summaryrefslogtreecommitdiff
path: root/paper/outfile.enriched.json
diff options
context:
space:
mode:
Diffstat (limited to 'paper/outfile.enriched.json')
-rw-r--r--paper/outfile.enriched.json1
1 files changed, 0 insertions, 1 deletions
diff --git a/paper/outfile.enriched.json b/paper/outfile.enriched.json
deleted file mode 100644
index a547003..0000000
--- a/paper/outfile.enriched.json
+++ /dev/null
@@ -1 +0,0 @@
-{"blocks":[{"t":"Header","c":[1,["introduction",[],[]],[{"t":"Str","c":"Introduction"}]]},{"t":"Para","c":[{"t":"Str","c":"TODO:"},{"t":"Space"},{"t":"Str","c":"algo"},{"t":"Space"},{"t":"Str","c":"history"}]},{"t":"Para","c":[{"t":"Str","c":"TODO:"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"history"}]},{"t":"Para","c":[{"t":"Str","c":"TODO:"},{"t":"Space"},{"t":"Str","c":"open"},{"t":"Space"},{"t":"Str","c":"problems"}]},{"t":"Header","c":[1,["materials-and-methods",[],[]],[{"t":"Str","c":"Materials"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Methods"}]]},{"t":"Header","c":[2,["mutagenicity-data",[],[]],[{"t":"Str","c":"Mutagenicity"},{"t":"Space"},{"t":"Str","c":"data"}]]},{"t":"Para","c":[{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"methods,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"same"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"SoftBreak"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"compiled"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"following"},{"t":"Space"},{"t":"Str","c":"sources:"}]},{"t":"BulletList","c":[[{"t":"Para","c":[{"t":"Str","c":"Kazius/Bursi"},{"t":"Space"},{"t":"Str","c":"Dataset"},{"t":"Space"},{"t":"Str","c":"(4337"},{"t":"Space"},{"t":"Str","c":"compounds,"},{"t":"Space"},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Kazius2005","citationHash":0}],[{"t":"Str","c":"@Kazius2005"}]]},{"t":"Str","c":"):"},{"t":"Space"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"http://cheminformatics.org/datasets/bursi/cas_4337.zip"}],["http://cheminformatics.org/datasets/bursi/cas_4337.zip",""]]}]}],[{"t":"Para","c":[{"t":"Str","c":"Hansen"},{"t":"Space"},{"t":"Str","c":"Dataset"},{"t":"Space"},{"t":"Str","c":"(6513"},{"t":"Space"},{"t":"Str","c":"compounds,"},{"t":"Space"},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Hansen2009","citationHash":0}],[{"t":"Str","c":"@Hansen2009"}]]},{"t":"Str","c":"):"},{"t":"Space"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv"}],["http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv",""]]}]}],[{"t":"Para","c":[{"t":"Str","c":"EFSA"},{"t":"Space"},{"t":"Str","c":"Dataset"},{"t":"Space"},{"t":"Str","c":"(695"},{"t":"Space"},{"t":"Str","c":"compounds):"},{"t":"Space"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://data.europa.eu/euodp/data/storage/f/2017-0719T142131/GENOTOX%20data%20and%20dictionary.xls"}],["https://data.europa.eu/euodp/data/storage/f/2017-0719T142131/GENOTOX%20data%20and%20dictionary.xls",""]]}]}]]},{"t":"Para","c":[{"t":"Str","c":"Mutagenicity"},{"t":"Space"},{"t":"Str","c":"classifications"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"Kazius"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Hansen"},{"t":"Space"},{"t":"Str","c":"datasets"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"SoftBreak"},{"t":"Str","c":"without"},{"t":"Space"},{"t":"Str","c":"further"},{"t":"Space"},{"t":"Str","c":"processing."},{"t":"Space"},{"t":"Str","c":"To"},{"t":"Space"},{"t":"Str","c":"achieve"},{"t":"Space"},{"t":"Str","c":"consistency"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"SoftBreak"},{"t":"Str","c":"datasets,"},{"t":"Space"},{"t":"Str","c":"EFSA"},{"t":"Space"},{"t":"Str","c":"compounds"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"classified"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"mutagenic,"},{"t":"Space"},{"t":"Str","c":"if"},{"t":"Space"},{"t":"Str","c":"at"},{"t":"Space"},{"t":"Str","c":"least"},{"t":"Space"},{"t":"Str","c":"one"},{"t":"SoftBreak"},{"t":"Str","c":"positive"},{"t":"Space"},{"t":"Str","c":"result"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"found"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"TA98"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"T100"},{"t":"Space"},{"t":"Str","c":"Salmonella"},{"t":"Space"},{"t":"Str","c":"strains."}]},{"t":"Para","c":[{"t":"Str","c":"Dataset"},{"t":"Space"},{"t":"Str","c":"merges"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"unique"},{"t":"Space"},{"t":"Str","c":"SMILES"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Emph","c":[{"t":"Str","c":"Simplified"},{"t":"Space"},{"t":"Str","c":"Molecular"},{"t":"Space"},{"t":"Str","c":"Input"},{"t":"SoftBreak"},{"t":"Str","c":"Line"},{"t":"Space"},{"t":"Str","c":"Entry"},{"t":"Space"},{"t":"Str","c":"Specification"}]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"strings"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"compound"},{"t":"Space"},{"t":"Str","c":"structures."},{"t":"SoftBreak"},{"t":"Str","c":"Duplicated"},{"t":"Space"},{"t":"Str","c":"experimental"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"same"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"merged"},{"t":"Space"},{"t":"Str","c":"into"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"single"},{"t":"Space"},{"t":"Str","c":"value,"},{"t":"Space"},{"t":"Str","c":"because"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"likely"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"originated"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"same"},{"t":"SoftBreak"},{"t":"Str","c":"experiment."},{"t":"Space"},{"t":"Str","c":"Contradictory"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"kept"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"multiple"},{"t":"Space"},{"t":"Str","c":"measurements"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"database."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"combined"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"contains"},{"t":"Space"},{"t":"Str","c":"8281"},{"t":"Space"},{"t":"Str","c":"unique"},{"t":"SoftBreak"},{"t":"Str","c":"structures."}]},{"t":"Para","c":[{"t":"Str","c":"Source"},{"t":"Space"},{"t":"Str","c":"code"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"download,"},{"t":"Space"},{"t":"Str","c":"extraction"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"merge"},{"t":"Space"},{"t":"Str","c":"operations"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"SoftBreak"},{"t":"Str","c":"publicly"},{"t":"Space"},{"t":"Str","c":"available"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"git"},{"t":"Space"},{"t":"Str","c":"repository"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://git.in-silico.ch/pyrrolizidine"}],["https://git.in-silico.ch/pyrrolizidine",""]]},{"t":"Space"},{"t":"Str","c":"under"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"GPL3"},{"t":"Space"},{"t":"Str","c":"License."}]},{"t":"Para","c":[{"t":"Str","c":"TODO:"},{"t":"Space"},{"t":"Str","c":"check/fix"},{"t":"Space"},{"t":"Str","c":"git"},{"t":"Space"},{"t":"Str","c":"repo"}]},{"t":"Para","c":[{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"Random"},{"t":"Space"},{"t":"Str","c":"Forest"},{"t":"Space"},{"t":"Str","c":"(RF),"},{"t":"Space"},{"t":"Str","c":"Support"},{"t":"Space"},{"t":"Str","c":"Vector"},{"t":"Space"},{"t":"Str","c":"Machines"},{"t":"Space"},{"t":"Str","c":"(SVM),"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Deep"},{"t":"SoftBreak"},{"t":"Str","c":"Learning"},{"t":"Space"},{"t":"Str","c":"(DL)"},{"t":"Space"},{"t":"Str","c":"models,"},{"t":"Space"},{"t":"Str","c":"molecular"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"SoftBreak"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"PaDEL-Descriptors"},{"t":"Space"},{"t":"Str","c":"program"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"http://www.yapcwsoft.com"}],["http://www.yapcwsoft.com",""]]},{"t":"Space"},{"t":"Str","c":"version"},{"t":"Space"},{"t":"Str","c":"2.21,"},{"t":"Space"},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Yap2011","citationHash":0}],[{"t":"Str","c":"@Yap2011"}]]},{"t":"Str","c":")."}]},{"t":"Para","c":[{"t":"Str","c":"TODO:"},{"t":"Space"},{"t":"Str","c":"sentence"},{"t":"Space"},{"t":"Str","c":"??"}]},{"t":"Para","c":[{"t":"Str","c":"From"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"SoftBreak"},{"t":"Str","c":"chosen,"},{"t":"Space"},{"t":"Str","c":"which"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"actually"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"generation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model."}]},{"t":"Header","c":[2,["algorithms",[],[]],[{"t":"Str","c":"Algorithms"}]]},{"t":"Header","c":[3,["lazar",[],[]],[{"t":"Code","c":[["",[],[]],"lazar"]}]]},{"t":"Para","c":[{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"("},{"t":"Emph","c":[{"t":"Str","c":"lazy"},{"t":"Space"},{"t":"Str","c":"structure"},{"t":"Space"},{"t":"Str","c":"activity"},{"t":"Space"},{"t":"Str","c":"relationships"}]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"modular"},{"t":"Space"},{"t":"Str","c":"framework"},{"t":"SoftBreak"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"read-across"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"development"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"validation."},{"t":"Space"},{"t":"Str","c":"It"},{"t":"Space"},{"t":"Str","c":"follows"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"following"},{"t":"Space"},{"t":"Str","c":"basic"},{"t":"Space"},{"t":"Str","c":"workflow:"},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"given"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"Space"},{"t":"Str","c":"structure"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Str","c":":"}]},{"t":"BulletList","c":[[{"t":"Para","c":[{"t":"Str","c":"searches"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"database"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"similar"},{"t":"Space"},{"t":"Str","c":"structures"},{"t":"Space"},{"t":"Str","c":"(neighbours)"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"SoftBreak"},{"t":"Str","c":"experimental"},{"t":"Space"},{"t":"Str","c":"data,"}]}],[{"t":"Para","c":[{"t":"Str","c":"builds"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"local"},{"t":"Space"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"neighbours"},{"t":"Space"},{"t":"Str","c":"and"}]}],[{"t":"Para","c":[{"t":"Str","c":"uses"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"predict"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"unknown"},{"t":"Space"},{"t":"Str","c":"activity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"query"},{"t":"SoftBreak"},{"t":"Str","c":"compound."}]}]]},{"t":"Para","c":[{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"procedure"},{"t":"Space"},{"t":"Str","c":"resembles"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"automated"},{"t":"Space"},{"t":"Str","c":"version"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"read"},{"t":"Space"},{"t":"Str","c":"across"},{"t":"Space"},{"t":"Str","c":"predictions"},{"t":"SoftBreak"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"toxicology,"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"machine"},{"t":"Space"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"terms"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"would"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"classified"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"k-nearest-neighbour"},{"t":"Space"},{"t":"Str","c":"algorithm."