In [1]:
from __future__ import print_function
import sys
import os
import time
import string
import numpy as np
import theano
import theano.tensor as T
import os; import sys; sys.path.append('..')
import gp
import gp.nets as nets
import gp.nets.BatchNormLayer as BatchNormLayer
import lasagne
sys.setrecursionlimit(10000)
In [2]:
%load_ext autoreload
%autoreload 2
In [2]:
# helper function for projection_b
def ceildiv(a, b):
return -(-a // b)
def build_cnn(input_var=None, n=1, num_filters=8, cudnn='no'):
import lasagne # For some odd reason it can't read the global import, please PR/Issue if you know why
projection_type = 'B'
# Setting up layers
if cudnn == 'yes':
import lasagne.layers.dnn
conv = lasagne.layers.dnn.Conv2DDNNLayer # cuDNN
else:
conv = lasagne.layers.Conv2DLayer
nonlin = lasagne.nonlinearities.rectify
nonlin_layer = lasagne.layers.NonlinearityLayer
sumlayer = lasagne.layers.ElemwiseSumLayer
#batchnorm = BatchNormLayer.BatchNormLayer
batchnorm = lasagne.layers.BatchNormLayer
# Setting the projection type for when reducing height/width
# and increasing dimensions.
# Default is 'B' as B performs slightly better
# and A requires newer version of lasagne with ExpressionLayer
projection_type = 'B'
if projection_type == 'A':
expression = lasagne.layers.ExpressionLayer
pad = lasagne.layers.PadLayer
if projection_type == 'A':
# option A for projection as described in paper
# (should perform slightly worse than B)
def projection(l_inp):
n_filters = l_inp.output_shape[1]*2
l = expression(l_inp, lambda X: X[:, :, ::2, ::2], lambda s: (s[0], s[1], ceildiv(s[2], 2), ceildiv(s[3], 2)))
l = pad(l, [n_filters//4,0,0], batch_ndim=1)
return l
if projection_type == 'B':
# option B for projection as described in paper
def projection(l_inp):
# twice normal channels when projecting!
n_filters = l_inp.output_shape[1]*2
l = conv(l_inp, num_filters=n_filters, filter_size=(1, 1),
stride=(2, 2), nonlinearity=None, pad='same', b=None)
l = batchnorm(l)
return l
# helper function to handle filters/strides when increasing dims
def filters_increase_dims(l, increase_dims):
in_num_filters = l.output_shape[1]
if increase_dims:
first_stride = (2, 2)
out_num_filters = in_num_filters*2
else:
first_stride = (1, 1)
out_num_filters = in_num_filters
return out_num_filters, first_stride
# block as described and used in cifar in the original paper:
# http://arxiv.org/abs/1512.03385
def res_block_v1(l_inp, nonlinearity=nonlin, increase_dim=False):
# first figure filters/strides
n_filters, first_stride = filters_increase_dims(l_inp, increase_dim)
# conv -> BN -> nonlin -> conv -> BN -> sum -> nonlin
l = conv(l_inp, num_filters=n_filters, filter_size=(3, 3),
stride=first_stride, nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=n_filters, filter_size=(3, 3),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
if increase_dim:
# Use projection (A, B) as described in paper
p = projection(l_inp)
else:
# Identity shortcut
p = l_inp
l = sumlayer([l, p])
l = nonlin_layer(l, nonlinearity=nonlin)
return l
# block as described in second paper on the subject (by same authors):
# http://arxiv.org/abs/1603.05027
def res_block_v2(l_inp, nonlinearity=nonlin, increase_dim=False):
# first figure filters/strides
n_filters, first_stride = filters_increase_dims(l_inp, increase_dim)
# BN -> nonlin -> conv -> BN -> nonlin -> conv -> sum
l = batchnorm(l_inp)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=n_filters, filter_size=(3, 3),
stride=first_stride, nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=n_filters, filter_size=(3, 3),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
if increase_dim:
# Use projection (A, B) as described in paper
p = projection(l_inp)
else:
# Identity shortcut
p = l_inp
l = sumlayer([l, p])
return l
def bottleneck_block(l_inp, nonlinearity=nonlin, increase_dim=False):
# first figure filters/strides
n_filters, first_stride = filters_increase_dims(l_inp, increase_dim)
