--- a/gradient_learner.py	Sat Jul 19 17:57:46 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-
-from learner import *
-from tensor import *
-import gradient
-from compile import Function
-
-class GradientLearner(Learner):
-    """
-    Base class for gradient-based optimization of a training criterion
-    that can consist in two parts, an additive part over examples, and
-    an example-independent part (usually called the regularizer).
-    The user provides a Theano formula that maps the fields of a minibatch (each being a tensor with the
-    same number of rows = minibatch size) and parameters to output fields (for the use function), one of which
-    must be a cost that is the training criterion to be minimized. Subclasses implement
-    a training strategy that uses the Theano formula to compute gradients and
-    to compute outputs in the update method.
-    The inputs, parameters, and outputs are lists of Theano tensors,
-    while the example_wise_cost and regularization_term are Theano tensors.
-    The user can specify a regularization coefficient that multiplies the regularization term.
-    The training algorithm looks for parameters that minimize
-       regularization_coefficient * regularization_term(parameters) +
-       sum_{inputs in training_set} example_wise_cost(inputs,parameters)
-    i.e. the regularization_term should not depend on the inputs, only on the parameters.
-    The learned function can map a subset of inputs to a subset of outputs (as long as the inputs subset
-    includes all the inputs required in the Theano expression for the selected outputs).
-    It is assumed that all the inputs are provided in the training set (as dataset fields
-    with the corresponding name), but not necessarily when using the learned function.
-    """
-    def __init__(self, inputs, parameters, outputs, example_wise_cost, regularization_term=astensor(0.0),
-                 regularization_coefficient = astensor(1.0)):
-        self.inputs = inputs
-        self.outputs = outputs
-        self.parameters = parameters
-        self.example_wise_cost = example_wise_cost
-        self.regularization_term = regularization_term
-        self.regularization_coefficient = regularization_coefficient
-        self.parameters_example_wise_gradient = gradient.grad(example_wise_cost, parameters)
-        self.parameters_regularization_gradient = gradient.grad(self.regularization_coefficient * regularization_term, parameters)
-        if example_wise_cost not in outputs:
-            outputs.append(example_wise_cost)
-        if regularization_term not in outputs:
-            outputs.append(regularization_term)
-        self.example_wise_gradient_fn = Function(inputs + parameters, 
-                                       [self.parameters_example_wise_gradient + self.parameters_regularization_gradient])
-        self.use_functions = {frozenset([input.name for input in inputs]+[output.name for output in outputs])
-                                        : Function(inputs, outputs)}
-
-    def use(self,input_dataset,output_fields=None,copy_inputs=True):
-        # obtain the function that maps the desired inputs to desired outputs
-        input_fields = input_dataset.fieldNames()
-        # map names of input fields to Theano tensors in self.inputs
-        input_variables = ???
-        if output_fields is None: output_fields = [output.name for output in outputs]
-        # handle special case of inputs that are directly copied into outputs
-        # map names of output fields to Theano tensors in self.outputs
-        output_variables = ???