}]},{"t":"Para","c":[{"t":"Str","c":"Apart"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"basic"},{"t":"Space"},{"t":"Str","c":"workflow,"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"completely"},{"t":"Space"},{"t":"Str","c":"modular"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"allows"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"researcher"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"use"},{"t":"Space"},{"t":"Str","c":"any"},{"t":"Space"},{"t":"Str","c":"algorithm"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"similarity"},{"t":"Space"},{"t":"Str","c":"searches"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"local"},{"t":"SoftBreak"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Emph","c":[{"t":"Str","c":"Quantitative"},{"t":"Space"},{"t":"Str","c":"structure–activity"},{"t":"Space"},{"t":"Str","c":"relationship"}]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"modelling."},{"t":"SoftBreak"},{"t":"Str","c":"Algorithms"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"within"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"study"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"described"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"following"},{"t":"SoftBreak"},{"t":"Str","c":"sections."}]},{"t":"Header","c":[4,["neighbour-identification",[],[]],[{"t":"Str","c":"Neighbour"},{"t":"Space"},{"t":"Str","c":"identification"}]]},{"t":"Para","c":[{"t":"Str","c":"Similarity"},{"t":"Space"},{"t":"Str","c":"calculations"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"MolPrint2D"},{"t":"Space"},{"t":"Str","c":"fingerprints"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Bender2004","citationHash":0}],[{"t":"Str","c":"@Bender2004"}]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"OpenBabel"},{"t":"Space"},{"t":"Str","c":"cheminformatics"},{"t":"Space"},{"t":"Str","c":"library"},{"t":"SoftBreak"},{"t":"Str","c":"("},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"OBoyle2011a","citationHash":0}],[{"t":"Str","c":"@OBoyle2011a"}]]},{"t":"Str","c":")."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"MolPrint2D"},{"t":"Space"},{"t":"Str","c":"fingerprint"},{"t":"Space"},{"t":"Str","c":"uses"},{"t":"SoftBreak"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"environments"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"molecular"},{"t":"Space"},{"t":"Str","c":"representation,"},{"t":"Space"},{"t":"Str","c":"which"},{"t":"Space"},{"t":"Str","c":"resembles"},{"t":"Space"},{"t":"Str","c":"basically"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"Space"},{"t":"Str","c":"concept"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"functional"},{"t":"Space"},{"t":"Str","c":"groups."},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"each"},{"t":"Space"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"molecule,"},{"t":"SoftBreak"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"represents"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"Space"},{"t":"Str","c":"environment"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"types"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"connected"},{"t":"SoftBreak"},{"t":"Str","c":"atoms."}]},{"t":"Para","c":[{"t":"Str","c":"MolPrint2D"},{"t":"Space"},{"t":"Str","c":"fingerprints"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"dynamically"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"SoftBreak"},{"t":"Str","c":"structures"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"do"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"rely"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"predefined"},{"t":"Space"},{"t":"Str","c":"lists"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"fragments"},{"t":"Space"},{"t":"Str","c":"(such"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"SoftBreak"},{"t":"Str","c":"OpenBabel"},{"t":"Space"},{"t":"Str","c":"FP3,"},{"t":"Space"},{"t":"Str","c":"FP4"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"MACCs"},{"t":"Space"},{"t":"Str","c":"fingerprints"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"lists"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"toxicophores/toxicophobes)."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"advantage"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"they"},{"t":"Space"},{"t":"Str","c":"may"},{"t":"Space"},{"t":"Str","c":"capture"},{"t":"SoftBreak"},{"t":"Str","c":"substructures"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"toxicological"},{"t":"Space"},{"t":"Str","c":"relevance"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"included"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"SoftBreak"},{"t":"Str","c":"fingerprints."}]},{"t":"Para","c":[{"t":"Str","c":"From"},{"t":"Space"},{"t":"Str","c":"MolPrint2D"},{"t":"Space"},{"t":"Str","c":"fingerprints"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"feature"},{"t":"Space"},{"t":"Str","c":"vector"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"environments"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"compound"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"constructed"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"calculate"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"SoftBreak"},{"t":"Str","c":"similarities."}]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"Space"},{"t":"Str","c":"similarity"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"two"},{"t":"Space"},{"t":"Str","c":"compounds"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"b"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"expressed"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"proportion"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"environments"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"both"},{"t":"Space"},{"t":"Str","c":"structures"},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"∩"},{"t":"Space"},{"t":"Str","c":"B"},{"t":"SoftBreak"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"total"},{"t":"Space"},{"t":"Str","c":"number"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"atom"},{"t":"Space"},{"t":"Str","c":"environments"},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"U"},{"t":"Space"},{"t":"Str","c":"B"},{"t":"Space"},{"t":"Str","c":"(Jaccard/Tanimoto"},{"t":"SoftBreak"},{"t":"Str","c":"index)."}]},{"t":"Para","c":[{"t":"Math","c":[{"t":"DisplayMath"},"sim = \\frac{\\left| A\\ \\cap B \\right|}{\\left| A\\ \\cup B \\right|}"]}]},{"t":"Para","c":[{"t":"Str","c":"Threshold"},{"t":"Space"},{"t":"Str","c":"selection"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"trade-off"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"prediction"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"(high"},{"t":"SoftBreak"},{"t":"Str","c":"threshold)"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"number"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"predictable"},{"t":"Space"},{"t":"Str","c":"compounds"},{"t":"Space"},{"t":"Str","c":"(low"},{"t":"Space"},{"t":"Str","c":"threshold)."},{"t":"Space"},{"t":"Str","c":"As"},{"t":"SoftBreak"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"many"},{"t":"Space"},{"t":"Str","c":"practical"},{"t":"Space"},{"t":"Str","c":"cases"},{"t":"Space"},{"t":"Str","c":"desirable"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"make"},{"t":"Space"},{"t":"Str","c":"predictions"},{"t":"Space"},{"t":"Str","c":"even"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"absence"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"closely"},{"t":"Space"},{"t":"Str","c":"related"},{"t":"Space"},{"t":"Str","c":"neighbours,"},{"t":"Space"},{"t":"Str","c":"we"},{"t":"Space"},{"t":"Str","c":"follow"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"tiered"},{"t":"Space"},{"t":"Str","c":"approach:"}]},{"t":"BulletList","c":[[{"t":"Para","c":[{"t":"Str","c":"First"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"similarity"},{"t":"Space"},{"t":"Str","c":"threshold"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"0.5"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"collect"},{"t":"Space"},{"t":"Str","c":"neighbours,"},{"t":"SoftBreak"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"create"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"local"},{"t":"Space"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"make"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"prediction"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"query"},{"t":"SoftBreak"},{"t":"Str","c":"compound."}]}],[{"t":"Para","c":[{"t":"Str","c":"If"},{"t":"Space"},{"t":"Str","c":"any"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"steps"},{"t":"Space"},{"t":"Str","c":"fails,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"procedure"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"repeated"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"similarity"},{"t":"Space"},{"t":"Str","c":"threshold"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"0.2"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"prediction"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"flagged"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"warning"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"might"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"out"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"applicability"},{"t":"Space"},{"t":"Str","c":"domain"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data."}]}],[{"t":"Para","c":[{"t":"Str","c":"Similarity"},{"t":"Space"},{"t":"Str","c":"thresholds"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"0.5"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"0.2"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"default"},{"t":"Space"},{"t":"Str","c":"values"},{"t":"Space"},{"t":"Str","c":"chosen"},{"t":"SoftBreak"},{"t":"Str","c":">"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"software"},{"t":"Space"},{"t":"Str","c":"developers"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"remained"},{"t":"Space"},{"t":"Str","c":"unchanged"},{"t":"Space"},{"t":"Str","c":"during"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":">"},{"t":"Space"},{"t":"Str","c":"course"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"experiments."}]}]]},{"t":"Para","c":[{"t":"Str","c":"Compounds"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"same"},{"t":"Space"},{"t":"Str","c":"structure"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"query"},{"t":"Space"},{"t":"Str","c":"structure"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"SoftBreak"},{"t":"Str","c":"automatically"},{"t":"Space"},{"t":"Str","c":"eliminated"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"neighbours"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"obtain"},{"t":"Space"},{"t":"Str","c":"unbiased"},{"t":"Space"},{"t":"Str","c":"predictions"},{"t":"SoftBreak"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"presence"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"duplicates."}]},{"t":"Header","c":[4,["local-qsar-models-and-predictions",[],[]],[{"t":"Str","c":"Local"},{"t":"Space"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"predictions"}]]},{"t":"Para","c":[{"t":"Str","c":"Only"},{"t":"Space"},{"t":"Str","c":"similar"},{"t":"Space"},{"t":"Str","c":"compounds"},{"t":"Space"},{"t":"Str","c":"(neighbours)"},{"t":"Space"},{"t":"Str","c":"above"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"threshold"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"SoftBreak"},{"t":"Str","c":"local"},{"t":"Space"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"models."},{"t":"Space"},{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"investigation,"},{"t":"Space"},{"t":"Str","c":"we"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"weighted"},{"t":"SoftBreak"},{"t":"Str","c":"majority"},{"t":"Space"},{"t":"Str","c":"vote"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"neighbour’s"},{"t":"Space"},{"t":"Str","c":"experimental"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"mutagenicity"},{"t":"SoftBreak"},{"t":"Str","c":"classifications."