scholarly journals Comparison of Regression and Machine Learning Methods in Depression Forecasting Among Home-Based Elderly Chinese: A Community Based Study

2022 ◽  
Vol 12 ◽  
Author(s):  
Shaowu Lin ◽  
Yafei Wu ◽  
Ya Fang
Keyword(s):  
Machine Learning ◽  
Life Satisfaction ◽  
Logistic Regression ◽  
Random Forest ◽  
Cognitive Ability ◽  
Characteristic Curve ◽  
Model Performance ◽  
Predictive Performance ◽  
Home Based ◽  
Elderly Chinese

BackgroundDepression is highly prevalent and considered as the most common psychiatric disorder in home-based elderly, while study on forecasting depression risk in the elderly is still limited. In an endeavor to improve accuracy of depression forecasting, machine learning (ML) approaches have been recommended, in addition to the application of more traditional regression approaches.MethodsA prospective study was employed in home-based elderly Chinese, using baseline (2011) and follow-up (2013) data of the China Health and Retirement Longitudinal Study (CHARLS), a nationally representative cohort study. We compared four algorithms, including the regression-based models (logistic regression, lasso, ridge) and ML method (random forest). Model performance was assessed using repeated nested 10-fold cross-validation. As the main measure of predictive performance, we used the area under the receiver operating characteristic curve (AUC).ResultsThe mean AUCs of the four predictive models, logistic regression, lasso, ridge, and random forest, were 0.795, 0.794, 0.794, and 0.769, respectively. The main determinants were life satisfaction, self-reported memory, cognitive ability, ADL (activities of daily living) impairment, CESD-10 score. Life satisfaction increased the odds ratio of a future depression by 128.6% (logistic), 13.8% (lasso), and 13.2% (ridge), and cognitive ability was the most important predictor in random forest.ConclusionsThe three regression-based models and one ML algorithm performed equally well in differentiating between a future depression case and a non-depression case in home-based elderly. When choosing a model, different considerations, however, such as easy operating, might in some instances lead to one model being prioritized over another.

scholarly journals A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Begüm D. Topçuoğlu ◽  
Nicholas A. Lesniak ◽  
Mack T. Ruffin ◽  
Jenna Wiens ◽  
Patrick D. Schloss
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Sequence Data ◽  
Characteristic Curve ◽  
Predictive Performance ◽  
Model Complexity ◽  
Support Vector ◽  
Classification Problems ◽  
Microbial Biomarkers

ABSTRACT Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability. IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.

scholarly journals Development of Machine Learning Models to Predict Probabilities and Types of Stroke at Prehospital Stage: the Japan Urgent Stroke Triage Score Using Machine Learning (JUST-ML)

2021 ◽  
Author(s):  
Kazutaka Uchida ◽  
Junichi Kouno ◽  
Shinichi Yoshimura ◽  
Norito Kinjo ◽  
Fumihiro Sakakibara ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forests ◽  
Prediction Models ◽  
Characteristic Curve ◽  
Predictive Performance ◽  
Vessel Occlusion ◽  
Predictive Values ◽  
Training Cohort ◽  
Sensitivity Specificity

AbstractIn conjunction with recent advancements in machine learning (ML), such technologies have been applied in various fields owing to their high predictive performance. We tried to develop prehospital stroke scale with ML. We conducted multi-center retrospective and prospective cohort study. The training cohort had eight centers in Japan from June 2015 to March 2018, and the test cohort had 13 centers from April 2019 to March 2020. We use the three different ML algorithms (logistic regression, random forests, XGBoost) to develop models. Main outcomes were large vessel occlusion (LVO), intracranial hemorrhage (ICH), subarachnoid hemorrhage (SAH), and cerebral infarction (CI) other than LVO. The predictive abilities were validated in the test cohort with accuracy, positive predictive value, sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and F score. The training cohort included 3178 patients with 337 LVO, 487 ICH, 131 SAH, and 676 CI cases, and the test cohort included 3127 patients with 183 LVO, 372 ICH, 90 SAH, and 577 CI cases. The overall accuracies were 0.65, and the positive predictive values, sensitivities, specificities, AUCs, and F scores were stable in the test cohort. The classification abilities were also fair for all ML models. The AUCs for LVO of logistic regression, random forests, and XGBoost were 0.89, 0.89, and 0.88, respectively, in the test cohort, and these values were higher than the previously reported prediction models for LVO. The ML models developed to predict the probability and types of stroke at the prehospital stage had superior predictive abilities.

