scholarly journals Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches

2020 ◽  
Vol 21 (4) ◽  
pp. 1523 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Hu Huang
Keyword(s):  
Machine Learning ◽  
Virtual Screening ◽  
In Silico ◽  
G6pd Deficiency ◽  
Binding Energies ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
In Silico Admet ◽  
Glucose 6 Phosphate Dehydrogenase

Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack of Nicotine Adenosine Dinucleotide Phosphate (NADPH) and produces stress conditions that can cause oxidative injury to photoreceptors, retinal cells, and blood barrier function. In this study, we constructed pharmacophore-based models based on the complex of G6PD with compound AG1 (G6PD activator) followed by virtual screening. Fifty-three hit molecules were mapped with core pharmacophore features. We performed molecular descriptor calculation, clustering, and principal component analysis (PCA) to pharmacophore hit molecules and further applied statistical machine learning methods. Optimal performance of pharmacophore modeling and machine learning approaches classified the 53 hits as drug-like (18) and nondrug-like (35) compounds. The drug-like compounds further evaluated our established cheminformatics pipeline (molecular docking and in silico ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis). Finally, five lead molecules with different scaffolds were selected by binding energies and in silico ADMET properties. This study proposes that the combination of machine learning methods with traditional structure-based virtual screening can effectively strengthen the ability to find potential G6PD activators used for G6PD deficiency diseases. Moreover, these compounds can be considered as safe agents for further validation studies at the cell level, animal model, and even clinic setting.

In Silico Machine Learning Methods in Drug Development

2014 ◽  
Vol 14 (16) ◽  
pp. 1913-1922 ◽  
Author(s):  
Dimitar Dobchev ◽  
Girinath Pillai ◽  
Mati Karelson
Keyword(s):  
Machine Learning ◽  
Drug Development ◽  
In Silico ◽  
Learning Methods ◽  
Machine Learning Methods

scholarly journals Machine Learning Methods Applied to the Prediction of Pseudo-nitzschia spp. Blooms in the Galician Rias Baixas (NW Spain)

2021 ◽  
Vol 10 (4) ◽  
pp. 199
Author(s):  
Francisco M. Bellas Aláez ◽  
Jesus M. Torres Palenzuela ◽  
Evangelos Spyrakos ◽  
Luis González Vilas
Keyword(s):  
Machine Learning ◽  
Performance Metrics ◽  
Prediction Models ◽  
Support Vector ◽  
False Alarms ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Rías Baixas ◽  
New Algorithms

This work presents new prediction models based on recent developments in machine learning methods, such as Random Forest (RF) and AdaBoost, and compares them with more classical approaches, i.e., support vector machines (SVMs) and neural networks (NNs). The models predict Pseudo-nitzschia spp. blooms in the Galician Rias Baixas. This work builds on a previous study by the authors (doi.org/10.1016/j.pocean.2014.03.003) but uses an extended database (from 2002 to 2012) and new algorithms. Our results show that RF and AdaBoost provide better prediction results compared to SVMs and NNs, as they show improved performance metrics and a better balance between sensitivity and specificity. Classical machine learning approaches show higher sensitivities, but at a cost of lower specificity and higher percentages of false alarms (lower precision). These results seem to indicate a greater adaptation of new algorithms (RF and AdaBoost) to unbalanced datasets. Our models could be operationally implemented to establish a short-term prediction system.

Machine Learning Approaches for Sentiment Analysis

2014 ◽  
pp. 193-208 ◽  
Author(s):  
Basant Agarwal ◽  
Namita Mittal
Keyword(s):  
Machine Learning ◽  
Sentiment Analysis ◽  
Opinion Mining ◽  
Machine Learning Algorithms ◽  
Sentiment Classification ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Knowledge Based ◽  
Semantic Orientation

Opinion Mining or Sentiment Analysis is the study that analyzes people's opinions or sentiments from the text towards entities such as products and services. It has always been important to know what other people think. With the rapid growth of availability and popularity of online review sites, blogs', forums', and social networking sites' necessity of analysing and understanding these reviews has arisen. The main approaches for sentiment analysis can be categorized into semantic orientation-based approaches, knowledge-based, and machine-learning algorithms. This chapter surveys the machine learning approaches applied to sentiment analysis-based applications. The main emphasis of this chapter is to discuss the research involved in applying machine learning methods mostly for sentiment classification at document level. Machine learning-based approaches work in the following phases, which are discussed in detail in this chapter for sentiment classification: (1) feature extraction, (2) feature weighting schemes, (3) feature selection, and (4) machine-learning methods. This chapter also discusses the standard free benchmark datasets and evaluation methods for sentiment analysis. The authors conclude the chapter with a comparative study of some state-of-the-art methods for sentiment analysis and some possible future research directions in opinion mining and sentiment analysis.

