Merging Branch 1.4.x

.gitignore

@@ -12,6 +12,9 @@ build/*.jar
 .settings
 .cache
 target/*
+dynaml-core/target/*
+dynaml-examples/target/*
+dynaml-pipes/target/*
 .DS_Store
 release.properties
 *.log

README.md

@@ -94,18 +94,22 @@ Steps
   You should get the following prompt.
 
 ```
-    ___       ___       ___       ___       ___       ___   
-   /\  \     /\__\     /\__\     /\  \     /\__\     /\__\  
-  /::\  \   |::L__L   /:| _|_   /::\  \   /::L_L_   /:/  /  
- /:/\:\__\  |:::\__\ /::|/\__\ /::\:\__\ /:/L:\__\ /:/__/   
- \:\/:/  /  /:;;/__/ \/|::/  / \/\::/  / \/_/:/  / \:\  \   
-  \::/  /   \/__/      |:/  /    /:/  /    /:/  /   \:\__\  
-   \/__/               \/__/     \/__/     \/__/     \/__/  
-
-Welcome to DynaML v 1.3
-Interactive Scala shell
-
-DynaML>
+      ___           ___           ___           ___           ___           ___
+     /\  \         |\__\         /\__\         /\  \         /\__\         /\__\
+    /::\  \        |:|  |       /::|  |       /::\  \       /::|  |       /:/  /
+   /:/\:\  \       |:|  |      /:|:|  |      /:/\:\  \     /:|:|  |      /:/  /
+  /:/  \:\__\      |:|__|__   /:/|:|  |__   /::\~\:\  \   /:/|:|__|__   /:/  /
+ /:/__/ \:|__|     /::::\__\ /:/ |:| /\__\ /:/\:\ \:\__\ /:/ |::::\__\ /:/__/
+ \:\  \ /:/  /    /:/~~/~    \/__|:|/:/  / \/__\:\/:/  / \/__/~~/:/  / \:\  \
+  \:\  /:/  /    /:/  /          |:/:/  /       \::/  /        /:/  /   \:\  \
+   \:\/:/  /     \/__/           |::/  /        /:/  /        /:/  /     \:\  \
+    \::/__/                      /:/  /        /:/  /        /:/  /       \:\__\
+     ~~                          \/__/         \/__/         \/__/         \/__/
+
+Welcome to DynaML v1.4-beta.8
+Interactive Scala shell for Machine Learning Research
+(Scala 2.11.7 Java 1.7.0_80)
+DynaML> 
 ```
 
 Getting Started

build.sbt

@@ -1,6 +1,8 @@
 import sbt._
 import java.io.File
 
+import sbtbuildinfo.BuildInfoPlugin.autoImport._
+
 maintainer := "Mandar Chandorkar <mandar2812@gmail.com>"
 
 packageSummary := "Scala Library/REPL for Machine Learning Research"
@@ -10,16 +12,17 @@ packageDescription := "DynaML is a scala library/repl for implementing and worki
   "which can be extended easily to implement advanced models for small and large scale applications.\n\n"+
   "But the library can also be used as an educational/research tool for data analysis."
 
+val mainVersion = "v1.4-beta.8"
+
 val dataDirectory = settingKey[File]("The directory holding the data files for running example scripts")
 
-lazy val commonSettings = Seq(
-  name := "DynaML",
+val baseSettings = Seq(
   organization := "io.github.mandar2812",
-  version := "v1.4-beta.7",
   scalaVersion in ThisBuild := "2.11.7",
-  mainClass in Compile := Some("io.github.mandar2812.dynaml.DynaML"),
-  fork in run := true,
-  resolvers in ThisBuild ++= Seq("jzy3d-releases" at "http://maven.jzy3d.org/releases"),
+  resolvers in ThisBuild ++= Seq("jzy3d-releases" at "http://maven.jzy3d.org/releases")
+)
+
+lazy val commonSettings = Seq(
   libraryDependencies ++= Seq(
     "org.scala-lang" % "scala-compiler" % scalaVersion.value % "compile",
     "org.scala-lang" % "scala-library" % scalaVersion.value % "compile",
@@ -42,15 +45,42 @@ lazy val commonSettings = Seq(
     "com.quantifind" % "wisp_2.11" % "0.0.4" % "compile",
     "org.jzy3d" % "jzy3d-api" % "0.9.1" % "compile",
     "com.lihaoyi" % "ammonite-repl_2.11.7" % "0.5.8"
-  ),
-  dataDirectory := new File("data/"),
-  initialCommands in console := """io.github.mandar2812.dynaml.DynaML.run(banner="""" +
-    target.value.getPath + """/universal/stage/conf/banner.txt");"""
+  )
 )
 