# conv -> BN -> nonlin -> conv -> BN -> nonlin -> conv -> BN -> sum
# -> nonlin
# first make the bottleneck, scale the filters ..!
scale = 4 # as per bottleneck architecture used in paper
scaled_filters = n_filters/scale
l = conv(l_inp, num_filters=scaled_filters, filter_size=(1, 1),
stride=first_stride, nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=scaled_filters, filter_size=(3, 3),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=n_filters, filter_size=(1, 1),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
if increase_dim:
# Use projection (A, B) as described in paper
p = projection(l_inp)
else:
# Identity shortcut
p = l_inp
l = sumlayer([l, p])
l = nonlin_layer(l, nonlinearity=nonlin)
return l
# Bottleneck architecture with more efficiency (the post with Kaiming He's response)
# https://www.reddit.com/r/MachineLearning/comments/3ywi6x/deep_residual_learning_the_bottleneck/
def bottleneck_block_fast(l_inp, nonlinearity=nonlin, increase_dim=False):
# first figure filters/strides
n_filters, last_stride = filters_increase_dims(l_inp, increase_dim)
# conv -> BN -> nonlin -> conv -> BN -> nonlin -> conv -> BN -> sum
# -> nonlin
# first make the bottleneck, scale the filters ..!
scale = 4 # as per bottleneck architecture used in paper
scaled_filters = n_filters/scale
l = conv(l_inp, num_filters=scaled_filters, filter_size=(1, 1),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=scaled_filters, filter_size=(3, 3),
stride=(1, 1), nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
l = batchnorm(l)
l = nonlin_layer(l, nonlinearity=nonlin)
l = conv(l, num_filters=n_filters, filter_size=(1, 1),
stride=last_stride, nonlinearity=None, pad='same',
W=lasagne.init.HeNormal(gain='relu'))
if increase_dim:
# Use projection (A, B) as described in paper
p = projection(l_inp)
else:
# Identity shortcut
p = l_inp
l = sumlayer([l, p])
l = nonlin_layer(l, nonlinearity=nonlin)
return l
res_block = res_block_v1
# Stacks the residual blocks, makes it easy to model size of architecture with int n
def blockstack(l, n, nonlinearity=nonlin):
for _ in range(n):
l = res_block(l, nonlinearity=nonlin)
return l
# Building the network
l_in = lasagne.layers.InputLayer(shape=(None, 4, 75, 75),
input_var=input_var)
# First layer! just a plain convLayer
l1 = conv(l_in, num_filters=num_filters, stride=(1, 1),
filter_size=(3, 3), nonlinearity=None, pad='same')
l1 = batchnorm(l1)
l1 = nonlin_layer(l1, nonlinearity=nonlin)
# Stacking bottlenecks and increasing dims! (while reducing shape size)
l1_bs = blockstack(l1, n=n)
l1_id = res_block(l1_bs, increase_dim=True)
l2_bs = blockstack(l1_id, n=n)
l2_id = res_block(l2_bs, increase_dim=True)
l3_bs = blockstack(l2_id, n=n)
# And, finally, the 10-unit output layer:
network = lasagne.layers.DenseLayer(
l3_bs,
num_units=2,
nonlinearity=lasagne.nonlinearities.softmax)
return network
# ############################# Batch iterator ###############################
# This is just a simple helper function iterating over training data in
# mini-batches of a particular size, optionally in random order. It assumes
# data is available as numpy arrays. For big datasets, you could load numpy
# arrays as memory-mapped files (np.load(..., mmap_mode='r')), or write your
# own custom data iteration function. For small datasets, you can also copy
# them to GPU at once for slightly improved performance. This would involve
# several changes in the main program, though, and is not demonstrated here.
def iterate_minibatches(inputs, targets, batchsize, shuffle=False):
assert len(inputs) == len(targets)
if shuffle:
indices = np.arange(len(inputs))
np.random.shuffle(indices)
for start_idx in range(0, len(inputs) - batchsize + 1, batchsize):
if shuffle:
excerpt = indices[start_idx:start_idx + batchsize]
else:
excerpt = slice(start_idx, start_idx + batchsize)
Xb = inputs[excerpt]
yb = targets[excerpt]
Xb = Xb - .5
k_s = np.array([0,1,2,3],dtype=np.uint8)
for i in range(len(Xb)):
k = np.random.choice(k_s)
for j in range(Xb.shape[1]):
Xb[j][0] = np.rot90(Xb[j][0], k)
yield Xb, yb
# yield inputs[excerpt], targets[excerpt]
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PATCH_PATH = ('ipmlb')
X_train, y_train, X_test, y_test = gp.Patch.load_rgba(PATCH_PATH)
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X_val = X_train[-X_train.shape[0]/4:]
y_val = y_train[-X_train.shape[0]/4:]
In [5]:
X_train2 = X_train[:-X_train.shape[0]/4]
y_train2 = y_train[:-X_train.shape[0]/4]
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n=1
num_filters=16
num_epochs=200
cudnn='yes'
In [7]:
# Prepare Theano variables for inputs and targets
input_var = T.tensor4('inputs')
target_var = T.ivector('targets')
# Create neural network model (depending on first command line parameter)
print("Building model and compiling functions...")
