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| author | Christoph Helma <helma@in-silico.ch> | 2013-07-17 14:50:35 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2013-07-17 14:50:35 +0200 |
| commit | 47140182b4b40573ecf199122e3687f885c5381d (patch) | |
| tree | 4291673caadb2893855ba25abb4140c35d030cb6 | |
| parent | 9838233bbc9ac5c88875f8001ec137274b24c57a (diff) | |
uri objects fixed in ntriples serialsiation
| -rw-r--r-- | lib/neighbors.rb | 1 | ||||
| -rw-r--r-- | lib/transform.rb | 4 |
2 files changed, 0 insertions, 5 deletions
diff --git a/lib/neighbors.rb b/lib/neighbors.rb index 285afa8..c77325a 100644 --- a/lib/neighbors.rb +++ b/lib/neighbors.rb @@ -69,7 +69,6 @@ module OpenTox # @param [Hash] params Keys `:props, :activities, :sims, :min_train_performance` are required # @return [Numeric] A prediction value. def self.local_svm_regression(params) - puts "SVM" confidence = 0.0 prediction = nil diff --git a/lib/transform.rb b/lib/transform.rb index 752f448..cb4fc87 100644 --- a/lib/transform.rb +++ b/lib/transform.rb @@ -242,7 +242,6 @@ module OpenTox # Transforms the model def transform get_matrices # creates @n_prop, @q_prop, @activities from ordered fingerprints - puts "MATRIX" @ids = (0..((@n_prop.length)-1)).to_a # surviving compounds; become neighbors if (@model.similarity_algorithm =~ /cosine/) @@ -277,16 +276,13 @@ module OpenTox @q_prop = svd.transform(gsl_q_prop).row(0).to_a $logger.debug "S: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}" else - puts "CONVERT NILS" convert_nils # convert nil cells (for tanimoto); leave @n_props, @q_props, @ids untouched end # neighbor calculation @ids = [] # surviving compounds become neighbors @sims = [] # calculated by neighbor routine - puts "NEIGHBORS" neighbors - puts "NEIGHBORS FINISHED" n_prop_tmp = []; @ids.each { |idx| n_prop_tmp << @n_prop[idx] }; @n_prop = n_prop_tmp # select neighbors from matrix acts_tmp = []; @ids.each { |idx| acts_tmp << @activities[idx] }; @activities = acts_tmp |