merge with upstream

GPy/inference/latent_function_inference/var_dtc.py

@@ -22,7 +22,7 @@ class VarDTC(LatentFunctionInference):
 
     """
     const_jitter = 1e-8
-    def __init__(self, limit=1):
+    def __init__(self, limit=3):
         from paramz.caching import Cacher
         self.limit = limit
         self.get_trYYT = Cacher(self._get_trYYT, limit)

GPy/inference/latent_function_inference/var_dtc_parallel.py

@@ -21,7 +21,7 @@ class VarDTC_minibatch(LatentFunctionInference):
 
     """
     const_jitter = 1e-8
-    def __init__(self, batchsize=None, limit=1, mpi_comm=None):
+    def __init__(self, batchsize=None, limit=3, mpi_comm=None):
 
         self.batchsize = batchsize
         self.mpi_comm = mpi_comm

GPy/inference/optimization/__init__.py

@@ -1,5 +1,8 @@
-from paramz.optimization import stochastics, Optimizer
+from paramz.optimization import Optimizer
+from . import stochastics
+
 from paramz.optimization import *
 import sys
+
 sys.modules['GPy.inference.optimization.stochastics'] = stochastics
-sys.modules['GPy.inference.optimization.Optimizer'] = Optimizer
+sys.modules['GPy.inference.optimization.Optimizer'] = Optimizer

GPy/inference/optimization/stochastics.py

@@ -0,0 +1,119 @@
+#===============================================================================
+# Copyright (c) 2015, Max Zwiessele
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+# 
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+# 
+# * Neither the name of paramax nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#===============================================================================
+
+class StochasticStorage(object):
+    '''
+    This is a container for holding the stochastic parameters,
+    such as subset indices or step length and so on.
+
+    self.d has to be a list of lists:
+    [dimension indices, nan indices for those dimensions]
+    so that the minibatches can be used as efficiently as possible.
+    '''
+    def __init__(self, model):
+        """
+        Initialize this stochastic container using the given model
+        """
+
+    def do_stochastics(self):
+        """
+        Update the internal state to the next batch of the stochastic
+        descent algorithm.
+        """
+        pass
+
+    def reset(self):
+        """
+        Reset the state of this stochastics generator.
+        """
+
+class SparseGPMissing(StochasticStorage):
+    def __init__(self, model, batchsize=1):
+        """
+        Here we want to loop over all dimensions everytime.
+        Thus, we can just make sure the loop goes over self.d every
+        time. We will try to get batches which look the same together
+        which speeds up calculations significantly.
+        """
+        import numpy as np
+        self.Y = model.Y_normalized
+        bdict = {}
+        #For N > 1000 array2string default crops
+        opt = np.get_printoptions()
+        np.set_printoptions(threshold=np.inf)
+        for d in range(self.Y.shape[1]):
+            inan = np.isnan(self.Y)[:, d]
+            arr_str = np.array2string(inan, np.inf, 0, True, '', formatter={'bool':lambda x: '1' if x else '0'})
+            try:
+                bdict[arr_str][0].append(d)
+            except:
+                bdict[arr_str] = [[d], ~inan]
+        np.set_printoptions(**opt)
+        self.d = bdict.values()
+
+class SparseGPStochastics(StochasticStorage):
+    """
+    For the sparse gp we need to store the dimension we are in,
+    and the indices corresponding to those
+    """
+    def __init__(self, model, batchsize=1, missing_data=True):
+        self.batchsize = batchsize
+        self.output_dim = model.Y.shape[1]
+        self.Y = model.Y_normalized
+        self.missing_data = missing_data
+        self.reset()
+        self.do_stochastics()
+
+    def do_stochastics(self):
+        import numpy as np
+        if self.batchsize == 1:
+            self.current_dim = (self.current_dim+1)%self.output_dim
+            self.d = [[[self.current_dim], np.isnan(self.Y[:, self.current_dim]) if self.missing_data else None]]
+        else:
+            self.d = np.random.choice(self.output_dim, size=self.batchsize, replace=False)
+            bdict = {}
+            if self.missing_data:
+                opt = np.get_printoptions()
+                np.set_printoptions(threshold=np.inf)
+                for d in self.d:
+                    inan = np.isnan(self.Y[:, d])
+                    arr_str = np.array2string(inan,np.inf, 0,True, '',formatter={'bool':lambda x: '1' if x else '0'})
+                    try:
+                        bdict[arr_str][0].append(d)
+                    except:
+                        bdict[arr_str] = [[d], ~inan]
+                np.set_printoptions(**opt)
+                self.d = bdict.values()
+            else:
+                self.d = [[self.d, None]]
+
+    def reset(self):
+        self.current_dim = -1
+        self.d = None