LOAEL(mg, corrected) 10-fold result of 33 jl2

Used corrected LOAEL data to create jl2 feature datasets.

6 files changed, 1986 insertions, 1987 deletions

diff --git a/cv/data/csv/LOAEL.csv b/cv/data/csv/LOAEL.csv
index d3c92a8..9e9c792 100644
--- a/cv/data/csv/LOAEL.csv
+++ b/cv/data/csv/LOAEL.csv
@@ -1,568 +1,568 @@
-SMILES,LOAEL_log_mg/kg_bw/day
-'COc1cc(c(C)cc1N=Nc2c(O)ccc3cc(ccc23)S(OH)(=O)=O)S(OH)(=O)=O',3.57275546515422
-'O1C(=O)C(O)=C(O)C1C(O)CO',3.48444220764241
-'C1(C)=C(C=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)C(=O)OC)C(C)(C)CCC1',2.69897000433602
-'c(cccc1)(c1)C(C)C',2.66464197555613
-'O=C(OCCCC)c(c(ccc1)C(=O)OCCCC)c1',2.77815125038364
-'O=C(OCC)c(c(ccc1)C(=O)OCC)c1',3.64689362416774
-'O=C(OC(OC(OC1C)C)C1)C',2.09691001300806
-'Oc(c(ccc1)C)c1C',0.778151250383644
-'Oc(ccc(c1C)C)c1',1.14612803567824
-'O=C(OCC)C=C',2.39445168082622
-'c(cccc1)(c1)CC',2.61066016308988
-'OCCO',2.39794000867204
-'c(ccc1C(=O)OCC(=O)OCC)cc1C(=O)OCC',3.39794000867204
-'O=C',1.91381385238372
-'O=C(O)C=CC(=O)O',3.03382569395331
-'OCC(O)CO',3.83777776955373
-'O=C(OC)c(ccc(O)c1)c1',3.17609125905568
-'O=C(OCCC)c(ccc(O)c1)c1',3.17609125905568
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-'OC(C(CCC1C)C(C)C)C1',2.77305469336426
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-'O=C(OCCC)c(cc(O)c(O)c1O)c1',2.93651374247889
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-'CN(C)(C)CCCl',2.43933269383026
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\ No newline at end of file
diff --git a/cv/data/csv/LOAEL_all_pc.csv b/cv/data/csv/LOAEL_all_pc.csv
index b9f70ed..8a736ec 100644
--- a/cv/data/csv/LOAEL_all_pc.csv
+++ b/cv/data/csv/LOAEL_all_pc.csv
@@ -1,440 +1,445 @@
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\ No newline at end of file
diff --git a/cv/data/csv/LOAEL_joelib.csv b/cv/data/csv/LOAEL_joelib.csv
index 141717b..04c87e9 100644
--- a/cv/data/csv/LOAEL_joelib.csv
+++ b/cv/data/csv/LOAEL_joelib.csv
@@ -1,440 +1,445 @@
-SMILES,NumberOfAtoms,KierShape3,NumberOfBonds,GraphShapeCoefficient,HeavyBonds,AliphaticOHGroups,HBD2,HBA1,RotatableBonds,HBA2,NumberOfHal,MolecularWeight,AromaticBonds,ZagrebIndex1,MolarRefractivity,FractionRotatableBonds,LogP,KierShape1,KierShape2,PolarSurfaceArea
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\ No newline at end of file
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\ No newline at end of file
diff --git a/cv/data/csv/LOAEL_topological.csv b/cv/data/csv/LOAEL_topological.csv
index cb583d4..c2105dc 100644
--- a/cv/data/csv/LOAEL_topological.csv
+++ b/cv/data/csv/LOAEL_topological.csv
@@ -1,440 +1,445 @@
-SMILES,SCH-6,VP-5,SP-2,geomShape,TopoPSA,ATSc1,khs.aaN,MDEC-22,SCH-7,VP-6,SP-3,ATSc2,Kier1,MDEC-23,VP-7,SP-4,ATSc3,Kier2,C2SP2,khs.dsssP,SP-5,Kier3,ATSc4,khs.dS,khs.sCl,ATSp1,khs.ssO,topoShape,ATSc5,VC-3,ATSp2,VC-4,ATSp3,SP-6,MDEO-22,WPATH,VC-5,ATSp4,SP-7,SPC-4,SC-3,ATSp5,khs.dsN,PetitjeanNumber,khs.aaCH,SPC-5,Zagreb,SPC-6,SC-5,khs.ssS,MDEC-12,VPC-4,MDEC-33,khs.dssC,VPC-5,ECCEN,VCH-5,VPC-6,MDEC-13,fragC,VCH-6,khs.ssCH2,VCH-7,ATSm1,VP-0,MDEO-11,C1SP2,khs.aasC,WPOL,MDEO-12,ATSm2,VP-1,khs.sOH,VP-2,ATSm3,khs.dO,VP-3,ATSm4,SP-0,SCH-5,MDEN-22,SP-1,khs.sssN,VP-4,ATSm5
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\ No newline at end of file
diff --git a/cv/data/datasets.yaml b/cv/data/datasets.yaml
index e47c3f9..a4f6172 100644
--- a/cv/data/datasets.yaml
+++ b/cv/data/datasets.yaml
@@ -1,45 +1,57 @@
 {
+
+  "MDD": {
+    "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/14"  #,
+#    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/",
+#    "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/",
+#    "topological": "http://toxcreate3.in-silico.ch:8080/dataset/",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/",
+#    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/",
+#    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/"
+  },
+  
   "FHM": {
-    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/84455",
-      "topological": "http://toxcreate3.in-silico.ch:8080/dataset/84456",
-      "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/6",
-      "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84457",
-      "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/46238",
-      "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/84458",
-      "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/84459"
+    "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/6",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/83",
+    "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/87",
+    "topological": "http://toxcreate3.in-silico.ch:8080/dataset/96",
+    "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/100",
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/115"
+  },
+  
+  "RAT": {
+    "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/7",
+    "training": "http://toxcreate3.in-silico.ch:8080/dataset/12",
+    "test": "http://toxcreate3.in-silico.ch:8080/dataset/13",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/99",
+    "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/112",
