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Spark MLlib KMeans聚类算法

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标签:spark   mllib   kmeans   聚类算法   

1.1 KMeans聚类算法

1.1.1 基础理论

KMeans算法的基本思想是初始随机给定K个簇中心,按照最邻近原则把待分类样本点分到各个簇。然后按平均法重新计算各个簇的质心,从而确定新的簇心。一直迭代,直到簇心的移动距离小于某个给定的值。

K-Means聚类算法主要分为三个步骤:

(1)第一步是为待聚类的点寻找聚类中心;

(2)第二步是计算每个点到聚类中心的距离,将每个点聚类到离该点最近的聚类中去;

(3)第三步是计算每个聚类中所有点的坐标平均值,并将这个平均值作为新的聚类中心;

反复执行(2)、(3),直到聚类中心不再进行大范围移动或者聚类次数达到要求为止。

1.1.2过程演示

下图展示了对n个样本点进行K-means聚类的效果,这里k取2:

(a)未聚类的初始点集;

(b)随机选取两个点作为聚类中心;

(c)计算每个点到聚类中心的距离,并聚类到离该点最近的聚类中去;

(d)计算每个聚类中所有点的坐标平均值,并将这个平均值作为新的聚类中心;

(e)重复(c),计算每个点到聚类中心的距离,并聚类到离该点最近的聚类中去;

(f)重复(d),计算每个聚类中所有点的坐标平均值,并将这个平均值作为新的聚类中心。

技术分享

参照以下文档:

http://blog.sina.com.cn/s/blog_62186b46010145ne.html

1.2 Spark Mllib KMeans源码分析

class KMeansprivate (

    privatevar k: Int,

    privatevar maxIterations: Int,

    privatevar runs: Int,

    privatevar initializationMode: String,

    privatevar initializationSteps: Int,

    privatevar epsilon: Double,

    privatevar seed: Long)extends Serializablewith Logging {

// KMeans类参数:

k:聚类个数,默认2maxIterations:迭代次数,默认20runs:并行度,默认1

initializationMode:初始中心算法,默认"k-means||"initializationSteps:初始步长,默认5epsilon:中心距离阈值,默认1e-4seed:随机种子。

  /**

   * Constructs a KMeans instance with default parameters: {k: 2, maxIterations: 20, runs: 1,

   * initializationMode: "k-means||", initializationSteps: 5, epsilon: 1e-4, seed: random}.

   */

  defthis() =this(2,20, 1, KMeans.K_MEANS_PARALLEL,5, 1e-4, Utils.random.nextLong())

// 参数设置

/** Set the number of clusters to create (k). Default: 2. */

  def setK(k: Int):this.type = {

    this.k = k

    this

  }

**省略各个参数设置代码**

// run方法,KMeans主入口函数

  /**

   * Train a K-means model on the given set of points; `data` should be cached for high

   * performance, because this is an iterative algorithm.

   */

  def run(data: RDD[Vector]): KMeansModel = {

 

    if (data.getStorageLevel == StorageLevel.NONE) {

      logWarning("The input data is not directly cached, which may hurt performance if its"

        + " parent RDDs are also uncached.")

    }

 

// Compute squared norms and cache them.

// 计算每行数据的L2范数,数据转换:data[Vector]=> data[(Vector, norms)],其中norms是Vector的L2范数,norms就是

    val norms = data.map(Vectors.norm(_,2.0))

    norms.persist()

    val zippedData = data.zip(norms).map {case (v, norm) =>

      new VectorWithNorm(v, norm)

    }

    val model = runAlgorithm(zippedData)

    norms.unpersist()

 

    // Warn at the end of the run as well, for increased visibility.

    if (data.getStorageLevel == StorageLevel.NONE) {

      logWarning("The input data was not directly cached, which may hurt performance if its"

        + " parent RDDs are also uncached.")

    }

    model

  }

// runAlgorithm方法,KMeans实现方法。

  /**

   * Implementation of K-Means algorithm.

   */

  privatedef runAlgorithm(data: RDD[VectorWithNorm]): KMeansModel = {

 

    val sc = data.sparkContext

 

    val initStartTime = System.nanoTime()

 

    val centers =if (initializationMode == KMeans.RANDOM) {

      initRandom(data)

    } else {

      initKMeansParallel(data)

    }

 

    val initTimeInSeconds = (System.nanoTime() - initStartTime) /1e9

    logInfo(s"Initialization with $initializationMode took " +"%.3f".format(initTimeInSeconds) +

      " seconds.")

