Comparative machine learning approach for biomarker identification using multiomics data from patients with endometriosis

2019 ◽  
Author(s):  
◽  
Sadia Akter
Keyword(s):  
Machine Learning ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Learning Tools ◽  
Next Generation ◽  
University Of Missouri ◽  
Gynecological Disorder ◽  
Ngs Data

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Endometriosis is a complex and common gynecological disorder yet a poorly understood disease affecting about 176 million women worldwide, and causing significant impact on their quality of life and economic burden. Neither a definitive clinical symptom nor a minimally invasive diagnostic method is available thus leading to an average of 10 years of diagnostic latency. Discovery of relevant biological patterns from microarray expression or next generation sequence (NGS) data has been advanced over the last several decades by applying various machine learning tools. The overall objective of this project was to identify diagnostic molecular mechanisms and biomarkers of endometriosis using a multi-omics approach and various machine learning classifiers. This objective was fulfilled by three related but independent aims: (1) mining rna-seq data to discover molecular mechanisms of endometriosis, (2) to discover diagnostics features of endometriosis in the DNA-methylation profile of the endometrium, and (3) develop innovative machine learning-based differential classification models using whole genome high throughput next generation sequence data. We experimented how well various supervised machine learning methods such as decision tree, Partial least squares-discriminant analysis, support vector machine, random forest and a newly developed method called GenomeForest perform in classifying endometriosis from the control samples trained on both transcriptomics and methylomics data.

Breast cancer prediction using an optimal machine learning technique for next generation sequences

2021 ◽  
pp. 1063293X2199180
Author(s):  
Babymol Kurian ◽  
VL Jyothi
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Decision Tree ◽  
Classification Model ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Next Generation ◽  
Machine Learning Technique ◽  
Cancer Prediction ◽  
Learning Technique

A wide reach on cancer prediction and detection using Next Generation Sequencing (NGS) by the application of artificial intelligence is highly appreciated in the current scenario of the medical field. Next generation sequences were extracted from NCBI (National Centre for Biotechnology Information) gene repository. Sequences of normal Homo sapiens (Class 1), BRCA1 (Class 2) and BRCA2 (Class 3) were extracted for Machine Learning (ML) purpose. The total volume of datasets extracted for the process were 1580 in number under four categories of 50, 100, 150 and 200 sequences. The breast cancer prediction process was carried out in three major steps such as feature extraction, machine learning classification and performance evaluation. The features were extracted with sequences as input. Ten features of DNA sequences such as ORF (Open Reading Frame) count, individual nucleobase average count of A, T, C, G, AT and GC-content, AT/GC composition, G-quadruplex occurrence, MR (Mutation Rate) were extracted from three types of sequences for the classification process. The sequence type was also included as a target variable to the feature set with values 0, 1 and 2 for classes 1, 2 and 3 respectively. Nine various supervised machine learning techniques like LR (Logistic Regression statistical model), LDA (Linear Discriminant analysis model), k-NN (k nearest neighbours’ algorithm), DT (Decision tree technique), NB (Naive Bayes classifier), SVM (Support-Vector Machine algorithm), RF (Random Forest learning algorithm), AdaBoost (AB) and Gradient Boosting (GB) were employed on four various categories of datasets. Of all supervised models, decision tree machine learning technique performed most with maximum accuracy in classification of 94.03%. Classification model performance was evaluated using precision, recall, F1-score and support values wherein F1-score was most similar to the classification accuracy.

scholarly journals Predictive Modelling of Employee Turnover in Indian IT Industry Using Machine Learning Techniques

2019 ◽  
Vol 23 (1) ◽  
pp. 12-21 ◽  
Author(s):  
Shikha N. Khera ◽  
Divya
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
Confusion Matrix ◽  
Predictive Modelling ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
It Industry ◽  
Knowledge Based ◽  
Employee Attrition

