diff options
| author | Andreas Maunz <andreas@maunz.de> | 2012-02-09 15:44:28 +0100 |
|---|---|---|
| committer | Andreas Maunz <andreas@maunz.de> | 2012-02-09 15:44:28 +0100 |
| commit | 7a37114695d783a770cdca854df36cc4ee347758 (patch) | |
| tree | 7c00197151b077646f9cb3c4e3406d0e6fd58781 | |
| parent | 1a0957e830030b9c376eb298f9e8a837249d3296 (diff) | |
| parent | 82f8512dc5e2de822433e2dcec3b579962e6ae2a (diff) | |
Merge branch 'pc_new_1' into development
Conflicts:
algorithm.rb
dataset.rb
lazar.rb
46 files changed, 14746 insertions, 269 deletions
diff --git a/5x_cv/check_datasets_inchi_equality.rb b/5x_cv/check_datasets_inchi_equality.rb new file mode 100644 index 0000000..7d38e96 --- /dev/null +++ b/5x_cv/check_datasets_inchi_equality.rb @@ -0,0 +1,98 @@ +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +@subjectid = nil + + + +def check_ds(t_ds_uri, f_ds_uri) + puts t_ds_uri + puts f_ds_uri + + regression_training_dataset = OpenTox::Dataset.find(t_ds_uri, @subjectid)#3963;1572; + regression_feature_dataset = OpenTox::Dataset.find(f_ds_uri, @subjectid)#3971;3946; + + train_ds = regression_training_dataset.data_entries.keys + train_cmds = regression_training_dataset.compounds + feature_ds = regression_feature_dataset.data_entries.keys + feature_cmds = regression_feature_dataset.compounds + + puts "----- Check activity inchi -----" + match=0 + mismatch=0 + train_ds.each { |i| + if feature_ds.include?(i) + match = match + 1 + else + mismatch = mismatch + 1 + end + } + if mismatch > 0 + puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0 + puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!" + else + puts "All training compounds represented in feature dataset." unless mismatch > 0 + puts "match: #{match}; mismatch: #{mismatch}" + puts "OK!!!" + end + + train_ds.sort! + feature_ds.sort! + + if train_ds == feature_ds + puts "train_ds == feature_ds" + else + a = train_ds - feature_ds + #puts "d: '#{a}'" + puts "train_ds: " + train_ds.size.to_s + "; feature_ds: "+ feature_ds.size.to_s + puts "train_ds =NOT feature_ds" + end + + + + puts "----- Check compound inchi -----" + match=0 + mismatch=0 + train_cmds.each { |i| + if feature_cmds.include?(i) + match = match + 1 + else + mismatch = mismatch + 1 + end + } + if mismatch > 0 + puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0 + puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!" + else + puts "All training compounds represented in feature dataset." unless mismatch > 0 + puts "match: #{match}; mismatch: #{mismatch}" + puts "OK!!!" + end + + + + feature_cmds.sort! + train_cmds.sort! + + if train_cmds == feature_cmds + puts "train_cmds == feature_cmds" + else + b = train_cmds - feature_cmds + #puts "d: '#{b}'" + puts "train_cmds: " + train_cmds.size.to_s + "; feature_cmds: " + feature_cmds.size.to_s + puts "train_cmds =NOT feature_cmds" + end + puts +end + + + + +ds = YAML::load_file("datasets_nestle.yaml") +ds.keys.each { |dataset| + ds[dataset].keys.each { |pc| + puts pc + check_ds(ds[dataset]["dataset"], ds[dataset][pc]) + } +} diff --git a/5x_cv/get_csv_versions.rb b/5x_cv/get_csv_versions.rb new file mode 100644 index 0000000..c09a46e --- /dev/null +++ b/5x_cv/get_csv_versions.rb @@ -0,0 +1,3 @@ +require 'yaml' +ds = YAML::load_file("datasets_nestle.yaml") +ds.keys.each { |d| puts d ; ds[d].keys.each {|t| puts " #{t}"; cmd = " curl -H 'accept:text/csv' #{ds[d][t]} > csv_file; mv -v --backup=numbered csv_file #{d}_#{t.gsub(/,/, '_')}.csv" unless t=="dataset"; puts cmd } } diff --git a/5x_cv/get_csv_versions.sh b/5x_cv/get_csv_versions.sh new file mode 100644 index 0000000..f3a29eb --- /dev/null +++ b/5x_cv/get_csv_versions.sh @@ -0,0 +1,20 @@ + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2902 > csv_file; mv -v --backup=numbered csv_file FHM_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1908 > csv_file; mv -v --backup=numbered csv_file FHM_geometrical.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1909 > csv_file; mv -v --backup=numbered csv_file FHM_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1910 > csv_file; mv -v --backup=numbered csv_file FHM_hybrid.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2903 > csv_file; mv -v --backup=numbered csv_file FHM_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2900 > csv_file; mv -v --backup=numbered csv_file MDD_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1905 > csv_file; mv -v --backup=numbered csv_file MDD_geometrical.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1906 > csv_file; mv -v --backup=numbered csv_file MDD_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1907 > csv_file; mv -v --backup=numbered csv_file MDD_hybrid.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2901 > csv_file; mv -v --backup=numbered csv_file MDD_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2904 > csv_file; mv -v --backup=numbered csv_file RAT_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1911 > csv_file; mv -v --backup=numbered csv_file RAT_geometrical.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1912 > csv_file; mv -v --backup=numbered csv_file RAT_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1913 > csv_file; mv -v --backup=numbered csv_file RAT_hybrid.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2905 > csv_file; mv -v --backup=numbered csv_file RAT_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2906 > csv_file; mv -v --backup=numbered csv_file MOU_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1914 > csv_file; mv -v --backup=numbered csv_file MOU_geometrical.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1915 > csv_file; mv -v --backup=numbered csv_file MOU_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/1916 > csv_file; mv -v --backup=numbered csv_file MOU_hybrid.