ALBD
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of a co-occurrence matrix
metaAnalysis.pl -- determines the number of rows, columns, vocabulary
size, and total number of co-occurrences of a co-occurrence file, or set
of co-occurrence files
There is another folder containing scripts to square co-occurrence
matrices. Squaring an explicit (A to B) co-occurrence matrix results in
a co-occurrence matrix containing all implicit (A to C) connections.
This is useful for time slicing and other analysis. Removal of the
original explicit matrix is an additional step that is required if you
wish to create a predictions matrix file for every CUI. This can be done
with the removeExplicit.pl script. Squaring a co-occurrence matrix can
be very computationally expensive, both in terms of ram and cpu. For
this reason MATLAB scripts are preferred over perl scripts. Even using
MATLAB ram can become an issue, and squaring sections of a matrix and
combining them into a single output matrix may be necassary, but takes
much longer. Scripts in the squaring folder include:
convertForSquaring_MATLAB.pl -- functions to convert to and from ALBD
and MATLAB sparse matrix formats
lib/LiteratureBasedDiscovery/Discovery.pm view on Meta::CPAN
######################################################################
# Description
######################################################################
# Discovery.pm - provides matrix operations from n11 counts from
# UMLS::Association
#
#TODO I think some of these notes should be elsewhere
# 'B' term filtering may be applied by removing elements from the
# explicit knowledge matrix before squaring. It is important to
# replicate the original matrix before filtering so that explicit
# knowledge can be removed from the implicit matrix.
# 'C' term filtering may be applied directly to the implicit
# knowledge matrix.
#
# A Typical workflow may look like:
# 1) load explicit knowledge from UMLS::Association
# 2) clone explicit knowledge (for removal from implicit)
# 3) apply filtering to explicit knowledge
# 4) square explicit knowledge to generate implicit knowledge
# 5) remove explicit knowledge from implicit knowledge
( run in 1.070 second using v1.01-cache-2.11-cpan-f985c23238c )