scholarly journals A Comparison of Different Approaches to Clinical Phenotyping of Lithium Response: A Proof of Principle Study Employing Genetic Variants of Three Candidate Circadian Genes

2021 ◽  
Vol 14 (11) ◽  
pp. 1072
Author(s):  
Jan Scott ◽  
Mohamed Lajnef ◽  
Romain Icick ◽  
Frank Bellivier ◽  
Cynthia Marie-Claire ◽  
...  
Keyword(s):  
Machine Learning ◽  
Significant Loss ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Circadian Genes ◽  
Retrospective Assessment ◽  
Misclassification Rates ◽  
Biomarker Research ◽  
Clinical Phenotyping

Optimal classification of the response to lithium (Li) is crucial in genetic and biomarker research. This proof of concept study aims at exploring whether different approaches to phenotyping the response to Li may influence the likelihood of detecting associations between the response and genetic markers. We operationalized Li response phenotypes using the Retrospective Assessment of Response to Lithium Scale (i.e., the Alda scale) in a sample of 164 cases with bipolar disorder (BD). Three phenotypes were defined using the established approaches, whilst two phenotypes were generated by machine learning algorithms. We examined whether these five different Li response phenotypes showed different levels of statistically significant associations with polymorphisms of three candidate circadian genes (RORA, TIMELESS and PPARGC1A), which were selected for this study because they were plausibly linked with the response to Li. The three original and two revised Alda ratings showed low levels of discordance (misclassification rates: 8–12%). However, the significance of associations with circadian genes differed when examining previously recommended categorical and continuous phenotypes versus machine-learning derived phenotypes. Findings using machine learning approaches identified more putative signals of the Li response. Established approaches to Li response phenotyping are easy to use but may lead to a significant loss of data (excluding partial responders) due to recent attempts to improve the reliability of the original rating system. While machine learning approaches require additional modeling to generate Li response phenotypes, they may offer a more nuanced approach, which, in turn, would enhance the probability of identifying significant signals in genetic studies.

scholarly journals Automating Visual Blockage Classification of Culverts with Deep Learning

2021 ◽  
Vol 11 (16) ◽  
pp. 7561
Author(s):  
Umair Iqbal ◽  
Johan Barthelemy ◽  
Wanqing Li ◽  
Pascal Perez
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
False Negative ◽  
Hydraulic Modeling ◽  
Machine Learning Algorithms ◽  
Visual Features ◽  
Learning Approaches ◽  
Learning Models ◽  
Conventional Machine

Blockage of culverts by transported debris materials is reported as the salient contributor in originating urban flash floods. Conventional hydraulic modeling approaches had no success in addressing the problem primarily because of the unavailability of peak floods hydraulic data and the highly non-linear behavior of debris at the culvert. This article explores a new dimension to investigate the issue by proposing the use of intelligent video analytics (IVA) algorithms for extracting blockage related information. The presented research aims to automate the process of manual visual blockage classification of culverts from a maintenance perspective by remotely applying deep learning models. The potential of using existing convolutional neural network (CNN) algorithms (i.e., DarkNet53, DenseNet121, InceptionResNetV2, InceptionV3, MobileNet, ResNet50, VGG16, EfficientNetB3, NASNet) is investigated over a dataset from three different sources (i.e., images of culvert openings and blockage (ICOB), visual hydrology-lab dataset (VHD), synthetic images of culverts (SIC)) to predict the blockage in a given image. Models were evaluated based on their performance on the test dataset (i.e., accuracy, loss, precision, recall, F1 score, Jaccard Index, region of convergence (ROC) curve), floating point operations per second (FLOPs) and response times to process a single test instance. Furthermore, the performance of deep learning models was benchmarked against conventional machine learning algorithms (i.e., SVM, RF, xgboost). In addition, the idea of classifying deep visual features extracted by CNN models (i.e., ResNet50, MobileNet) using conventional machine learning approaches was also implemented in this article. From the results, NASNet was reported most efficient in classifying the blockage images with the 5-fold accuracy of 85%; however, MobileNet was recommended for the hardware implementation because of its improved response time with 5-fold accuracy comparable to NASNet (i.e., 78%). Comparable performance to standard CNN models was achieved for the case where deep visual features were classified using conventional machine learning approaches. False negative (FN) instances, false positive (FP) instances and CNN layers activation suggested that background noise and oversimplified labelling criteria were two contributing factors in the degraded performance of existing CNN algorithms. A framework for partial automation of the visual blockage classification process was proposed, given that none of the existing models was able to achieve high enough accuracy to completely automate the manual process. In addition, a detection-classification pipeline with higher blockage classification accuracy (i.e., 94%) has been proposed as a potential future direction for practical implementation.