},{"t":"Space"},{"t":"Str","c":"Probabilities"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"both"},{"t":"Space"},{"t":"Str","c":"classes"},{"t":"SoftBreak"},{"t":"Str","c":"(mutagenic/non-mutagenic)"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"Space"},{"t":"Str","c":"according"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"following"},{"t":"SoftBreak"},{"t":"Str","c":"formula"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"class"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"higher"},{"t":"Space"},{"t":"Str","c":"probability"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"prediction"},{"t":"SoftBreak"},{"t":"Str","c":"outcome."}]},{"t":"Para","c":[{"t":"Math","c":[{"t":"DisplayMath"},"p_{c} = \\ \\frac{\\sum_{}^{}\\text{sim}_{n,c}}{\\sum_{}^{}\\text{sim}_{n}}"]}]},{"t":"Para","c":[{"t":"Math","c":[{"t":"InlineMath"},"p_{c}"]},{"t":"Space"},{"t":"Str","c":"Probability"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"class"},{"t":"Space"},{"t":"Str","c":"c"},{"t":"Space"},{"t":"Str","c":"(e.g. mutagenic"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"non-mutagenic)"},{"t":"LineBreak"},{"t":"Math","c":[{"t":"InlineMath"},"\\sum_{}^{}\\text{sim}_{n,c}"]},{"t":"Space"},{"t":"Str","c":"Sum"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"similarities"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"neighbours"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"SoftBreak"},{"t":"Str","c":"class"},{"t":"Space"},{"t":"Str","c":"c"},{"t":"LineBreak"},{"t":"Math","c":[{"t":"InlineMath"},"\\sum_{}^{}\\text{sim}_{n}"]},{"t":"Space"},{"t":"Str","c":"Sum"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"neighbours"}]},{"t":"Header","c":[4,["applicability-domain",[],[]],[{"t":"Str","c":"Applicability"},{"t":"Space"},{"t":"Str","c":"domain"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"applicability"},{"t":"Space"},{"t":"Str","c":"domain"},{"t":"Space"},{"t":"Str","c":"(AD)"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"determined"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"structural"},{"t":"Space"},{"t":"Str","c":"diversity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data."},{"t":"Space"},{"t":"Str","c":"If"},{"t":"Space"},{"t":"Str","c":"no"},{"t":"Space"},{"t":"Str","c":"similar"},{"t":"Space"},{"t":"Str","c":"compounds"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"SoftBreak"},{"t":"Str","c":"found"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"no"},{"t":"Space"},{"t":"Str","c":"predictions"},{"t":"Space"},{"t":"Str","c":"will"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"generated."},{"t":"Space"},{"t":"Str","c":"Warnings"},{"t":"SoftBreak"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"issued"},{"t":"Space"},{"t":"Str","c":"if"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"similarity"},{"t":"Space"},{"t":"Str","c":"threshold"},{"t":"Space"},{"t":"Str","c":"had"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"lowered"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"0.5"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"0.2"},{"t":"SoftBreak"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"order"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"enable"},{"t":"Space"},{"t":"Str","c":"predictions."},{"t":"Space"},{"t":"Str","c":"Predictions"},{"t":"Space"},{"t":"Str","c":"without"},{"t":"Space"},{"t":"Str","c":"warnings"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"SoftBreak"},{"t":"Str","c":"considered"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"close"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"applicability"},{"t":"Space"},{"t":"Str","c":"domain"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"predictions"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"SoftBreak"},{"t":"Str","c":"warnings"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"more"},{"t":"Space"},{"t":"Str","c":"distant"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"applicability"},{"t":"Space"},{"t":"Str","c":"domain."},{"t":"Space"},{"t":"Str","c":"Quantitative"},{"t":"SoftBreak"},{"t":"Str","c":"applicability"},{"t":"Space"},{"t":"Str","c":"domain"},{"t":"Space"},{"t":"Str","c":"information"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"obtained"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"similarities"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"individual"},{"t":"Space"},{"t":"Str","c":"neighbours."}]},{"t":"Header","c":[4,["availability",[],[]],[{"t":"Str","c":"Availability"}]]},{"t":"BulletList","c":[[{"t":"Para","c":[{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"experiments"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"manuscript:"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://git.in-silico.ch/pyrrolizidine"}],["https://git.in-silico.ch/pyrrolizidine",""]]},{"t":"SoftBreak"},{"t":"Str","c":"(source"},{"t":"Space"},{"t":"Str","c":"code,"},{"t":"Space"},{"t":"Str","c":"GPL3)"}]}],[{"t":"Para","c":[{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"framework:"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://git.in-silico.ch/lazar"}],["https://git.in-silico.ch/lazar",""]]},{"t":"SoftBreak"},{"t":"Str","c":"(source"},{"t":"Space"},{"t":"Str","c":"code,"},{"t":"Space"},{"t":"Str","c":"GPL3)"}]}],[{"t":"Para","c":[{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"GUI:"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://git.in-silico.ch/lazar-gui"}],["https://git.in-silico.ch/lazar-gui",""]]},{"t":"SoftBreak"},{"t":"Str","c":"(source"},{"t":"Space"},{"t":"Str","c":"code,"},{"t":"Space"},{"t":"Str","c":"GPL3)"}]}],[{"t":"Para","c":[{"t":"Str","c":"Public"},{"t":"Space"},{"t":"Str","c":"web"},{"t":"Space"},{"t":"Str","c":"interface:"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://lazar.in-silico.ch"}],["https://lazar.in-silico.ch",""]]}]}]]},{"t":"Header","c":[3,["random-forest-support-vector-machines-and-deep-learning-in-r-project",[],[]],[{"t":"Str","c":"Random"},{"t":"Space"},{"t":"Str","c":"Forest,"},{"t":"Space"},{"t":"Str","c":"Support"},{"t":"Space"},{"t":"Str","c":"Vector"},{"t":"Space"},{"t":"Str","c":"Machines,"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Deep"},{"t":"Space"},{"t":"Str","c":"Learning"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"R-project"}]]},{"t":"Para","c":[{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"comparison"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Str","c":","},{"t":"Space"},{"t":"Str","c":"three"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"(Random"},{"t":"Space"},{"t":"Str","c":"Forest"},{"t":"Space"},{"t":"Str","c":"(RF),"},{"t":"Space"},{"t":"Str","c":"Support"},{"t":"SoftBreak"},{"t":"Str","c":"Vector"},{"t":"Space"},{"t":"Str","c":"Machines"},{"t":"Space"},{"t":"Str","c":"(SVM),"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Deep"},{"t":"Space"},{"t":"Str","c":"Learning"},{"t":"Space"},{"t":"Str","c":"(DL))"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"evaluated."}]},{"t":"Para","c":[{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"generation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"models,"},{"t":"Space"},{"t":"Str","c":"molecular"},{"t":"Space"},{"t":"Str","c":"1D"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"2D"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"PaDEL-Descriptors"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"http://www.yapcwsoft.com"}],["http://www.yapcwsoft.com",""]]},{"t":"Space"},{"t":"Str","c":"version"},{"t":"SoftBreak"},{"t":"Str","c":"2.21,"},{"t":"Space"},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Yap2011","citationHash":0}],[{"t":"Str","c":"@Yap2011"}]]},{"t":"Str","c":")."}]},{"t":"Para","c":[{"t":"Str","c":"As"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"contained"},{"t":"Space"},{"t":"Str","c":"over"},{"t":"Space"},{"t":"Str","c":"8280"},{"t":"Space"},{"t":"Str","c":"instances,"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"decided"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"SoftBreak"},{"t":"Str","c":"delete"},{"t":"Space"},{"t":"Str","c":"instances"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"missing"},{"t":"Space"},{"t":"Str","c":"values"},{"t":"Space"},{"t":"Str","c":"during"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"pre-processing."},{"t":"SoftBreak"},{"t":"Str","c":"Furthermore,"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"equivocal"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"removed."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"final"},{"t":"SoftBreak"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"contained"},{"t":"Space"},{"t":"Str","c":"8080"},{"t":"Space"},{"t":"Str","c":"instances"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"known"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"SoftBreak"},{"t":"Str","c":"potential."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"RF,"},{"t":"Space"},{"t":"Str","c":"SVM,"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"R"},{"t":"SoftBreak"},{"t":"Str","c":"software"},{"t":"Space"},{"t":"Str","c":"(R-project"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"Statistical"},{"t":"Space"},{"t":"Str","c":"Computing,"},{"t":"SoftBreak"},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://www.r-project.org/"}],["https://www.r-project.org/",""]]},{"t":"Emph","c":[{"t":"Str","c":";"}]},{"t":"Space"},{"t":"Str","c":"version"},{"t":"Space"},{"t":"Str","c":"3.3.1),"},{"t":"Space"},{"t":"Str","c":"specific"},{"t":"Space"},{"t":"Str","c":"R"},{"t":"Space"},{"t":"Str","c":"packages"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"SoftBreak"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"identified"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"each"},{"t":"Space"},{"t":"Str","c":"step"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"description"},{"t":"Space"},{"t":"Str","c":"below."},{"t":"Space"},{"t":"Str","c":"During"},{"t":"Space"},{"t":"Str","c":"feature"},{"t":"SoftBreak"},{"t":"Str","c":"selection,"},{"t":"Space"},{"t":"Str","c":"descriptor"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"near"},{"t":"Space"},{"t":"Str","c":"zero"},{"t":"Space"},{"t":"Str","c":"variance"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"removed"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"SoftBreak"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"NearZeroVar"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"caret"}]]},{"t":"Str","c":")."},{"t":"Space"},{"t":"Str","c":"If"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"percentage"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"most"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"value"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"more"},{"t":"Space"},{"t":"Str","c":"than"},{"t":"Space"},{"t":"Str","c":"90%"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"when"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"frequency"},{"t":"Space"},{"t":"Str","c":"ratio"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"most"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"value"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"second"},{"t":"Space"},{"t":"Str","c":"most"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"value"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"greater"},{"t":"Space"},{"t":"Str","c":"than"},{"t":"Space"},{"t":"Str","c":"95:5"},{"t":"SoftBreak"},{"t":"Str","c":"(e.g. 95"},{"t":"Space"},{"t":"Str","c":"instances"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"most"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"value"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"only"},{"t":"Space"},{"t":"Str","c":"5"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"less"},{"t":"Space"},{"t":"Str","c":"instances"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"second"},{"t":"Space"},{"t":"Str","c":"most"},{"t":"Space"},{"t":"Str","c":"common"},{"t":"Space"},{"t":"Str","c":"value),"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"descriptor"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"classified"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"having"},{"t":"SoftBreak"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"near"},{"t":"Space"},{"t":"Str","c":"zero"},{"t":"Space"},{"t":"Str","c":"variance."