scholarly journals Identifying Essential Proteins in Dynamic PPI Network with Improved FOA

2018 ◽  
Vol 13 (3) ◽  
pp. 365-382 ◽  
Author(s):  
Xiujuan Lei ◽  
Siguo Wang ◽  
Linqiang Pan
Keyword(s):  
Fruit Fly ◽  
Biological Information ◽  
Detection Methods ◽  
Fruit Fly Optimization Algorithm ◽  
Fruit Fly Optimization ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Cellular Life ◽  
Ppi Networks ◽  
Ranking Score

Identification of essential proteins plays an important role for understanding the cellular life activity and development in postgenomic era. Identification of essential proteins from the protein-protein interaction (PPI) networks has become a hot topic in recent years. In this work, fruit fly optimization algorithm (FOA) is extended for identifying essential proteins, the extended algorithm is called EPFOA, which merges FOA with topological properties and biological information for essential proteins identification. The algorithm EPFOA has the advantage of identifying multiple essential proteins simultaneously rather than completely relying on ranking score identification individually. The performance of EPFOA is analyzed on dynamic PPI networks, which are constructed by combining the gene expression data. The experimental results demonstrate that EPFOA is more efficient in detecting essential proteins than the state-of-the-art essential proteins detection methods.

scholarly journals A Non-negative Matrix Factorization Based Method for Identifying Essential Proteins

2021 ◽  
Author(s):  
Zhihong Zhang ◽  
Sai Hu ◽  
Wei Yan ◽  
Bihai Zhao ◽  
Lei Wang
Keyword(s):  
Protein Interaction ◽  
Matrix Factorization ◽  
Biological Data ◽  
Protein Domain ◽  
Biological Information ◽  
Ppi Network ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Non Negative Matrix Factorization

Abstract BackgroundIdentification of essential proteins is very important for understanding the basic requirements to sustain a living organism. In recent years, various different computational methods have been proposed to identify essential proteins based on protein-protein interaction (PPI) networks. However, there has been reliable evidence that a huge amount of false negatives and false positives exist in PPI data. Therefore, it is necessary to reduce the influence of false data on accuracy of essential proteins prediction by integrating multi-source biological information with PPI networks.ResultsIn this paper, we proposed a non-negative matrix factorization and multiple biological information based model (NDM) for identifying essential proteins. The first stage in this progress was to construct a weighted PPI network by combing the information of protein domain, protein complex and the topology characteristic of the original PPI network. Then, the non-negative matrix factorization technique was used to reconstruct an optimized PPI network with whole enough weight of edges. In the final stage, the ranking score of each protein was computed by the PageRank algorithm in which the initial scores were calculated with homologous and subcellular localization information. In order to verify the effectiveness of the NDM method, we compared the NDM with other state-of-the-art essential proteins prediction methods. The comparison of the results obtained from different methods indicated that our NDM model has better performance in predicting essential proteins.ConclusionEmploying the non-negative matrix factorization and integrating multi-source biological data can effectively improve quality of the PPI network, which resulted in the led to optimization of the performance essential proteins identification. This will also provide a new perspective for other prediction based on protein-protein interaction networks.

scholarly journals A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhihong Zhang ◽  
Meiping Jiang ◽  
Dongjie Wu ◽  
Wang Zhang ◽  
Wei Yan ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Negative Impact ◽  
False Negative ◽  
Interaction Network ◽  
Biological Information ◽  
Ppi Network ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Ppi Networks

Identification of essential proteins is very important for understanding the basic requirements to sustain a living organism. In recent years, there has been an increasing interest in using computational methods to predict essential proteins based on protein–protein interaction (PPI) networks or fusing multiple biological information. However, it has been observed that existing PPI data have false-negative and false-positive data. The fusion of multiple biological information can reduce the influence of false data in PPI, but inevitably more noise data will be produced at the same time. In this article, we proposed a novel non-negative matrix tri-factorization (NMTF)-based model (NTMEP) to predict essential proteins. Firstly, a weighted PPI network is established only using the topology features of the network, so as to avoid more noise. To reduce the influence of false data (existing in PPI network) on performance of identify essential proteins, the NMTF technique, as a widely used recommendation algorithm, is performed to reconstruct a most optimized PPI network with more potential protein–protein interactions. Then, we use the PageRank algorithm to compute the final ranking score of each protein, in which subcellular localization and homologous information of proteins were used to calculate the initial scores. In addition, extensive experiments are performed on the publicly available datasets and the results indicate that our NTMEP model has better performance in predicting essential proteins against the start-of-the-art method. In this investigation, we demonstrated that the introduction of non-negative matrix tri-factorization technology can effectively improve the condition of the protein–protein interaction network, so as to reduce the negative impact of noise on the prediction. At the same time, this finding provides a more novel angle of view for other applications based on protein–protein interaction networks.

scholarly journals A mixed clustering coefficient centrality for identifying essential proteins

2020 ◽  
Vol 34 (10) ◽  
pp. 2050090
Author(s):  
Pengli Lu ◽  
JingJuan Yu
Keyword(s):  
Drug Target ◽  
Protein Complexes ◽  
Biological Evolution ◽  
Clustering Coefficient ◽  
Biological Information ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Cell Life ◽  
Definition Of

Essential protein plays a crucial role in the process of cell life. The identification of essential proteins not only promotes the development of drug target technology, but also contributes to the mechanism of biological evolution. There are plenty of scholars who pay attention to discover essential proteins according to the topological structure of protein network and biological information. The accuracy of protein recognition still demands to be improved. In this paper, we propose a method which integrates the clustering coefficient in protein complexes and topological properties to determine the essentiality of proteins. First, we give the definition of In-clustering coefficient (IC) to describe the properties of protein complexes. Then we propose a new method, complex edge and node clustering (CENC) coefficient, to identify essential proteins. Different Protein–Protein Interaction (PPI) networks of Saccharomyces cerevisiae, MIPS and DIP are used as experimental materials. Through some experiments of logistic regression model, the results show that the method of CENC can promote the ability of recognizing essential proteins by comparing with the existing methods DC, BC, EC, SC, LAC, NC and the recent UC method.

Research on Enhancement Technology of Conveyor Belt Fault Images Based on Fruit Fly Optimization Algorithm

2014 ◽  
Vol 8 (1) ◽  
pp. 685-689
Author(s):  
Chunqing Ye ◽  
Changyun Miao ◽  
Xianguo Li ◽  
Yanli Yang
Keyword(s):  
Optimization Algorithm ◽  
Detection System ◽  
Fruit Fly ◽  
Conveyor Belt ◽  
Recognition Algorithm ◽  
Fruit Fly Optimization Algorithm ◽  
Fruit Fly Optimization ◽  
Wire Ropes ◽  
Fault Recognition ◽  
Steel Cord

In this research, we studied the fault recognition algorithm of steel cord conveyor belt, and obtained the wire ropes image by adopting the detection system of steel cord conveyor belt, so that the fault recognition algorithm of steel cord conveyor belt was proposed based on Fruit fly optimization algorithm. As we know that the fruit fly optimization algorithm is used for fault detection of the processing steel cord conveyor belt image and for obtaining the fault image. In the MATLAB environment, the algorithm process was designed and verified in terms of the effectiveness and accuracy. The experimental results show that with fast speed and high accuracy in detecting the fault image of steel cord conveyor belt rapidly and accurately, and in classifying scratch from fracture the proposed algorithm is suitable for the fault recognition of steel cord conveyor belt automatically.

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