diff --git a/GPy/examples/dimensionality_reduction.py b/GPy/examples/dimensionality_reduction.py index 6230ef3a..1f30a67f 100644 --- a/GPy/examples/dimensionality_reduction.py +++ b/GPy/examples/dimensionality_reduction.py @@ -131,7 +131,7 @@ def BGPLVM_oil(optimize=True, N=100, Q=5, M=25, max_f_eval=4e3, plot=False, **k) m = GPy.models.Bayesian_GPLVM(Yn, Q, kernel=kernel, M=M, **k) m.data_labels = data['Y'][:N].argmax(axis=1) - m.constrain('variance|leng', logexp_clipped()) + # m.constrain('variance|leng', logexp_clipped()) m['lengt'] = m.X.var(0).max() / m.X.var(0) m['noise'] = Yn.var() / 100. @@ -246,7 +246,7 @@ def bgplvm_simulation_matlab_compare(): def bgplvm_simulation(optimize='scg', plot=True, max_f_eval=2e4): - from GPy.core.transformations import logexp_clipped +# from GPy.core.transformations import logexp_clipped D1, D2, D3, N, M, Q = 15, 8, 8, 100, 3, 5 slist, Slist, Ylist = _simulate_sincos(D1, D2, D3, N, M, Q, plot) @@ -259,8 +259,8 @@ def bgplvm_simulation(optimize='scg', k = kern.linear(Q, ARD=True) + kern.bias(Q, np.exp(-2)) + kern.white(Q, np.exp(-2)) # + kern.bias(Q) m = Bayesian_GPLVM(Y, Q, init="PCA", M=M, kernel=k, _debug=True) - m.constrain('variance|noise', logexp_clipped()) -# m.ensure_default_constraints() + # m.constrain('variance|noise', logexp_clipped()) + m.ensure_default_constraints() m['noise'] = Y.var() / 100. m['linear_variance'] = .01 @@ -273,8 +273,8 @@ def bgplvm_simulation(optimize='scg', pylab.figure(); pylab.axis(); m.kern.plot_ARD() return m -def mrd_simulation(optimize=True, plot_sim=False): - D1, D2, D3, N, M, Q = 150, 250, 30, 300, 3, 7 +def mrd_simulation(optimize=True, plot_sim=False, **kw): + D1, D2, D3, N, M, Q = 150, 250, 30, 200, 3, 7 slist, Slist, Ylist = _simulate_sincos(D1, D2, D3, N, M, Q, plot_sim) from GPy.models import mrd @@ -284,12 +284,12 @@ def mrd_simulation(optimize=True, plot_sim=False): 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') + 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