},{"t":"Space"},{"t":"Str","c":"After"},{"t":"Space"},{"t":"Str","c":"that,"},{"t":"Space"},{"t":"Str","c":"highly"},{"t":"Space"},{"t":"Str","c":"correlated"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"SoftBreak"},{"t":"Str","c":"removed"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"findCorrelation"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"caret"}]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"cut-off"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"0.9."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"resulted"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"516"},{"t":"SoftBreak"},{"t":"Str","c":"descriptors."},{"t":"Space"},{"t":"Str","c":"These"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"scaled"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"range"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"0"},{"t":"SoftBreak"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"1"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"preProcess"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"caret"}]]},{"t":"Str","c":")."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"scaling"},{"t":"SoftBreak"},{"t":"Str","c":"routine"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"saved"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"order"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"apply"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"same"},{"t":"Space"},{"t":"Str","c":"scaling"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"testing"},{"t":"SoftBreak"},{"t":"Str","c":"dataset."},{"t":"Space"},{"t":"Str","c":"As"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"three"},{"t":"Space"},{"t":"Str","c":"steps"},{"t":"Space"},{"t":"Str","c":"did"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"consider"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome,"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"SoftBreak"},{"t":"Str","c":"decided"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"they"},{"t":"Space"},{"t":"Str","c":"do"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"need"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"included"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model."},{"t":"Space"},{"t":"Str","c":"To"},{"t":"Space"},{"t":"Str","c":"further"},{"t":"Space"},{"t":"Str","c":"reduce"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"number"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"features,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"LASSO"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Emph","c":[{"t":"Str","c":"least"},{"t":"SoftBreak"},{"t":"Str","c":"absolute"},{"t":"Space"},{"t":"Str","c":"shrinkage"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"selection"},{"t":"Space"},{"t":"Str","c":"operator"}]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"regression"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"performed"},{"t":"SoftBreak"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"glmnet"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"glmnet"}]}]]},{"t":"Str","c":")."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"reduced"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"SoftBreak"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"generation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"pre-trained"},{"t":"Space"},{"t":"Str","c":"models."}]},{"t":"Para","c":[{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"RF"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"randomForest"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"SoftBreak"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"randomForest"}]}]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"forest"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"1000"},{"t":"Space"},{"t":"Str","c":"trees"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"maximal"},{"t":"SoftBreak"},{"t":"Str","c":"terminal"},{"t":"Space"},{"t":"Str","c":"nodes"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"200"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"grown"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"prediction."}]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"svm"}]}]]},{"t":"Str","c":"-function"},{"t":"Space"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"e1071"}]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Emph","c":[{"t":"Str","c":"radial"},{"t":"Space"},{"t":"Str","c":"basis"},{"t":"Space"},{"t":"Str","c":"function"},{"t":"SoftBreak"},{"t":"Str","c":"kernel"}]},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"SVM"},{"t":"Space"},{"t":"Str","c":"model."}]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"h2o.deeplearning"}]}]]},{"t":"Str","c":"-function"},{"t":"SoftBreak"},{"t":"Str","c":"(package"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"h2o"}]}]]},{"t":"Str","c":")."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"contained"},{"t":"Space"},{"t":"Str","c":"four"},{"t":"Space"},{"t":"Str","c":"hidden"},{"t":"Space"},{"t":"Str","c":"layer"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"70,"},{"t":"Space"},{"t":"Str","c":"50,"},{"t":"Space"},{"t":"Str","c":"50,"},{"t":"SoftBreak"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"10"},{"t":"Space"},{"t":"Str","c":"neurons,"},{"t":"Space"},{"t":"Str","c":"respectively."},{"t":"Space"},{"t":"Str","c":"Other"},{"t":"Space"},{"t":"Str","c":"hyperparameter"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"set"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"follows:"},{"t":"SoftBreak"},{"t":"Str","c":"l1=1.0E-7,"},{"t":"Space"},{"t":"Str","c":"l2=1.0E-11,"},{"t":"Space"},{"t":"Str","c":"epsilon"},{"t":"Space"},{"t":"Str","c":"="},{"t":"Space"},{"t":"Str","c":"1.0E-10,"},{"t":"Space"},{"t":"Str","c":"rho"},{"t":"Space"},{"t":"Str","c":"="},{"t":"Space"},{"t":"Str","c":"0.8,"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"quantile_alpha"},{"t":"SoftBreak"},{"t":"Str","c":"="},{"t":"Space"},{"t":"Str","c":"0.5."},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"Space"},{"t":"Str","c":"hyperparameter,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"default"},{"t":"Space"},{"t":"Str","c":"values"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"SoftBreak"},{"t":"Str","c":"Weights"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"biases"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"first"},{"t":"Space"},{"t":"Str","c":"step"},{"t":"Space"},{"t":"Str","c":"determined"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"unsupervised"},{"t":"SoftBreak"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model."},{"t":"Space"},{"t":"Str","c":"These"},{"t":"Space"},{"t":"Str","c":"values"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"then"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"actual,"},{"t":"Space"},{"t":"Str","c":"supervised"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"SoftBreak"},{"t":"Str","c":"model."}]},{"t":"Para","c":[{"t":"Str","c":"To"},{"t":"Space"},{"t":"Str","c":"validate"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"models,"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"internal"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"approach"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"SoftBreak"},{"t":"Str","c":"chosen."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"randomly"},{"t":"Space"},{"t":"Str","c":"split"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data,"},{"t":"Space"},{"t":"Str","c":"which"},{"t":"SoftBreak"},{"t":"Str","c":"contained"},{"t":"Space"},{"t":"Str","c":"95%"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"data,"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"data,"},{"t":"Space"},{"t":"Str","c":"which"},{"t":"Space"},{"t":"Str","c":"contain"},{"t":"Space"},{"t":"Str","c":"5%"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"data."},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"feature"},{"t":"Space"},{"t":"Str","c":"selection"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"LASSO"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"performed,"},{"t":"SoftBreak"},{"t":"Str","c":"reducing"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"number"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"descriptors"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"approximately"},{"t":"Space"},{"t":"Str","c":"100."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"step"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"SoftBreak"},{"t":"Str","c":"repeated"},{"t":"Space"},{"t":"Str","c":"five"},{"t":"Space"},{"t":"Str","c":"times."},{"t":"Space"},{"t":"Str","c":"Based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"each"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"five"},{"t":"Space"},{"t":"Str","c":"different"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"data,"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"predictive"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"trained"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"performance"},{"t":"Space"},{"t":"Str","c":"tested"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"data."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"step"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"repeated"},{"t":"Space"},{"t":"Str","c":"10"},{"t":"Space"},{"t":"Str","c":"times."},{"t":"Space"},{"t":"Str","c":"Furthermore,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"y-randomisation"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"RF"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"performed."},{"t":"Space"},{"t":"Str","c":"During"},{"t":"SoftBreak"},{"t":"Str","c":"y-randomisation,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"(y-variable)"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"randomly"},{"t":"Space"},{"t":"Str","c":"permuted."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"SoftBreak"},{"t":"Str","c":"theory"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"after"},{"t":"Space"},{"t":"Str","c":"randomisation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"should"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"SoftBreak"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"able"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"correlate"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"properties"},{"t":"Space"},{"t":"Str","c":"(descriptor"},{"t":"Space"},{"t":"Str","c":"values)"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"substances."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"performance"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"should"},{"t":"Space"},{"t":"Str","c":"therefore"},{"t":"SoftBreak"},{"t":"Str","c":"indicate"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"change"},{"t":"Space"},{"t":"Str","c":"prediction"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"about"},{"t":"Space"},{"t":"Str","c":"50%."},{"t":"Space"},{"t":"Str","c":"If"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"SoftBreak"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"true,"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"concluded"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"correlation"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"actual"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"SoftBreak"},{"t":"Str","c":"properties"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"real"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"chance"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Cite","c":[[{"citationSuffix":[],"citationNoteNum":0,"citationMode":{"t":"AuthorInText"},"citationPrefix":[],"citationId":"Rücker2007","citationHash":0}],[{"t":"Str","c":"@Rücker2007"}]]},{"t":"Str","c":")."