scholarly journals How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

2020 ◽  
Vol 21 (20) ◽  
pp. 7501
Author(s):  
Magdalena Góralska ◽  
Jan Bińkowski ◽  
Natalia Lenarczyk ◽  
Anna Bienias ◽  
Agnieszka Grądzielewska ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Maximum Likelihood ◽  
Random Forest ◽  
Diversity Array Technology ◽  
Gene Encoding ◽  
Putative Gene ◽  
Machine Learning Methods ◽  
F2 Population ◽  
Array Technology

The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.

Detecting Face Touching Using Smartwatches to Mitigate the Spread of COVID-19: Pilot Study (Preprint)

2021 ◽  
Author(s):  
Chen Bai ◽  
Yu-Peng Chen ◽  
Adam Wolach ◽  
Lisa Anthony ◽  
Mamoun Mardini
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
Respiratory Diseases ◽  
Window Size ◽  
Support Vector ◽  
Accelerometer Data ◽  
Respiratory Illnesses ◽  
Motion Data ◽  
Machine Learning Methods

BACKGROUND Frequent spontaneous facial self-touches, predominantly during outbreaks, have the theoretical potential to be a mechanism of contracting and transmitting diseases. Despite the recent advent of vaccines, behavioral approaches remain an integral part of reducing the spread of COVID-19 and other respiratory illnesses. Real-time biofeedback of face touching can potentially mitigate the spread of respiratory diseases. The gap addressed in this study is the lack of an on-demand platform that utilizes motion data from smartwatches to accurately detect face touching. OBJECTIVE The aim of this study was to utilize the functionality and the spread of smartwatches to develop a smartwatch application to identifying motion signatures that are mapped accurately to face touching. METHODS Participants (n=10, 50% women, aged 20-83) performed 10 physical activities classified into: face touching (FT) and non-face touching (NFT) categories, in a standardized laboratory setting. We developed a smartwatch application on Samsung Galaxy Watch to collect raw accelerometer data from participants. Then, data features were extracted from consecutive non-overlapping windows varying from 2-16 seconds. We examined the performance of state-of-the-art machine learning methods on face touching movements recognition (FT vs NFT) and individual activity recognition (IAR): logistic regression, support vector machine, decision trees and random forest. RESULTS Machine learning models were accurate in recognizing face touching categories; logistic regression achieved the best performance across all metrics (Accuracy: 0.93 +/- 0.08, Recall: 0.89 +/- 0.16, Precision: 0.93 +/- 0.08, F1-score: 0.90 +/- 0.11, AUC: 0.95 +/- 0.07) at the window size of 5 seconds. IAR models resulted in lower performance; the random forest classifier achieved the best performance across all metrics (Accuracy: 0.70 +/- 0.14, Recall: 0.70 +/- 0.14, Precision: 0.70 +/- 0.16, F1-score: 0.67 +/- 0.15) at the window size of 9 seconds. CONCLUSIONS Wearable devices, powered with machine learning, are effective in detecting facial touches. This is highly significant during respiratory infection outbreaks, as it has a great potential to refrain people from touching their faces and potentially mitigate the possibility of transmitting COVID-19 and future respiratory diseases.

scholarly journals Comparative Analysis of Intellectual Methods for Muscular Contraction Interpretation for Gesture Interface Implementation

2021 ◽  
Vol 2096 (1) ◽  
pp. 012190
Author(s):  
E V Bunyaeva ◽  
I V Kuznetsov ◽  
Y V Ponomarchuk ◽  
P S Timosh
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Logistic Regression ◽  
Comparative Analysis ◽  
Random Forest ◽  
Decision Tree ◽  
Single Channel ◽  
Muscular Contraction ◽  
Support Vector ◽  
Machine Learning Methods

Abstract The paper considers comparative analysis results of the machine learning methods used for the gesture recognition based on the surface single-channel electromyography (sEMG) data. The data were processed using multilayer perceptron, support vector machine, decision tree ensemble (Random Forest) and logistic regression for the chosen four gesture types. The conclusion was derived on the analysis efficiency of these methods using commonly recommended accuracy metrics.

scholarly journals Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men

2019 ◽  
Vol 26 (11) ◽  
pp. 1263-1271 ◽  
Author(s):  
Yang Xiang ◽  
Kayo Fujimoto ◽  
John Schneider ◽  
Yuxi Jia ◽  
Degui Zhi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Social Network ◽  
Random Forest ◽  
Hiv Infections ◽  
Hiv Status ◽  
Learning Methods ◽  
Network Information ◽  
Machine Learning Methods ◽  
Sex With Men