scholarly journals Machine Learning-based in-hospital Mortality Prediction Models for Patients With Acute Coronary Syndrome

2020 ◽  
Author(s):  
Jun Ke ◽  
Yiwei Chen ◽  
Xiaoping Wang ◽  
Zhiyong Wu ◽  
qiongyao Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Hospital Mortality ◽  
Operating Characteristic ◽  
Prediction Models ◽  
Characteristic Curve ◽  
Multivariate Logistic Regression Analysis ◽  
Hdl Cholesterol ◽  
Coronary Syndrome

Abstract BackgroundThe purpose of this study is to identify the risk factors of in-hospital mortality in patients with acute coronary syndrome (ACS) and to evaluate the performance of traditional regression and machine learning prediction models.MethodsThe data of ACS patients who entered the emergency department of Fujian Provincial Hospital from January 1, 2017 to March 31, 2020 for chest pain were retrospectively collected. The study used univariate and multivariate logistic regression analysis to identify risk factors for in-hospital mortality of ACS patients. The traditional regression and machine learning algorithms were used to develop predictive models, and the sensitivity, specificity, and receiver operating characteristic curve were used to evaluate the performance of each model.ResultsA total of 7810 ACS patients were included in the study, and the in-hospital mortality rate was 1.75%. Multivariate logistic regression analysis found that age and levels of D-dimer, cardiac troponin I, N-terminal pro-B-type natriuretic peptide (NT-proBNP), lactate dehydrogenase (LDH), high-density lipoprotein (HDL) cholesterol, and calcium channel blockers were independent predictors of in-hospital mortality. The study found that the area under the receiver operating characteristic curve of the models developed by logistic regression, gradient boosting decision tree (GBDT), random forest, and support vector machine (SVM) for predicting the risk of in-hospital mortality were 0.963, 0.960, 0.963, and 0.959, respectively. Feature importance evaluation found that NT-proBNP, LDH, and HDL cholesterol were top three variables that contribute the most to the prediction performance of the GBDT model and random forest model.ConclusionsThe predictive model developed using logistic regression, GBDT, random forest, and SVM algorithms can be used to predict the risk of in-hospital death of ACS patients. Based on our findings, we recommend that clinicians focus on monitoring the changes of NT-proBNP, LDH, and HDL cholesterol, as this may improve the clinical outcomes of ACS patients.

scholarly journals A framework for effective application of machine learning to microbiome-based classification problems

2019 ◽  
Author(s):  
Begüm D. Topçuoğlu ◽  
Nicholas A. Lesniak ◽  
Mack Ruffin ◽  
Jenna Wiens ◽  
Patrick D. Schloss
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Sequence Data ◽  
Predictive Performance ◽  
Model Complexity ◽  
Support Vector ◽  
Classification Problems ◽  
16S Rrna Sequence ◽  
Microbial Biomarkers

AbstractMachine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made towards developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs; n=490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1 and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, decision trees, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an AUROC of 0.695 [IQR 0.651-0.739] but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 [IQR 0.625-0.735], trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.ImportanceDiagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely over-optimistic. Moreover, there is a trend towards using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step towards developing more reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.

scholarly journals CT-Based Radiomics Signature With Machine Learning Predicts MYCN Amplification in Pediatric Abdominal Neuroblastoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Xin Chen ◽  
Haoru Wang ◽  
Kaiping Huang ◽  
Huan Liu ◽  
Hao Ding ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Predictive Performance ◽  
Training Group ◽  
Clinicopathological Parameters ◽  
Mycn Amplification ◽  
Clinical Model ◽  
Radiomics Signature ◽  
Better Than