}]},{"t":"Para","c":[{"t":"Image","c":[["",[],[["width","6.26875in"],["height","5.486111111111111in"]]],[],["media/image1.png",""]]}]},{"t":"Para","c":[{"t":"Str","c":"Figure"},{"t":"Space"},{"t":"Str","c":"1:"},{"t":"Space"},{"t":"Str","c":"Flowchart"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"generation"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"SoftBreak"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"R-project"}]},{"t":"Header","c":[4,["applicability-domain-1",[],[]],[{"t":"Str","c":"Applicability"},{"t":"Space"},{"t":"Str","c":"domain"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"AD"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"PA"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"evaluated"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"Jaccard"},{"t":"Space"},{"t":"Str","c":"distance."},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"Jaccard"},{"t":"Space"},{"t":"Str","c":"distance"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"0"}]]},{"t":"Space"},{"t":"Str","c":"indicates"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"similar,"},{"t":"Space"},{"t":"Str","c":"whereas"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"value"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"1"}]]},{"t":"Space"},{"t":"Str","c":"shows"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"SoftBreak"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"different."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"Jaccard"},{"t":"Space"},{"t":"Str","c":"distance"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"below"},{"t":"Space"},{"t":"Str","c":"0.2"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"PAs"},{"t":"Space"},{"t":"Str","c":"relative"},{"t":"SoftBreak"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset."},{"t":"Space"},{"t":"Str","c":"Therefore,"},{"t":"Space"},{"t":"Str","c":"PA"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"within"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"AD"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"predict"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"genotoxic"},{"t":"SoftBreak"},{"t":"Str","c":"potential"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"PA"},{"t":"Space"},{"t":"Str","c":"dataset."}]},{"t":"Header","c":[4,["y-randomisation",[],[]],[{"t":"Str","c":"y-randomisation"}]]},{"t":"Para","c":[{"t":"Str","c":"After"},{"t":"Space"},{"t":"Str","c":"y-randomisation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"CCR"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"around"},{"t":"SoftBreak"},{"t":"Str","c":"50%,"},{"t":"Space"},{"t":"Str","c":"indicating"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"chance"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"distribution"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"results."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"shows,"},{"t":"SoftBreak"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"actually"},{"t":"Space"},{"t":"Str","c":"related"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"predictors"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"SoftBreak"},{"t":"Str","c":"chance."}]},{"t":"Header","c":[3,["deep-learning-in-tensorflow",[],[]],[{"t":"Str","c":"Deep"},{"t":"Space"},{"t":"Str","c":"Learning"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"TensorFlow"}]]},{"t":"Para","c":[{"t":"Str","c":"Alternatively,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"established"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"Python-based"},{"t":"Space"},{"t":"Str","c":"TensorFlow"},{"t":"SoftBreak"},{"t":"Str","c":"program"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://www.tensorflow.org/"}],["https://www.tensorflow.org/",""]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"high-level"},{"t":"Space"},{"t":"Str","c":"API"},{"t":"Space"},{"t":"Str","c":"Keras"},{"t":"SoftBreak"},{"t":"Str","c":"("},{"t":"Link","c":[["",["uri"],[]],[{"t":"Str","c":"https://www.tensorflow.org/guide/keras"}],["https://www.tensorflow.org/guide/keras",""]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"build"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"models."}]},{"t":"Para","c":[{"t":"Str","c":"Data"},{"t":"Space"},{"t":"Str","c":"pre-processing"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"done"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"rank"},{"t":"Space"},{"t":"Str","c":"transformation"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"QuantileTransformer"}]}]]},{"t":"Space"},{"t":"Str","c":"procedure."},{"t":"Space"},{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"sequential"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"been"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"SoftBreak"},{"t":"Str","c":"Four"},{"t":"Space"},{"t":"Str","c":"layers"},{"t":"Space"},{"t":"Str","c":"have"},{"t":"Space"},{"t":"Str","c":"been"},{"t":"Space"},{"t":"Str","c":"used:"},{"t":"Space"},{"t":"Str","c":"input"},{"t":"Space"},{"t":"Str","c":"layer,"},{"t":"Space"},{"t":"Str","c":"two"},{"t":"Space"},{"t":"Str","c":"hidden"},{"t":"Space"},{"t":"Str","c":"layers"},{"t":"Space"},{"t":"Str","c":"(with"},{"t":"Space"},{"t":"Str","c":"12,"},{"t":"Space"},{"t":"Str","c":"8"},{"t":"SoftBreak"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"8"},{"t":"Space"},{"t":"Str","c":"nodes,"},{"t":"Space"},{"t":"Str","c":"respectively)"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"one"},{"t":"Space"},{"t":"Str","c":"output"},{"t":"Space"},{"t":"Str","c":"layer."},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"output"},{"t":"Space"},{"t":"Str","c":"layer,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"sigmoidal"},{"t":"Space"},{"t":"Str","c":"activation"},{"t":"Space"},{"t":"Str","c":"function"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"Space"},{"t":"Str","c":"layers"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"ReLU"},{"t":"SoftBreak"},{"t":"Str","c":"("},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Emph","c":[{"t":"Str","c":"Rectified"},{"t":"Space"},{"t":"Str","c":"Linear"},{"t":"Space"},{"t":"Str","c":"Unit"}]}]]},{"t":"Str","c":")"},{"t":"Space"},{"t":"Str","c":"activation"},{"t":"Space"},{"t":"Str","c":"function"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"Space"},{"t":"Str","c":"Additionally,"},{"t":"SoftBreak"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"L"},{"t":"Superscript","c":[{"t":"Str","c":"2"}]},{"t":"Str","c":"-penalty"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"0.001"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"input"},{"t":"Space"},{"t":"Str","c":"layer."},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"ADAM"},{"t":"Space"},{"t":"Str","c":"algorithm"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"minimise"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"cross-entropy"},{"t":"SoftBreak"},{"t":"Str","c":"loss"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"default"},{"t":"Space"},{"t":"Str","c":"parameters"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"Keras."},{"t":"Space"},{"t":"Str","c":"Training"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"performed"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"SoftBreak"},{"t":"Str","c":"100"},{"t":"Space"},{"t":"Str","c":"epochs"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"batch"},{"t":"Space"},{"t":"Str","c":"size"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"64."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"implemented"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"SoftBreak"},{"t":"Str","c":"Python"},{"t":"Space"},{"t":"Str","c":"3.6"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"Keras."},{"t":"Space"},{"t":"Str","c":"For"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"6-fold"},{"t":"SoftBreak"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"used."},{"t":"Space"},{"t":"Str","c":"Accuracy"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"estimated"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"ROC-AUC"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"SoftBreak"},{"t":"Str","c":"confusion"},{"t":"Space"},{"t":"Str","c":"matrix."}]},{"t":"Header","c":[2,["validation",[],[]],[{"t":"Str","c":"Validation"}]]},{"t":"Header","c":[1,["results",[],[]],[{"t":"Str","c":"Results"}]]},{"t":"Header","c":[2,["lazar-1",[],[]],[{"t":"Code","c":[["",[],[]],"lazar"]}]]},{"t":"Header","c":[2,["random-forest",[],[]],[{"t":"Str","c":"Random"},{"t":"Space"},{"t":"Str","c":"Forest"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"showed"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"RF"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"64%,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"66%"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"63%."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"8080"},{"t":"Space"},{"t":"Str","c":"instances,"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"provided"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"1."}]},{"t":"Para","c":[{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"1:"},{"t":"Space"},{"t":"Str","c":"Confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"RF"},{"t":"Space"},{"t":"Str","c":"model"}]},{"t":"Table","c":[[],[{"t":"AlignDefault"},{"t":"AlignLeft"},{"t":"AlignDefault"},{"t":"AlignDefault"},{"t":"AlignDefault"}],[0,0,0,0,0],[[],[{"t":"Plain","c":[{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[],[]],[[[{"t":"Plain","c":[{"t":"Str","c":"Measured"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PP"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PN"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TP"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"2274"}]}],[{"t":"Plain","c":[{"t":"Str","c":"1163"}]}],[{"t":"Plain","c":[{"t":"Str","c":"3437"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TN"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"1736"}]}],[{"t":"Plain","c":[{"t":"Str","c":"2907"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4643"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"4010"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4070"}]}],[{"t":"Plain","c":[{"t":"Str","c":"8080"}]}]]]]},{"t":"Para","c":[{"t":"Str","c":"PP:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"positive;"},{"t":"Space"},{"t":"Str","c":"PN:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"negative,"},{"t":"Space"},{"t":"Str","c":"TP:"},{"t":"Space"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"positive,"},{"t":"Space"},{"t":"Str","c":"TN:"},{"t":"SoftBreak"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"negative"}]},{"t":"Header","c":[2,["support-vector-machines",[],[]],[{"t":"Str","c":"Support"},{"t":"Space"},{"t":"Str","c":"Vector"},{"t":"Space"},{"t":"Str","c":"Machines"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"showed"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"SVM"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"62%,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"65%"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"60%."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"SVM"},{"t":"SoftBreak"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"8080"},{"t":"Space"},{"t":"Str","c":"instances,"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"provided"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"2."