-        use_function_key = input_fields+output_fields
-        if not self.use_functions.has_key(use_function_key):
-            self.use_function[use_function_key]=Function(input_variables,output_variables)
-        use_function = self.use_functions[use_function_key]
-        # return a dataset that computes the outputs
-        return input_dataset.apply_function(use_function,input_fields,output_fields,copy_inputs,compute_now=True)
-    
-
-class StochasticGradientDescent(object):
-    def update_parameters(self):
-        
-class StochasticGradientLearner(GradientLearner,StochasticGradientDescent):
-    def __init__(self,inputs, parameters, outputs, example_wise_cost, regularization_term=astensor(0.0),
-                 regularization_coefficient = astensor(1.0),)
-    def update()

--- a/kernel_regression.py	Sat Jul 19 17:57:46 2008 -0400
+++ b/kernel_regression.py	Tue Jul 22 15:20:25 2008 -0400
@@ -82,9 +82,11 @@
        - 'squared_error' (optionally produced by learned model if 'target' is provided)
           = example-wise squared error
     """
-    def __init__(self, kernel=None, L2_regularizer=0, gamma=1):
+    def __init__(self, kernel=None, L2_regularizer=0, gamma=1, use_bias=False):
+        # THE VERSION WITH BIAS DOES NOT SEEM RIGHT
         self.kernel = kernel
         self.L2_regularizer=L2_regularizer
+        self.use_bias=use_bias
         self.gamma = gamma # until we fix things, the kernel type is fixed, Gaussian
         self.equations = KernelRegressionEquations()
 
@@ -93,19 +95,22 @@
         first_example = trainset[0]
         n_inputs = first_example['input'].size
         n_outputs = first_example['target'].size
-        M = numpy.zeros((n_examples+1,n_examples+1))
-        Y = numpy.zeros((n_examples+1,n_outputs))
+        b1=1 if self.use_bias else 0
+        M = numpy.zeros((n_examples+b1,n_examples+b1))
+        Y = numpy.zeros((n_examples+b1,n_outputs))
         for i in xrange(n_examples):
-            M[i+1,i+1]=self.L2_regularizer
+            M[i+b1,i+b1]=self.L2_regularizer
         data = trainset.fields()
         train_inputs = numpy.array(data['input'])
-        Y[0]=1
-        Y[1:,:] = numpy.array(data['target'])
+        if self.use_bias:
+            Y[0]=1
+        Y[b1:,:] = numpy.array(data['target'])
         train_inputs_square,sumG,G=self.equations.compute_system_matrix(train_inputs,self.gamma)
-        M[1:,1:] += G 
-        M[0,1:] = sumG
-        M[1:,0] = 1
-        M[0,0] = M.shape[0]
+        M[b1:,b1:] += G
+        if self.use_bias:
+            M[0,1:] = sumG
+            M[1:,0] = 1
+            M[0,0] = M.shape[0]
         self.M=M
         self.Y=Y
         theta=numpy.linalg.solve(M,Y)
@@ -117,10 +122,11 @@
     inputs = T.matrix() # minibatchsize x n_inputs
     targets = T.matrix() # minibatchsize x n_outputs
     theta = T.matrix() # (n_examples+1) x n_outputs
+    b1 = T.shape(train_inputs_square)[0]<T.shape(theta)[0]
     gamma = T.scalar()
     inv_gamma2 = 1./(gamma*gamma)
-    b = theta[0]
-    alpha = theta[1:,:]
+    b = b1*theta[0]
+    alpha = theta[b1:,:]
     inputs_square = T.sum(inputs*inputs,axis=1)
     Kx = T.exp(-(row_vector(train_inputs_square)-2*T.dot(inputs,train_inputs.T)+col_vector(inputs_square))*inv_gamma2)
     outputs = T.dot(Kx,alpha) + b # minibatchsize x n_outputs

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sandbox/gradient_learner.py	Tue Jul 22 15:20:25 2008 -0400
@@ -0,0 +1,71 @@
+
+from learner import *
+from tensor import *
+import gradient
+from compile import Function
+
+class GradientLearner(Learner):
+    """
+    Base class for gradient-based optimization of a training criterion
+    that can consist in two parts, an additive part over examples, and
+    an example-independent part (usually called the regularizer).
+    The user provides a Theano formula that maps the fields of a minibatch (each being a tensor with the
+    same number of rows = minibatch size) and parameters to output fields (for the use function), one of which
+    must be a cost that is the training criterion to be minimized. Subclasses implement
+    a training strategy that uses the Theano formula to compute gradients and
+    to compute outputs in the update method.
+    The inputs, parameters, and outputs are lists of Theano tensors,
+    while the example_wise_cost and regularization_term are Theano tensors.
+    The user can specify a regularization coefficient that multiplies the regularization term.
+    The training algorithm looks for parameters that minimize
+       regularization_coefficient * regularization_term(parameters) +
+       sum_{inputs in training_set} example_wise_cost(inputs,parameters)
+    i.e. the regularization_term should not depend on the inputs, only on the parameters.
+    The learned function can map a subset of inputs to a subset of outputs (as long as the inputs subset
+    includes all the inputs required in the Theano expression for the selected outputs).
+    It is assumed that all the inputs are provided in the training set (as dataset fields
+    with the corresponding name), but not necessarily when using the learned function.