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/2907 > csv_file; mv -v --backup=numbered csv_file MOU_constitutional.csv @@ -23,12 +23,14 @@ task :setup do @@classification_training_dataset = OpenTox::Dataset.create_from_csv_file("data/hamster_carcinogenicity.csv", @@subjectid) @@multinomial_training_dataset = OpenTox::Dataset.create_from_csv_file("data/ISSCAN-multi.csv", @@subjectid) @@regression_training_dataset = OpenTox::Dataset.create_from_csv_file("data/EPAFHM.csv", @@subjectid) + @@regression_feature_dataset = OpenTox::Dataset.create_from_csv_file("data/EPAFHM-constitutional.csv", @@subjectid) end task :teardown do @@classification_training_dataset.delete(@@subjectid) @@multinomial_training_dataset.delete(@@subjectid) @@regression_training_dataset.delete(@@subjectid) + @@regression_feature_dataset.delete(@@subjectid) OpenTox::Authorization.logout(@@subjectid) end diff --git a/algorithm.rb b/algorithm.rb index ceee1fa..6c6ba73 100644 --- a/algorithm.rb +++ b/algorithm.rb @@ -24,57 +24,6 @@ class AlgorithmTest < Test::Unit::TestCase end end - def test_p_sum_support - params = {} - params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2} - params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2" - params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2} - params[:weights] = { "c:c" => 0.95, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98} - params[:features] = (params[:compound_features_hits].keys + params[:training_compound_features_hits].keys).uniq - 2.times{ - params[:mode] = "min" - assert_in_delta OpenTox::Algorithm.p_sum_support(params), 12.48, 0.001 - params[:mode] = "max" - assert_in_delta OpenTox::Algorithm.p_sum_support(params), 18,2, 0.001 - } - end - - def test_tanimoto - params = {} - params[:training_compound] = "http://localhost/compound/InChI=1S/CH2O/c1-2/h1H2" - weights = { "c:c" => 0.9, "c:c:c" => 0.96, "O:N" => 0.97, "O:O" => 0.98} - params[:compound_features_hits] = { "c:c" => 10, "c:c:c" => 5, "O:N" => 2} - features_a = params[:compound_features_hits].keys - params[:training_compound_features_hits] = {"c:c" => 6, "c:c:c" => 3, "O:O" => 2} - features_b = params[:training_compound_features_hits].keys - 2.times{ - params[:nr_hits] = false - #test without weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, nil, params), 0.5, 0.0001 - - #test with weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.488188976377953, 0.0001 - - #test with weights and nr_hits true - params[:nr_hits] = true - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_b, weights, params), 0.467796610169492, 0.0001 - } - - params[:training_compound_features_hits] = {"c:c" => 2, "O:N" => 2} - features_c = params[:training_compound_features_hits].keys - - 2.times{ - params[:nr_hits] = false - #test without weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, nil, params), 0.666666666666667, 0.0001 - #test with weights - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.660777385159011, 0.0001 - - #test with weights and nr_hits true - params[:nr_hits] = true - assert_in_delta OpenTox::Algorithm::Similarity.tanimoto(features_a, features_c, weights, params), 0.237611181702668, 0.0001 - } - end =begin def test_clustering # Parameters diff --git a/cv/data/csv/FHM.csv b/cv/data/csv/FHM.csv new file mode 100644 index 0000000..a6c3c0f --- /dev/null +++ b/cv/data/csv/FHM.csv @@ -0,0 +1,536 @@ +STRUCTURE_SMILES,LOGINV_TD50_mmol +NC1=CC=C(CCCCCCCCCC)C=C1,3.57511836336893 +C=CC=O,3.51855737149769 +CCCCCCCCCCCCCN,3.48412615628832 +Cl\C(Cl)=C(Cl)/C(Cl)=C(Cl)\Cl,3.46218090492673 +[H][C@]1(CC2)C(C)(C)CCC[C@@](C)1[C@@H](CC[C@@](O)(C)C=C)C2=C,3.3840499483436 +C1=CC=CC=C1SSC2=CC=CC=C2,3.29756946355447 +CCCCCCCCCCCCN,3.25492520841794 +NC1=CC=C(CCCCCCCC)C=C1,3.2335871528876 +CCCCCCCCCC1=CC=C(O)C=C1,3.19722627470802 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\ No newline at end of file diff --git a/cv/data/csv/FHM_electronic_cpsa.csv b/cv/data/csv/FHM_electronic_cpsa.csv new file mode 100644 index 0000000..5d53192 --- /dev/null +++ b/cv/data/csv/FHM_electronic_cpsa.csv @@ -0,0 +1,568 @@ +SMILES,TPSA,WNSA-2,apol,bpol,RNCG,WNSA-3,RPSA,RNCS,THSA,RPCG,WPSA-1,RPCS,WPSA-2,nHBAcc,RHSA,WPSA-3,PNSA-1,nHBDon,PNSA-2,FNSA-1,FPSA-1,DPSA-1,PNSA-3,PPSA-1,FNSA-2,FPSA-2,DPSA-2,PPSA-2,WNSA-1,FNSA-3,FPSA-3,DPSA-3,PPSA-3 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\ No newline at end of file diff --git a/cv/data/csv/FHM_topological.csv b/cv/data/csv/FHM_topological.csv new file mode 100644 index 0000000..25c3fab --- /dev/null +++ b/cv/data/csv/FHM_topological.csv @@ -0,0 +1,536 @@ +SMILES,VPC-6,C3SP3,VCH-6,fragC,khs.dO,MDEO-22,WPOL,VCH-7,MDEN-22,VP-0,khs.sBr,ATSm1,MDEN-23,MDEC-22,VP-1,ATSm2,C1SP2,MDEC-23,VP-2,VAdjMat,MDEC-44,khs.aasC,ATSm3,C1SP3,MDEC-24,VP-3,SP-0,khs.sCH3,SCH-5,ATSm4,VP-4,SP-1,khs.sCl,SCH-6,Zagreb,ATSm5,VP-5,SP-2,khs.sssCH,khs.ssO,VP-6,topoShape,SP-3,ATSc1,SCH-7,VP-7,SP-4,ATSc2,Kier1,SP-5,khs.dsN,ATSc3,Kier2,C2SP2,VC-3,ATSp1,MDEN-11,MDEO-11,SP-6,Kier3,ATSc4,PetitjeanNumber,C2SP3,khs.ssS,khs.tN,VC-4,ATSp2,MDEC-11,MDEN-33,MDEN-12,ATSc5,SP-7,khs.dsCH,VC-5,MDEO-12,SC-3,MDEC-33,MDEC-12,MDEN-13,WPATH,khs.sF,VC-6,ATSp3,SPC-4,SC-4,MDEC-34,MDEC-13,ATSp4,khs.ssssC,khs.ddsN,SPC-5,SC-5,MDEC-14,ATSp5,khs.ssCH2,khs.sssN,khs.aaCH,TopoPSA,SPC-6,SC-6,khs.aaN,VPC-4,khs.ssNH,VCH-5,ECCEN,C3SP2,VPC-5,khs.dssC,khs.aaNH,khs.sOH,khs.sNH2 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\ No newline at end of file diff --git a/cv/data/csv/LOAEL.csv b/cv/data/csv/LOAEL.csv new file mode 100644 index 0000000..2a8db92 --- /dev/null +++ b/cv/data/csv/LOAEL.csv @@ -0,0 +1,568 @@ +STRUCTURE_SMILES,LOAEL_mg_kg_bw_day +COc1cc(c(C)cc1N=Nc2c(O)ccc3cc(ccc23)S(OH)(=O)=O)S(OH)(=O)=O,3739 +O1C(=O)C(O)=C(O)C1C(O)CO,3051 +C1(C)=C(C=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)C(=O)OC)C(C)(C)CCC1,500 +c(cccc1)(c1)C(C)C,462 +O=C(OCCCC)c(c(ccc1)C(=O)OCCCC)c1,600 +O=C(OCC)c(c(ccc1)C(=O)OCC)c1,4435 +O=C(OC(OC(OC1C)C)C1)C,125 +Oc(c(ccc1)C)c1C,6 +Oc(ccc(c1C)C)c1,14 +O=C(OCC)C=C,248 +c(cccc1)(c1)CC,408 +OCCO,250 +c(ccc1C(=O)OCC(=O)OCC)cc1C(=O)OCC,2500 +O=C,82 +O=C(O)C=CC(=O)O,1081 +OCC(O)CO,6883 +O=C(OC)c(ccc(O)c1)c1,1500 +O=C(OCCC)c(ccc(O)c1)c1,1500 +CC(CCC(=O)(O))C3CCC4C2CCC1CC(O)CCC1(C)C2CCC34C,500 +OC(C(CCC1C)C(C)C)C1,593 +O=C(O)C(=C)C,248 +O=C(OC)c(c(O)ccc1)c1,360 +Oc(cccc1)c1,344 +O=C(OCCC)c(cc(O)c(O)c1O)c1,864 +OCC(O)C1C(O)=C(O)C(=O)O1,1554 +c(cccc1)(c1)C=C,21 +O=Cc(occ1)c1,60 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+C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl,15 +CC1=NC=C(N1C)[N+](=O)[O-],15 +CCN1CCN(CC1)C2=C(C=C3C(=C2)N(C=C(C3=O)C(=O)O)C4CC4)F,26 +CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O,1 +COCC(=O)NC1=C(C=CC(=C1)SC2=CC=CC=C2)NC(=NC(=O)OC)NC(=O)OC,40 +CC1CCC2=C3N1C=C(C(=O)C3=CC(=C2)F)C(=O)O,400 +COC(=O)NC1=NC2=C(N1)C=C(C=C2)S(=O)C3=CC=CC=C3,2 +CC1(C2CC3C(C(=O)C(=C(N)O)C(=O)C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)N(C)C)O,150 +C1CN(CCN1CCCC(=O)C2=CC=C(C=C2)F)C3=CC=CC=N3,30 +CC(C)NCC(COC1=CC=CC2=C1C3=CC=CC=C3N2)O,7 +C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl,23 +CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O,2.5 +COP(=S)(OC)Oc1ccc(SC)c(C)c1,0.45 +C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl,8 +C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl,4 +CC(N(C)C)CN(C(=CC=C3)C1=C3)C(=CC=C2)C(=C2)S1,16.6 +C1=C(C=C(C(=C1Cl)N)Cl)[N+](=O)[O-],240 +c(cccc1)(c1)C=C,400 diff --git a/cv/data/csv/LOAEL_constitutional.csv b/cv/data/csv/LOAEL_constitutional.csv new file mode 100644 index 0000000..a2244bc --- /dev/null +++ b/cv/data/csv/LOAEL_constitutional.csv @@ -0,0 +1,440 @@ +SMILES,nB,AMR,nAtom,nAtomLC,nAtomLAC,nAromBond,nHBDon,ALogP,ALogp2,nAtomP,naAromAtom,nRotB,MLogP,XLogP +InChI%3D1S%2FC6H10N6%2Fc7-4-10-5%288%2912-6%2811-4%299-3-1-2-3%2Fh3H%2C1-2H2%2C%28H5%2C7%2C8%2C9%2C10%2C11%2C12%29,13,35.2267990112305,22,0,0,0,5,-0.613099992275238,0.375891596078873,9,0,1,1.46000003814697,2.08200001716614 +InChI%3D1S%2FC14H21N3O4%2Fc1-6-9%282%2915-13-11%2816%2818%2919%297-10%2814%283%2C4%295%298-12%2813%2917%2820%2921%2Fh7-9%2C15H%2C6H2%2C1-5H3,21,46.3053016662598,42,5,4,6,1,0.80680000782013,0.650926232337952,13,6,6,2.23000001907349,6.89300012588501 +InChI%3D1S%2FC8H8Cl3O3PS%2Fc1-12-15%2816%2C13-2%2914-8-4-6%2810%295%289%293-7%288%2911%2Fh3-4H%2C1-2H3,16,47.2397994995117,24,7,0,6,0,3.23790001869202,10.4839963912964,11,6,4,1.46000003814697,3.88100004196167 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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 new file mode 100644 index 0000000..44f13d6 --- /dev/null +++ b/cv/data/csv/LOAEL_topological.csv @@ -0,0 +1,440 @@ 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\ No newline at end of file diff --git a/cv/data/csv/MDD_electronic_cpsa.csv b/cv/data/csv/MDD_electronic_cpsa.csv new file mode 100644 index 0000000..18e61e2 --- /dev/null +++ b/cv/data/csv/MDD_electronic_cpsa.csv @@ -0,0 +1,1196 @@ +SMILES,nHBDon,RPCS,RHSA,FNSA-1,FNSA-2,FPSA-1,PNSA-1,PPSA-1,FPSA-2,PNSA-2,PPSA-2,WNSA-1,FNSA-3,FPSA-3,DPSA-1,PNSA-3,PPSA-3,TPSA,WNSA-2,DPSA-2,WNSA-3,DPSA-3,apol,bpol,THSA,RNCG,WPSA-1,nHBAcc,RPSA,RNCS,WPSA-2,RPCG,WPSA-3 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\ No newline at end of file diff --git a/cv/data/csv/MDD_topological.csv b/cv/data/csv/MDD_topological.csv new file mode 100644 index 0000000..8cbb2b1 --- /dev/null +++ b/cv/data/csv/MDD_topological.csv @@ -0,0 +1,1196 @@ 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\ No newline at end of file diff --git a/cv/data/csv/MOU_electronic_cpsa.csv b/cv/data/csv/MOU_electronic_cpsa.csv new file mode 100644 index 0000000..99212f2 --- /dev/null +++ b/cv/data/csv/MOU_electronic_cpsa.csv @@ -0,0 +1,402 @@ +SMILES,RNCG,THSA,WPSA-3,bpol,WNSA-3,DPSA-3,apol,RNCS,FNSA-1,RPSA,RPCG,RHSA,RPCS,FNSA-3,nHBAcc,PPSA-1,PNSA-1,FPSA-1,TPSA,FPSA-2,FPSA-3,WPSA-1,PPSA-3,PNSA-3,DPSA-1,WNSA-1 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\ No newline at end of file diff --git a/cv/data/csv/MOU_test.csv b/cv/data/csv/MOU_test.csv new file mode 100644 index 0000000..7ca8555 --- /dev/null +++ b/cv/data/csv/MOU_test.csv @@ -0,0 +1,41 @@ +SMILES,pTD50 +InChI%3D1S%2FC24H31Cl2N5O7%2Fc1-2-14-21%2835%2930-16%2810-32%2922%2836%2929-15%2812-6-4-3-5-7-12%298-18%2834%2927-17%2811-33%2924%2838%2931-9-13%2825%2919%2826%2920%2831%2923%2837%2928-14%2Fh3-7%2C13-17%2C19-20%2C32-33H%2C2%2C8-11H2%2C1H3%2C%28H%2C27%2C34%29%28H%2C28%2C37%29%28H%2C29%2C36%29%28H%2C30%2C35%29,4.38481637686251 +InChI%3D1S%2FC2H5NO%2Fc1-2%283%294%2Fh1H3%2C%28H2%2C3%2C4%29,1.29278018271655 +InChI%3D1S%2FC9H10O2%2Fc1-8%2810%2911-7-9-5-3-2-4-6-9%2Fh2-6H%2C7H2%2C1H3,2.01823370256042 +InChI%3D1S%2FC14H16N2%2Fc1-9-7-11%283-5-13%289%2915%2912-4-6-14%2816%2910%282%298-12%2Fh3-8H%2C15-16H2%2C1-2H3,3.87056411764216 +InChI%3D1S%2FC8H13NO2%2Fc1-9-5-3-4-7%286-9%298%2810%2911-2%2Fh4H%2C3%2C5-6H2%2C1-2H3,3.59427895059354 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\ No newline at end of file diff --git a/cv/data/csv/MOU_topological.csv b/cv/data/csv/MOU_topological.csv new file mode 100644 index 0000000..f648d86 --- /dev/null +++ b/cv/data/csv/MOU_topological.csv @@ -0,0 +1,402 @@ +SMILES,Kier3,VP-1,VC-3,SC-3,SCH-7,C1SP2,VP-2,VC-5,MDEO-11,C1SP3,VP-3,MDEC-22,MDEN-23,MDEC-23,ATSc1,VPC-4,MDEC-12,VP-4,ATSc2,ATSm1,TopoPSA,VPC-5,MDEC-13,MDEN-13,ATSc3,ATSm2,VPC-6,VP-6,ATSc4,fragC,ATSm3,VCH-6,C2SP2,ATSc5,VCH-7,ATSm4,C2SP3,ATSm5,Kier2,VP-0 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\ No newline at end of file diff --git a/cv/data/csv/RAT_electronic_cpsa.csv b/cv/data/csv/RAT_electronic_cpsa.csv new file mode 100644 index 0000000..876c6d7 --- /dev/null +++ b/cv/data/csv/RAT_electronic_cpsa.csv @@ -0,0 +1,512 @@ +SMILES,WPSA-3,TPSA,apol,bpol,RNCG,PPSA-3,DPSA-1,RNCS,RPSA,FNSA-1,RPCG,THSA,RPCS,FNSA-3,nHBAcc,RHSA,FPSA-1,FPSA-2,FPSA-3,PNSA-3 +InChI%3D1S%2FC19H27NO7%2Fc1-11-9-19%2812%282%2927-19%2917%2823%2926-14-6-8-20%284%297-5-13%2815%2814%2921%2910-25-16%2822%2918%2811%2C3%2924%2Fh5%2C11-12%2C14%2C24H%2C6-10H2%2C1-4H3,11.1058168411255,140.182739257812,58.1574096679688,40.1185874938965,0.141917109489441,19.0705699920654,274.479400634766,2.39669132232666,0.240717515349388,0.264336168766022,0.111287288367748,442.170989990234,0.0,-0.0675310268998146,8.0,0.759282469749451,0.735663831233978,1.96453440189362,0.0327473990619183,-39.3269424438477 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\ No newline at end of file diff --git a/cv/data/csv/RAT_test.csv b/cv/data/csv/RAT_test.csv new file mode 100644 index 0000000..27bd96d --- /dev/null +++ b/cv/data/csv/RAT_test.csv @@ -0,0 +1,52 @@ +SMILES,pTD50 +InChI%3D1S%2FC5H10N2O2%2Fc1-2-3-7%286-9%294-5-8%2Fh2%2C8H%2C1%2C3-5H2,5.42334666301952 +InChI%3D1S%2FC9H13ClN6%2Fc1-4-12-7-13-6%2810%2914-8%2815-7%2916-9%282%2C3%295-11%2Fh4H2%2C1-3H3%2C%28H2%2C12%2C13%2C14%2C15%2C16%29,4.58005920868396 +InChI%3D1S%2FC13H14O5%2Fc1-5-7%283%2918-4-8-9%285%296%282%2911%2814%2910%2812%288%2915%2913%2816%2917%2Fh4-5%2C7%2C16-17H%2C1-3H3,4.52446780256691 +InChI%3D1S%2FC5H10N2O3%2Fc1-3-7%286-9%295%288%2910-4-2%2Fh3-4H2%2C1-2H3,6.20861434246114 +InChI%3D1S%2FC7H7FN2O%2Fc1-10%289-11%297-4-2-6%288%293-5-7%2Fh2-5H%2C1H3,5.78138024574518 +InChI%3D1S%2FC14H9Cl5%2Fc15-11-5-1-9%282-6-11%2913%2814%2817%2C18%2919%2910-3-7-12%2816%298-4-10%2Fh1-8%2C13H,3.62171420741785 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\ No newline at end of file diff --git a/cv/data/csv/RAT_topological.csv b/cv/data/csv/RAT_topological.csv new file mode 100644 index 0000000..d707006 --- /dev/null +++ b/cv/data/csv/RAT_topological.csv @@ -0,0 +1,512 @@ +SMILES,ATSc5,ATSm5,C1SP3,VP-3,SC-4,fragC,SP-3,SCH-5,SC-5,SCH-6,SCH-7,ECCEN,VCH-5,SP-6,ATSp1,VCH-6,ATSp2,VCH-7,MDEC-22,MDEC-33,MDEC-11,MDEN-23,ATSc1,TopoPSA,ATSm1,MDEC-23,MDEO-11,Kier1,MDEC-12,Kier2,ATSc2,VC-3,MDEC-13,ATSm2,MDEO-12,SPC-6,ATSc3,Kier3,SC-3,VPC-4,ATSm3,ATSc4,C1SP2,ATSm4,VC-5 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\ No newline at end of file diff --git a/cv/data/datasets.yaml b/cv/data/datasets.yaml new file mode 100644 index 0000000..f922ea4 --- /dev/null +++ b/cv/data/datasets.yaml @@ -0,0 +1,44 @@ +{ + + "MDD": { + "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/6248", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/6250", + "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/6249", + "topological": "http://toxcreate3.in-silico.ch:8086/dataset/6251" + }, + + "FHM": { + "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/6244", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/6246", + "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/6245", + "topological": "http://toxcreate3.in-silico.ch:8086/dataset/6247" + }, + + "RAT": { + "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/6258", + "training": "http://toxcreate3.in-silico.ch:8086/dataset/6263", + "test": "http://toxcreate3.in-silico.ch:8086/dataset/6261", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/6260", # A + "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/6259", # A + "topological": "http://toxcreate3.in-silico.ch:8086/dataset/6262" # N + }, + + "MOU": { + "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/6252", + "training": "http://toxcreate3.in-silico.ch:8086/dataset/6257", + "test": "http://toxcreate3.in-silico.ch:8086/dataset/6255", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/6254", # A + "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/6253", # ALL + "topological": "http://toxcreate3.in-silico.ch:8086/dataset/6256" # A + }, + + "LOAEL": { + "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/6576", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/6714", + "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/6716", + "topological": "http://toxcreate3.in-silico.ch:8086/dataset/6717" + } + + + +} diff --git a/cv/data/sources/Bercu_CPDB_9March2010_mouseTD50_mgkg_pTD50.xls b/cv/data/sources/Bercu_CPDB_9March2010_mouseTD50_mgkg_pTD50.xls Binary files differnew file mode 100644 index 0000000..31fc047 --- /dev/null +++ b/cv/data/sources/Bercu_CPDB_9March2010_mouseTD50_mgkg_pTD50.xls diff --git a/cv/data/sources/Bercu_CPDB_9March2010_ratTD50_mgkg_pTD50.xls b/cv/data/sources/Bercu_CPDB_9March2010_ratTD50_mgkg_pTD50.xls Binary files differnew file mode 100644 index 0000000..9a5df64 --- /dev/null +++ b/cv/data/sources/Bercu_CPDB_9March2010_ratTD50_mgkg_pTD50.xls diff --git a/cv/data/sources/CPDBAS_v5d_1547_20Nov2008_nostructures.xls b/cv/data/sources/CPDBAS_v5d_1547_20Nov2008_nostructures.xls Binary files differnew file mode 100644 index 0000000..a2bf88a --- /dev/null +++ b/cv/data/sources/CPDBAS_v5d_1547_20Nov2008_nostructures.xls diff --git a/cv/data/sources/Data_sources.txt b/cv/data/sources/Data_sources.txt new file mode 100644 index 0000000..b40de41 --- /dev/null +++ b/cv/data/sources/Data_sources.txt @@ -0,0 +1,16 @@ +CPDBAS_v5d_1547_20Nov2008_nostructures.xls +from: +http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html + +Bercu_CPDB_9March2010_mouseTD50_mgkg_pTD50.xls initially mmc1.xls +Bercu_CPDB_9March2010_ratTD50_mgkg_pTD50.xls initially mmc1.xls +both from: +http://www.sciencedirect.com/science/article/pii/S0273230010000589 + +FDAMDD_v3b_1216_15Feb2008_nostructures.xls +from: +http://www.epa.gov/ncct/dsstox/sdf_fdamdd.html + +EPAFHM_v4b_617_15Feb2008_nostructures.xls +from: +http://www.epa.gov/ncct/dsstox/sdf_epafhm.html diff --git a/cv/data/sources/EPAFHM_v4b_617_15Feb2008_nostructures.xls b/cv/data/sources/EPAFHM_v4b_617_15Feb2008_nostructures.xls Binary files differnew file mode 100644 index 0000000..cc5102d --- /dev/null +++ b/cv/data/sources/EPAFHM_v4b_617_15Feb2008_nostructures.xls diff --git a/cv/data/sources/FDAMDD_v3b_1216_15Feb2008_nostructures.xls b/cv/data/sources/FDAMDD_v3b_1216_15Feb2008_nostructures.xls Binary files differnew file mode 100644 index 0000000..e80d144 --- /dev/null +++ b/cv/data/sources/FDAMDD_v3b_1216_15Feb2008_nostructures.xls diff --git a/cv/data/utils/check_datasets_inchi_equality.rb b/cv/data/utils/check_datasets_inchi_equality.rb new file mode 100644 index 0000000..75d6558 --- /dev/null +++ b/cv/data/utils/check_datasets_inchi_equality.rb @@ -0,0 +1,98 @@ +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +@subjectid = nil + + + +def check_ds(t_ds_uri, f_ds_uri) + puts t_ds_uri + puts f_ds_uri + + regression_training_dataset = OpenTox::Dataset.find(t_ds_uri, @subjectid) + regression_feature_dataset = OpenTox::Dataset.find(f_ds_uri, @subjectid) + + train_ds = regression_training_dataset.data_entries.keys + train_cmds = regression_training_dataset.compounds + feature_ds = regression_feature_dataset.data_entries.keys + feature_cmds = regression_feature_dataset.compounds + + puts "----- Check activity inchi -----" + match=0 + mismatch=0 + train_ds.each { |i| + if feature_ds.include?(i) + match = match + 1 + else + mismatch = mismatch + 1 + end + } + if mismatch > 0 + puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0 + puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!" + else + puts "All training compounds represented in feature dataset." unless mismatch > 0 + puts "match: #{match}; mismatch: #{mismatch}" + puts "OK!!!" + end + + train_ds.sort! + feature_ds.sort! + + if train_ds == feature_ds + puts "train_ds == feature_ds" + else + a = train_ds - feature_ds + #puts "d: '#{a}'" + puts "train_ds: " + train_ds.size.to_s + "; feature_ds: "+ feature_ds.size.to_s + puts "train_ds =NOT feature_ds" + end + + + + puts "----- Check compound inchi -----" + match=0 + mismatch=0 + train_cmds.each { |i| + if feature_cmds.include?(i) + match = match + 1 + else + mismatch = mismatch + 1 + end + } + if mismatch > 0 + puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0 + puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!" + else + puts "All training compounds represented in feature dataset." unless mismatch > 0 + puts "match: #{match}; mismatch: #{mismatch}" + puts "OK!!!" + end + + + + feature_cmds.sort! + train_cmds.sort! + + if train_cmds == feature_cmds + puts "train_cmds == feature_cmds" + else + b = train_cmds - feature_cmds + #puts "d: '#{b}'" + puts "train_cmds: " + train_cmds.size.to_s + "; feature_cmds: " + feature_cmds.size.to_s + puts "train_cmds =NOT feature_cmds" + end + puts +end + + + + +ds = YAML::load_file("../datasets.yaml") +ds.keys.each { |dataset| + ds[dataset].keys.each { |pc| + puts pc + check_ds(ds[dataset]["dataset"], ds[dataset][pc]) + } +} diff --git a/cv/data/utils/get_csv.sh b/cv/data/utils/get_csv.sh new file mode 100755 index 0000000..0ca8129 --- /dev/null +++ b/cv/data/utils/get_csv.sh @@ -0,0 +1,20 @@ + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5263 > csv_file; mv -v --backup=numbered csv_file FHM_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5765 > csv_file; mv -v --backup=numbered csv_file FHM_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5262 > csv_file; mv -v --backup=numbered csv_file FHM_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5266 > csv_file; mv -v --backup=numbered csv_file FHM_constitutional_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5478 > csv_file; mv -v --backup=numbered csv_file MDD_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5766 > csv_file; mv -v --backup=numbered csv_file MDD_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5475 > csv_file; mv -v --backup=numbered csv_file MDD_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5479 > csv_file; mv -v --backup=numbered csv_file MDD_constitutional_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/6230 > csv_file; mv -v --backup=numbered csv_file RAT_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/6243 > csv_file; mv -v --backup=numbered csv_file RAT_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5465 > csv_file; mv -v --backup=numbered csv_file RAT_training.