Artificial Intelligence Applications in Type 2 Diabetes Mellitus Care: Focus on Machine Learning Methods

Abhari, Shahabeddin; Kalhori, Sharareh R. Niakan; Ebrahimi, Mehdi; Hasannejadasl, Hajar; Garavand, Ali

doi:10.4258/hir.2019.25.4.248

Cited by 75 publications

(55 citation statements)

References 67 publications

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“…To classify people into cases or controls rather than using genotype data most of the researchers used different factors like gender, age, body mass index, environmental effects, daily routine, and food consumption [ 28 – 30 ].…”

Section: Introductionmentioning

confidence: 99%

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Muneeb

Henschel

2021

BMC Bioinformatics

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Background Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the association which can be broadly categorized into two classes, statistical techniques, and machine learning. Statistical techniques are good for finding the actual SNPs causing variation where Machine Learning techniques are good where we just want to classify the people into different categories. In this article, we examined the Eye-color and Type-2 diabetes phenotype. The proposed technique is a hybrid approach consisting of some parts from statistical techniques and remaining from Machine learning. Results The main dataset for Eye-color phenotype consists of 806 people. 404 people have Blue-Green eyes where 402 people have Brown eyes. After preprocessing we generated 8 different datasets, containing different numbers of SNPs, using the mutation difference and thresholding at individual SNP. We calculated three types of mutation at each SNP no mutation, partial mutation, and full mutation. After that data is transformed for machine learning algorithms. We used about 9 classifiers, RandomForest, Extreme Gradient boosting, ANN, LSTM, GRU, BILSTM, 1DCNN, ensembles of ANN, and ensembles of LSTM which gave the best accuracy of 0.91, 0.9286, 0.945, 0.94, 0.94, 0.92, 0.95, and 0.96% respectively. Stacked ensembles of LSTM outperformed other algorithms for 1560 SNPs with an overall accuracy of 0.96, AUC = 0.98 for brown eyes, and AUC = 0.97 for Blue-Green eyes. The main dataset for Type-2 diabetes consists of 107 people where 30 people are classified as cases and 74 people as controls. We used different linear threshold to find the optimal number of SNPs for classification. The final model gave an accuracy of 0.97%. Conclusion Genotype–phenotype predictions are very useful especially in forensic. These predictions can help to identify SNP variant association with traits and diseases. Given more datasets, machine learning model predictions can be increased. Moreover, the non-linearity in the Machine learning model and the combination of SNPs Mutations while training the model increases the prediction. We considered binary classification problems but the proposed approach can be extended to multi-class classification.

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Section: Introductionmentioning

confidence: 99%

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Muneeb

Henschel

2021

BMC Bioinformatics

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Section: Methodsmentioning

confidence: 99%

Eye-Color and Type-2 Diabetes Phenotype Prediction From Genotype Data Using Deep Learning Methods

Muneeb

Henschel

2020

Preprint

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Background: Genotype-Phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the association which can be broadly categorized into two classes, statistical techniques, and machine learning. Statistical techniques are good for finding the actual SNPs causing variation where Machine Learning techniques are good where we just want to classify the people into different categories. In this article, we examined the Eye-color and Type-2 diabetes phenotype. The proposed technique is a hybrid approach consisting of some parts from statistical techniques and remaining from Machine learning. Results: The main dataset for Eye-color phenotype consists of 806 people. 404 people have Blue-Green eyes where 402 people have Brown eyes. After preprocessing we generated 8 different datasets, containing different numbers of SNPs, using the mutation difference and thresholding at individual SNP. We calculated three types of mutation at each SNP no mutation, partial mutation, and full mutation. After that data is transformed for machine learning algorithms. We used about 9 classifiers, RandomForest, Extreme Gradient boosting, ANN, LSTM, GRU, BILSTM, 1DCNN, ensembles of ANN, and ensembles of LSTM which gave the best accuracy of 0.91, 0.9286, 0.945, 0.94, 0.94, 0.92, 0.95, and 0.96 percent respectively. Stacked ensembles of LSTM outperformed other algorithms for 1560 SNPs with an overall accuracy of 0.96, AUC = 0.98 for brown eyes, and AUC = 0.97 for Blue-Green eyes. The main dataset for Type-2 diabetes consists of 107 people where 30 people are classified as cases and 74 people as controls. We used different linear threshold to find the optimal number of SNPs for classification. The final model gave an accuracy of 0.97 percent. Conclusion: Genotype-phenotype predictions are very useful especially in forensic. These predictions can help to identify SNP variant association with traits and diseases. Given more datasets, machine learning model predictions can be increased. Moreover, the non-linearity in the Machine learning model and the combination of SNPs Mutations while training the model increases the prediction. We considered binary classification problems but the proposed approach can be extended to multi-class classification.

