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authorChristoph Helma <helma@in-silico.ch>2021-06-25 12:44:49 +0200
committerChristoph Helma <helma@in-silico.ch>2021-06-25 12:44:49 +0200
commitfbeb14b83a03a2ebff3ec2f0e52b57bb6954d454 (patch)
treeb49c334a318fdf4ab565e0cdeb56cd2b5d29fa95
parent83591831c6e36c36d87159acba6afdfedab95522 (diff)
model validations and pa predictions addedmutagenicity-paper
-rw-r--r--.gitignore1
-rw-r--r--ext/lazar/Makefile5
-rw-r--r--ext/lazar/extconf.rb32
-rw-r--r--ext/lazar/rinstall.R14
-rw-r--r--models/mutagenicity-cdk/. non-redundant1
-rw-r--r--models/mutagenicity-cdk/.RDatabin0 -> 110206063 bytes
-rw-r--r--models/mutagenicity-cdk/.Rhistory138
-rw-r--r--models/mutagenicity-cdk/Makefile10
-rw-r--r--models/mutagenicity-cdk/crossvalidation/0/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/0/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/0/test-prediction.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/0/test.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/0/train.csv7275
-rw-r--r--models/mutagenicity-cdk/crossvalidation/1/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/1/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/1/test-prediction.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/1/test.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/1/train.csv7275
-rw-r--r--models/mutagenicity-cdk/crossvalidation/2/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/2/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/2/test-prediction.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/2/test.csv810
-rw-r--r--models/mutagenicity-cdk/crossvalidation/2/train.csv7275
-rw-r--r--models/mutagenicity-cdk/crossvalidation/3/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/3/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/3/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/3/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/3/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/4/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/4/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/4/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/4/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/4/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/5/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/5/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/5/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/5/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/5/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/6/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/6/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/6/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/6/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/6/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/7/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/7/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/7/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/7/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/7/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/8/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/8/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/8/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/8/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/8/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/9/common-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/9/scaled-variables.csv8084
-rw-r--r--models/mutagenicity-cdk/crossvalidation/9/test-prediction.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/9/test.csv809
-rw-r--r--models/mutagenicity-cdk/crossvalidation/9/train.csv7276
-rw-r--r--models/mutagenicity-cdk/crossvalidation/confusion-matrices/all2
-rw-r--r--models/mutagenicity-cdk/crossvalidation/confusion-matrices/high_confidence2
-rw-r--r--models/mutagenicity-cdk/crossvalidation/confusion-matrices/low_confidence2
-rw-r--r--models/mutagenicity-cdk/crossvalidation/confusion-matrix-all.csv2
-rw-r--r--models/mutagenicity-cdk/crossvalidation/confusion-matrix-high-confidence.csv2
-rw-r--r--models/mutagenicity-cdk/crossvalidation/predictions.csv8083
-rw-r--r--models/mutagenicity-cdk/crossvalidation/summary-all.csv5
-rw-r--r--models/mutagenicity-cdk/crossvalidation/summary-high-confidence.csv5
-rw-r--r--models/mutagenicity-cdk/metadata.json1
-rw-r--r--models/mutagenicity-cdk/mutagenicity-mod-2.new.csv8084
-rw-r--r--models/mutagenicity-cdk/nohup.out114