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/6226 > csv_file; mv -v --backup=numbered csv_file RAT_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5464 > csv_file; mv -v --backup=numbered csv_file RAT_constitutional_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5466 > csv_file; mv -v --backup=numbered csv_file RAT_test.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/6231 > csv_file; mv -v --backup=numbered csv_file MOU_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/6229 > csv_file; mv -v --backup=numbered csv_file MOU_topological.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5467 > csv_file; mv -v --backup=numbered csv_file MOU_training.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5459 > csv_file; mv -v --backup=numbered csv_file MOU_constitutional.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5461 > csv_file; mv -v --backup=numbered csv_file MOU_constitutional_electronic_cpsa.csv + curl -H 'accept:text/csv' http://toxcreate3.in-silico.ch:8086/dataset/5468 > csv_file; mv -v --backup=numbered csv_file MOU_test.csv diff --git a/cv/data/utils/get_csv_versions.rb b/cv/data/utils/get_csv_versions.rb new file mode 100644 index 0000000..4fa360f --- /dev/null +++ b/cv/data/utils/get_csv_versions.rb @@ -0,0 +1,3 @@ +require 'yaml' +ds = YAML::load_file("../datasets.yaml") +ds.keys.each { |d| puts d ; ds[d].keys.each {|t| puts " #{t}"; cmd = " curl -H 'accept:text/csv' #{ds[d][t]} > csv_file; mv -v --backup=numbered csv_file #{d}_#{t.gsub(/,/, '_')}.csv" unless t=="dataset"; puts cmd } } diff --git a/cv/scripts/CV_ds_pctype_algo_rseed.rb b/cv/scripts/CV_ds_pctype_algo_rseed.rb new file mode 100644 index 0000000..36adb6f --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed.rb @@ -0,0 +1,58 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first + + +# Ready +cv_args = {} +cv_args[:dataset_uri] = ds_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:80XX/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +cv_args[:stratified] = false +cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +#cv = OpenTox::Crossvalidation.create(cv_args).uri +#puts cv + +#cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri +#puts cvr diff --git a/cv/scripts/factors_config b/cv/scripts/factors_config new file mode 100644 index 0000000..83bb54c --- /dev/null +++ b/cv/scripts/factors_config @@ -0,0 +1,17 @@ +#Dataset pc_type prediction_algorithm +MDD constitutional local_svm_regression +MDD electronic,cpsa local_svm_regression +MDD topological local_svm_regression +MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU nil local_svm_regression diff --git a/cv/scripts/wrapper_pc_cv.sh b/cv/scripts/wrapper_pc_cv.sh new file mode 100755 index 0000000..ed13122 --- /dev/null +++ b/cv/scripts/wrapper_pc_cv.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Wrapper Skript for CV +# Reads factors_config, ../data/datasets.yaml and performs cv's +# Andreas Maunz, David Vorgrimmler, 2012 + +if [ $# -lt 1 ]; then + echo "Usage: $0 factors" + exit +fi + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../data/datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +CV="CV_ds_pctype_algo_rseed.rb" +FACTORS="$1" + +# Don't start when running +while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done + +LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv.log" +rm "$LOGFILE" >/dev/null 2>&1 + + +cat $FACTORS | while read factor; do + if ! [[ "$factor" =~ "#" ]]; then # allow comments + for r_seed in 1 #2 3 4 5 + do + factor="$factor $r_seed" + echo "${THIS_DATE}: $factor" >> $LOGFILE>&1 + echo "ruby $CV $factor" >> $LOGFILE 2>&1 + ruby $CV $factor >> $LOGFILE 2>&1 + echo >> $LOGFILE 2>&1 + done + fi +done + diff --git a/data/EPAFHM-constitutional.csv b/data/EPAFHM-constitutional.csv new file mode 100644 index 0000000..369b3c1 --- /dev/null +++ b/data/EPAFHM-constitutional.csv @@ -0,0 +1,581 @@ +SMILES,nAtom,LipinskiFailures,nAromBond,nAtomLC,ALogP,nAtomLAC,nHBDon,nAtomP,nRotB,MLogP,naAromAtom,AMR,ALogp2,XLogP,nB,LipinksiFailures +InChI%3D1S%2FC10H9NO6%2Fc1-16-9%2812%296-3-4-7%2810%2813%2917-2%298%285-6%2911%2814%2915%2Fh3-5H%2C1-2H3, 26.0, 0.0, 6.0, 4.0, -0.0241999998688698, 0.0, 0.0, 15.0, 5.0, 1.78999996185303, 6.0, 26.8626003265381, 0.000585640023928136, 1.79900002479553, 17.0, +InChI%3D1S%2FC12H17NO%2Fc1-4-13%285-2%2912%2814%2911-8-6-7-10%283%299-11%2Fh6-9H%2C4-5H2%2C1-3H3, 31.0, 0.0, 6.0, 7.0, 0.712599992752075, 2.0, 0.0, 9.0, 4.0, 2.55999994277954, 6.0, 32.9245986938477, 0.507798731327057, 3.76699995994568, 14.0, +InChI%3D1S%2FC5H4ClNO%2Fc6-4-1-2-5%288%297-3-4%2Fh1-3H%2C%28H%2C7%2C8%29, 12.0, 0.0, 6.0, 0.0, 0.284000009298325, 0.0, 1.0, 7.0, 0.0, 1.67999994754791, 6.0, 8.18019962310791, 0.080655999481678, 1.03299999237061, 8.0, +InChI%3D1S%2FC8H8Cl2%2Fc9-5-7-1-2-8%286-10%294-3-7%2Fh1-4H%2C5-6H2, 18.0, 0.0, 6.0, 2.0, 1.51180005073547, 0.0, 0.0, 6.0, 2.0, 2.11999988555908, 6.0, 20.6555995941162, 2.28553915023804, 3.7039999961853, 10.0, +InChI%3D1S%2FC9H11N%2Fc1-2-8-10-9-6-4-3-5-7-9%2Fh2-7%2C10H%2C1%2C8H2, 21.0, 0.0, 6.0, 4.0, 0.298700004816055, 3.0, 1.0, 7.0, 3.0, 2.33999991416931, 6.0, 18.1594009399414, 0.0892216935753822, 2.98200011253357, 10.0, +InChI%3D1S%2FC7H8O%2Fc1-6-2-4-7%288%295-3-6%2Fh2-5%2C8H%2C1H3, 16.0, 0.0, 6.0, 0.0, 0.181700006127357, 0.0, 1.0, 7.0, 0.0, 2.11999988555908, 6.0, 8.06669998168945, 0.033014889806509, 2.36700010299683, 8.0, 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\ No newline at end of file @@ -28,8 +28,13 @@ class DatasetTest < Test::Unit::TestCase #@new_dataset.delete end -=begin -=end +# def test_get_pc +# ds_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"], {:file => File.new("data/EPAFHM.csv")} ,{:accept => "text/uri-list", :subjectid => @@subjectid}).to_s.chomp +# puts "DS: #{ds_uri}" +# fds_uri = OpenTox::Algorithm.pc_descriptors( { :dataset_uri => ds_uri, :pc_type => "constitutional" } ) +# puts "FDS: #{fds_uri}" +# end + def test_save_external @dataset = OpenTox::Dataset.find "http://apps.ideaconsult.net:8080/ambit2/dataset/2698" @@ -220,9 +225,7 @@ class DatasetTest < Test::Unit::TestCase end end -=begin -=end - + def test_merge() #upload dataset1 = OpenTox::Dataset.create_from_csv_file(File.new("data/hamster_carcinogenicity.csv").path, @@subjectid) @@ -54,182 +54,95 @@ class LazarTest < Test::Unit::TestCase FileUtils.cp f, reference FileUtils.rm f end - @predictions.each do |dataset| - dataset.delete(@@subjectid) - end + #@predictions.each do |dataset| + # dataset.delete(@@subjectid) + #end @model.delete(@@subjectid) end -=begin -=end - def test_create_regression_model - create_model :dataset_uri => @@regression_training_dataset.uri - predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") - assert_in_delta @predictions.first.value(@compounds.first), 0.517, 0.1 - assert_equal 0.61.