PurposeMYCN amplification plays a critical role in defining high-risk subgroup of patients with neuroblastoma. We aimed to develop and validate the CT-based machine learning models for predicting MYCN amplification in pediatric abdominal neuroblastoma.MethodsA total of 172 patients with MYCN amplified (n = 47) and non-amplified (n = 125) were enrolled. The cohort was randomly stratified sampling into training and testing groups. Clinicopathological parameters and radiographic features were selected to construct the clinical predictive model. The regions of interest (ROIs) were segmented on three-phrase CT images to extract first-, second- and higher-order radiomics features. The ICCs, mRMR and LASSO methods were used for dimensionality reduction. The selected features from the training group were used to establish radiomics models using Logistic regression, Support Vector Machine (SVM), Bayes and Random Forest methods. The performance of four different radiomics models was evaluated according to the area under the receiver operator characteristic (ROC) curve (AUC), and then compared by Delong test. The nomogram incorporated of clinicopathological parameters, radiographic features and radiomics signature was developed through multivariate logistic regression. Finally, the predictive performance of the clinical model, radiomics models, and nomogram was evaluated in both training and testing groups.ResultsIn total, 1,218 radiomics features were extracted from the ROIs on three-phrase CT images, and then 14 optimal features, including one original first-order feature and eight wavelet-transformed features and five LoG-transformed features, were identified and selected to construct the radiomics models. In the training group, the AUC of the Logistic, SVM, Bayes and Random Forest model was 0.940, 0.940, 0.780 and 0.927, respectively, and the corresponding AUC in the testing group was 0.909, 0.909, 0.729, 0.851, respectively. There was no significant difference among the Logistic, SVM and Random Forest model, but all better than the Bayes model (p <0.005). The predictive performance of the Logistic radiomics model based on three-phrase is similar to nomogram, but both better than the clinical model and radiomics model based on single venous phase.ConclusionThe CT-based radiomics signature is able to predict MYCN amplification of pediatric abdominal NB with high accuracy based on SVM, Logistic and Random Forest classifiers, while Bayes classifier yields lower predictive performance. When combined with clinical and radiographic qualitative features, the clinics-radiomics nomogram can improve the performance of predicting MYCN amplification.

A proof-of-concept study applying machine learning methods to putative risk factors for eating disorders: results from the multi-centre European project on healthy eating

2021 ◽  
pp. 1-10
Author(s):  
I. Krug ◽  
J. Linardon ◽  
C. Greenwood ◽  
G. Youssef ◽  
J. Treasure ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Logistic Regression ◽  
Predictive Accuracy ◽  
Area Under The Curve ◽  
Prediction Rule ◽  
Predictive Performance ◽  
Individual Risk ◽  
European Project ◽  
Wide Range

Abstract Background Despite a wide range of proposed risk factors and theoretical models, prediction of eating disorder (ED) onset remains poor. This study undertook the first comparison of two machine learning (ML) approaches [penalised logistic regression (LASSO), and prediction rule ensembles (PREs)] to conventional logistic regression (LR) models to enhance prediction of ED onset and differential ED diagnoses from a range of putative risk factors. Method Data were part of a European Project and comprised 1402 participants, 642 ED patients [52% with anorexia nervosa (AN) and 40% with bulimia nervosa (BN)] and 760 controls. The Cross-Cultural Risk Factor Questionnaire, which assesses retrospectively a range of sociocultural and psychological ED risk factors occurring before the age of 12 years (46 predictors in total), was used. Results All three statistical approaches had satisfactory model accuracy, with an average area under the curve (AUC) of 86% for predicting ED onset and 70% for predicting AN v. BN. Predictive performance was greatest for the two regression methods (LR and LASSO), although the PRE technique relied on fewer predictors with comparable accuracy. The individual risk factors differed depending on the outcome classification (EDs v. non-EDs and AN v. BN). Conclusions Even though the conventional LR performed comparably to the ML approaches in terms of predictive accuracy, the ML methods produced more parsimonious predictive models. ML approaches offer a viable way to modify screening practices for ED risk that balance accuracy against participant burden.

