Correction: Comparison of risk models for mortality and cardiovascular events between machine learning and conventional logistic regression analysis.
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ABSTRACT:
SUBMITTER: PLOS ONE Staff
PROVIDER: S-EPMC6786577 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Correction: Comparison of risk models for mortality and cardiovascular events between machine learning and conventional logistic regression analysis.
PloS one 20191010 10
[This corrects the article DOI: 10.1371/journal.pone.0221911.]. ...[more]
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Project description:(1) Medical research has shown an increasing interest in machine learning, permitting massive multivariate data analysis. Thus, we developed drug intoxication mortality prediction models, and compared machine learning models and traditional logistic regression. (2) Categorized as drug intoxication, 8,937 samples were extracted from the Korea Centers for Disease Control and Prevention (2008-2017). We trained, validated, and tested each model through data and compared their performance using three measures: Brier score, calibration slope, and calibration-in-the-large. (3) A chi-square test demonstrated that mortality risk statistically significantly differed according to severity, intent, toxic substance, age, and sex. The multilayer perceptron model (MLP) had the highest area under the curve (AUC), and lowest Brier score in training and validation phases, while the logistic regression model (LR) showed the highest AUC (0.827) and lowest Brier score (0.0307) in the testing phase. MLP also had the second-highest AUC (0.816) and second-lowest Brier score (0.003258) in the testing phase, demonstrating better performance than the decision-making tree model. (4) Given the complexity of choosing tuning parameters, LR proved competitive when using medical datasets, which require strict accuracy.
| S-EPMC7037603 | biostudies-literature
Project description:Bronchopulmonary dysplasia (BPD) is the most prevalent and clinically significant complication of prematurity. Accurate identification of at-risk infants would enable ongoing intervention to improve outcomes. Although postnatal exposures are known to affect an infant's likelihood of developing BPD, most existing BPD prediction models do not allow risk to be evaluated at different time points, and/or are not suitable for use in ethno-diverse populations. A comprehensive approach to developing clinical prediction models avoids assumptions as to which method will yield the optimal results by testing multiple algorithms/models. We compared the performance of machine learning and logistic regression models in predicting BPD/death. Our main cohort included infants <33 weeks' gestational age (GA) admitted to a Canadian Neonatal Network site from 2016 to 2018 (n = 9,006) with all analyses repeated for the <29 weeks' GA subcohort (n = 4,246). Models were developed to predict, on days 1, 7, and 14 of admission to neonatal intensive care, the composite outcome of BPD/death prior to discharge. Ten-fold cross-validation and a 20% hold-out sample were used to measure area under the curve (AUC). Calibration intercepts and slopes were estimated by regressing the outcome on the log-odds of the predicted probabilities. The model AUCs ranged from 0.811 to 0.886. Model discrimination was lower in the <29 weeks' GA subcohort (AUCs 0.699-0.790). Several machine learning models had a suboptimal calibration intercept and/or slope (k-nearest neighbor, random forest, artificial neural network, stacking neural network ensemble). The top-performing algorithms will be used to develop multinomial models and an online risk estimator for predicting BPD severity and death that does not require information on ethnicity.