+lazy val pipes = (project in file("dynaml-pipes")).settings(baseSettings:_*)
+  .settings(
+    name := "dynaml-pipes",
+    version := "1.0"
+  )
+
+lazy val core = (project in file("dynaml-core")).settings(baseSettings)
+  .settings(commonSettings:_*)
+  .enablePlugins(JavaAppPackaging, BuildInfoPlugin)
+  .dependsOn(pipes)
+  .settings(
+    name := "dynaml-core",
+    version := mainVersion
+  )
+
+lazy val examples = (project in file("dynaml-examples"))
+  .settings(baseSettings:_*)
+  .settings(commonSettings:_*)
+  .settings(
+    name := "dynaml-examples",
+    version := "1.0"
+  ).dependsOn(pipes, core)
+
 lazy val DynaML = (project in file(".")).enablePlugins(JavaAppPackaging, BuildInfoPlugin)
+  .settings(baseSettings:_*)
   .settings(commonSettings: _*)
+  .dependsOn(core, examples, pipes)
   .settings(
+    //aggregate in update := false,
+    name := "DynaML",
+    version := mainVersion,
+    fork in run := true,
+    mainClass in Compile := Some("io.github.mandar2812.dynaml.DynaML"),
     buildInfoKeys := Seq[BuildInfoKey](name, version, scalaVersion, sbtVersion),
     buildInfoPackage := "io.github.mandar2812.dynaml.repl",
     buildInfoUsePackageAsPath := true,
@@ -67,6 +97,10 @@ lazy val DynaML = (project in file(".")).enablePlugins(JavaAppPackaging, BuildIn
       // -J params will be added as jvm parameters
       "-J-Xmx2048m",
       "-J-Xms64m"
-    )
-  )
+    ),
+    dataDirectory := new File("data/"),
+    initialCommands in console := """io.github.mandar2812.dynaml.DynaML.run(banner="""" +
+      target.value.getPath + """/universal/stage/conf/banner.txt");"""
+
+)
 

src/main/scala/io/github/mandar2812/dynaml/pipes/DynaMLPipe.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/DynaMLPipe.scala

@@ -1,35 +1,14 @@
-/*
-Licensed to the Apache Software Foundation (ASF) under one
-or more contributor license agreements.  See the NOTICE file
-distributed with this work for additional information
-regarding copyright ownership.  The ASF licenses this file
-to you under the Apache License, Version 2.0 (the
-"License"); you may not use this file except in compliance
-with the License.  You may obtain a copy of the License at
-
-  http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing,
-software distributed under the License is distributed on an
-"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-KIND, either express or implied.  See the License for the
-specific language governing permissions and limitations
-under the License.
-* */
-package io.github.mandar2812.dynaml.pipes
+package io.github.mandar2812.dynaml
 
+import scala.collection.mutable.{MutableList => ML}
 import breeze.linalg.DenseVector
 import io.github.mandar2812.dynaml.evaluation.RegressionMetrics
 import io.github.mandar2812.dynaml.models.ParameterizedLearner
 import io.github.mandar2812.dynaml.models.gp.AbstractGPRegressionModel
-import io.github.mandar2812.dynaml.optimization.{
-CoupledSimulatedAnnealing, GPMLOptimizer,
-GloballyOptWithGrad, GridSearch}
-import io.github.mandar2812.dynaml.utils
+import io.github.mandar2812.dynaml.optimization.{CoupledSimulatedAnnealing, GPMLOptimizer, GloballyOptWithGrad, GridSearch}
+import io.github.mandar2812.dynaml.pipes.{DataPipe, StreamDataPipe}
 import org.apache.log4j.Logger
 
-import scala.collection.mutable.{MutableList => ML}
-
 /**
   * @author mandar2812 datum 3/2/16.
   *
@@ -325,7 +304,7 @@ object DynaMLPipe {
     * Takes a base pipe and creates a parallel pipe by duplicating it.
     *
     * @param pipe The base data pipe
-    * @return a [[ParallelPipe]] object.
+    * @return a [[io.github.mandar2812.dynaml.pipes.ParallelPipe]] object.
     * */
   def duplicate[Source, Destination](pipe: DataPipe[Source, Destination]) =
     DataPipe(pipe, pipe)

src/main/scala/io/github/mandar2812/dynaml/graphutils/CausalEdge.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/CausalEdge.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.frames.{Property, OutVertex, InVertex, EdgeFrame}
 