}]},{"t":"Para","c":[{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"2:"},{"t":"Space"},{"t":"Str","c":"Confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"SVM"},{"t":"Space"},{"t":"Str","c":"model"}]},{"t":"Table","c":[[],[{"t":"AlignDefault"},{"t":"AlignLeft"},{"t":"AlignDefault"},{"t":"AlignDefault"},{"t":"AlignDefault"}],[0,0,0,0,0],[[],[{"t":"Plain","c":[{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[],[]],[[[{"t":"Plain","c":[{"t":"Str","c":"Measured"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PP"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PN"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TP"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"2057"}]}],[{"t":"Plain","c":[{"t":"Str","c":"1107"}]}],[{"t":"Plain","c":[{"t":"Str","c":"3164"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TN"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"1953"}]}],[{"t":"Plain","c":[{"t":"Str","c":"2963"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4916"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"4010"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4070"}]}],[{"t":"Plain","c":[{"t":"Str","c":"8080"}]}]]]]},{"t":"Para","c":[{"t":"Str","c":"PP:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"positive;"},{"t":"Space"},{"t":"Str","c":"PN:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"negative,"},{"t":"Space"},{"t":"Str","c":"TP:"},{"t":"Space"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"positive,"},{"t":"Space"},{"t":"Str","c":"TN:"},{"t":"SoftBreak"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"negative"}]},{"t":"Header","c":[2,["deep-learning-r-project",[],[]],[{"t":"Str","c":"Deep"},{"t":"Space"},{"t":"Str","c":"Learning"},{"t":"Space"},{"t":"Str","c":"(R-project)"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"showed"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"R"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"59%,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"89%"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"30%."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"confusion"},{"t":"SoftBreak"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"normalised"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"8080"},{"t":"Space"},{"t":"Str","c":"instances,"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"provided"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"Table"},{"t":"SoftBreak"},{"t":"Str","c":"3."}]},{"t":"Para","c":[{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"3:"},{"t":"Space"},{"t":"Str","c":"Confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"(R-project)"}]},{"t":"Table","c":[[],[{"t":"AlignDefault"},{"t":"AlignLeft"},{"t":"AlignDefault"},{"t":"AlignDefault"},{"t":"AlignDefault"}],[0,0,0,0,0],[[],[{"t":"Plain","c":[{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[],[]],[[[{"t":"Plain","c":[{"t":"Str","c":"Measured"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PP"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PN"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TP"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"3575"}]}],[{"t":"Plain","c":[{"t":"Str","c":"435"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4010"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TN"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"2853"}]}],[{"t":"Plain","c":[{"t":"Str","c":"1217"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4070"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"6428"}]}],[{"t":"Plain","c":[{"t":"Str","c":"1652"}]}],[{"t":"Plain","c":[{"t":"Str","c":"8080"}]}]]]]},{"t":"Para","c":[{"t":"Str","c":"PP:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"positive;"},{"t":"Space"},{"t":"Str","c":"PN:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"negative,"},{"t":"Space"},{"t":"Str","c":"TP:"},{"t":"Space"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"positive,"},{"t":"Space"},{"t":"Str","c":"TN:"},{"t":"SoftBreak"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"negative"}]},{"t":"Header","c":[2,["dl-model-tensorflow",[],[]],[{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"(TensorFlow)"}]]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"showed"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"TensorFlow"},{"t":"Space"},{"t":"Str","c":"has"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"SoftBreak"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"68%,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"70%"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"46%."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"SoftBreak"},{"t":"Str","c":"confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"normalised"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"8080"},{"t":"Space"},{"t":"Str","c":"instances,"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"provided"},{"t":"SoftBreak"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"4."}]},{"t":"Para","c":[{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"4:"},{"t":"Space"},{"t":"Str","c":"Confusion"},{"t":"Space"},{"t":"Str","c":"matrix"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"(TensorFlow)"}]},{"t":"Table","c":[[],[{"t":"AlignDefault"},{"t":"AlignLeft"},{"t":"AlignDefault"},{"t":"AlignDefault"},{"t":"AlignDefault"}],[0,0,0,0,0],[[],[{"t":"Plain","c":[{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[],[]],[[[{"t":"Plain","c":[{"t":"Str","c":"Measured"},{"t":"Space"},{"t":"Str","c":"genotoxicity"}]}],[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PP"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"PN"}]}]}]}],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TP"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"2851"}]}],[{"t":"Plain","c":[{"t":"Str","c":"1227"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4078"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"TN"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"1825"}]}],[{"t":"Plain","c":[{"t":"Str","c":"2177"}]}],[{"t":"Plain","c":[{"t":"Str","c":"4002"}]}]],[[],[{"t":"Plain","c":[{"t":"Strong","c":[{"t":"Emph","c":[{"t":"Str","c":"Total"}]}]}]}],[{"t":"Plain","c":[{"t":"Str","c":"4676"}]}],[{"t":"Plain","c":[{"t":"Str","c":"3404"}]}],[{"t":"Plain","c":[{"t":"Str","c":"8080"}]}]]]]},{"t":"Para","c":[{"t":"Str","c":"PP:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"positive;"},{"t":"Space"},{"t":"Str","c":"PN:"},{"t":"Space"},{"t":"Str","c":"Predicted"},{"t":"Space"},{"t":"Str","c":"negative,"},{"t":"Space"},{"t":"Str","c":"TP:"},{"t":"Space"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"positive,"},{"t":"Space"},{"t":"Str","c":"TN:"},{"t":"SoftBreak"},{"t":"Str","c":"True"},{"t":"Space"},{"t":"Str","c":"negative"}]},{"t":"Para","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"ROC"},{"t":"Space"},{"t":"Str","c":"curves"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"6-fold"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"shown"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"Figure"},{"t":"Space"},{"t":"Str","c":"7."}]},{"t":"Para","c":[{"t":"Image","c":[["",[],[["width","3.825in"],["height","2.7327045056867894in"]]],[],["media/image7.png",""]]}]},{"t":"Para","c":[{"t":"Str","c":"Figure"},{"t":"Space"},{"t":"Str","c":"7:"},{"t":"Space"},{"t":"Str","c":"Six-fold"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"TensorFlow"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"show"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"SoftBreak"},{"t":"Str","c":"average"},{"t":"Space"},{"t":"Str","c":"area"},{"t":"Space"},{"t":"Str","c":"under"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"ROC-curve"},{"t":"Space"},{"t":"Str","c":"(ROC-AUC;"},{"t":"Space"},{"t":"Str","c":"measure"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"accuracy)"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"68%."}]},{"t":"Para","c":[{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"summary,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"four"},{"t":"Space"},{"t":"Str","c":"methods"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"presented"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"following"},{"t":"Space"},{"t":"Str","c":"table."}]},{"t":"Para","c":[{"t":"Str","c":"Table"},{"t":"Space"},{"t":"Str","c":"5"},{"t":"Space"},{"t":"Str","c":"Results"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"four"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"after"},{"t":"SoftBreak"},{"t":"Str","c":"y-randomisation"}]},{"t":"Table","c":[[],[{"t":"AlignDefault"},{"t":"AlignLeft"},{"t":"AlignLeft"},{"t":"AlignLeft"},{"t":"AlignLeft"}],[0.3287671232876712,0.1506849315068493,0.1095890410958904,0.1917808219178082,0.1917808219178082],[[],[{"t":"Plain","c":[{"t":"Str","c":"Accuracy"}]}],[{"t":"Plain","c":[{"t":"Str","c":"CCR"}]}],[{"t":"Plain","c":[{"t":"Str","c":"Sensitivity"}]}],[{"t":"Plain","c":[{"t":"Str","c":"Specificity"}]}]],[[[{"t":"Plain","c":[{"t":"Str","c":"RF"},{"t":"Space"},{"t":"Str","c":"model"}]}],[{"t":"Plain","c":[{"t":"Str","c":"64.1%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"64.4%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"66.2%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"62.6%"}]}]],[[{"t":"Plain","c":[{"t":"Str","c":"SVM"},{"t":"Space"},{"t":"Str","c":"model"}]}],[{"t":"Plain","c":[{"t":"Str","c":"62.1%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"62.6%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"65.0%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"60.3%"}]}]],[[{"t":"Plain","c":[{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"LineBreak"},{"t":"Str","c":"(R-project)"}]}],[{"t":"Plain","c":[{"t":"Str","c":"59.3%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"59.5%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"89.2%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"29.9%"}]}]],[[{"t":"Plain","c":[{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"(TensorFlow)"}]}],[{"t":"Plain","c":[{"t":"Str","c":"68%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"62.2%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"69.9%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"45.6%"}]}]],[[{"t":"Plain","c":[{"t":"Str","c":"y-randomisation"}]}],[{"t":"Plain","c":[{"t":"Str","c":"50.5%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"50.4%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"50.3%"}]}],[{"t":"Plain","c":[{"t":"Str","c":"50.6%"}]}]]]]},{"t":"Para","c":[{"t":"Str","c":"CCR"},{"t":"Space"},{"t":"Str","c":"(correct"},{"t":"Space"},{"t":"Str","c":"classification"},{"t":"Space"},{"t":"Str","c":"rate)"}]},{"t":"Header","c":[1,["discussion",[],[]],[{"t":"Str","c":"Discussion"}]]},{"t":"Para","c":[{"t":"Str","c":"General"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"performance"}]},{"t":"Para","c":[{"t":"Str","c":"Based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"models,"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Str","c":","},{"t":"Space"},{"t":"Str","c":"RF,"},{"t":"SoftBreak"},{"t":"Str","c":"SVM,"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"(R-project)"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"(TensorFlow)"},{"t":"Space"},{"t":"Str","c":"it"},{"t":"Space"},{"t":"Str","c":"can"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"state"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"prediction"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"optimal"},{"t":"Space"},{"t":"Str","c":"due"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"different"},{"t":"Space"},{"t":"Str","c":"reasons."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"SoftBreak"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"measured"},{"t":"Space"},{"t":"Str","c":"during"},{"t":"Space"},{"t":"Str","c":"cross-validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"four"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"(RF,"},{"t":"SoftBreak"},{"t":"Str","c":"SVM,"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"(R-project"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"TensorFlow))"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"partly"},{"t":"Space"},{"t":"Str","c":"low"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"CCR"},{"t":"Space"},{"t":"Str","c":"values"},{"t":"SoftBreak"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"59.3"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"68%,"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"R-generated"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"TensorFlow-generated"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"showing"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"worst"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"best"},{"t":"SoftBreak"},{"t":"Str","c":"performance,"},{"t":"Space"},{"t":"Str","c":"respectively."