local_fingerprint_regression with svm radial basis

11 files changed, 762 insertions, 762 deletions

diff --git a/Makefile b/Makefile
index 2e6b333..0025ed7 100644
--- a/Makefile
+++ b/Makefile
@@ -29,14 +29,14 @@ figure/test-correlation.pdf: data/combined-test-predictions.csv data/median-corr
 
 # Validations
 
-validations: data/combined-cv.csv data/combined-test-predictions.csv
-
-data/combined-cv.csv: crossvalidation.rb data/combined.csv
-	ruby crossvalidation.rb combined.csv
+validations: data/combined-test-predictions.csv data/combined-cv.csv
 
 data/combined-test-predictions.csv: test-validation.rb data/test.csv data/combined.csv
 	ruby test-validation.rb combined.csv
 
+data/combined-cv.csv: crossvalidation.rb data/combined.csv
+	ruby crossvalidation.rb combined.csv
+
 # Datasets
 
 datasets: data/median-correlation.csv data/test.csv data/combined.csv data/mazzatorta.csv data/swiss.csv data/test.json data/combined.json data/mazzatorta.json data/swiss.json
diff --git a/crossvalidation.rb b/crossvalidation.rb
index eb0c098..00fab96 100644
--- a/crossvalidation.rb
+++ b/crossvalidation.rb
@@ -5,8 +5,8 @@ file = File.join DATA,ARGV[0]
 csv_file = File.join(DATA,ARGV[0].sub(/.csv/,'-cv.csv'))
 id_file = File.join(DATA,ARGV[0].sub(/.csv/,'-cv.id'))
 dataset = Dataset.from_csv_file file
-#model = Model::LazarRegression.create(dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
 model = Model::LazarRegression.create(dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression")
+#model = Model::LazarRegression.create(dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
 #model = Model::LazarRegression.create(dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_weighted_average")
 cv = RegressionCrossValidation.create model
 File.open(id_file,"w+"){|f| f.puts cv.id}
diff --git a/data/combined-cv.csv b/data/combined-cv.csv
index b065b56..7d6359b 100644
--- a/data/combined-cv.csv
+++ b/data/combined-cv.csv
@@ -1,634 +1,634 @@
 SMILES,LOAEL_measured_median,LOAEL_predicted,Confidence
 ClC12C3C4(C(C1(Cl)Cl)(C1(C2(C3(Cl)C(C41Cl)(Cl)Cl)Cl)Cl)Cl)Cl,1.9566e-05,0.0014217916687719956,0.625
-ClC1=C(Cl)C2(C(C1(Cl)C1C2C2CC1C=C2)(Cl)Cl)Cl,2.7404e-05,0.0013618384919362545,1
-N#Cc1nn(c(c1S(=O)C(F)(F)F)N)c1c(Cl)cc(cc1Cl)C(F)(F)F,0.00013611,0.02280039754243981,1
-Clc1ccc2c(c1)[n+]([O-])nc(n2)n1cncc1,0.00020191,0.036072045935982476,1
-OC(=O)C(Oc1ccc(cc1)Oc1ncc(cc1Cl)C(F)(F)F)C,0.00027647,0.010022237178723312,1
-CCOP(=S)(SCSC(C)(C)C)OCC,0.00027736000000000004,0.0035114324579501584,1
-ClC1C2OC2C2C1C1(Cl)C(=C(C2(C1(Cl)Cl)Cl)Cl)Cl,0.00028896749999999995,0.00127489457568648,1
-ClC1=C(Cl)C2(C(C1(Cl)C1C2C2CC1C1C2O1)(Cl)Cl)Cl,0.000295345,0.0013908113005169935,1
-CCSCCSP(=S)(OCC)OCC,0.00036443,0.00316231172071027,1
-CNC(=O)ON=CC(SC)(C)C,0.00052559,0.03599307284127598,1
-COC(=O)C(Oc1ccc(cc1)Oc1ccc(cc1Cl)Cl)C,0.00058619,0.04581631659416678,1
-CCSCSP(=S)(OCC)OCC,0.00061449,0.0010182908439074832,1
-OC1CCCCCc2cc(O)cc(c2C(=O)OC(CCC1)C)O,0.00062036,0.5980317768795744,1
-ClC1C=CC2C1C1(Cl)C(=C(C2(C1(Cl)Cl)Cl)Cl)Cl,0.000843785,0.0002461160399892707,1
-c1ccc(cc1)[Sn](c1ccccc1)c1ccccc1,0.00085711,0.4743457265368468,1
-CCOP(=O)(SC(CC)C)SC(CC)C,0.000872805,0.020254725397746965,1
-CCS(=O)CCSP(=O)(OC)OC,0.00089328,0.001392136051857325,1
-ClC1CC2C(C1Cl)C1(C(C2(Cl)C(=C1Cl)Cl)(Cl)Cl)Cl,0.000939545,0.0005483941672543966,1
