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From m...@apache.org
Subject spark git commit: [SPARK-8998] [MLLIB] Distribute PrefixSpan computation for large projected databases
Date Thu, 30 Jul 2015 15:14:14 GMT
Repository: spark
Updated Branches:
  refs/heads/master c5815930b -> d212a3142


[SPARK-8998] [MLLIB] Distribute PrefixSpan computation for large projected databases

Continuation of work by zhangjiajin

Closes #7412

Author: zhangjiajin <zhangjiajin@huawei.com>
Author: Feynman Liang <fliang@databricks.com>
Author: zhang jiajin <zhangjiajin@huawei.com>

Closes #7783 from feynmanliang/SPARK-8998-improve-distributed and squashes the following commits:

a61943d [Feynman Liang] Collect small patterns to local
4ddf479 [Feynman Liang] Parallelize freqItemCounts
ad23aa9 [zhang jiajin] Merge pull request #1 from feynmanliang/SPARK-8998-collectBeforeLocal
87fa021 [Feynman Liang] Improve extend prefix readability
c2caa5c [Feynman Liang] Readability improvements and comments
1235cfc [Feynman Liang] Use Iterable[Array[_]] over Array[Array[_]] for database
da0091b [Feynman Liang] Use lists for prefixes to reuse data
cb2a4fc [Feynman Liang] Inline code for readability
01c9ae9 [Feynman Liang] Add getters
6e149fa [Feynman Liang] Fix splitPrefixSuffixPairs
64271b3 [zhangjiajin] Modified codes according to comments.
d2250b7 [zhangjiajin] remove minPatternsBeforeLocalProcessing, add maxSuffixesBeforeLocalProcessing.
b07e20c [zhangjiajin] Merge branch 'master' of https://github.com/apache/spark into CollectEnoughPrefixes
095aa3a [zhangjiajin] Modified the code according to the review comments.
baa2885 [zhangjiajin] Modified the code according to the review comments.
6560c69 [zhangjiajin] Add feature: Collect enough frequent prefixes before projection in PrefixeSpan
a8fde87 [zhangjiajin] Merge branch 'master' of https://github.com/apache/spark
4dd1c8a [zhangjiajin] initialize file before rebase.
078d410 [zhangjiajin] fix a scala style error.
22b0ef4 [zhangjiajin] Add feature: Collect enough frequent prefixes before projection in PrefixSpan.
ca9c4c8 [zhangjiajin] Modified the code according to the review comments.
574e56c [zhangjiajin] Add new object LocalPrefixSpan, and do some optimization.
ba5df34 [zhangjiajin] Fix a Scala style error.
4c60fb3 [zhangjiajin] Fix some Scala style errors.
1dd33ad [zhangjiajin] Modified the code according to the review comments.
89bc368 [zhangjiajin] Fixed a Scala style error.
a2eb14c [zhang jiajin] Delete PrefixspanSuite.scala
951fd42 [zhang jiajin] Delete Prefixspan.scala
575995f [zhangjiajin] Modified the code according to the review comments.
91fd7e6 [zhangjiajin] Add new algorithm PrefixSpan and test file.


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/d212a314
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/d212a314
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/d212a314

Branch: refs/heads/master
Commit: d212a314227dec26c0dbec8ed3422d0ec8f818f9
Parents: c581593
Author: zhangjiajin <zhangjiajin@huawei.com>
Authored: Thu Jul 30 08:14:09 2015 -0700
Committer: Xiangrui Meng <meng@databricks.com>
Committed: Thu Jul 30 08:14:09 2015 -0700

