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From chiwanp...@apache.org
Subject flink git commit: [FLINK-3919] [ml] Implement DistributedRowMatrix
Date Thu, 23 Jun 2016 02:08:13 GMT
Repository: flink
Updated Branches:
  refs/heads/master 08b075aa5 -> 63504a3cb


[FLINK-3919] [ml] Implement DistributedRowMatrix

This closes #1996.


Project: http://git-wip-us.apache.org/repos/asf/flink/repo
Commit: http://git-wip-us.apache.org/repos/asf/flink/commit/63504a3c
Tree: http://git-wip-us.apache.org/repos/asf/flink/tree/63504a3c
Diff: http://git-wip-us.apache.org/repos/asf/flink/diff/63504a3c

Branch: refs/heads/master
Commit: 63504a3cb331b9fb29cf833eeaa66afe5ba5d5f1
Parents: 08b075a
Author: chobeat <simone.robutti@gmail.com>
Authored: Tue May 17 14:19:15 2016 +0200
Committer: Chiwan Park <chiwanpark@apache.org>
Committed: Thu Jun 23 11:01:33 2016 +0900

----------------------------------------------------------------------
 .../ml/math/distributed/DistributedMatrix.scala |  39 +++++
 .../math/distributed/DistributedRowMatrix.scala | 161 +++++++++++++++++++
 .../distributed/DistributedRowMatrixSuite.scala | 104 ++++++++++++
 3 files changed, 304 insertions(+)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/flink/blob/63504a3c/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedMatrix.scala
----------------------------------------------------------------------
diff --git a/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedMatrix.scala
b/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedMatrix.scala
new file mode 100644
index 0000000..f34641e
--- /dev/null
+++ b/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedMatrix.scala
@@ -0,0 +1,39 @@
+/*
+ * 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 org.apache.flink.ml.math.distributed
+
+/** Common trait used by distributed data structures representing a matrix. */
+trait DistributedMatrix {
+  /** Returns number of rows in matrix.
+    *
+    * @return Number of rows
+    */
+  def numRows: Int
+
+  /** Returns number of columns in matrix.
+    *
+    * @return Number of columns
+    */
+  def numCols: Int
+}
+
+object DistributedMatrix {
+  type MatrixColIndex = Int
+  type MatrixRowIndex = Int
+}

