ALBD
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method, a different command may be needed. As long as the resulting
co-occurrence matrix is in the correct format LBD may be run on it. This
allows flexibility in where co-occurrence information comes from.
Note: utils/datasetCreator/fromMySQL/removeQuotes.pl may need to be run
on the resulting tab seperated file, if quotes are inlcuded in the
resulting co-ocurrence matrix file.
Stage 5: Set up Dummy UMLS::Association Database
UMLS::Association requires that a database can be connected to that is
in the correct format. Although this database is not required for ALBD
(since co-occurrence data is loaded from a co-occurrence matrix), it is
required to run UMLS:Association. If you ran UMLS::Association to
generate a co-occurrence matrix, you should be fine. Otherwise you will
need to create a dummy database that it can connect to. This can be done
in a few steps:
1) open mysql type mysql at the terminal
2) create the default database in the correct format, type: CREATE
DATABASE cuicounts; use cuicounts; CREATE TABLE N_11(cui_1 CHAR(10),
cui_2 CHAR(10), n_11 BIGINT(20));
method, a different command may be needed. As long as the resulting
co-occurrence matrix is in the correct format LBD may be run on it. This
allows flexibility in where co-occurrence information comes from.
Note: utils/datasetCreator/fromMySQL/removeQuotes.pl may need to be run
on the resulting tab seperated file, if quotes are inlcuded in the
resulting co-ocurrence matrix file.
Set Up Dummy UMLS::Association Database
UMLS::Association requires that a database can be connected to that is
in the correct format. Although this database is not required for ALBD
(since co-occurrence data is loaded from a co-occurrence matrix), it is
required to run UMLS:Association. If you ran UMLS::Association to
generate a co-occurrence matrix, you should be fine. Otherwise you will
need to create a dummy database that it can connect to. This can be done
in a few steps:
1) open mysql type mysql at the terminal
2) create the default database in the correct format, type: CREATE
DATABASE cuicounts; use cuicounts; CREATE TABLE N_11(cui_1 CHAR(10),
cui_2 CHAR(10), n_11 BIGINT(20));
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
samples/configFileSamples/UMLSAssociationConfig view on Meta::CPAN
# the line "<database>bigrams" will pass the 'database' parameter with a
# value of 'bigrams' to the UMLS::Association options hash for its
# initialization.
#
# For parameters where no value is needed, just write the name of the
# parameter in '<>' (e.g. '<debug>')
#
#
# See UMLS::Association for more detailed
# Database of Association Scores. Not used, but required to initialize
# UMLS::Association
<database>CUI_Bigram
# If the UMLS::Association Database is not installed on the local machine
# The following parameters may be needed to connect to the server
<hostname>192.168.00.00
<username>username
<password>password
<socket>/var/run/mysqld.sock
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