From 3922c8e5fcb9fbe6ddedab9f70e114717ff33a60 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 26 May 2011 14:28:19 +0200 Subject: 8th v --- lib/model.rb | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) (limited to 'lib/model.rb') diff --git a/lib/model.rb b/lib/model.rb index 7c2ef58..28c05a9 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -69,7 +69,7 @@ module OpenTox include Model include Algorithm - attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid + attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :subjectid, :prop_kernel def initialize(uri=nil) @@ -92,6 +92,7 @@ module OpenTox @prediction_algorithm = "Neighbors.weighted_majority_vote" @min_sim = 0.3 + @prop_kernel = false end @@ -219,7 +220,11 @@ module OpenTox (i == modulo[0]) && (slack>0) ? lr_size = s.size + slack : lr_size = s.size + addon # determine fraction LOGGER.info "BLAZAR: Neighbors round #{i}: #{position} + #{lr_size}." neighbors_balanced(s, l, position, lr_size) # get ratio fraction of larger part - (@prediction_algorithm.include? "svm" and params[:prop_kernel] == "true") ? props = get_props : props = nil + if @prop_kernel && @prediction_algorithm.include?("svm") + props = get_props + else + props = nil + end prediction = eval("#{@prediction_algorithm}(@neighbors,{:similarity_algorithm => @similarity_algorithm, :p_values => @p_values}, props)") if prediction_best.nil? || prediction[:confidence].abs > prediction_best[:confidence].abs prediction_best=prediction @@ -235,10 +240,14 @@ module OpenTox @neighbors=neighbors_best ### END AM balanced predictions - else # regression case: no balancing + else # AM: no balancing LOGGER.info "LAZAR: Unbalanced." neighbors - (@prediction_algorithm.include? "svm" and params[:prop_kernel] == "true") ? props = get_props : props = nil + if @prop_kernel && @prediction_algorithm.include?("svm") + props = get_props + else + props = nil + end prediction = eval("#{@prediction_algorithm}(@neighbors,{:similarity_algorithm => @similarity_algorithm, :p_values => @p_values}, props)") end -- cgit v1.2.3