scholarly journals VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data

2021 ◽  
Author(s):  
Evan McCartney-Melstad ◽  
Ke Bi ◽  
James Han ◽  
Catherine K. Foo
Keyword(s):  
Dna Sequencing ◽  
Genetic Material ◽  
Support Vector ◽  
Learning Approach ◽  
Sequencing Data ◽  
Support Vector Regression Model ◽  
Variant Call ◽  
Sample Contamination ◽  
Machine Learning Approach

AbstractThe quality of genotyping calls resulting from DNA sequencing is reliant on high quality starting genetic material. One factor that can reduce sample quality and lead to misleading genotyping results is genetic contamination of a sample by another source, such as cells or DNA from another sample of the same or different species. Cross-sample contamination by individuals of the same species is particularly difficult to detect in DNA sequencing data, because the contaminating sequence reads look very similar to those of the intended base sample. We introduce a new method that uses a support vector regression model trained on in silico contaminated datasets to predict empirical contamination using a collection of variables drawn from VCF files, including the fraction of sites that are heterozygous, the fraction of heterozygous sites with imbalanced allele counts, and parameters describing distributions fit to heterozygous allele fractions in a sample. We use the method described here to train a model that can accurately predict the extent of cross-sample contamination within 1% of the actual fraction, for simulated contaminated samples in the 0-5% contamination range, directly from the VCF file.DefinitionsLesser alleleThe allele in a heterozygous position that received less sequencing read support (which may be either the REF or ALT allele).Lesser allele fraction (LAF)The number of sequencing reads supporting the less frequently observed allele divided by the sum of reads supporting both alleles in the genotype at a given genomic position.

A Support-Vector-Machine Method for Precisely Evaluating Planar Straightness Error

2012 ◽  
Vol 220-223 ◽  
pp. 1611-1614
Author(s):  
Jiang Meng
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Evaluation Method ◽  
Support Vector ◽  
Learning Approach ◽  
Support Vector Regression Model ◽  
Machine Method ◽  
Support Vector Machine Method ◽  
Machine Learning Approach ◽  
Straightness Error

To present a precise and efficient algorithm to solve planar straightness error problems, a machine-learning approach to evaluate planar straightness error was presented in this paper. According to the similarity between the least envelope zone and the support vector regression model, the SVR-based method was developed to solve the problem of straightness error. The evaluation method was compared to some existing techniques. According to the results from three datasets, it is shown that the SVR-based method can provide precise and exact values of planar straightness error.

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 Arabic English Cross-Lingual Plagiarism Detection Based on Keyphrases Extraction, Monolingual and Machine Learning Approach

2019 ◽  
pp. 1-12
Author(s):  
Mokhtar Al-Suhaiqi ◽  
Muneer A. S. Hazaa ◽  
Mohammed Albared
Keyword(s):  
Machine Learning ◽  
Machine Learning Techniques ◽  
Detection Methods ◽  
Support Vector ◽  
Svm Classifier ◽  
Learning Approach ◽  
Plagiarism Detection ◽  
Machine Learning Approach ◽  
Cross Lingual ◽  
Cross Language

Due to rapid growth of research articles in various languages, cross-lingual plagiarism detection problem has received increasing interest in recent years. Cross-lingual plagiarism detection is more challenging task than monolingual plagiarism detection. This paper addresses the problem of cross-lingual plagiarism detection (CLPD) by proposing a method that combines keyphrases extraction, monolingual detection methods and machine learning approach. The research methodology used in this study has facilitated to accomplish the objectives in terms of designing, developing, and implementing an efficient Arabic – English cross lingual plagiarism detection. This paper empirically evaluates five different monolingual plagiarism detection methods namely i)N-Grams Similarity, ii)Longest Common Subsequence, iii)Dice Coefficient, iv)Fingerprint based Jaccard Similarity  and v) Fingerprint based Containment Similarity. In addition, three machine learning approaches namely i) naïve Bayes, ii) Support Vector Machine, and iii) linear logistic regression classifiers are used for Arabic-English Cross-language plagiarism detection. Several experiments are conducted to evaluate the performance of the key phrases extraction methods. In addition, Several experiments to investigate the performance of machine learning techniques to find the best method for Arabic-English Cross-language plagiarism detection. According to the experiments of Arabic-English Cross-language plagiarism detection, the highest result was obtained using SVM   classifier with 92% f-measure. In addition, the highest results were obtained by all classifiers are achieved, when most of the monolingual plagiarism detection methods are used. 

