CompFilter compares two networks.

Introduction

This filter compares the input network with another network and pass the input network to the next filter without any modification.

This is originally designed to perform the comparison of the estimated network from the simulated data with the true structure. Therefore, the comparison result is shown by the sensitivity and the specificity, that are popular measures of evaluating the performance of machine learning algorithms.

Output

The comparison result is output to the standard error (log file). The lines beginning with "COML:" and "COMP:" are the main part of the result. They are tab-delimited text. The line COML: shows the column label showing the meanings of the tab-delimited columns. The line COMP: shows values of the comparison result.

TP : True positive edges. The number of edges that exist both in the input network and the second network (network read from the file).
RTP : Reversed positive edges. The number of edges that exist both in the input and second networks but the edge directions are different.
FP : False positive edges. The number of edges that exist in the input network but do not in the second network.
FN : False negative edges. The number of edges that do not exist in the input network but exist in the second network.
TN : True negative edges. The number of edge that do not exist both in the input and second networks.
Sn : Sensitivity = TP / (TP + FN).
Sp : Specificty = TP / (TP + RTP + FP).
Snr : Sensitivity allowing reverse edges = (TP + RTP) / (TP + RTP + FN).
Spr : Specifity allowing reverse edges = (TP + RTP) / (TP + RTP + FP).

The comparison result can be output in network files. Use the tp, fp, and fn options for saving true positive, false positive, and false negative edges in files.

Arguments

file=file

File name of the network to read and compare.

type=format

Network file format type. See Network File Formats for available formats. If this is omitted, the extension of the file name given by file is used to determine the format type.

args={key [ =values,... ]}

Arguments for the network file format.

tp=file

Saves true positive edges in file.

tptype=format

Network file format for saving true positive edges. See Network File Formats for available format types.

tpargs={key=value,...}

Arguments for the network file format used to save true positive edges.

fp=file

Saves false positive edges in file.

fptype=format

Network file format for saving false positive edges. See Network File Formats for available format types.

fpargs={key=value,...}

Arguments for the network file format used to save false positive edges.

fn=file

Saves false negative edges in file.

fntype=format

Network file format for saving false negative edges. See Network File Formats for available format types.

fnargs={key=value,...}

Arguments for the network file format used to save false negative edges.

output=file

Saves the comparison result in the specified file.

show_not_found

Outputs names of nodes that are not found in the true network.

Filters | INGOR Manual