scholarly journals iAIPs: Identifying Anti-Inflammatory Peptides Using Random Forest

2021 ◽  
Vol 12 ◽  
Author(s):  
Dongxu Zhao ◽  
Zhixia Teng ◽  
Yanjuan Li ◽  
Dong Chen
Keyword(s):  
Feature Selection ◽  
Amino Acid ◽  
Random Forest ◽  
Feature Selection Method ◽  
Selection Strategy ◽  
Feature Subset ◽  
Evolutionary Analysis ◽  
Anti Inflammatory ◽  
Optimal Feature Subset ◽  
Optimal Feature

Recently, several anti-inflammatory peptides (AIPs) have been found in the process of the inflammatory response, and these peptides have been used to treat some inflammatory and autoimmune diseases. Therefore, identifying AIPs accurately from a given amino acid sequences is critical for the discovery of novel and efficient anti-inflammatory peptide-based therapeutics and the acceleration of their application in therapy. In this paper, a random forest-based model called iAIPs for identifying AIPs is proposed. First, the original samples were encoded with three feature extraction methods, including g-gap dipeptide composition (GDC), dipeptide deviation from the expected mean (DDE), and amino acid composition (AAC). Second, the optimal feature subset is generated by a two-step feature selection method, in which the feature is ranked by the analysis of variance (ANOVA) method, and the optimal feature subset is generated by the incremental feature selection strategy. Finally, the optimal feature subset is inputted into the random forest classifier, and the identification model is constructed. Experiment results showed that iAIPs achieved an AUC value of 0.822 on an independent test dataset, which indicated that our proposed model has better performance than the existing methods. Furthermore, the extraction of features for peptide sequences provides the basis for evolutionary analysis. The study of peptide identification is helpful to understand the diversity of species and analyze the evolutionary history of species.

PREDAIP: Computational Prediction and Analysis for Anti-inflammatory Peptide via a Hybrid Feature Selection Technique

2021 ◽  
Vol 16 ◽  
Author(s):  
Dan Lin ◽  
Jialin Yu ◽  
Ju Zhang ◽  
Huan He ◽  
Xinyun Guo ◽  
...  
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Machine Learning Algorithms ◽  
Selection Strategy ◽  
Feature Subset ◽  
Feature Selection Technique ◽  
Selection Technique ◽  
Anti Inflammatory ◽  
Optimal Feature Subset ◽  
Optimal Feature

Background: Anti-inflammatory peptides (AIPs) are potent therapeutic agents for inflammatory and autoimmune disorders due to their high specificity and minimal toxicity under normal conditions. Therefore, it is greatly significant and beneficial to identify AIPs for further discovering novel and efficient AIPs-based therapeutics. Recently, three computational approaches, which can effectively identify potential AIPs, have been developed based on machine learning algorithms. However, there are several challenges with the existing three predictors. Objective: A novel machine learning algorithm needs to be proposed to improve the AIPs prediction accuracy. Methods: This study attempts to improve the recognition of AIPs by employing multiple primary sequence-based feature descriptors and an efficient feature selection strategy. By sorting features through four enhanced minimal redundancy maximal relevance (emRMR) methods, and then attaching seven different classifiers wrapper methods based on the sequential forward selection algorithm (SFS), we proposed a hybrid feature selection technique emRMR-SFS to optimize feature vectors. Furthermore, by evaluating seven classifiers trained with the optimal feature subset, we developed the extremely randomized tree (ERT) based predictor named PREDAIP for identifying AIPs. Results: We systematically compared the performance of PREDAIP with the existing tools on an independent test dataset. It demonstrates the effectiveness and power of the PREDAIP. The correlation criteria used in emRMR would affect the selection results of the optimal feature subset at the SFS-wrapper stage, which justifies the necessity for considering different correlation criteria in emRMR. Conclusion: We expect that PREDAIP will be useful for the high-throughput prediction of AIPs and the development of AIPs therapeutics.

scholarly journals Accelerated Simulated Annealing and Mutation Operator Feature Selection method for Big Data

