From b56222969d7534a0bcf62b2696159765ed1b95b7 Mon Sep 17 00:00:00 2001
From: kimsoohwan <kimsoohwan@naver.com>
Date: Wed, 16 Jul 2014 14:52:14 +1000
Subject: [PATCH] Added meanGP.m

---
 main/main_prediction.m | 77 +++++++++++++++++++++++++++++++++++++++---
 mean/meanGP.m          | 26 ++++++++++++++
 2 files changed, 98 insertions(+), 5 deletions(-)
 create mode 100644 mean/meanGP.m

diff --git a/main/main_prediction.m b/main/main_prediction.m
index 82daa84..2240c15 100644
--- a/main/main_prediction.m
+++ b/main/main_prediction.m
@@ -48,8 +48,8 @@
 dy_dx = [41.704618124666638; -28.757549228476215; 14.122022625746855; -52.574386176465111; 15.885794730520876; -27.330344334593999; 43.308255238127209; -20.443387861589134; 22.877410410575429; -52.447400235726114];
  
 % plot
-figure('position', [0, 0, 1200, 400]);
-subplot(1, 3, 1);
+figure('position', [0, 0, 1600, 400]);
+subplot(1, 4, 1);
 hold on
 delta_x = 0.03;
 plot(xs, ys, 'k-');
@@ -90,7 +90,7 @@
 [dummy, dummy, fmu, fs2] = gp(hyp1, inf_method, mean_func, cov_func, lik_func, x, y, xs);
 
 % plot
-subplot(1, 3, 2);
+subplot(1, 4, 2);
 hold on;
 ff = [fmu+2*sqrt(fs2); flipdim(fmu-2*sqrt(fs2),1)]; 
 fill([xs; flipdim(xs,1)], ff, [7 7 7]/8)
@@ -113,7 +113,6 @@
 cov_func  = {@covSEisoDerObs};
 lik_func  = @likGaussDerObs;
 inf_method = @infExactDerObs;
-likstr = func2str(lik_func);
 
 % data
 xxd = [zeros(length(x), 1), x;
@@ -133,16 +132,84 @@
 disp(['hyp2.cov.ell = ',        num2str(exp(hyp2.cov(1)), precision)]);
 disp(['hyp2.cov.sf = ',         num2str(exp(hyp2.cov(2)), precision)]);
 disp(['hyp2.lik.sigma_n = ',    num2str(exp(hyp2.lik(1)), precision)]);
+disp(['hyp2.lik.sigma_nd = ',   num2str(exp(hyp2.lik(2)), precision)]);
 disp(['nlZ2 = ',                num2str(nlZ2, precision)]);
 disp(['dnlZ2.cov.ell = ',       num2str(dnlZ2.cov(1), precision)]);
 disp(['dnlZ2.cov.sf = ',        num2str(dnlZ2.cov(2), precision)]);
 disp(['dnlZ2.lik.sigma_n = ',   num2str(dnlZ2.lik(1), precision)]);
+disp(['dnlZ2.lik.sigma_nd = ',  num2str(dnlZ2.lik(2), precision)]);
 
 % prediction - regression
 [dummy, dummy, fmu, fs2] = gp(hyp2, inf_method, mean_func, cov_func, lik_func, xxd, yyd, xs);
 
