Computational Method for Distinguishing Lysine Acetylation, Sumoylation, and Ubiquitination using the Random Forest Algorithm with a Feature Selection Procedure

2018 ◽  
Vol 20 (10) ◽  
pp. 886-895 ◽  
Author(s):  
ShaoPeng Wang ◽  
JiaRui Li ◽  
Fei Yuan ◽  
Lei Chen ◽  
Tao Huang ◽  
...  
Keyword(s):  
Feature Selection ◽  
Random Forest ◽  
Selection Procedure ◽  
Computational Method ◽  
Lysine Acetylation ◽  
Random Forest Algorithm

Computational Method for Identifying Malonylation Sites by Using Random Forest Algorithm

2020 ◽  
Vol 23 (4) ◽  
pp. 304-312
Author(s):  
ShaoPeng Wang ◽  
JiaRui Li ◽  
Xijun Sun ◽  
Yu-Hang Zhang ◽  
Tao Huang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Random Forest ◽  
Learning Algorithms ◽  
Selection Procedure ◽  
Machine Learning Algorithms ◽  
Computational Method ◽  
Feature Subset ◽  
Random Forest Algorithm ◽  
Post Translational Modification

Background: As a newly uncovered post-translational modification on the ε-amino group of lysine residue, protein malonylation was found to be involved in metabolic pathways and certain diseases. Apart from experimental approaches, several computational methods based on machine learning algorithms were recently proposed to predict malonylation sites. However, previous methods failed to address imbalanced data sizes between positive and negative samples. Objective: In this study, we identified the significant features of malonylation sites in a novel computational method which applied machine learning algorithms and balanced data sizes by applying synthetic minority over-sampling technique. Method: Four types of features, namely, amino acid (AA) composition, position-specific scoring matrix (PSSM), AA factor, and disorder were used to encode residues in protein segments. Then, a two-step feature selection procedure including maximum relevance minimum redundancy and incremental feature selection, together with random forest algorithm, was performed on the constructed hybrid feature vector. Results: An optimal classifier was built from the optimal feature subset, which featured an F1-measure of 0.356. Feature analysis was performed on several selected important features. Conclusion: Results showed that certain types of PSSM and disorder features may be closely associated with malonylation of lysine residues. Our study contributes to the development of computational approaches for predicting malonyllysine and provides insights into molecular mechanism of malonylation.

Prediction of Heart Disease Using Random Forest and Rough Set Based Feature Selection

2018 ◽  
Vol 3 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Indu Yekkala ◽  
Sunanda Dixit
Keyword(s):  
Feature Selection ◽  
Heart Disease ◽  
Random Forest ◽  
Causes Of Death ◽  
Electronic Records ◽  
Complex Nature ◽  
Random Forest Algorithm ◽  
Multiple Sources ◽  
Artery Disease ◽  
Single Data

Data is generated by the medical industry. Often this data is of very complex nature—electronic records, handwritten scripts, etc.—since it is generated from multiple sources. Due to the Complexity and sheer volume of this data necessitates techniques that can extract insight from this data in a quick and efficient way. These insights not only diagnose the diseases but also predict and can prevent disease. One such use of these techniques is cardiovascular diseases. Heart disease or coronary artery disease (CAD) is one of the major causes of death all over the world. Comprehensive research using single data mining techniques have not resulted in an acceptable accuracy. Further research is being carried out on the effectiveness of hybridizing more than one technique for increasing accuracy in the diagnosis of heart disease. In this article, the authors worked on heart stalog dataset collected from the UCI repository, used the Random Forest algorithm and Feature Selection using rough sets to accurately predict the occurrence of heart disease

scholarly journals Phishing Detection Based on Machine Learning and Feature Selection Methods

2019 ◽  
Vol 13 (12) ◽  
pp. 171 ◽  
Author(s):  
Mohammad Almseidin ◽  
AlMaha Abu Zuraiq ◽  
Mouhammd Al-kasassbeh ◽  
Nidal Alnidami
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Random Forest ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Web Pages ◽  
Selection Methods ◽  
Random Forest Algorithm ◽  
Phishing Detection ◽  
Enormous Number

With increasing technology developments, the Internet has become everywhere and accessible by everyone. There are a considerable number of web-pages with different benefits. Despite this enormous number, not all of these sites are legitimate. There are so-called phishing sites that deceive users into serving their interests. This paper dealt with this problem using machine learning algorithms in addition to employing a novel dataset that related to phishing detection, which contains 5000 legitimate web-pages and 5000 phishing ones. In order to obtain the best results, various machine learning algorithms were tested. Then J48, Random forest, and Multilayer perceptron were chosen. Different feature selection tools were employed to the dataset in order to improve the efficiency of the models. The best result of the experiment achieved by utilizing 20 features out of 48 features and applying it to Random forest algorithm. The accuracy was 98.11%.

scholarly journals A Study of the Classification of Motor Imagery Signals using Machine Learning Tools

2021 ◽  
Author(s):  
Anam Hashmi ◽  
Bilal Alam Khan ◽  
Omar Farooq
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Wavelet Transform ◽  
Random Forest ◽  
Random Forest Algorithm ◽  
Eeg Signals ◽  
Relaxation State ◽  
Wavelet Transform Analysis ◽  
Imagined Movement

In this paper, we propose a system for the purpose of classifying Electroencephalography (EEG) signals associated with imagined movement of right hand and relaxation state using machine learning algorithm namely Random Forest Algorithm. The EEG dataset used in this research was created by the University of Tubingen, Germany. EEG signals associated with the imagined movement of right hand and relaxation state were processed using wavelet transform analysis with Daubechies orthogonal wavelet as the mother wavelet. After the wavelet transform analysis, eight features were extracted. Subsequently, a feature selection method based on Random Forest Algorithm was employed giving us the best features out of the eight proposed features. The feature selection stage was followed by classification stage in which eight different models combining the different features based on their importance were constructed. The optimum classification performance of 85.41% was achieved with the Random Forest classifier. This research shows that this system of classification of motor movements can be used in a Brain Computer Interface system (BCI) to mentally control a robotic device or an exoskeleton.

scholarly journals Modify Random Forest Algorithm Using Hybrid Feature Selection Method

2018 ◽  
Vol 4 (2) ◽  
pp. 1-6
Author(s):  
Ahmed T. Sadiq‎ ◽  
Karrar Shareef Musawi
Keyword(s):  
Feature Selection ◽  
Random Forest ◽  
Gini Index ◽  
Feature Selection Method ◽  
Selection Method ◽  
Random Selection ◽  
Experimental Results ◽  
Random Forest Algorithm ◽  
Selection For

The Importance of Random Forrest(RF) is one of the most powerful ‎methods ‎of ‎machine learning in ‎Decision Tree.‎ The Proposed hybrid feature selection for Random Forest depend on ‎two ‎measure ‎‎Information Gain and Gini Index in varying percentages ‎based on ‎weight.‎ In this paper, we tend to ‎propose a modify Random Forrest‏ ‏‎algorithm named ‎Random Forest algorithm using hybrid ‎feature ‎‎selection ‎that uses hybrid feature ‎selection instead of ‎using ‎one feature selection. The ‎main plan is to ‎computation the ‎‎ Information ‎Gain for all random selection ‎feature then search for ‎the best split ‎‎point in ‎the node that gives the best ‎value for a hybrid ‎equation with ‎Gini Index. ‎The experimental results on the ‎dataset ‎showed that the proposed ‎modification is ‎better than the classic Random ‎Forest compared to ‎the standard static Random ‎Forest the hybrid feature ‎‎selection Random Forrest shows significant ‎improvement ‎in accuracy measure.‎

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