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"validation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"R-generated"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"SoftBreak"},{"t":"Str","c":"revealed"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"high"},{"t":"Space"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"(89.2%)"},{"t":"Space"},{"t":"Str","c":"but"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"unacceptably"},{"t":"Space"},{"t":"Str","c":"low"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"SoftBreak"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"29.9%"},{"t":"Space"},{"t":"Str","c":"indicating"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"high"},{"t":"Space"},{"t":"Str","c":"number"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"false"},{"t":"Space"},{"t":"Str","c":"positive"},{"t":"Space"},{"t":"Str","c":"estimates."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"SoftBreak"},{"t":"Str","c":"TensorFlow-generated"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model,"},{"t":"Space"},{"t":"Str","c":"however,"},{"t":"Space"},{"t":"Str","c":"showed"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"acceptable"},{"t":"Space"},{"t":"Str","c":"but"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"SoftBreak"},{"t":"Str","c":"optimal"},{"t":"Space"},{"t":"Str","c":"accuracy"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"68%,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"sensitivity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"69.9%"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"45.6%."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"low"},{"t":"Space"},{"t":"Str","c":"specificity"},{"t":"Space"},{"t":"Str","c":"indicates"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"both"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"tends"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"SoftBreak"},{"t":"Str","c":"predict"},{"t":"Space"},{"t":"Str","c":"too"},{"t":"Space"},{"t":"Str","c":"many"},{"t":"Space"},{"t":"Str","c":"instances"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"positive"},{"t":"Space"},{"t":"Str","c":"(genotoxic),"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"therefore"},{"t":"Space"},{"t":"Str","c":"have"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"high"},{"t":"Space"},{"t":"Str","c":"false"},{"t":"Space"},{"t":"Str","c":"positive"},{"t":"Space"},{"t":"Str","c":"rate."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"allows"},{"t":"Space"},{"t":"Str","c":"at"},{"t":"Space"},{"t":"Str","c":"least"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"TensorFlow"},{"t":"SoftBreak"},{"t":"Str","c":"generated"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"make"},{"t":"Space"},{"t":"Str","c":"group"},{"t":"Space"},{"t":"Str","c":"statements,"},{"t":"Space"},{"t":"Str","c":"but"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"confidence"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"SoftBreak"},{"t":"Str","c":"estimations"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"single"},{"t":"Space"},{"t":"Str","c":"PAs"},{"t":"Space"},{"t":"Str","c":"appears"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"insufficiently"},{"t":"Space"},{"t":"Str","c":"low."}]},{"t":"Para","c":[{"t":"Str","c":"Several"},{"t":"Space"},{"t":"Str","c":"factors"},{"t":"Space"},{"t":"Str","c":"have"},{"t":"Space"},{"t":"Str","c":"likely"},{"t":"Space"},{"t":"Str","c":"contributed"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"low"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"moderate"},{"t":"SoftBreak"},{"t":"Str","c":"performance"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"methods"},{"t":"Space"},{"t":"Str","c":"as"},{"t":"Space"},{"t":"Str","c":"shown"},{"t":"Space"},{"t":"Str","c":"during"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"cross-validation:"}]},{"t":"OrderedList","c":[[1,{"t":"Decimal"},{"t":"Period"}],[[{"t":"Plain","c":[{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"AMES"},{"t":"SoftBreak"},{"t":"Str","c":"tests"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"genotoxicity"},{"t":"Space"},{"t":"Link","c":[["",[],[]],[{"t":"Str","c":"ICH"},{"t":"Space"},{"t":"Str","c":"2011"}],["#_ENREF_63",""]]},{"t":"Str","c":"(),"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Emph","c":[{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"vitro"}]},{"t":"Space"},{"t":"Str","c":"test"},{"t":"SoftBreak"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"different"},{"t":"Space"},{"t":"Str","c":"strains"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"bacteria"},{"t":"Space"},{"t":"Emph","c":[{"t":"Str","c":"Salmonella"},{"t":"Space"},{"t":"Str","c":"typhimurium"}]},{"t":"Str","c":"."},{"t":"Space"},{"t":"Str","c":"In"},{"t":"SoftBreak"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"test,"},{"t":"Space"},{"t":"Str","c":"mutagenicity"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"evaluated"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"without"},{"t":"Space"},{"t":"Str","c":"prior"},{"t":"SoftBreak"},{"t":"Str","c":"metabolic"},{"t":"Space"},{"t":"Str","c":"activation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"test"},{"t":"Space"},{"t":"Str","c":"substance."},{"t":"Space"},{"t":"Str","c":"Metabolic"},{"t":"Space"},{"t":"Str","c":"activation"},{"t":"SoftBreak"},{"t":"Str","c":"could"},{"t":"Space"},{"t":"Str","c":"result"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"formation"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"genotoxic"},{"t":"Space"},{"t":"Str","c":"metabolites"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"SoftBreak"},{"t":"Str","c":"non-genotoxic"},{"t":"Space"},{"t":"Str","c":"parent"},{"t":"Space"},{"t":"Str","c":"compounds."},{"t":"Space"},{"t":"Str","c":"However,"},{"t":"Space"},{"t":"Str","c":"no"},{"t":"Space"},{"t":"Str","c":"distinction"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"made"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"between"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"needed"},{"t":"Space"},{"t":"Str","c":"metabolic"},{"t":"SoftBreak"},{"t":"Str","c":"activation"},{"t":"Space"},{"t":"Str","c":"before"},{"t":"Space"},{"t":"Str","c":"being"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"those"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"SoftBreak"},{"t":"Str","c":"without"},{"t":"Space"},{"t":"Str","c":"metabolic"},{"t":"Space"},{"t":"Str","c":"activation."},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"able"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"handle"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"SoftBreak"},{"t":"Quoted","c":[{"t":"SingleQuote"},[{"t":"Str","c":"inaccuracy"}]]},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"well"},{"t":"Space"},{"t":"Str","c":"due"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"way"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"algorithm"},{"t":"Space"},{"t":"Str","c":"works:"},{"t":"Space"},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Space"},{"t":"Str","c":"predicts"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"genotoxic"},{"t":"Space"},{"t":"Str","c":"potential"},{"t":"Space"},{"t":"Str","c":"based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"neighbours"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"comparable"},{"t":"Space"},{"t":"Str","c":"structural"},{"t":"Space"},{"t":"Str","c":"features,"},{"t":"SoftBreak"},{"t":"Str","c":"considering"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"Space"},{"t":"Str","c":"neighbours."},{"t":"Space"},{"t":"Str","c":"Based"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"structural"},{"t":"Space"},{"t":"Str","c":"similarity,"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"probability"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"mutagenicity"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"no"},{"t":"SoftBreak"},{"t":"Str","c":"mutagenicity"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"calculated"},{"t":"Space"},{"t":"Str","c":"independently"},{"t":"Space"},{"t":"Str","c":"from"},{"t":"Space"},{"t":"Str","c":"each"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"Space"},{"t":"Str","c":"(meaning"},{"t":"SoftBreak"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"sum"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"probabilities"},{"t":"Space"},{"t":"Str","c":"does"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"necessarily"},{"t":"Space"},{"t":"Str","c":"adds"},{"t":"Space"},{"t":"Str","c":"up"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"100%)."},{"t":"SoftBreak"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"class"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"higher"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"is"},{"t":"Space"},{"t":"Str","c":"then"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"overall"},{"t":"Space"},{"t":"Str","c":"outcome"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"substance."}]}]]]},{"t":"BlockQuote","c":[{"t":"Para","c":[{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"contrast,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"other"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"need"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"trained"},{"t":"Space"},{"t":"Str","c":"first"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"recognise"},{"t":"SoftBreak"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"structural"},{"t":"Space"},{"t":"Str","c":"features"},{"t":"Space"},{"t":"Str","c":"that"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"responsible"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"genotoxicity."},{"t":"SoftBreak"},{"t":"Str","c":"Therefore,"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"mixture"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"being"},{"t":"Space"},{"t":"Str","c":"mutagenic"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"without"},{"t":"SoftBreak"},{"t":"Str","c":"metabolic"},{"t":"Space"},{"t":"Str","c":"activation"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"may"},{"t":"Space"},{"t":"Str","c":"have"},{"t":"Space"},{"t":"Str","c":"adversely"},{"t":"SoftBreak"},{"t":"Str","c":"affected"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"ability"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"separate"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"two"},{"t":"Space"},{"t":"Str","c":"distinct"},{"t":"Space"},{"t":"Str","c":"classes"},{"t":"SoftBreak"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"thus"},{"t":"Space"},{"t":"Str","c":"explains"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"relatively"},{"t":"Space"},{"t":"Str","c":"low"},{"t":"Space"},{"t":"Str","c":"performance"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"models."}]}]},{"t":"OrderedList","c":[[2,{"t":"Decimal"},{"t":"Period"}],[[{"t":"Plain","c":[{"t":"Str","c":"Machine"},{"t":"Space"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"algorithms"},{"t":"Space"},{"t":"Str","c":"try"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"find"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"optimized"},{"t":"Space"},{"t":"Str","c":"solution"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"SoftBreak"},{"t":"Str","c":"high-dimensional"},{"t":"Space"},{"t":"Str","c":"(one"},{"t":"Space"},{"t":"Str","c":"dimension"},{"t":"Space"},{"t":"Str","c":"per"},{"t":"Space"},{"t":"Str","c":"each"},{"t":"Space"},{"t":"Str","c":"predictor)"},{"t":"Space"},{"t":"Str","c":"space."