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3) - assert_equal 253, @predictions.first.neighbors(@compounds.first).size - cleanup - end - - def test_create_regression_prop_model - create_model :dataset_uri => @@regression_training_dataset.uri, :local_svm_kernel => "propositionalized" - predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") - assert_equal 0.61.round_to(3), @predictions.first.confidence(@compounds.first).round_to(3) - assert_equal 253, @predictions.first.neighbors(@compounds.first).size - assert_equal 131, @model.features.size - cleanup - end - - def test_classification_model - create_model :dataset_uri => @@classification_training_dataset.uri - # single prediction - predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") - # dataset activity - predict_compound OpenTox::Compound.from_smiles("CNN") - # dataset prediction - predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid) - # assertions - # single prediction - assert_equal "false", @predictions[0].value(@compounds[0]) - assert_equal 0.3383.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4) - assert_equal 16, @predictions[0].neighbors(@compounds[0]).size - # dataset activity - assert !@predictions[1].measured_activities(@compounds[1]).empty? - assert_equal "true", @predictions[1].measured_activities(@compounds[1]).first.to_s - assert @predictions[1].value(@compounds[1]).nil? - # dataset prediction - c = OpenTox::Compound.from_smiles("CC(=Nc1ccc2c(c1)Cc1ccccc21)O") - assert_equal nil, @predictions[2].value(c) - assert_equal "true", @predictions[2].measured_activities(c).first.to_s - c = OpenTox::Compound.from_smiles("c1ccccc1NN") - assert_equal "false", @predictions[2].value(c) - assert_equal 0.3383.round_to(4) , @predictions[2].confidence(c).round_to(4) - # model - assert_equal 41, @model.features.size - cleanup - end - - def test_classification_svm_model - - create_model :dataset_uri => @@classification_training_dataset.uri, :prediction_algorithm => "local_svm_classification" - predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") - predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid) - - assert_equal "false", @predictions[0].value(@compounds[0]) - assert_equal 0.5587.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4) - assert_equal 16, @predictions[0].neighbors(@compounds[0]).size - - c = OpenTox::Compound.from_smiles("c1ccccc1NN") - assert_equal 4, @predictions[1].compounds.size - assert_equal "false", @predictions[1].value(c) - - assert_equal 41, @model.features.size - cleanup - end - - def test_classification_svm_prop_model - - create_model :dataset_uri => @@classification_training_dataset.uri, :prediction_algorithm => "local_svm_classification", :local_svm_kernel => "propositionalized" - predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") - predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid) - - assert_equal "false", @predictions[0].value(@compounds[0]) - #assert_equal 0.2938.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4) - assert_equal 0.5587.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4) - assert_equal 16, @predictions[0].neighbors(@compounds[0]).size - c = OpenTox::Compound.from_smiles("c1ccccc1NN") - assert_equal 4, @predictions[1].compounds.size - assert_equal "false", @predictions[1].value(c) +## Regression +def test_create_regression_svm_pc_model + create_model :dataset_uri => @@regression_training_dataset.uri, :feature_dataset_uri => @@regression_feature_dataset.uri, :pc_type => "constitutional" + predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") + assert_in_delta @predictions.first.value(@compounds.first), 7.8, 0.1 + assert_equal 0.603, @predictions.first.confidence(@compounds.first).round_to(3) + assert_equal 74, @predictions.first.neighbors(@compounds.first).size + cleanup +end - assert_equal 41, @model.features.size - cleanup - end -# def test_regression_mlr_prop_model -# create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop" -# predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") -# assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3) -# assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3) -# assert_equal 253, @predictions.first.neighbors(@compounds.first).size -# assert_equal 131, @model.features.size -# end +##Classification +def test_classification_model + create_model :dataset_uri => @@classification_training_dataset.uri + # single prediction + predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") + # dataset activity + predict_compound OpenTox::Compound.from_smiles("CNN") + # dataset prediction + predict_dataset OpenTox::Dataset.create_from_csv_file("data/multicolumn.csv", @@subjectid) + # assertions + # single prediction + assert_equal "false", @predictions[0].value(@compounds[0]) + assert_equal 0.3383.round_to(4), @predictions[0].confidence(@compounds[0]).round_to(4) + assert_equal 16, @predictions[0].neighbors(@compounds[0]).size + # dataset activity + assert !