| S-EPMC8688959 | biostudies-literature
Project description:BackgroundMachine learning (ML) algorithms have been trained to early predict critical in-hospital events from COVID-19 using patient data at admission, but little is known on how their performance compares with each other and/or with statistical logistic regression (LR). This prospective multicentre cohort study compares the performance of a LR and five ML models on the contribution of influencing predictors and predictor-to-event relationships on prediction model´s performance.MethodsWe used 25 baseline variables of 490 COVID-19 patients admitted to 8 hospitals in Germany (March-November 2020) to develop and validate (75/25 random-split) 3 linear (L1 and L2 penalty, elastic net [EN]) and 2 non-linear (support vector machine [SVM] with radial kernel, random forest [RF]) ML approaches for predicting critical events defined by intensive care unit transfer, invasive ventilation and/or death (composite end-point: 181 patients). Models were compared for performance (area-under-the-receiver-operating characteristic-curve [AUC], Brier score) and predictor importance (performance-loss metrics, partial-dependence profiles).ResultsModels performed close with a small benefit for LR (utilizing restricted cubic splines for non-linearity) and RF (AUC means: 0.763-0.731 [RF-L1]); Brier scores: 0.184-0.197 [LR-L1]). Top ranked predictor variables (consistently highest importance: C-reactive protein) were largely identical across models, except creatinine, which exhibited marginal (L1, L2, EN, SVM) or high/non-linear effects (LR, RF) on events.ConclusionsAlthough the LR and ML models analysed showed no strong differences in performance and the most influencing predictors for COVID-19-related event prediction, our results indicate a predictive benefit from taking account for non-linear predictor-to-event relationships and effects. Future efforts should focus on leveraging data-driven ML technologies from static towards dynamic modelling solutions that continuously learn and adapt to changes in data environments during the evolving pandemic.Trial registration numberNCT04659187.
| S-EPMC9702742 | biostudies-literature
Project description:BackgroundTimely and accurate prediction of delayed cerebral ischemia is critical for improving the prognosis of patients with aneurysmal subarachnoid hemorrhage. Machine learning (ML) algorithms are increasingly regarded as having a higher prediction power than conventional logistic regression (LR). This study aims to construct LR and ML models and compare their prediction power on delayed cerebral ischemia (DCI) after aneurysmal subarachnoid hemorrhage (aSAH).MethodsThis was a multicenter, retrospective, observational cohort study that enrolled patients with aneurysmal subarachnoid hemorrhage from five hospitals in China. A total of 404 aSAH patients were prospectively enrolled. We randomly divided the patients into training (N = 303) and validation cohorts (N = 101) according to a ratio of 75-25%. One LR and six popular ML algorithms were used to construct models. The area under the receiver operating characteristic curve (AUC), accuracy, balanced accuracy, confusion matrix, sensitivity, specificity, calibration curve, and Hosmer-Lemeshow test were used to assess and compare the model performance. Finally, we calculated each feature of importance.ResultsA total of 112 (27.7%) patients developed DCI. Our results showed that conventional LR with an AUC value of 0.824 (95%CI: 0.73-0.91) in the validation cohort outperformed k-nearest neighbor, decision tree, support vector machine, and extreme gradient boosting model with the AUCs of 0.792 (95%CI: 0.68-0.9, P = 0.46), 0.675 (95%CI: 0.56-0.79, P < 0.01), 0.677 (95%CI: 0.57-0.77, P < 0.01), and 0.78 (95%CI: 0.68-0.87, P = 0.50). However, random forest (RF) and artificial neural network model with the same AUC (0.858, 95%CI: 0.78-0.93, P = 0.26) were better than the LR. The accuracy and the balanced accuracy of the RF were 20.8% and 11% higher than the latter, and the RF also showed good calibration in the validation cohort (Hosmer-Lemeshow: P = 0.203). We found that the CT value of subarachnoid hemorrhage, WBC count, neutrophil count, CT value of cerebral edema, and monocyte count were the five most important features for DCI prediction in the RF model. We then developed an online prediction tool (https://dynamic-nomogram.shinyapps.io/DynNomapp-DCI/) based on important features to calculate DCI risk precisely.ConclusionsIn this multicenter study, we found that several ML methods, particularly RF, outperformed conventional LR. Furthermore, an online prediction tool based on the RF model was developed to identify patients at high risk for DCI after SAH and facilitate timely interventions.Clinical trial registrationhttp://www.chictr.org.cn, Unique identifier: ChiCTR2100044448.
