 ± 0.17 | AUC, 0.77 ± 0.15 | AUC, 0.77 ± 0.15 | AUC, 0.83 ± 0.14 |
| Se, 76.5% | Se, 74% | Se, 71% | Se, 71% | Se, 79% | |
| Sp, 61% | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 71% | |
| PPV, 54.5% | PPV, 61.1% | PPV, 60.1% | PPV, 60.1% | PPV, 62.6% | |
| NPV, 80.5% | NPV, 81.6% | NPV, 79.9% | NPV, 79.9% | NPV, 84.6% | |
| Nagelkerke R2, 0.43 | Nagelkerke R2, 0.59 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.46 | |
| Number input, 6 | Number input, 9 | Number input, 6 | Number input, 6 | Number input, 2 | |
| RF | AUC, 0.77 ± 0.13 | AUC, 0.84 ± 0.14 | AUC, 0.84 ± 0.16 | AUC, 0.86 ± 0.14 | AUC, 0.9 ± 0.12 |
| Se, 78 % | Se, 81% | Se, 81% | Se, 87% | Se, 89% | |
| Sp, 62 % | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 75% | |
| PPV, 55.8% | PPV, 63.2% | PPV, 63.2% | PPV, 64.9% | PPV, 68.7% | |
| NPV, 82.1% | NPV, 85.9% | NPV, 85.9% | NPV, 89.9% | NPV, 91.7% | |
| Number input, 7 | Number input, 2 | Number input, 4 | Number input, 5 | Number input, 3 | |
| GBDT | AUC, 0.74 ± 0.16 | AUC, 0.81 ± 0.14 | AUC, 0.81 ± 0.14 | AUC, 0.83 ± 0.15 | AUC, 0.88 ± 0.1 |
| Se, 72 % | Se, 78% | Se, 79% | Se, 87% | Se, 86% | |
| Sp, 70 % | Sp, 74% | Sp, 72% | Sp, 62% | Sp, 75% | |
| PPV, 59.6% | PPV, 64.9% | PPV, 63.5% | PPV, 58.5% | PPV, 67.9% | |
| NPV, 80.2% | NPV, 84.5% | NPV, 84.8% | NPV, 88.5% | NPV, 89.7% | |
| Number input, 2 | Number input, 2 | Number input, 2 | Number input, 3 | Number input, 3 | |
| Input Variables Selected at Different Timepoints for LR, RF, and GBDT | |||||
| Baseline | Week 1 | Week 2 | Week 3 | Week 6 | |
| LR | Use of IMM | Eosinophil count at baseline | CRP level at week 1 | CRP level at week 1 | Neutrophil count at week 1 |
| Eosinophil count | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 | IFX trough level at week 6† | |
| Lymphocyte count | CRP level at week 1 | Monocyte count at week 1 | Monocyte count at week 1 | ||
| Monocyte count | Neutrophil count at week 1 | Eosinophil count at week 1 | Eosinophil count at week 1 | ||
| Albumin level | Leukocyte count at week 1 | Leukocyte count at week 1 | Leukocyte count at week 1 | ||
| Height | Eosinophil count at week 1 | Albumin level at baseline | Albumin level at baseline | ||
| Monocyte count at week 1 | |||||
| Albumin level at baseline | |||||
| Height | |||||
| RF | Neutrophil count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Lymphocyte count | Lymphocyte count at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| Eosinophil count | Platelet count at week 2 | FC level at week 2 | IFX trough level at week 6† | ||
| Albumin level | Age at diagnosis | Eosinophil count at week 1 | |||
| Age at diagnosis | IFX level at week 3† | ||||
| Age at IFX start | |||||
| GBDT | Lymphocyte count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Albumin level | Lymphocyte at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| FC level at week 2 | IFX trough level at week 6† |
*Nagelkerke R2 (for LR) is a measure between 0 and 1, with 0 meaning that the model does not predict anything and 1 meaning that it perfectly predicts the remission. AUC values (for both LR and tree-based models) between 0.5 and 1.0, with 0.5 meaning that the model does not predict remission and 1.0 meaning that it perfectly predicts remission. PPV and NPV calculated using remission prevalence of 38.1% at week 30.
†Infliximab measurements.
IFX indicates infliximab; IMM, immunomodulators; NPV, negative predictive value; PPV, positive predictive value; SE, sensitivity; Sp, specificity.
