--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline/conv_mlp/convolutional_mlp.py	Fri Feb 26 14:24:11 2010 -0500
@@ -0,0 +1,472 @@
+"""
+This tutorial introduces the LeNet5 neural network architecture using Theano.  LeNet5 is a
+convolutional neural network, good for classifying images. This tutorial shows how to build the
+architecture, and comes with all the hyper-parameters you need to reproduce the paper's MNIST
+results.
+
+The best results are obtained after X iterations of the main program loop, which takes ***
+minutes on my workstation (an Intel Core i7, circa July 2009), and *** minutes on my GPU (an
+NVIDIA GTX 285 graphics processor).
+
+This implementation simplifies the model in the following ways:
+
+ - LeNetConvPool doesn't implement location-specific gain and bias parameters
+ - LeNetConvPool doesn't implement pooling by average, it implements pooling by max.
+ - Digit classification is implemented with a logistic regression rather than an RBF network
+ - LeNet5 was not fully-connected convolutions at second layer
+
+References:
+ - Y. LeCun, L. Bottou, Y. Bengio and P. Haffner: Gradient-Based Learning Applied to Document
+   Recognition, Proceedings of the IEEE, 86(11):2278-2324, November 1998.
+   http://yann.lecun.com/exdb/publis/pdf/lecun-98.pdf
+"""
+
+import numpy, theano, cPickle, gzip, time
+import theano.tensor as T
+import theano.sandbox.softsign
+import pylearn.datasets.MNIST
+from pylearn.io import filetensor as ft
+from theano.sandbox import conv, downsample
+
+class LeNetConvPoolLayer(object):
+
+    def __init__(self, rng, input, filter_shape, image_shape, poolsize=(2,2)):
+        """
+        Allocate a LeNetConvPoolLayer with shared variable internal parameters.
+        :type rng: numpy.random.RandomState
+        :param rng: a random number generator used to initialize weights
+        :type input: theano.tensor.dtensor4
+        :param input: symbolic image tensor, of shape image_shape
+        :type filter_shape: tuple or list of length 4
+        :param filter_shape: (number of filters, num input feature maps,
+                              filter height,filter width)
+        :type image_shape: tuple or list of length 4
+        :param image_shape: (batch size, num input feature maps,
+                             image height, image width)
+        :type poolsize: tuple or list of length 2
+        :param poolsize: the downsampling (pooling) factor (#rows,#cols)
+        """
+        assert image_shape[1]==filter_shape[1]
+        self.input = input
+   
+        # initialize weight values: the fan-in of each hidden neuron is
+        # restricted by the size of the receptive fields.
+        fan_in =  numpy.prod(filter_shape[1:])
+        W_values = numpy.asarray( rng.uniform( \
+              low = -numpy.sqrt(3./fan_in), \
+              high = numpy.sqrt(3./fan_in), \
+              size = filter_shape), dtype = theano.config.floatX)
+        self.W = theano.shared(value = W_values)
+
+        # the bias is a 1D tensor -- one bias per output feature map
+        b_values = numpy.zeros((filter_shape[0],), dtype= theano.config.floatX)
+        self.b = theano.shared(value= b_values)
+
+        # convolve input feature maps with filters
+        conv_out = conv.conv2d(input, self.W, 
+                filter_shape=filter_shape, image_shape=image_shape)
+
+        # downsample each feature map individually, using maxpooling
+        pooled_out = downsample.max_pool2D(conv_out, poolsize, ignore_border=True)
+
+        # add the bias term. Since the bias is a vector (1D array), we first
+        # reshape it to a tensor of shape (1,n_filters,1,1). Each bias will thus
+        # be broadcasted across mini-batches and feature map width & height
+        self.output = T.tanh(pooled_out + self.b.dimshuffle('x', 0, 'x', 'x'))
+
+        # store parameters of this layer
+        self.params = [self.W, self.b]
+
+
+class SigmoidalLayer(object):
+    def __init__(self, rng, input, n_in, n_out):
+        """
+        Typical hidden layer of a MLP: units are fully-connected and have
+        sigmoidal activation function. Weight matrix W is of shape (n_in,n_out)
+        and the bias vector b is of shape (n_out,).