----------------------------------------------------------------------
 .../spark/mllib/fpm/LocalPrefixSpan.scala       |   6 +-
 .../org/apache/spark/mllib/fpm/PrefixSpan.scala | 203 ++++++++++++++-----
 .../spark/mllib/fpm/PrefixSpanSuite.scala       |  21 +-
 3 files changed, 161 insertions(+), 69 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/d212a314/mllib/src/main/scala/org/apache/spark/mllib/fpm/LocalPrefixSpan.scala
----------------------------------------------------------------------
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/fpm/LocalPrefixSpan.scala b/mllib/src/main/scala/org/apache/spark/mllib/fpm/LocalPrefixSpan.scala
index 7ead632..0ea7920 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/fpm/LocalPrefixSpan.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/fpm/LocalPrefixSpan.scala
@@ -40,7 +40,7 @@ private[fpm] object LocalPrefixSpan extends Logging with Serializable {
       minCount: Long,
       maxPatternLength: Int,
       prefixes: List[Int],
-      database: Array[Array[Int]]): Iterator[(List[Int], Long)] = {
+      database: Iterable[Array[Int]]): Iterator[(List[Int], Long)] = {
     if (prefixes.length == maxPatternLength || database.isEmpty) return Iterator.empty
     val frequentItemAndCounts = getFreqItemAndCounts(minCount, database)
     val filteredDatabase = database.map(x => x.filter(frequentItemAndCounts.contains))
@@ -67,7 +67,7 @@ private[fpm] object LocalPrefixSpan extends Logging with Serializable {
     }
   }
 
-  def project(database: Array[Array[Int]], prefix: Int): Array[Array[Int]] = {
+  def project(database: Iterable[Array[Int]], prefix: Int): Iterable[Array[Int]] = {
     database
       .map(getSuffix(prefix, _))
       .filter(_.nonEmpty)
@@ -81,7 +81,7 @@ private[fpm] object LocalPrefixSpan extends Logging with Serializable {
    */
   private def getFreqItemAndCounts(
       minCount: Long,
-      database: Array[Array[Int]]): mutable.Map[Int, Long] = {
+      database: Iterable[Array[Int]]): mutable.Map[Int, Long] = {
     // TODO: use PrimitiveKeyOpenHashMap
     val counts = mutable.Map[Int, Long]().withDefaultValue(0L)
     database.foreach { sequence =>

http://git-wip-us.apache.org/repos/asf/spark/blob/d212a314/mllib/src/main/scala/org/apache/spark/mllib/fpm/PrefixSpan.scala
----------------------------------------------------------------------
diff --git a/mllib/src/main/scala/org/apache/spark/mllib/fpm/PrefixSpan.scala b/mllib/src/main/scala/org/apache/spark/mllib/fpm/PrefixSpan.scala
index 6f52db7..e675233 100644
--- a/mllib/src/main/scala/org/apache/spark/mllib/fpm/PrefixSpan.scala
+++ b/mllib/src/main/scala/org/apache/spark/mllib/fpm/PrefixSpan.scala
@@ -17,6 +17,8 @@
 
 package org.apache.spark.mllib.fpm
 
+import scala.collection.mutable.ArrayBuffer
+
 import org.apache.spark.Logging
 import org.apache.spark.annotation.Experimental
 import org.apache.spark.rdd.RDD
@@ -44,27 +46,44 @@ class PrefixSpan private (
     private var maxPatternLength: Int) extends Logging with Serializable {
 
   /**
+   * The maximum number of items allowed in a projected database before local processing.
If a
+   * projected database exceeds this size, another iteration of distributed PrefixSpan is
run.
+   */
+  // TODO: make configurable with a better default value, 10000 may be too small
+  private val maxLocalProjDBSize: Long = 10000
+
+  /**
    * Constructs a default instance with default parameters
    * {minSupport: `0.1`, maxPatternLength: `10`}.
    */
   def this() = this(0.1, 10)
 
   /**
+   * Get the minimal support (i.e. the frequency of occurrence before a pattern is considered
+   * frequent).
+   */
+  def getMinSupport: Double = this.minSupport
+
+  /**
    * Sets the minimal support level (default: `0.1`).
    */
   def setMinSupport(minSupport: Double): this.type = {
-    require(minSupport >= 0 && minSupport <= 1,
-      "The minimum support value must be between 0 and 1, including 0 and 1.")
+    require(minSupport >= 0 && minSupport <= 1, "The minimum support value
must be in [0, 1].")
     this.minSupport = minSupport
     this
   }
 