scholarly journals Machine learning for identification of surgeries with high risks of cancellation

2018 ◽  
Vol 26 (1) ◽  
pp. 141-155 ◽  
Author(s):  
Li Luo ◽  
Fengyi Zhang ◽  
Yao Yao ◽  
RenRong Gong ◽  
Martina Fu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Predictive Value ◽  
Operating Characteristic ◽  
Sampling Methods ◽  
Characteristic Curve ◽  
Support Vector ◽  
Chi Square ◽  
Stable Performance ◽  
Operating Characteristic Curve

Surgery cancellations waste scarce operative resources and hinder patients’ access to operative services. In this study, the Wilcoxon and chi-square tests were used for predictor selection, and three machine learning models – random forest, support vector machine, and XGBoost – were used for the identification of surgeries with high risks of cancellation. The optimal performances of the identification models were as follows: sensitivity − 0.615; specificity − 0.957; positive predictive value − 0.454; negative predictive value − 0.904; accuracy − 0.647; and area under the receiver operating characteristic curve − 0.682. Of the three models, the random forest model achieved the best performance. Thus, the effective identification of surgeries with high risks of cancellation is feasible with stable performance. Models and sampling methods significantly affect the performance of identification. This study is a new application of machine learning for the identification of surgeries with high risks of cancellation and facilitation of surgery resource management.

scholarly journals A machine learning approach for identification of gastrointestinal predictors for the risk of COVID-19 related hospitalization

2021 ◽  
Author(s):  
Peter Liptak ◽  
Peter Banovcin ◽  
Robert Rosolanka ◽  
Michal Prokopic ◽  
Ivan Kocan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Emergency Department ◽  
Random Forest ◽  
Gastrointestinal Symptoms ◽  
Machine Learning Algorithms ◽  
Important Predictor ◽  
University Hospital ◽  
Home Based ◽  
Severity Of The Disease ◽  
The University

Background and aim: COVID-19 can be presented with various gastrointestinal symptoms. Shortly after the pandemic outbreak several machine learning algorithms have been implemented to assess new diagnostic and therapeutic methods for this disease. Aim of this study is to assess gas-trointestinal and liver related predictive factors for SARS-CoV-2 associated risk of hospitalization. Methods: Data collection was based on questionnaire from the COVID-19 outpatient test center and from the emergency department at the University hospital in combination with data from inter-nal hospital information system and from the mobile application used for telemedicine follow-up of patients. For statistical analysis SARS-CoV-2 negative patients were considered as controls to three different SARS-CoV-2 positive patient groups (divided based on severity of the disease). Results: Total of 710 patients were enrolled in the study. Presence of diarrhea and nausea was significantly higher in emergency department group than in the COVID-19 outpatient test center. Among liver enzymes only aspartate transaminase (AST) has been significantly elevated in the hospitalized group compared to patients discharged home. Based on random forest algorithm, AST has been identified as the most important predictor followed by age or diabetes mellitus. Diarrhea and bloating have also predictive importance although much lower than AST. Conclusion: SARS-CoV-2 positivity is connected with isolated AST elevation and the level is linked with the severity of the disease. Furthermore, using machine learning random forest algo-rithm, we have identified elevated AST as the most important predictor for COVID-19 related hos-pitalizations.

scholarly journals Machine learning approaches revealed metabolic signatures of incident chronic kidney disease in persons with pre-and type 2 diabetes

2020 ◽  
Author(s):  
Ada Admin ◽  
Jialing Huang ◽  
Cornelia Huth ◽  
Marcela Covic ◽  
Martina Troll ◽  
...  
Keyword(s):  
Machine Learning ◽  
Type 2 Diabetes ◽  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Characteristic Curve ◽  
Predictive Performance ◽  
Population Based ◽  
Learning Approaches ◽  
Clinical Variables