src/main/scala/io/github/mandar2812/dynaml/graphutils/Label.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/Label.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.blueprints.Direction
 import com.tinkerpop.frames.{Adjacency, VertexFrame, Property}

src/main/scala/io/github/mandar2812/dynaml/graphutils/Neuron.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/Neuron.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.blueprints.Direction
 import com.tinkerpop.frames.{Incidence, Property, VertexFrame}

src/main/scala/io/github/mandar2812/dynaml/graphutils/ParamEdge.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/ParamEdge.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.frames.{InVertex, OutVertex, EdgeFrame}
 

src/main/scala/io/github/mandar2812/dynaml/graphutils/Parameter.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/Parameter.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.blueprints.Direction
 import com.tinkerpop.frames.{Adjacency, VertexFrame, Property}

src/main/scala/io/github/mandar2812/dynaml/graphutils/Point.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/Point.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.blueprints.Direction
 import com.tinkerpop.frames.{Adjacency, VertexFrame, Property}

src/main/scala/io/github/mandar2812/dynaml/graphutils/Synapse.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/graph/Synapse.scala

@@ -16,7 +16,7 @@ KIND, either express or implied.  See the License for the
 specific language governing permissions and limitations
 under the License.
 * */
-package io.github.mandar2812.dynaml.graphutils
+package io.github.mandar2812.dynaml.graph
 
 import com.tinkerpop.frames.{Property, InVertex, OutVertex, EdgeFrame}
 

dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/DLSSVMPipe.scala

@@ -0,0 +1,22 @@
+package io.github.mandar2812.dynaml.models
+
+import breeze.linalg.{DenseMatrix, DenseVector}
+import io.github.mandar2812.dynaml.kernels.CovarianceFunction
+import io.github.mandar2812.dynaml.models.svm.DLSSVM
+
+/**
+  * Created by mandar on 15/6/16.
+  */
+class DLSSVMPipe[Source](pre: (Source) => Stream[(DenseVector[Double], Double)],
+                         cov: CovarianceFunction[DenseVector[Double], Double, DenseMatrix[Double]],
+                         task: String = "regression") extends
+  ModelPipe[Source, Stream[(DenseVector[Double], Double)],
+    DenseVector[Double], Double, DLSSVM] {
+
+  override val preProcess = pre
+
+  override def run(data: Source) = {
+    val training = preProcess(data)
+    new DLSSVM(training, training.length, cov, task)
+  }
+}

dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/GLMPipe.scala

@@ -0,0 +1,23 @@
+package io.github.mandar2812.dynaml.models
+
+import breeze.linalg.DenseVector
+import io.github.mandar2812.dynaml.models.lm.GeneralizedLinearModel
+
+/**
+  * Created by mandar on 15/6/16.
+  */
+class GLMPipe[T, Source](pre: (Source) => Stream[(DenseVector[Double], Double)],
+                         map: (DenseVector[Double]) => (DenseVector[Double]) = identity _,
+                         task: String = "regression", modelType: String = "") extends
+  ModelPipe[Source, Stream[(DenseVector[Double], Double)],
+    DenseVector[Double], Double,
+    GeneralizedLinearModel[T]] {
+
+  override val preProcess = pre
+
+  override def run(data: Source) = {
+    val training = preProcess(data)
+    GeneralizedLinearModel[T](training, task, map, modelType)
+  }
+
+}

dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/GPRegressionPipe.scala

@@ -0,0 +1,24 @@
+package io.github.mandar2812.dynaml.models
+
+import breeze.linalg.{DenseMatrix, DenseVector}
+import io.github.mandar2812.dynaml.kernels.CovarianceFunction
+import io.github.mandar2812.dynaml.models.gp.AbstractGPRegressionModel
+
+/**
+  * Created by mandar on 15/6/16.
+  */
+class GPRegressionPipe[M <:
+AbstractGPRegressionModel[Seq[(DenseVector[Double], Double)],
+  DenseVector[Double]], Source](pre: (Source) => Seq[(DenseVector[Double], Double)],
+                                cov: CovarianceFunction[DenseVector[Double], Double, DenseMatrix[Double]],
+                                n: CovarianceFunction[DenseVector[Double], Double, DenseMatrix[Double]],
+                                order: Int = 0, ex: Int = 0)
+  extends ModelPipe[Source, Seq[(DenseVector[Double], Double)],
+    DenseVector[Double], Double, M] {
+
+  override val preProcess: (Source) => Seq[(DenseVector[Double], Double)] = pre
+
+  override def run(data: Source): M =
+    AbstractGPRegressionModel[M](preProcess(data), cov, n, order, ex)
+
+}

dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/ModelPipe.scala

@@ -0,0 +1,14 @@
+package io.github.mandar2812.dynaml.models
+
+import io.github.mandar2812.dynaml.pipes.DataPipe
+
+/**
+  * Top level trait for Pipes involving ML models.
+  */
+trait ModelPipe[Source, T, Q, R, M <: Model[T, Q, R]]
+  extends DataPipe[Source, M]{
+
+  val preProcess: (Source) => T
+
+  override def run(data: Source): M
+}

src/main/scala/io/github/mandar2812/dynaml/models/ensemble/CommitteeModel.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/ensemble/CommitteeModel.scala