-COP(=S)(Oc1ccc(cc1)N(=O)=O)OC,0.00094982,0.02033309300106236,1
-Clc1c(Cl)c(Cl)c(c(c1Cl)Cl)Cl,0.0010183,0.11955050452253108,1
-CNC(=O)CSP(=S)(OC)OC,0.0010905,0.010363449559145924,1
+ClC1=C(Cl)C2(C(C1(Cl)C1C2C2CC1C=C2)(Cl)Cl)Cl,2.7404e-05,0.002387671183307973,0.4375
+N#Cc1nn(c(c1S(=O)C(F)(F)F)N)c1c(Cl)cc(cc1Cl)C(F)(F)F,0.00013611,0.03806504214723742,0.7272727272727273
+Clc1ccc2c(c1)[n+]([O-])nc(n2)n1cncc1,0.00020191,0.044090771816319076,0.18181818181818182
+OC(=O)C(Oc1ccc(cc1)Oc1ncc(cc1Cl)C(F)(F)F)C,0.00027647,0.037229670092100806,0.6521739130434783
+CCOP(=S)(SCSC(C)(C)C)OCC,0.00027736000000000004,0.004010065596865467,0.5454545454545454
+ClC1C2OC2C2C1C1(Cl)C(=C(C2(C1(Cl)Cl)Cl)Cl)Cl,0.00028896749999999995,0.001107636536884408,0.5
+ClC1=C(Cl)C2(C(C1(Cl)C1C2C2CC1C1C2O1)(Cl)Cl)Cl,0.000295345,0.002061537057415606,0.5
+CCSCCSP(=S)(OCC)OCC,0.00036443,0.0045393269903714764,0.5
+CNC(=O)ON=CC(SC)(C)C,0.00052559,0.058837247552187444,0.35294117647058826
+COC(=O)C(Oc1ccc(cc1)Oc1ccc(cc1Cl)Cl)C,0.00058619,0.05432467306381369,0.4230769230769231
+CCSCSP(=S)(OCC)OCC,0.00061449,0.0033397489227135033,0.5454545454545454
+OC1CCCCCc2cc(O)cc(c2C(=O)OC(CCC1)C)O,0.00062036,1.0415534190320412,0.17391304347826086
+ClC1C=CC2C1C1(Cl)C(=C(C2(C1(Cl)Cl)Cl)Cl)Cl,0.000843785,0.0003704141467113901,0.4375
+c1ccc(cc1)[Sn](c1ccccc1)c1ccccc1,0.00085711,0.5799160071304471,0.16666666666666666
+CCOP(=O)(SC(CC)C)SC(CC)C,0.000872805,0.004760493760561179,0.46153846153846156
+CCS(=O)CCSP(=O)(OC)OC,0.00089328,0.0014369137370621636,0.29411764705882354
+ClC1CC2C(C1Cl)C1(C(C2(Cl)C(=C1Cl)Cl)(Cl)Cl)Cl,0.000939545,0.0013512631119732106,0.375
+COP(=S)(Oc1ccc(cc1)N(=O)=O)OC,0.00094982,0.011744057540543631,0.6428571428571429
+Clc1c(Cl)c(Cl)c(c(c1Cl)Cl)Cl,0.0010183,0.10771356141815085,0.4
+CNC(=O)CSP(=S)(OC)OC,0.0010905,0.008598461399213199,0.2222222222222222
 COP(=O)(SCCS(=O)(=O)CC)OC,0.0011438,0.001174623533543087,0.3125
-COC1CC(OC2C(C)C=CC=C3COC4C3(O)C(C=C(C4O)C)C(=O)OC3CC(CC=C2C)OC2(C3)C=CC(C(O2)C(CC)C)C)OC(C1OC1CC(OC)C(C(O1)C)O)C.COC1CC(OC(C1OC1CC(OC)C(C(O1)C)O)C)OC1C(C)C=CC=C2COC3C2(O)C(C=C(C3O)C)C(=O)OC2CC(CC=C1C)OC1(C2)C=CC(C(O1)C(C)C)C,0.0011546,0.0022361066689595625,1
+COC1CC(OC2C(C)C=CC=C3COC4C3(O)C(C=C(C4O)C)C(=O)OC3CC(CC=C2C)OC2(C3)C=CC(C(O2)C(CC)C)C)OC(C1OC1CC(OC)C(C(O1)C)O)C.COC1CC(OC(C1OC1CC(OC)C(C(O1)C)O)C)OC1C(C)C=CC=C2COC3C2(O)C(C=C(C3O)C)C(=O)OC2CC(CC=C1C)OC1(C2)C=CC(C(O1)C(C)C)C,0.0011546,0.007054323504366715,0.7818181818181819
 ClC12C(Cl)(Cl)C3(C4(C1(Cl)C1(C2(Cl)C3(C4(C1(Cl)Cl)Cl)Cl)Cl)Cl)Cl,0.0012831,6.240058509303287e-05,0.625
-CCOP(=O)(N1CCSC1=O)SC(CC)C,0.0013411,0.018751518589811837,1
-O=C1CCCC(=O)C1C(=O)c1ccc(cc1[N+](=O)[O-])S(=O)(=O)C,0.0014146,0.010571230016176134,1
-CCOP(=S)(Oc1ccccc1C(=O)OC(C)C)NC(C)C,0.0014476,0.09120206260700489,1
-CCSCCSP(=O)(OC)OC,0.0015199,0.0008906250834214297,1
-CCOc1cc(nc(n1)CC)OP(=S)(OC)OC,0.0015396,0.008978274823277978,1
-COC(=O)C=C(OP(=O)(OC)OC)C,0.0015615,0.025123689238209644,1
-COC(=O)/C=C(/OP(=O)(OC)OC)\C,0.0015615,0.020027335083149144,1
-OC(=O)c1ccccc1.CCC(C1OC2(C=CC1C)OC1CC=C(C)C(OC3CC(OC)C(C(O3)C)OC3CC(OC)C(C(O3)C)NC)C(C)C=CC=C3C4(C(C(=O)OC(C2)C1)C=C(C)C(C4OC3)O)O)C,0.001735715,0.002019549613558084,1
-C1CCC(CC1)[Sn](n1ncnc1)(C1CCCCC1)C1CCCCC1,0.001811,0.009696985421986192,1