+        
+        Hidden unit activation is given by: sigmoid(dot(input,W) + b)
+
+        :type rng: numpy.random.RandomState
+        :param rng: a random number generator used to initialize weights
+        :type input: theano.tensor.dmatrix
+        :param input: a symbolic tensor of shape (n_examples, n_in)
+        :type n_in: int
+        :param n_in: dimensionality of input
+        :type n_out: int
+        :param n_out: number of hidden units
+        """
+        self.input = input
+
+        W_values = numpy.asarray( rng.uniform( \
+              low = -numpy.sqrt(6./(n_in+n_out)), \
+              high = numpy.sqrt(6./(n_in+n_out)), \
+              size = (n_in, n_out)), dtype = theano.config.floatX)
+        self.W = theano.shared(value = W_values)
+
+        b_values = numpy.zeros((n_out,), dtype= theano.config.floatX)
+        self.b = theano.shared(value= b_values)
+
+        self.output = T.tanh(T.dot(input, self.W) + self.b)
+        self.params = [self.W, self.b]
+
+
+class LogisticRegression(object):
+    """Multi-class Logistic Regression Class
+
+    The logistic regression is fully described by a weight matrix :math:`W` 
+    and bias vector :math:`b`. Classification is done by projecting data 
+    points onto a set of hyperplanes, the distance to which is used to 
+    determine a class membership probability. 
+    """
+
+    def __init__(self, input, n_in, n_out):
+        """ Initialize the parameters of the logistic regression
+        :param input: symbolic variable that describes the input of the 
+                      architecture (one minibatch)
+        :type n_in: int
+        :param n_in: number of input units, the dimension of the space in 
+                     which the datapoints lie
+        :type n_out: int
+        :param n_out: number of output units, the dimension of the space in 
+                      which the labels lie
+        """ 
+
+        # initialize with 0 the weights W as a matrix of shape (n_in, n_out) 
+        self.W = theano.shared( value=numpy.zeros((n_in,n_out),
+                                            dtype = theano.config.floatX) )
+        # initialize the baises b as a vector of n_out 0s
+        self.b = theano.shared( value=numpy.zeros((n_out,), 
+                                            dtype = theano.config.floatX) )
+        # compute vector of class-membership probabilities in symbolic form
+        self.p_y_given_x = T.nnet.softmax(T.dot(input, self.W)+self.b)
+        
+        # compute prediction as class whose probability is maximal in 
+        # symbolic form
+        self.y_pred=T.argmax(self.p_y_given_x, axis=1)
+
+        # list of parameters for this layer
+        self.params = [self.W, self.b]
+
+    def negative_log_likelihood(self, y):
+        """Return the mean of the negative log-likelihood of the prediction
+        of this model under a given target distribution.
+        :param y: corresponds to a vector that gives for each example the
+                  correct label
+        Note: we use the mean instead of the sum so that
+        the learning rate is less dependent on the batch size
+        """
+        return -T.mean(T.log(self.p_y_given_x)[T.arange(y.shape[0]),y])
+
+    def errors(self, y):
+        """Return a float representing the number of errors in the minibatch 
+        over the total number of examples of the minibatch ; zero one
+        loss over the size of the minibatch
+        """
+        # check if y has same dimension of y_pred 
+        if y.ndim != self.y_pred.ndim:
+            raise TypeError('y should have the same shape as self.y_pred', 
+                ('y', target.type, 'y_pred', self.y_pred.type))
+
+        # check if y is of the correct datatype        
+        if y.dtype.startswith('int'):
+            # the T.neq operator returns a vector of 0s and 1s, where 1
+            # represents a mistake in prediction
+            return T.mean(T.neq(self.y_pred, y))
+        else:
+            raise NotImplementedError()
+
+
+def load_dataset(fname,batch=20):
+
+    # repertoire qui contient les donnees NIST
+    # le repertoire suivant va fonctionner si vous etes connecte sur un ordinateur
+    # du reseau DIRO
+    datapath = '/data/lisa/data/nist/by_class/'
+    # le fichier .ft contient chiffres NIST dans un format efficace. Les chiffres
+    # sont stockes dans une matrice de NxD, ou N est le nombre d'images, est D est
+    # le nombre de pixels par image (32x32 = 1024). Chaque pixel de l'image est une
+    # valeur entre 0 et 255, correspondant a un niveau de gris. Les valeurs sont
+    # stockees comme des uint8, donc des bytes.
