NAME
create-icpropagation.pl - This program determines the probability of the CUIs in a specified set of sources and relations.
SYNOPSIS
This program determines the probability of the CUIs in a specified set of sources and relations.
USAGE
Usage: create-icpropagation.pl [OPTIONS] OUTPUTFILE ICFREQUENCY_FILE
OUTPUTFILE
File in which the probability of the CUIs will be stored.
The ouput file containing the probability of the CUIs has the following format:
SMOOTH :: <0|1>
SAB :: (include|exclude) <sources>
REL :: (include|exclude) <relations>
N :: NUMBER
REL :: <relations>
RELA :: <relas> <- if any are specified in the config
CUI<>probability
CUI<>probability
...ICFREQUENCY FILE
File containing the icfrequency counts
The input file contains frequency counts for CUIs in the following format:
SAB :: (include|exclude) <sources>
REL :: (include|exclude) <relations>
N :: NUMBER
CUI<>freq
CUI<>freq
...N is the total number of ngrams that occurred in the text used to create the icfrequency file.
Optional Arguments:
--st
This outputs the probability of the concepts semantic types rather than the concepts themselves. The frequencies for the st are propagated up the semantic network and therefore are source independent. Note, that the semantic types are expected in the icfrequency input file. This can be created using the create-icfrequency.pl program with the --st option.
If you are erroring out due to the header information on the top of the icfrequency file, try using the --disregard option.
--smooth
Incorporate Laplace smoothing, where the frequency count of each of the concepts in the taxonomy is incremented by one. The advantage of doing this is that it avoides having a concept that has a probability of zero. The disadvantage is that it can shift the overall probability mass of the concepts from what is actually seen in the corpus.
--config FILE
This is the configuration file. The format of the configuration file is as follows:
SAB :: <include|exclude> <source1, source2, ... sourceN>
REL :: <include|exclude> <relation1, relation2, ... relationN>
For example, if we wanted to use the MSH vocabulary with only the RB/RN relations, the configuration file would be:
SAB :: include MSH REL :: include RB, RN
or
SAB :: include MSH REL :: exclude PAR, CHD
If you go to the configuration file directory, there will be example configuration files for the different runs that you have performed.
Note: You can use relations other than PAR/CHD and RB/RN for propagation but we do not recommend it. The PAR/CHD and RB/RN relations are considered the heirarchical relations in the UMLS which is required for propagation to perform correctly.
--disregard
This ignores the SAB configuration that the icfrequency file was created with
--precision N
Displays values upto N places of decimal.
--username STRING
Username is required to access the umls database on MySql
--password STRING
Password is required to access the umls database on MySql
--hostname STRING
Hostname where mysql is located. DEFAULT: localhost
--database STRING
Database contain UMLS DEFAULT: umls
--debug
Sets the UMLS-Interface debug flag on for testing
--help
Displays the quick summary of program options.
--version
Displays the version information.
PROPAGATION
The Information Content (IC) is defined as the negative log of the probability of a concept.
The probability of a concept, c, is determine by summing the probability of the concept (P(c)) ocurring in some text plus the probability its decendants (P(d)) occuring in some text as see in below:
P(c*) = P(c) + \sum_{d\exists decendant(c)} P(d)The initial probability of a concept (P(c)) and its decendants (P(d)) is obtained by dividing the number of times a concept is seen in the corpus (freq(d)) by the total number of concepts (N) as seen below:
P(d) = freq(d) / NNot all of the concepts in the taxonomy will be seen in the corpus. The package includes the option of using Laplace smoothing, where the frequency count of each of the concepts in the taxonomy is incremented by one. The advantage of doing this is that it avoides having a concept that has a probability of zero. The disadvantage is that it can shift the overall probability mass of the concepts from what is actually seen in the corpus.
For more information on how this is calculated please see the README file.
SYSTEM REQUIREMENTS
Perl (version 5.8.5 or better) - http://www.perl.org
UMLS::Interface - http://search.cpan.org/dist/UMLS-Interface
UMLS::Similarity - http://search.cpan.org/dist/UMLS-Similarity
Text::NSP - http://search.cpan.org/dist/Text-NSP
MetaMap - http://mmtx.nlm.nih.gov/
CONTACT US
If you have any trouble installing and using CreatePropagationFile,
please contact us via the users mailing list :
umls-similarity@yahoogroups.com
You can join this group by going to:
http://tech.groups.yahoo.com/group/umls-similarity/
You may also contact us directly if you prefer :
Bridget T. McInnes: bthomson at cs.umn.edu
Ted Pedersen : tpederse at d.umn.eduAUTHOR
Bridget T. McInnes, University of MinnesotaCOPYRIGHT
Copyright (c) 2007-2011,
Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Siddharth Patwardhan, University of Utah, Salt Lake City
sidd@cs.utah.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002@umn.eduThis program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to:
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.