},{"t":"Space"},{"t":"Str","c":"Sometimes"},{"t":"SoftBreak"},{"t":"Str","c":"these"},{"t":"Space"},{"t":"Str","c":"methods"},{"t":"Space"},{"t":"Str","c":"do"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"find"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"global"},{"t":"Space"},{"t":"Str","c":"optimum"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"estimates"},{"t":"Space"},{"t":"Str","c":"but"},{"t":"Space"},{"t":"Str","c":"only"},{"t":"SoftBreak"},{"t":"Str","c":"local"},{"t":"Space"},{"t":"Str","c":"(not"},{"t":"Space"},{"t":"Str","c":"optimal)"},{"t":"Space"},{"t":"Str","c":"solutions."},{"t":"Space"},{"t":"Str","c":"Strategies"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"find"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"global"},{"t":"SoftBreak"},{"t":"Str","c":"solutions"},{"t":"Space"},{"t":"Str","c":"are"},{"t":"Space"},{"t":"Str","c":"systematic"},{"t":"Space"},{"t":"Str","c":"variation"},{"t":"Space"},{"t":"Str","c":"(grid"},{"t":"Space"},{"t":"Str","c":"search)"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"hyperparameters"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"methods,"},{"t":"Space"},{"t":"Str","c":"which"},{"t":"Space"},{"t":"Str","c":"may"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"very"},{"t":"Space"},{"t":"Str","c":"time"},{"t":"Space"},{"t":"Str","c":"consuming"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"SoftBreak"},{"t":"Str","c":"particular"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"large"},{"t":"Space"},{"t":"Str","c":"datasets."}]}]]]},{"t":"Header","c":[1,["conclusions",[],[]],[{"t":"Str","c":"Conclusions"}]]},{"t":"Para","c":[{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"this"},{"t":"Space"},{"t":"Str","c":"study,"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"attempt"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"made"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"predict"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"genotoxic"},{"t":"Space"},{"t":"Str","c":"potential"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"PAs"},{"t":"Space"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"five"},{"t":"Space"},{"t":"Str","c":"different"},{"t":"Space"},{"t":"Str","c":"machine"},{"t":"Space"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"techniques"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Str","c":","},{"t":"Space"},{"t":"Str","c":"RF,"},{"t":"Space"},{"t":"Str","c":"SVM,"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"SoftBreak"},{"t":"Str","c":"(R-project"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"TensorFlow)."},{"t":"Space"},{"t":"Str","c":"The"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"all"},{"t":"Space"},{"t":"Str","c":"models"},{"t":"Space"},{"t":"Str","c":"fitted"},{"t":"Space"},{"t":"Str","c":"only"},{"t":"Space"},{"t":"Str","c":"partly"},{"t":"SoftBreak"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"findings"},{"t":"Space"},{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"literature,"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"best"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"Space"},{"t":"Str","c":"obtained"},{"t":"Space"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"TensorFlow"},{"t":"Space"},{"t":"Str","c":"DL"},{"t":"Space"},{"t":"Str","c":"model."},{"t":"Space"},{"t":"Str","c":"Therefore,"},{"t":"Space"},{"t":"Str","c":"modelling"},{"t":"Space"},{"t":"Str","c":"allows"},{"t":"Space"},{"t":"Str","c":"statements"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"relative"},{"t":"Space"},{"t":"Str","c":"risks"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"genotoxicity"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"different"},{"t":"Space"},{"t":"Str","c":"PA"},{"t":"Space"},{"t":"Str","c":"groups."},{"t":"Space"},{"t":"Str","c":"Individual"},{"t":"SoftBreak"},{"t":"Str","c":"predictions"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"selective"},{"t":"Space"},{"t":"Str","c":"PAs"},{"t":"Space"},{"t":"Str","c":"appear,"},{"t":"Space"},{"t":"Str","c":"however,"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"reliable"},{"t":"Space"},{"t":"Str","c":"on"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"SoftBreak"},{"t":"Str","c":"current"},{"t":"Space"},{"t":"Str","c":"basis"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset."}]},{"t":"Para","c":[{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"study"},{"t":"Space"},{"t":"Str","c":"emphasises"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"importance"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"critical"},{"t":"Space"},{"t":"Str","c":"assessment"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"SoftBreak"},{"t":"Str","c":"predictions"},{"t":"Space"},{"t":"Str","c":"by"},{"t":"Space"},{"t":"Str","c":"QSAR"},{"t":"Space"},{"t":"Str","c":"models."},{"t":"Space"},{"t":"Str","c":"This"},{"t":"Space"},{"t":"Str","c":"includes"},{"t":"Space"},{"t":"Str","c":"not"},{"t":"Space"},{"t":"Str","c":"only"},{"t":"Space"},{"t":"Str","c":"extensive"},{"t":"Space"},{"t":"Str","c":"literature"},{"t":"SoftBreak"},{"t":"Str","c":"research"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"assess"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"plausibility"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"predictions,"},{"t":"Space"},{"t":"Str","c":"but"},{"t":"Space"},{"t":"Str","c":"also"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"good"},{"t":"SoftBreak"},{"t":"Str","c":"knowledge"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"metabolism"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"test"},{"t":"Space"},{"t":"Str","c":"substances"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"understanding"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"SoftBreak"},{"t":"Str","c":"possible"},{"t":"Space"},{"t":"Str","c":"mechanisms"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"toxicity."}]},{"t":"Para","c":[{"t":"Str","c":"In"},{"t":"Space"},{"t":"Str","c":"further"},{"t":"Space"},{"t":"Str","c":"studies,"},{"t":"Space"},{"t":"Str","c":"additional"},{"t":"Space"},{"t":"Str","c":"machine"},{"t":"Space"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"techniques"},{"t":"Space"},{"t":"Str","c":"or"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"modified"},{"t":"SoftBreak"},{"t":"Str","c":"(extended)"},{"t":"Space"},{"t":"Str","c":"training"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"Space"},{"t":"Str","c":"should"},{"t":"Space"},{"t":"Str","c":"be"},{"t":"Space"},{"t":"Str","c":"used"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"an"},{"t":"Space"},{"t":"Str","c":"additional"},{"t":"Space"},{"t":"Str","c":"attempt"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"SoftBreak"},{"t":"Str","c":"predict"},{"t":"Space"},{"t":"Str","c":"the"},{"t":"Space"},{"t":"Str","c":"genotoxic"},{"t":"Space"},{"t":"Str","c":"potential"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"PAs."}]},{"t":"Header","c":[1,["references",[],[]],[{"t":"Str","c":"References"}]]}],"pandoc-api-version":[1,17,5,4],"meta":{"bibliography":{"t":"MetaInlines","c":[{"t":"Str","c":"bibliography.bib"}]},"documentclass":{"t":"MetaInlines","c":[{"t":"Str","c":"scrartcl"}]},"keywords":{"t":"MetaInlines","c":[{"t":"Str","c":"mutagenicity,"},{"t":"Space"},{"t":"Str","c":"(Q)SAR,"},{"t":"Space"},{"t":"Str","c":"lazar,"},{"t":"Space"},{"t":"Str","c":"random"},{"t":"Space"},{"t":"Str","c":"forest,"},{"t":"Space"},{"t":"Str","c":"support"},{"t":"Space"},{"t":"Str","c":"vector"},{"t":"Space"},{"t":"Str","c":"machine,"},{"t":"Space"},{"t":"Str","c":"deep"},{"t":"Space"},{"t":"Str","c":"learning"}]},"author":{"t":"MetaList","c":[{"t":"MetaMap","c":{"email":{"t":"MetaInlines","c":[{"t":"Str","c":"helma@in-silico.ch"}]},"name":{"t":"MetaInlines","c":[{"t":"Str","c":"Christoph Helma"}]},"correspondence":{"t":"MetaInlines","c":[{"t":"Str","c":"yes"}]},"id":{"t":"MetaString","c":"Christoph Helma"},"institute":{"t":"MetaList","c":[{"t":"MetaString","c":"1"}]}}},{"t":"MetaMap","c":{"name":{"t":"MetaInlines","c":[{"t":"Str","c":"Verena Schöning"}]},"id":{"t":"MetaString","c":"Verena Schöning"},"institute":{"t":"MetaList","c":[{"t":"MetaString","c":"2"}]}}},{"t":"MetaMap","c":{"name":{"t":"MetaInlines","c":[{"t":"Str","c":"Philipp Boss"}]},"id":{"t":"MetaString","c":"Philipp Boss"},"institute":{"t":"MetaList","c":[{"t":"MetaString","c":"2"}]}}},{"t":"MetaMap","c":{"name":{"t":"MetaInlines","c":[{"t":"Str","c":"Jürgen Drewe"}]},"id":{"t":"MetaString","c":"Jürgen Drewe"},"institute":{"t":"MetaList","c":[{"t":"MetaString","c":"2"}]}}}]},"abstract":{"t":"MetaBlocks","c":[{"t":"Para","c":[{"t":"Str","c":"k-nearest"},{"t":"Space"},{"t":"Str","c":"neighbor"},{"t":"Space"},{"t":"Str","c":"("},{"t":"Code","c":[["",[],[]],"lazar"]},{"t":"Str","c":"),"},{"t":"Space"},{"t":"Str","c":"random"},{"t":"Space"},{"t":"Str","c":"forest,"},{"t":"Space"},{"t":"Str","c":"support"},{"t":"Space"},{"t":"Str","c":"vector"},{"t":"Space"},{"t":"Str","c":"machine"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"deep"},{"t":"SoftBreak"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"algorithms"},{"t":"Space"},{"t":"Str","c":"were"},{"t":"Space"},{"t":"Str","c":"applied"},{"t":"Space"},{"t":"Str","c":"to"},{"t":"Space"},{"t":"Str","c":"a"},{"t":"Space"},{"t":"Str","c":"new"},{"t":"Space"},{"t":"Emph","c":[{"t":"Str","c":"Salmonella"}]},{"t":"Space"},{"t":"Str","c":"mutagenicity"},{"t":"Space"},{"t":"Str","c":"dataset"},{"t":"SoftBreak"},{"t":"Str","c":"with"},{"t":"Space"},{"t":"Str","c":"8281"},{"t":"Space"},{"t":"Str","c":"unique"},{"t":"Space"},{"t":"Str","c":"chemical"},{"t":"Space"},{"t":"Str","c":"structures."},{"t":"Space"},{"t":"Str","c":"Algorithm"},{"t":"Space"},{"t":"Str","c":"performance"},{"t":"Space"},{"t":"Str","c":"was"},{"t":"Space"},{"t":"Str","c":"evaluated"},{"t":"SoftBreak"},{"t":"Str","c":"using"},{"t":"Space"},{"t":"Str","c":"5-fold"},{"t":"Space"},{"t":"Str","c":"crossvalidation."},{"t":"SoftBreak"},{"t":"Str","c":"TODO"},{"t":"SoftBreak"},{"t":"Str","c":"-"},{"t":"Space"},{"t":"Str","c":"results"},{"t":"SoftBreak"},{"t":"Str","c":"-"},{"t":"Space"},{"t":"Str","c":"conclusion"}]}]},"title":{"t":"MetaInlines","c":[{"t":"Str","c":"A"},{"t":"Space"},{"t":"Str","c":"comparison"},{"t":"Space"},{"t":"Str","c":"of"},{"t":"Space"},{"t":"Str","c":"random"},{"t":"Space"},{"t":"Str","c":"forest,"},{"t":"Space"},{"t":"Str","c":"support"},{"t":"Space"},{"t":"Str","c":"vector"},{"t":"Space"},{"t":"Str","c":"machine,"},{"t":"Space"},{"t":"Str","c":"deep"},{"t":"Space"},{"t":"Str","c":"learning"},{"t":"Space"},{"t":"Str","c":"and"},{"t":"Space"},{"t":"Str","c":"lazar"},{"t":"Space"},{"t":"Str","c":"algorithms"},{"t":"Space"},{"t":"Str","c":"for"},{"t":"Space"},{"t":"Str","c":"predicting"},{"t":"Space"},{"t":"Str","c":"mutagenicity"}]},"cito_cites":{"t":"MetaMap","c":{"citation":{"t":"MetaList","c":[{"t":"MetaString","c":"Kazius2005"},{"t":"MetaString","c":"Hansen2009"},{"t":"MetaString","c":"Yap2011"},{"t":"MetaString","c":"Bender2004"},{"t":"MetaString","c":"OBoyle2011a"},{"t":"MetaString","c":"Yap2011"},{"t":"MetaString","c":"Rücker2007"}]}}},"institute":{"t":"MetaList","c":[{"t":"MetaMap","c":{"address":{"t":"MetaInlines","c":[{"t":"Str","c":"Rastatterstrasse"},{"t":"Space"},{"t":"Str","c":"41,"},{"t":"Space"},{"t":"Str","c":"4057"},{"t":"Space"},{"t":"Str","c":"Basel,"},{"t":"Space"},{"t":"Str","c":"Switzerland"}]},"name":{"t":"MetaInlines","c":[{"t":"Str","c":"in"},{"t":"Space"},{"t":"Str","c":"silico"},{"t":"Space"},{"t":"Str","c":"toxicology"},{"t":"Space"},{"t":"Str","c":"gmbh"}]},"id":{"t":"MetaString","c":"ist"}}},{"t":"MetaMap","c":{"address":{"t":"MetaInlines","c":[{"t":"Str","c":"Seeblickstrasse"},{"t":"Space"},{"t":"Str","c":"4,"},{"t":"Space"},{"t":"Str","c":"8590"},{"t":"Space"},{"t":"Str","c":"Romanshorn,"},{"t":"Space"},{"t":"Str","c":"Switzerland"}]},"name":{"t":"MetaInlines","c":[{"t":"Str","c":"Zeller"},{"t":"Space"},{"t":"Str","c":"AG"}]},"id":{"t":"MetaString","c":"zeller"}}}]}}}