+    f = open(datapath+'digits/digits_train_data.ft')
+    # Verifier que vous avez assez de memoire pour loader les donnees au complet
+    # dans le memoire. Sinon, utilisez ft.arraylike, une classe construite
+    # specialement pour des fichiers qu'on ne souhaite pas loader dans RAM.
+    d = ft.read(f)
+
+    # NB: N'oubliez pas de diviser les valeurs des pixels par 255. si jamais vous
+    # utilisez les donnees commes entrees dans un reseaux de neurones et que vous 
+    # voulez des entres entre 0 et 1.
+    # digits_train_data.ft contient les images, digits_train_labels.ft contient les
+    # etiquettes
+    f = open(datapath+'digits/digits_train_labels.ft')
+    labels = ft.read(f)
+
+
+    # Load the dataset 
+    #f = gzip.open(fname,'rb')
+    #train_set, valid_set, test_set = cPickle.load(f)
+    #f.close()
+
+    # make minibatches of size 20 
+    batch_size = batch   # sized of the minibatch
+
+    # Dealing with the training set
+    # get the list of training images (x) and their labels (y)
+    (train_set_x, train_set_y) = (d[:4000,:],labels[:4000])
+    # initialize the list of training minibatches with empty list
+    train_batches = []
+    for i in xrange(0, len(train_set_x), batch_size):
+        # add to the list of minibatches the minibatch starting at 
+        # position i, ending at position i+batch_size
+        # a minibatch is a pair ; the first element of the pair is a list 
+        # of datapoints, the second element is the list of corresponding 
+        # labels
+        train_batches = train_batches + \
+               [(train_set_x[i:i+batch_size], train_set_y[i:i+batch_size])]
+
+    #print train_batches[500]
+
+    # Dealing with the validation set
+    (valid_set_x, valid_set_y) = (d[4000:5000,:],labels[4000:5000])
+    # initialize the list of validation minibatches 
+    valid_batches = []
+    for i in xrange(0, len(valid_set_x), batch_size):
+        valid_batches = valid_batches + \
+               [(valid_set_x[i:i+batch_size], valid_set_y[i:i+batch_size])]
+
+    # Dealing with the testing set
+    (test_set_x, test_set_y) = (d[5000:6000,:],labels[5000:6000])
+    # initialize the list of testing minibatches 
+    test_batches = []
+    for i in xrange(0, len(test_set_x), batch_size):
+        test_batches = test_batches + \
+              [(test_set_x[i:i+batch_size], test_set_y[i:i+batch_size])]
+
+    return train_batches, valid_batches, test_batches
+
+
+def evaluate_lenet5(learning_rate=0.1, n_iter=1, batch_size=20, n_kern0=20,n_kern1=50,filter_shape=5,n_layer=3, dataset='mnist.pkl.gz'):
+    rng = numpy.random.RandomState(23455)
+
+    print 'Before load dataset'
+    train_batches, valid_batches, test_batches = load_dataset(dataset,batch_size)
+    print 'After load dataset'
+
+    ishape = (32,32)     # this is the size of NIST images
+    n_kern2=80
+
+    # allocate symbolic variables for the data
+    x = T.matrix('x')  # rasterized images
+    y = T.lvector()  # the labels are presented as 1D vector of [long int] labels
+
+
+    ######################
+    # BUILD ACTUAL MODEL #
+    ######################
+
+    # Reshape matrix of rasterized images of shape (batch_size,28*28)
+    # to a 4D tensor, compatible with our LeNetConvPoolLayer
+    layer0_input = x.reshape((batch_size,1,32,32))
+
+    # Construct the first convolutional pooling layer:
+    # filtering reduces the image size to (32-5+1,32-5+1)=(28,28)