2019 ◽  
Vol 8 (2) ◽  
pp. 910-916
Keyword(s):  
Feature Selection ◽  
Simulated Annealing ◽  
Feature Selection Method ◽  
Classification Problem ◽  
Feature Subset Selection ◽  
Feature Subset ◽  
Mutation Operator ◽  
Knn Classifier ◽  
Optimal Feature Subset ◽  
Optimal Feature

The optimal feature subset selection over very high dimensional data is a vital issue. Even though the optimal features are selected, the classification of those selected features becomes a key complicated task. In order to handle these problems, a novel, Accelerated Simulated Annealing and Mutation Operator (ASAMO) feature selection algorithm is suggested in this work. For solving the classification problem, the Fuzzy Minimal Consistent Class Subset Coverage (FMCCSC) problem is introduced. In FMCCSC, consistent subset is combined with the K-Nearest Neighbour (KNN) classifier known as FMCCSC-KNN classifier. The two data sets Dorothea and Madelon from UCI machine repository are experimented for optimal feature selection and classification. The experimental results substantiate the efficiency of proposed ASAMO with FMCCSC-KNN classifier compared to Particle Swarm Optimization (PSO) and Accelerated PSO feature selection algorithms.

Research of Red Tide Algae Images Feature Selection Method Based on ReliefF and SBS

2014 ◽  
Vol 507 ◽  
pp. 806-809
Author(s):  
Shu Fang Li ◽  
Qin Jia ◽  
Hong Liang
Keyword(s):  
Feature Selection ◽  
Red Tide ◽  
Feature Selection Method ◽  
Original Data ◽  
Feature Subset ◽  
Data Set ◽  
Before And After ◽  
Optimal Feature Subset ◽  
Optimal Feature ◽  
Original Feature

In order to Red Tide algae present real-time automatic classification method of high accuracy rate, this paper proposes using ReliefF-SBS for feature selection. Namely feature analysis about Red Tide algae image original data set. And on this basis, feature selection to remove the irrelevant features and redundant features from the original feature set feature, to get the optimal feature subset, and reduce their impact on the classification accuracy. Meanwhile compare the classification results before and after SVM and KNN two kinds feature selection classifiers.

A Multilevel Optimal Feature Selection and Ensemble Learning for a Specific CAD System-Pulmonary Nodule Detection

2013 ◽  
Vol 380-384 ◽  
pp. 1593-1599
Author(s):  
Hao Yan Guo ◽  
Da Zheng Wang
Keyword(s):  
Feature Selection ◽  
Learning Algorithm ◽  
Feature Selection Method ◽  
Feature Subset ◽  
Cad System ◽  
Optimal Feature Selection ◽  
Optimal Feature Subset ◽  
Feature Selection Approach ◽  
Selection Algorithms ◽  
Optimal Feature

The traditional motivation behind feature selection algorithms is to find the best subset of features for a task using one particular learning algorithm. However, it has been often found that no single classifier is entirely satisfactory for a particular task. Therefore, how to further improve the performance of these single systems on the basis of the previous optimal feature subset is a very important issue.We investigate the notion of optimal feature selection and present a practical feature selection approach that is based on an optimal feature subset of a single CAD system, which is referred to as a multilevel optimal feature selection method (MOFS) in this paper. Through MOFS, we select the different optimal feature subsets in order to eliminate features that are redundant or irrelevant and obtain optimal features.

scholarly journals Succinylation Site Prediction Based on Protein Sequences Using the IFS-LightGBM (BO) Model

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Lu Zhang ◽  
Min Liu ◽  
Xinyi Qin ◽  
Guangzhong Liu
Keyword(s):  
Feature Selection ◽  
Amino Acid ◽  
Optimization Algorithm ◽  
Feature Selection Method ◽  
Selection Method ◽  
Bayesian Optimization ◽  
Feature Subset ◽  
Bayesian Optimization Algorithm ◽  
Incremental Feature Selection ◽  
Optimal Feature Subset