   /**
+   * Gets the maximal pattern length (i.e. the length of the longest sequential pattern to
consider.
+   */
+  def getMaxPatternLength: Double = this.maxPatternLength
+
+  /**
    * Sets maximal pattern length (default: `10`).
    */
   def setMaxPatternLength(maxPatternLength: Int): this.type = {
-    require(maxPatternLength >= 1,
-      "The maximum pattern length value must be greater than 0.")
+    // TODO: support unbounded pattern length when maxPatternLength = 0
+    require(maxPatternLength >= 1, "The maximum pattern length value must be greater than
0.")
     this.maxPatternLength = maxPatternLength
     this
   }
@@ -78,81 +97,153 @@ class PrefixSpan private (
    *         the value of pair is the pattern's count.
    */
   def run(sequences: RDD[Array[Int]]): RDD[(Array[Int], Long)] = {
+    val sc = sequences.sparkContext
+
     if (sequences.getStorageLevel == StorageLevel.NONE) {
       logWarning("Input data is not cached.")
     }
-    val minCount = getMinCount(sequences)
-    val lengthOnePatternsAndCounts =
-      getFreqItemAndCounts(minCount, sequences).collect()
-    val prefixAndProjectedDatabase = getPrefixAndProjectedDatabase(
-      lengthOnePatternsAndCounts.map(_._1), sequences)
-    val groupedProjectedDatabase = prefixAndProjectedDatabase
-      .map(x => (x._1.toSeq, x._2))
-      .groupByKey()
-      .map(x => (x._1.toArray, x._2.toArray))
-    val nextPatterns = getPatternsInLocal(minCount, groupedProjectedDatabase)
-    val lengthOnePatternsAndCountsRdd =
-      sequences.sparkContext.parallelize(
-        lengthOnePatternsAndCounts.map(x => (Array(x._1), x._2)))
-    val allPatterns = lengthOnePatternsAndCountsRdd ++ nextPatterns
-    allPatterns
+
+    // Convert min support to a min number of transactions for this dataset
+    val minCount = if (minSupport == 0) 0L else math.ceil(sequences.count() * minSupport).toLong
+
+    // (Frequent items -> number of occurrences, all items here satisfy the `minSupport`
threshold
+    val freqItemCounts = sequences
+      .flatMap(seq => seq.distinct.map(item => (item, 1L)))
+      .reduceByKey(_ + _)
+      .filter(_._2 >= minCount)
+      .collect()
+
+    // Pairs of (length 1 prefix, suffix consisting of frequent items)
+    val itemSuffixPairs = {
+      val freqItems = freqItemCounts.map(_._1).toSet
+      sequences.flatMap { seq =>
+        val filteredSeq = seq.filter(freqItems.contains(_))
+        freqItems.flatMap { item =>
+          val candidateSuffix = LocalPrefixSpan.getSuffix(item, filteredSeq)
+          candidateSuffix match {
+            case suffix if !suffix.isEmpty => Some((List(item), suffix))
+            case _ => None
+          }
+        }
+      }
+    }
+
+    // Accumulator for the computed results to be returned, initialized to the frequent items
(i.e.
+    // frequent length-one prefixes)
+    var resultsAccumulator = freqItemCounts.map(x => (List(x._1), x._2))
+
+    // Remaining work to be locally and distributively processed respectfully
+    var (pairsForLocal, pairsForDistributed) = partitionByProjDBSize(itemSuffixPairs)
+
+    // Continue processing until no pairs for distributed processing remain (i.e. all prefixes
have
+    // projected database sizes <= `maxLocalProjDBSize`)
+    while (pairsForDistributed.count() != 0) {
+      val (nextPatternAndCounts, nextPrefixSuffixPairs) =
+        extendPrefixes(minCount, pairsForDistributed)
+      pairsForDistributed.unpersist()
+      val (smallerPairsPart, largerPairsPart) = partitionByProjDBSize(nextPrefixSuffixPairs)
+      pairsForDistributed = largerPairsPart
+      pairsForDistributed.persist(StorageLevel.MEMORY_AND_DISK)
+      pairsForLocal ++= smallerPairsPart
+      resultsAccumulator ++= nextPatternAndCounts.collect()
+    }
+
+    // Process the small projected databases locally
+    val remainingResults = getPatternsInLocal(
+      minCount, sc.parallelize(pairsForLocal, 1).groupByKey())
+
+    (sc.parallelize(resultsAccumulator, 1) ++ remainingResults)
+      .map { case (pattern, count) => (pattern.toArray, count) }
   }
 