scholarly journals Driver Stress State Evaluation by Means of Thermal Imaging: A Supervised Machine Learning Approach Based on ECG Signal

2020 ◽  
Vol 10 (16) ◽  
pp. 5673 ◽  
Author(s):  
Daniela Cardone ◽  
David Perpetuini ◽  
Chiara Filippini ◽  
Edoardo Spadolini ◽  
Lorenza Mancini ◽  
...  
Keyword(s):  
Machine Learning ◽  
Stress State ◽  
Thermal Imaging ◽  
Driving Simulator ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Learning Approach ◽  
Machine Learning Approach ◽  
Thermal Features ◽  
Driver Stress

Traffic accidents determine a large number of injuries, sometimes fatal, every year. Among other factors affecting a driver’s performance, an important role is played by stress which can decrease decision-making capabilities and situational awareness. In this perspective, it would be beneficial to develop a non-invasive driver stress monitoring system able to recognize the driver’s altered state. In this study, a contactless procedure for drivers’ stress state assessment by means of thermal infrared imaging was investigated. Thermal imaging was acquired during an experiment on a driving simulator, and thermal features of stress were investigated with comparison to a gold-standard metric (i.e., the stress index, SI) extracted from contact electrocardiography (ECG). A data-driven multivariate machine learning approach based on a non-linear support vector regression (SVR) was employed to estimate the SI through thermal features extracted from facial regions of interest (i.e., nose tip, nostrils, glabella). The predicted SI showed a good correlation with the real SI (r = 0.61, p = ~0). A two-level classification of the stress state (STRESS, SI ≥ 150, versus NO STRESS, SI < 150) was then performed based on the predicted SI. The ROC analysis showed a good classification performance with an AUC of 0.80, a sensitivity of 77%, and a specificity of 78%.

scholarly journals Validation of miRNAs as Breast Cancer Biomarkers with a Machine Learning Approach

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 431 ◽  
Author(s):  
Oneeb Rehman ◽  
Hanqi Zhuang ◽  
Ali Muhamed Ali ◽  
Ali Ibrahim ◽  
Zhongwei Li
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Information Gain ◽  
Support Vector ◽  
Learning Approach ◽  
Breast Cancers ◽  
Functional Studies ◽  
Normal Tissues ◽  
Machine Learning Approach ◽  
Chi Squared

Certain small noncoding microRNAs (miRNAs) are differentially expressed in normal tissues and cancers, which makes them great candidates for biomarkers for cancer. Previously, a selected subset of miRNAs has been experimentally verified to be linked to breast cancer. In this paper, we validated the importance of these miRNAs using a machine learning approach on miRNA expression data. We performed feature selection, using Information Gain (IG), Chi-Squared (CHI2) and Least Absolute Shrinkage and Selection Operation (LASSO), on the set of these relevant miRNAs to rank them by importance. We then performed cancer classification using these miRNAs as features using Random Forest (RF) and Support Vector Machine (SVM) classifiers. Our results demonstrated that the miRNAs ranked higher by our analysis had higher classifier performance. Performance becomes lower as the rank of the miRNA decreases, confirming that these miRNAs had different degrees of importance as biomarkers. Furthermore, we discovered that using a minimum of three miRNAs as biomarkers for breast cancers can be as effective as using the entire set of 1800 miRNAs. This work suggests that machine learning is a useful tool for functional studies of miRNAs for cancer detection and diagnosis.

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