+    """
+    def __init__(self, inputs, parameters, outputs, example_wise_cost, regularization_term=astensor(0.0),
+                 regularization_coefficient = astensor(1.0)):
+        self.inputs = inputs
+        self.outputs = outputs
+        self.parameters = parameters
+        self.example_wise_cost = example_wise_cost
+        self.regularization_term = regularization_term
+        self.regularization_coefficient = regularization_coefficient
+        self.parameters_example_wise_gradient = gradient.grad(example_wise_cost, parameters)
+        self.parameters_regularization_gradient = gradient.grad(self.regularization_coefficient * regularization_term, parameters)
+        if example_wise_cost not in outputs:
+            outputs.append(example_wise_cost)
+        if regularization_term not in outputs:
+            outputs.append(regularization_term)
+        self.example_wise_gradient_fn = Function(inputs + parameters, 
+                                       [self.parameters_example_wise_gradient + self.parameters_regularization_gradient])
+        self.use_functions = {frozenset([input.name for input in inputs]+[output.name for output in outputs])
+                                        : Function(inputs, outputs)}
+
+    def use(self,input_dataset,output_fields=None,copy_inputs=True):
+        # obtain the function that maps the desired inputs to desired outputs
+        input_fields = input_dataset.fieldNames()
+        # map names of input fields to Theano tensors in self.inputs
+        input_variables = ???
+        if output_fields is None: output_fields = [output.name for output in outputs]
+        # handle special case of inputs that are directly copied into outputs
+        # map names of output fields to Theano tensors in self.outputs
+        output_variables = ???
+        use_function_key = input_fields+output_fields
+        if not self.use_functions.has_key(use_function_key):
+            self.use_function[use_function_key]=Function(input_variables,output_variables)
+        use_function = self.use_functions[use_function_key]
+        # return a dataset that computes the outputs
+        return input_dataset.apply_function(use_function,input_fields,output_fields,copy_inputs,compute_now=True)
+    
+
+class StochasticGradientDescent(object):
+    def update_parameters(self):
+        
+class StochasticGradientLearner(GradientLearner,StochasticGradientDescent):
+    def __init__(self,inputs, parameters, outputs, example_wise_cost, regularization_term=astensor(0.0),
+                 regularization_coefficient = astensor(1.0),)
+    def update()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sandbox/statscollector.py	Tue Jul 22 15:20:25 2008 -0400
@@ -0,0 +1,127 @@
+
+# Here is how I see stats collectors:
+
+def my_stats(graph):
+    graph.mse=examplewise_mean(square_norm(graph.residue))
+    graph.training_loss=graph.regularizer+examplewise_sum(graph.nll)
+    return [graph.mse,graph.training_loss]
+    
+
+#    def my_stats(residue,nll,regularizer):
+#            mse=examplewise_mean(square_norm(residue))
+#            training_loss=regularizer+examplewise_sum(nll)
+#            set_names(locals())
+#            return ((residue,nll),(regularizer),(),(mse,training_loss))
+#    my_stats_collector = make_stats_collector(my_stats)
+#
+# where make_stats_collector calls my_stats(examplewise_fields, attributes) to
+# construct its update function, and figure out what are the input fields (here "residue"
+# and "nll") and input attributes (here "regularizer") it needs, and the output
+# attributes that it computes (here "mse" and "training_loss"). Remember that
+# fields are examplewise quantities, but attributes are not, in my jargon.
+# In the above example, I am highlighting that some operations done in my_stats
+# are examplewise and some are not.  I am hoping that theano Ops can do these
+# kinds of internal side-effect operations (and proper initialization of these hidden
+# variables). I expect that a StatsCollector (returned by make_stats_collector)
+# knows the following methods:
+#     stats_collector.input_fieldnames
+#     stats_collector.input_attribute_names
+#     stats_collector.output_attribute_names
+#     stats_collector.update(mini_dataset)
+#     stats_collector['mse']
+# where mini_dataset has the input_fieldnames() as fields and the input_attribute_names()
+# as attributes, and in the resulting dataset the output_attribute_names() are set to the
+# proper numeric values.
