From 063acd4dc63e9287287cc1ff78fff2064ff74e4f Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 7 Apr 2016 17:39:14 +0200 Subject: initial ambit import --- lib/lazar.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index a28ba3a..39dd8fa 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -61,7 +61,7 @@ suppressPackageStartupMessages({ " # OpenTox classes and includes -CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment","Nanoparticle"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites "overwrite.rb", @@ -71,6 +71,7 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveO "feature.rb", "physchem.rb", "compound.rb", + "nanoparticle.rb", "dataset.rb", "algorithm.rb", "model.rb", -- cgit v1.2.3 From f3780d7507092b643216054fa3ca1e6146281e43 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 8 Apr 2016 13:04:56 +0200 Subject: enm import test --- lib/lazar.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 39dd8fa..0e2cec2 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -81,5 +81,6 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveO "crossvalidation.rb", "leave-one-out-validation.rb", "experiment.rb", + "import.rb", ].each{ |f| require_relative f } OpenTox::PhysChem.descriptors # load descriptor features -- cgit v1.2.3 From 84222bae2bbb9fb3e0ce3e65de1be8e7f94d2147 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 12 Apr 2016 12:37:37 +0200 Subject: new dataset structure --- lib/lazar.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 0e2cec2..2bcecc5 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -61,7 +61,8 @@ suppressPackageStartupMessages({ " # OpenTox classes and includes -CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment","Nanoparticle"]# Algorithm and Models are modules +#CLASSES = ["Feature","Substance::Compound","Substance::Nanoparticle","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Substance","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites "overwrite.rb", -- cgit v1.2.3 From a8368dda776c05331474adf7eaf9a6e413a3b1eb Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 13 Apr 2016 15:15:51 +0200 Subject: validation tests pass --- lib/lazar.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 2bcecc5..a1ad551 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -62,7 +62,7 @@ suppressPackageStartupMessages({ # OpenTox classes and includes #CLASSES = ["Feature","Substance::Compound","Substance::Nanoparticle","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules -CLASSES = ["Feature","Substance","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites "overwrite.rb", @@ -81,6 +81,7 @@ CLASSES = ["Feature","Substance","Dataset","Validation","CrossValidation","Leave "validation.rb", "crossvalidation.rb", "leave-one-out-validation.rb", + "validation-statistics.rb", "experiment.rb", "import.rb", ].each{ |f| require_relative f } -- cgit v1.2.3 From 64f1f32ced77afb278bdb7c27397c5299a73675c Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 13 Apr 2016 18:18:36 +0200 Subject: improved enm import --- lib/lazar.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index a1ad551..8eb46e0 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -71,6 +71,7 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","Cross "opentox.rb", "feature.rb", "physchem.rb", + "substance.rb", "compound.rb", "nanoparticle.rb", "dataset.rb", -- cgit v1.2.3 From 51f57e2858b60bed74ebcc97189b2188c900c283 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 6 May 2016 12:49:28 +0200 Subject: dataset tests cleanup --- lib/lazar.rb | 1 - 1 file changed, 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 8eb46e0..8daaaa1 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -86,4 +86,3 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","Cross "experiment.rb", "import.rb", ].each{ |f| require_relative f } -OpenTox::PhysChem.descriptors # load descriptor features -- cgit v1.2.3 From 48234554ea99b972a01718ac36c4e8332dd9159b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sat, 7 May 2016 10:34:03 +0200 Subject: -log10 for regression datasets, test cleanups --- lib/lazar.rb | 1 - 1 file changed, 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 8daaaa1..140bca3 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -61,7 +61,6 @@ suppressPackageStartupMessages({ " # OpenTox classes and includes -#CLASSES = ["Feature","Substance::Compound","Substance::Nanoparticle","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites -- cgit v1.2.3 From b8bb12c8a163c238d7d4387c1914e2100bb660df Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 12 May 2016 15:23:01 +0200 Subject: enm study import fixed --- lib/lazar.rb | 2 ++ 1 file changed, 2 insertions(+) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 140bca3..55de511 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -48,6 +48,7 @@ NR_CORES = `getconf _NPROCESSORS_ONLN`.to_i R = Rserve::Connection.new R.eval " suppressPackageStartupMessages({ + library(labeling,lib=\"#{rlib}\") library(iterators,lib=\"#{rlib}\") library(foreach,lib=\"#{rlib}\") library(ggplot2,lib=\"#{rlib}\") @@ -75,6 +76,7 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","Cross "nanoparticle.rb", "dataset.rb", "algorithm.rb", + "similarity", "model.rb", "classification.rb", "regression.rb", -- cgit v1.2.3 From c90644211e214a50f6fdb3a936bf247f45f1f4be Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 13 May 2016 13:38:24 +0200 Subject: compound tests fixed --- lib/lazar.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 55de511..7bd87f4 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -80,10 +80,10 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","Cross "model.rb", "classification.rb", "regression.rb", + "validation-statistics.rb", "validation.rb", "crossvalidation.rb", "leave-one-out-validation.rb", - "validation-statistics.rb", "experiment.rb", "import.rb", ].each{ |f| require_relative f } -- cgit v1.2.3 From b515a0cfedb887a2af753db6e4a08ae1af430cad Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 31 May 2016 18:08:08 +0200 Subject: cleanup of validation modules/classes --- lib/lazar.rb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 7bd87f4..1853aba 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -62,7 +62,7 @@ suppressPackageStartupMessages({ " # OpenTox classes and includes -CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Substance","Dataset","LazarPrediction","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites "overwrite.rb", @@ -82,8 +82,9 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","Validation","Cross "regression.rb", "validation-statistics.rb", "validation.rb", - "crossvalidation.rb", + "train-test-validation.rb", "leave-one-out-validation.rb", - "experiment.rb", + "crossvalidation.rb", + #"experiment.rb", "import.rb", ].each{ |f| require_relative f } -- cgit v1.2.3 From 290c7f86950c4051d018b8019ff4e72ec406c58c Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 3 Jun 2016 19:15:36 +0200 Subject: random forest regression --- lib/lazar.rb | 2 ++ 1 file changed, 2 insertions(+) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 1853aba..46605d3 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -57,6 +57,8 @@ suppressPackageStartupMessages({ library(pls,lib=\"#{rlib}\") library(caret,lib=\"#{rlib}\") library(doMC,lib=\"#{rlib}\") + library(randomForest,lib=\"#{rlib}\") + library(plyr,lib=\"#{rlib}\") registerDoMC(#{NR_CORES}) }) " -- cgit v1.2.3 From 5d4e5e463c2b87241bbb56e4658e1e26c0ed084f Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 5 Oct 2016 13:22:12 +0200 Subject: substance and nanoparticle model creation and predictions --- lib/lazar.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index 46605d3..d0f05c0 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -78,7 +78,8 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","CrossValidation"," "nanoparticle.rb", "dataset.rb", "algorithm.rb", - "similarity", + "similarity.rb", + "feature_selection.rb", "model.rb", "classification.rb", "regression.rb", -- cgit v1.2.3 From 4348eec89033e6677c9f628646fc67bd03c73fe6 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Thu, 6 Oct 2016 19:14:10 +0200 Subject: nano caret regression fixed --- lib/lazar.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'lib/lazar.rb') diff --git a/lib/lazar.rb b/lib/lazar.rb index d0f05c0..f251379 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -83,6 +83,7 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","CrossValidation"," "model.rb", "classification.rb", "regression.rb", + "caret.rb", "validation-statistics.rb", "validation.rb", "train-test-validation.rb", -- cgit v1.2.3