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/0/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/0/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/0/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/1/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/1/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/1/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/2/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/2/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/2/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/3/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/3/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/3/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/4/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/4/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/4/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/5/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/5/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/5/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/6/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/6/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/6/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/7/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/7/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/7/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/8/test-prediction.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/8/test.csv832
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/8/train.csv7479
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/9/test-prediction.csv831
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/9/test.csv831
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/9/train.csv7480
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/confusion-matrix-all.csv2
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/confusion-matrix-high-confidence.csv2
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/predictions.csv8309
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/summary-all.csv5
-rw-r--r--models/mutagenicity-mp2d/crossvalidation/summary-high-confidence.csv5
-rw-r--r--models/mutagenicity-mp2d/mutagenicity.csv8310
-rw-r--r--predictions/pa-cdk/Makefile4
-rw-r--r--predictions/pa-cdk/common-variables.csv8686
-rw-r--r--predictions/pa-cdk/nohup.out10
-rw-r--r--predictions/pa-cdk/pa-cdk-prediction.csv603
-rw-r--r--predictions/pa-cdk/pa-cdk.csv603
-rw-r--r--predictions/pa-cdk/scaled-variables.csv8686
-rw-r--r--predictions/pa-mp2d/Makefile4
-rw-r--r--predictions/pa-mp2d/pa-mp2d-prediction.csv603
-rw-r--r--predictions/pa-mp2d/pa-mp2d.csv603
114 files changed, 394938 insertions, 52 deletions
diff --git a/.gitignore b/.gitignore
index dac2e93..81855ba 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,3 @@
-models
R
openbabel
Gemfile.lock
diff --git a/ext/lazar/Makefile b/ext/lazar/Makefile
deleted file mode 100644
index 1d51914..0000000
--- a/ext/lazar/Makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-all:
- true
-
-install:
- true
diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
deleted file mode 100644
index aa031e5..0000000
--- a/ext/lazar/extconf.rb
+++ /dev/null
@@ -1,32 +0,0 @@
-require 'fileutils'
-require 'rbconfig'
-require 'mkmf'
-
-main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
-
-# check for required programs
-programs = ["R","Rscript","mongod","java","getconf","wget","unzip","xls2csv","xlsx2csv"]
-programs.each do |program|
- abort "Please install #{program} on your system." unless find_executable program
-end
-
-abort "Please install the latest Rserve version on your system (the CRAN version is outdated). Execute 'install.packages('Rserve',,'http://www.rforge.net/')' in a R console running as root ('sudo R')." unless `R CMD Rserve --version`.match(/^Rserve v1.8/)
-
-# install R packages
-r_dir = File.join main_dir, "R"
-FileUtils.mkdir_p r_dir
-#FileUtils.mkdir_p File.join(main_dir,"bin") # for Rserve binary
-rinstall = File.expand_path(File.join(File.dirname(__FILE__),"rinstall.R"))
-puts `Rscript --vanilla #{rinstall} #{r_dir}`
-
-r_libs = Dir[File.join(r_dir,"*")].collect{|l| l.sub(r_dir, '').sub('/','')}.sort
-["caret","doMC","foreach","ggplot2","gridExtra","iterators","pls"].each do |lib|
- abort "Failed to install R package '#{lib}'." unless r_libs.include?(lib)
-end
-
-# create a fake Makefile
-File.open(File.join(File.dirname(__FILE__),"Makefile"),"w+") do |makefile|
- makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
-end
-
-$makefile_created = true
diff --git a/ext/lazar/rinstall.R b/ext/lazar/rinstall.R
deleted file mode 100644
index 17c2e61..0000000
--- a/ext/lazar/rinstall.R
+++ /dev/null
@@ -1,14 +0,0 @@
-libdir = commandArgs(trailingOnly=TRUE)[1]
-repo = "https://stat.ethz.ch/CRAN/"
-#install.packages("Rserve",lib=libdir,repos=)
-# dependencies=TRUE installs unnecessary Suggests packages. The default, NA, means c("Depends", "Imports", "LinkingTo").