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“…Machine learning, which can learn patterns and decision rules from data [6][7][8][9], has been used in clinical practice. Applications of machine learning for the early detection of diabetic retinopathy and cancer, for which clear-cut diagnostic gold standards exist, have been evaluated [10][11][12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Machine Learning Approach to Decision Making for Insulin Initiation in Japanese Patients With Type 2 Diabetes (JDDM 58): Model Development and Validation Study

Fujihara¹,

Matsubayashi²,

Yamada³

et al. 2021

JMIR Med Inform

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Background Applications of machine learning for the early detection of diseases for which a clear-cut diagnostic gold standard exists have been evaluated. However, little is known about the usefulness of machine learning approaches in the decision-making process for decisions such as insulin initiation by diabetes specialists for which no absolute standards exist in clinical settings. Objective The objectives of this study were to examine the ability of machine learning models to predict insulin initiation by specialists and whether the machine learning approach could support decision making by general physicians for insulin initiation in patients with type 2 diabetes. Methods Data from patients prescribed hypoglycemic agents from December 2009 to March 2015 were extracted from diabetes specialists’ registries, resulting in a sample size of 4860 patients who had received initial monotherapy with either insulin (n=293) or noninsulin (n=4567). Neural network output was insulin initiation ranging from 0 to 1 with a cutoff of >0.5 for the dichotomous classification. Accuracy, recall, and area under the receiver operating characteristic curve (AUC) were calculated to compare the ability of machine learning models to make decisions regarding insulin initiation to the decision-making ability of logistic regression and general physicians. By comparing the decision-making ability of machine learning and logistic regression to that of general physicians, 7 cases were chosen based on patient information as the gold standard based on the agreement of 8 of the 9 specialists. Results The AUCs, accuracy, and recall of logistic regression were higher than those of machine learning (AUCs of 0.89-0.90 for logistic regression versus 0.67-0.74 for machine learning). When the examination was limited to cases receiving insulin, discrimination by machine learning was similar to that of logistic regression analysis (recall of 0.05-0.68 for logistic regression versus 0.11-0.52 for machine learning). Accuracies of logistic regression, a machine learning model (downsampling ratio of 1:8), and general physicians were 0.80, 0.70, and 0.66, respectively, for 43 randomly selected cases. For the 7 gold standard cases, the accuracies of logistic regression and the machine learning model were 1.00 and 0.86, respectively, with a downsampling ratio of 1:8, which were higher than the accuracy of general physicians (ie, 0.43). Conclusions Although we found no superior performance of machine learning over logistic regression, machine learning had higher accuracy in prediction of insulin initiation than general physicians, defined by diabetes specialists’ choice of the gold standard. Further study is needed before the use of machine learning–based decision support systems for insulin initiation can be incorporated into clinical practice.

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Artificial Intelligence Applications in Type 2 Diabetes Mellitus Care: Focus on Machine Learning Methods

Cited by 75 publications

References 67 publications

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Eye-Color and Type-2 Diabetes Phenotype Prediction From Genotype Data Using Deep Learning Methods

Machine Learning Approach to Decision Making for Insulin Initiation in Japanese Patients With Type 2 Diabetes (JDDM 58): Model Development and Validation Study

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