Merge 04bd9a6 into 8e34b01

pymc3/step_methods/nuts.py

@@ -1,11 +1,11 @@
 from .quadpotential import quad_potential
-from .arraystep import ArrayStepShared, ArrayStep, SamplerHist, Competence
+from .arraystep import ArrayStepShared, SamplerHist, Competence
 from ..model import modelcontext, Point
 from ..vartypes import continuous_types
-from numpy import exp, log, array
-from numpy.random import uniform
-from .hmc import leapfrog, Hamiltonian, bern, energy
+from .hmc import leapfrog, Hamiltonian, energy, bern
 from ..tuning import guess_scaling
+import numpy as np
+import numpy.random as nr
 import theano
 from ..theanof import (make_shared_replacements, join_nonshared_inputs, CallableTensor,
                        gradient, inputvars)
@@ -26,7 +26,7 @@ class NUTS(ArrayStepShared):
     default_blocked = True
 
     def __init__(self, vars=None, scaling=None, step_scale=0.25, is_cov=False, state=None,
-                 Emax=1000,
+                 max_energy=1000,
                  target_accept=0.8,
                  gamma=0.05,
                  k=0.75,
@@ -42,10 +42,11 @@ def __init__(self, vars=None, scaling=None, step_scale=0.25, is_cov=False, state
             step_scale : float, default=.25
                 Size of steps to take, automatically scaled down by 1/n**(1/4)
             is_cov : bool, default=False
-                Treat C as a covariance matrix/vector if True, else treat it as a precision matrix/vector
+                Treat C as a covariance matrix/vector if True, else treat it as a
+                precision matrix/vector
             state
                 state to start from
-            Emax : float, default 1000
+            max_energy : float, default 1000
                 maximum energy
             target_accept : float (0,1) default .8
                 target for avg accept probability between final branch and initial position
@@ -68,27 +69,19 @@ def __init__(self, vars=None, scaling=None, step_scale=0.25, is_cov=False, state
             scaling = model.test_point
 
         if isinstance(scaling, dict):
-            scaling = guess_scaling(
-                Point(scaling, model=model), model=model, vars=vars)
-
-        n = scaling.shape[0]
-
-        self.step_size = step_scale / n**(1 / 4.)
-
+            scaling = guess_scaling(Point(scaling, model=model), model=model, vars=vars)
+        self.step_size = step_scale / scaling.shape[0]**0.25
         self.potential = quad_potential(scaling, is_cov, as_cov=False)
-
         if state is None:
             state = SamplerHist()
         self.state = state
-        self.Emax = Emax
-
+        self.max_energy = max_energy
         self.target_accept = target_accept
         self.gamma = gamma
         self.t0 = t0
         self.k = k
-
-        self.Hbar = 0
-        self.u = log(self.step_size * 10)
+        self.h_bar = 0
+        self.u = np.log(self.step_size * 10)
         self.m = 1
 
         shared = make_shared_replacements(vars, model)
@@ -97,97 +90,80 @@ def __init__(self, vars=None, scaling=None, step_scale=0.25, is_cov=False, state
 
         super(NUTS, self).__init__(vars, shared, **kwargs)
 
-    def astep(self, q0):
-        # Hamiltonian(self.logp, self.dlogp, self.potential)
-        H = self.leapfrog1_dE
-        Emax = self.Emax
-        e = self.step_size
-
-        p0 = self.potential.random()
-        u = uniform()
-        q = qn = qp = q0
-        p = pn = pp = p0
-
-        n, s, j = 1, 1, 0
-
-        while s == 1:
-            v = bern(.5) * 2 - 1
-
-            if v == -1:
-                qn, pn, _, _, q1, n1, s1, a, na = buildtree(
-                    H, qn, pn, u, v, j, e, Emax, q0, p0)
-            else:
-                _, _, qp, pp, q1, n1, s1, a, na = buildtree(
-                    H, qp, pp, u, v, j, e, Emax, q0, p0)
-
-            if s1 == 1 and bern(min(1, n1 * 1. / n)):
-                q = q1
+    @staticmethod
+    def competence(var):
+        if var.dtype in continuous_types:
+            return Competence.IDEAL
+        return Competence.INCOMPATIBLE
 
-            n = n + n1
+    def astep(self, initial_position):
+        log_slice_var = np.log(nr.uniform())
+        initial_momentum = self.potential.random()
+        position = back_position = forward_position = initial_position
+        back_momentum = forward_momentum = initial_momentum
+        should_continue = True
+        trials = 1
+        depth = 0
+        while should_continue:
+            direction = nr.choice((-1, 1))
+            step = np.array(direction * self.step_size)
+            new_trials = 0
+            metropolis_acceptance = 0
+            steps = 0
+            for _ in range(2 ** depth):
+                if not should_continue:
+                    break
+                if direction == 1:
+                    forward_position, forward_momentum, energy_change = self.leapfrog1_dE(
+                        forward_position, forward_momentum, step,
+                        initial_position, initial_momentum)
+                else:
+                    back_position, back_momentum, energy_change = self.leapfrog1_dE(
+                        back_position, back_momentum, step, initial_position, initial_momentum)
+                new_trials += int(log_slice_var + energy_change <= 0)
+                if should_update_position(new_trials, trials):
+                    if direction == 1:
+                        position = forward_position
+                    else:
+                        position = back_position
+
+                should_continue = (self._energy_is_bounded(log_slice_var, energy_change) and
+                                   no_u_turns(forward_position, forward_momentum,
+                                              back_position, back_momentum))
+                metropolis_acceptance += min(1., np.exp(-energy_change))
+                steps += 1
+            trials += new_trials
+            depth += 1
+        w = 1. / (self.m + self.t0)
+        self.h_bar = (1 - w) * self.h_bar + w * (self.target_accept - metropolis_acceptance / steps)
+        self.step_size = np.exp(self.u - (self.m ** 0.5 / self.gamma) * self.h_bar)
+        self.m += 1
+        return position
 