-install.packages("caret",lib=libdir,repos=repo);
-install.packages("stringi",lib=libdir,repos=repo);
-install.packages("iterators",lib=libdir,repos=repo);
-install.packages("labeling",lib=libdir,repos=repo);
-install.packages("foreach",lib=libdir,repos=repo);
-install.packages("gridExtra",lib=libdir,repos=repo);
-install.packages("ggplot2",lib=libdir,repos=repo);
-install.packages("pls",lib=libdir,repos=repo);
-install.packages("randomForest",lib=libdir,repos=repo);
-install.packages("doMC",lib=libdir,repos=repo);
diff --git a/models/mutagenicity-cdk/. non-redundant b/models/mutagenicity-cdk/. non-redundant
new file mode 100644
index 0000000..6efb5d5
--- /dev/null
+++ b/models/mutagenicity-cdk/. non-redundant
@@ -0,0 +1 @@
+V1 V2 V3 V4 V10 V13 V14 V15 V21 V25 V26 V30 V77 V78 V79 V80 V81 V82 V83 V84 V97 V98 V99 V103 V107 V108 V109 V110 V111 V112 V113 V115 V116 V117 V118 V119 V120 V122 V123 V124 V125 V126 V127 V128 V129 V132 V133 V134 V135 V136 V137 V138 V139 V140 V141 V142 V143 V144 V145 V146 V147 V149 V150 V151 V152 V153 V154 V155 V156 V158 V159 V160 V161 V162 V163 V164 V165 V166 V167 V168 V169 V170 V171 V172 V173 V174 V175 V176 V177 V178 V179 V180 V181 V182 V183 V184 V185 V186 V187 V188 V189 V190 V191 V192 V194 V196 V197 V198 V199 V200 V201 V202 V203 V204 V205 V206 V207 V208 V209 V210 V211 V212 V214 V215 V218 V221 V222 V223 V224 V225 V226 V227 V228 V229 V230 V231 V232 V233 V234 V235 V236 V237 V238 V239 V240 V241 V242 V243 V244 V245 V246 V248 V249 V250 V251 V252 V253 V254 V255 V256 V257 V258 V259 V260 V261 V262 V263 V264 V265 V266 V267 V268 V269 V270 V271 V273 V276 V277 V279 V280 V281 V282 V283 V284 V287 V288 V290 V291 V297 V298 V299 V304 V305 V306 V307 V308 V309 V310 V311 V312 V313 V314 V315 V316 V317 V318 V319 V320 V321 V322 V323 V324 V325 V326 V327 V328 V330 V331 V332 V333 V336 V337 V338 V339 V340 V341 V342 V344 V345 V346 V347 V348 V349 V350 V351 V352 V353 V354 V355 V356 V357 V358 V359 V360 V361 V362 V363 V364 V365 V366 V367 V376 V378 V379 V387 V388 V401 V402 V415 V427 V428 V429 V430 V431 V439 V440 V450 V452 V453 V454 V455 V456 V457 V459 V460 V461 V462 V464 V465 V472 V477 V478 V479 V486 V487 V488 V489 V490 V491 V492 V524 V525 V538 V539 V552 V553 V554 V555 V557 V558 V559 V565 V568 V569 V570 V571 V572 V575 V577 V578 V579 V580 V584 V585 V591 V594 V596 V598 V605 V616 V617 V618 V619 V620 V621 V629 V632 V633 V634 V635 V636 V637 V650 V657 V658 V659 V660 V661 V666 V668 V669 V670 V673 V690 V692 V693 V709 V712 V713 V715 V717 V724 V725 V726 V731 V732 V735 V783 V788 V789 V790 V791 V792 V793 V796 V800 V807 V822 V824 V827 V828 V831 V832 V833 V834 V839 V874 V904 V905 V906 V907 V908 V909 V910 V911 V912 V915 V919 V926 