diff --git a/GPy/examples/GP_regression_demo.py b/GPy/examples/GP_regression_demo.py index 0fe2fabd..96bd6dc3 100644 --- a/GPy/examples/GP_regression_demo.py +++ b/GPy/examples/GP_regression_demo.py @@ -1,7 +1,6 @@ # Copyright (c) 2012, GPy authors (see AUTHORS.txt). # Licensed under the BSD 3-clause license (see LICENSE.txt) - """ Simple Gaussian Processes regression with an RBF kernel """ @@ -19,8 +18,11 @@ pb.close('all') X = np.random.uniform(-3.,3.,(20,1)) Y = np.sin(X)+np.random.randn(20,1)*0.05 +# define kernel +ker = GPy.kern.rbf(1,ARD=False) + GPy.kern.white(1) + # create simple GP model -m = GPy.models.GP_regression(X,Y) +m = GPy.models.GP_regression(X,Y,ker) # contrain all parameters to be positive m.constrain_positive('') @@ -30,6 +32,7 @@ m.optimize('tnc', max_f_eval = 1000) m.plot() print(m) + ###################################### ## 2 dimensional example @@ -37,8 +40,11 @@ print(m) X = np.random.uniform(-3.,3.,(40,2)) Y = np.sin(X[:,0:1]) * np.sin(X[:,1:2])+np.random.randn(40,1)*0.05 +# define kernel +ker = GPy.kern.rbf(2,ARD=True) + GPy.kern.white(2) + # create simple GP model -m = GPy.models.GP_regression(X,Y) +m = GPy.models.GP_regression(X,Y,ker) # contrain all parameters to be positive m.constrain_positive('') diff --git a/GPy/examples/sparse_GPLVM_demo.py b/GPy/examples/sparse_GPLVM_demo.py index 6ca6c941..3f1969fe 100644 --- a/GPy/examples/sparse_GPLVM_demo.py +++ b/GPy/examples/sparse_GPLVM_demo.py @@ -10,11 +10,11 @@ print "sparse GPLVM with RBF kernel" N = 100 M = 4 -Q = 1 +Q = 2 D = 2 #generate GPLVM-like data X = np.random.rand(N, Q) -k = GPy.kern.rbf(Q, 1.0, 2.0) + GPy.kern.white(Q, 0.00001) +k = GPy.kern.rbf(Q,1.,2*np.ones((1,))) + GPy.kern.white(Q, 0.00001) K = k.K(X) Y = np.random.multivariate_normal(np.zeros(N),K,D).T diff --git a/GPy/kern/constructors.py b/GPy/kern/constructors.py index 0ddc09e3..e1304f11 100644 --- a/GPy/kern/constructors.py +++ b/GPy/kern/constructors.py @@ -22,7 +22,7 @@ from Brownian import Brownian as Brownianpart #using meta-classes to make the objects construct properly wthout them. -def rbf(D,variance=1., lengthscale=1.): +def rbf(D,variance=1., lengthscale=None,ARD=False): """ Construct an RBF kernel @@ -33,7 +33,7 @@ def rbf(D,variance=1., lengthscale=1.): :param lengthscale: the lengthscale of the kernel :type lengthscale: float """ - part = rbfpart(D,variance,lengthscale) + part = rbfpart(D,variance,lengthscale,ARD) return kern(D, [part]) def rbf_ARD(D,variance=1., lengthscales=None): diff --git a/GPy/kern/rbf.py b/GPy/kern/rbf.py index 9e2bb509..775bb797 100644 --- a/GPy/kern/rbf.py +++ b/GPy/kern/rbf.py @@ -20,17 +20,33 @@ class rbf(kernpart): :type D: int :param variance: the variance of the kernel :type variance: float - :param lengthscale: the lengthscale of the kernel - :type lengthscale: float + :param lengthscale: the vector of lengthscale of the kernel + :type lengthscale: np.ndarray + :param ARD: Auto Relevance Determination. If equal to "False", the kernel is isotropic (ie. one single lengthscale parameter \ell), otherwise there is one lengthscale parameter per dimension. + :type ARD: Boolean - .. Note: for rbf with different lengthscale on each dimension, see rbf_ARD """ - def __init__(self,D,variance=1.,lengthscale=1.): + def __init__(self,D,variance=1.,lengthscale=None,ARD=False): self.D = D - self.Nparam = 2 - self.name = 'rbf' - self.set_param(np.hstack((variance,lengthscale))) + self.ARD = ARD + if ARD == False: + self.Nparam = 2 + self.name = 'rbf' + if lengthscale is not None: + assert lengthscale.shape == (1,) + else: + lengthscale = np.ones(1) + + else: + self.Nparam = self.D + 1 + self.name = 'rbf_ARD' + if lengthscale is not None: + assert lengthscale.shape == (self.D,) + else: + lengthscale = np.ones(self.D) + + self.set_param(np.hstack((variance,lengthscale))) #initialize cache self._Z, self._mu, self._S = np.empty(shape=(3,1)) @@ -40,14 +56,19 @@ class rbf(kernpart): return np.hstack((self.variance,self.lengthscale)) def set_param(self,x): - self.variance, self.lengthscale = x + assert x.size==(self.Nparam) + self.variance = x[0] + self.lengthscale = x[1:] self.lengthscale2 = np.square(self.lengthscale) #reset cached results self._X, self._X2, self._params = np.empty(shape=(3,1)) self._Z, self._mu, self._S = np.empty(shape=(3,1)) # cached versions of Z,mu,S def get_param_names(self): - return ['variance','lengthscale'] + if self.Nparam == 2: + return ['variance','lengthscale'] + else: + return ['variance']+['lengthscale_%i'%i for i in range(self.lengthscale.size)] def K(self,X,X2,target): if X2 is None: @@ -61,7 +82,12 @@ class rbf(kernpart): def dK_dtheta(self,partial,X,X2,target): self._K_computations(X,X2) target[0] += np.sum(self._K_dvar*partial) - target[1] += np.sum(self._K_dvar*self.variance*self._K_dist2/self.lengthscale*partial) + if self.ARD == True: + dl = self._K_dvar[:,:,None]*self.variance*self._K_dist2/self.lengthscale + target[1:] += (dl*partial[:,:,None]).sum(0).sum(0) + else: + target[1] += np.sum(self._K_dvar*self.variance*(self._K_dist2.sum(-1))/self.lengthscale*partial) + #np.sum(self._K_dvar*self.variance*self._K_dist2/self.lengthscale*partial) def dKdiag_dtheta(self,partial,X,target): #NB: derivative of diagonal elements wrt lengthscale is 0 @@ -81,15 +107,13 @@ class rbf(kernpart): self._X = X self._X2 = X2 if X2 is None: X2 = X - XXT = np.dot(X,X2.T) - if X is X2: - self._K_dist2 = (-2.*XXT + np.diag(XXT)[:,np.newaxis] + np.diag(XXT)[np.newaxis,:])/self.lengthscale2 - else: - self._K_dist2 = (-2.*XXT + np.sum(np.square(X),1)[:,None] + np.sum(np.square(X2),1)[None,:])/self.lengthscale2 - # TODO Remove comments if this is fine. - # Commented out by Neil as doesn't seem to be used elsewhere. - #self._K_exponent = -0.5*self._K_dist2 - self._K_dvar = np.exp(-0.5*self._K_dist2) + self._K_dist = X[:,None,:]-X2[None,:,:] # this can be computationally heavy + self._params = np.empty(shape=(1,0))#ensure the next section gets called + if not np.all(self._params == self.get_param()): + self._params == self.get_param() + self._K_dist2 = np.square(self._K_dist/self.lengthscale) + #self._K_exponent = -0.5*self._K_dist2.sum(-1) #ND: commented out because seems not to be used + self._K_dvar = np.exp(-0.5*self._K_dist2.sum(-1)) def psi0(self,Z,mu,S,target): target += self.variance @@ -132,7 +156,7 @@ class rbf(kernpart): d_length = self._psi2[:,:,:,None]*(0.5*self._psi2_Zdist_sq*self._psi2_denom + 2.*self._psi2_mudist_sq + 2.*S[:,None,None,:]/self.lengthscale2)/(self.lengthscale*self._psi2_denom) d_length = d_length.sum(0) target[0] += np.sum(partial*d_var) - target[1] += np.sum(d_length*partial) + target[1:] += (d_length*partial[:,:,None]).sum(0).sum(0) def dpsi2_dZ(self,partial,Z,mu,S,target): """Returns shape N,M,M,Q""" @@ -175,4 +199,3 @@ class rbf(kernpart): self._psi2 = np.square(self.variance)*np.exp(self._psi2_exponent) # N,M,M self._Z, self._mu, self._S = Z, mu,S -