Java library of multi-way algorithms.
Home Page: https://waikato-datamining.github.io/multiway-algorithms/
License: GNU General Public License v3.0
Java library of multi-way algorithms.
For more documentation, go to:
waikato-datamining.github.io/multiway-algorithms
Available algorithms:
Add the following dependency in your pom.xml:
<dependency>
<groupId>nz.ac.waikato.cms.adams</groupId>
<artifactId>multiway-algorithms</artifactId>
<version>0.0.7</version>
</dependency>
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
stopExecution() (or similar method) that allows an external process to stop the build and/or filter process in a controlled fashionHello, I really appreciated this library although I know it is just very young.
I think I will greatly benefit of such platform written in Java. I have real-time data in multidimensional data running in simulators which I use for testing, but in our lab great deal of the data acquired is multidimensional.
Currently, the biggest issue I see in the application of multiway algorithms is that they usually are not easily generalised for multiway (>3 modes) datasets. I've done a small literature review and I always find reports of incredible improvements (very "occult" benchmarks). These decomposition algorithms are rarely open source (TensorPy being an exception) and I think the major improvements have resulted almost exclusively of distributed vectorization in MPPs. I have collected a list of these algorithms (unfortunately not all the code) and I really want to contribute to this project.
My main question over this specific implementation is related to the interface Tensor. Why is it needed? Why cannot one just use the FeatureVectors (INDArrays) of a DataSet (nd4j, I saw that you contribute to both projects)? If I'm not mistaken you use it to obtain data in other modality but shouldn't these algorithms work independently of the modality?
Best regards,
Andre
On Java 10.0.1, mvn clean package generates the following error:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.0:compile (default-compile) on project multiway-algorithms: Fatal error compiling: java.lang.ExceptionInInitializerError: com.sun.tools.javac.code.TypeTags -> [Help 1]
When running mvn clean package -e, it looks like lombok is the issue (see also this lombok issue):
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.0:compile (default-compile) on project multiway-algorithms: Fatal error compiling: java.lang.ExceptionInInitializerError: com.sun.tools.javac.code.TypeTags -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.0:compile (default-compile) on project multiway-algorithms: Fatal error compiling
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Fatal error compiling
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:695)
at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:118)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
... 20 more
Caused by: org.codehaus.plexus.compiler.CompilerException: java.lang.ExceptionInInitializerError
at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:191)
at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile(JavacCompiler.java:170)
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:684)
... 23 more
Caused by: java.lang.RuntimeException: java.lang.ExceptionInInitializerError
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.handleExceptions(JavacTaskImpl.java:158)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.doCall(JavacTaskImpl.java:96)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:90)
at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:126)
... 25 more
Caused by: java.lang.ExceptionInInitializerError
at lombok.javac.handlers.HandleGetter.<clinit>(HandleGetter.java:303)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:374)
at lombok.core.SpiLoadUtil$1$1.next(SpiLoadUtil.java:111)
at lombok.javac.HandlerLibrary.loadAnnotationHandlers(HandlerLibrary.java:171)
at lombok.javac.HandlerLibrary.load(HandlerLibrary.java:156)
at lombok.javac.JavacTransformer.<init>(JavacTransformer.java:44)
at lombok.javac.apt.LombokProcessor.init(LombokProcessor.java:87)
at lombok.core.AnnotationProcessor$JavacDescriptor.want(AnnotationProcessor.java:87)
at lombok.core.AnnotationProcessor.init(AnnotationProcessor.java:140)
at lombok.launch.AnnotationProcessorHider$AnnotationProcessor.init(AnnotationProcessor.java:69)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment$ProcessorState.<init>(JavacProcessingEnvironment.java:674)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment$DiscoveredProcessors$ProcessorStateIterator.next(JavacProcessingEnvironment.java:771)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:866)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment.access$2100(JavacProcessingEnvironment.java:110)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment$Round.run(JavacProcessingEnvironment.java:1202)
at jdk.compiler/com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:1311)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.processAnnotations(JavaCompiler.java:1250)
at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:928)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.lambda$doCall$0(JavacTaskImpl.java:100)
at jdk.compiler/com.sun.tools.javac.api.JavacTaskImpl.handleExceptions(JavacTaskImpl.java:142)
... 28 more
Caused by: java.lang.ClassNotFoundException: com.sun.tools.javac.code.TypeTags
at java.base/java.lang.ClassLoader.findClass(ClassLoader.java:711)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:566)
at lombok.launch.ShadowClassLoader.loadClass(ShadowClassLoader.java:422)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:291)
at lombok.javac.JavacTreeMaker$SchroedingerType.getFieldCached(JavacTreeMaker.java:156)
at lombok.javac.JavacTreeMaker$TypeTag.typeTag(JavacTreeMaker.java:244)
at lombok.javac.Javac.<clinit>(Javac.java:155)
... 49 more
calculate scores from loadings applied to spectra
PARAFAC support for missing values can be added quite easily as follows:
In each iteration a missing value x_ijk can be estimated by x_ijk = sum_{1..F} (a_if * b_jf * c_kf)
The easiest approach would be to store a mask in the beginning that indicates which indices ijk had missing values and update the X tensor after each iteration with the reconstructed values from A,B,C. The reconstruction is calculated in each iteration anyway to compute the loss so this only needs to be cached and used for value estimation in a second step.
Below are some enhancements that should be implemented to further extend the PARAFAC algorithm.
The loading matrices can be initialized in a few different ways. Currently available are:
PARAFAC.Initialization.RANDOMPARAFAC.Initialization.SVDLooking at the nway toolbox, there are two more initialization methods possible:
The loading matrices can be further constrained as shown here:
% const A vector telling type of constraints put on the loadings of the
% different modes. Same size as DimX but the i'th element tells
% what constraint is on that mode.
% 0 => no constraint,
% 1 => orthogonality
% 2 => nonnegativity
% 3 => unimodality (and nonnegativitiy)
% 4 => L1 fitting (will be imposed in all modes)
% 5 => L1 fitting and nonnegativity (will be imposed in all modes)
% If const is not defined, no constraints are used.
% For no constraints in a threeway problem const = [0 0 0]
PARAFAC support for missing values can be added quite easily as follows:
In each iteration a missing value x_ijk can be estimated by x_ijk = sum_{1..F} (a_if * b_jf * c_kf)
The easiest approach would be to store a mask in the beginning that indicates which indices ijk had missing values and update the X tensor after each iteration with the reconstructed values from A,B,C. The reconstruction is calculated in each iteration anyway to compute the loss so this only needs to be cached and used for value estimation in a second step.
(See also #1)
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