+
   /**
-   * Get the minimum count (sequences count * minSupport).
-   * @param sequences input data set, contains a set of sequences,
-   * @return minimum count,
+   * Partitions the prefix-suffix pairs by projected database size.
+   * @param prefixSuffixPairs prefix (length n) and suffix pairs,
+   * @return prefix-suffix pairs partitioned by whether their projected database size is
<= or
+   *         greater than [[maxLocalProjDBSize]]
    */
-  private def getMinCount(sequences: RDD[Array[Int]]): Long = {
-    if (minSupport == 0) 0L else math.ceil(sequences.count() * minSupport).toLong
+  private def partitionByProjDBSize(prefixSuffixPairs: RDD[(List[Int], Array[Int])])
+    : (Array[(List[Int], Array[Int])], RDD[(List[Int], Array[Int])]) = {
+    val prefixToSuffixSize = prefixSuffixPairs
+      .aggregateByKey(0)(
+        seqOp = { case (count, suffix) => count + suffix.length },
+        combOp = { _ + _ })
+    val smallPrefixes = prefixToSuffixSize
+      .filter(_._2 <= maxLocalProjDBSize)
+      .keys
+      .collect()
+      .toSet
+    val small = prefixSuffixPairs.filter { case (prefix, _) => smallPrefixes.contains(prefix)
}
+    val large = prefixSuffixPairs.filter { case (prefix, _) => !smallPrefixes.contains(prefix)
}
+    (small.collect(), large)
   }
 
   /**
-   * Generates frequent items by filtering the input data using minimal count level.
-   * @param minCount the absolute minimum count
-   * @param sequences original sequences data
-   * @return array of item and count pair
+   * Extends all prefixes by one item from their suffix and computes the resulting frequent
prefixes
+   * and remaining work.
+   * @param minCount minimum count
+   * @param prefixSuffixPairs prefix (length N) and suffix pairs,
+   * @return (frequent length N+1 extended prefix, count) pairs and (frequent length N+1
extended
+   *         prefix, corresponding suffix) pairs.
    */
-  private def getFreqItemAndCounts(
+  private def extendPrefixes(
       minCount: Long,
-      sequences: RDD[Array[Int]]): RDD[(Int, Long)] = {
-    sequences.flatMap(_.distinct.map((_, 1L)))
+      prefixSuffixPairs: RDD[(List[Int], Array[Int])])
+    : (RDD[(List[Int], Long)], RDD[(List[Int], Array[Int])]) = {
+
+    // (length N prefix, item from suffix) pairs and their corresponding number of occurrences
+    // Every (prefix :+ suffix) is guaranteed to have support exceeding `minSupport`
+    val prefixItemPairAndCounts = prefixSuffixPairs
+      .flatMap { case (prefix, suffix) => suffix.distinct.map(y => ((prefix, y), 1L))
}
       .reduceByKey(_ + _)
       .filter(_._2 >= minCount)
-  }
 
-  /**
-   * Get the frequent prefixes' projected database.
-   * @param frequentPrefixes frequent prefixes
-   * @param sequences sequences data
-   * @return prefixes and projected database
-   */
-  private def getPrefixAndProjectedDatabase(
-      frequentPrefixes: Array[Int],
-      sequences: RDD[Array[Int]]): RDD[(Array[Int], Array[Int])] = {
-    val filteredSequences = sequences.map { p =>
-      p.filter (frequentPrefixes.contains(_) )
-    }
-    filteredSequences.flatMap { x =>
-      frequentPrefixes.map { y =>
-        val sub = LocalPrefixSpan.getSuffix(y, x)
-        (Array(y), sub)
-      }.filter(_._2.nonEmpty)
-    }
+    // Map from prefix to set of possible next items from suffix
+    val prefixToNextItems = prefixItemPairAndCounts
+      .keys
+      .groupByKey()
+      .mapValues(_.toSet)
+      .collect()
+      .toMap
+
+
+    // Frequent patterns with length N+1 and their corresponding counts
+    val extendedPrefixAndCounts = prefixItemPairAndCounts
+      .map { case ((prefix, item), count) => (item :: prefix, count) }
+
+    // Remaining work, all prefixes will have length N+1
+    val extendedPrefixAndSuffix = prefixSuffixPairs
+      .filter(x => prefixToNextItems.contains(x._1))
+      .flatMap { case (prefix, suffix) =>
+        val frequentNextItems = prefixToNextItems(prefix)
+        val filteredSuffix = suffix.filter(frequentNextItems.contains(_))
+        frequentNextItems.flatMap { item =>
+          LocalPrefixSpan.getSuffix(item, filteredSuffix) match {
+            case suffix if !suffix.isEmpty => Some(item :: prefix, suffix)
+            case _ => None
+          }
+        }
+      }
+
+    (extendedPrefixAndCounts, extendedPrefixAndSuffix)
   }
 
