17amd64Cp1252en_GBc:\Program Files\KNIME\plugins64file:/C:/Users/User/knime-workspace/true-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx4026m
-Dorg.eclipse.swt.browser.IEVersion=11001
-Dsun.awt.noerasebackground=true
-Dequinox.statechange.timeout=30000
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=C:\Program Files\KNIME\\plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
truehttps://adoptium.net/osgi.ee; osgi.ee="OSGi/Minimum"; version:List<Version>="1.0, 1.1, 1.2", osgi.ee; osgi.ee="JRE"; version:List<Version>="1.0, 1.1", osgi.ee; osgi.ee="JavaSE"; version:List<Version>="1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0",osgi.ee; osgi.ee="JavaSE/compact1"; version:List<Version>="1.8, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0",osgi.ee; osgi.ee="JavaSE/compact2"; version:List<Version>="1.8, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0",osgi.ee; osgi.ee="JavaSE/compact3"; version:List<Version>="1.8, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0"org.apache.cxf.jaxrs.impl.RuntimeDelegateImpl4000MC:\Program Files\KNIME\plugins\org.knime.binary.jre.win32.x86_64_17.0.3.20220621\jre\binreleasec:\Program Files\KNIME\plugins\org.knime.product_4.6.3.v202209271303\splash.bmptruex86_64file:org.eclipse.equinox.simpleconfigurator/bundles.infoOracle Corporationencom.sun.java.accessibility.util, 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org.xml.sax, org.xml.sax.ext, org.xml.sax.helpers, sun.misc, sun.reflectorg.knime.product.KNIME_APPLICATION--nointeractive2022-04-19KnimeC:\Program Files\KNIME\plugins\org.knime.binary.jre.win32.x86_64_17.0.3.20220621\jre\Zero based
OSGi/Minimum-1.0, OSGi/Minimum-1.1, OSGi/Minimum-1.2, JavaSE/compact1-1.8, JavaSE/compact2-1.8, JavaSE/compact3-1.8, JRE-1.1, J2SE-1.2, J2SE-1.3, J2SE-1.4, J2SE-1.5, JavaSE-1.6, JavaSE-1.7, JavaSE-1.8, JavaSE-9, JavaSE-10, JavaSE-11, JavaSE-12, JavaSE-13, JavaSE-14, JavaSE-15, JavaSE-16, JavaSE-17Oracle CorporationJava Platform API SpecificationtrueclassnameHotSpot 64-Bit Tiered Compilers17.0.3+7100UsertruetrueEclipseCp1252org.knime.workbench.ui.ModellerPerspectiveTemurin-17.0.3+7reference:file:org.eclipse.osgi.compatibility.state_1.2.300.v20210212-1137.jar,reference:file:javax.transaction_1.1.1.v201105210645.jarC:\Users\User\AppData\Local\Tempfile:/C:/Program Files/KNIME/17.0.34Java Virtual Machine SpecificationCp1252C:\Program Files\KNIME;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\Python39\Scripts\;C:\Python39\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\ProgramData\chocolatey\bin;C:\Users\User\anaconda3;C:\Users\User\anaconda3\Library\mingw-w64\bin;C:\Users\User\anaconda3\Library\usr\bin;C:\Users\User\anaconda3\Library\bin;C:\Users\User\anaconda3\Scripts;C:\Users\User\AppData\Local\Microsoft\WindowsApps;C:\Program Files\heroku\bin;C:\Users\User\AppData\Local\Programs\Python\Python38\;C:\Users\User\AppData\Roaming\Python\Python38\ScriptsC:\Users\User\AppData\Roaming\Python\Python38\Scripts;C:\Users\User\AppData\Local\GitHubDesktop\bin;.Eclipse AdoptiumUnicodeLittle300001.10.0C:\Program Files\KNIME\\plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jartrueEclipse AdoptiumEurope/Londontrue090d1348-d874-4358-ac81-59b9235cc61817Windows 10x86-640GBlittleC:\Users\User\knime-workspace\.metadata\.logC:\Users\Userfile:/C:/Program Files/KNIME/enC:\Users\User\knime-workspace\.metadata\trace.logorg.apache.poi.util.NullLoggertruetruetrue3000011001C:\Program Files\KNIME\\plugins/org.knime.binary.jre.win32.x86_64_17.0.3.20220621/jre/bin/server/jvm.dllorg.knime.product.KNIME_PRODUCT--disable-web-securityfalsefalse-os
