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#   ltcAssociation (LTA) - association measures that use linking terms as inputs
#   ltc_AMW - linking term count with AMW as a tie-breaker
#
#   *all procedures require a measure to be specified except LTC and freq
<rankingProcedure>averageMinimumWeight

# The association measure to use as a value in the ranking procedure.
# The string is passed directly to UMLS::Association, so as that gets
# updated, new associatio measures will work automatically.
# At the time of this writing, valid arguments are:
# freq - Frequency
# dice - Dice Coefficient
# left - Fishers exact test - left sided 
# right - Fishers exact test - right sided 
# twotailed - Fishers twotailed test
# jaccard - Jaccard Coefficient
# ll - Log-likelihood ratio
# tmi - Mutual Information
# odds - Odds Ratio
# pmi - Pointwise Mutual Information
# phi - Phi Coefficient
# chi - Pearson's Chi Squared Test
# ps - Poisson Stirling Measure 
# tscore - T-score
<rankingMeasure>ll

# a comma seperated list of linking (B) term accept semantic groups, which 
# restricts the linking terms to the semantic groups specified. Group names
# come directly from the UMLS. 
# See https://metamap.nlm.nih.gov/Docs/SemGroups_2013.txt for a list
#<linkingAcceptGroups>CHEM,DISO,GENE,PHYS,ANAT

# similar to linking accept groups, this restricts the acceptable linking (B) 
# terms to terms within the semantic types listed
# See http://metampa.nlm.gov/Docs/SemanticTypes_2013AA.txt for a list
#<linkingAcceptGroups>clnd,chem

# a comma seperated list of target (C) term accept semantic groups, which 
# restricts the linking terms to the semantic groups specified. Group names
# come directly from the UMLS. 
# See https://metamap.nlm.nih.gov/Docs/SemGroups_2013.txt for a list
#<targetAcceptGroups>CHEM,GENE

# similar to target termcept groups, this restricts the acceptable target (C) 
# terms to terms within the semantic types listed
# See http://metampa.nlm.gov/Docs/SemanticTypes_2013AA.txt for a list
#<linkingAcceptGroups>clnd,chem

# Input file path for the explicit co-occurrence matrix used in LBD
<explicitInputFile>sampleExplicitMatrix

# Input file path for the gold standard matrix (matrix of true predictions)
# See utils/datasetCreator on how to make this
<goldInputFile>sampleGoldMatrix

# Input file path of the pre-computed predictions file
# This is optional, but can speed up computation time, since computing the 
# prediction matrix can be time consuming.
# The prediction matrix is all predicted discoveries. It is easiest to generate
# by running timeslicing first with the predictionsOutFile specified, then
# in subsequent runs using that as an input
# <predictionsInFile>predictionsMatrix

# Output file path of the pre-computed predictions file
# This is optional, but can speed up computation time, since computing the 
# prediction matrix can be time consuming.
# The prediction matrix is all predicted discoveries
<predictionsOutFile>predictionsMatrix

# A thresholded matrix to use for computing association measure values. The
# user must specify a non-thresholded matrix in order to properly compute 
# predictions. The thresholded matrix file is optional, and is used only
# for the values in ranking procedures
# <thresholdedMatrix>thresholdMatrix