Distributed Stochastic PCA


Mahout has a distributed implementation of Stochastic PCA[1]. This algorithm computes the exact equivalent of Mahout's dssvd(\(\mathbf{A-1\mu^\top}\)) by modifying the dssvd algorithm so as to avoid forming \(\mathbf{A-1\mu^\top}\), which would densify a sparse input. Thus, it is suitable for work with both dense and sparse inputs.


Given an m \(\times\) n matrix \(\mathbf{A}\), a target rank k, and an oversampling parameter p, this procedure computes a k-rank PCA by finding the unknowns in \(\mathbf{A−1\mu^\top \approx U\Sigma V^\top}\):

  1. Create seed for random n \(\times\) (k+p) matrix \(\Omega\).
  2. \(\mathbf{s_\Omega \leftarrow \Omega^\top \mu}\).
  3. \(\mathbf{Y_0 \leftarrow A\Omega − 1 {s_\Omega}^\top, Y \in \mathbb{R}^{m\times(k+p)}}\).
  4. Column-orthonormalize \(\mathbf{Y_0} \rightarrow \mathbf{Q}\) by computing thin decomposition \(\mathbf{Y_0} = \mathbf{QR}\). Also, \(\mathbf{Q}\in\mathbb{R}^{m\times(k+p)}, \mathbf{R}\in\mathbb{R}^{(k+p)\times(k+p)}\).
  5. \(\mathbf{s_Q \leftarrow Q^\top 1}\).
  6. \(\mathbf{B_0 \leftarrow Q^\top A: B \in \mathbb{R}^{(k+p)\times n}}\).
  7. \(\mathbf{s_B \leftarrow {B_0}^\top \mu}\).
  8. For i in 1..q repeat (power iterations):
    • For j in 1..n apply \(\mathbf{(B_{i−1})_{∗j} \leftarrow (B_{i−1})_{∗j}−\mu_j s_Q}\).
    • \(\mathbf{Y_i \leftarrow A{B_{i−1}}^\top−1(s_B−\mu^\top \mu s_Q)^\top}\).
    • Column-orthonormalize \(\mathbf{Y_i} \rightarrow \mathbf{Q}\) by computing thin decomposition \(\mathbf{Y_i = QR}\).
    • \(\mathbf{s_Q \leftarrow Q^\top 1}\).
    • \(\mathbf{B_i \leftarrow Q^\top A}\).
    • \(\mathbf{s_B \leftarrow {B_i}^\top \mu}\).
  9. Let \(\mathbf{C \triangleq s_Q {s_B}^\top}\). \(\mathbf{M \leftarrow B_q {B_q}^\top − C − C^\top + \mu^\top \mu s_Q {s_Q}^\top}\).
  10. Compute an eigensolution of the small symmetric \(\mathbf{M = \hat{U} \Lambda \hat{U}^\top: M \in \mathbb{R}^{(k+p)\times(k+p)}}\).
  11. The singular values \(\Sigma = \Lambda^{\circ 0.5}\), or, in other words, \(\mathbf{\sigma_i= \sqrt{\lambda_i}}\).
  12. If needed, compute \(\mathbf{U = Q\hat{U}}\).
  13. If needed, compute \(\mathbf{V = B^\top \hat{U} \Sigma^{−1}}\).
  14. If needed, items converted to the PCA space can be computed as \(\mathbf{U\Sigma}\).


Mahout dspca(...) is implemented in the mahout math-scala algebraic optimizer which translates Mahout's R-like linear algebra operators into a physical plan for both Spark and H2O distributed engines.

def dspca[K](drmA: DrmLike[K], k: Int, p: Int = 15, q: Int = 0): 
(DrmLike[K], DrmLike[Int], Vector) = {

    // Some mapBlock() calls need it
    implicit val ktag =  drmA.keyClassTag

    val drmAcp = drmA.checkpoint()
    implicit val ctx = drmAcp.context

    val m = drmAcp.nrow
    val n = drmAcp.ncol
    assert(k <= (m min n), "k cannot be greater than smaller of m, n.")
    val pfxed = safeToNonNegInt((m min n) - k min p)

