The influence maximization problem aims to select a small set of influential nodes, termed a seed set, to maximize their influence coverage in social networks. Although the methods that are based on a greedy strategy ...The influence maximization problem aims to select a small set of influential nodes, termed a seed set, to maximize their influence coverage in social networks. Although the methods that are based on a greedy strategy can obtain good accuracy, they come at the cost of enormous computational time, and are therefore not applicable to practical scenarios in large-scale networks. In addition, the centrality heuristic algorithms that are based on network topology can be completed in relatively less time. However, they tend to fail to achieve satisfactory results because of drawbacks such as overlapped influence spread. In this work, we propose a discrete two-stage metaheuristic optimization combining quantum-behaved particle swarm optimization with Lévy flight to identify a set of the most influential spreaders. According to the framework,first, the particles in the population are tasked to conduct an exploration in the global solution space to eventually converge to an acceptable solution through the crossover and replacement operations. Second, the Lévy flight mechanism is used to perform a wandering walk on the optimal candidate solution in the population to exploit the potentially unidentified influential nodes in the network. Experiments on six real-world social networks show that the proposed algorithm achieves more satisfactory results when compared to other well-known algorithms.展开更多
Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have b...Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.展开更多
Finding crucial vertices is a key problem for improving the reliability and ensuring the effective operation of networks,solved by approaches based on multiple attribute decision that suffer from ignoring the correlat...Finding crucial vertices is a key problem for improving the reliability and ensuring the effective operation of networks,solved by approaches based on multiple attribute decision that suffer from ignoring the correlation among each attribute or the heterogeneity between attribute and structure. To overcome these problems, a novel vertex centrality approach, called VCJG, is proposed based on joint nonnegative matrix factorization and graph embedding. The potential attributes with linearly independent and the structure information are captured automatically in light of nonnegative matrix factorization for factorizing the weighted adjacent matrix and the structure matrix, which is generated by graph embedding. And the smoothness strategy is applied to eliminate the heterogeneity between attributes and structure by joint nonnegative matrix factorization. Then VCJG integrates the above steps to formulate an overall objective function, and obtain the ultimately potential attributes fused the structure information of network through optimizing the objective function. Finally, the attributes are combined with neighborhood rules to evaluate vertex's importance. Through comparative analyses with experiments on nine real-world networks, we demonstrate that the proposed approach outperforms nine state-of-the-art algorithms for identification of vital vertices with respect to correlation, monotonicity and accuracy of top-10 vertices ranking.展开更多
Essential proteins play an important role in disease diagnosis and drug development.Many methods have been devoted to the essential protein prediction by using some kinds of biological information.However,they either ...Essential proteins play an important role in disease diagnosis and drug development.Many methods have been devoted to the essential protein prediction by using some kinds of biological information.However,they either ignore the noise presented in the biological information itself or the noise generated during feature extraction.To overcome these problems,in this paper,we propose a novel method for predicting essential proteins called attention gate-graph attention network and temporal convolutional network(AG-GATCN).In AG-GATCN method,we use improved temporal convolutional network(TCN)to extract features from gene expression sequence.To address the noise in the gene expression sequence itself and the noise generated after the dilated causal convolution,we introduce attention mechanism and gating mechanism in TCN.In addition,we use graph attention network(GAT)to extract protein–protein interaction(PPI)network features,in which we construct the feature matrix by introducing node2vec technique and 7 centrality metrics,and to solve the GAT oversmoothing problem,we introduce gated tanh unit(GTU)in GAT.Finally,two types of features are integrated by us to predict essential proteins.Compared with the existing methods for predicting essential proteins,the experimental results show that AG-GATCN achieves better performance.展开更多
Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,th...Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal,neglecting the influence of the similarity structure on the transition probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,compared with the contrast methods,the improvements of BRWR in terms of the ACC results range in 1.4%–5.7%,1.3%–11.9%,2.4%–8.8%,and 0.8%–14.2%,respectively.Therefore,BRWR is effective and reasonable.展开更多
基金Project supported by the Zhejiang Provincial Natural Science Foundation (Grant No.LQ20F020011)the Gansu Provincial Foundation for Distinguished Young Scholars (Grant No.23JRRA766)+1 种基金the National Natural Science Foundation of China (Grant No.62162040)the National Key Research and Development Program of China (Grant No.2020YFB1713600)。
文摘The influence maximization problem aims to select a small set of influential nodes, termed a seed set, to maximize their influence coverage in social networks. Although the methods that are based on a greedy strategy can obtain good accuracy, they come at the cost of enormous computational time, and are therefore not applicable to practical scenarios in large-scale networks. In addition, the centrality heuristic algorithms that are based on network topology can be completed in relatively less time. However, they tend to fail to achieve satisfactory results because of drawbacks such as overlapped influence spread. In this work, we propose a discrete two-stage metaheuristic optimization combining quantum-behaved particle swarm optimization with Lévy flight to identify a set of the most influential spreaders. According to the framework,first, the particles in the population are tasked to conduct an exploration in the global solution space to eventually converge to an acceptable solution through the crossover and replacement operations. Second, the Lévy flight mechanism is used to perform a wandering walk on the optimal candidate solution in the population to exploit the potentially unidentified influential nodes in the network. Experiments on six real-world social networks show that the proposed algorithm achieves more satisfactory results when compared to other well-known algorithms.