Information technology (IT) industry in India has been facing a systemic issue of high attrition in the past few years, resulting in monetary and knowledge-based loses to the companies. The aim of this research is to develop a model to predict employee attrition and provide the organizations opportunities to address any issue and improve retention. Predictive model was developed based on supervised machine learning algorithm, support vector machine (SVM). Archival employee data (consisting of 22 input features) were collected from Human Resource databases of three IT companies in India, including their employment status (response variable) at the time of collection. Accuracy results from the confusion matrix for the SVM model showed that the model has an accuracy of 85 per cent. Also, results show that the model performs better in predicting who will leave the firm as compared to predicting who will not leave the company.

scholarly journals Supervised Machine Learning Methods and Hyperspectral Imaging Techniques Jointly Applied for Brain Cancer Classification

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3827
Author(s):  
Gemma Urbanos ◽  
Alberto Martín ◽  
Guillermo Vázquez ◽  
Marta Villanueva ◽  
Manuel Villa ◽  
...  
Keyword(s):  
Machine Learning ◽  
Blood Vessel ◽  
Hyperspectral Imaging ◽  
Imaging Techniques ◽  
Venous Blood ◽  
Healthy Tissue ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Arterial Blood

Hyperspectral imaging techniques (HSI) do not require contact with patients and are non-ionizing as well as non-invasive. As a consequence, they have been extensively applied in the medical field. HSI is being combined with machine learning (ML) processes to obtain models to assist in diagnosis. In particular, the combination of these techniques has proven to be a reliable aid in the differentiation of healthy and tumor tissue during brain tumor surgery. ML algorithms such as support vector machine (SVM), random forest (RF) and convolutional neural networks (CNN) are used to make predictions and provide in-vivo visualizations that may assist neurosurgeons in being more precise, hence reducing damages to healthy tissue. In this work, thirteen in-vivo hyperspectral images from twelve different patients with high-grade gliomas (grade III and IV) have been selected to train SVM, RF and CNN classifiers. Five different classes have been defined during the experiments: healthy tissue, tumor, venous blood vessel, arterial blood vessel and dura mater. Overall accuracy (OACC) results vary from 60% to 95% depending on the training conditions. Finally, as far as the contribution of each band to the OACC is concerned, the results obtained in this work are 3.81 times greater than those reported in the literature.

scholarly journals Financial Context News Sentiment Analysis for the Lithuanian Language

2021 ◽  
Vol 11 (10) ◽  
pp. 4443
Author(s):  
Rokas Štrimaitis ◽  
Pavel Stefanovič ◽  
Simona Ramanauskaitė ◽  
Asta Slotkienė
Keyword(s):  
Machine Learning ◽  
Sentiment Analysis ◽  
Short Term Memory ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Experimental Investigations ◽  
Support Vector ◽  
Applied Machine Learning ◽  
Bayes Algorithm ◽  
Website Content

Financial area analysis is not limited to enterprise performance analysis. It is worth analyzing as wide an area as possible to obtain the full impression of a specific enterprise. News website content is a datum source that expresses the public’s opinion on enterprise operations, status, etc. Therefore, it is worth analyzing the news portal article text. Sentiment analysis in English texts and financial area texts exist, and are accurate, the complexity of Lithuanian language is mostly concentrated on sentiment analysis of comment texts, and does not provide high accuracy. Therefore in this paper, the supervised machine learning model was implemented to assign sentiment analysis on financial context news, gathered from Lithuanian language websites. The analysis was made using three commonly used classification algorithms in the field of sentiment analysis. The hyperparameters optimization using the grid search was performed to discover the best parameters of each classifier. All experimental investigations were made using the newly collected datasets from four Lithuanian news websites. The results of the applied machine learning algorithms show that the highest accuracy is obtained using a non-balanced dataset, via the multinomial Naive Bayes algorithm (71.1%). The other algorithm accuracies were slightly lower: a long short-term memory (71%), and a support vector machine (70.4%).

scholarly journals Phenotyping Women Based on Dietary Macronutrients, Physical Activity, and Body Weight Using Machine Learning Tools