win32
-ws
win32
-arch
x86_64
-showsplash
-launcher
C:\Program Files\KNIME\knime.exe
-name
Knime
--launcher.library
C:\Program Files\KNIME\\plugins/org.eclipse.equinox.launcher.win32.win32.x86_64_1.2.100.v20210209-1541\eclipse_11301.dll
-startup
C:\Program Files\KNIME\\plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
--launcher.overrideVmargs
-vm
C:\Program Files\KNIME\\plugins/org.knime.binary.jre.win32.x86_64_17.0.3.20220621/jre/bin/server/jvm.dll
;true10.0OpenJDK Runtime Environmentorg.apache.cxf.jaxrs.client.spec.ClientBuilderImpltruereference:file:org.eclipse.osgi.compatibility.state_1.2.300.v20210212-1137.jar,reference:file:javax.transaction_1.1.1.v201105210645.jar,reference:file:org.eclipse.equinox.simpleconfigurator_1.3.600.v20200721-1308.jar@1:startfalsejarOpenJDK 64-Bit Server VMKNIMEProfilefile:/c:/Program Files/KNIME/plugins/org.eclipse.osgi_3.16.200.v20210226-1447.jarfile:/C:/Users/User/.eclipse/903338280_win32_win32_x86_64/configuration/win32https://github.com/adoptium/adoptium-support/issuesc:\Program Files\KNIME\plugins\org.knime.product_4.6.3.v202209271303\splash.bmpWindows10platform:/base/plugins/org.knime.producttrueorg.eclipse.ui.workbench/LegacyIDE.e4xmiC:\Users\User\.eclipse\903338280_win32_win32_x86_64\configurationC:\Program Files\KNIMEamd64file:/c:/Program Files/KNIME/configuration/win32file:/C:/Users/User/knime-workspace/C:\Program Files\KNIME\knime.exe., file:c:/Program Files/KNIME/plugins/org.eclipse.osgi.compatibility.state_1.2.300.v20210212-1137.jar, file:c:/Program Files/KNIME/plugins/javax.transaction_1.1.1.v201105210645.jar171232234194310.0.0mixed mode, sharing17.0.3+7@config.dir/../p2/61.0Auto conversion in column 'Smiles' failed: SMILES Parsing Error (MolSanitizeException (Explicit valence for atom # 1 N, 5, is greater than permitted)) - Using empty cell. [1 of 5395 rows]
Auto conversion in column 'Smiles' failed: SMILES Parsing Error (MolSanitizeException (Explicit valence for atom # 8 N, 5, is greater than permitted)) - Using empty cell. [2 of 5395 rows]
Encountered empty input cell. [3 of 5395 rows]Encountered empty input cell. [3 of 5395 rows]The current settings use missing value handling methods that cannot be represented in PMML 4.2The current settings use missing value handling methods that cannot be represented in PMML 4.20.63840399002493765240.17241379310344830.8275862068965517Notes from more layer network
Accuracy around 50 % more layers -neurons increasing by times 2. Acitvation Tanh
Reduced the number of neurons per each layer around 30 - 30 - 10 -10 - 5 - 2. Activation all linear but the last one - Accuracy around 63 %
tried to change all neurons but last one to Tanh. for most layers - Reduced the number of neurons to even below 10 ( first layer has 20 ) - Acc 50 %
Tried to change all activation function but last one to Hard sigmoid - Acc 58 %
Linear except last one sigmoid - Acc 40 %
Last one to tanh - Acc 51 %
Inreased the number of neurons and Relu - Acc around 40 %ceTesting combining all descript and fingerprint - (first has 245 neurons )100 and 50 neurons All tanh. The optimzer is set on ADAM - 98 % accuracy (However, i have noticed that the predictions are either negative or close to one and then the rule engine determine the class. Not sure why the are negative ).
With stoch grad and learn rate 0.001 - acc 98 %
- whole database used - massive drop in accuracies (below 50 % )
tried to increase epochs and training batch and valida - 200 - 50 - 15 - ACC 92 %DATA INPUTMODEL LEARNINGEXTERNAL VALIDATIONPERFORMANCE EVALUATION