+    "topological": "http://toxcreate3.in-silico.ch:8080/dataset/109",
+    "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/107",
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/90",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/3409"
+  },
+
+  "MOU": {
+    "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/8",
+    "training": "http://toxcreate3.in-silico.ch:8080/dataset/10",
+    "test": "http://toxcreate3.in-silico.ch:8080/dataset/11",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/97",
+    "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/102",
+    "topological": "http://toxcreate3.in-silico.ch:8080/dataset/108",
+    "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/103",
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/94",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/2273"
   },
-    "MDD": {
-      "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/14"
-    },
-    "RAT": {
-      "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/84460",
-      "topological": "http://toxcreate3.in-silico.ch:8080/dataset/84461",
-      "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/7",
-      "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84462",
-      "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/52151",
-      "training": "http://toxcreate3.in-silico.ch:8080/dataset/12",
-      "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/84463",
-      "test": "http://toxcreate3.in-silico.ch:8080/dataset/13",
-      "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/84464"
-    },
-    "LOAEL": {
-      "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/84465",
-      "topological": "http://toxcreate3.in-silico.ch:8080/dataset/84466",
-      "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/84400",
-      "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84467",
-      "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/49285",
-      "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/84468",
-      "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/84469"
-    },
-    "MOU": {
-      "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/84470",
-      "topological": "http://toxcreate3.in-silico.ch:8080/dataset/84471",
-      "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/8",
-      "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84472",
-      "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/49337",
-      "training": "http://toxcreate3.in-silico.ch:8080/dataset/10",
-      "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/84473",
-      "test": "http://toxcreate3.in-silico.ch:8080/dataset/11",
-      "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/84474"
-    }
+
+  "LOAEL": {
+    "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/120089",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/141114",
+    "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/141120",
+    "topological": "http://toxcreate3.in-silico.ch:8080/dataset/185800",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/",
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/185802",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/185805"
+  }
+
 }
diff --git a/cv/scripts/logs/LOAEL.log b/cv/scripts/logs/LOAEL.log
index 2d47481..5c01ad1 100644
--- a/cv/scripts/logs/LOAEL.log
+++ b/cv/scripts/logs/LOAEL.log
@@ -1,70 +1,42 @@
-20120319_07_: LOAEL constitutional local_svm_regression 1
-ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL constitutional local_svm_regression 1
-datasets.yaml exists
---- prediction_algorithm=local_svm_regression;pc_type=constitutional;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84468
---- 
+20120325_22_: LOAEL topological local_svm_regression nil 1
+ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL topological local_svm_regression nil 1 ../data/datasets_new_LOAEL_mg_allnum_old_rfe2.yaml
+[2012-03-25T20:20:07.3443Z] datasets_new_LOAEL_mg_allnum_old_rfe2.yaml exists.
+[2012-03-25T20:20:07.3445Z] --- prediction_algorithm=local_svm_regression;pc_type=topological;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185800
+[2012-03-25T20:20:07.3818Z] --- 
+:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/120089
+:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/120089/feature/LOAEL_log_mg_kg_bw_day
 :algorithm_uri: http://toxcreate3.in-silico.ch:8080/algorithm/lazar
-:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=constitutional;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84468
+:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=topological;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185800
 :stratified: false
 :random_seed: "1"
-:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/84400
-:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/84400/feature/LOAEL_log_mg/kg_bw/day
-http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/259
-http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/343
+[2012-03-25T21:40:23.6780Z] http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/385
+[2012-03-25T21:40:45.0129Z] http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/444
 