http://git-wip-us.apache.org/repos/asf/flink/blob/63504a3c/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrix.scala
----------------------------------------------------------------------
diff --git a/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrix.scala
b/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrix.scala
new file mode 100644
index 0000000..9092e5c
--- /dev/null
+++ b/flink-libraries/flink-ml/src/main/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrix.scala
@@ -0,0 +1,161 @@
+/*
+ * 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 org.apache.flink.ml.math.distributed
+
+import org.apache.flink.api.scala._
+import org.apache.flink.ml.math.Breeze._
+import org.apache.flink.ml.math.distributed.DistributedMatrix._
+import org.apache.flink.ml.math._
+
+/** Represents distributed row-major matrix.
+  *
+  * @param data    [[DataSet]] which contains [[IndexedRow]]s
+  * @param numRows Number of rows
+  * @param numCols Number of columns
+  */
+class DistributedRowMatrix(
+  val data: DataSet[IndexedRow],
+  val numRows: Int,
+  val numCols: Int
+) extends DistributedMatrix {
+
+  /** Collects the data in the form of a sequence of coordinates associated with their values.
+    * This operation immediately triggers program execution.
+    */
+  def toCOO: Seq[(MatrixRowIndex, MatrixColIndex, Double)] = {
+    val localRows = data.collect()
+
+    for {
+      IndexedRow(rowIndex, vector) <- localRows
+      (columnIndex, value) <- vector
+    } yield (rowIndex, columnIndex, value)
+  }
+
+  /** Collects the data in the form of a SparseMatrix. This operation immediately triggers
program
+    * execution.
+    */
+  def toLocalSparseMatrix: SparseMatrix = {
+    val localMatrix = SparseMatrix.fromCOO(this.numRows, this.numCols, this.toCOO)
+    require(localMatrix.numRows == this.numRows)
+    require(localMatrix.numCols == this.numCols)
+
+    localMatrix
+  }
+
+  // TODO: convert to dense representation on the distributed matrix and collect it afterward
+  /** Collects the data in the form of a DenseMatrix. This operation immediately triggers
program
+    * execution.
+    */
+  def toLocalDenseMatrix: DenseMatrix = this.toLocalSparseMatrix.toDenseMatrix
+
+  /** Applies a high-order function to couple of rows.
+    *
+    * @param func  a function to be applied
+    * @param other a [[DistributedRowMatrix]] to apply the function together
+    */
+  def byRowOperation(
+    func: (Vector, Vector) => Vector,
+    other: DistributedRowMatrix
+  ): DistributedRowMatrix = {
+    val otherData = other.data
+    require(this.numCols == other.numCols)
+    require(this.numRows == other.numRows)
+
+    val result = this.data
+      .fullOuterJoin(otherData)
+      .where("rowIndex")
+      .equalTo("rowIndex")(
+        (left: IndexedRow, right: IndexedRow) => {
+          val row1 = Option(left) match {
+            case Some(row: IndexedRow) => row
+            case None =>
+              IndexedRow(right.rowIndex, SparseVector.fromCOO(right.values.size, List((0,
0.0))))
+          }
+          val row2 = Option(right) match {
+            case Some(row: IndexedRow) => row
+            case None =>
+              IndexedRow(left.rowIndex, SparseVector.fromCOO(left.values.size, List((0, 0.0))))
+          }
+          IndexedRow(row1.rowIndex, func(row1.values, row2.values))
+        }
+      )
+    new DistributedRowMatrix(result, numRows, numCols)
+  }
+
+  /** Adds this matrix to another matrix.
+    *
+    * @param other a [[DistributedRowMatrix]] to be added
+    */
+  def add(other: DistributedRowMatrix): DistributedRowMatrix = {
+    val addFunction = (x: Vector, y: Vector) => (x.asBreeze + y.asBreeze).fromBreeze
+    this.byRowOperation(addFunction, other)
+  }
+
+  /** Subtracts another matrix from this matrix.
+    *
+    * @param other a [[DistributedRowMatrix]] to be subtracted from this matrix
+    */
+  def subtract(other: DistributedRowMatrix): DistributedRowMatrix = {
+    val subFunction = (x: Vector, y: Vector) => (x.asBreeze - y.asBreeze).fromBreeze
+    this.byRowOperation(subFunction, other)
+  }
+}
+
+object DistributedRowMatrix {
+
+  /** Builds a [[DistributedRowMatrix]] from a [[DataSet]] in COO.
+    *
+    * @param data     [[DataSet]] which contains matrix elements in the form of
+    *                 (row index, column index, value)
+    * @param numRows  Number of rows
+    * @param numCols  Number of columns
+    * @param isSorted If false, sorts the row to properly build the matrix representation.
+    *                 If already sorted, set this parameter to true to skip sorting.
+    */
+  def fromCOO(data: DataSet[(MatrixRowIndex, MatrixColIndex, Double)],
+    numRows: Int,
+    numCols: Int,
+    isSorted: Boolean = false
+  ): DistributedRowMatrix = {
+    val vectorData: DataSet[(MatrixRowIndex, SparseVector)] = data
+      .groupBy(0)
+      .reduceGroup(sparseRow => {
+        require(sparseRow.nonEmpty)
+        val sortedRow =
+          if (isSorted) {
+            sparseRow.toList
+          } else {
+            sparseRow.toList.sortBy(row => row._2)
+          }
+        val (indices, values) = sortedRow.map(x => (x._2, x._3)).unzip
+        (sortedRow.head._1, SparseVector(numCols, indices.toArray, values.toArray))
+      })
+
+    val zippedData = vectorData.map(x => IndexedRow(x._1.toInt, x._2))
+
+    new DistributedRowMatrix(zippedData, numRows, numCols)
+  }
+}
+
+/** Represents a row in row-major matrix. */
+case class IndexedRow(rowIndex: MatrixRowIndex, values: Vector) extends Ordered[IndexedRow]
{
+  def compare(other: IndexedRow) = this.rowIndex.compare(other.rowIndex)
+
+  override def toString: String = s"($rowIndex, ${values.toString})"
+}