基金Project supported by the Gansu Province Industrial Support Plan (Grant No.2023CYZC-25)the Natural Science Foundation of Gansu Province (Grant No.23JRRA770)the National Natural Science Foundation of China (Grant No.62162040)。
文摘Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.
基金Project supported by the National Natural Science Foundation of China (Grant Nos.62162040 and 11861045)。
文摘Finding crucial vertices is a key problem for improving the reliability and ensuring the effective operation of networks,solved by approaches based on multiple attribute decision that suffer from ignoring the correlation among each attribute or the heterogeneity between attribute and structure. To overcome these problems, a novel vertex centrality approach, called VCJG, is proposed based on joint nonnegative matrix factorization and graph embedding. The potential attributes with linearly independent and the structure information are captured automatically in light of nonnegative matrix factorization for factorizing the weighted adjacent matrix and the structure matrix, which is generated by graph embedding. And the smoothness strategy is applied to eliminate the heterogeneity between attributes and structure by joint nonnegative matrix factorization. Then VCJG integrates the above steps to formulate an overall objective function, and obtain the ultimately potential attributes fused the structure information of network through optimizing the objective function. Finally, the attributes are combined with neighborhood rules to evaluate vertex's importance. Through comparative analyses with experiments on nine real-world networks, we demonstrate that the proposed approach outperforms nine state-of-the-art algorithms for identification of vital vertices with respect to correlation, monotonicity and accuracy of top-10 vertices ranking.
基金the National Natural Science Foundation of China(Grant Nos.11861045,11361033,and 62162040)。
文摘Essential proteins play an important role in disease diagnosis and drug development.Many methods have been devoted to the essential protein prediction by using some kinds of biological information.However,they either ignore the noise presented in the biological information itself or the noise generated during feature extraction.To overcome these problems,in this paper,we propose a novel method for predicting essential proteins called attention gate-graph attention network and temporal convolutional network(AG-GATCN).In AG-GATCN method,we use improved temporal convolutional network(TCN)to extract features from gene expression sequence.To address the noise in the gene expression sequence itself and the noise generated after the dilated causal convolution,we introduce attention mechanism and gating mechanism in TCN.In addition,we use graph attention network(GAT)to extract protein–protein interaction(PPI)network features,in which we construct the feature matrix by introducing node2vec technique and 7 centrality metrics,and to solve the GAT oversmoothing problem,we introduce gated tanh unit(GTU)in GAT.Finally,two types of features are integrated by us to predict essential proteins.Compared with the existing methods for predicting essential proteins,the experimental results show that AG-GATCN achieves better performance.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11861045 and 62162040)。
文摘Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal,neglecting the influence of the similarity structure on the transition probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,compared with the contrast methods,the improvements of BRWR in terms of the ACC results range in 1.4%–5.7%,1.3%–11.9%,2.4%–8.8%,and 0.8%–14.2%,respectively.Therefore,BRWR is effective and reasonable.