    // Actual decomposition rank
    val r = k + pfxed

    // Dataset mean
    val mu = drmAcp.colMeans

    val mtm = mu dot mu

    // We represent Omega by its seed.
    val omegaSeed = RandomUtils.getRandom().nextInt()
    val omega = Matrices.symmetricUniformView(n, r, omegaSeed)

    // This done in front in a single-threaded fashion for now. Even though it doesn't require any
    // memory beyond that is required to keep xi around, it still might be parallelized to backs
    // for significantly big n and r. TODO
    val s_o = omega.t %*% mu

    val bcastS_o = drmBroadcast(s_o)
    val bcastMu = drmBroadcast(mu)

    var drmY = drmAcp.mapBlock(ncol = r) {
        case (keys, blockA) ⇒
            val s_o:Vector = bcastS_o
            val blockY = blockA %*% Matrices.symmetricUniformView(n, r, omegaSeed)
            for (row ← 0 until blockY.nrow) blockY(row, ::) -= s_o
            keys → blockY
            // Checkpoint Y

    var drmQ = dqrThin(drmY, checkRankDeficiency = false)._1.checkpoint()

    var s_q = drmQ.colSums()
    var bcastVarS_q = drmBroadcast(s_q)

    // This actually should be optimized as identically partitioned map-side A'B since A and Q should
    // still be identically partitioned.
    var drmBt = (drmAcp.t %*% drmQ).checkpoint()

    var s_b = (drmBt.t %*% mu).collect(::, 0)
    var bcastVarS_b = drmBroadcast(s_b)

    for (i ← 0 until q) {

        // These closures don't seem to live well with outside-scope vars. This doesn't record closure
        // attributes correctly. So we create additional set of vals for broadcast vars to properly
        // create readonly closure attributes in this very scope.
        val bcastS_q = bcastVarS_q
        val bcastMuInner = bcastMu

        // Fix Bt as B' -= xi cross s_q
        drmBt = drmBt.mapBlock() {
            case (keys, block) ⇒
                val s_q: Vector = bcastS_q
                val mu: Vector = bcastMuInner
                keys.zipWithIndex.foreach {
                    case (key, idx) ⇒ block(idx, ::) -= s_q * mu(key)
                keys → block


        val bCastSt_b = drmBroadcast(s_b -=: mtm * s_q)

        drmY = (drmAcp %*% drmBt)
            // Fix Y by subtracting st_b from each row of the AB'
            .mapBlock() {
            case (keys, block) ⇒
                val st_b: Vector = bCastSt_b
                block := { (_, c, v) ⇒ v - st_b(c) }
                keys → block
        // Checkpoint Y

        drmQ = dqrThin(drmY, checkRankDeficiency = false)._1.checkpoint()

        s_q = drmQ.colSums()
        bcastVarS_q = drmBroadcast(s_q)

        // This on the other hand should be inner-join-and-map A'B optimization since A and Q_i are not
        // identically partitioned anymore.
        drmBt = (drmAcp.t %*% drmQ).checkpoint()

        s_b = (drmBt.t %*% mu).collect(::, 0)
        bcastVarS_b = drmBroadcast(s_b)

    val c = s_q cross s_b
    val inCoreBBt = (drmBt.t %*% drmBt).checkpoint(CacheHint.NONE).collect -=:
        c -=: c.t +=: mtm *=: (s_q cross s_q)
    val (inCoreUHat, d) = eigen(inCoreBBt)
    val s = d.sqrt

    // Since neither drmU nor drmV are actually computed until actually used, we don't need the flags
    // instructing compute (or not compute) either of the U,V outputs anymore. Neat, isn't it?
    val drmU = drmQ %*% inCoreUHat
    val drmV = drmBt %*% (inCoreUHat %*% diagv(1 / s))

    (drmU(::, 0 until k), drmV(::, 0 until k), s(0 until k))


The scala dspca(...) method can easily be called in any Spark, Flink, or H2O application built with the math-scala library and the corresponding Spark, Flink, or H2O engine module as follows:

import org.apache.mahout.math._
import decompositions._
import drm._

val (drmU, drmV, s) = dspca(drmA, k=200, q=1)

Note the parameter is optional and its default value is zero.


[1]: Lyubimov and Palumbo, "Apache Mahout: Beyond MapReduce; Distributed Algorithm Design"