summaryrefslogtreecommitdiff
path: root/lib
diff options
context:
space:
mode:
authorhelma@in-silico.ch <helma@in-silico.ch>2018-08-14 12:02:03 +0000
committerhelma@in-silico.ch <helma@in-silico.ch>2018-08-14 12:02:03 +0000
commit13e7865f386603fb784e62feef2ee2a56c015b45 (patch)
treea02269ca52a03c5c676e56047e62a38aa8a67268 /lib
parent15054eab1c3444bc7a602596b08c4656d324f44b (diff)
classification min_sim=0.5, 5 repeated cvs
Diffstat (limited to 'lib')
-rw-r--r--lib/crossvalidation.rb2
-rw-r--r--lib/model.rb2
-rw-r--r--lib/train-test-validation.rb2
3 files changed, 3 insertions, 3 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 06a1e2a..e94864a 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -103,7 +103,7 @@ module OpenTox
# @param [Fixnum] number of folds
# @param [Fixnum] number of repeats
# @return [OpenTox::Validation::RepeatedCrossValidation]
- def self.create model, folds=10, repeats=3
+ def self.create model, folds=10, repeats=5
repeated_cross_validation = self.new
repeats.times do |n|
$logger.debug "Crossvalidation #{n+1} for #{model.name}"
diff --git a/lib/model.rb b/lib/model.rb
index dce53a9..0ed70f2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -80,7 +80,7 @@ module OpenTox
}
model.algorithms[:similarity] = {
:method => "Algorithm::Similarity.tanimoto",
- :min => 0.1,
+ :min => 0.5,
}
elsif model.class == LazarRegression
model.algorithms[:prediction] = {
diff --git a/lib/train-test-validation.rb b/lib/train-test-validation.rb
index 9a5532d..8231728 100644
--- a/lib/train-test-validation.rb
+++ b/lib/train-test-validation.rb
@@ -28,7 +28,7 @@ module OpenTox
end
predictions.select!{|cid,p| p[:value] and p[:measurements]}
# hack to avoid mongos file size limit error on large datasets
- #predictions.each{|cid,p| p[:neighbors] = []} if model.training_dataset.name.match(/mutagenicity/i)
+ predictions.each{|cid,p| p[:neighbors] = []} #if model.training_dataset.name.match(/mutagenicity/i)
validation = self.new(
:model_id => validation_model.id,
:test_dataset_id => test_set.id,