 

    val active = Array.fill(runs)(true)

    val costs = Array.fill(runs)(0.0)

 

    var activeRuns =new ArrayBuffer[Int] ++ (0 until runs)

    var iteration =0

 

    val iterationStartTime = System.nanoTime()

//KMeans迭代执行,计算每个样本属于哪个中心点,中心点累加样本的值及计数,然后根据中心点的所有的样本数据进行中心点的更新,并比较更新前的数值,判断是否完成。其中runs代表并行度。

    // Execute iterations of Lloyd‘s algorithm until all runs have converged

    while (iteration < maxIterations && !activeRuns.isEmpty) {

      type WeightedPoint = (Vector, Long)

      def mergeContribs(x: WeightedPoint, y: WeightedPoint): WeightedPoint = {

        axpy(1.0, x._1, y._1)

        (y._1, x._2 + y._2)

      }

 

      val activeCenters = activeRuns.map(r => centers(r)).toArray

      val costAccums = activeRuns.map(_ => sc.accumulator(0.0))

 

      val bcActiveCenters = sc.broadcast(activeCenters)

 

      // Find the sum and count of points mapping to each center

//计算属于每个中心点的样本,对每个中心点的样本进行累加和计算;

runs代表并行度,k中心点个数,sums代表中心点样本累加值,counts代表中心点样本计数;

contribs代表((并行度I,中心J),(中心J样本之和,中心J样本计数和));

findClosest方法:找到点与所有聚类中心最近的一个中心

      val totalContribs = data.mapPartitions { points =>

        val thisActiveCenters = bcActiveCenters.value

        val runs = thisActiveCenters.length

        val k = thisActiveCenters(0).length

        val dims = thisActiveCenters(0)(0).vector.size

 

        val sums = Array.fill(runs, k)(Vectors.zeros(dims))

        val counts = Array.fill(runs, k)(0L)

 

        points.foreach { point =>

          (0 until runs).foreach { i =>

           val (bestCenter, cost) = KMeans.findClosest(thisActiveCenters(i), point)

           costAccums(i) += cost

           val sum = sums(i)(bestCenter)

           axpy(1.0, point.vector, sum)

           counts(i)(bestCenter) += 1

          }

        }

 

        val contribs =for (i <-0 until runs; j <-0 until k) yield {

          ((i, j), (sums(i)(j), counts(i)(j)))

        }

        contribs.iterator

      }.reduceByKey(mergeContribs).collectAsMap()

//更新中心点,更新中心点= sum/count

判断newCentercenters之间的距离是否 > epsilon * epsilon;

      // Update the cluster centers and costs for each active run

      for ((run, i) <- activeRuns.zipWithIndex) {

        var changed =false

        var j =0

        while (j < k) {

          val (sum, count) = totalContribs((i, j))

          if (count !=0) {

           scal(1.0 / count, sum)

           val newCenter =new VectorWithNorm(sum)

           if (KMeans.fastSquaredDistance(newCenter, centers(run)(j)) > epsilon * epsilon) {

             changed = true

           }

           centers(run)(j) = newCenter

          }

          j += 1

        }

        if (!changed) {

          active(run) = false

          logInfo("Run " + run +" finished in " + (iteration +1) + " iterations")

        }

        costs(run) = costAccums(i).value

      }

 

      activeRuns = activeRuns.filter(active(_))

      iteration += 1

    }

 

    val iterationTimeInSeconds = (System.nanoTime() - iterationStartTime) /1e9

    logInfo(s"Iterations took " +"%.3f".format(iterationTimeInSeconds) +" seconds.")

 

    if (iteration == maxIterations) {

      logInfo(s"KMeans reached the max number of iterations: $maxIterations.")

    } else {

      logInfo(s"KMeans converged in $iteration iterations.")

    }

 

    val (minCost, bestRun) = costs.zipWithIndex.min

 

    logInfo(s"The cost for the best run is $minCost.")

 

    new KMeansModel(centers(bestRun).map(_.vector))

  }

//findClosest方法:找到点与所有聚类中心最近的一个中心

/**

   * Returns the index of the closest center to the given point, as well as the squared distance.

   */

  private[mllib]def findClosest(

      centers: TraversableOnce[VectorWithNorm],

      point: VectorWithNorm): (Int, Double) = {

    var bestDistance = Double.PositiveInfinity

    var bestIndex =0

    var i =0

    centers.foreach { center =>

      // Since `\|a - b\| \geq |\|a\| - \|b\||`, we can use this lower bound to avoid unnecessary

      // distance computation.

      var lowerBoundOfSqDist = center.norm - point.norm

      lowerBoundOfSqDist = lowerBoundOfSqDist * lowerBoundOfSqDist

      if (lowerBoundOfSqDist < bestDistance) {

        val distance: Double = fastSquaredDistance(center, point)

        if (distance < bestDistance) {

          bestDistance = distance

          bestIndex = i

        }

      }

      i += 1

    }

    (bestIndex, bestDistance)

  }

findClosest方法中:var lowerBoundOfSqDist = center.norm - point.norm

lowerBoundOfSqDist = lowerBoundOfSqDist * lowerBoundOfSqDist

如果中心点center是(a1,b1),需要计算的点point是(a2,b2),那么lowerBoundOfSqDist是:

技术分享

如下是展开式,第二个是真正计算欧式距离时的除去开平方的公式。(在查找最短距离的时候无需计算开方,因为只需要计算出开方里面的式子就可以进行比较了,mllib也是这样做的)