Nutrients ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 1681 ◽  
Author(s):  
Ramyaa Ramyaa ◽  
Omid Hosseini ◽  
Giri P. Krishnan ◽  
Sridevi Krishnan
Keyword(s):  
Physical Activity ◽  
Machine Learning ◽  
Cluster Analysis ◽  
Body Weight ◽  
Energy Balance ◽  
Numerical Data ◽  
Support Vector ◽  
Learning Tools ◽  
K Nearest Neighbor ◽  
Numerical Predictions

Nutritional phenotyping can help achieve personalized nutrition, and machine learning tools may offer novel means to achieve phenotyping. The primary aim of this study was to use energy balance components, namely input (dietary energy intake and macronutrient composition) and output (physical activity) to predict energy stores (body weight) as a way to evaluate their ability to identify potential phenotypes based on these parameters. From the Women’s Health Initiative Observational Study (WHI OS), carbohydrates, proteins, fats, fibers, sugars, and physical activity variables, namely energy expended from mild, moderate, and vigorous intensity activity, were used to predict current body weight (both as body weight in kilograms and as a body mass index (BMI) category). Several machine learning tools were used for this prediction. Finally, cluster analysis was used to identify putative phenotypes. For the numerical predictions, the support vector machine (SVM), neural network, and k-nearest neighbor (kNN) algorithms performed modestly, with mean approximate errors (MAEs) of 6.70 kg, 6.98 kg, and 6.90 kg, respectively. For categorical prediction, SVM performed the best (54.5% accuracy), followed closely by the bagged tree ensemble and kNN algorithms. K-means cluster analysis improved prediction using numerical data, identified 10 clusters suggestive of phenotypes, with a minimum MAE of ~1.1 kg. A classifier was used to phenotype subjects into the identified clusters, with MAEs <5 kg for 15% of the test set (n = ~2000). This study highlights the challenges, limitations, and successes in using machine learning tools on self-reported data to identify determinants of energy balance.

scholarly journals Optimizing machine learning models for granular NdFeB magnets by very fast simulated annealing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyeon-Kyu Park ◽  
Jae-Hyeok Lee ◽  
Jehyun Lee ◽  
Sang-Koog Kim
Keyword(s):  
Machine Learning ◽  
Simulated Annealing ◽  
Permanent Magnets ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Micromagnetic Simulations ◽  
Ndfeb Magnets ◽  
Average Grain Size ◽  
Macroscopic Properties ◽  
Very Fast Simulated Annealing

AbstractThe macroscopic properties of permanent magnets and the resultant performance required for real implementations are determined by the magnets’ microscopic features. However, earlier micromagnetic simulations and experimental studies required relatively a lot of work to gain any complete and comprehensive understanding of the relationships between magnets’ macroscopic properties and their microstructures. Here, by means of supervised learning, we predict reliable values of coercivity (μ0Hc) and maximum magnetic energy product (BHmax) of granular NdFeB magnets according to their microstructural attributes (e.g. inter-grain decoupling, average grain size, and misalignment of easy axes) based on numerical datasets obtained from micromagnetic simulations. We conducted several tests of a variety of supervised machine learning (ML) models including kernel ridge regression (KRR), support vector regression (SVR), and artificial neural network (ANN) regression. The hyper-parameters of these models were optimized by a very fast simulated annealing (VFSA) algorithm with an adaptive cooling schedule. In our datasets of randomly generated 1,000 polycrystalline NdFeB cuboids with different microstructural attributes, all of the models yielded similar results in predicting both μ0Hc and BHmax. Furthermore, some outliers, which deteriorated the normality of residuals in the prediction of BHmax, were detected and further analyzed. Based on all of our results, we can conclude that our ML approach combined with micromagnetic simulations provides a robust framework for optimal design of microstructures for high-performance NdFeB magnets.