+    # maxpooling reduces this further to (28/2,28/2) = (14,14)
+    # 4D output tensor is thus of shape (20,20,14,14)
+    layer0 = LeNetConvPoolLayer(rng, input=layer0_input,
+            image_shape=(batch_size,1,32,32), 
+            filter_shape=(n_kern0,1,filter_shape,filter_shape), poolsize=(2,2))
+
+    if(n_layer>2):
+
+	# Construct the second convolutional pooling layer
+	# filtering reduces the image size to (14-5+1,14-5+1)=(10,10)
+	# maxpooling reduces this further to (10/2,10/2) = (5,5)
+	# 4D output tensor is thus of shape (20,50,5,5)
+	fshape=(32-filter_shape+1)/2
+	layer1 = LeNetConvPoolLayer(rng, input=layer0.output,
+		image_shape=(batch_size,n_kern0,fshape,fshape), 
+		filter_shape=(n_kern1,n_kern0,filter_shape,filter_shape), poolsize=(2,2))
+
+    else:
+
+	fshape=(32-filter_shape+1)/2
+	layer1_input = layer0.output.flatten(2)
+		# construct a fully-connected sigmoidal layer
+	layer1 = SigmoidalLayer(rng, input=layer1_input,n_in=n_kern0*fshape*fshape, n_out=500)
+
+	layer2 = LogisticRegression(input=layer1.output, n_in=500, n_out=10)
+	cost = layer2.negative_log_likelihood(y)
+	test_model = theano.function([x,y], layer2.errors(y))
+	params = layer2.params+ layer1.params + layer0.params
+
+
+    if(n_layer>3):
+
+	fshape=(32-filter_shape+1)/2
+	fshape2=(fshape-filter_shape+1)/2
+	fshape3=(fshape2-filter_shape+1)/2
+	layer2 = LeNetConvPoolLayer(rng, input=layer1.output,
+		image_shape=(batch_size,n_kern1,fshape2,fshape2), 
+		filter_shape=(n_kern2,n_kern1,filter_shape,filter_shape), poolsize=(2,2))
+
+	layer3_input = layer2.output.flatten(2)
+
+	layer3 = SigmoidalLayer(rng, input=layer3_input, 
+					n_in=n_kern2*fshape3*fshape3, n_out=500)
+
+  
+	layer4 = LogisticRegression(input=layer3.output, n_in=500, n_out=10)
+
+	cost = layer4.negative_log_likelihood(y)
+
+	test_model = theano.function([x,y], layer4.errors(y))
+
+	params = layer4.params+ layer3.params+ layer2.params+ layer1.params + layer0.params
+
+ 
+    elif(n_layer>2):
+
+	fshape=(32-filter_shape+1)/2
+	fshape2=(fshape-filter_shape+1)/2
+
+	# the SigmoidalLayer being fully-connected, it operates on 2D matrices of
+	# shape (batch_size,num_pixels) (i.e matrix of rasterized images).
+	# This will generate a matrix of shape (20,32*4*4) = (20,512)
+	layer2_input = layer1.output.flatten(2)
+
+	# construct a fully-connected sigmoidal layer
+	layer2 = SigmoidalLayer(rng, input=layer2_input, 
+					n_in=n_kern1*fshape2*fshape2, n_out=500)
+
+  
+	# classify the values of the fully-connected sigmoidal layer
+	layer3 = LogisticRegression(input=layer2.output, n_in=500, n_out=10)
+
+	# the cost we minimize during training is the NLL of the model
+	cost = layer3.negative_log_likelihood(y)
+
+	# create a function to compute the mistakes that are made by the model
+	test_model = theano.function([x,y], layer3.errors(y))
+
+	# create a list of all model parameters to be fit by gradient descent
+	params = layer3.params+ layer2.params+ layer1.params + layer0.params
+    	
+      
+  
+		
+    
+    # create a list of gradients for all model parameters
+    grads = T.grad(cost, params)
+
+    # train_model is a function that updates the model parameters by SGD
+    # Since this model has many parameters, it would be tedious to manually
+    # create an update rule for each model parameter. We thus create the updates
+    # dictionary by automatically looping over all (params[i],grads[i])  pairs.