-ClC1C2(Cl)C3C4C5C1(Cl)C(C2(Cl)C5C3C1C4O1)(Cl)Cl,0.0018377,0.0001308233255598207,1
-CNC(=O)CCSCCSP(=O)(OC)OC,0.0018793,0.0041661125577594224,1
-COC1CC(OC2C(C)C=CC=C3COC4C3(O)C(C=C(C4O)C)C(=O)OC3CC(CC=C2C)OC2(C3)C=CC(C(O2)C(C)C)C)OC(C1OC1CC(OC)C(C(O1)C)NC(=O)C)C,0.00194425,0.0021990193765551013,1
-N#CC(c1cccc(c1)Oc1ccccc1)OC(=O)[C@H](C(C)C)Nc1ccc(cc1Cl)C(F)(F)F,0.0019884,0.008357689310140923,1
-CNC(=O)C=C(OP(=O)(OC)OC)C,0.0020165,0.007629651235905489,1
-COP(=O)(SC)N,0.0020549,0.31875673049140224,1
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-CO[C@H]1C[C@H](O[C@H]2[C@@H](C)C=CC=C3CO[C@H]4[C@]3(O)[C@@H](C=C([C@H]4O)C)C(=O)O[C@H]3C[C@@H](CC=C2C)O[C@]2(C3)C=C[C@@H]([C@H](O2)[C@H](CC)C)C)O[C@H]([C@@H]1O[C@H]1C[C@H](OC)[C@H]([C@@H](O1)C)O)C,0.0022907,0.011593437850191157,1
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-CC1C=CC=C2COC3C2(O)C(C=C(C3O)C)C(=O)OC2CC(CC=C(C1)C)OC1(C2)CCC(C(O1)C)C,0.012862,0.004182750580056495,1
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-[S-]C(=S)NCCNC(=S)[S-].[Zn+2],0.044607,0.04442239106782064,1
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+OC(=O)c1ccc(cc1N)N(=O)=O,6.5062,0.35101047887427045,0.5833333333333334
+Oc1cc(O)c2c(c1)oc(c(c2=O)O)c1ccc(c(c1)O)O,6.7298,0.1547408403789841,0.16666666666666666
+ClCC(=O)c1ccc(cc1)NC(=O)C,7.4653,0.21162029854797587,0.3
+O=C1OC(=O)c2c1cccc2,8.0005,0.44857150383371225,0.4
+CCCOC(=O)c1ccc(cc1)O,8.3241,0.8190167516728168,0.5714285714285714
+CCOC(=O)COC(=O)c1ccccc1C(=O)OCC,8.9199,0.26571277447074904,0.6153846153846154
+O=C1CCCCC1,9.2722,0.6964108675677542,0.18181818181818182
 OC(=O)C=CC(=O)O,9.3132,2.880700000000001,0.14285714285714285
-COC(=O)c1ccc(cc1)O,9.8589,0.5041426979007558,1
-COC(=O)c1ccccc1C(=O)OC,10.3,0.8561575030005575,1
+COC(=O)c1ccc(cc1)O,9.8589,0.5445964595249081,0.6666666666666666
+COC(=O)c1ccccc1C(=O)OC,10.3,0.4137775820588338,0.625
 OC1C2C(N(C)C)C(=O)C(=C(O)N)C(=O)C2(O)C(=O)C2=C(O)c3c(C(C12)(C)O)c(Cl)ccc3O,10.508,0.33751,0.6216216216216216
-OCC(C1OC(=O)C(=C1O)O)O,13.07315,3.70421978143881,1
-OCCO,14.822,2.46791420903979,1
-CCCCCCCCCCCCCCCCCC(=O)OCC(C1OCC(C1O)O)O,16.727,0.3141167570299539,1
-[O-]S(=O)(=O)NC1CCCCC1.[Na+],17.901,0.028489155298906475,1
-O=C1NS(=O)(=O)c2c1cccc2,19.663,0.32691285919713825,1
-CCCCCCCCCCCC(=O)OCC(C1OCC(C1O)O)O,19.867,0.3141167570299539,1
-CCOC(=O)c1ccccc1C(=O)OCC,19.956,0.23807316673019932,1
-OC(=O)c1ccccc1N,20.06,0.6835612141548324,1
-OCC(CO)O,74.739,1.181179898642482,1
+OCC(C1OC(=O)C(=C1O)O)O,13.07315,0.8547324122721407,0.23076923076923078
+OCCO,14.822,1.0671047873220199,0.2
+CCCCCCCCCCCCCCCCCC(=O)OCC(C1OCC(C1O)O)O,16.727,0.4341973519193462,1
+[O-]S(=O)(=O)NC1CCCCC1.[Na+],17.901,0.014887180676877398,0.15384615384615385
+O=C1NS(=O)(=O)c2c1cccc2,19.663,0.2316225122795419,0.23076923076923078
+CCCCCCCCCCCC(=O)OCC(C1OCC(C1O)O)O,19.867,0.3964148587369233,1
+CCOC(=O)c1ccccc1C(=O)OCC,19.956,0.31768146687053195,0.6153846153846154
+OC(=O)c1ccccc1N,20.06,0.4100698203820209,0.5833333333333334
+OCC(CO)O,74.739,1.6124273227552521,0.42857142857142855
diff --git a/data/combined-cv.id b/data/combined-cv.id
index f731528..9d5207e 100644
--- a/data/combined-cv.id
+++ b/data/combined-cv.id
@@ -1 +1 @@
-56d46da02b72ed687e000003
+56d483392b72ed7887000001
diff --git a/data/combined-test-predictions.csv b/data/combined-test-predictions.csv
index db503b2..a39bc69 100644