Early and precise identification of individuals with pre-diabetes and type 2 diabetes (T2D) at risk of progressing to chronic kidney disease (CKD) is essential to prevent complications of diabetes. Here, we identify and evaluate prospective metabolite biomarkers and the best set of predictors of CKD in the longitudinal, population-based Cooperative Health Research in the Region of Augsburg (KORA) cohort by targeted metabolomics and machine learning approaches. Out of 125 targeted metabolites, sphingomyelin (SM) C18:1 and phosphatidylcholine diacyl (PC aa) C38:0 were identified as candidate metabolite biomarkers of incident CKD specifically in hyperglycemic individuals followed during 6.5 years. Sets of predictors for incident CKD developed from 125 metabolites and 14 clinical variables showed highly stable performances in all three machine learning approaches and outperformed the currently established clinical algorithm for CKD. The two metabolites in combination with five clinical variables were identified as the best set of predictors and their predictive performance yielded a mean area value under the receiver operating characteristic curve of 0.857. The inclusion of metabolite variables in the clinical prediction of future CKD may thus improve the risk prediction in persons with pre- and T2D. The metabolite link with hyperglycemia-related early kidney dysfunction warrants further investigation.

scholarly journals Development of an ensemble machine learning prognostic model to predict 60-day risk of major adverse cardiac events in adults with chest pain

2021 ◽  
Author(s):  
Chris J. Kennedy ◽  
Dustin G. Mark ◽  
Jie Huang ◽  
Mark J. van der Laan ◽  
Alan E. Hubbard ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Chest Pain ◽  
Random Forest ◽  
Decision Trees ◽  
Low Risk ◽  
Major Adverse Cardiac Events ◽  
Risk Scores ◽  
Cardiac Events ◽  
Adverse Cardiac Events

Background: Chest pain is the second leading reason for emergency department (ED) visits and is commonly identified as a leading driver of low-value health care. Accurate identification of patients at low risk of major adverse cardiac events (MACE) is important to improve resource allocation and reduce over-treatment. Objectives: We sought to assess machine learning (ML) methods and electronic health record (EHR) covariate collection for MACE prediction. We aimed to maximize the pool of low-risk patients that are accurately predicted to have less than 0.5% MACE risk and may be eligible for reduced testing. Population Studied: 116,764 adult patients presenting with chest pain in the ED and evaluated for potential acute coronary syndrome (ACS). 60-day MACE rate was 1.9%. Methods: We evaluated ML algorithms (lasso, splines, random forest, extreme gradient boosting, Bayesian additive regression trees) and SuperLearner stacked ensembling. We tuned ML hyperparameters through nested ensembling, and imputed missing values with generalized low-rank models (GLRM). We benchmarked performance to key biomarkers, validated clinical risk scores, decision trees, and logistic regression. We explained the models through variable importance ranking and accumulated local effect visualization. Results: The best discrimination (area under the precision-recall [PR-AUC] and receiver operating characteristic [ROC-AUC] curves) was provided by SuperLearner ensembling (0.148, 0.867), followed by random forest (0.146, 0.862). Logistic regression (0.120, 0.842) and decision trees (0.094, 0.805) exhibited worse discrimination, as did risk scores [HEART (0.064, 0.765), EDACS (0.046, 0.733)] and biomarkers [serum troponin level (0.064, 0.708), electrocardiography (0.047, 0.686)]. The ensemble's risk estimates were miscalibrated by 0.2 percentage points. The ensemble accurately identified 50% of patients to be below a 0.5% 60-day MACE risk threshold. The most important predictors were age, peak troponin, HEART score, EDACS score, and electrocardiogram. GLRM imputation achieved 90% reduction in root mean-squared error compared to median-mode imputation. Conclusion: Use of ML algorithms, combined with broad predictor sets, improved MACE risk prediction compared to simpler alternatives, while providing calibrated predictions and interpretability. Standard risk scores may neglect important health information available in other characteristics and combined in nuanced ways via ML.

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