To conduct a systemic analysis of biological networks function distribution and function modules, we present a semiautomatic method to achieve independent and intact GO slim (InitGO) based on graph operations and GO h...
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ISBN:
(纸本)9781424441334
To conduct a systemic analysis of biological networks function distribution and function modules, we present a semiautomatic method to achieve independent and intact GO slim (InitGO) based on graph operations and GO hierarchy structure. Our method is packed into a user-friendly Cytoscape plugin named InitGO. The application of InitGO to yeast transcriptional factors regulatory network shows that the network has function modularity, offering evidence that our method is effective for defining function modules. InitGO plugin and source codes are available on request from the authors.
It has been reported that function implementations in biological systems, including transcriptional regulatory networks (TRN), show modular architecture. Analyzing functional modularity of biological networks can desc...
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ISBN:
(纸本)9781424445189
It has been reported that function implementations in biological systems, including transcriptional regulatory networks (TRN), show modular architecture. Analyzing functional modularity of biological networks can describe characteristics of function implementation and their "position" in biology systems from the systems perspective. Defining functional modules naturally, we bring up a novel measurement, cohesive degree (CD), to characterize the modularity. From this character, we know that not all of the corresponding modules of function annotations take on good modularity. Considering the ratio of the non-cohesive (zero-CD value) modules, TRN's functional modularity is also weaker than that of other biological network and integral ones. And, this is not caused by data integrity, but by the topology of itself. In fact, the modularity implementation of biological systems is mainly accomplished through the cooperation of several types of networks, not by TRN alonely.
The Weapon-Target Assignment (WTA) problem is a fundamental problem arising in defense-related applications of operations research. The WTA problem can be formulated as a nonlinear integer programming problem and is k...
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ISBN:
(纸本)9780769532905
The Weapon-Target Assignment (WTA) problem is a fundamental problem arising in defense-related applications of operations research. The WTA problem can be formulated as a nonlinear integer programming problem and is known to be NP-complete. We present firstly a technique founded on the use weapon cell, which enables one-to-many mapping about weapon-target to become one-to-one mapping. Next, we introduce a framework of solving the WTA problem. Based on this framework, an approximation algorithm that is grounded on the rules about weapon cells and targets is proposed Finally, the simulative results show that the proposed algorithm indeed is very efficient
Peer-to-peer distributed storage systems usually replicate data objects on multi-node to improve the performance and availability. However, updates may be delayed for P2P systems are generally large-scale and strong d...
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ISBN:
(纸本)9783540747413
Peer-to-peer distributed storage systems usually replicate data objects on multi-node to improve the performance and availability. However, updates may be delayed for P2P systems are generally large-scale and strong distributed, and then the performance of resource location in Internet would be depressed. According to that, an optimistic data consistency maintenance method based on key-attributes is proposed. In the method, updates about key-attributes are separated from user request. key-updates are propagated by latency-overlay update propagation model, that is, updates are always propagated to nodes having maximum or minimal latency, and assured and uncertain propagation paths of updates are all taken into account. Based on classifying key-update conflicts, a double-level reconciling mechanism including the preprocessing of buffer and the processing of update-log is applied to detect and reconcile conflicts, and then conflicts are solved by policies of last-writer-win and divide-and-rule. Lastly, the technique of managing and maintaining update-log is discussed for the above is deployed based on the information storied in update-log. Delaying key-attributes updates cannot occur by the optimistic disposal method, and then it cannot depress efficiency of resource location based on key-attributes, which adapts well to P2P systems in Internet. The simulation results show it is an effective optimistic consistency maintenance method, achieves good consistency overhead, resource location and access overhead, and has strong robustness.
Recently superpeers are introduced to improve the performance of P2P systems. A superpeer is a node in a P2P system that operates as a server for a set of clients. By exploiting heterogeneity, the superpeer paradigm a...
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ISBN:
(纸本)9783540747413
Recently superpeers are introduced to improve the performance of P2P systems. A superpeer is a node in a P2P system that operates as a server for a set of clients. By exploiting heterogeneity, the superpeer paradigm allows P2P systems to run more efficiently. This paper proposes a hierarchy-adaptive P2P topology DAHP2P and a hierarchical routing, algorithm Hroute. Peers are grouped into clusters according to proximity and super peers form the upper-level overlay, the number of hierarchy is self-adaptively changed according to the number of nodes in the system, a hierarchical routing algorithm is designed to reduce the routing hops. Simulation results show that Hroute can significantly reduce the expected number of hops and latency of message routing, and loads of peers at different layers are relatively balanceable.
In parallel database systems, parallelism is utilized to improve the efficiency of query processing. However, parallelism is not equal to high efficiency. Therefore, query optimization techniques should be utilized to...
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In parallel database systems, parallelism is utilized to improve the efficiency of query processing. However, parallelism is not equal to high efficiency. Therefore, query optimization techniques should be utilized to improve the efficiency of parallel query processing. In this paper, according to the characteristic of the object-oriented database and its query, based on the semi-join-based parallel query processing algorithm, the information flow based query optimization techniques are proposed, and the results of performance evaluation show that they are efficient and practical.
Recently Tao Guo proposed a stochastic search algorithm in his PhD thesis for solving function optimization problems. He combined the subspace search method (a general multi-parent recombination strategy) with the pop...
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ISBN:
(纸本)0780363752
Recently Tao Guo proposed a stochastic search algorithm in his PhD thesis for solving function optimization problems. He combined the subspace search method (a general multi-parent recombination strategy) with the population hill-climbing method. The former keeps a global search for overall situation,and the latter keeps the convergence of the algorithm. Guo's algorithm has many advantages,such as the simplicity of its structure,the higher accuracy of its results, the wide range of its applications, and the robustness of its use. In this paper a preliminary theoretical analysis of the algorithm is given and some numerical experiments has been done by using Guo's algorithm for demostrating the theoretical results. Three asynchronous parallel algorithms with different granularities for MIMD machines are designed by parallelizing Guo's Algorithm.
parallel query processing is one of the research emphases of the parallel database, but the traditional parallel query processing techniques can not capture the intrinsic characteristic of object-oriented database and...
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parallel query processing is one of the research emphases of the parallel database, but the traditional parallel query processing techniques can not capture the intrinsic characteristic of object-oriented database and its query, so the efficiency of the traditional techniques is low. In this paper, according to the characteristic of the object-oriented database and its query a series of parallel query processing techniques for object-oriented database are proposed, including the stage-by-stage executing strategy, the class-based hybrid data placement strategy, the mark-based data operation parallel executing algorithm and the semi-join-based parallel query processing algorithm. The results of performance evaluation are given.
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