-20120319_07_: LOAEL electronic,cpsa local_svm_regression 1
-ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL electronic,cpsa local_svm_regression 1
-datasets.yaml exists
---- prediction_algorithm=local_svm_regression;pc_type=electronic,cpsa;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84465
---- 
+20120325_22_: LOAEL joelib local_svm_regression nil 1
+ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL joelib local_svm_regression nil 1 ../data/datasets_new_LOAEL_mg_allnum_old_rfe2.yaml
+[2012-03-25T21:40:46.3455Z] datasets_new_LOAEL_mg_allnum_old_rfe2.yaml exists.
+[2012-03-25T21:40:46.3458Z] --- prediction_algorithm=local_svm_regression;pc_type=joelib;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185802
+[2012-03-25T21:40:46.3540Z] --- 
+:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/120089
+:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/120089/feature/LOAEL_log_mg_kg_bw_day
 :algorithm_uri: http://toxcreate3.in-silico.ch:8080/algorithm/lazar
-:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=electronic,cpsa;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84465
+:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=joelib;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185802
 :stratified: false
 :random_seed: "1"
-:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/84400
-:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/84400/feature/LOAEL_log_mg/kg_bw/day
-http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/262
-http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/345
+[2012-03-25T22:30:06.3168Z] http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/387
+[2012-03-25T22:30:18.5146Z] http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/446
 
-20120319_07_: LOAEL topological local_svm_regression 1
-ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL topological local_svm_regression 1
-datasets.yaml exists
---- prediction_algorithm=local_svm_regression;pc_type=topological;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84466
---- 
+20120325_22_: LOAEL all_pc local_svm_regression nil 1
+ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL all_pc local_svm_regression nil 1 ../data/datasets_new_LOAEL_mg_allnum_old_rfe2.yaml
+[2012-03-25T22:30:19.4904Z] datasets_new_LOAEL_mg_allnum_old_rfe2.yaml exists.
+[2012-03-25T22:30:19.4907Z] --- prediction_algorithm=local_svm_regression;pc_type=all_pc;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185805
+[2012-03-25T22:30:19.4973Z] --- 
+:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/120089
+:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/120089/feature/LOAEL_log_mg_kg_bw_day
 :algorithm_uri: http://toxcreate3.in-silico.ch:8080/algorithm/lazar
-:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=topological;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84466
+:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=all_pc;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/185805
 :stratified: false
 :random_seed: "1"
-:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/84400
-:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/84400/feature/LOAEL_log_mg/kg_bw/day
-http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/263
-http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/347
-
-20120319_07_: LOAEL joelib local_svm_regression 1
-ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL joelib local_svm_regression 1
-datasets.yaml exists
---- prediction_algorithm=local_svm_regression;pc_type=joelib;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84467
---- 
-:algorithm_uri: http://toxcreate3.in-silico.ch:8080/algorithm/lazar
-:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=joelib;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84467
-:stratified: false
-:random_seed: "1"
-:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/84400
-:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/84400/feature/LOAEL_log_mg/kg_bw/day
-http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/266
-http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/348
-
-20120318_23_: LOAEL all_pc local_svm_regression 1
-ruby CV_ds_pctype_algo_rseed_LOAEL.rb LOAEL all_pc local_svm_regression 1
-datasets.yaml exists
---- prediction_algorithm=local_svm_regression;pc_type=all_pc;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84469
---- 
-:algorithm_uri: http://toxcreate3.in-silico.ch:8080/algorithm/lazar
-:algorithm_params: prediction_algorithm=local_svm_regression;pc_type=all_pc;feature_dataset_uri=http://toxcreate3.in-silico.ch:8080/dataset/84469
-:stratified: false
-:random_seed: "1"
-:dataset_uri: http://toxcreate3.in-silico.ch:8080/dataset/84400
-:prediction_feature: http://toxcreate3.in-silico.ch:8080/dataset/84400/feature/LOAEL_log_mg/kg_bw/day
-http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/256
-http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/339
+[2012-03-26T00:11:45.5506Z] http://toxcreate3.in-silico.ch:8080/validation/crossvalidation/389
+[2012-03-26T00:12:11.3307Z] http://toxcreate3.in-silico.ch:8080/validation/report/crossvalidation/448