From 56ff88eeec52baffa6f93c2150e9c3e8d2bf4065 Mon Sep 17 00:00:00 2001
From: Amit Kumar Jaiswal <amitkumarj441@gmail.com>
Date: Wed, 22 Feb 2017 10:06:33 +0530
Subject: [PATCH] Create HMC.scala

Dislocation of implicits
---
 .../mandar2812/dynaml/probability/HMC.scala   | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/probability/HMC.scala

diff --git a/dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/probability/HMC.scala b/dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/probability/HMC.scala
new file mode 100644
index 000000000..8c8805dd0
--- /dev/null
+++ b/dynaml-core/src/main/scala-2.11/io/github/mandar2812/dynaml/probability/HMC.scala
@@ -0,0 +1,51 @@
+package io.github.mandar2812.dynaml.probability
+
+import org.apache.commons.math3.linear.{Array2DRowRealMatrix, CholeskyDecomposition, LUDecomposition}
+import shapeless.Witness
+import spire.algebra._
+import spire.random.{Dist, Gaussian, Generator, Uniform}
+import spire.std.seq._
+import spire.syntax.innerProductSpace._
+import spire.syntax.order._
+
+abstract class HMC[R : Uniform : Gaussian, N, G, D <: Int with Singleton : Witness.Aux](val posterior: Tree[R, N] => (R, G), val M: Matrix[D, R], val alpha: R, val eps: R, val L: Int, val RToDouble: R => Double)(implicit val rng: Generator, implicit val f: Field[R], implicit val trig: Trig[R], implicit val n: NRoot[R], implicit val s: Signed[R], implicit val o: Order[R]) extends (Z[R, N, G] => Z[R, N, G]) {
+
+  type ZZ = Z[R, N, G]
+
+  val (invM, choleskyL): (Matrix[D, R], Matrix[D, R]) = {
+    val apacheM = new Array2DRowRealMatrix(M.size, M.size)
+    M.indices.foreach(Function.tupled((i, j) => apacheM.setEntry(i, j, RToDouble(M(i, j)))))
+    val apacheInvM = new LUDecomposition(apacheM).getSolver.getInverse
+    val apacheCholeskyL = new CholeskyDecomposition(apacheM).getL
+    (Matrix[D, R]((i: Int, j: Int) => Field[R].fromDouble(apacheInvM.getEntry(i, j))), Matrix[D, R]((i: Int, j: Int) => Field[R].fromDouble(apacheCholeskyL.getEntry(i, j))))
+  }
+
+  val uniform = Dist.uniform(Field[R].zero, Field[R].one)
+  val gaussian = Dist.gaussian(Field[R].zero, Field[R].one)
+  val sqrtalpha = NRoot[R].sqrt(alpha)
+  val sqrt1malpha = NRoot[R].sqrt(1 - alpha)
+
+  def U(q: Tree[R, N]): (R, G)
+
+  def K(p: IndexedSeq[R]): (R, G)
+
+  def flipMomentum(z: ZZ): ZZ = {
+    val pp = -z.p
+    z.copy(p = pp)(_K = K(pp))
+  }
+
+  def corruptMomentum(z: ZZ): ZZ = {
+    val r = IndexedSeq.fill(z.p.size)(rng.next(gaussian))
+    val pp = sqrt1malpha *: z.p + sqrtalpha *: (choleskyL * r)
+    z.copy(p = pp)(_K = K(pp))
+  }
+
+  def simulateDynamics(z: ZZ): ZZ
+
+  override def apply(z: ZZ): ZZ = {
+    val zp = flipMomentum(simulateDynamics(z))
+    val a = Trig[R].exp(z.H - zp.H) min 1
+    corruptMomentum(flipMomentum(if (rng.next(uniform) < a) zp else z))
+  }
+
+}