network = build_cnn(input_var, n, num_filters, cudnn)
all_layers = lasagne.layers.get_all_layers(network)
num_params = lasagne.layers.count_params(network)
num_conv = 0
num_nonlin = 0
num_input = 0
num_batchnorm = 0
num_elemsum = 0
num_dense = 0
num_unknown = 0
print(" layer output shapes:")
for layer in all_layers:
name = string.ljust(layer.__class__.__name__, 32)
print(" %s %s" %(name, lasagne.layers.get_output_shape(layer)))
if "Conv2D" in name:
num_conv += 1
elif "NonlinearityLayer" in name:
num_nonlin += 1
elif "InputLayer" in name:
num_input += 1
elif "BatchNormLayer" in name:
num_batchnorm += 1
elif "ElemwiseSumLayer" in name:
num_elemsum += 1
elif "DenseLayer" in name:
num_dense += 1
else:
num_unknown += 1
print(" no. of InputLayers: %d" % num_input)
print(" no. of Conv2DLayers: %d" % num_conv)
print(" no. of BatchNormLayers: %d" % num_batchnorm)
print(" no. of NonlinearityLayers: %d" % num_nonlin)
print(" no. of DenseLayers: %d" % num_dense)
print(" no. of ElemwiseSumLayers: %d" % num_elemsum)
print(" no. of Unknown Layers: %d" % num_unknown)
print(" total no. of layers: %d" % len(all_layers))
print(" no. of parameters: %d" % num_params)
# Create a loss expression for training, i.e., a scalar objective we want
# to minimize (for our multi-class problem, it is the cross-entropy loss):
prediction = lasagne.layers.get_output(network)
loss = lasagne.objectives.categorical_crossentropy(prediction, target_var)
loss = loss.mean()
# We could add some weight decay as well here, see lasagne.regularization.
# Create update expressions for training, i.e., how to modify the
# parameters at each training step. Here, we'll use Stochastic Gradient
# Descent (SGD) with Nesterov momentum, but Lasagne offers plenty more.
params = lasagne.layers.get_all_params(network, trainable=True)
# several learning rates for low initial learning rates and
# learning rate anealing (id is epoch)
learning_rate_schedule = {
0: 0.0001, # low initial learning rate as described in paper
2: 0.01,
100: 0.001,
150: 0.0001
}
learning_rate = theano.shared(np.float32(learning_rate_schedule[0]))
updates = lasagne.updates.nesterov_momentum(
loss, params, learning_rate=learning_rate, momentum=0.9)
# Create a loss expression for validation/testing. The crucial difference
# here is that we do a deterministic forward pass through the network,
# disabling dropout layers.
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.categorical_crossentropy(test_prediction,
target_var)
test_loss = test_loss.mean()
# As a bonus, also create an expression for the classification accuracy:
test_acc = T.mean(T.eq(T.argmax(test_prediction, axis=1), target_var),
dtype=theano.config.floatX)
# Compile a function performing a training step on a mini-batch (by giving
# the updates dictionary) and returning the corresponding training loss:
train_fn = theano.function([input_var, target_var], loss, updates=updates)
# Compile a second function computing the validation loss and accuracy:
val_fn = theano.function([input_var, target_var], [test_loss, test_acc])
In [49]:
# Finally, launch the training loop.
print("Starting training...")
# We iterate over epochs:
for epoch in range(num_epochs):
if epoch in learning_rate_schedule:
lr = np.float32(learning_rate_schedule[epoch])
print(" setting learning rate to %.7f" % lr)
learning_rate.set_value(lr)
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(X_train2, y_train2, 500, shuffle=False):
inputs, targets = batch
train_err += train_fn(inputs, targets)
train_batches += 1
# And a full pass over the validation data:
val_err = 0
val_acc = 0
val_batches = 0
for batch in iterate_minibatches(X_val, y_val, 500, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
val_err += err
val_acc += acc
val_batches += 1
# Then we print the results for this epoch:
print("Epoch {} of {} took {:.3f}s".format(
epoch + 1, num_epochs, time.time() - start_time))
print(" training loss:\t\t{:.6f}".format(train_err / train_batches))
print(" validation loss:\t\t{:.6f}".format(val_err / val_batches))
print(" validation accuracy:\t\t{:.2f} %".format(
val_acc / val_batches * 100))
In [50]:
# After training, we compute and print the test error:
test_err = 0
test_acc = 0
test_batches = 0
for batch in iterate_minibatches(X_test, y_test, 500, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
test_err += err
test_acc += acc
test_batches += 1
print("Final results:")
print(" test loss:\t\t\t{:.6f}".format(test_err / test_batches))
print(" test accuracy:\t\t{:.2f} %".format(
test_acc / test_batches * 100))
In [65]:
# Finally, launch the training loop.
print("Starting training...")