V927 V929 V930 V932 V941 V943 V945 V946 V947 V950 V951 V952 V953 V955 V958 V962 V963 V964 V969 V970 V973 V993 V1021 V1023 V1024 V1025 V1026 V1027 V1028 V1029 V1030 V1031 V1062 V1066 V1069 V1070 V1142 V1144 V1145 V1146 V1154 V1156 V1161 V1163 V1165 V1166 V1169 V1170 V1171 V1175 V1178 V1180 V1183 V1186 V1188 V1192 V1193 V1195 V1196 V1197 V1203 V1204 V1205 V1206 V1216 V1217 V1218 V1231 V1234 V1235 V1244 V1247 V1248 V1249 V1250 V1251 V1253 V1254 V1255 V1257 V1258 V1260 V1263 V1272 V1273 V1275 V1285 V1296 V1299 V1304 V1305 V1319 V1323 V1331 V1335 V1336 V1353 V1357 V1360 V1361 V1365 V1369 V1370 V1372 V1373 V1376 V1384 V1388 V1389 V1390 V1391 V1392 V1393 V1394 V1395 V1396 V1397 V1403 V1404 V1405 V1406 V1407 V1408 V1409 V1425 V1439 V1441 \ No newline at end of file
diff --git a/models/mutagenicity-cdk/.RData b/models/mutagenicity-cdk/.RData
new file mode 100644
index 0000000..2e75e75
--- /dev/null
+++ b/models/mutagenicity-cdk/.RData
Binary files differ
diff --git a/models/mutagenicity-cdk/.Rhistory b/models/mutagenicity-cdk/.Rhistory
new file mode 100644
index 0000000..4de9cdf
--- /dev/null
+++ b/models/mutagenicity-cdk/.Rhistory
@@ -0,0 +1,138 @@
+independent_variables = read.csv("/home/ch/src/lazar/models/mutagenicity-cdk/independent-variables",header=F)
+independent_variables[1,]
+independent_variables[,1]
+near_zero_var <- nearZeroVar(independent_variables)
+library(caret)
+install.packages('caret')
+q()
+library(caret)
+independent_variables = read.csv("independent-variables",header=F)
+independent_variables
+near_zero_var <- nearZeroVar(independent_variables)
+near_zero_var
+near_zero_var <- nearZeroVar(independent_variables,allowParallel=T)
+near_zero_var
+independent_variables.class
+class(independent_variables)
+names(independent_variables)
+non_zero_var = subset(independent_variables,select = -near_zero_var
+non_zero_var
+class(non_zero_var)
+names(non_zero_var)
+correlation = cor(non_zero_var)
+correlation
+correlated = findCorrelation(correlated)
+ls()
+correlated = findCorrelation(correlation)
+correlated
+print(correlated)
+?findCorrelation
+correlation = cor(independent_variables)
+correlated = findCorrelation(correlation)
+correlation
+?cor
+correlation = cor(non_zero_var)
+correlated = findCorrelation(correlation)
+correlated
+class(correlated)
+names(correlated)
+near_zero_var
+class(near_zero_var)
+names(non_zero_var)
+subset(non_zero_var,-correlated)
+subset(non_zero_var,select=-correlated)
+non_correlated = subset(non_zero_var,select=-correlated)
+names(non_correlated)
+names(non_correlated)[1..10]
+names(non_correlated)[1:10]
+names[independent_variables][0..10]
+names[independent_variables][0:10]