+
+
+
+import theano
+from theano import tensor as t
+from Learner import Learner
+from lookup_list import LookupList
+
+class StatsCollectorModel(AttributesHolder):
+    def __init__(self,stats_collector):
+        self.stats_collector = stats_collector
+        self.outputs = LookupList(stats_collector.output_names,[None for name in stats_collector.output_names])
+        # the statistics get initialized here
+        self.update_function = theano.function(input_attributes+input_fields,output_attributes+output_fields,linker="c|py")
+        for name,value in self.outputs.items():
+            self.__setattribute__(name,value)
+    def update(self,dataset):
+        input_fields = dataset.fields()(self.stats_collector.input_field_names)
+        input_attributes = dataset.getAttributes(self.stats_collector.input_attribute_names)
+        self.outputs._values = self.update_function(input_attributes+input_fields)
+        for name,value in self.outputs.items():
+            self.__setattribute__(name,value)
+    def __call__(self):
+        return self.outputs
+    def attributeNames(self):
+        return self.outputs.keys()
+    
+class StatsCollector(AttributesHolder):
+        
+    def __init__(self,input_attributes, input_fields, outputs):
+        self.input_attributes = input_attributes
+        self.input_fields = input_fields
+        self.outputs = outputs
+        self.input_attribute_names = [v.name for v in input_attributes]
+        self.input_field_names = [v.name for v in input_fields]
+        self.output_names = [v.name for v in output_attributes]
+            
+    def __call__(self,dataset=None):
+        model = StatsCollectorModel(self)
+        if dataset:
+            self.update(dataset)
+        return model
+
+if __name__ == '__main__':
+    def my_statscollector():
+        regularizer = t.scalar()
+        nll = t.matrix()
+        class_error = t.matrix()
+        total_loss = regularizer+t.examplewise_sum(nll)
+        avg_nll = t.examplewise_mean(nll)
+        avg_class_error = t.examplewise_mean(class_error)
+        for name,val in locals().items(): val.name = name
+        return StatsCollector([regularizer],[nll,class_error],[total_loss,avg_nll,avg_class_error])
+    
+
+
+
+# OLD DESIGN:
+#
+# class StatsCollector(object):
+#     """A StatsCollector object is used to record performance statistics during training
+#     or testing of a learner. It can be configured to measure different things and
+#     accumulate the appropriate statistics. From these statistics it can be interrogated
+#     to obtain performance measures of interest (such as maxima, minima, mean, standard
+#     deviation, standard error, etc.). Optionally, the observations can be weighted
+#     (yielded weighted mean, weighted variance, etc., where applicable). The statistics
+#     that are desired can be specified among a list supported by the StatsCollector
+#     class or subclass. When some statistics are requested, others become automatically
+#     available (e.g., sum or mean)."""
+#
+#     default_statistics = [mean,standard_deviation,min,max]
+#    
+#     __init__(self,n_quantities_observed, statistics=default_statistics):
+#         self.n_quantities_observed=n_quantities_observed
+#
+#     clear(self):
+#         raise NotImplementedError
+#
+#     update(self,observations):
+#         """The observations is a numpy vector of length n_quantities_observed. Some
+#         entries can be 'missing' (with a NaN entry) and will not be counted in the
+#         statistics."""
+#         raise NotImplementedError
+#
+#     __getattr__(self, statistic)
+#         """Return a particular statistic, which may be inferred from the collected statistics.
+#         The argument is a string naming that statistic."""
+        
+
+    
+
+    
+    

--- a/statscollector.py	Sat Jul 19 17:57:46 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-
-# Here is how I see stats collectors:
-
-def my_stats(graph):
-    graph.mse=examplewise_mean(square_norm(graph.residue))
-    graph.training_loss=graph.regularizer+examplewise_sum(graph.nll)
-    return [graph.mse,graph.training_loss]
-    
-
-#    def my_stats(residue,nll,regularizer):
-#            mse=examplewise_mean(square_norm(residue))
-#            training_loss=regularizer+examplewise_sum(nll)
-#            set_names(locals())
-#            return ((residue,nll),(regularizer),(),(mse,training_loss))
-#    my_stats_collector = make_stats_collector(my_stats)
-#
-# where make_stats_collector calls my_stats(examplewise_fields, attributes) to
-# construct its update function, and figure out what are the input fields (here "residue"
-# and "nll") and input attributes (here "regularizer") it needs, and the output
-# attributes that it computes (here "mse" and "training_loss"). Remember that
-# fields are examplewise quantities, but attributes are not, in my jargon.
