net_align: Network alignment method based on conditional random fields

In wulingyun/Corbi: Collection of Rudimentary Bioinformatics Tools

Network alignment method based on conditional random fields

Description

Find the maximal matching subnetworks from a target network for a query network based on the conditional random fields (CRF) model.

Usage

net_align(
  query.net,
  target.net,
  node.sim,
  query.type = 4,
  delta.d = 1e-10,
  delta.c = 0.5,
  delta.e = 1,
  delta.s = 1,
  output = "result.txt"
)

Arguments

query.net	The input file name of the query network.
target.net	The input file name of the target network.
node.sim	The input file name of the node similarity scores between the query network and the target network.
query.type	The querying network type: 1 - general, 2 - chain, 3 - tree, 4 - heuristic.
delta.d	The parameter delta.d is a parameter for deletions.
delta.c	The parameter delta.c is a parameter for consecutive deletions.
delta.e	The parameter delta.e is a parameter for single deletion.
delta.s	The parameter delta.s is a parameter for insertions.
output	The suffix of output file name. The output contains two files in the working directory. One is the matching nodes and edges between query network and target network, the other is the unique matching node pairs.

Details

This is an approach for network alignment problem based on conditional random field (CRF) model which uses the node similarity and structure information equally. This method is based on our network querying method net_query. This method uses an iterative strategy to get the one-to-one map between the query network and target netowrk.

More details can be seen in net_query.

References

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. CNetA: Network alignment by combining biological and topological features. In Proceedings of 2012 IEEE International Conference on Systems Biology (ISB), 220-225, IEEE, 2012.

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. Corbi: A new R package for biological network alignment and querying. BMC Systems Biology, 7(Suppl 2):S6, 2013.

Examples

## Not run: 
library(Corbi)

## An example: "querynet.txt", "targetnet.txt", "nodesim.txt" are
## three input files in the working directory
net_align("querynet.txt", "targetnet.txt", "nodesim.txt")

## End(Not run)

wulingyun/Corbi documentation built on May 11, 2022, 11:32 p.m.