@@ -21,8 +21,7 @@ package io.github.mandar2812.dynaml.models.ensemble
 import breeze.linalg.DenseVector
 import io.github.mandar2812.dynaml.models.gp.GPRegression
 import io.github.mandar2812.dynaml.models.neuralnets.FeedForwardNetwork
-import io.github.mandar2812.dynaml.models.{LinearModel, Model}
-import io.github.mandar2812.dynaml.pipes.ModelPipe
+import io.github.mandar2812.dynaml.models.{LinearModel, Model, ModelPipe}
 
 /**
   * Defines an abstract implementation of a "committee-model".

src/main/scala/io/github/mandar2812/dynaml/models/ensemble/MetaModel.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/ensemble/MetaModel.scala

@@ -19,10 +19,9 @@ under the License.
 package io.github.mandar2812.dynaml.models.ensemble
 
 import breeze.linalg.DenseVector
-import io.github.mandar2812.dynaml.models.Model
+import io.github.mandar2812.dynaml.models.{Model, ModelPipe}
 import io.github.mandar2812.dynaml.models.gp.GPRegression
 import io.github.mandar2812.dynaml.models.neuralnets.FeedForwardNetwork
-import io.github.mandar2812.dynaml.pipes.ModelPipe
 
 /**
   *

src/main/scala/io/github/mandar2812/dynaml/models/gp/GPCommitteeRegression.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/gp/GPCommitteeRegression.scala

@@ -19,8 +19,7 @@ under the License.
 package io.github.mandar2812.dynaml.models.gp
 
 import breeze.linalg.DenseVector
-import io.github.mandar2812.dynaml.models.LinearModel
-import io.github.mandar2812.dynaml.pipes.GPRegressionPipe
+import io.github.mandar2812.dynaml.models.{GPRegressionPipe, LinearModel}
 
 /**
   * Created by mandar on 9/2/16.

src/main/scala/io/github/mandar2812/dynaml/models/neuralnets/AutoEncoder.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/neuralnets/AutoEncoder.scala

@@ -19,7 +19,7 @@ under the License.
 package io.github.mandar2812.dynaml.models.neuralnets
 
 import breeze.linalg.DenseVector
-import io.github.mandar2812.dynaml.pipes.ModelPipe
+import io.github.mandar2812.dynaml.models.ModelPipe
 
 /**
   * Created by mandar on 23/2/16.

src/main/scala/io/github/mandar2812/dynaml/models/neuralnets/FFNeuralGraph.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/neuralnets/FFNeuralGraph.scala

@@ -21,7 +21,7 @@ package io.github.mandar2812.dynaml.models.neuralnets
 import breeze.linalg.DenseVector
 import com.tinkerpop.blueprints.{GraphFactory, Graph}
 import com.tinkerpop.frames.{FramedGraphFactory, FramedGraph}
-import io.github.mandar2812.dynaml.graphutils.{Neuron, Synapse}
+import io.github.mandar2812.dynaml.graph.{Neuron, Synapse}
 import org.apache.log4j.Logger
 
 import scala.collection.JavaConversions

src/main/scala/io/github/mandar2812/dynaml/models/svm/KernelLSSVMModel.scala → dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/models/svm/KernelLSSVMModel.scala

@@ -19,7 +19,7 @@ package io.github.mandar2812.dynaml.models.svm
 import breeze.linalg.{DenseMatrix, DenseVector, norm}
 import com.tinkerpop.blueprints.Graph
 import com.tinkerpop.frames.FramedGraph
-import io.github.mandar2812.dynaml.graphutils.{CausalEdge, Parameter, Point}
+import io.github.mandar2812.dynaml.graph.{CausalEdge, Parameter, Point}
 import io.github.mandar2812.dynaml.kernels.{GaussianDensityKernel, RBFKernel, SVMKernel}
 import io.github.mandar2812.dynaml.models.KernelizedModel
 import io.github.mandar2812.dynaml.optimization.ConjugateGradient