技术分享

可轻易证明上面两式的第一式将会小于等于第二式,因此在进行距离比较的时候,先计算很容易计算的lowerBoundOfSqDist,如果lowerBoundOfSqDist都不小于之前计算得到的最小距离bestDistance,那真正的欧式距离也不可能小于bestDistance了,因此这种情况下就不需要去计算欧式距离,省去很多计算工作。

如果lowerBoundOfSqDist小于了bestDistance,则进行距离的计算,调用fastSquaredDistance,这个方法将调用MLUtils.scala里面的fastSquaredDistance方法,计算真正的欧式距离,代码如下:

/**

   * Returns the squared Euclidean distance between two vectors. The following formula will be used

   * if it does not introduce too much numerical error:

   * <pre>

   *   \|a - b\|_2^2 = \|a\|_2^2 + \|b\|_2^2 - 2 a^T b.

   * </pre>

   * When both vector norms are given, this is faster than computing the squared distance directly,

   * especially when one of the vectors is a sparse vector.

   *

   * @param v1 the first vector

   * @param norm1 the norm of the first vector, non-negative

   * @param v2 the second vector

   * @param norm2 the norm of the second vector, non-negative

   * @param precision desired relative precision for the squared distance

   * @return squared distance between v1 and v2 within the specified precision

   */

  private[mllib]def fastSquaredDistance(

      v1: Vector,

      norm1: Double,

      v2: Vector,

      norm2: Double,

      precision: Double = 1e-6): Double = {

    val n = v1.size

    require(v2.size == n)

    require(norm1 >= 0.0 && norm2 >=0.0)

    val sumSquaredNorm = norm1 * norm1 + norm2 * norm2

    val normDiff = norm1 - norm2

    var sqDist =0.0

    /*

     * The relative error is

     * <pre>

     * EPSILON * ( \|a\|_2^2 + \|b\\_2^2 + 2 |a^T b|) / ( \|a - b\|_2^2 ),

     * </pre>

     * which is bounded by

     * <pre>

     * 2.0 * EPSILON * ( \|a\|_2^2 + \|b\|_2^2 ) / ( (\|a\|_2 - \|b\|_2)^2 ).

     * </pre>

     * The bound doesn‘t need the inner product, so we can use it as a sufficient condition to

     * check quickly whether the inner product approach is accurate.

     */

    val precisionBound1 =2.0 * EPSILON * sumSquaredNorm / (normDiff * normDiff + EPSILON)

    if (precisionBound1 < precision) {

      sqDist = sumSquaredNorm - 2.0 * dot(v1, v2)

    } elseif (v1.isInstanceOf[SparseVector] || v2.isInstanceOf[SparseVector]) {

      val dotValue = dot(v1, v2)

      sqDist = math.max(sumSquaredNorm - 2.0 * dotValue,0.0)

      val precisionBound2 = EPSILON * (sumSquaredNorm +2.0 * math.abs(dotValue)) /

        (sqDist + EPSILON)

      if (precisionBound2 > precision) {

        sqDist = Vectors.sqdist(v1, v2)

      }

    } else {

      sqDist = Vectors.sqdist(v1, v2)

    }

    sqDist

  }

fastSquaredDistance方法会先计算一个精度,有关精度的计算val precisionBound1 = 2.0 * EPSILON * sumSquaredNorm / (normDiff * normDiff + EPSILON),如果在精度满足条件的情况下,欧式距离sqDist = sumSquaredNorm - 2.0 * v1.dot(v2),sumSquaredNorm即为技术分享,2.0 * v1.dot(v2)即为技术分享。这也是之前将norm计算出来的好处。如果精度不满足要求,则进行原始的距离计算公式了技术分享,即调用Vectors.sqdist(v1, v2)。

1.3 Mllib KMeans实例

1、数据

数据格式为:特征1 特征2 特征3

0.0 0.0 0.0

0.1 0.1 0.1

0.2 0.2 0.2

9.0 9.0 9.0

9.1 9.1 9.1

9.2 9.2 9.2

2、代码

  //1读取样本数据

  valdata_path ="/home/jb-huangmeiling/kmeans_data.txt"

  valdata =sc.textFile(data_path)

  valexamples =data.map { line =>

    Vectors.dense(line.split(‘ ‘).map(_.toDouble))

  }.cache()

  valnumExamples =examples.count()

  println(s"numExamples = $numExamples.")

  //2建立模型

  valk =2

  valmaxIterations =20

  valruns =2

  valinitializationMode ="k-means||"

  valmodel = KMeans.train(examples,k, maxIterations,runs, initializationMode)

  //3计算测试误差

  valcost =model.computeCost(examples)

  println(s"Total cost = $cost.")

Spark MLlib KMeans聚类算法

标签:spark   mllib   kmeans   聚类算法   

原文地址:http://blog.csdn.net/sunbow0/article/details/45673613

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