# We iterate over epochs:
for epoch in range(num_epochs):
if epoch in learning_rate_schedule:
lr = np.float32(learning_rate_schedule[epoch])
print(" setting learning rate to %.7f" % lr)
learning_rate.set_value(lr)
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(X_train2, y_train2, 500, shuffle=False):
inputs, targets = batch
train_err += train_fn(inputs, targets)
train_batches += 1
# And a full pass over the validation data:
val_err = 0
val_acc = 0
val_batches = 0
for batch in iterate_minibatches(X_val, y_val, 500, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
val_err += err
val_acc += acc
val_batches += 1
# Then we print the results for this epoch:
print("Epoch {} of {} took {:.3f}s".format(
epoch + 1, num_epochs, time.time() - start_time))
print(" training loss:\t\t{:.6f}".format(train_err / train_batches))
print(" validation loss:\t\t{:.6f}".format(val_err / val_batches))
print(" validation accuracy:\t\t{:.2f} %".format(
val_acc / val_batches * 100))
In [67]:
# After training, we compute and print the test error:
test_err = 0
test_acc = 0
test_batches = 0
for batch in iterate_minibatches(X_test, y_test, 500, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
test_err += err
test_acc += acc
test_batches += 1
print("Final results:")
print(" test loss:\t\t\t{:.6f}".format(test_err / test_batches))
print(" test accuracy:\t\t{:.2f} %".format(
test_acc / test_batches * 100))
In [80]:
# Finally, launch the training loop.
print("Starting training...")
# We iterate over epochs:
for epoch in range(num_epochs):
if epoch in learning_rate_schedule:
lr = np.float32(learning_rate_schedule[epoch])
print(" setting learning rate to %.7f" % lr)
learning_rate.set_value(lr)
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(X_train2, y_train2, 128, shuffle=False):
inputs, targets = batch
train_err += train_fn(inputs, targets)
train_batches += 1
# And a full pass over the validation data:
val_err = 0
val_acc = 0
val_batches = 0
for batch in iterate_minibatches(X_val, y_val, 128, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
val_err += err
val_acc += acc
val_batches += 1
# Then we print the results for this epoch:
print("Epoch {} of {} took {:.3f}s".format(
epoch + 1, num_epochs, time.time() - start_time))
print(" training loss:\t\t{:.6f}".format(train_err / train_batches))
print(" validation loss:\t\t{:.6f}".format(val_err / val_batches))
print(" validation accuracy:\t\t{:.2f} %".format(
val_acc / val_batches * 100))
In [81]:
# After training, we compute and print the test error:
test_err = 0
test_acc = 0
test_batches = 0
for batch in iterate_minibatches(X_test, y_test, 128, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
test_err += err
test_acc += acc
test_batches += 1
print("Final results:")
print(" test loss:\t\t\t{:.6f}".format(test_err / test_batches))
print(" test accuracy:\t\t{:.2f} %".format(
test_acc / test_batches * 100))
In [82]:
np.savez('/home/d/resnet.npz', *lasagne.layers.get_all_param_values(network))
In [84]:
network.input_layer
Out[84]:
In [8]:
with np.load('/home/d/resnet.npz') as f:
param_values = [f['arr_%d' % i] for i in range(len(f.files))]
lasagne.layers.set_all_param_values(network, param_values)
In [9]:
from sklearn.metrics import classification_report, accuracy_score, roc_curve, auc, precision_recall_fscore_support, f1_score, precision_recall_curve, average_precision_score, zero_one_loss
In [10]:
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.categorical_crossentropy(test_prediction,
target_var)
test_loss = test_loss.mean()
# As a bonus, also create an expression for the classification accuracy:
test_acc = T.mean(T.eq(T.argmax(test_prediction, axis=1), target_var),
dtype=theano.config.floatX)
pred_fn = theano.function([input_var, target_var], [test_prediction, test_loss, test_acc])
pred2_fn = theano.function([input_var], [test_prediction])
In [11]:
all_preds = []
for i,p in enumerate(X_test):
pred = pred2_fn(p.reshape(1,4,75,75))
all_preds.append(pred[0][:,1][0].astype(np.uint8))
if i % 1000 == 0:
print(i)
In [12]:
print(classification_report(y_test, all_preds))
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