Performance of Predictive Models and Input Variables Selected at Different Timepoints for LR, RF, and GBDT
| Performance of Predictive Models for LR, RF, and GBDT at Different Timepoints* . | . | . | . | . | . |
|---|---|---|---|---|---|
| . | Baseline . | Week 1 . | Week 2 . | Week 3 . | Week 6 . |
| LR | AUC, 0.74 ± 0.14 | AUC, 0.79 ± 0.17 | AUC, 0.77 ± 0.15 | AUC, 0.77 ± 0.15 | AUC, 0.83 ± 0.14 |
| Se, 76.5% | Se, 74% | Se, 71% | Se, 71% | Se, 79% | |
| Sp, 61% | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 71% | |
| PPV, 54.5% | PPV, 61.1% | PPV, 60.1% | PPV, 60.1% | PPV, 62.6% | |
| NPV, 80.5% | NPV, 81.6% | NPV, 79.9% | NPV, 79.9% | NPV, 84.6% | |
| Nagelkerke R2, 0.43 | Nagelkerke R2, 0.59 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.46 | |
| Number input, 6 | Number input, 9 | Number input, 6 | Number input, 6 | Number input, 2 | |
| RF | AUC, 0.77 ± 0.13 | AUC, 0.84 ± 0.14 | AUC, 0.84 ± 0.16 | AUC, 0.86 ± 0.14 | AUC, 0.9 ± 0.12 |
| Se, 78 % | Se, 81% | Se, 81% | Se, 87% | Se, 89% | |
| Sp, 62 % | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 75% | |
| PPV, 55.8% | PPV, 63.2% | PPV, 63.2% | PPV, 64.9% | PPV, 68.7% | |
| NPV, 82.1% | NPV, 85.9% | NPV, 85.9% | NPV, 89.9% | NPV, 91.7% | |
| Number input, 7 | Number input, 2 | Number input, 4 | Number input, 5 | Number input, 3 | |
| GBDT | AUC, 0.74 ± 0.16 | AUC, 0.81 ± 0.14 | AUC, 0.81 ± 0.14 | AUC, 0.83 ± 0.15 | AUC, 0.88 ± 0.1 |
| Se, 72 % | Se, 78% | Se, 79% | Se, 87% | Se, 86% | |
| Sp, 70 % | Sp, 74% | Sp, 72% | Sp, 62% | Sp, 75% | |
| PPV, 59.6% | PPV, 64.9% | PPV, 63.5% | PPV, 58.5% | PPV, 67.9% | |
| NPV, 80.2% | NPV, 84.5% | NPV, 84.8% | NPV, 88.5% | NPV, 89.7% | |
| Number input, 2 | Number input, 2 | Number input, 2 | Number input, 3 | Number input, 3 | |
| Input Variables Selected at Different Timepoints for LR, RF, and GBDT | |||||
| Baseline | Week 1 | Week 2 | Week 3 | Week 6 | |
| LR | Use of IMM | Eosinophil count at baseline | CRP level at week 1 | CRP level at week 1 | Neutrophil count at week 1 |
| Eosinophil count | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 | IFX trough level at week 6† | |
| Lymphocyte count | CRP level at week 1 | Monocyte count at week 1 | Monocyte count at week 1 | ||
| Monocyte count | Neutrophil count at week 1 | Eosinophil count at week 1 | Eosinophil count at week 1 | ||
| Albumin level | Leukocyte count at week 1 | Leukocyte count at week 1 | Leukocyte count at week 1 | ||
| Height | Eosinophil count at week 1 | Albumin level at baseline | Albumin level at baseline | ||
| Monocyte count at week 1 | |||||
| Albumin level at baseline | |||||
| Height | |||||
| RF | Neutrophil count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Lymphocyte count | Lymphocyte count at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| Eosinophil count | Platelet count at week 2 | FC level at week 2 | IFX trough level at week 6† | ||
| Albumin level | Age at diagnosis | Eosinophil count at week 1 | |||
| Age at diagnosis | IFX level at week 3† | ||||
| Age at IFX start | |||||
| GBDT | Lymphocyte count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Albumin level | Lymphocyte at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| FC level at week 2 | IFX trough level at week 6† |
| Performance of Predictive Models for LR, RF, and GBDT at Different Timepoints* . | . | . | . | . | . |
|---|---|---|---|---|---|
| . | Baseline . | Week 1 . | Week 2 . | Week 3 . | Week 6 . |
| LR | AUC, 0.74 ± 0.14 | AUC, 0.79 ± 0.17 | AUC, 0.77 ± 0.15 | AUC, 0.77 ± 0.15 | AUC, 0.83 ± 0.14 |
| Se, 76.5% | Se, 74% | Se, 71% | Se, 71% | Se, 79% | |
