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Neighbor-first Biomolecular Subnetwork Search Method Based on Expert Knowledge and Topological Similarity

An expert knowledge, biomolecular technology, applied in the computer field

Inactive Publication Date: 2016-02-17
SHANGHAI UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] The object of the present invention is to provide a neighbor priority biomolecular subnet search method based on expert knowledge and topology similarity in order to solve the above problems, which can search for the most similar result subnet to the target subnet in a complex biomolecular network , which avoids the blindness of calculation caused by the failure of the previous algorithm to make reasonable use of expert knowledge, and reduces the error caused by the lack of original information, so it has high stability

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  • Neighbor-first Biomolecular Subnetwork Search Method Based on Expert Knowledge and Topological Similarity
  • Neighbor-first Biomolecular Subnetwork Search Method Based on Expert Knowledge and Topological Similarity
  • Neighbor-first Biomolecular Subnetwork Search Method Based on Expert Knowledge and Topological Similarity

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Embodiment Construction

[0093] Preferred embodiments of the present invention will be further described in detail below in conjunction with the accompanying drawings.

[0094] In this embodiment, the experiment of the neighbor priority biomolecular subnet search method based on expert knowledge and topological similarity of the present invention is completed on a cluster computer of the Institute of Systems Biotechnology of Shanghai University. The cluster consists of 14 IBMHS21 blade servers and 2 The x3650 server forms computing and management nodes, and the network connection adopts Gigabit Ethernet and infiniband2.5G network. Each node is configured with two dual-core CPUs and 4GB of memory, each CPU is intelxeon51502.66GMhz main frequency, and two graphics workstations are used as front-end machines for scientific data visualization.

[0095] For network A (G A ), Network B (G B ) and Network A (G A ) in the target subnet T (G t ), the present invention's neighbor-first biomolecular subnet s...

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Abstract

The invention discloses a neighbor priority biomolecular subnet searching method based on expert knowledge and similar to topology. The method includes the following steps: A. constructing an initial similar matrix of biomolecules in networks T (Gt) and B (GB); B. calculating a similar matrix S of the biomolecules according to similar characteristics of the topology of the biomolecules in the networks; C. constructing an expert knowledge dictionary; D. conducting searching through the neighbor priority strategy based on expert knowledge to obtain a result subnet; E. calculating similarity scores of a result subnet R (Gr) and a target subnet T (Gt); F. calculating P value; and G. conducting visualization on the result subnet. Compared with a similar method, the method is high in calculation accuracy, high in stability, capable of better processing 'gaps' (Gap) among the networks of the biomolecules to obtain more conservative sides and nodes and capable of well reflecting change condition between the networks of the biomolecules.

Description

technical field [0001] The invention relates to the computer field, and proposes a neighbor priority biomolecular subnet search method based on expert knowledge and topology similarity. Background technique [0002] Biomolecular networks are complex networks. Searching for the subnetwork most similar to the target subnetwork in a complex network is a local network comparison problem, which involves a lot of calculations, and has been proven to be a NP-complete problem (Non-deterministicPolynomial problem, that is, a non-deterministic polynomial complexity problem). certainty issues). At present, researchers generally use graphs to represent complex networks and study them with graph theory. For a biomolecular network, the nodes in the graph represent biomolecules, and the edges represent various relationships such as regulation and interaction between biomolecules. [0003] Due to the unique biological significance of biomolecular networks, it is not enough to study them ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/24
Inventor 谢江谭军马进张武文铁桥
Owner SHANGHAI UNIV
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