| S-EPMC9247265 | biostudies-literature
Project description:BackgroundThe study aims to compare the prognostic performance of conventional scoring systems to a machine learning (ML) model on coronary computed tomography angiography (CCTA) to discriminate between the patients with and without major adverse cardiovascular events (MACEs) and to find the most important contributing factor of MACE.Materials and methodsFrom November to December 2019, 500 of 1586 CCTA scans were included and analyzed, then six conventional scores were calculated for each participant, and seven ML models were designed. Our study endpoints were all-cause mortality, non-fatal myocardial infarction, late coronary revascularization, and hospitalization for unstable angina or heart failure. Score performance was assessed by area under the curve (AUC) analysis.ResultsOf 500 patients (mean age: 60 ± 10; 53.8% male subjects) referred for CCTA, 416 patients have met inclusion criteria, 46 patients with early (<90 days) cardiac evaluation (due to the inability to clarify the reason for the assessment, deterioration of the symptoms vs. the CCTA result), and 38 patients because of missed follow-up were not enrolled in the final analysis. Forty-six patients (11.0%) developed MACE within 20.5 ± 7.9 months of follow-up. Compared to conventional scores, ML models showed better performance, except only one model which is eXtreme Gradient Boosting had lower performance than conventional scoring systems (AUC:0.824, 95% confidence interval (CI): 0.701-0.947). Between ML models, random forest, ensemble with generalized linear, and ensemble with naive Bayes were shown to have higher prognostic performance (AUC: 0.92, 95% CI: 0.85-0.99, AUC: 0.90, 95% CI: 0.81-0.98, and AUC: 0.89, 95% CI: 0.82-0.97), respectively. Coronary artery calcium score (CACS) had the highest correlation with MACE.ConclusionCompared to the conventional scoring system, ML models using CCTA scans show improved prognostic prediction for MACE. Anatomical features were more important than clinical characteristics.
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Project description:In medical research, there is great interest in developing methods for combining biomarkers. We argue that selection of markers should also be considered in the process. Traditional model/variable selection procedures ignore the underlying uncertainty after model selection. In this work, we propose a novel model-combining algorithm for classification in biomarker studies. It works by considering weighted combinations of various logistic regression models; five different weighting schemes are considered in the article. The weights and algorithm are justified using decision theory and risk-bound results. Simulation studies are performed to assess the finite-sample properties of the proposed model-combining method. It is illustrated with an application to data from an immunohistochemical study in prostate cancer.
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Project description:Genome-wide association studies (GWAS) are a widely used study design for detecting genetic causes of complex diseases. Current studies provide good coverage of common causal SNPs, but not rare ones. A popular method to detect rare causal variants is haplotype testing. A disadvantage of this approach is that many parameters are estimated simultaneously, which can mean a loss of power and slower fitting to large datasets.Haplotype testing effectively tests both the allele frequencies and the linkage disequilibrium (LD) structure of the data. LD has previously been shown to be mostly attributable to LD between adjacent SNPs. We propose a generalised linear model (GLM) which models the effects of each SNP in a region as well as the statistical interactions between adjacent pairs. This is compared to two other commonly used multimarker GLMs: one with a main-effect parameter for each SNP; one with a parameter for each haplotype.We show the haplotype model has higher power for rare untyped causal SNPs, the main-effects model has higher power for common untyped causal SNPs, and the proposed model generally has power in between the two others. We show that the relative power of the three methods is dependent on the number of marker haplotypes the causal allele is present on, which depends on the age of the mutation. Except in the case of a common causal variant in high LD with markers, all three multimarker models are superior in power to single-SNP tests.Including the adjacent statistical interactions results in lower inflation in test statistics when a realistic level of population stratification is present in a dataset.Using the multimarker models, we analyse data from the Molecular Genetics of Schizophrenia study. The multimarker models find potential associations that are not found by single-SNP tests. However, multimarker models also require stricter control of data quality since biases can have a larger inflationary effect on multimarker test statistics than on single-SNP test statistics.Analysing a GWAS with multimarker models can yield candidate regions which may contain rare untyped causal variants. This is useful for increasing prior odds of association in future whole-genome sequence analyses.