Succinylation is an important posttranslational modification of proteins, which plays a key role in protein conformation regulation and cellular function control. Many studies have shown that succinylation modification on protein lysine residue is closely related to the occurrence of many diseases. To understand the mechanism of succinylation profoundly, it is necessary to identify succinylation sites in proteins accurately. In this study, we develop a new model, IFS-LightGBM (BO), which utilizes the incremental feature selection (IFS) method, the LightGBM feature selection method, the Bayesian optimization algorithm, and the LightGBM classifier, to predict succinylation sites in proteins. Specifically, pseudo amino acid composition (PseAAC), position-specific scoring matrix (PSSM), disorder status, and Composition of k -spaced Amino Acid Pairs (CKSAAP) are firstly employed to extract feature information. Then, utilizing the combination of the LightGBM feature selection method and the incremental feature selection (IFS) method selects the optimal feature subset for the LightGBM classifier. Finally, to increase prediction accuracy and reduce the computation load, the Bayesian optimization algorithm is used to optimize the parameters of the LightGBM classifier. The results reveal that the IFS-LightGBM (BO)-based prediction model performs better when it is evaluated by some common metrics, such as accuracy, recall, precision, Matthews Correlation Coefficient (MCC), and F -measure.

A Hybrid Feature Selection Method for Effective Data Classification in Data Mining Applications

2019 ◽  
Vol 11 (1) ◽  
pp. 1-16
Author(s):  
Ilangovan Sangaiya ◽  
A. Vincent Antony Kumar
Keyword(s):  
Data Mining ◽  
Feature Selection ◽  
Classification Accuracy ◽  
Feature Selection Method ◽  
Original Data ◽  
Selection Method ◽  
Feature Subset ◽  
Data Set ◽  
Optimal Feature Subset ◽  
Optimal Feature

In data mining, people require feature selection to select relevant features and to remove unimportant irrelevant features from a original data set based on some evolution criteria. Filter and wrapper are the two methods used but here the authors have proposed a hybrid feature selection method to take advantage of both methods. The proposed method uses symmetrical uncertainty and genetic algorithms for selecting the optimal feature subset. This has been done so as to improve processing time by reducing the dimension of the data set without compromising the classification accuracy. This proposed hybrid algorithm is much faster and scales well to the data set in terms of selected features, classification accuracy and running time than most existing algorithms.

Feature distillation and accumulated selection for automated fraudulent publisher classification from user click data of online advertising

2022 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Deepti Sisodia ◽  
Dilip Singh Sisodia
Keyword(s):  
Feature Selection ◽  
Online Advertising ◽  
Feature Selection Method ◽  
Majority Voting ◽  
Feature Subset ◽  
Relevant Feature ◽  
Selection Methods ◽  
Content Type ◽  
Optimal Feature Subset ◽  
Optimal Feature

PurposeThe problem of choosing the utmost useful features from hundreds of features from time-series user click data arises in online advertising toward fraudulent publisher's classification. Selecting feature subsets is a key issue in such classification tasks. Practically, the use of filter approaches is common; however, they neglect the correlations amid features. Conversely, wrapper approaches could not be applied due to their complexities. Moreover, in particular, existing feature selection methods could not handle such data, which is one of the major causes of instability of feature selection.Design/methodology/approachTo overcome such issues, a majority voting-based hybrid feature selection method, namely feature distillation and accumulated selection (FDAS), is proposed to investigate the optimal subset of relevant features for analyzing the publisher's fraudulent conduct. FDAS works in two phases: (1) feature distillation, where significant features from standard filter and wrapper feature selection methods are obtained using majority voting; (2) accumulated selection, where we enumerated an accumulated evaluation of relevant feature subset to search for an optimal feature subset using effective machine learning (ML) models.FindingsEmpirical results prove enhanced classification performance with proposed features in average precision, recall, f1-score and AUC in publisher identification and classification.Originality/valueThe FDAS is evaluated on FDMA2012 user-click data and nine other benchmark datasets to gauge its generalizing characteristics, first, considering original features, second, with relevant feature subsets selected by feature selection (FS) methods, third, with optimal feature subset obtained by the proposed approach. ANOVA significance test is conducted to demonstrate significant differences between independent features.