Machine Learning Approaches for Sentiment Analysis

Big Data ◽  
2016 ◽  
pp. 1917-1933
Author(s):  
Basant Agarwal ◽  
Namita Mittal
Keyword(s):  
Machine Learning ◽  
Sentiment Analysis ◽  
Opinion Mining ◽  
Machine Learning Algorithms ◽  
Sentiment Classification ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Knowledge Based ◽  
Semantic Orientation

Opinion Mining or Sentiment Analysis is the study that analyzes people's opinions or sentiments from the text towards entities such as products and services. It has always been important to know what other people think. With the rapid growth of availability and popularity of online review sites, blogs', forums', and social networking sites' necessity of analysing and understanding these reviews has arisen. The main approaches for sentiment analysis can be categorized into semantic orientation-based approaches, knowledge-based, and machine-learning algorithms. This chapter surveys the machine learning approaches applied to sentiment analysis-based applications. The main emphasis of this chapter is to discuss the research involved in applying machine learning methods mostly for sentiment classification at document level. Machine learning-based approaches work in the following phases, which are discussed in detail in this chapter for sentiment classification: (1) feature extraction, (2) feature weighting schemes, (3) feature selection, and (4) machine-learning methods. This chapter also discusses the standard free benchmark datasets and evaluation methods for sentiment analysis. The authors conclude the chapter with a comparative study of some state-of-the-art methods for sentiment analysis and some possible future research directions in opinion mining and sentiment analysis.

scholarly journals Machine Learning Methods for Precision Medicine Research Designed to Reduce Health Disparities: A Structured Tutorial

2020 ◽  
Vol 30 (Suppl 1) ◽  
pp. 217-228 ◽  
Author(s):  
Sanjay Basu ◽  
James H. Faghmous ◽  
Patrick Doupe
Keyword(s):  
Machine Learning ◽  
Health Disparities ◽  
Precision Medicine ◽  
Learning Approaches ◽  
Learning Methods ◽  
Medicine Research ◽  
Machine Learning Methods ◽  
Box Models ◽  
Precision Medicine Research ◽  
Key Terms

  Precision medicine research designed to reduce health disparities often involves studying multi-level datasets to understand how diseases manifest disproportionately in one group over another, and how scarce health care resources can be directed precisely to those most at risk for disease. In this article, we provide a structured tutorial for medical and public health research­ers on the application of machine learning methods to conduct precision medicine research designed to reduce health dispari­ties. We review key terms and concepts for understanding machine learning papers, including supervised and unsupervised learning, regularization, cross-validation, bagging, and boosting. Metrics are reviewed for evaluating machine learners and major families of learning approaches, including tree-based learning, deep learning, and ensemble learning. We highlight the advan­tages and disadvantages of different learning approaches, describe strategies for interpret­ing “black box” models, and demonstrate the application of common methods in an example dataset with open-source statistical code in R.Ethn Dis. 2020;30(Suppl 1):217-228; doi:10.18865/ed.30.S1.217

In Silico Prediction of Metabolic Epoxidation for Drug‐like Molecules via Machine Learning Methods

2020 ◽  
Vol 39 (8) ◽  
pp. 1900178
Author(s):  
Jiajing Hu ◽  
Yingchun Cai ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Machine Learning ◽  
In Silico ◽  
In Silico Prediction ◽  
Learning Methods ◽  
Machine Learning Methods

scholarly journals Evaluation of machine-learning methods for ligand-based virtual screening

2007 ◽  
Vol 21 (1-3) ◽  
pp. 53-62 ◽  
Author(s):  
Beining Chen ◽  
Robert F. Harrison ◽  
George Papadatos ◽  
Peter Willett ◽  
David J. Wood ◽  
...  
Keyword(s):  
Machine Learning ◽  
Virtual Screening ◽  
Learning Methods ◽  
Machine Learning Methods
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