+    updates = {}
+    for param_i, grad_i in zip(params, grads):
+        updates[param_i] = param_i - learning_rate * grad_i
+    train_model = theano.function([x, y], cost, updates=updates)
+
+
+    ###############
+    # TRAIN MODEL #
+    ###############
+
+    n_minibatches        = len(train_batches) 
+
+    # early-stopping parameters
+    patience              = 10000 # look as this many examples regardless
+    patience_increase     = 2     # wait this much longer when a new best is 
+                                  # found
+    improvement_threshold = 0.995 # a relative improvement of this much is 
+                                  # considered significant
+    validation_frequency  = n_minibatches  # go through this many 
+                                  # minibatche before checking the network 
+                                  # on the validation set; in this case we 
+                                  # check every epoch 
+
+    best_params          = None
+    best_validation_loss = float('inf')
+    best_iter            = 0
+    test_score           = 0.
+    start_time = time.clock()
+
+    # have a maximum of `n_iter` iterations through the entire dataset
+    for iter in xrange(n_iter * n_minibatches):
+
+        # get epoch and minibatch index
+        epoch           = iter / n_minibatches
+        minibatch_index =  iter % n_minibatches
+
+        # get the minibatches corresponding to `iter` modulo
+        # `len(train_batches)`
+        x,y = train_batches[ minibatch_index ]
+	
+        if iter %100 == 0:
+            print 'training @ iter = ', iter
+        cost_ij = train_model(x,y)
+
+        if (iter+1) % validation_frequency == 0: 
+
+            # compute zero-one loss on validation set 
+            this_validation_loss = 0.
+            for x,y in valid_batches:
+                # sum up the errors for each minibatch
+                this_validation_loss += test_model(x,y)
+
+            # get the average by dividing with the number of minibatches
+            this_validation_loss /= len(valid_batches)
+            print('epoch %i, minibatch %i/%i, validation error %f %%' % \
+                   (epoch, minibatch_index+1, n_minibatches, \
+                    this_validation_loss*100.))
+
+
+            # if we got the best validation score until now
+            if this_validation_loss < best_validation_loss:
+
+                #improve patience if loss improvement is good enough
+                if this_validation_loss < best_validation_loss *  \
+                       improvement_threshold :
+                    patience = max(patience, iter * patience_increase)
+
+                # save best validation score and iteration number
+                best_validation_loss = this_validation_loss
+                best_iter = iter
+
+                # test it on the test set
+                test_score = 0.
+                for x,y in test_batches:
+                    test_score += test_model(x,y)
+                test_score /= len(test_batches)
+                print(('     epoch %i, minibatch %i/%i, test error of best '
+                      'model %f %%') % 
+                             (epoch, minibatch_index+1, n_minibatches,
+                              test_score*100.))
+
+        if patience <= iter :
+            break
+
+    end_time = time.clock()
+    print('Optimization complete.')
+    print('Best validation score of %f %% obtained at iteration %i,'\
+          'with test performance %f %%' %  
+          (best_validation_loss * 100., best_iter, test_score*100.))
+    print('The code ran for %f minutes' % ((end_time-start_time)/60.))
+
+    return (best_validation_loss * 100., test_score*100., (end_time-start_time)/60., best_iter)
+
+if __name__ == '__main__':
+    evaluate_lenet5()
+
+def experiment(state, channel):
+    print 'start experiment'
+    (best_validation_loss, test_score, minutes_trained, iter) = evaluate_lenet5(state.learning_rate, state.n_iter, state.batch_size, state.n_kern0, state.n_kern1, state.filter_shape, state.n_layer)
+    print 'end experiment'
+    
+    state.best_validation_loss = best_validation_loss
+    state.test_score = test_score
+    state.minutes_trained = minutes_trained
+    state.iter = iter
+
+    return channel.COMPLETE