--- a/data/combined-test-predictions.csv
+++ b/data/combined-test-predictions.csv
@@ -1,151 +1,151 @@
 SMILES,LOAEL_measured_median,LOAEL_predicted,Confidence,Dataset
-N#Cc1nn(c(c1S(=O)C(F)(F)F)N)c1c(Cl)cc(cc1Cl)C(F)(F)F,0.00013611,0.022613188319232452,1,combined-prediction
-OC(=O)C(Oc1ccc(cc1)Oc1ncc(cc1Cl)C(F)(F)F)C,0.00027647,0.01427623251867895,1,combined-prediction
-CCOP(=S)(SCSC(C)(C)C)OCC,0.00027736000000000004,0.0039055723532512654,1,combined-prediction
-CCSCSP(=S)(OCC)OCC,0.00061449,0.0013412206725761037,1,combined-prediction
-CCOP(=O)(SC(CC)C)SC(CC)C,0.000872805,0.017329999717435547,1,combined-prediction
-CNC(=O)CSP(=S)(OC)OC,0.0010905,0.011060482604012548,1,combined-prediction
-COP(=O)(SC)N,0.0020549,0.32686975597991175,1,combined-prediction
-CSc1ccc(cc1C)OP(=S)(OC)OC,0.00210185,0.010081251478298994,1,combined-prediction
-CCOP(=S)(Oc1ccc2c(c1)oc(=O)c(c2C)Cl)OCC,0.0033631,0.014776291625072534,1,combined-prediction
-CCOP(=S)(Oc1ncn(n1)c1ccccc1)OCC,0.0041492,0.021227133218238135,1,combined-prediction
-COc1sc(=O)n(n1)CSP(=S)(OC)OC,0.00471335,0.011073485220332436,1,combined-prediction
-CCOP(=S)(OCC)SCSP(=S)(OCC)OCC,0.0049418,0.002033337677017067,1,combined-prediction
-CCOP(=O)(Oc1ccc(c(c1)C)SC)NC(C)C,0.0049447,0.009081872831360313,1,combined-prediction
-CC(Cc1ccc(cc1)C(C)(C)C)CN1CC(C)OC(C1)C,0.0056016,0.13115549471565732,1,combined-prediction
-COP(=S)(Oc1nc(Cl)c(cc1Cl)Cl)OC,0.00620095,0.025034719479014724,1,combined-prediction
-OC(C(Cl)(Cl)Cl)(c1ccc(cc1)Cl)c1ccc(cc1)Cl,0.0067479,0.05111523136561661,1,combined-prediction
-COC(=O)N(C(=O)N1COC2(C(=N1)c1ccc(cc1C2)Cl)C(=O)OC)c1ccc(cc1)OC(F)(F)F,0.0068203,0.056514606119788334,1,combined-prediction
-Clc1ccc(cc1)C(c1ccccc1Cl)(c1cncnc1)O,0.0075484,0.04628306576789365,1,combined-prediction
-COP(=S)(SCn1nnc2c(c1=O)cccc2)OC,0.0076105,0.02591746392416698,1,combined-prediction
-N#CC(c1cccc(c1)Oc1ccccc1)OC(=O)C1C(C1(C)C)C=C(Br)Br,0.00781875,0.021878276593749975,1,combined-prediction
-CCN(c1nc(cc(n1)C)OP(=S)(OC)OC)CC,0.0081878,0.022310762222922397,1,combined-prediction
-CCCCOC(=O)C(Oc1ccc(cc1)Oc1ccc(cn1)C(F)(F)F)C,0.00885585,0.028183985852508562,1,combined-prediction
-COP(=O)(OC=C(Cl)Cl)OC,0.0100688,0.024813932884041406,1,combined-prediction
-CCCSP(=O)(SCCC)OCC,0.010069,0.008592333628124936,1,combined-prediction
-O=S1OCC2C(CO1)C1(C(C2(Cl)C(=C1Cl)Cl)(Cl)Cl)Cl,0.012287,0.00036386866340140173,1,combined-prediction
-CC(Oc1cc(c(cc1Cl)Cl)n1nc(oc1=O)C(C)(C)C)C,0.0124555,0.12216512349844322,1,combined-prediction
-CNC(=O)Oc1cccc2c1OC(C2)(C)C,0.01394355,0.037241106707072084,1,combined-prediction
-N#Cc1c(Cl)c(C#N)c(c(c1Cl)Cl)Cl,0.015043,0.06184952661439345,1,combined-prediction
-Fc1ccc(cc1)[Si](c1ccc(cc1)F)(Cn1cncn1)C,0.015853,0.018138810281156853,1,combined-prediction
-CCOP(=S)(Oc1cc(C)nc(n1)C(C)C)OCC,0.016429,0.016587213739035486,1,combined-prediction
-N#Cc1c(Cl)cccc1Cl,0.0165685,0.1054800864156153,1,combined-prediction
-CCOP(=S)(Oc1nc(Cl)c(cc1Cl)Cl)OCC,0.017114,0.013303480728567664,1,combined-prediction
-BrC1COC(C1)(Cn1cncn1)c1ccc(cc1Cl)Cl,0.017185,0.03617135710333624,1,combined-prediction
-CCN(C(=O)SCc1ccc(cc1)Cl)CC,0.0180385,0.037898508979231846,1,combined-prediction
-CCCN(C(=O)n1cncc1)CCOc1c(Cl)cc(cc1Cl)Cl,0.019912,0.05289083531396049,1,combined-prediction
-CCOC(=O)c1cn2nc(cc2nc1C)OP(=S)(OCC)OCC,0.0200875,0.05180011405744196,1,combined-prediction
