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Prediction of delayed graft function after kidney transplantation : comparison between logistic regression and machine learning methods

Alexander Decruyenaere (UGent) , Philippe Decruyenaere (UGent) , Patrick Peeters (UGent) , Frank Vermassen (UGent) , Tom Dhaene (UGent) and Ivo Couckuyt (UGent)
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Abstract
Background: Predictive models for delayed graft function (DGF) after kidney transplantation are usually developed using logistic regression. We want to evaluate the value of machine learning methods in the prediction of DGF. Methods: 497 kidney transplantations from deceased donors at the Ghent University Hospital between 2005 and 2011 are included. A feature elimination procedure is applied to determine the optimal number of features, resulting in 20 selected parameters (24 parameters after conversion to indicator parameters) out of 55 retrospectively collected parameters. Subsequently, 9 distinct types of predictive models are fitted using the reduced data set: logistic regression (LR), linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), support vector machines (SVMs; using linear, radial basis function and polynomial kernels), decision tree (DT), random forest (RF), and stochastic gradient boosting (SGB). Performance of the models is assessed by computing sensitivity, positive predictive values and area under the receiver operating characteristic curve (AUROC) after 10-fold stratified cross-validation. AUROCs of the models are pairwise compared using Wilcoxon signed-rank test. Results: The observed incidence of DGF is 12.5 %. DT is not able to discriminate between recipients with and without DGF (AUROC of 52.5 %) and is inferior to the other methods. SGB, RF and polynomial SVM are mainly able to identify recipients without DGF (AUROC of 77.2, 73.9 and 79.8 %, respectively) and only outperform DT. LDA, QDA, radial SVM and LR also have the ability to identify recipients with DGF, resulting in higher discriminative capacity (AUROC of 82.2, 79.6, 83.3 and 81.7 %, respectively), which outperforms DT and RF. Linear SVM has the highest discriminative capacity (AUROC of 84.3 %), outperforming each method, except for radial SVM, polynomial SVM and LDA. However, it is the only method superior to LR. Conclusions: The discriminative capacities of LDA, linear SVM, radial SVM and LR are the only ones above 80 %. None of the pairwise AUROC comparisons between these models is statistically significant, except linear SVM outperforming LR. Additionally, the sensitivity of linear SVM to identify recipients with DGF is amongst the three highest of all models. Due to both reasons, the authors believe that linear SVM is most appropriate to predict DGF.
Keywords
ISCHEMIA-REPERFUSION INJURY, ARTIFICIAL NEURAL-NETWORK, Support vector machines, Sensitivity and specificity, ROC curve, Predictive analysis, Machine learning, Logistic models, Kidney transplantation, Discriminant analysis, Decision trees, Delayed graft function, IBCN, PRETRANSPLANT VARIABLES, RENAL-TRANSPLANTATION, DIALYSIS, ALLOGRAFT, RISK, MODEL, SURVIVAL

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Chicago
Decruyenaere, Alexander, Philippe Decruyenaere, Patrick Peeters, Frank Vermassen, Tom Dhaene, and Ivo Couckuyt. 2015. “Prediction of Delayed Graft Function After Kidney Transplantation : Comparison Between Logistic Regression and Machine Learning Methods.” Bmc Medical Informatics and Decision Making 15.
APA
Decruyenaere, A., Decruyenaere, P., Peeters, P., Vermassen, F., Dhaene, T., & Couckuyt, I. (2015). Prediction of delayed graft function after kidney transplantation : comparison between logistic regression and machine learning methods. BMC MEDICAL INFORMATICS AND DECISION MAKING, 15.
Vancouver
1.
Decruyenaere A, Decruyenaere P, Peeters P, Vermassen F, Dhaene T, Couckuyt I. Prediction of delayed graft function after kidney transplantation : comparison between logistic regression and machine learning methods. BMC MEDICAL INFORMATICS AND DECISION MAKING. 2015;15.
MLA
Decruyenaere, Alexander, Philippe Decruyenaere, Patrick Peeters, et al. “Prediction of Delayed Graft Function After Kidney Transplantation : Comparison Between Logistic Regression and Machine Learning Methods.” BMC MEDICAL INFORMATICS AND DECISION MAKING 15 (2015): n. pag. Print.
@article{6973986,
  abstract     = {Background: Predictive models for delayed graft function (DGF) after kidney transplantation are usually developed using logistic regression. We want to evaluate the value of machine learning methods in the prediction of DGF. 
Methods: 497 kidney transplantations from deceased donors at the Ghent University Hospital between 2005 and 2011 are included. A feature elimination procedure is applied to determine the optimal number of features, resulting in 20 selected parameters (24 parameters after conversion to indicator parameters) out of 55 retrospectively collected parameters. Subsequently, 9 distinct types of predictive models are fitted using the reduced data set: logistic regression (LR), linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), support vector machines (SVMs; using linear, radial basis function and polynomial kernels), decision tree (DT), random forest (RF), and stochastic gradient boosting (SGB). Performance of the models is assessed by computing sensitivity, positive predictive values and area under the receiver operating characteristic curve (AUROC) after 10-fold stratified cross-validation. AUROCs of the models are pairwise compared using Wilcoxon signed-rank test. 
Results: The observed incidence of DGF is 12.5 \%. DT is not able to discriminate between recipients with and without DGF (AUROC of 52.5 \%) and is inferior to the other methods. SGB, RF and polynomial SVM are mainly able to identify recipients without DGF (AUROC of 77.2, 73.9 and 79.8 \%, respectively) and only outperform DT. LDA, QDA, radial SVM and LR also have the ability to identify recipients with DGF, resulting in higher discriminative capacity (AUROC of 82.2, 79.6, 83.3 and 81.7 \%, respectively), which outperforms DT and RF. Linear SVM has the highest discriminative capacity (AUROC of 84.3 \%), outperforming each method, except for radial SVM, polynomial SVM and LDA. However, it is the only method superior to LR. 
Conclusions: The discriminative capacities of LDA, linear SVM, radial SVM and LR are the only ones above 80 \%. None of the pairwise AUROC comparisons between these models is statistically significant, except linear SVM outperforming LR. Additionally, the sensitivity of linear SVM to identify recipients with DGF is amongst the three highest of all models. Due to both reasons, the authors believe that linear SVM is most appropriate to predict DGF.},
  articleno    = {83},
  author       = {Decruyenaere, Alexander and Decruyenaere, Philippe and Peeters, Patrick and Vermassen, Frank and Dhaene, Tom and Couckuyt, Ivo},
  issn         = {1472-6947},
  journal      = {BMC MEDICAL INFORMATICS AND DECISION MAKING},
  language     = {eng},
  pages        = {10},
  title        = {Prediction of delayed graft function after kidney transplantation : comparison between logistic regression and machine learning methods},
  url          = {http://dx.doi.org/10.1186/s12911-015-0206-y},
  volume       = {15},
  year         = {2015},
}

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