+names(independent_variables)[0:10]
+names(independent_variables)[1:10]
+?read.csv
+sink(tmp)
+sink("tmp")
+names(non_correlated)
+sink()
+cat(names(non_correlated))
+
+sink("tmp")
+cat(names(non_correlated))
+sink()
+near_zero_var
+correlated
+q()
+library(caret)
+independent_variables = read.csv("independent-variables",header=F)
+dependent_variables = read.csv("dependent-variables",header=F)
+dependent_variables
+dependent_variables[,1]
+?varImp
+importance = varImp(x=independent_variables,y=dependent_variables)
+importance = varImp(x=independent_variables,y=dependent_variables[,1])
+importance = fiterVarImp(x=independent_variables,y=dependent_variables[,1])
+importance = filterVarImp(x=independent_variables,y=dependent_variables[,1])
+importance = filterVarImp(x=independent_variables,y=as.factor(dependent_variables[,1]))
+importance
+importance = varImp(x=independent_variables,y=dependent_variables[,1],useModel=F)
+importance = filterVarImp(x=independent_variables,y=as.factor(dependent_variables[,1]))
+near_zero_var = nearZeroVar(independent_variables)
+non_zero_var = subset(independent_variables,select = -near_zero_var)
+correlation = cor(non_zero_var)
+correlated = findCorrelation(correlation)
+non_correlated = subset(non_zero_var,select=-correlated)
+importance = filterVarImp(x=non_correlated,y=as.factor(dependent_variables[,1]))
+importance
+importance$X0
+class(importance)
+importance[with(importance,order(X0)]
+importance[with(importance,order(X0))]
+arrange(importance,X0)
+importance[order(importance$X1)]
+names(importance)
+importance$X0
+importance[order(importance$X0)]
+importance[order(importance$X0),]
+importance[order(importance$X0),]
+length(importance$X0)
+importance[importance[,1] %in% c(0.6,1)]
+importance[importance$X0 %in% c(0.6,1),]
+importance[importance$X0 %in% c(0.6:1),]
+importance[importance$X0 %in% c(0.6:1)]
+importance[,importance$X0 %in% c(0.6:1)]
+subset(importance,importance$X0 > 0.6)
+selected = subset(importance,importance$X0 > 0.6)
+selected[order(selected$X0),]
+length(selected)
+length(selected$X0)
+selected = subset(importance,importance$X0 > 0.55)
+length(selected$X0)
+q()
+names(importance)
+importance = subset(importance,-c(2))
+importance = subset(importance,select=-c(2))
+importance
+selected = subset(importance,importance[,1] > 0.55)
+length(selected$X0)
+cat(selected)
+selected
+dependent_variables = read.csv("dependent-variables",header=F)
+dependent_variables = read.csv("dependent-variables",header=F)[,1]
+dependent_variables
+importance = filterVarImp(x=non_correlated,y=as.factor(dependent_variables[,1]),nonpara=T)
+library(caret)