-COP(=S)(SCN1C(=O)c2c(C1=O)cccc2)OC,0.020484,0.05421868262555557,1,combined-prediction
-CNC(=O)ON=C(C(=O)N(C)C)SC,0.022348,0.0237270686589673,1,combined-prediction
-COC(=O)N(c1ccccc1COc1ccn(n1)c1ccc(cc1)Cl)OC,0.023207,0.1423704290587658,1,combined-prediction
-CON(C(=O)Nc1ccc(c(c1)Cl)Cl)C,0.025091,0.035121486796294954,1,combined-prediction
-O=C(NC(=O)c1c(F)cccc1F)Nc1ccc(cc1)Cl,0.025428,0.14981414669522117,1,combined-prediction
-O=C(N(C)C)Nc1ccc(c(c1)Cl)Cl,0.025741,0.10878500256007394,1,combined-prediction
-CCOC(=O)C(Oc1ccc(cc1)Oc1cnc2c(n1)ccc(c2)Cl)C,0.0257509,0.014081655883317851,1,combined-prediction
-N#Cc1sc2=c(sc1C#N)c(=O)c1c(c2=O)cccc1,0.0269975,0.16746185893696108,1,combined-prediction
-C=CC1(C)OC(=O)N(C1=O)c1cc(Cl)cc(c1)Cl,0.027961,0.11945370218702653,1,combined-prediction
-N#CC(c1ccc(c(c1)Oc1ccccc1)F)OC(=O)C1C(C1(C)C)C=C(Cl)Cl,0.028207,0.014219028445680626,1,combined-prediction
-CCOC(=O)C(Cc1cc(c(cc1Cl)F)n1nc(n(c1=O)C(F)F)C)Cl,0.029113,0.15247632763725313,1,combined-prediction
-CON(C(=O)Nc1ccc(cc1)Br)C,0.0313005,0.04467487171287893,1,combined-prediction
-CN1CN(C)CSC1=S,0.03266,0.052056702348718106,1,combined-prediction
-ClCC1CN(C(=O)C1Cl)c1cccc(c1)C(F)(F)F,0.033160999999999996,0.08725712740853743,1,combined-prediction
-CCCCC(c1ccc(cc1)Cl)(Cn1cncn1)C#N,0.034179,0.0771974306341176,1,combined-prediction
-CCOP(=S)(SCn1c(=O)oc2c1ccc(c2)Cl)OCC,0.0345288,0.007143322378582819,1,combined-prediction
-CCOCn1c(c2ccc(cc2)Cl)c(c(c1C(F)(F)F)Br)C#N,0.0350825,0.05518424645194078,1,combined-prediction
-Clc1ccc(c(c1)Cl)C1(OCCO1)Cn1cncn1,0.0379825,0.04379693313132412,1,combined-prediction
-CC(C(c1cncnc1)(c1ccc(cc1)OC(F)(F)F)O)C,0.038746,0.035079804408126004,1,combined-prediction
-CC(N(C(=O)SCC(=C(Cl)Cl)Cl)C(C)C)C,0.041029,0.031010804072697008,1,combined-prediction
-COP(=S)(Oc1ccc(c(c1)C)[N+](=O)[O-])OC,0.0424911,0.010255605293952691,1,combined-prediction
-O=C1OC(C(=O)N1Nc1ccccc1)(C)c1ccc(cc1)Oc1ccccc1,0.04514,0.1155080006805767,1,combined-prediction
-CN(C(=S)SSC(=S)N(C)C)C,0.04783,0.05133696427232243,1,combined-prediction
-CN(C(=O)Oc1nc(nc(c1C)C)N(C)C)C,0.0520385,0.03465891885594715,1,combined-prediction
-C=CCOC(c1ccc(cc1Cl)Cl)Cn1cncc1,0.053503,0.016391136261299098,1,combined-prediction
-COCN(c1c(CC)cccc1CC)C(=O)CCl,0.0537505,0.3706946785186903,1,combined-prediction
-CCOc1ccc2c(c1)C(=CC(N2)(C)C)C,0.055221,0.27942157494105746,1,combined-prediction
-O=C(c1ccc(cc1S(=O)(=O)C)C(F)(F)F)c1cnoc1C1CC1,0.055661,0.028836462363937342,1,combined-prediction
-OC(=O)COc1ccc(cc1C)Cl,0.0573225,0.09302559055397255,1,combined-prediction
-CCOC(=O)NCCOc1ccc(cc1)Oc1ccccc1,0.0575765,0.19073701124003703,1,combined-prediction
-N#CC(c1cccc(c1)Oc1ccccc1)OC(=O)C(c1ccc(cc1)Cl)C(C)C,0.059538,0.015717797785230917,1,combined-prediction
-N#CC(c1cccc(c1)Oc1ccccc1)OC(=O)C1C(C1(C)C)(C)C,0.060099,0.02342509771890023,1,combined-prediction
-CC(OC(=O)C(c1ccc(cc1)Br)(c1ccc(cc1)Br)O)C,0.0606145,0.07815017836186108,1,combined-prediction
-Clc1ccccc1c1nnc(nn1)c1ccccc1Cl,0.06152150000000001,0.10254821536612242,1,combined-prediction
-Clc1cc(ccc1Oc1ccc(c(c1)C(=O)NS(=O)(=O)C)[N+](=O)[O-])C(F)(F)F,0.062678,0.13311561685727313,1,combined-prediction
-COc1nc(nc(n1)C)NC(=O)NS(=O)(=O)c1ccccc1Cl,0.062889,0.23152239748840012,1,combined-prediction
-CCCCN(SN(C(=O)Oc1cccc2c1OC(C2)(C)C)C)CCCC,0.065695,0.02729751820103898,1,combined-prediction