Forecasting Repair and Maintenance Services of Medical Devices Using Support Vector Machine

2021 ◽  
Author(s):  
Hao-yu Liao ◽  
Willie Cade ◽  
Sara Behdad
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Medical Devices ◽  
Kernel Functions ◽  
Support Vector ◽  
Quality Level ◽  
Learning Tools ◽  
Physical Damage ◽  
Repair Service ◽  
Product Failure

Abstract Accurate prediction of product failures and the need for repair services become critical for various reasons, including understanding the warranty performance of manufacturers, defining cost-efficient repair strategies, and compliance with safety standards. The purpose of this study is to use machine learning tools to analyze several parameters crucial for achieving a robust repair service system, including the number of repairs, the time of the next repair ticket or product failure, and the time to repair. A large dataset of over 530,000 repairs and maintenance of medical devices has been investigated by employing the Support Vector Machine (SVM) tool. SVM with four kernel functions is used to forecast the timing of the next failure or repair request in the system for two different products and two different failure types, namely random failure and physical damage. A frequency analysis is also conducted to explore the product quality level based on product failure and the time to repair it. Besides, the best probability distributions are fitted for the number of failures, the time between failures, and the time to repair. The results reveal the value of data analytics and machine learning tools in analyzing post-market product performance and the cost of repair and maintenance operations.

Prediction of CO2 Minimum Miscibility Pressure Using an Augmented Machine-Learning-Based Model

SPE Journal ◽  
2021 ◽  
pp. 1-13
Author(s):  
Utkarsh Sinha ◽  
Birol Dindoruk ◽  
Mohamed Soliman
Keyword(s):  
Machine Learning ◽  
Phase Behavior ◽  
Hybrid Method ◽  
Gas Injection ◽  
Supervised Machine Learning ◽  
Design Parameters ◽  
Support Vector ◽  
Hydrocarbon Gases ◽  
Minimum Miscibility Pressure ◽  
Analytical Correlation

Summary Minimum miscibility pressure (MMP) is one of the key design parameters for gas injection projects. It is a physical parameter that is a measure of local displacement efficiency while subject to some constraints due to its definition. Also, the MMP value is used to tune compositional models along with proper fluid description constrained with other available basic phase behavior data, such as bubble point pressure and volumetric properties. In general, carbon dioxide (CO2) and hydrocarbon gases are the most common gases used for (or screened for) gas injection processes, and because of recent focus, they are used to screen for the coupling of CO2-sequestration and CO2-enhanced oil recovery (EOR) projects. Because the CO2/oil phase behavior is quite different than the hydrocarbon gas/oil phase behavior, researchers developed specialized correlations for CO2 or CO2-rich streams. Therefore, there is a need for a tool with expanded range capabilities for the estimation of MMP for CO2 gas streams. The only known and widely accepted measurement technique for MMP that is coherent with its formal definition is the use of a slimtube apparatus. However, the use of slimtube restricts the amount of data available, even though there are other alternative techniques presented over the last three decades, which all have various limitations (Dindoruk et al. 2021). Due to some of the complexities highlighted in Dindoruk et al. (2021) and time and resource requirements, there have been a number of correlations developed in the literature using mostly classical regression techniques with relatively sparse data using various combinations of limited input data (Cronquist 1978; Lee 1979; Yellig and Metcalfe 1980; Alston et al. 1985; Glaso 1985; Jaubert et al. 1998; Emera and Sarma 2005; Yuan et al. 2005; Ahmadi et al. 2010; Ahmadi and Johns 2011). In this paper, we present two separate approaches for the calculation of the MMP of an oil for CO2 injection: analytical correlation in which the correlation coefficients were tuned using linear support vector machines (SVMs) (Press et al. 2007; MathWorks 2020; RDocumentation 2020b; Cortes and Vapnik 1995) and using a hybrid method (i.e., superlearner model), which consists of the combination of random forest (RF) regression (Breiman 2001) and the proposed analytical correlation. Both models take the compositional analysis of oils up to heptane plus fraction, molecular weight of oil, and the reservoir temperature as input parameters. Based on statistical and data analysis techniques in combination with the help of corresponding crossplots, we showed that the performance of the final proposed method (hybrid method) is superior to all the leading correlations (Cronquist 1978; Lee 1979; Yellig and Metcalfe 1980; Alston et al. 1985; Glaso 1985; Emera and Sarma 2005; Yuan et al. 2005) and supervised machine-learning (Metcalfe 1982) methods considered in the literature (Altman 1992; Chambers and Hastie 1992; Chapelle and Vapnik 2000; Breiman 2001; Press et al. 2007; MathWorks 2020). The proposed model works for the widest spectrum of MMPs from 1,000 to 4,900 psia, which covers the entire range of oils within the scope of CO2 EOR based on the widely used screening criteria (Taber et al. 1997a, 1997b).

