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https://issues.apache.org/jira/browse/MAHOUT-1746?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14600675#comment-14600675
]
ASF GitHub Bot commented on MAHOUT-1746:
----------------------------------------
Github user andrewpalumbo commented on a diff in the pull request:
https://github.com/apache/mahout/pull/145#discussion_r33221710
--- Diff:
math-scala/src/main/scala/org/apache/mahout/math/drm/package.scala ---
@@ -160,6 +160,165 @@ package object drm {
def dsqrt[K: ClassTag](drmA: DrmLike[K]): DrmLike[K] = new
OpAewUnaryFunc[K](drmA, math.sqrt)
def dsignum[K: ClassTag](drmA: DrmLike[K]): DrmLike[K] = new
OpAewUnaryFunc[K](drmA, math.signum)
+
+ ///////////////////////////////////////////////////////////
+ // Misc. math utilities.
+
+ /**
+ * Compute column wise means and variances -- distributed version.
+ *
+ * @param drmA Note: will pin input to cache if not yet pinned.
+ * @tparam K
+ * @return colMeans → colVariances
+ */
+ def dcolMeanVars[K: ClassTag](drmA: DrmLike[K]): (Vector, Vector) = {
+
+ import RLikeDrmOps._
+
+ val drmAcp = drmA.checkpoint()
+
+ val mu = drmAcp colMeans
+
+ // Compute variance using mean(x^2) - mean(x)^2
+ val variances = (drmAcp ^ 2 colMeans) -=: mu * mu
+
+ mu → variances
+ }
+
+ /**
+ * Compute column wise means and standard deviations -- distributed
version.
+ * @param drmA note: input will be pinned to cache if not yet pinned
+ * @return colMeans → colStdevs
+ */
+ def dcolMeanStdevs[K: ClassTag](drmA: DrmLike[K]): (Vector, Vector) = {
+ val (mu, vars) = dcolMeanVars(drmA)
+ mu → (vars ::= math.sqrt _)
+ }
+
+ /**
+ * Thin column-wise mean and covariance matrix computation. Same as
[[dcolMeanCov()]] but suited for
+ * thin and tall inputs where covariance matrix can be reduced and
finalized in driver memory.
+ *
+ * @param drmA note: will pin input to cache if not yet pinned.
+ * @return mean → covariance matrix (in core)
+ */
+ def dcolMeanCovThin[K: ClassTag](drmA: DrmLike[K]):(Vector, Matrix) = {
+
+ import RLikeDrmOps._
+
+ val drmAcp = drmA.checkpoint()
+ val mu = drmAcp colMeans
+ val mxCov = (drmAcp.t %*% drmAcp).collect /= drmAcp.nrow -= (mu cross
mu)
+ mu → mxCov
+ }
+
+ /**
+ * Compute COV(X) matrix and mean of row-wise data set. X is presented
as row-wise input matrix A.
+ *
+ * This is a "wide" procedure, covariance matrix is returned as a DRM.
+ *
+ * @param drmA note: will pin input into cache if not yet pinned.
+ * @return mean → covariance DRM
+ */
+ def dcolMeanCov[K: ClassTag](drmA: DrmLike[K]): (Vector, DrmLike[Int]) =
{
+
+ import RLikeDrmOps._
+
+ implicit val ctx = drmA.context
+ val drmAcp = drmA.checkpoint()
+
+ val bcastMu = drmBroadcast(drmAcp colMeans)
+
+ // We use multivaraite analogue COV(X)=E(XX')-mu*mu'. In our case
E(XX') = (A'A)/A.nrow.
+ // Compute E(XX')
+ val drmSigma = (drmAcp.t %*% drmAcp / drmAcp.nrow)
+
+ // Subtract mu*mu'. In this case we assume mu*mu' may still be big
enough to be treated by
+ // driver alone, so we redistribute this operation as well. Hence it
may look a bit cryptic.
+ .mapBlock() { case (keys, block) ⇒
+
+ // Pin mu as vector reference to memory.
+ val mu:Vector = bcastMu
+
+ keys → (block := { (r, c, v) ⇒ v - mu(keys(r)) * mu(c) })
+ }
+
+ // return (mu, cov(X) ("bigSigma")).
+ (bcastMu: Vector) → drmSigma
+ }
+
+ /** Distributed Squared distance matrix computation. */
+ def dsqDist(drmX: DrmLike[Int]): DrmLike[Int] = {
+
+ // This is a specific case of pairwise distances of X and Y.
+
+ import RLikeDrmOps._
+
+ // Context needed
+ implicit val ctx = drmX.context
+
+ // Pin to cache if hasn't been pinned yet
+ val drmXcp = drmX.checkpoint()
+
+ // Compute column sum of squares
+ val s = drmXcp ^ 2 rowSums
+
+ val sBcast = drmBroadcast(s)
+
+ (drmXcp %*% drmXcp.t)
+
+ // Apply second part of the formula as per in-core algorithm
+ .mapBlock() { case (keys, block) ⇒
+
+ // Slurp broadcast to memory
+ val s = sBcast: Vector
+
+ // Update in-place
+ block := { (r, c, x) ⇒ s(keys(r)) + s(c) - 2 * x}
+
+ keys → block
+ }
+ }
+
+
+ /**
+ * Compute fold-in distances (distributed version). Here, we use pretty
much the same math as with
+ * squared distances.
+ *
+ * D_sq = s*1' + 1*t' - 2*X*Y'
+ *
+ * where s is row sums of hadamard product(X, X), and, similarly,
+ * s is row sums of Hadamard product(Y, Y).
+ *
+ * @param drmX m x d row-wise dataset. Pinned to cache if not yet pinned.
+ * @param drmY n x d row-wise dataset. Pinned to cache if not yet pinned.
+ * @return m x d pairwise squared distance matrix (between rows of X and
Y)
+ */
+ def dsqDist(drmX: DrmLike[Int], drmY: DrmLike[Int]): DrmLike[Int] = {
+
+ import RLikeDrmOps._
+
+ implicit val ctx = drmX.context
+
+ val drmXcp = drmX.checkpoint()
+ val drmYcp = drmY.checkpoint()
+
+ val sBcast = drmBroadcast(drmXcp ^ 2 rowSums)
+ val tBcast = drmBroadcast(drmYcp ^ 2 rowSums)
+
+ (drmX %*% drmY.t)
+
+ // Apply the rest of the formula
+ .mapBlock() { case (keys, block) =>
+
+ // Cache broadcast representations in local task variable
+ val s = tBcast: Vector
--- End diff --
Yeah- definite copy/paste typo. The h2o/spark tests catch it. After
changing it, the tests run fine.
> Fix: mxA ^ 2, mxA ^ 0.5 to mean the same thing as mxA * mxA and mxA ::= sqrt _
> ------------------------------------------------------------------------------
>
> Key: MAHOUT-1746
> URL: https://issues.apache.org/jira/browse/MAHOUT-1746
> Project: Mahout
> Issue Type: Blog - New Blog Request
> Reporter: Dmitriy Lyubimov
> Assignee: Dmitriy Lyubimov
> Fix For: 0.10.2
>
>
> it so happens that in java, if x is of double type, Math.pow(x,2.0) and x * x
> produce different values approximately once in million random values.
> This is extremely annoying as it creates rounding errors, especially with
> things like euclidean distance computations, which eventually may produce
> occasional NaNs.
> This issue suggests to get special treatment on vector and matrix dsl to make
> sure identical fpu algorithms are running as follows:
> x ^ 2 <=> x * x
> x ^ 0.5 <=> sqrt(x)
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