-O=C(NC(=O)c1c(F)cccc1F)Nc1cc(Cl)c(c(c1F)Cl)F,0.06691,0.06304495071113188,1,combined-prediction
+N#Cc1nn(c(c1S(=O)C(F)(F)F)N)c1c(Cl)cc(cc1Cl)C(F)(F)F,0.00013611,0.04202666947504676,0.7272727272727273,combined-prediction
+OC(=O)C(Oc1ccc(cc1)Oc1ncc(cc1Cl)C(F)(F)F)C,0.00027647,0.03837316659754307,0.6521739130434783,combined-prediction
+CCOP(=S)(SCSC(C)(C)C)OCC,0.00027736000000000004,0.006244785277908732,0.5454545454545454,combined-prediction
+CCSCSP(=S)(OCC)OCC,0.00061449,0.0033397489227135033,0.5454545454545454,combined-prediction
+CCOP(=O)(SC(CC)C)SC(CC)C,0.000872805,0.004760493760561179,0.46153846153846156,combined-prediction
+CNC(=O)CSP(=S)(OC)OC,0.0010905,0.008598461399213199,0.2222222222222222,combined-prediction
+COP(=O)(SC)N,0.0020549,0.07267302761993463,0.13333333333333333,combined-prediction
+CSc1ccc(cc1C)OP(=S)(OC)OC,0.00210185,0.007885803202315566,0.45,combined-prediction
+CCOP(=S)(Oc1ccc2c(c1)oc(=O)c(c2C)Cl)OCC,0.0033631,0.008074684367671859,0.34782608695652173,combined-prediction
+CCOP(=S)(Oc1ncn(n1)c1ccccc1)OCC,0.0041492,0.019419668559497557,0.3333333333333333,combined-prediction
+COc1sc(=O)n(n1)CSP(=S)(OC)OC,0.00471335,0.014453233387553464,0.25,combined-prediction
+CCOP(=S)(OCC)SCSP(=S)(OCC)OCC,0.0049418,0.003882603616523481,0.5454545454545454,combined-prediction
+CCOP(=O)(Oc1ccc(c(c1)C)SC)NC(C)C,0.0049447,0.00588887528527483,0.391304347826087,combined-prediction
+CC(Cc1ccc(cc1)C(C)(C)C)CN1CC(C)OC(C1)C,0.0056016,0.09684939846922258,0.5882352941176471,combined-prediction
+COP(=S)(Oc1nc(Cl)c(cc1Cl)Cl)OC,0.00620095,0.01263784329125101,0.6875,combined-prediction
+OC(C(Cl)(Cl)Cl)(c1ccc(cc1)Cl)c1ccc(cc1)Cl,0.0067479,0.06035236375493807,0.4166666666666667,combined-prediction
+COC(=O)N(C(=O)N1COC2(C(=N1)c1ccc(cc1C2)Cl)C(=O)OC)c1ccc(cc1)OC(F)(F)F,0.0068203,0.06690498702032557,0.25,combined-prediction
+Clc1ccc(cc1)C(c1ccccc1Cl)(c1cncnc1)O,0.0075484,0.06510030909231854,0.7647058823529411,combined-prediction
+COP(=S)(SCn1nnc2c(c1=O)cccc2)OC,0.0076105,0.02533556283830024,0.25,combined-prediction
+N#CC(c1cccc(c1)Oc1ccccc1)OC(=O)C1C(C1(C)C)C=C(Br)Br,0.00781875,0.05246941081941809,0.7391304347826086,combined-prediction
+CCN(c1nc(cc(n1)C)OP(=S)(OC)OC)CC,0.0081878,0.011238266231223978,0.30434782608695654,combined-prediction
+CCCCOC(=O)C(Oc1ccc(cc1)Oc1ccc(cn1)C(F)(F)F)C,0.00885585,0.04770077107958393,0.5,combined-prediction
+COP(=O)(OC=C(Cl)Cl)OC,0.0100688,0.012690525889265763,0.25,combined-prediction
+CCCSP(=O)(SCCC)OCC,0.010069,0.0026313189577840735,0.46153846153846156,combined-prediction
+O=S1OCC2C(CO1)C1(C(C2(Cl)C(=C1Cl)Cl)(Cl)Cl)Cl,0.012287,0.0004368725355889385,0.4,combined-prediction
+CC(Oc1cc(c(cc1Cl)Cl)n1nc(oc1=O)C(C)(C)C)C,0.0124555,0.1026953824737063,0.4074074074074074,combined-prediction
+CNC(=O)Oc1cccc2c1OC(C2)(C)C,0.01394355,0.11577740543838756,0.5,combined-prediction
+N#Cc1c(Cl)c(C#N)c(c(c1Cl)Cl)Cl,0.015043,0.051870479532762394,0.4,combined-prediction
+Fc1ccc(cc1)[Si](c1ccc(cc1)F)(Cn1cncn1)C,0.015853,0.05068240975245326,0.5625,combined-prediction
+CCOP(=S)(Oc1cc(C)nc(n1)C(C)C)OCC,0.016429,0.00967740922944127,0.30434782608695654,combined-prediction
+N#Cc1c(Cl)cccc1Cl,0.0165685,0.0700468589441214,0.4,combined-prediction
+CCOP(=S)(Oc1nc(Cl)c(cc1Cl)Cl)OCC,0.017114,0.01226732331072138,0.6875,combined-prediction