Abstract Objective HIV infection risk can be estimated based on not only individual features but also social network information. However, there have been insufficient studies using n machine learning methods that can maximize the utility of such information. Leveraging a state-of-the-art network topology modeling method, graph convolutional networks (GCN), our main objective was to include network information for the task of detecting previously unknown HIV infections. Materials and Methods We used multiple social network data (peer referral, social, sex partners, and affiliation with social and health venues) that include 378 young men who had sex with men in Houston, TX, collected between 2014 and 2016. Due to the limited sample size, an ensemble approach was engaged by integrating GCN for modeling information flow and statistical machine learning methods, including random forest and logistic regression, to efficiently model sparse features in individual nodes. Results Modeling network information using GCN effectively increased the prediction of HIV status in the social network. The ensemble approach achieved 96.6% on accuracy and 94.6% on F1 measure, which outperformed the baseline methods (GCN, logistic regression, and random forest: 79.0%, 90.5%, 94.4% on accuracy, respectively; and 57.7%, 80.2%, 90.4% on F1). In the networks with missing HIV status, the ensemble also produced promising results. Conclusion Network context is a necessary component in modeling infectious disease transmissions such as HIV. GCN, when combined with traditional machine learning approaches, achieved promising performance in detecting previously unknown HIV infections, which may provide a useful tool for combatting the HIV epidemic.

scholarly journals Using Smartwatches to Detect Face Touching

Sensors ◽  
2021 ◽  
Vol 21 (19) ◽  
pp. 6528
Author(s):  
Chen Bai ◽  
Yu-Peng Chen ◽  
Adam Wolach ◽  
Lisa Anthony ◽  
Mamoun T. Mardini
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forest ◽  
State Of The Art ◽  
Window Size ◽  
Support Vector ◽  
Accelerometer Data ◽  
Respiratory Illnesses ◽  
Machine Learning Methods ◽  
Movement Recognition

Frequent spontaneous facial self-touches, predominantly during outbreaks, have the theoretical potential to be a mechanism of contracting and transmitting diseases. Despite the recent advent of vaccines, behavioral approaches remain an integral part of reducing the spread of COVID-19 and other respiratory illnesses. The aim of this study was to utilize the functionality and the spread of smartwatches to develop a smartwatch application to identify motion signatures that are mapped accurately to face touching. Participants (n = 10, five women, aged 20–83) performed 10 physical activities classified into face touching (FT) and non-face touching (NFT) categories in a standardized laboratory setting. We developed a smartwatch application on Samsung Galaxy Watch to collect raw accelerometer data from participants. Data features were extracted from consecutive non-overlapping windows varying from 2 to 16 s. We examined the performance of state-of-the-art machine learning methods on face-touching movement recognition (FT vs. NFT) and individual activity recognition (IAR): logistic regression, support vector machine, decision trees, and random forest. While all machine learning models were accurate in recognizing FT categories, logistic regression achieved the best performance across all metrics (accuracy: 0.93 ± 0.08, recall: 0.89 ± 0.16, precision: 0.93 ± 0.08, F1-score: 0.90 ± 0.11, AUC: 0.95 ± 0.07) at the window size of 5 s. IAR models resulted in lower performance, where the random forest classifier achieved the best performance across all metrics (accuracy: 0.70 ± 0.14, recall: 0.70 ± 0.14, precision: 0.70 ± 0.16, F1-score: 0.67 ± 0.15) at the window size of 9 s. In conclusion, wearable devices, powered by machine learning, are effective in detecting facial touches. This is highly significant during respiratory infection outbreaks as it has the potential to limit face touching as a transmission vector.

scholarly journals Apply Machine Learning Methods to Predict Failure of Glaucoma Drainage

2021 ◽  
Vol 11 (1) ◽  
pp. 1-12
Author(s):  
Paul Morrison ◽  
Maxwell Dixon ◽  
Arsham Sheybani ◽  
Bahareh Rahmani
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Intraocular Pressure ◽  
Random Forest ◽  
Glaucoma Drainage Device ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Demographic Information ◽  
Drainage Device ◽  
Machine Learning Methods

The purpose of this retrospective study is to measure machine learning models' ability to predict glaucoma drainage device failure based on demographic information and preoperative measurements. The medical records of 165 patients were used. Potential predictors included the patients' race, age, sex, preoperative intraocular pressure (IOP), preoperative visual acuity, number of IOP-lowering medications, and number and type of previous ophthalmic surgeries. Failure was defined as final IOP greater than 18 mm Hg, reduction in intraocular pressure less than 20% from baseline, or need for reoperation unrelated to normal implant maintenance. Five classifiers were compared: logistic regression, artificial neural network, random forest, decision tree, and support vector machine. Recursive feature elimination was used to shrink the number of predictors and grid search was used to choose hyperparameters. To prevent leakage, nested cross-validation was used throughout. With a small amount of data, the best classfier was logistic regression, but with more data, the best classifier was the random forest.

scholarly journals Integrating Machine/Deep Learning Methods and Filtering Techniques for Reliable Mineral Phase Segmentation of 3D X-ray Computed Tomography Images

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4595
Author(s):  
Parisa Asadi ◽  
Lauren E. Beckingham
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Random Forest ◽  
Ct Images ◽  
Ct Imaging ◽  
Learning Method ◽  
Learning Methods ◽  
X Ray ◽  
Machine Learning Methods ◽  
Filtering Techniques