   /**
-   * calculate the patterns in local.
+   * Calculate the patterns in local.
    * @param minCount the absolute minimum count
-   * @param data patterns and projected sequences data data
+   * @param data prefixes and projected sequences data data
    * @return patterns
    */
   private def getPatternsInLocal(
       minCount: Long,
-      data: RDD[(Array[Int], Array[Array[Int]])]): RDD[(Array[Int], Long)] = {
-    data.flatMap { case (prefix, projDB) =>
-      LocalPrefixSpan.run(minCount, maxPatternLength, prefix.toList, projDB)
-        .map { case (pattern: List[Int], count: Long) => (pattern.toArray.reverse, count)
}
+      data: RDD[(List[Int], Iterable[Array[Int]])]): RDD[(List[Int], Long)] = {
+    data.flatMap {
+      case (prefix, projDB) =>
+        LocalPrefixSpan.run(minCount, maxPatternLength, prefix.toList.reverse, projDB)
+          .map { case (pattern: List[Int], count: Long) =>
+          (pattern.reverse, count)
+        }
     }
   }
 }

http://git-wip-us.apache.org/repos/asf/spark/blob/d212a314/mllib/src/test/scala/org/apache/spark/mllib/fpm/PrefixSpanSuite.scala
----------------------------------------------------------------------
diff --git a/mllib/src/test/scala/org/apache/spark/mllib/fpm/PrefixSpanSuite.scala b/mllib/src/test/scala/org/apache/spark/mllib/fpm/PrefixSpanSuite.scala
index 9f107c8..6dd2dc9 100644
--- a/mllib/src/test/scala/org/apache/spark/mllib/fpm/PrefixSpanSuite.scala
+++ b/mllib/src/test/scala/org/apache/spark/mllib/fpm/PrefixSpanSuite.scala
@@ -44,13 +44,6 @@ class PrefixSpanSuite extends SparkFunSuite with MLlibTestSparkContext
{
 
     val rdd = sc.parallelize(sequences, 2).cache()
 
-    def compareResult(
-        expectedValue: Array[(Array[Int], Long)],
-        actualValue: Array[(Array[Int], Long)]): Boolean = {
-      expectedValue.map(x => (x._1.toSeq, x._2)).toSet ==
-        actualValue.map(x => (x._1.toSeq, x._2)).toSet
-    }
-
     val prefixspan = new PrefixSpan()
       .setMinSupport(0.33)
       .setMaxPatternLength(50)
@@ -76,7 +69,7 @@ class PrefixSpanSuite extends SparkFunSuite with MLlibTestSparkContext {
       (Array(4, 5), 2L),
       (Array(5), 3L)
     )
-    assert(compareResult(expectedValue1, result1.collect()))
+    assert(compareResults(expectedValue1, result1.collect()))
 
     prefixspan.setMinSupport(0.5).setMaxPatternLength(50)
     val result2 = prefixspan.run(rdd)
@@ -87,7 +80,7 @@ class PrefixSpanSuite extends SparkFunSuite with MLlibTestSparkContext {
       (Array(4), 4L),
       (Array(5), 3L)
     )
-    assert(compareResult(expectedValue2, result2.collect()))
+    assert(compareResults(expectedValue2, result2.collect()))
 
     prefixspan.setMinSupport(0.33).setMaxPatternLength(2)
     val result3 = prefixspan.run(rdd)
@@ -107,6 +100,14 @@ class PrefixSpanSuite extends SparkFunSuite with MLlibTestSparkContext
{
       (Array(4, 5), 2L),
       (Array(5), 3L)
     )
-    assert(compareResult(expectedValue3, result3.collect()))
+    assert(compareResults(expectedValue3, result3.collect()))
+  }
+
+  private def compareResults(
+    expectedValue: Array[(Array[Int], Long)],
+    actualValue: Array[(Array[Int], Long)]): Boolean = {
+    expectedValue.map(x => (x._1.toSeq, x._2)).toSet ==
+      actualValue.map(x => (x._1.toSeq, x._2)).toSet
   }
+
 }


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