+BrC1COC(C1)(Cn1cncn1)c1ccc(cc1Cl)Cl,0.017185,0.05948653474874811,0.52,combined-prediction
+CCN(C(=O)SCc1ccc(cc1)Cl)CC,0.0180385,0.058932449375049684,0.4375,combined-prediction
+CCCN(C(=O)n1cncc1)CCOc1c(Cl)cc(cc1Cl)Cl,0.019912,0.05048182950992367,0.21212121212121213,combined-prediction
+CCOC(=O)c1cn2nc(cc2nc1C)OP(=S)(OCC)OCC,0.0200875,0.02036221800054178,0.25,combined-prediction
+COP(=S)(SCN1C(=O)c2c(C1=O)cccc2)OC,0.020484,0.03712628100411957,0.35,combined-prediction
+CNC(=O)ON=C(C(=O)N(C)C)SC,0.022348,0.04646395325144057,0.35294117647058826,combined-prediction
+COC(=O)N(c1ccccc1COc1ccn(n1)c1ccc(cc1)Cl)OC,0.023207,0.06976594438403964,0.1935483870967742,combined-prediction
+CON(C(=O)Nc1ccc(c(c1)Cl)Cl)C,0.025091,0.0672942260939406,0.7857142857142857,combined-prediction
+O=C(NC(=O)c1c(F)cccc1F)Nc1ccc(cc1)Cl,0.025428,0.07143486542742777,0.5454545454545454,combined-prediction
+O=C(N(C)C)Nc1ccc(c(c1)Cl)Cl,0.025741,0.08763643148617718,0.75,combined-prediction
+CCOC(=O)C(Oc1ccc(cc1)Oc1cnc2c(n1)ccc(c2)Cl)C,0.0257509,0.03950626192412149,0.7142857142857143,combined-prediction
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-CCCCOCCOCCOCc1cc2OCOc2cc1CCC,0.51708,0.3407671414577521,1,combined-prediction
-COCC(N(c1c(C)cccc1CC)C(=O)CCl)C,0.52855,0.10057456723782453,1,combined-prediction
+ClC(SN1C(=O)C2C(C1=O)CC=CC2)(Cl)Cl,0.32935499999999995,0.11145687673563447,0.42857142857142855,combined-prediction
+CC(=CC1C(C1(C)C)C(=O)OCc1cccc(c1)Oc1ccccc1)C,0.42802,0.05666640235782462,0.7142857142857143,combined-prediction
+CC(Oc1ccccn1)COc1ccc(cc1)Oc1ccccc1,0.433615,0.06767869983880132,0.2608695652173913,combined-prediction
+N#Cc1c[nH]cc1c1cccc2c1OC(O2)(F)F,0.449265,0.2537231165733238,0.45454545454545453,combined-prediction
+Clc1c(Cl)c([N+](=O)[O-])c(c(c1Cl)Cl)Cl,0.47404,0.06739399960905106,0.3333333333333333,combined-prediction
+COc1nc(nc(n1)C)NC(=O)NS(=O)(=O)c1ccccc1C(=O)OC,0.48379,0.2526657114703754,0.7586206896551724,combined-prediction
+Nc1nc(NC2CC2)nc(n1)N,0.514491,0.054311082810879936,0.3076923076923077,combined-prediction
+CCCCOCCOCCOCc1cc2OCOc2cc1CCC,0.51708,0.28615321598312393,0.22727272727272727,combined-prediction
+COCC(N(c1c(C)cccc1CC)C(=O)CCl)C,0.52855,0.14073564290622803,0.5238095238095238,combined-prediction
 O=Cc1ccco1,0.62445,0.12487,0.1111111111111111,combined-prediction
-[O-][N+](=O)c1cc(Cl)c(c(c1)Cl)N,0.72459,0.12418355176644183,1,combined-prediction
-COC(=O)c1c(Cl)c(Cl)c(c(c1Cl)Cl)C(=O)OC,0.768162,0.7718941842378951,1,combined-prediction
-COC(=O)NS(=O)(=O)c1ccc(cc1)N,0.78179,0.47721321130047156,1,combined-prediction
-OC(=O)c1nc(Cl)c(c(c1Cl)N)Cl,0.8283,0.6037122433930873,1,combined-prediction
-CC(C1(C)N=C(NC1=O)c1nc2ccccc2cc1C(=O)O)C,0.8351195,0.8106366739911756,1,combined-prediction
-COC(=O)Nc1nc2c([nH]1)cccc2,0.8499450000000001,0.0833355353580093,1,combined-prediction
-CC(Oc1cccc(c1)NC(=O)c1ccccc1C(F)(F)F)C,0.907795,0.10858688334353366,1,combined-prediction
-O=C(C1(C)CCCCC1)Nc1ccc(c(c1Cl)Cl)O,0.96626,0.45051257469048867,1,combined-prediction
-ClCCP(=O)(O)O,0.9723550000000001,2.4009973601180943,1,combined-prediction
-COc1cccc(c1C)C(=O)NN(C(C)(C)C)C(=O)c1cc(C)cc(c1)C,1.1154,0.27892917563036485,1,combined-prediction
-CCC(c1noc(c1)NC(=O)c1c(OC)cccc1OC)(CC)C,1.5855,0.4457808075272036,1,combined-prediction
-OC(=O)COc1nc(F)c(c(c1Cl)N)Cl,1.9605,0.12629032616320499,1,combined-prediction