Modulation Recognition of Digital Multimedia Signal Based on Data Feature Selection

2017 ◽  
Vol 8 (3) ◽  
pp. 90-111 ◽  
Author(s):  
Hui Wang ◽  
Li Li Guo ◽  
Yun Lin
Keyword(s):  
Feature Selection ◽  
Information Entropy ◽  
Feature Subset ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Modulation Recognition ◽  
Signal Modulation ◽  
Digital Multimedia ◽  
Optimal Feature Subset ◽  
Optimal Feature

Automatic modulation recognition is very important for the receiver design in the broadband multimedia communication system, and the reasonable signal feature extraction and selection algorithm is the key technology of Digital multimedia signal recognition. In this paper, the information entropy is used to extract the single feature, which are power spectrum entropy, wavelet energy spectrum entropy, singular spectrum entropy and Renyi entropy. And then, the feature selection algorithm of distance measurement and Sequential Feature Selection(SFS) are presented to select the optimal feature subset. Finally, the BP neural network is used to classify the signal modulation. The simulation result shows that the four-different information entropy can be used to classify different signal modulation, and the feature selection algorithm is successfully used to choose the optimal feature subset and get the best performance.

scholarly journals An Optimal Burn-In Policy for Cellular Phone Lithium-Ion Batteries Using a Feature Selection Strategy and Relevance Vector Machine

Energies ◽  
2018 ◽  
Vol 11 (11) ◽  
pp. 3021 ◽  
Author(s):  
Jinsong Yu ◽  
Jie Yang ◽  
Diyin Tang ◽  
Jing Dai
Keyword(s):  
Feature Selection ◽  
Lithium Ion Batteries ◽  
Feature Selection Method ◽  
Lithium Ion ◽  
Cellular Phone ◽  
Relevance Vector Machine ◽  
Test Method ◽  
Selection Strategy ◽  
Feature Subset ◽  
Cellular Phones

The early detection of defective lithium-ion batteries in cellular phones is critical due to the rapid increase in popularity and mass production of cellular phones. It is essential for manufacturers to design an optimal burn-in policy to differentiate between normal and weak batteries in short cycles prior to shipping them to the marketplace. A novel approach to determine the optimal burn-in policy using a feature selection strategy and relevance vector machine (RVM) is proposed. The sequential floating forward search (SFFS) is used as the feature selection method to find an optimal feature subset from the entire sequence of the batteries’ quality characteristics while preserving the original variables. Given the selected feature subset, the RVM is applied to classify batteries into two groups and simultaneously obtain the posterior probabilities. To achieve better discrimination performance with less risk, a new characteristic is extracted from the discharge profile. Subsequently, an optimization cost model is developed by introducing a classification instability penalty to ensure the stability of the optimal number of burn-in cycles. A case study utilizing cellular phone lithium-ion batteries randomly selected from manufactured lots is presented to illustrate the proposed methodology. Furthermore, we conduct a comparison with the cumulative degradation (CD) method and non-cumulative degradation (NCD) method based on the Wiener process. The results show that our proposed burn-in test method performs better than comparable methods.

scholarly journals Optimal Feature Subset Selection for Imbalanced Class Data using SMOTE and Binary ALO Algorithm

2020 ◽  
Vol 9 (3) ◽  
pp. 344-349
Keyword(s):  
Feature Selection ◽  
Class Imbalance ◽  
Classification Performance ◽  
Selection Model ◽  
Feature Subset Selection ◽  
Feature Subset ◽  
Spatial Features ◽  
Imbalanced Classes ◽  
Optimal Feature Subset ◽  
Optimal Feature

Feature selection in multispectral high dimensional information is a hard labour machine learning problem because of the imbalanced classes present in the data. The existing Most of the feature selection schemes in the literature ignore the problem of class imbalance by choosing the features from the classes having more instances and avoiding significant features of the classes having less instances. In this paper, SMOTE concept is exploited to produce the required samples form minority classes. Feature selection model is formulated with the objective of reducing number of features with improved classification performance. This model is based on dimensionality reduction by opt for a subset of relevant spectral, textural and spatial features while eliminating the redundant features for the purpose of improved classification performance. Binary ALO is engaged to solve the feature selection model for optimal selection of features. The proposed ALO-SVM with wrapper concept is applied to each potential solution obtained during optimization step. The working of this methodology is tested on LANDSAT multispectral image.

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