diff options
author | Christoph Helma <helma@in-silico.ch> | 2015-09-17 14:56:25 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-09-17 14:56:25 +0200 |
commit | 6ac119c32cef094d4f1c2fb5c2daa4e274401f70 (patch) | |
tree | 9028a2922b68a5e2175687fe48caa1b1119e5939 /test/experiment.rb | |
parent | 2fdecbed76c4db8dfe3f10f825fed9772e653197 (diff) |
neighbor calculation moved to Compound class
Diffstat (limited to 'test/experiment.rb')
-rw-r--r-- | test/experiment.rb | 31 |
1 files changed, 29 insertions, 2 deletions
diff --git a/test/experiment.rb b/test/experiment.rb index cad4fa7..4b54768 100644 --- a/test/experiment.rb +++ b/test/experiment.rb @@ -18,7 +18,7 @@ class ExperimentTest < MiniTest::Test } ] ) - experiment.run + #experiment.run puts experiment.report.to_yaml assert_equal datasets.size, experiment.results.size experiment.results.each do |dataset_id, result| @@ -48,7 +48,7 @@ class ExperimentTest < MiniTest::Test #} ] ) - experiment.run + #experiment.run =begin experiment = Experiment.find "55f944a22b72ed7de2000000" =end @@ -61,4 +61,31 @@ class ExperimentTest < MiniTest::Test end end end + + def test_regression_fingerprints + datasets = [ + "LOAEL_mmol_corrected_smiles.csv" + ] + min_sims = [0.3,0.7] + types = ["FP2","FP3","FP4","MACCS"] + experiment = Experiment.create( + :name => "Fminer vs fingerprint classification for datasets #{datasets}.", + :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id}, + ) + types.each do |type| + min_sims.each do |min_sim| + experiment.model_settings << { + :algorithm => "OpenTox::Model::LazarRegression", + :neighbor_algorithm => "fingerprint_neighbors", + :neighbor_algorithm_parameter => { + :type => type, + :min_sim => min_sim, + } + } + end + end + experiment.run + p experiment.report + + end end |