-CC(OC(=O)Nc1cccc(c1)Cl)C,2.3402,0.12374297824529319,1,combined-prediction
-Oc1ccccc1c1ccccc1,3.1197,0.23249187284217376,1,combined-prediction
+[O-][N+](=O)c1cc(Cl)c(c(c1)Cl)N,0.72459,0.08483486708186733,0.4,combined-prediction
+COC(=O)c1c(Cl)c(Cl)c(c(c1Cl)Cl)C(=O)OC,0.768162,0.7882747528257691,0.4444444444444444,combined-prediction
+COC(=O)NS(=O)(=O)c1ccc(cc1)N,0.78179,0.30789314787939004,0.2,combined-prediction
+OC(=O)c1nc(Cl)c(c(c1Cl)N)Cl,0.8283,0.22921095816235462,0.5714285714285714,combined-prediction
+CC(C1(C)N=C(NC1=O)c1nc2ccccc2cc1C(=O)O)C,0.8351195,0.776601225740296,0.5416666666666666,combined-prediction
+COC(=O)Nc1nc2c([nH]1)cccc2,0.8499450000000001,0.0782700957052491,0.7647058823529411,combined-prediction
+CC(Oc1cccc(c1)NC(=O)c1ccccc1C(F)(F)F)C,0.907795,0.09902360209177057,0.30303030303030304,combined-prediction
+O=C(C1(C)CCCCC1)Nc1ccc(c(c1Cl)Cl)O,0.96626,0.31948866306169044,0.20833333333333334,combined-prediction
+ClCCP(=O)(O)O,0.9723550000000001,3.5513890262080436,0.16666666666666666,combined-prediction
+COc1cccc(c1C)C(=O)NN(C(C)(C)C)C(=O)c1cc(C)cc(c1)C,1.1154,0.19278665189974828,0.6153846153846154,combined-prediction
+CCC(c1noc(c1)NC(=O)c1c(OC)cccc1OC)(CC)C,1.5855,0.5622280221828752,0.15789473684210525,combined-prediction
+OC(=O)COc1nc(F)c(c(c1Cl)N)Cl,1.9605,0.11355586792202625,0.3157894736842105,combined-prediction
+CC(OC(=O)Nc1cccc(c1)Cl)C,2.3402,0.06474733012562413,0.6923076923076923,combined-prediction
+Oc1ccccc1c1ccccc1,3.1197,0.14128212505165622,0.42857142857142855,combined-prediction
 OC(=O)CNCP(=O)(O)O,5.5597,0.7008374592406027,0.16666666666666666,combined-prediction
diff --git a/data/combined-test-predictions.id b/data/combined-test-predictions.id
index beb87b2..c8a8308 100644
--- a/data/combined-test-predictions.id
+++ b/data/combined-test-predictions.id
@@ -1 +1 @@
-56d470502b72ed6930000006
+56d482c02b72ed77ae000004
diff --git a/figure/crossvalidation.pdf b/figure/crossvalidation.pdf
index 03f324c..7ca7827 100644
--- a/figure/crossvalidation.pdf
+++ b/figure/crossvalidation.pdf
diff --git a/figure/test-correlation.pdf b/figure/test-correlation.pdf
index 6e0ed2e..45f61ff 100644
--- a/figure/test-correlation.pdf
+++ b/figure/test-correlation.pdf
diff --git a/figure/test-prediction.pdf b/figure/test-prediction.pdf
index 361145d..2fd5761 100644
--- a/figure/test-prediction.pdf
+++ b/figure/test-prediction.pdf
diff --git a/loael.md b/loael.md
index 2cb3014..6e6db6d 100644
--- a/loael.md
+++ b/loael.md
@@ -311,7 +311,7 @@ These results are presented in [@fig:corr] and [@tbl:cv]. Please bear in mind th
 Training data | $r^2$                     | RMSE                    
 --------------|---------------------------|-------------------------
 Experimental | 0.49      | 1.41           
-Combined             | 0.38 | 1.48 
+Combined             | 0.38 | 1.47 
 
 : Comparison of model predictions with experimental variability. {#tbl:common-pred}
 
@@ -325,7 +325,7 @@ All correlations are statistically highly significant with a p-value < 2.2e-16.
 
 Training dataset | $r^2$ | RMSE 
 -----------------|-------|------
-Combined | 0.37  | 1.84 
+Combined | 0.33  | 1.9 
 
 : 10-fold crossvalidation results {#tbl:cv}
 
diff --git a/loael.pdf b/loael.pdf
index 8147805..e8cc2d2 100644
--- a/loael.pdf
+++ b/loael.pdf