-            span = qp - qn
-            s = s1 * (span.dot(pn) >= 0) * (span.dot(pp) >= 0)
-            j = j + 1
+    def _energy_is_bounded(self, log_slice_var, energy_change):
+        return log_slice_var + energy_change < self.max_energy
 
-        p = -p
 
-        w = 1. / (self.m + self.t0)
-        self.Hbar = (1 - w) * self.Hbar + w * \
-            (self.target_accept - a * 1. / na)
+def no_u_turns(forward_position, forward_momentum, back_position, back_momentum):
+    span = forward_position - back_position
+    return span.dot(back_momentum) >= 0 and span.dot(forward_momentum) >= 0
 
-        self.step_size = exp(self.u - (self.m**.5 / self.gamma) * self.Hbar)
-        self.m += 1
 
-        return q
+def should_update_position(new_trials, trials):
+    return bern(float(new_trials) / max(trials, 1.))
 
-    @staticmethod
-    def competence(var):
-        if var.dtype in continuous_types:
-            return Competence.IDEAL
-        return Competence.INCOMPATIBLE
 
+def leapfrog1_dE(logp, vars, shared, quad_potential, profile):
+    """Computes a theano function that computes one leapfrog step and the energy
+    difference between the beginning and end of the trajectory.
 
-def buildtree(H, q, p, u, v, j, e, Emax, q0, p0):
-    if j == 0:
-        leapfrog1_dE = H
-        q1, p1, dE = leapfrog1_dE(q, p, array(v * e), q0, p0)
-
-        n1 = int(log(u) + dE <= 0)
-        s1 = int(log(u) + dE < Emax)
-        return q1, p1, q1, p1, q1, n1, s1, min(1, exp(-dE)), 1
-    else:
-        qn, pn, qp, pp, q1, n1, s1, a1, na1 = buildtree(
-            H, q, p, u, v, j - 1, e, Emax, q0, p0)
-        if s1 == 1:
-            if v == -1:
-                qn, pn, _, _, q11, n11, s11, a11, na11 = buildtree(
-                    H, qn, pn, u, v, j - 1, e, Emax, q0, p0)
-            else:
-                _, _, qp, pp, q11, n11, s11, a11, na11 = buildtree(
-                    H, qp, pp, u, v, j - 1, e, Emax, q0, p0)
-
-            if bern(n11 * 1. / (max(n1 + n11, 1))):
-                q1 = q11
-
-            a1 = a1 + a11
-            na1 = na1 + na11
-
-            span = qp - qn
-            s1 = s11 * (span.dot(pn) >= 0) * (span.dot(pp) >= 0)
-            n1 = n1 + n11
-        return qn, pn, qp, pp, q1, n1, s1, a1, na1
-    return
-
-
-def leapfrog1_dE(logp, vars, shared, pot, profile):
-    """Computes a theano function that computes one leapfrog step and the energy difference between the beginning and end of the trajectory.
     Parameters
     ----------
     logp : TensorVariable
     vars : list of tensor variables
     shared : list of shared variables not to compute leapfrog over
-    pot : quadpotential
-    porifle : Boolean
+    quad_potential : quadpotential
+    profile : Boolean
 
     Returns
     -------
@@ -199,7 +175,7 @@ def leapfrog1_dE(logp, vars, shared, pot, profile):
     logp = CallableTensor(logp)
     dlogp = CallableTensor(dlogp)
 
-    H = Hamiltonian(logp, dlogp, pot)
+    hamiltonian = Hamiltonian(logp, dlogp, quad_potential)
 
     p = tt.dvector('p')
     p.tag.test_value = q.tag.test_value
@@ -212,11 +188,9 @@ def leapfrog1_dE(logp, vars, shared, pot, profile):
     e = tt.dscalar('e')
     e.tag.test_value = 1
 
-    q1, p1 = leapfrog(H, q, p, 1, e)
-    E = energy(H, q1, p1)
-    E0 = energy(H, q0, p0)
-    dE = E - E0
+    q1, p1 = leapfrog(hamiltonian, q, p, 1, e)
+    energy_change = energy(hamiltonian, q1, p1) - energy(hamiltonian, q0, p0)
 
-    f = theano.function([q, p, e, q0, p0], [q1, p1, dE], profile=profile)
+    f = theano.function([q, p, e, q0, p0], [q1, p1, energy_change], profile=profile)
     f.trust_input = True
     return f

pymc3/tests/test_sampling.py

@@ -19,8 +19,6 @@
 except:
     test_parallel = False
 
-RSEED = 20090425
-
 
 def test_sample():
     model, start, step, _ = simple_init()
@@ -38,13 +36,13 @@ def test_iter_sample():
         assert i == len(trace) - 1, "Trace does not have correct length."
 
 
-def test_parallel_start():
-    model, _, _, _ = simple_init()
-    with model:
-        tr = sample(5, njobs=2, start=[{'x': [10, 10]}, {
-                    'x': [-10, -10]}], random_seed=RSEED)
-    assert tr.get_values('x', chains=0)[0][0] > 0
-    assert tr.get_values('x', chains=1)[0][0] < 0
+class TestParallelStart(SeededTest):
+    def test_parallel_start(self):
+        model, _, _, _ = simple_init()
+        with model:
+            tr = sample(5, njobs=2, start=[{'x': [10, 10]}, {'x': [-10, -10]}])
+        self.assertGreater(tr.get_values('x', chains=0)[0][0], 0)
+        self.assertLess(tr.get_values('x', chains=1)[0][0], 0)
 
 
 def test_soft_update_all_present():