scholarly journals Classification of Phonocardiography Signals Using Imbalanced Machine Learning Techniques

2020 ◽  
pp. 103-106
Author(s):  
Mustafa Berkant Selek ◽  
Sude Pehlivan ◽  
Yalcin Isler
Keyword(s):  
Machine Learning ◽  
Frequency Domain ◽  
Cardiovascular Health ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Random Forest Algorithm ◽  
Learning Techniques ◽  
Machine Learning Applications

Cardiovascular diseases, which involve heart and blood vessel dysfunctions, cause a higher number of deaths than any other disease in the world. Throughout history, many approaches have been developed to analyze cardiovascular health by diagnosing such conditions. One of the methodologies is recording and analyzing heart sounds to distinguish normal and abnormal functioning of the heart, which is called Phonocardiography. With the emergence of machine learning applications in healthcare, this process can be automated via the extraction of various features from phonocardiography signals and performing classification with several machine learning algorithms. Many studies have been conducted to extract time and frequency domain features from the phonocardiography signals by segmenting them first into individual heart cycles, and then by classifying them using different machine learning and deep learning approaches. In this study, various time and frequency domain features have been extracted using the complete signal rather than just segments of it. Random Forest algorithm was found to be the most successful algorithm in terms of accuracy as well as recall and precision.

Prediction of K562 Cells Functional Inhibitors Based on Machine Learning Approaches

2020 ◽  
Vol 25 (40) ◽  
pp. 4296-4302 ◽  
Author(s):  
Yuan Zhang ◽  
Zhenyan Han ◽  
Qian Gao ◽  
Xiaoyi Bai ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Inclusion Bodies ◽  
Cross Validation ◽  
Independent Set ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Validation Test ◽  
Excess Number ◽  
Fold Cross Validation

Background: β thalassemia is a common monogenic genetic disease that is very harmful to human health. The disease arises is due to the deletion of or defects in β-globin, which reduces synthesis of the β-globin chain, resulting in a relatively excess number of α-chains. The formation of inclusion bodies deposited on the cell membrane causes a decrease in the ability of red blood cells to deform and a group of hereditary haemolytic diseases caused by massive destruction in the spleen. Methods: In this work, machine learning algorithms were employed to build a prediction model for inhibitors against K562 based on 117 inhibitors and 190 non-inhibitors. Results: The overall accuracy (ACC) of a 10-fold cross-validation test and an independent set test using Adaboost were 83.1% and 78.0%, respectively, surpassing Bayes Net, Random Forest, Random Tree, C4.5, SVM, KNN and Bagging. Conclusion: This study indicated that Adaboost could be applied to build a learning model in the prediction of inhibitors against K526 cells.

scholarly journals Classification of Brainwaves for Sleep Stages by High-Dimensional FFT Features from EEG Signals

2020 ◽  
Vol 10 (5) ◽  
pp. 1797 ◽  
Author(s):  
Mera Kartika Delimayanti ◽  
Bedy Purnama ◽  
Ngoc Giang Nguyen ◽  
Mohammad Reza Faisal ◽  
Kunti Robiatul Mahmudah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Sleep Stage ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Sleep Stages ◽  
Eeg Signals ◽  
Stage Classification ◽  
Sleep Stage Classification ◽  
Low Dimensional

Manual classification of sleep stage is a time-consuming but necessary step in the diagnosis and treatment of sleep disorders, and its automation has been an area of active study. The previous works have shown that low dimensional fast Fourier transform (FFT) features and many machine learning algorithms have been applied. In this paper, we demonstrate utilization of features extracted from EEG signals via FFT to improve the performance of automated sleep stage classification through machine learning methods. Unlike previous works using FFT, we incorporated thousands of FFT features in order to classify the sleep stages into 2–6 classes. Using the expanded version of Sleep-EDF dataset with 61 recordings, our method outperformed other state-of-the art methods. This result indicates that high dimensional FFT features in combination with a simple feature selection is effective for the improvement of automated sleep stage classification.

