scholarly journals Developing Gene-Specific Meta-Predictor of Variant Pathogenicity

2017 ◽  
Author(s):  
Anna Rychkova ◽  
MyMy C. Buu ◽  
Curt Scharfe ◽  
Martina I. Lefterova ◽  
Justin I. Odegaard ◽  
...  
Keyword(s):  
Machine Learning ◽  
Allele Frequency ◽  
Genomic Medicine ◽  
Structural Features ◽  
Machine Learning Algorithms ◽  
Genomic Variation ◽  
Supervised Machine Learning ◽  
Internal Resources ◽  
Variants Of Unknown Significance ◽  
A Genome

AbstractRapid, accurate, and inexpensive genome sequencing promises to transform medical care. However, a critical hurdle to enabling personalized genomic medicine is predicting the functional impact of novel genomic variation. Various methods of missense variants pathogenicity prediction have been developed by now. Here we present a new strategy for developing a pathogenicity predictor of improved accuracy by applying and training a supervised machine learning model in a gene-specific manner. Our meta-predictor combines outputs of various existing predictors, supplements them with an extended set of stability and structural features of the protein, as well as its physicochemical properties, and adds information about allele frequency from various datasets. We used such a supervised gene-specific meta-predictor approach to train the model on the CFTR gene, and to predict pathogenicity of about 1,000 variants of unknown significance that we collected from various publicly available and internal resources. Our CFTR-specific meta-predictor based on the Random Forest model performs better than other machine learning algorithms that we tested, and also outperforms other available tools, such as CADD, MutPred, SIFT, and PolyPhen-2. Our predicted pathogenicity probability correlates well with clinical measures of Cystic Fibrosis patients and experimental functional measures of mutated CFTR proteins. Training the model on one gene, in contrast to taking a genome wide approach, allows taking into account structural features specific for a particular protein, thus increasing the overall accuracy of the predictor. Collecting data from several separate resources, on the other hand, allows to accumulate allele frequency information, estimated as the most important feature by our approach, for a larger set of variants. Finally, our predictor will be hosted on the ClinGen Consortium database to make it available to CF researchers and to serve as a feasibility pilot study for other Mendelian diseases.

Exploring the Use of Machine Learning to Automate the Qualitative Coding of Church-related Tweets

2020 ◽  
Vol 14 (2) ◽  
pp. 140-159
Author(s):  
Anthony-Paul Cooper ◽  
Emmanuel Awuni Kolog ◽  
Erkki Sutinen
Keyword(s):  
Machine Learning ◽  
Online Community ◽  
High Volume ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Social Media Data ◽  
Twitter Data ◽  
Resource Intensity ◽  
Media Data ◽  
Better Than

This article builds on previous research around the exploration of the content of church-related tweets. It does so by exploring whether the qualitative thematic coding of such tweets can, in part, be automated by the use of machine learning. It compares three supervised machine learning algorithms to understand how useful each algorithm is at a classification task, based on a dataset of human-coded church-related tweets. The study finds that one such algorithm, Naïve-Bayes, performs better than the other algorithms considered, returning Precision, Recall and F-measure values which each exceed an acceptable threshold of 70%. This has far-reaching consequences at a time where the high volume of social media data, in this case, Twitter data, means that the resource-intensity of manual coding approaches can act as a barrier to understanding how the online community interacts with, and talks about, church. The findings presented in this article offer a way forward for scholars of digital theology to better understand the content of online church discourse.

scholarly journals Crop price prediction using supervised machine learning algorithms

2021 ◽  
Vol 1916 (1) ◽  
pp. 012042
Author(s):  
Ranjani Dhanapal ◽  
A AjanRaj ◽  
S Balavinayagapragathish ◽  
J Balaji
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Price Prediction

scholarly journals Application of Supervised Machine Learning to Recognize Competent Level and Mixed Antinuclear Antibody Patterns Based on ICAP International Consensus

Diagnostics ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 642
Author(s):  
Yi-Da Wu ◽  
Ruey-Kai Sheu ◽  
Chih-Wei Chung ◽  
Yen-Ching Wu ◽  
Chiao-Chi Ou ◽  
...  
Keyword(s):  
Machine Learning ◽  
Pattern Recognition ◽  
Excellent Agreement ◽  
Antinuclear Antibody ◽  
Disease Diagnosis ◽  
Machine Learning Algorithms ◽  
Observer Agreement ◽  
Supervised Machine Learning ◽  
International Consensus ◽  
Testing Data

