Molecular Docking Improvement: Coefficient Adaptive Genetic Algorithms for Multiple Scoring Functions

In this paper, a coefficient adaptive scoring method of molecular docking is presented to improve the docking accuracy with multiple available scoring functions. Based on force-field scoring function, we considered hydrophobic and deformation as well in the proposed method, Instead of simple combination with fixed weights, coefficients of each factor are adaptive in searching procedure. In order to improve the docking accuracy and stability, knowledge-based scoring function is used as another scoring factor. Genetic algorithm with the multi-population evolution and entropy-based searching technique with narrowing down space is used to solve the optimization model for molecular docking. To evaluate the method, we carried out a numerical experiment with 134 protein- ligand complexes of the publicly available GOLD test set. The results validated that it improved the docking accuracy over the individual force-field scoring. In addition, analyses were given to show the disadvantage of individual scoring model. Through the comparison with other popular docking software, the proposed method showed higher accuracy. Among more than 77% of the complexes, the docked results were within 1.0 Å according to Root- Mean-Square Deviation (RMSD) of the X-ray structure. The average computing time obtained here is 563.9 s

Efficient k-means++ approximation with MapReduce

PublishedJournal Articlek-means is undoubtedly one of the most popular clustering algorithms owing to its simplicity and efficiency. However, this algorithm is highly sensitive to the chosen initial centers and thus a proper initialization is crucial for obtaining an ideal solution. To address this problem, k-means++ is proposed to sequentially choose the centers so as to achieve a solution that is provably close to the optimal one. However, due to its weak scalability, k-means++ becomes inefficient as the size of data increases. To improve its scalability and efficiency, this paper presents MapReduce k-means++ method which can drastically reduce the number of MapReduce jobs by using only one MapReduce job to obtain k centers. The k-means++ initialization algorithm is executed in the Mapper phase and the weighted k-means++ initialization algorithm is run in the Reducer phase. As this new MapReduce k-means++ method replaces the iterations among multiple machines with a single machine, it can reduce the communication and I/O costs significantly. We also prove that the proposed MapReduce k-means++ method obtains O(α2) approximation to the optimal solution of k-means. To reduce the expensive distance computation of the proposed method, we further propose a pruning strategy that can greatly avoid a large number of redundant distance computations. Extensive experiments on real and synthetic data are conducted and the performance results indicate that the proposed MapReduce k-means++ method is much more efficient and can achieve a good approximation.This work was supported by the National Science Foundation for Distinguished Young Scholars of China under Grant No. of 61225010, National Nature Science Foundation of China (Nos. 61173162, 61173165, 61370199, 61300187, 61300189, and 61370198), New Century Excellent Talents (No. NCET-10-0095), the Fundamental Research Funds for the Central Universities (Nos. 2013QN044 and 2012TD008)

Performance Guaranteed Computation Offloading for Mobile-Edge Cloud Computing

In this letter, we investigate an energy efficiency with performance guaranteed problem in mobile-edge computing. The mobile users desire lower energy consumption with better performance of tasks, for that we propose an energy minimizing optimization problem for mobile-edge cloud computing. We apply KKT conditions to solve it, and also present a request offloading scheme for this issue. In particular, the offloading scheme is determined by energy consumption and bandwidth capacity at each time slot. Numerical results demonstrate that our proposed offloading scheme outperforms local computing and entirely offloading method on energy consumption and performance on delay

Applications of Federated Learning in Smart Cities: Recent Advances, Taxonomy, and Open Challenges

Federated learning plays an important role in the process of smart cities. With the development of big data and artificial intelligence, there is a problem of data privacy protection in this process. Federated learning is capable of solving this problem. This paper starts with the current developments of federated learning and its applications in various fields. We conduct a comprehensive investigation. This paper summarize the latest research on the application of federated learning in various fields of smart cities. In-depth understanding of the current development of federated learning from the Internet of Things, transportation, communications, finance, medical and other fields. Before that, we introduce the background, definition and key technologies of federated learning. Further more, we review the key technologies and the latest results. Finally, we discuss the future applications and research directions of federated learning in smart cities

Dynamically Selecting Distribution Strategies for Web Documents According to Access Pattern

Abstract. Web caching and replication are efficient techniques for reducing web traffic, user access latency, and server load. In this paper we present a group-based method for dynamically selecting distribution strategies for web documents according to access patterns. The documents are divided into groups according to access patterns and the documents in each group are assigned to the same distribution strategy. Our group-based model combines performance metrics with the different weights assigned to each of them. We use both trace data and statistical data to simulate our methods. The experimental results show that our group-based method for document distribution strategy selection can improve several performance metrics, while keeping others almost the same

A Cascading Failure Model for Command and Control Networks with Hierarchy Structure

Cascading failures in the command and control networks (C2 networks) could substantially affect the network invulnerability to some extent. In particular, without considering the characteristics of hierarchy structure, it is quite misleading to employ the existing cascading failure models and effectively analyze the invulnerability of C2 networks. Therefore, a novel cascading failure model for command and control networks with hierarchy structure is proposed in this paper. Firstly, a method of defining the node’s initial load in C2 networks based on hierarchy-degree is proposed. By applying the method, the impact of organizational positions and the degree of the node on its initial load could be highlighted. Secondly, a nonuniform adjustable load redistribution strategy (NALR strategy) is put forward in this paper. More specifically, adjusting the redistribution coefficient could allocate the load from failure nodes to the higher and the same level neighboring nodes according to different proportions. It could be demonstrated by simulation results that the robustness of C2 networks against cascading failures could be dramatically improved by adjusting the initial load adjustment coefficient, the tolerance parameter, and the load redistribution coefficient. And finally, comparisons with other relational models are provided to verify the rationality and effectiveness of the model proposed in this paper. Subsequently, the invulnerability of C2 networks could be enhanced

Optimal methods for coordinated en-route web caching for tree networks

Web caching is an important technology for improving the scalability of Web services. One of the key problems in coordinated enroute Web caching is to compute the locations for storing copies of an object among the enroute caches so that some specified objectives are achieved. In this article, we address this problem for tree networks, and formulate it as a maximization problem. We consider this problem for both unconstrained and constrained cases. The constrained case includes constraints on the cost gain per node and on the number of object copies to be placed. We present dynamic programming-based solutions to this problem for different cases and theoretically show that the solutions are either optimal or convergent to optimal solutions. We derive efficient algorithms that produce these solutions. Based on our mathematical model, we also present a solution to coordinated enroute Web caching for autonomous systems as a natural extension of the solution for tree networks. We implement our algorithms and evaluate our model on different performance metrics through extensive simulation experiments. The implementation results show that our methods outperform the existing algorithms of either coordinated enroute Web caching for linear topology or object placement (replacement) at individual nodes only.Keqiu Li, Hong Shen, Francis Y. L. Chin, Si Qing Zhen

Software defined networking applications in distributed datacenters

This SpringerBrief provides essential insights on the SDN application designing and deployment in distributed datacenters. In this book, three key problems are discussed: SDN application designing, SDN deployment and SDN management. This book demonstrates how to design the SDN-based request allocation application in distributed datacenters. It also presents solutions for SDN controller placement to deploy SDN in distributed datacenters. Finally, an SDN management system is proposed to guarantee the performance of datacenter networks which are covered and controlled by many heterogeneous controllers. Researchers and practitioners alike will find this book a valuable resource for further study on Software Defined Networking.