X-ray CT imaging provides a 3D view of a sample and is a powerful tool for investigating the internal features of porous rock. Reliable phase segmentation in these images is highly necessary but, like any other digital rock imaging technique, is time-consuming, labor-intensive, and subjective. Combining 3D X-ray CT imaging with machine learning methods that can simultaneously consider several extracted features in addition to color attenuation, is a promising and powerful method for reliable phase segmentation. Machine learning-based phase segmentation of X-ray CT images enables faster data collection and interpretation than traditional methods. This study investigates the performance of several filtering techniques with three machine learning methods and a deep learning method to assess the potential for reliable feature extraction and pixel-level phase segmentation of X-ray CT images. Features were first extracted from images using well-known filters and from the second convolutional layer of the pre-trained VGG16 architecture. Then, K-means clustering, Random Forest, and Feed Forward Artificial Neural Network methods, as well as the modified U-Net model, were applied to the extracted input features. The models’ performances were then compared and contrasted to determine the influence of the machine learning method and input features on reliable phase segmentation. The results showed considering more dimensionality has promising results and all classification algorithms result in high accuracy ranging from 0.87 to 0.94. Feature-based Random Forest demonstrated the best performance among the machine learning models, with an accuracy of 0.88 for Mancos and 0.94 for Marcellus. The U-Net model with the linear combination of focal and dice loss also performed well with an accuracy of 0.91 and 0.93 for Mancos and Marcellus, respectively. In general, considering more features provided promising and reliable segmentation results that are valuable for analyzing the composition of dense samples, such as shales, which are significant unconventional reservoirs in oil recovery.

scholarly journals Machine Learning in Aging: An Example of Developing Prediction Models for Serious Fall Injury in Older Adults

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 268-269
Author(s):  
Jaime Speiser ◽  
Kathryn Callahan ◽  
Jason Fanning ◽  
Thomas Gill ◽  
Anne Newman ◽  
...  
Keyword(s):  
Machine Learning ◽  
Older Adults ◽  
Random Forest ◽  
Decision Tree ◽  
Prediction Models ◽  
Receiver Operating Curve ◽  
Learning Methods ◽  
Life Study ◽  
Fall Injury ◽  
Machine Learning Methods

Abstract Advances in computational algorithms and the availability of large datasets with clinically relevant characteristics provide an opportunity to develop machine learning prediction models to aid in diagnosis, prognosis, and treatment of older adults. Some studies have employed machine learning methods for prediction modeling, but skepticism of these methods remains due to lack of reproducibility and difficulty understanding the complex algorithms behind models. We aim to provide an overview of two common machine learning methods: decision tree and random forest. We focus on these methods because they provide a high degree of interpretability. We discuss the underlying algorithms of decision tree and random forest methods and present a tutorial for developing prediction models for serious fall injury using data from the Lifestyle Interventions and Independence for Elders (LIFE) study. Decision tree is a machine learning method that produces a model resembling a flow chart. Random forest consists of a collection of many decision trees whose results are aggregated. In the tutorial example, we discuss evaluation metrics and interpretation for these models. Illustrated in data from the LIFE study, prediction models for serious fall injury were moderate at best (area under the receiver operating curve of 0.54 for decision tree and 0.66 for random forest). Machine learning methods may offer improved performance compared to traditional models for modeling outcomes in aging, but their use should be justified and output should be carefully described. Models should be assessed by clinical experts to ensure compatibility with clinical practice.

scholarly journals Possibility of Autonomous Estimation of Shiba Goat’s Estrus and Non-Estrus Behavior by Machine Learning Methods

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 771
Author(s):  
Toshiya Arakawa
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Random Forest ◽  
Markov Models ◽  
Tracking System ◽  
Video Tracking ◽  
Training Data ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

Mammalian behavior is typically monitored by observation. However, direct observation requires a substantial amount of effort and time, if the number of mammals to be observed is sufficiently large or if the observation is conducted for a prolonged period. In this study, machine learning methods as hidden Markov models (HMMs), random forests, support vector machines (SVMs), and neural networks, were applied to detect and estimate whether a goat is in estrus based on the goat’s behavior; thus, the adequacy of the method was verified. Goat’s tracking data was obtained using a video tracking system and used to estimate whether they, which are in “estrus” or “non-estrus”, were in either states: “approaching the male”, or “standing near the male”. Totally, the PC of random forest seems to be the highest. However, The percentage concordance (PC) value besides the goats whose data were used for training data sets is relatively low. It is suggested that random forest tend to over-fit to training data. Besides random forest, the PC of HMMs and SVMs is high. However, considering the calculation time and HMM’s advantage in that it is a time series model, HMM is better method. The PC of neural network is totally low, however, if the more goat’s data were acquired, neural network would be an adequate method for estimation.

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 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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