minor changes, dimensionality reduction tests

GPy/examples/dimensionality_reduction.py

@@ -266,15 +266,19 @@ def bgplvm_simulation(optimize='scg',
 
     if optimize:
         print "Optimizing model:"
-        m.optimize('scg', max_iters=max_f_eval, max_f_eval=max_f_eval, messages=True)
+        m.optimize('bfgs', max_iters=max_f_eval,
+                   max_f_eval=max_f_eval,
+                   messages=True, gtol=1e-2)
     if plot:
         import pylab
         m.plot_X_1d()
-        pylab.figure(); pylab.axis(); m.kern.plot_ARD()
+        pylab.figure('BGPLVM Simulation ARD Parameters');
+        pylab.axis();
+        m.kern.plot_ARD()
     return m
 
 def mrd_simulation(optimize=True, plot_sim=False, **kw):
-    D1, D2, D3, N, M, Q = 150, 250, 30, 200, 3, 7
+    D1, D2, D3, N, M, Q = 15, 8, 8, 100, 3, 7
     slist, Slist, Ylist = _simulate_sincos(D1, D2, D3, N, M, Q, plot_sim)
 
     from GPy.models import mrd
@@ -284,20 +288,20 @@ def mrd_simulation(optimize=True, plot_sim=False, **kw):
     reload(mrd); reload(kern)
 
     k = kern.linear(Q, [0.01] * Q, True) + kern.bias(Q, np.exp(-2)) + kern.white(Q, np.exp(-2))
-    m = mrd.MRD(*Ylist, Q=Q, M=M, kernel=k, initx="concat", initz='permute', **kw)
+    m = mrd.MRD(Ylist, Q=Q, M=M, kernel=k, initx="concat", initz='permute', **kw)
 
     for i, Y in enumerate(Ylist):
         m['{}_noise'.format(i + 1)] = Y.var() / 100.
 
-    # m.constrain('variance|noise', logexp_clipped())
+    m.constrain('variance|noise', logexp_clipped())
     m.ensure_default_constraints()
 
     # DEBUG
-    np.seterr("raise")
+    # np.seterr("raise")
 
     if optimize:
         print "Optimizing Model:"
-        m.optimize('scg', messages=1, max_iters=3e3)
+        m.optimize('bfgs', messages=1, max_iters=3e3)
 
     return m
 

GPy/inference/SCG.py

@@ -25,6 +25,13 @@
 import numpy as np
 import sys
 
+
+def print_out(len_maxiters, display, fnow, current_grad, beta, iteration):
+    if display:
+        print '\r',
+        print '{0:>0{mi}g}  {1:> 12e}  {2:> 12e}  {3:> 12e}'.format(iteration, float(fnow), float(beta), float(current_grad), mi=len_maxiters), # print 'Iteration:', iteration, ' Objective:', fnow, '  Scale:', beta, '\r',
+        sys.stdout.flush()
+
 def SCG(f, gradf, x, optargs=(), maxiters=500, max_f_eval=500, display=True, xtol=None, ftol=None, gtol=None):
     """
     Optimisation through Scaled Conjugate Gradients (SCG)
@@ -65,7 +72,8 @@ def SCG(f, gradf, x, optargs=(), maxiters=500, max_f_eval=500, display=True, xto
     iteration = 0
 
     if display:
-        print ' {0:{mi}s}   {1:11s}    {2:11s}    {3:11s}'.format("I", "F", "Scale", "|g|", mi=len(str(maxiters)))
+        len_maxiters = len(str(maxiters))
+        print ' {0:{mi}s}   {1:11s}    {2:11s}    {3:11s}'.format("I", "F", "Scale", "|g|", mi=len_maxiters)
 
     # Main optimization loop.
     while iteration < maxiters:
@@ -113,11 +121,7 @@ def SCG(f, gradf, x, optargs=(), maxiters=500, max_f_eval=500, display=True, xto
         flog.append(fnow) # Current function value
 
         iteration += 1
-        if display:
+        print_out(len_maxiters, display, fnow, current_grad, beta, iteration)
-            print '\r',
-            print '{0:>0{mi}g}  {1:> 12e}  {2:> 12e}  {3:> 12e}'.format(iteration, float(fnow), float(beta), float(current_grad), mi=len(str(maxiters))),
-            # print 'Iteration:', iteration, ' Objective:', fnow, '  Scale:', beta, '\r',
-            sys.stdout.flush()
 
         if success:
             # Test for termination
@@ -158,5 +162,6 @@ def SCG(f, gradf, x, optargs=(), maxiters=500, max_f_eval=500, display=True, xto
         status = "maxiter exceeded"
 
     if display:
+        print_out(len_maxiters, display, fnow, current_grad, beta, iteration)
         print ""
     return x, flog, function_eval, status

GPy/likelihoods/Gaussian.py

@@ -53,7 +53,7 @@ class Gaussian(likelihood):
     def _set_params(self, x):
         x = float(x)
         if self._variance != x:
-            self.precision = 1. / max(x, 1e-6)
+            self.precision = 1. / x
             self.covariance_matrix = np.eye(self.N) * x
             self.V = (self.precision) * self.Y
             self._variance = x

GPy/models/Bayesian_GPLVM.py

@@ -93,8 +93,12 @@ class Bayesian_GPLVM(sparse_GP, GPLVM):
         x = np.hstack((self.X.flatten(), self.X_variance.flatten(), sparse_GP._get_params(self)))
         return x
 
+    def _clipped(self, x):
+        return x # np.clip(x, -1e100, 1e100)
+    
     def _set_params(self, x, save_old=True, save_count=0):
 #         try:
+            x = self._clipped(x)
             N, Q = self.N, self.Q
             self.X = x[:self.X.size].reshape(N, Q).copy()
             self.X_variance = x[(N * Q):(2 * N * Q)].reshape(N, Q).copy()
@@ -176,7 +180,7 @@ class Bayesian_GPLVM(sparse_GP, GPLVM):
         # ========================
         self.dbound_dmuS = np.hstack((d_dmu, d_dS))
         self.dbound_dZtheta = sparse_GP._log_likelihood_gradients(self)
-        return np.hstack((self.dbound_dmuS.flatten(), self.dbound_dZtheta))
+        return self._clipped(np.hstack((self.dbound_dmuS.flatten(), self.dbound_dZtheta)))
 
     def plot_latent(self, which_indices=None, *args, **kwargs):
 

GPy/models/GPLVM.py

@@ -119,7 +119,7 @@ class GPLVM(GP):
             else:
                 x = self.X[index,input_1]
                 y = self.X[index,input_2]
-            ax.scatter(x, y, marker=m, s=s, color=util.plot.Tango.nextMedium(), mew=1.3, label=this_label)
+            ax.scatter(x, y, marker=m, s=s, color=util.plot.Tango.nextMedium(), label=this_label)
 
         ax.set_xlabel('latent dimension %i'%input_1)
         ax.set_ylabel('latent dimension %i'%input_2)