| Sp, 61% | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 71% | |
| PPV, 54.5% | PPV, 61.1% | PPV, 60.1% | PPV, 60.1% | PPV, 62.6% | |
| NPV, 80.5% | NPV, 81.6% | NPV, 79.9% | NPV, 79.9% | NPV, 84.6% | |
| Nagelkerke R2, 0.43 | Nagelkerke R2, 0.59 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.49 | Nagelkerke R2, 0.46 | |
| Number input, 6 | Number input, 9 | Number input, 6 | Number input, 6 | Number input, 2 | |
| RF | AUC, 0.77 ± 0.13 | AUC, 0.84 ± 0.14 | AUC, 0.84 ± 0.16 | AUC, 0.86 ± 0.14 | AUC, 0.9 ± 0.12 |
| Se, 78 % | Se, 81% | Se, 81% | Se, 87% | Se, 89% | |
| Sp, 62 % | Sp, 71% | Sp, 71% | Sp, 71% | Sp, 75% | |
| PPV, 55.8% | PPV, 63.2% | PPV, 63.2% | PPV, 64.9% | PPV, 68.7% | |
| NPV, 82.1% | NPV, 85.9% | NPV, 85.9% | NPV, 89.9% | NPV, 91.7% | |
| Number input, 7 | Number input, 2 | Number input, 4 | Number input, 5 | Number input, 3 | |
| GBDT | AUC, 0.74 ± 0.16 | AUC, 0.81 ± 0.14 | AUC, 0.81 ± 0.14 | AUC, 0.83 ± 0.15 | AUC, 0.88 ± 0.1 |
| Se, 72 % | Se, 78% | Se, 79% | Se, 87% | Se, 86% | |
| Sp, 70 % | Sp, 74% | Sp, 72% | Sp, 62% | Sp, 75% | |
| PPV, 59.6% | PPV, 64.9% | PPV, 63.5% | PPV, 58.5% | PPV, 67.9% | |
| NPV, 80.2% | NPV, 84.5% | NPV, 84.8% | NPV, 88.5% | NPV, 89.7% | |
| Number input, 2 | Number input, 2 | Number input, 2 | Number input, 3 | Number input, 3 | |
| Input Variables Selected at Different Timepoints for LR, RF, and GBDT | |||||
| Baseline | Week 1 | Week 2 | Week 3 | Week 6 | |
| LR | Use of IMM | Eosinophil count at baseline | CRP level at week 1 | CRP level at week 1 | Neutrophil count at week 1 |
| Eosinophil count | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 | IFX trough level at week 6† | |
| Lymphocyte count | CRP level at week 1 | Monocyte count at week 1 | Monocyte count at week 1 | ||
| Monocyte count | Neutrophil count at week 1 | Eosinophil count at week 1 | Eosinophil count at week 1 | ||
| Albumin level | Leukocyte count at week 1 | Leukocyte count at week 1 | Leukocyte count at week 1 | ||
| Height | Eosinophil count at week 1 | Albumin level at baseline | Albumin level at baseline | ||
| Monocyte count at week 1 | |||||
| Albumin level at baseline | |||||
| Height | |||||
| RF | Neutrophil count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Lymphocyte count | Lymphocyte count at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| Eosinophil count | Platelet count at week 2 | FC level at week 2 | IFX trough level at week 6† | ||
| Albumin level | Age at diagnosis | Eosinophil count at week 1 | |||
| Age at diagnosis | IFX level at week 3† | ||||
| Age at IFX start | |||||
| GBDT | Lymphocyte count | Neutrophil count at week 1 | Lymphocyte count at baseline | Neutrophil count at week 1 | Neutrophil count at week 1 |
| Albumin level | Lymphocyte at baseline | Neutrophil count at week 1 | Lymphocyte count at baseline | Lymphocyte count at baseline | |
| FC level at week 2 | IFX trough level at week 6† |
*Nagelkerke R2 (for LR) is a measure between 0 and 1, with 0 meaning that the model does not predict anything and 1 meaning that it perfectly predicts the remission. AUC values (for both LR and tree-based models) between 0.5 and 1.0, with 0.5 meaning that the model does not predict remission and 1.0 meaning that it perfectly predicts remission. PPV and NPV calculated using remission prevalence of 38.1% at week 30.
†Infliximab measurements.
IFX indicates infliximab; IMM, immunomodulators; NPV, negative predictive value; PPV, positive predictive value; SE, sensitivity; Sp, specificity.
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