@predictions[1].measured_activities(@compounds[1]).empty? + assert_equal "true", @predictions[1].measured_activities(@compounds[1]).first.to_s + assert @predictions[1].value(@compounds[1]).nil? + # dataset prediction + c = OpenTox::Compound.from_smiles("CC(=Nc1ccc2c(c1)Cc1ccccc21)O") + assert_equal nil, @predictions[2].value(c) + assert_equal "true", @predictions[2].measured_activities(c).first.to_s + c = OpenTox::Compound.from_smiles("c1ccccc1NN") + assert_equal "false", @predictions[2].value(c) + assert_equal 0.3383 , @predictions[2].confidence(c).round_to(4) + # model + assert_equal 41, @model.features.size + cleanup +end + +# DISABLED TEMPORARILY +# def test_ambit_classification_model # -# def test_regression_mlr_prop_conf_stdev -# create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :conf_stdev => "true" -# predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") -# assert_equal 0.154, @predictions.first.confidence(@compounds.first).round_to(3) -# assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3) -# assert_equal 253, @predictions.first.neighbors(@compounds.first).size -# assert_equal 131, @model.features.size -# end +# # create model +# dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=400" +# feature_uri ="http://apps.ideaconsult.net:8080/ambit2/feature/2153" +# #model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri}).to_s +# #lazar = OpenTox::Model::Lazar.find model_uri +# model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri, :subjectid => @@subjectid}).to_s +# validate_owl model_uri,@@subjectid +# lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid +# puts lazar.features.size +# assert_equal lazar.features.size, 1874 +# #puts "Model: #{lazar.uri}" +# #puts lazar.features.size # +# # single prediction +# compound = OpenTox::Compound.from_smiles("c1ccccc1NN") +# #prediction_uri = lazar.run(:compound_uri => compound.uri) +# #prediction = OpenTox::LazarPrediction.find(prediction_uri) +# prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) +# prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid) +# #puts "Prediction: #{prediction.uri}" +# #puts prediction.value(compound) +# assert_equal prediction.value(compound), "3.0" +# #puts @prediction.confidence(compound).round_to(4) +# #assert_equal @prediction.confidence(compound).round_to(4), 0.3005.round_to(4) +# #assert_equal @prediction.neighbors(compound).size, 15 +# #@prediction.delete(@@subjectid) # -# def test_regression_mlr_prop_weighted_model -# create_model :dataset_uri => @@regression_training_dataset.uri, :prediction_algorithm => "local_mlr_prop", :nr_hits => "true" -# predict_compound OpenTox::Compound.from_smiles("c1ccccc1NN") -# assert_equal 0.453, @predictions.first.confidence(@compounds.first).round_to(3) -# assert_equal 0.265, @predictions.first.value(@compounds.first).round_to(3) -# assert_equal 253, @predictions.first.neighbors(@compounds.first).size -# assert_equal 131, @model.features.size -# end - - def test_conf_stdev - params = {:sims => [0.6,0.72,0.8], :acts => [1,1,1], :neighbors => [1,1,1], :conf_stdev => true} # stdev = 0 - params2 = {:sims => [0.6,0.7,0.8], :acts => [3.4,2,0.6], :neighbors => [1,1,1,1], :conf_stdev => true } # stev ~ 1.4 - params3 = {:sims => [0.6,0.7,0.8], :acts => [1,1,1], :neighbors => [1,1,1], } - params4 = {:sims => [0.6,0.7,0.8], :acts => [3.4,2,0.6], :neighbors => [1,1,1] } - 2.times { - assert_in_delta OpenTox::Algorithm::Neighbors::get_confidence(params), 0.72, 0.0001 - assert_in_delta OpenTox::Algorithm::Neighbors::get_confidence(params2), 0.172617874759125, 0.0001 - assert_in_delta OpenTox::Algorithm::Neighbors::get_confidence(params3), 0.7, 0.0001 - assert_in_delta OpenTox::Algorithm::Neighbors::get_confidence(params4), 0.7, 0.0001 - } - end - - -=begin - def test_ambit_classification_model - - # create model - dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=400" - feature_uri ="http://apps.ideaconsult.net:8080/ambit2/feature/21573" - #model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri}).to_s - #lazar = OpenTox::Model::Lazar.find model_uri - model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => dataset_uri, :prediction_feature => feature_uri, :subjectid => @@subjectid}).to_s - validate_owl model_uri,@@subjectid - lazar = OpenTox::Model::Lazar.find model_uri, @@subjectid - puts lazar.features.size - assert_equal lazar.features.size, 1874 - #puts "Model: #{lazar.uri}" - #puts lazar.features.size - - # single prediction - compound = OpenTox::Compound.from_smiles("c1ccccc1NN") - #prediction_uri = lazar.run(:compound_uri => compound.uri) - #prediction = OpenTox::LazarPrediction.find(prediction_uri) - prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) - prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid) - #puts "Prediction: #{prediction.uri}" - #puts prediction.value(compound) - assert_equal prediction.value(compound), "3.0" - #puts @prediction.confidence(compound).round_to(4) - #assert_equal @prediction.confidence(compound).round_to(4), 0.3005.round_to(4) - #assert_equal @prediction.neighbors(compound).size, 15 - #@prediction.delete(@@subjectid) - - # dataset activity - #compound = OpenTox::Compound.from_smiles("CNN") - #prediction_uri = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) - #@prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid - #assert !@prediction.measured_activities(compound).empty? - #assert_equal @prediction.measured_activities(compound).first, true - #assert @prediction.value(compound).nil? - #@prediction.delete(@@subjectid) - - # dataset prediction - #@lazar.delete(@@subjectid) - end -=end +# # dataset activity +# #compound = OpenTox::Compound.from_smiles("CNN") +# #prediction_uri = @lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid) +# #@prediction = OpenTox::LazarPrediction.find prediction_uri, @@subjectid +# #assert !@prediction.measured_activities(compound).empty? +# #assert_equal @prediction.measured_activities(compound).first, true +# #assert @prediction.value(compound).nil? +# #@prediction.delete(@@subjectid) +# +# # dataset prediction +# #@lazar.delete(@@subjectid) +# end end diff --git a/transform.rb b/transform.rb index a00f87d..5754393 100644 --- a/transform.rb +++ b/transform.rb @@ -2,54 +2,207 @@ require 'rubygems' require 'opentox-ruby' require 'test/unit' +class Float + def round_to(x) + (self * 10**x).round.to_f / 10**x + end +end class TransformTest < Test::Unit::TestCase -def test_mlr - 2.times { - n_prop = [ [1,1], [2,2], [3,3] ] # erste WH - acts = [ 3,2,3 ] # should yield a constant y=2.8 - sims = [ 4,2,4 ] # move constant closer to 3.0 - q_prop = [0.5,0.5] # extrapolation - params={:n_prop => n_prop, :q_prop => q_prop, :sims => sims, :acts => acts} - - prediction = OpenTox::Algorithm::Neighbors.mlr(params) - assert_in_delta prediction, 2.8, 1.0E-10 # small deviations, don't know why - - q_prop = [1.5,1.5] # interpolation - prediction = OpenTox::Algorithm::Neighbors.mlr(params) - assert_in_delta prediction, 2.8, 1.0E-10 # small deviations, don't know why - } -end + #def test_mlr + # 2.times { + # n_prop = [ [1,1], [2,2], [3,3] ] # erste WH + # acts = [ 3,2,3 ] # should yield a constant y=2.8 + # sims = [ 4,2,4 ] # move constant closer to 3.0 + # q_prop = [0.5,0.5] # extrapolation + # params={:n_prop => n_prop, :q_prop => q_prop, :sims => sims, :acts => acts} + # + # prediction = OpenTox::Algorithm::Neighbors.mlr(params) + # assert_in_delta prediction, 2.8, 1.0E-10 # small deviations, don't know why + # + # q_prop = [1.5,1.5] # interpolation + # prediction = OpenTox::Algorithm::Neighbors.mlr(params) + # assert_in_delta prediction, 2.8, 1.0E-10 # small deviations, don't know why + # } + #end + + def test_pca + + d = GSL::Matrix.alloc([1.0, -5, 1.1, 2.0, -5, 1.9, 3.0, -5, 3.3], 3, 3) # 2nd col is const -5, gets removed + rd = GSL::Matrix.alloc([1.0, 1.1, 1.9, 2.0, 3.1, 3.2], 3, 2) + td = GSL::Matrix.alloc([-1.4142135623731, -0.14142135623731, 1.5556349186104],3,1) + ev = GSL::Matrix.alloc([0.707106781186548, 0.707106781186548], 2, 1) + + # Lossy + 2.times do # repeat to ensure idempotency + pca = OpenTox::Transform::PCA.new(d, 0.05) + assert_equal pca.data_matrix, d + assert_equal pca.data_transformed_matrix, td + assert_equal pca.transform(d), td + assert_equal pca.eigenvector_matrix, ev + assert_equal pca.restore, rd + end + + rd = GSL::Matrix.alloc([1.0, 1.1, 2.0, 1.9, 3.0, 3.3], 3, 2) # 2nd col of d is const -5, gets removed on rd + td = GSL::Matrix.alloc([-1.4142135623731, -7.84962372879505e-17, -0.14142135623731, -0.14142135623731, 1.5556349186104, 0.141421356237309],3,2) + ev = GSL::Matrix.alloc([0.707106781186548, -0.707106781186548, 0.707106781186548, 0.707106781186548], 2, 2) + + # Lossless + 2.times do + pca = OpenTox::Transform::PCA.new(d, 0.0) + assert_equal pca.data_matrix, d + assert_equal pca.data_transformed_matrix, td + assert_equal pca.transform(d), td + assert_equal pca.eigenvector_matrix, ev + assert_equal pca.restore, rd + end + + rd = GSL::Matrix.alloc([1.0, 1.1, 1.9, 2.0, 3.1, 3.2], 3, 2) + td = GSL::Matrix.alloc([-1.4142135623731, -0.14142135623731, 1.5556349186104],3,1) + ev = GSL::Matrix.alloc([0.707106781186548, 0.707106781186548], 2, 1) + # Lossy, but using maxcols constraint + 2.times do + pca = OpenTox::Transform::PCA.new(d, 0.0, 1) # 1 column + assert_equal pca.data_matrix, d + assert_equal pca.data_transformed_matrix, td + assert_equal pca.transform(d), td + assert_equal pca.eigenvector_matrix, ev + assert_equal pca.restore, rd + end + + + end + + def test_svd + + m = GSL::Matrix[ + [5,5,0,5], + [5,0,3,4], + [3,4,0,3], + [0,0,5,3], + [5,4,4,5], + [5,4,5,5] + ] + + + foo = GSL::Matrix[[5,5,3,0,5,5]] + bar = GSL::Matrix[[5,4,5,5]] + + + + # AutoScale (mean and center) to improve on representation + nr_cases, nr_features = m.size1, m.size2 + (0..nr_features-1).each { |i| + autoscaler = OpenTox::Transform::AutoScale.new(m.col(i)) + m.col(i)[0..nr_cases-1] = autoscaler.vs + bar.col(i)[0..0] = autoscaler.transform bar.col(i) + } + autoscaler = OpenTox::Transform::AutoScale.new(foo.transpose.col(0)) + foo = GSL::Matrix[autoscaler.vs] + + + #puts + #puts m.to_a.collect { |r| r.collect{ |v| sprintf("%.2f", v) }.join(", ") }.join("\n") + #puts + #puts foo.to_a.collect { |r| r.collect{ |v| sprintf("%.2f", v) }.join(", ") }.join("\n") + #puts + #puts bar.to_a.collect { |r| r.collect{ |v| sprintf("%.2f", v) }.join(", ") }.join("\n") + + + + # run SVD + svd = OpenTox::Algorithm::Transform::SVD.new m, 0.2 + #puts + #puts svd.restore.to_a.collect { |r| r.collect{ |v| sprintf("%.2f", v) }.join(", ") }.join("\n") + + + #puts + #puts svd.data_transformed_matrix.to_a.collect { |r| r.collect{ |v| sprintf("%.2f", v) }.join(", ") }.join("\n") + + # instance transform + bar = svd.transform bar # alias for svd.transform_instance bar + sim = [] + svd.uk.each_row { |x| + sim << OpenTox::Algorithm::Similarity.cosine_num(x,bar.row(0)) + } + + # # # NO AUTOSCALE + #assert_equal sim[0].round_to(3), 0.346 + #assert_equal sim[1].round_to(3), 0.966 + #assert_equal sim[2].round_to(3), 0.282 + #assert_equal sim[3].round_to(3), 0.599 + #assert_equal sim[4].round_to(3), 0.975 + #assert_equal sim[5].round_to(3), 1.000 + + # # # AUTOSCALE + assert_equal sim[0].round_to(3), -0.115 + assert_equal sim[1].round_to(3), 0.425 + assert_equal sim[2].round_to(3), -0.931 + assert_equal sim[3].round_to(3), -0.352 + assert_equal sim[4].round_to(3), 0.972 + assert_equal sim[5].round_to(3), 1.000 + + + # feature transform, only for demonstration of concept + foo = svd.transform_feature foo + sim = [] + svd.vk.each_row { |x| + sim << OpenTox::Algorithm::Similarity.cosine_num(x,foo.row(0)) + } + + # # # NO AUTOSCALE + #assert_equal sim[0].round_to(3), 1.000 + #assert_equal sim[1].round_to(3), 0.874 + #assert_equal sim[2].round_to(3), 0.064 + #assert_equal sim[3].round_to(3), 0.895 + + # # # AUTOSCALE + assert_equal sim[0].round_to(3), 1.000 + assert_equal sim[1].round_to(3), 0.705 + assert_equal sim[2].round_to(3), 0.023 + assert_equal sim[3].round_to(3), 0.934 + + end + + def test_logas + + d1 = [ 1,2,3 ].to_gv + d2 = [ -1,0,1 ].to_gv + d3 = [ -2,3,8 ].to_gv + d4 = [ -20,30,80 ].to_gv + d5 = [ 0.707, 0.7071].to_gv + + d1la = [ -1.31668596949013, 0.211405021140643, 1.10528094834949 ].to_gv + d2la = d1la + d3la = [ -1.37180016053906, 0.388203523926062, 0.983596636612997 ].to_gv + d4la = [ -1.40084731572532, 0.532435269814955, 0.868412045910369 ].to_gv + d5la = [ -1.0, 1.0 ].to_gv + + 2.times { + + logas = OpenTox::Transform::LogAutoScale.new(d1) + assert_equal logas.vs, d1la + assert_equal logas.restore(logas.vs), d1 + + logas = OpenTox::Transform::LogAutoScale.new(d2) + assert_equal logas.vs, d2la + assert_equal logas.restore(logas.vs), d2 + + logas = OpenTox::Transform::LogAutoScale.new(d3) + assert_equal logas.vs, d3la + assert_equal logas.restore(logas.vs), d3 + + logas = OpenTox::Transform::LogAutoScale.new(d4) + assert_equal logas.vs, d4la + assert_equal logas.restore(logas.vs), d4 -# def test_pca -# -# d = GSL::Matrix.alloc([1,1.1,2,1.9,3,3.3], 3, 2) -# td = GSL::Matrix.alloc([-1.3421074161875, -0.127000127000191, 1.46910754318769],3,1) -# ev = GSL::Matrix.alloc([0.707106781186548, 0.707106781186548], 2, 1) -# rd = GSL::Matrix.alloc([1.05098674493306, 1.043223563717, 1.91019734898661, 2.0, 3.03881590608033, 3.256776436283], 3, 2) -# -# # Lossy -# 2.times do # repeat to ensure idempotency -# pca = OpenTox::Algorithm::Transform::PCA.new(d, 0.05) -# assert_equal pca.data_matrix, d -# assert_equal pca.data_transformed_matrix, td -# assert_equal pca.eigenvector_matrix, ev -# assert_equal pca.restore, rd -# end -# -# td = GSL::Matrix.alloc([-1.3421074161875, 0.0721061461855949, -0.127000127000191, -0.127000127000191, 1.46910754318769, 0.0548939808145955],3,2) -# ev = GSL::Matrix.alloc([0.707106781186548, -0.707106781186548, 0.707106781186548, 0.707106781186548], 2, 2) -# -# # Lossless -# 2.times do -# pca = OpenTox::Algorithm::Transform::PCA.new(d, 0.0) -# assert_equal pca.data_matrix, d -# assert_equal pca.data_transformed_matrix, td -# assert_equal pca.eigenvector_matrix, ev -# assert_equal pca.restore, d -# end -# -# end + logas = OpenTox::Transform::LogAutoScale.new(d5) + assert_equal logas.vs, d5la + assert_equal logas.restore(logas.vs), d5 + + } + + end end |