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Project description: Not available
| S-EPMC7568985 | biostudies-literature
Project description:OBJECTIVES:Predictive models for hepatocellular carcinoma (HCC) have been limited by modest accuracy and lack of validation. Machine-learning algorithms offer a novel methodology, which may improve HCC risk prognostication among patients with cirrhosis. Our study's aim was to develop and compare predictive models for HCC development among cirrhotic patients, using conventional regression analysis and machine-learning algorithms. METHODS:We enrolled 442 patients with Child A or B cirrhosis at the University of Michigan between January 2004 and September 2006 (UM cohort) and prospectively followed them until HCC development, liver transplantation, death, or study termination. Regression analysis and machine-learning algorithms were used to construct predictive models for HCC development, which were tested on an independent validation cohort from the Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial. Both models were also compared with the previously published HALT-C model. Discrimination was assessed using receiver operating characteristic curve analysis, and diagnostic accuracy was assessed with net reclassification improvement and integrated discrimination improvement statistics. RESULTS:After a median follow-up of 3.5 years, 41 patients developed HCC. The UM regression model had a c-statistic of 0.61 (95% confidence interval (CI) 0.56-0.67), whereas the machine-learning algorithm had a c-statistic of 0.64 (95% CI 0.60-0.69) in the validation cohort. The HALT-C model had a c-statistic of 0.60 (95% CI 0.50-0.70) in the validation cohort and was outperformed by the machine-learning algorithm. The machine-learning algorithm had significantly better diagnostic accuracy as assessed by net reclassification improvement (P<0.001) and integrated discrimination improvement (P=0.04). CONCLUSIONS:Machine-learning algorithms improve the accuracy of risk stratifying patients with cirrhosis and can be used to accurately identify patients at high-risk for developing HCC.
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Project description:BackgroundLogistic random effects models are a popular tool to analyze multilevel also called hierarchical data with a binary or ordinal outcome. Here, we aim to compare different statistical software implementations of these models.MethodsWe used individual patient data from 8509 patients in 231 centers with moderate and severe Traumatic Brain Injury (TBI) enrolled in eight Randomized Controlled Trials (RCTs) and three observational studies. We fitted logistic random effects regression models with the 5-point Glasgow Outcome Scale (GOS) as outcome, both dichotomized as well as ordinal, with center and/or trial as random effects, and as covariates age, motor score, pupil reactivity or trial. We then compared the implementations of frequentist and Bayesian methods to estimate the fixed and random effects. Frequentist approaches included R (lme4), Stata (GLLAMM), SAS (GLIMMIX and NLMIXED), MLwiN ([R]IGLS) and MIXOR, Bayesian approaches included WinBUGS, MLwiN (MCMC), R package MCMCglmm and SAS experimental procedure MCMC.Three data sets (the full data set and two sub-datasets) were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial. For the ordinal outcome in the full data set also a proportional odds model with a random center effect was fitted.ResultsThe packages gave similar parameter estimates for both the fixed and random effects and for the binary (and ordinal) models for the main study and when based on a relatively large number of level-1 (patient level) data compared to the number of level-2 (hospital level) data. However, when based on relatively sparse data set, i.e. when the numbers of level-1 and level-2 data units were about the same, the frequentist and Bayesian approaches showed somewhat different results. The software implementations differ considerably in flexibility, computation time, and usability. There are also differences in the availability of additional tools for model evaluation, such as diagnostic plots. The experimental SAS (version 9.2) procedure MCMC appeared to be inefficient.ConclusionsOn relatively large data sets, the different software implementations of logistic random effects regression models produced similar results. Thus, for a large data set there seems to be no explicit preference (of course if there is no preference from a philosophical point of view) for either a frequentist or Bayesian approach (if based on vague priors). The choice for a particular implementation may largely depend on the desired flexibility, and the usability of the package. For small data sets the random effects variances are difficult to estimate. In the frequentist approaches the MLE of this variance was often estimated zero with a standard error that is either zero or could not be determined, while for Bayesian methods the estimates could depend on the chosen "non-informative" prior of the variance parameter. The starting value for the variance parameter may be also critical for the convergence of the Markov chain.
| S-EPMC3112198 | biostudies-literature