+importance = filterVarImp(x=non_correlated,y=as.factor(dependent_variables[,1]),nonpara=T)
+importance = filterVarImp(x=non_correlated,y=as.factor(dependent_variables),nonpara=T)
+selected = subset(importance,importance[,1] > 0.55)
+length(selected)
+selected
+length(selected$X0)
+selected = subset(importance,importance[,1] > 0.6)
+length(selected$X0)
+importanceF = filterVarImp(x=non_correlated,y=as.factor(dependent_variables),nonpara=F)
+selectedF = subset(importance,importance[,1] > 0.6)
+length(selectedF$X0)
+selected == selectedF
+write.csv(selected,"tmp.csv",col.names=F)
+write.table(selected,"tmp.csv",sep=",",col.names=F)
+q()
diff --git a/models/mutagenicity-cdk/Makefile b/models/mutagenicity-cdk/Makefile
new file mode 100644
index 0000000..2153e30
--- /dev/null
+++ b/models/mutagenicity-cdk/Makefile
@@ -0,0 +1,10 @@
+all: crossvalidation/summary-all.csv metadata.json
+
+crossvalidation/summary-all.csv: mutagenicity-mod-2.new.csv
+ ../../bin/lazar -t $< -x
+
+# Metadata
+
+metadata.json:
+ echo '{"species":"Salmonella typhimurium","endpoint":"Mutagenicity","source":"http://cheminformatics.org/datasets/bursi/cas_4337.zip, http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv, https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX data and dictionary.xls","qmrf":{"group":"QMRF 4.10. Mutagenicity","name":"OECD 471 Bacterial Reverse Mutation Test"}}' > $@
+
diff --git a/models/mutagenicity-cdk/crossvalidation/0/common-variables.csv b/models/mutagenicity-cdk/crossvalidation/0/common-variables.csv
new file mode 100644
index 0000000..7754f9e
--- /dev/null
+++ b/models/mutagenicity-cdk/crossvalidation/0/common-variables.csv
@@ -0,0 +1,8084 @@
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_Dt,SpMAD_Dt,EE_Dt,VE1_Dt,VE2_Dt,VE3_Dt,VR1_Dt,VR2_Dt,VR3_Dt,ECCEN,nHBd,nwHBd,nHBa,nwHBa,nHBint2,nHBint3,nHBint4,nHBint5,nHBint6,nHBint7,nHBint8,nHBint9,nHBint10,nHsOH,nHdNH,nHsSH,nHsNH2,nHssNH,nHaaNH,nHsNH3p,nHssNH2p,nHsssNHp,nHtCH,nHdCH2,nHdsCH,nHaaCH,nHCHnX,nHCsats,nHCsatu,nHAvin,nHother,nHmisc,nsLi,nssBe,nssssBem,nsBH2,nssBH,nsssB,nssssBm,nsCH3,ndCH2,nssCH2,ntCH,ndsCH,naaCH,nsssCH,nddC,ntsC,ndssC,naasC,naaaC,nssssC,nsNH3p,nsNH2,nssNH2p,ndNH,nssNH,naaNH,ntN,nsssNHp,ndsN,naaN,nsssN,nddsN,naasN,nssssNp,nsOH,ndO,nssO,naaO,naOm,nsOm,nsF,nsSiH3,nssSiH2,nsssSiH,nssssSi,nsPH2,nssPH,nsssP,ndsssP,nddsP,nsssssP,nsSH,ndS,nssS,naaS,ndssS,nddssS,nssssssS,nSm,nsCl,nsGeH3,nssGeH2,nsssGeH,nssssGe,nsAsH2,nssAsH,nsssAs,ndsssAs,nddsAs,nsssssAs,nsSeH,ndSe,nssSe,naaSe,ndssSe,nssssssSe,nddssSe,nsBr,nsSnH3,nssSnH2,nsssSnH,nssssSn,nsI,nsPbH3,nssPbH2,nsssPbH,nssssPb,SHBd,SwHBd,SHBa,SwHBa,SHBint2,SHBint3,SHBint4,SHBint5,SHBint6,SHBint7,SHBint8,SHBint9,SHBint10,SHsOH,SHdNH,SHsSH,SHsNH2,SHssNH,SHaaNH,SHsNH3p,SHssNH2p,SHsssNHp,SHtCH,SHdCH2,SHdsCH,SHaaCH,SHCHnX,SHCsats,SHCsatu,SHAvin,SHother,SHmisc,SsLi,SssBe,SssssBem,SsBH2,SssBH,SsssB,SssssBm,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,SssssC,SsNH3p,SsNH2,SssNH2p,SdNH,SssNH,SaaNH,StN,SsssNHp,SdsN,SaaN,SsssN,SddsN,SaasN,SssssNp,SsOH,SdO,SssO,SaaO,SaOm,SsOm,SsF,SsSiH3,SssSiH2,SsssSiH,SssssSi,SsPH2,SssPH,SsssP,SdsssP,SddsP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SssssssS,SSm,SsCl,SsGeH3,SssGeH2,SsssGeH,SssssGe,SsAsH2,SssAsH,SsssAs,SdsssAs,SddsAs,SsssssAs,SsSeH,SdSe,SssSe,SaaSe,SdssSe,SssssssSe,SddssSe,SsBr,SsSnH3,SssSnH2,SsssSnH,SssssSn,SsI,SsPbH3,SssPbH2,SsssPbH,SssssPb,minHBd,minwHBd,minHBa,minwHBa,minHBint2,minHBint3,minHBint4,minHBint5,minHBint6,minHBint7,minHBint8,minHBint9,minHBint10,minHsOH,minHdNH,minHsSH,minHsNH2,minHssNH,minHaaNH,minHsNH3p,minHssNH2p,minHsssNHp,minHtCH,minHdCH2,minHdsCH,minHaaCH,minHCHnX,minHCsats,minHCsatu,minHAvin,minHother,minHmisc,minsLi,minssBe,minssssBem,minsBH2,minssBH,minsssB,minssssBm,minsCH3,mindCH2,minssCH2,mintCH,mindsCH,minaaCH,minsssCH,minddC,mintsC,mindssC,minaasC,minaaaC,minssssC,minsNH3p,minsNH2,minssNH2p,mindNH,minssNH,minaaNH,mintN,minsssNHp,mindsN,minaaN,minsssN,minddsN,minaasN,minssssNp,minsOH,mindO,minssO,minaaO,minaOm,minsOm,minsF,minsSiH3,minssSiH2,minsssSiH,minssssSi,minsPH2,minssPH,minsssP,mindsssP,minddsP,minsssssP,minsSH,mindS,minssS,minaaS,mindssS,minddssS,minssssssS,minSm,minsCl,minsGeH3,minssGeH2,minsssGeH,minssssGe,minsAsH2,minssAsH,minsssAs,mindsssAs,minddsAs,minsssssAs,minsSeH,mindSe,minssSe,minaaSe,mindssSe,minssssssSe,minddssSe,minsBr,minsSnH3,minssSnH2,minsssSnH,minssssSn,minsI,minsPbH3,minssPbH2,minsssPbH,minssssPb,maxHBd,maxwHBd,maxHBa,maxwHBa,maxHBint2,maxHBint3,maxHBint4,maxHBint5,maxHBint6,maxHBint7,maxHBint8,maxHBint9,maxHBint10,maxHsOH,maxHdNH,maxHsSH,maxHsNH2,maxHssNH,maxHaaNH,maxHsNH3p,maxHssNH2p,maxHsssNHp,maxHtCH,maxHdCH2,maxHdsCH,maxHaaCH,maxHCHnX,maxHCsats,maxHCsatu,maxHAvin,maxHother,maxHmisc,maxsLi,maxssBe,maxssssBem,maxsBH2,maxssBH,maxsssB,maxssssBm,maxsCH3,maxdCH2,maxssCH2,maxtCH,maxdsCH,maxaaCH,maxsssCH,maxddC,maxtsC,maxdssC,maxaasC,maxaaaC,maxssssC,maxsNH3p,maxsNH2,maxssNH2p,maxdNH,maxssNH,maxaaNH,maxtN,maxsssNHp,maxdsN,maxaaN,maxsssN,maxddsN,maxaasN,maxssssNp,maxsOH,maxdO,maxssO,maxaaO,maxaOm,maxsOm,maxsF,maxsSiH3,maxssSiH2,maxsssSiH,maxssssSi,maxsPH2,maxssPH,maxsssP,maxdsssP,maxddsP,maxsssssP,maxsSH,maxdS,maxssS,maxaaS,maxdssS,maxddssS,maxssssssS,maxSm,maxsCl,maxsGeH3,maxssGeH2,maxsssGeH,maxssssGe,maxsAsH2,maxssAsH,maxsssAs,maxdsssAs,maxddsAs,maxsssssAs,maxsSeH,maxdSe,maxssSe,maxaaSe,maxdssSe,maxssssssSe,maxddssSe,maxsBr,maxsSnH3,maxssSnH2,maxsssSnH,maxssssSn,maxsI,maxsPbH3,maxssPbH2,maxsssPbH,maxssssPb,sumI,meanI,hmax,gmax,hmin,gmin,LipoaffinityIndex,MAXDN,MAXDP,DELS,MAXDN2,MAXDP2,DELS2,ETA_Alpha,ETA_AlphaP,ETA_dAlpha_A,ETA_dAlpha_B,ETA_Epsilon_1,ETA_Epsilon_2,ETA_Epsilon_3,ETA_Epsilon_4,ETA_Epsilon_5,ETA_dEpsilon_A,ETA_dEpsilon_B,ETA_dEpsilon_C,ETA_dEpsilon_D,ETA_Psi_1,ETA_dPsi_A,ETA_dPsi_B,ETA_Shape_P,ETA_Shape_Y,ETA_Shape_X,ETA_Beta,ETA_BetaP,ETA_Beta_s,ETA_BetaP_s,ETA_Beta_ns,ETA_BetaP_ns,ETA_dBeta,ETA_dBetaP,ETA_Beta_ns_d,ETA_BetaP_ns_d,ETA_Eta,ETA_EtaP,ETA_Eta_R,ETA_Eta_F,ETA_EtaP_F,ETA_Eta_L,ETA_EtaP_L,ETA_Eta_R_L,ETA_Eta_F_L,ETA_EtaP_F_L,ETA_Eta_B,ETA_EtaP_B,ETA_Eta_B_RC,ETA_EtaP_B_RC,fragC,nHBAcc,nHBAcc2,nHBAcc3,nHBAcc_Lipinski,nHBDon,nHBDon_Lipinski,HybRatio,IC0,IC1,IC2,IC3,IC4,IC5,TIC0,TIC1,TIC2,TIC3,TIC4,TIC5,SIC0,SIC1,SIC2,SIC3,SIC4,SIC5,CIC0,CIC1,CIC2,CIC3,CIC4,CIC5,BIC0,BIC1,BIC2,BIC3,BIC4,BIC5,MIC0,MIC1,MIC2,MIC3,MIC4,MIC5,ZMIC0,ZMIC1,ZMIC2,ZMIC3,ZMIC4,ZMIC5,Kier1,Kier2,nAtomLC,nAtomP,nAtomLAC,MLogP,McGowan_Volume,MDEC-11,MDEC-12,MDEC-13,MDEC-14,MDEC-22,MDEC-23,MDEC-24,MDEC-33,MDEC-34,MDEC-44,MDEO-11,MDEO-12,MDEO-22,MDEN-11,MDEN-12,MDEN-13,MDEN-22,MDEN-23,MDEN-33,MLFER_A,MLFER_BH,MLFER_BO,MLFER_S,MLFER_E,MLFER_L,MPC2,MPC3,MPC4,MPC5,MPC6,MPC7,MPC8,MPC9,MPC10,TPC,piPC1,piPC2,piPC3,piPC4,piPC5,piPC6,piPC7,piPC8,piPC9,piPC10,TpiPC,R_TpiPCTPC,PetitjeanNumber,nRing,n3Ring,n4Ring,n5Ring,n6Ring,n7Ring,n8Ring,n9Ring,n10Ring,n11Ring,n12Ring,nG12Ring,nFRing,nF4Ring,nF5Ring,nF6Ring,nF7Ring,nF8Ring,nF9Ring,nF10Ring,nF11Ring,nF12Ring,nFG12Ring,nTRing,nT4Ring,nT5Ring,nT6Ring,nT7Ring,nT8Ring,nT9Ring,nT10Ring,nT11Ring,nT12Ring,nTG12Ring,nHeteroRing,n3HeteroRing,n4HeteroRing,n5HeteroRing,n6HeteroRing,n7HeteroRing,n8HeteroRing,n9HeteroRing,n10HeteroRing,n11HeteroRing,n12HeteroRing,nG12HeteroRing,nFHeteroRing,nF4HeteroRing,nF5HeteroRing,nF6HeteroRing,nF7HeteroRing,nF8HeteroRing,nF9HeteroRing,nF10HeteroRing,nF11HeteroRing,nF12HeteroRing,nFG12HeteroRing,nTHeteroRing,nT4HeteroRing,nT5HeteroRing,nT6HeteroRing,nT7HeteroRing,nT8HeteroRing,nT9HeteroRing,nT10HeteroRing,nT11HeteroRing,nT12HeteroRing,nTG12HeteroRing,nRotB,RotBFrac,nRotBt,RotBtFrac,LipinskiFailures,topoRadius,topoDiameter,topoShape,GGI1,GGI2,GGI3,GGI4,GGI5,GGI6,GGI7,GGI8,GGI9,GGI10,JGI1,JGI2,JGI3,JGI4,JGI5,JGI6,JGI7,JGI8,JGI9,JGI10,JGT,SpMax_D,SpDiam_D,SpAD_D,SpMAD_D,EE_D,VE1_D,VE2_D,VE3_D,VR1_D,VR2_D,VR3_D,TopoPSA,VABC,VAdjMat,MWC2,MWC3,MWC4,MWC5,MWC6,MWC7,MWC8,MWC9,MWC10,TWC,SRW2,SRW3,SRW4,SRW5,SRW6,SRW7,SRW8,SRW9,SRW10,TSRW,MW,AMW,WTPT-1,WTPT-2,WTPT-3,WTPT-4,WTPT-5,WPATH,WPOL,XLogP,Zagreb
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