re-init

1 files changed, 66 insertions, 0 deletions

diff --git a/create_prediction_models.rb b/create_prediction_models.rb
new file mode 100644
index 0000000..0ec5e25
--- /dev/null
+++ b/create_prediction_models.rb
@@ -0,0 +1,66 @@
+ENV["LAZAR_ENV"] = "development"
+require_relative '../lazar/lib/lazar'
+#require 'lazar'
+include OpenTox
+#$mongo.database.drop
+#$gridfs = $mongo.database.fs # recreate GridFS indexes
+
+=begin
+# classification models
+Dir["classification/*csv"].each do |file|
+  unless file.match(/hamster/)
+    Model::Prediction.from_csv_file file
+  end
+end
+
+# regression models
+Dir["regression/*log10.csv"].each do |file|
+  Model::Prediction.from_csv_file file
+end
+=end
+
+## nano-lazar
+=begin
+
+# creates 3 models: one with physchem, one with proteomics, one with fingerprints
+feature_categories = ["fingerprint", "P-CHEM", "Proteomics"]
+
+feature_categories.each do |category|
+  if category == "fingerprint"
+		algorithms = {
+			:descriptors => { :method => "fingerprint", :type => "MP2D", },
+			:feature_selection => nil,
+			:similarity => {
+				:method => "Algorithm::Similarity.tanimoto",
+				:min => 0.1
+			}
+		}
+		
+		OpenTox::Model::Validation.from_enanomapper algorithms: algorithms
+	else
+		algorithms = {
+			:descriptors => {
+				:method => "properties",
+				:categories => (category.is_a?(Array) ? [category].flatten : [category]),
+			},
+			:similarity => {
+				:method => "Algorithm::Similarity.weighted_cosine",
+				:min => 0.5
+			},
+			:prediction => {
+				:method => "Algorithm::Caret.rf",
+			},
+			:feature_selection => {
+				:method => "Algorithm::FeatureSelection.correlation_filter",
+			},
+		}
+
+		OpenTox::Model::Validation.from_enanomapper algorithms: algorithms
+	end
+end
+=end
+
+# save
+
+#`mongodump -h 127.0.0.1 -d development`
+#`mongorestore --host 127.0.0.1`