diff --git a/GPy/inference/likelihoods.py b/GPy/inference/likelihoods.py index 023f00ae..5f0eb7ff 100644 --- a/GPy/inference/likelihoods.py +++ b/GPy/inference/likelihoods.py @@ -122,36 +122,50 @@ class poisson(likelihood): mu = v_i/tau_i sigma = np.sqrt(1./tau_i) def poisson_norm(f): + """ + Product of the likelihood and the cavity distribution + """ pdf_norm_f = stats.norm.pdf(f,loc=mu,scale=sigma) rate = np.exp( (f*self.scale)+self.location) poisson = stats.poisson.pmf(float(self.Y[i]),rate) return pdf_norm_f*poisson def log_pnm(f): + """ + Log of poisson_norm + """ return -(-.5*(f-mu)**2/sigma**2 - np.exp( (f*self.scale)+self.location) + ( (f*self.scale)+self.location)*self.Y[i]) - golden_A = -1 if self.Y[i] == 0 else np.array([np.log(self.Y[i]),mu]).min() - golden_B = np.array([np.log(self.Y[i]),mu]).max() + """ + Golden Search and Simpson's Rule + -------------------------------- + Simpson's Rule is used to calculate the moments mumerically, it needs a grid of points as input. + Golden Search is used to find the mode in the poisson_norm distribution and define around it the grid for Simpson's Rule + """ + #TODO golden search & simpson's rule can be defined in the general likelihood class, rather than in each specific case. + + #Golden search + golden_A = -1 if self.Y[i] == 0 else np.array([np.log(self.Y[i]),mu]).min() #Lower limit + golden_B = np.array([np.log(self.Y[i]),mu]).max() #Upper limit golden_A = (golden_A - self.location)/self.scale golden_B = (golden_B - self.location)/self.scale - opt = sp.optimize.golden(log_pnm,brack=(golden_A,golden_B)) - width = 3./np.log(max(self.Y[i],2)) + opt = sp.optimize.golden(log_pnm,brack=(golden_A,golden_B)) #Better to work with log_pnm than with poisson_norm - # Simpson's approximamtion - #TODO explain this algorithm - A = opt - width - B = opt + width - K = 10*int(np.log(max(self.Y[i],150))) - h = (B-A)/K - grid_x = np.hstack([np.linspace(opt-width,opt,K/2+1)[1:-1], np.linspace(opt,opt+width,K/2+1)]) - x = np.hstack([A,B,grid_x[range(1,K,2)],grid_x[range(2,K-1,2)]]) - zeroth = np.hstack([poisson_norm(A),poisson_norm(B),[4*poisson_norm(f) for f in grid_x[range(1,K,2)]],[2*poisson_norm(f) for f in grid_x[range(2,K-1,2)]]]) + # Simpson's approximation + width = 3./np.log(max(self.Y[i],2)) + A = opt - width #Lower limit + B = opt + width #Upper limit + K = 10*int(np.log(max(self.Y[i],150))) #Number of points in the grid, we DON'T want K to be the same number for every case + h = (B-A)/K # length of the intervals + grid_x = np.hstack([np.linspace(opt-width,opt,K/2+1)[1:-1], np.linspace(opt,opt+width,K/2+1)]) # grid of points (X axis) + x = np.hstack([A,B,grid_x[range(1,K,2)],grid_x[range(2,K-1,2)]]) # grid_x rearranged, just to make Simpson's algorithm easier + zeroth = np.hstack([poisson_norm(A),poisson_norm(B),[4*poisson_norm(f) for f in grid_x[range(1,K,2)]],[2*poisson_norm(f) for f in grid_x[range(2,K-1,2)]]]) # grid of points (Y axis) rearranged like x first = zeroth*x second = first*x - Z_hat = sum(zeroth)*h/3 - mu_hat = sum(first)*h/(3*Z_hat) - m2 = sum(second)*h/(3*Z_hat) - sigma2_hat = m2 - mu_hat**2 + Z_hat = sum(zeroth)*h/3 # Zero-th moment + mu_hat = sum(first)*h/(3*Z_hat) # First moment + m2 = sum(second)*h/(3*Z_hat) # Second moment + sigma2_hat = m2 - mu_hat**2 # Second central moment return float(Z_hat), float(mu_hat), float(sigma2_hat) def plot1Db(self,X,X_new,F_new,F2_new=None,U=None): @@ -201,4 +215,3 @@ class gaussian(likelihood): def _log_likelihood_gradients(): raise NotImplementedError -#This is just a test