1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
|
require_relative "setup.rb"
class LazarClassificationTest < MiniTest::Test
def test_lazar_classification
training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv")
model = Model::LazarClassification.create training_dataset#, feature_dataset
#assert_equal 'C-C-C=C', feature_dataset.features.first.smarts
[ {
:compound => OpenTox::Compound.from_inchi("InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"),
:prediction => "false",
:confidence => 0.25281385281385277,
:nr_neighbors => 11
},{
:compound => OpenTox::Compound.from_smiles("c1ccccc1NN"),
:prediction => "false",
:confidence => 0.3639589577089577,
:nr_neighbors => 14
} ].each do |example|
prediction = model.predict example[:compound]
assert_equal example[:prediction], prediction[:value]
#assert_equal example[:confidence], prediction[:confidence]
#assert_equal example[:nr_neighbors], prediction[:neighbors].size
end
compound = Compound.from_smiles "CCO"
prediction = model.predict compound
assert_equal ["false"], prediction[:database_activities]
assert_equal "true", prediction[:value]
# make a dataset prediction
compound_dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
prediction = model.predict compound_dataset
assert_equal compound_dataset.compounds, prediction.compounds
assert_equal "Cound not find similar compounds.", prediction.data_entries[7][2]
assert_equal "measured", prediction.data_entries[14][1]
# cleanup
[training_dataset,model,compound_dataset].each{|o| o.delete}
end
end
|