From bdc6b5b40437896384561d74a510560e9e592364 Mon Sep 17 00:00:00 2001 From: "helma@in-silico.ch" Date: Tue, 9 Oct 2018 18:20:27 +0200 Subject: tentative random forest classification: hangs unpredictably during caret model generation/optimization for some (inorganic?) compounds. --- test/model-classification.rb | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'test/model-classification.rb') diff --git a/test/model-classification.rb b/test/model-classification.rb index f75598b..232ee3f 100644 --- a/test/model-classification.rb +++ b/test/model-classification.rb @@ -2,6 +2,42 @@ require_relative "setup.rb" class LazarClassificationTest < MiniTest::Test + def test_carcinogenicity_rf_classification + skip "Caret rf may run into a (endless?) loop for some compounds." + dataset = Dataset.from_csv_file "#{DATA_DIR}/multi_cell_call.csv" + algorithms = { + :prediction => { + :method => "Algorithm::Caret.rf", + }, + } + model = Model::Lazar.create training_dataset: dataset, algorithms: algorithms + substance = Compound.from_smiles "[O-]S(=O)(=O)[O-].[Mn+2].O" + prediction = model.predict substance + p prediction + + end + + def test_rf_classification + skip "Caret rf may run into a (endless?) loop for some compounds." + algorithms = { + :prediction => { + :method => "Algorithm::Caret.rf", + }, + } + training_dataset = Dataset.from_sdf_file File.join(DATA_DIR,"cas_4337.sdf") + model = Model::Lazar.create training_dataset: training_dataset, algorithms: algorithms + #p model.id.to_s + #model = Model::Lazar.find "5bbb4c0cca626909f6c8a924" + assert_kind_of Model::LazarClassification, model + assert_equal algorithms[:prediction][:method], model.algorithms["prediction"]["method"] + substance = Compound.from_smiles "Clc1ccc(cc1)C(=O)c1ccc(cc1)OC(C(=O)O)(C)C" + prediction = model.predict substance + assert_equal 51, prediction[:neighbors].size + assert_equal "nonmutagen", prediction[:value] + assert_equal 0.1, prediction[:probabilities]["mutagen"].round(1) + assert_equal 0.9, prediction[:probabilities]["nonmutagen"].round(1) + end + def test_classification_default algorithms = { :descriptors => { -- cgit v1.2.3