scholarly journals A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium

2021 ◽  
Vol 9 (5) ◽  
pp. 1034
Author(s):  
Carlos Sabater ◽  
Lorena Ruiz ◽  
Abelardo Margolles
Keyword(s):  
Machine Learning ◽  
Supervised Classification ◽  
Machine Learning Algorithms ◽  
Learning Approach ◽  
Human Milk Oligosaccharides ◽  
Future Studies ◽  
High Fiber ◽  
Machine Learning Approach ◽  
Prebiotic Oligosaccharides

This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies.

scholarly journals Classification of Oil Palm Female Inflorescences Anthesis Stages Using Machine Learning Approaches

2020 ◽  
Author(s):  
Mamehgol Yousefi ◽  
Azmin Shakrine ◽  
Samsuzana bt. Abd Aziz ◽  
Syaril Azrad ◽  
Mohamed Mazmira ◽  
...  
Keyword(s):  
Machine Learning ◽  
Oil Palm ◽  
Learning Approaches

scholarly journals Delineating Smallholder Maize Farms from Sentinel-1 Coupled with Sentinel-2 Data Using Machine Learning

2021 ◽  
Vol 13 (9) ◽  
pp. 4728
Author(s):  
Zinhle Mashaba-Munghemezulu ◽  
George Johannes Chirima ◽  
Cilence Munghemezulu
Keyword(s):  
Machine Learning ◽  
Food Security ◽  
Rural Communities ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Subsistence Agriculture ◽  
Smallholder Farms ◽  
Main Driver ◽  
Sentinel 2

Rural communities rely on smallholder maize farms for subsistence agriculture, the main driver of local economic activity and food security. However, their planted area estimates are unknown in most developing countries. This study explores the use of Sentinel-1 and Sentinel-2 data to map smallholder maize farms. The random forest (RF), support vector (SVM) machine learning algorithms and model stacking (ST) were applied. Results show that the classification of combined Sentinel-1 and Sentinel-2 data improved the RF, SVM and ST algorithms by 24.2%, 8.7%, and 9.1%, respectively, compared to the classification of Sentinel-1 data individually. Similarities in the estimated areas (7001.35 ± 1.2 ha for RF, 7926.03 ± 0.7 ha for SVM and 7099.59 ± 0.8 ha for ST) show that machine learning can estimate smallholder maize areas with high accuracies. The study concludes that the single-date Sentinel-1 data were insufficient to map smallholder maize farms. However, single-date Sentinel-1 combined with Sentinel-2 data were sufficient in mapping smallholder farms. These results can be used to support the generation and validation of national crop statistics, thus contributing to food security.

scholarly journals 174 A comparison of machine learning algorithms in the classification of beef steers finished in feedlot

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 126-127
Author(s):  
Lucas S Lopes ◽  
Christine F Baes ◽  
Dan Tulpan ◽  
Luis Artur Loyola Chardulo ◽  
Otavio Machado Neto ◽  
...  
Keyword(s):  
Machine Learning ◽  
Decision Tree ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Final Decision ◽  
Relevant Parameter ◽  
Good Prediction ◽  
Quality Traits ◽  
C4.5 Decision Tree

Abstract The aim of this project is to compare some of the state-of-the-art machine learning algorithms on the classification of steers finished in feedlots based on performance, carcass and meat quality traits. The precise classification of animals allows for fast, real-time decision making in animal food industry, such as culling or retention of herd animals. Beef production presents high variability in its numerous carcass and beef quality traits. Machine learning algorithms and software provide an opportunity to evaluate the interactions between traits to better classify animals. Four different treatment levels of wet distiller’s grain were applied to 97 Angus-Nellore animals and used as features for the classification problem. The C4.5 decision tree, Naïve Bayes (NB), Random Forest (RF) and Multilayer Perceptron (MLP) Artificial Neural Network algorithms were used to predict and classify the animals based on recorded traits measurements, which include initial and final weights, sheer force and meat color. The top performing classifier was the C4.5 decision tree algorithm with a classification accuracy of 96.90%, while the RF, the MLP and NB classifiers had accuracies of 55.67%, 39.17% and 29.89% respectively. We observed that the final decision tree model constructed with C4.5 selected only the dry matter intake (DMI) feature as a differentiator. When DMI was removed, no other feature or combination of features was sufficiently strong to provide good prediction accuracies for any of the classifiers. We plan to investigate in a follow-up study on a significantly larger sample size, the reasons behind DMI being a more relevant parameter than the other measurements.

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