-# In the above example, I am highlighting that some operations done in my_stats
-# are examplewise and some are not.  I am hoping that theano Ops can do these
-# kinds of internal side-effect operations (and proper initialization of these hidden
-# variables). I expect that a StatsCollector (returned by make_stats_collector)
-# knows the following methods:
-#     stats_collector.input_fieldnames
-#     stats_collector.input_attribute_names
-#     stats_collector.output_attribute_names
-#     stats_collector.update(mini_dataset)
-#     stats_collector['mse']
-# where mini_dataset has the input_fieldnames() as fields and the input_attribute_names()
-# as attributes, and in the resulting dataset the output_attribute_names() are set to the
-# proper numeric values.
-
-
-
-import theano
-from theano import tensor as t
-from Learner import Learner
-from lookup_list import LookupList
-
-class StatsCollectorModel(AttributesHolder):
-    def __init__(self,stats_collector):
-        self.stats_collector = stats_collector
-        self.outputs = LookupList(stats_collector.output_names,[None for name in stats_collector.output_names])
-        # the statistics get initialized here
-        self.update_function = theano.function(input_attributes+input_fields,output_attributes+output_fields,linker="c|py")
-        for name,value in self.outputs.items():
-            self.__setattribute__(name,value)
-    def update(self,dataset):
-        input_fields = dataset.fields()(self.stats_collector.input_field_names)
-        input_attributes = dataset.getAttributes(self.stats_collector.input_attribute_names)
-        self.outputs._values = self.update_function(input_attributes+input_fields)
-        for name,value in self.outputs.items():
-            self.__setattribute__(name,value)
-    def __call__(self):
-        return self.outputs
-    def attributeNames(self):
-        return self.outputs.keys()
-    
-class StatsCollector(AttributesHolder):
-        
-    def __init__(self,input_attributes, input_fields, outputs):
-        self.input_attributes = input_attributes
-        self.input_fields = input_fields
-        self.outputs = outputs
-        self.input_attribute_names = [v.name for v in input_attributes]
-        self.input_field_names = [v.name for v in input_fields]
-        self.output_names = [v.name for v in output_attributes]
-            
-    def __call__(self,dataset=None):
-        model = StatsCollectorModel(self)
-        if dataset:
-            self.update(dataset)
-        return model
-
-if __name__ == '__main__':
-    def my_statscollector():
-        regularizer = t.scalar()
-        nll = t.matrix()
-        class_error = t.matrix()
-        total_loss = regularizer+t.examplewise_sum(nll)
-        avg_nll = t.examplewise_mean(nll)
-        avg_class_error = t.examplewise_mean(class_error)
-        for name,val in locals().items(): val.name = name
-        return StatsCollector([regularizer],[nll,class_error],[total_loss,avg_nll,avg_class_error])
-    
-
-
-
-# OLD DESIGN:
-#
-# class StatsCollector(object):
-#     """A StatsCollector object is used to record performance statistics during training
-#     or testing of a learner. It can be configured to measure different things and
-#     accumulate the appropriate statistics. From these statistics it can be interrogated
-#     to obtain performance measures of interest (such as maxima, minima, mean, standard
-#     deviation, standard error, etc.). Optionally, the observations can be weighted
-#     (yielded weighted mean, weighted variance, etc., where applicable). The statistics
-#     that are desired can be specified among a list supported by the StatsCollector
-#     class or subclass. When some statistics are requested, others become automatically
-#     available (e.g., sum or mean)."""
-#
-#     default_statistics = [mean,standard_deviation,min,max]
-#    
-#     __init__(self,n_quantities_observed, statistics=default_statistics):
-#         self.n_quantities_observed=n_quantities_observed
-#
-#     clear(self):
-#         raise NotImplementedError
-#
-#     update(self,observations):
-#         """The observations is a numpy vector of length n_quantities_observed. Some
-#         entries can be 'missing' (with a NaN entry) and will not be counted in the
-#         statistics."""
-#         raise NotImplementedError
-#
-#     __getattr__(self, statistic)
-#         """Return a particular statistic, which may be inferred from the collected statistics.
-#         The argument is a string naming that statistic."""
-        
-
-    
-
-    
-