scholarly journals Computational method for predicting Self-Interactions Protein using Recurrent Neural Network from Protein Evolutionary Information

2020 ◽  
Author(s):  
Ji-Yong An
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Biological Activities ◽  
Back Propagation ◽  
Back Propagation Neural Network ◽  
Computational Method ◽  
Evolutionary Information ◽  
Support Vector ◽  
Scale Invariant ◽  
Average Accuracy

Abstract Self-interactions Protein (SIPs) play crucial roles in biological activities of organisms. Many high-throughput methods can be used to identify SIPs. However, these methods are both time-consuming and expensive. How to develop effective computational approaches for identifying SIPs is a challenging task. In the paper, we presented a novelty computational method called RRN-SIFT, which combines the Recurrent Neural Network (RNN) with Scale Invariant Feature Transform (SIFT) to predict SIPs based on protein evolutionary information. The main advantage of the proposed RNN-SIFT model is that it used SIFT for extracting key feature by exploring the evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix (PSSM) and employed RNN classifier to carry out classification based on extracted features. Extensive experiments show that the RRN-SIFT obtained average accuracy of 94.34% and 97.12% on yeast and human dataset. We also compared our performance with the Back Propagation Neural Network (BPNN), the state-of-the-art support vector machine (SVM) and other exiting methods. By comparing with experimental results, the performance of RNN-SIFT is significantly better than those of the BPNN, SVM and other previous methods in the domain. Therefore, we can come to the conclusion that the proposed RNN-SIFT model is useful tools and can execute incredibly well for predicting SIPs, as well as other bioinformatics tasks. In order to facilitate widely studies and encourage future proteomics research, a freely available web server called RNN-SIFT-SIPs was developed, and is available at http://219.219.62.123:8888/RNNSIFT/ and includes source code and SIPs datasets.

scholarly journals Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information

2020 ◽  
Vol 16 ◽  
pp. 117693432092467
Author(s):  
Ji-Yong An ◽  
Yong Zhou ◽  
Zi-Ji Yan ◽  
Yu-Jun Zhao
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Biological Activities ◽  
Back Propagation ◽  
Back Propagation Neural Network ◽  
Computational Method ◽  
Evolutionary Information ◽  
Support Vector ◽  
Interacting Proteins ◽  
Scale Invariant

Self-interacting proteins (SIPs) play crucial roles in biological activities of organisms. Many high-throughput methods can be used to identify SIPs. However, these methods are both time-consuming and expensive. How to develop effective computational approaches for identifying SIPs is a challenging task. In the article, we present a novel computational method called RRN-SIFT, which combines the recurrent neural network (RNN) with scale invariant feature transform (SIFT) to predict SIPs based on protein evolutionary information. The main advantage of the proposed RNN-SIFT model is that it uses SIFT for extracting key feature by exploring the evolutionary information embedded in Position-Specific Iterated BLAST–constructed position-specific scoring matrix and employs an RNN classifier to perform classification based on extracted features. Extensive experiments show that the RRN-SIFT obtained average accuracy of 94.34% and 97.12% on the yeast and human dataset, respectively. We also compared our performance with the back propagation neural network (BPNN), the state-of-the-art support vector machine (SVM), and other existing methods. By comparing with experimental results, the performance of RNN-SIFT is significantly better than that of the BPNN, SVM, and other previous methods in the domain. Therefore, we conclude that the proposed RNN-SIFT model is a useful tool for predicting SIPs, as well to solve other bioinformatics tasks. To facilitate widely studies and encourage future proteomics research, a freely available web server called RNN-SIFT-SIPs was developed at http://219.219.62.123:8888/RNNSIFT/ including the source code and the SIP datasets.

ARRHYTHMIA DISEASE DIAGNOSIS USING NEURAL NETWORK, SVM, AND GENETIC ALGORITHM-OPTIMIZED k-MEANS CLUSTERING

2011 ◽  
Vol 11 (04) ◽  
pp. 897-915 ◽  
Author(s):  
ROSHAN JOY MARTIS ◽  
CHANDAN CHAKRABORTY
Keyword(s):  
Neural Network ◽  
Genetic Algorithm ◽  
Normal Sinus Rhythm ◽  
Optimization Technique ◽  
Back Propagation ◽  
Principal Component ◽  
Disease Diagnosis ◽  
Back Propagation Neural Network ◽  
Polynomial Kernel ◽  
Support Vector

This work aims at presenting a methodology for electrocardiogram (ECG)-based arrhythmia disease detection using genetic algorithm (GA)-optimized k-means clustering. The open-source ECG data from MIT-BIH arrhythmia database and MIT-BIH normal sinus rhythm database are subjected to a sequence of steps including segmentation using R-point detection, extraction of features using principal component analysis (PCA), and pattern classification. Here, the classical classifiers viz., k-means clustering, error back propagation neural network (EBPNN), and support vector machine (SVM) have been initially attempted and subsequently m-fold (m = 3) cross validation is used to reduce the bias during training of the classifier. The average classification accuracy is computed as the average over all the three folds. It is observed that EBPNN and SVM with different order polynomial kernel provide significant accuracies in comparison with k-means one. In fact, the parameters (centroids) of k-means algorithm are locally optimized by minimizing its objective function. In order to overcome this limitation, a global optimization technique viz., GA is suggested here and implemented to find more robust parameters of k-means clustering. Finally, it is shown that GA-optimized k-means algorithm enhances its accuracy to those of other classifiers. The results are discussed and compared. It is concluded that the GA-optimized k-means algorithm is an alternate approach for classification whose accuracy will be near to that of supervised (viz., EBPNN and SVM) classifiers.

scholarly journals LBP and GLCM Based Image Forgery Recognition

2018 ◽  
Vol 7 (4.6) ◽  
pp. 217
Author(s):  
D. Vaishnavi ◽  
T. S. Subashini ◽  
G. N. Balaji ◽  
D. Mahalakshmi
Keyword(s):  
Neural Network ◽  
Local Binary Pattern ◽  
Back Propagation ◽  
Back Propagation Neural Network ◽  
Support Vector ◽  
Gray Level ◽  
Image Splicing ◽  
Naked Eye ◽  
Occurrence Matrix

The forgery of digital images became very easy and it’s very difficult to ascertain the authenticity of such images by naked eye. Among the various kinds of image forgeries, image splicing is a frequent and widely used technique. Even though various methods are available to detect image splicing forgery, authors have attempted to provide a novel hybrid method which can yield greater accuracy, sensitivity and specificity. In this method, gray level co-occurrence matrix (GLCM) features are extracted using local binary pattern (LBP) operator on the image and the detection of the splicing forged images among the authentic images is done using the popular pattern recognition algorithms such as combined k-NN (Comb-KNN), back propagation neural network (BPNN) and support vector machine (SVM). The recorded results are also compared with the existing results of the previous studies to ascertain the quality of the results.  

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