http://git-wip-us.apache.org/repos/asf/flink/blob/63504a3c/flink-libraries/flink-ml/src/test/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrixSuite.scala
----------------------------------------------------------------------
diff --git a/flink-libraries/flink-ml/src/test/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrixSuite.scala
b/flink-libraries/flink-ml/src/test/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrixSuite.scala
new file mode 100644
index 0000000..598b0f3
--- /dev/null
+++ b/flink-libraries/flink-ml/src/test/scala/org/apache/flink/ml/math/distributed/DistributedRowMatrixSuite.scala
@@ -0,0 +1,104 @@
+/*
+ * 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 org.apache.flink.ml.math.distributed
+
+import org.apache.flink.api.scala._
+import org.apache.flink.test.util.FlinkTestBase
+import org.scalatest.{FlatSpec, Matchers}
+
+class DistributedRowMatrixSuite extends FlatSpec with Matchers with FlinkTestBase {
+  behavior of "DistributedRowMatrix"
+
+  val rawSampleData = List(
+    (0, 0, 3.0),
+    (0, 1, 3.0),
+    (0, 3, 4.0),
+    (2, 3, 4.0),
+    (1, 4, 3.0),
+    (1, 1, 3.0),
+    (2, 1, 3.0),
+    (2, 2, 3.0)
+  )
+
+  it should "contain the initialization data" in {
+    val env = ExecutionEnvironment.getExecutionEnvironment
+    val rowDataset = env.fromCollection(rawSampleData)
+    val dmatrix = DistributedRowMatrix.fromCOO(rowDataset, 3, 5)
+
+    dmatrix.toCOO.toSet.filter(_._3 != 0) shouldBe rawSampleData.toSet
+  }
+
+  it should "return the correct dimensions when provided by the user" in {
+    val env = ExecutionEnvironment.getExecutionEnvironment
+    val rowDataset = env.fromCollection(rawSampleData)
+    val dmatrix = DistributedRowMatrix.fromCOO(rowDataset, 3, 5)
+
+    dmatrix.numCols shouldBe 5
+    dmatrix.numRows shouldBe 3
+  }
+
+
+  it should "return a sparse local matrix containing the initialization data" in {
+    val env = ExecutionEnvironment.getExecutionEnvironment
+    val rowDataset = env.fromCollection(rawSampleData)
+    val dmatrix = DistributedRowMatrix.fromCOO(rowDataset, 3, 5)
+
+    dmatrix.toLocalSparseMatrix.iterator.filter(_._3 != 0).toSet shouldBe rawSampleData.toSet
+  }
+
+  it should "return a dense local matrix containing the initialization data" in {
+    val env = ExecutionEnvironment.getExecutionEnvironment
+    val rowDataset = env.fromCollection(rawSampleData)
+    val dmatrix = DistributedRowMatrix.fromCOO(rowDataset, 3, 5)
+
+    dmatrix.toLocalDenseMatrix.iterator.filter(_._3 != 0).toSet shouldBe rawSampleData.toSet
+  }
+
+  "add" should "correctly add two distributed row matrices" in {
+    val env = ExecutionEnvironment.getExecutionEnvironment
+    val rawSampleSum1 = List(
+      (0, 0, 1.0),
+      (7, 4, 3.0),
+      (0, 1, 8.0),
+      (2, 8, 12.0)
+    )
+
+    val rawSampleSum2 = List(
+      (0, 0, 2.0),
+      (3, 4, 4.0),
+      (2, 8, 8.0)
+    )
+
+    val addBlockMatrix1 = DistributedRowMatrix.fromCOO(env.fromCollection(rawSampleSum1),
10, 10)
+    val addBlockMatrix2 = DistributedRowMatrix.fromCOO(env.fromCollection(rawSampleSum2),
10, 10)
+
+    val expected = List(
+      (0, 0, 3.0),
+      (0, 1, 8.0),
+      (3, 4, 4.0),
+      (2, 8, 20.0),
+      (7, 4, 3.0)
+    )
+    val result = addBlockMatrix1
+      .add(addBlockMatrix2)
+      .toLocalSparseMatrix
+      .filter(_._3 != 0.0)
+    result.toSet shouldEqual expected.toSet
+  }
+}


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