logexp_clipped adjust & mrd error messages

GPy/core/transformations.py

@@ -39,7 +39,7 @@ class logexp(transformation):
         return '(+ve)'
 
 class logexp_clipped(transformation):
-    max_bound = 1e300
+    max_bound = 1e100
     min_bound = 1e-10
     log_max_bound = np.log(max_bound)
     log_min_bound = np.log(min_bound)
@@ -53,11 +53,11 @@ class logexp_clipped(transformation):
 #             import ipdb;ipdb.set_trace()
         return np.clip(f, self.min_bound, self.max_bound)
     def finv(self, f):
-        return np.log(np.exp(np.clip(f, self.min_bound, self.max_bound)) - 1.)
+        return np.log(np.exp(f - 1.))
     def gradfactor(self, f):
         ef = np.exp(f) # np.clip(f, self.min_bound, self.max_bound))
         gf = (ef - 1.) / ef
-        return np.where(f < self.lower, 0, gf)
+        return gf # np.where(f < self.lower, 0, gf)
     def initialize(self, f):
         if np.any(f < 0.):
             print "Warning: changing parameters to satisfy constraints"

GPy/examples/dimensionality_reduction.py

@@ -278,7 +278,7 @@ def bgplvm_simulation(optimize='scg',
     return m
 
 def mrd_simulation(optimize=True, plot_sim=False, **kw):
-    D1, D2, D3, N, M, Q = 150, 200, 400, 700, 3, 7
+    D1, D2, D3, N, M, Q = 150, 200, 400, 300, 3, 7
     slist, Slist, Ylist = _simulate_sincos(D1, D2, D3, N, M, Q, plot_sim)
 
     from GPy.models import mrd
@@ -287,7 +287,7 @@ 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))
+    k = kern.linear(Q, [0.05] * Q, True) + kern.bias(Q, np.exp(-2)) + kern.white(Q, np.exp(-2))
     m = mrd.MRD(Ylist, Q=Q, M=M, kernels=k, initx="concat", initz='permute', **kw)
 
     for i, Y in enumerate(Ylist):

GPy/models/mrd.py

@@ -56,6 +56,7 @@ class MRD(model):
         else:
             assert len(kernels) == len(likelihood_or_Y_list), "need one kernel per output"
             assert all([isinstance(k, kern) for k in kernels]), "invalid kernel object detected!"
+        assert not ('kernel' in kw), "pass kernels through `kernels` argument"
 
         self.Q = Q
         self.M = M