Background: Antinuclear antibody pattern recognition is vital for autoimmune disease diagnosis but labor-intensive for manual interpretation. To develop an automated pattern recognition system, we established machine learning models based on the International Consensus on Antinuclear Antibody Patterns (ICAP) at a competent level, mixed patterns recognition, and evaluated their consistency with human reading. Methods: 51,694 human epithelial cells (HEp-2) cell images with patterns assigned by experienced medical technologists collected in a medical center were used to train six machine learning algorithms and were compared by their performance. Next, we choose the best performing model to test the consistency with five experienced readers and two beginners. Results: The mean F1 score in each classification of the best performing model was 0.86 evaluated by Testing Data 1. For the inter-observer agreement test on Testing Data 2, the average agreement was 0.849 (?) among five experienced readers, 0.844 between the best performing model and experienced readers, 0.528 between experienced readers and beginners. The results indicate that the proposed model outperformed beginners and achieved an excellent agreement with experienced readers. Conclusions: This study demonstrated that the developed model could reach an excellent agreement with experienced human readers using machine learning methods.

scholarly journals Improving Manufacturing Applications of Machine Learning by Understanding Defect Classification and the Critical Error Threshold

2021 ◽  
Author(s):  
David Blondheim
Keyword(s):  
Machine Learning ◽  
Machine Learning Algorithms ◽  
Error Threshold ◽  
Supervised Machine Learning ◽  
Secondary Process ◽  
Defect Classification ◽  
Critical Error ◽  
Manufacturing Applications ◽  
Applications Of Machine Learning ◽  
Manufacturing Environments

AbstractMachine learning (ML) is unlocking patterns and insight into data to provide financial value and knowledge for organizations. Use of machine learning in manufacturing environments is increasing, yet sometimes these applications fail to produce meaningful results. A critical review of how defects are classified is needed to appropriately apply machine learning in a production foundry and other manufacturing processes. Four elements associated with defect classification are proposed: Binary Acceptance Specifications, Stochastic Formation of Defects, Secondary Process Variation, and Visual Defect Inspection. These four elements create data space overlap, which influences the bias associated with training supervised machine learning algorithms. If this influence is significant enough, the predicted error of the model exceeds a critical error threshold (CET). There is no financial motivation to implement the ML model in the manufacturing environment if its error is greater than the CET. The goal is to bring awareness to these four elements, define the critical error threshold, and offer guidance and future study recommendations on data collection and machine learning that will increase the success of ML within manufacturing.

scholarly journals Performance Improvement of Decision Tree: A Robust Classifier Using Tabu Search Algorithm

2021 ◽  
Vol 11 (15) ◽  
pp. 6728
Author(s):  
Muhammad Asfand Hafeez ◽  
Muhammad Rashid ◽  
Hassan Tariq ◽  
Zain Ul Abideen ◽  
Saud S. Alotaibi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Tabu Search ◽  
Decision Tree ◽  
Decision Trees ◽  
Search Algorithm ◽  
Learning Algorithms ◽  
Performance Comparison ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Tabu Search Algorithm

Classification and regression are the major applications of machine learning algorithms which are widely used to solve problems in numerous domains of engineering and computer science. Different classifiers based on the optimization of the decision tree have been proposed, however, it is still evolving over time. This paper presents a novel and robust classifier based on a decision tree and tabu search algorithms, respectively. In the aim of improving performance, our proposed algorithm constructs multiple decision trees while employing a tabu search algorithm to consistently monitor the leaf and decision nodes in the corresponding decision trees. Additionally, the used tabu search algorithm is responsible to balance the entropy of the corresponding decision trees. For training the model, we used the clinical data of COVID-19 patients to predict whether a patient is suffering. The experimental results were obtained using our proposed classifier based on the built-in sci-kit learn library in Python. The extensive analysis for the performance comparison was presented using Big O and statistical analysis for conventional supervised machine learning algorithms. Moreover, the performance comparison to optimized state-of-the-art classifiers is also presented. The achieved accuracy of 98%, the required execution time of 55.6 ms and the area under receiver operating characteristic (AUROC) for proposed method of 0.95 reveals that the proposed classifier algorithm is convenient for large datasets.

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 Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 241
Author(s):  
Dongwon Seo ◽  
Sunghyun Cho ◽  
Prabuddha Manjula ◽  
Nuri Choi ◽  
Young-Kuk Kim ◽  
...  
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Fixation Index ◽  
Machine Learning Classification ◽  
Genetic Components ◽  
Marker Combination ◽  
A Genome ◽  
Minimum Number ◽  
Native Chickens

A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

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