 % plot
-subplot(1, 3, 3);
+subplot(1, 4, 3);
+hold on;
+ff = [fmu+2*sqrt(fs2); flipdim(fmu-2*sqrt(fs2),1)]; 
+fill([xs; flipdim(xs,1)], ff, [7 7 7]/8)
+plot(xs, fmu, 'b-');
+plot(xs, ys, 'k-');
+plot(x, y, 'or');
+axis([0, 1, min(ys)-0.1, max(ys)+0.1]);
+
+% print
+print_matrix_for_reference(yyd, 'yyd');
+print_matrix_for_reference(fmu, 'fmu', 10);
+print_matrix_for_reference(fs2, 'fs2', 10);
+
+
+%% GP - Derivative and Function Observations with Global GP
+% global GP
+global global_mean_func;
+global global_cov_func;
+global global_lik_func;
+global global_inf_method;
+global global_hyp;
+global global_x;
+global global_y;
+
+% global_mean_func    = @meanZero;
+% global_cov_func     = {@covSEiso}; %{@covMaterniso, 3}
+% global_lik_func     = @likGauss;
+% global_inf_method   = @infExact;
+% global_hyp          = hyp1;
+% global_x            = x;
+% global_y            = y;
+
+global_mean_func    = @meanZeroDerObs;
+global_cov_func     = {@covSEisoDerObs};
+global_lik_func     = @likGaussDerObs;
+global_inf_method   = @infExactDerObs;
+global_hyp          = hyp1;
+global_hyp.lik(2)   = global_hyp.lik(1);
+global_x            = [zeros(length(x), 1), x];
+global_y            = y;
+
+% local GP
+mean_func = @meanGP; % Global GP 
+
+% hyperparameter
+hyp.cov = log([ell, sf]);
+hyp.lik = log([sn, sn]);
+
+% training
+hyp3 = minimize(hyp, @gp, -100, inf_method, mean_func, cov_func, lik_func, xxd, yyd);
+[nlZ3, dnlZ3] = gp(hyp3, inf_method, mean_func, cov_func, lik_func, xxd, yyd);
+disp(['hyp3.cov.ell = ',        num2str(exp(hyp3.cov(1)), precision)]);
+disp(['hyp3.cov.sf = ',         num2str(exp(hyp3.cov(2)), precision)]);
+disp(['hyp3.lik.sigma_n = ',    num2str(exp(hyp3.lik(1)), precision)]);
+disp(['hyp3.lik.sigma_nd = ',   num2str(exp(hyp3.lik(2)), precision)]);
+disp(['nlZ3 = ',                num2str(nlZ3, precision)]);
+disp(['dnlZ3.cov.ell = ',       num2str(dnlZ3.cov(1), precision)]);
+disp(['dnlZ3.cov.sf = ',        num2str(dnlZ3.cov(2), precision)]);
+disp(['dnlZ3.lik.sigma_n = ',   num2str(dnlZ3.lik(1), precision)]);
+disp(['dnlZ3.lik.sigma_nd = ',  num2str(dnlZ3.lik(2), precision)]);
+
+% prediction - regression
+[dummy, dummy, fmu, fs2] = gp(hyp3, inf_method, mean_func, cov_func, lik_func, xxd, yyd, xs);
+
+% plot
+subplot(1, 4, 4);
 hold on;
 ff = [fmu+2*sqrt(fs2); flipdim(fmu-2*sqrt(fs2),1)]; 
 fill([xs; flipdim(xs,1)], ff, [7 7 7]/8)
diff --git a/mean/meanGP.m b/mean/meanGP.m
new file mode 100644
index 0000000..77f077e
--- /dev/null
+++ b/mean/meanGP.m
@@ -0,0 +1,26 @@
+function A = meanGP(hyp, x, i)
+% GP mean function. The mean function does not have any parameters.
+
+% global variables
+global global_mean_func;
+global global_cov_func;
+global global_lik_func;
+global global_inf_method;
+global global_hyp;
+global global_x;
+global global_y;
+
+if nargin<2, A = '0'; return; end             % report number of hyperparameters 
+
+% % for now, it only works for 1D cases
+% if size(x, 2) > 2
+%     error('For now, it only works for 1D cases')
+% end
+% 
+% if size(x, 2) == 2
+%     mask = x(:, 1) == 0;
+%     x = x(mask, 2);
+% end
+    
+% mean
+[dummy, dummy, A, dummy] = gp(global_hyp, global_inf_method, global_mean_func, global_cov_func, global_lik_func, global_x, global_y, x);