scholarly journals Distribution Grids Fault Location employing ST based Optimized Machine Learning Approach

Energies ◽  
2018 ◽  
Vol 11 (9) ◽  
pp. 2328 ◽  
Author(s):  
Md Shafiullah ◽  
M. Abido ◽  
Taher Abdel-Fattah
Keyword(s):  
Machine Learning ◽  
Fault Location ◽  
Percentage Error ◽  
Support Vector ◽  
Learning Approach ◽  
Efficiency Coefficient ◽  
Learning Tools ◽  
Performance Indices ◽  
Machine Learning Approach ◽  
Distribution Grids

Precise information of fault location plays a vital role in expediting the restoration process, after being subjected to any kind of fault in power distribution grids. This paper proposed the Stockwell transform (ST) based optimized machine learning approach, to locate the faults and to identify the faulty sections in the distribution grids. This research employed the ST to extract useful features from the recorded three-phase current signals and fetches them as inputs to different machine learning tools (MLT), including the multilayer perceptron neural networks (MLP-NN), support vector machines (SVM), and extreme learning machines (ELM). The proposed approach employed the constriction-factor particle swarm optimization (CF-PSO) technique, to optimize the parameters of the SVM and ELM for their better generalization performance. Hence, it compared the obtained results of the test datasets in terms of the selected statistical performance indices, including the root mean squared error (RMSE), mean absolute percentage error (MAPE), percent bias (PBIAS), RMSE-observations to standard deviation ratio (RSR), coefficient of determination (R2), Willmott’s index of agreement (WIA), and Nash–Sutcliffe model efficiency coefficient (NSEC) to confirm the effectiveness of the developed fault location scheme. The satisfactory values of the statistical performance indices, indicated the superiority of the optimized machine learning tools over the non-optimized tools in locating faults. In addition, this research confirmed the efficacy of the faulty section identification scheme based on overall accuracy. Furthermore, the presented results validated the robustness of the developed approach against the measurement noise and uncertainties associated with pre-fault loading condition, fault resistance, and inception angle.

scholarly journals Sentiment Analysis using various Machine Learning and Deep Learning Techniques

2021 ◽  
pp. 385-394
Author(s):  
V Umarani ◽  
A Julian ◽  
J Deepa
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Analysis Process ◽  
Learning Techniques

Sentiment analysis has gained a lot of attention from researchers in the last year because it has been widely applied to a variety of application domains such as business, government, education, sports, tourism, biomedicine, and telecommunication services. Sentiment analysis is an automated computational method for studying or evaluating sentiments, feelings, and emotions expressed as comments, feedbacks, or critiques. The sentiment analysis process can be automated using machine learning techniques, which analyses text patterns faster. The supervised machine learning technique is the most used mechanism for sentiment analysis. The proposed work discusses the flow of sentiment analysis process and investigates the common supervised machine learning techniques such as multinomial naive bayes, Bernoulli naive bayes, logistic regression, support vector machine, random forest, K-nearest neighbor, decision tree, and deep learning techniques such as Long Short-Term Memory and Convolution Neural Network. The work examines such learning methods using standard data set and the experimental results of sentiment analysis demonstrate the performance of various classifiers taken in terms of the precision, recall, F1-score, RoC-Curve, accuracy, running time and k fold cross validation and helps in appreciating the novelty of the several deep learning techniques and also giving the user an overview of choosing the right technique for their application.

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