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author | Thomas Mesnard <thomas.mesnard@ens.fr> | 2015-12-20 10:58:07 +0100 |
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committer | Thomas Mesnard <thomas.mesnard@ens.fr> | 2015-12-20 10:58:07 +0100 |

commit | e4d1c9c632158d7f40d26567d10c558c8815b84d (patch) | |

tree | 0e823d931ea18cbd69fbad05c7cd17baeba0c528 | |

parent | 2142359b779519dab8b31a7b04c17c8539942a77 (diff) | |

download | pgm-ctc-e4d1c9c632158d7f40d26567d10c558c8815b84d.tar.gz pgm-ctc-e4d1c9c632158d7f40d26567d10c558c8815b84d.zip |

Add some random code

-rw-r--r-- | .gitignore | 3 | ||||

-rw-r--r-- | README.md | 2 | ||||

-rw-r--r-- | mohammad/LICENSE | 201 | ||||

-rw-r--r-- | mohammad/README.md | 33 | ||||

-rw-r--r-- | mohammad/ctc_cost.py | 206 | ||||

-rw-r--r-- | mohammad/ctc_test_data.pkl | bin | 0 -> 2080084 bytes | |||

-rw-r--r-- | mohammad/test_ctc.py | 135 |

7 files changed, 580 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5942bbc --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +__pycache__/ +*.pyc +*.swp @@ -1,2 +1,4 @@ # pgm Projet PGM + +Thomas Mesnard, Alex Auvolat diff --git a/mohammad/LICENSE b/mohammad/LICENSE new file mode 100644 index 0000000..5c304d1 --- /dev/null +++ b/mohammad/LICENSE @@ -0,0 +1,201 @@ +Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/mohammad/README.md b/mohammad/README.md new file mode 100644 index 0000000..8c553c3 --- /dev/null +++ b/mohammad/README.md @@ -0,0 +1,33 @@ +CTC-Connectionist Temporal Classification +========================================= + +-CTC cost is implemented in pure [Theano](https://github.com/Theano/Theano). + +-Supports mini-batch. + +-Supports both normal- and log-scale. + +-"apple" problem (two same consecutive labels) is solved. + +-Test file is implemented using [Blocks](https://github.com/bartvm/blocks). + + + + +Reference +========= +Graves, Alex, et al. "Connectionist temporal classification: labelling unsegmented sequence data with recurrent neural networks." Proceedings of the 23rd international conference on Machine learning. ACM, 2006. + + +Credits +======= +Theano implementation of CTC by [Shawn Tan](https://github.com/shawntan/rnn-experiment/) + +Theano implementation of CTC by [Rakesh Var](https://github.com/rakeshvar/rnn_ctc) + + +Special thanks to +================= +[Kyle Kastner](https://github.com/kastnerkyle) + +Pascal Lambdin diff --git a/mohammad/ctc_cost.py b/mohammad/ctc_cost.py new file mode 100644 index 0000000..979ed93 --- /dev/null +++ b/mohammad/ctc_cost.py @@ -0,0 +1,206 @@ +""" +CTC-Connectionist Temporal Classification + +Code provided by Mohammad Pezeshki - May. 2015 - +Montreal Institute for Learning Algorithms + +Referece: Graves, Alex, et al. "Connectionist temporal classification: +labelling unsegmented sequence data with recurrent neural networks." +Proceedings of the 23rd international conference on Machine learning. +ACM, 2006. + +Credits: Shawn Tan, Rakesh Var + +This code is distributed without any warranty, express or implied. +""" + +import theano +from theano import tensor + +floatX = theano.config.floatX + + +# T: INPUT_SEQUENCE_LENGTH +# B: BATCH_SIZE +# L: OUTPUT_SEQUENCE_LENGTH +# C: NUM_CLASSES +class CTC(object): + """Connectionist Temporal Classification + y_hat : T x B x C+1 + y : L x B + y_hat_mask : T x B + y_mask : L x B + """ + @staticmethod + def add_blanks(y, blank_symbol, y_mask=None): + """Add blanks to a matrix and updates mask + + Input shape: L x B + Output shape: 2L+1 x B + + """ + # for y + y_extended = y.T.dimshuffle(0, 1, 'x') + blanks = tensor.zeros_like(y_extended) + blank_symbol + concat = tensor.concatenate([y_extended, blanks], axis=2) + res = concat.reshape((concat.shape[0], + concat.shape[1] * concat.shape[2])).T + begining_blanks = tensor.zeros((1, res.shape[1])) + blank_symbol + blanked_y = tensor.concatenate([begining_blanks, res], axis=0) + # for y_mask + if y_mask is not None: + y_mask_extended = y_mask.T.dimshuffle(0, 1, 'x') + concat = tensor.concatenate([y_mask_extended, + y_mask_extended], axis=2) + res = concat.reshape((concat.shape[0], + concat.shape[1] * concat.shape[2])).T + begining_blanks = tensor.ones((1, res.shape[1]), dtype=floatX) + blanked_y_mask = tensor.concatenate([begining_blanks, res], axis=0) + else: + blanked_y_mask = None + return blanked_y, blanked_y_mask + + @staticmethod + def class_batch_to_labeling_batch(y, y_hat, y_hat_mask=None): + y_hat = y_hat * y_hat_mask.dimshuffle(0, 'x', 1) + batch_size = y_hat.shape[2] + res = y_hat[:, y.astype('int32'), tensor.arange(batch_size)] + return res + + @staticmethod + def recurrence_relation(y, y_mask, blank_symbol): + n_y = y.shape[0] + blanks = tensor.zeros((2, y.shape[1])) + blank_symbol + ybb = tensor.concatenate((y, blanks), axis=0).T + sec_diag = (tensor.neq(ybb[:, :-2], ybb[:, 2:]) * + tensor.eq(ybb[:, 1:-1], blank_symbol) * + y_mask.T) + + # r1: LxL + # r2: LxL + # r3: LxLxB + r2 = tensor.eye(n_y, k=1) + r3 = (tensor.eye(n_y, k=2).dimshuffle(0, 1, 'x') * + sec_diag.dimshuffle(1, 'x', 0)) + + return r2, r3 + + @classmethod + def path_probabs(cls, y, y_hat, y_mask, y_hat_mask, blank_symbol): + pred_y = cls.class_batch_to_labeling_batch(y, y_hat, y_hat_mask) + + r2, r3 = cls.recurrence_relation(y, y_mask, blank_symbol) + + def step(p_curr, p_prev): + # instead of dot product, we * first + # and then sum oven one dimension. + # objective: T.dot((p_prev)BxL, LxLxB) + # solusion: Lx1xB * LxLxB --> LxLxB --> (sumover)xLxB + dotproduct = (p_prev + tensor.dot(p_prev, r2) + + (p_prev.dimshuffle(1, 'x', 0) * r3).sum(axis=0).T) + return p_curr.T * dotproduct * y_mask.T # B x L + + probabilities, _ = theano.scan( + step, + sequences=[pred_y], + outputs_info=[tensor.eye(y.shape[0])[0] * tensor.ones(y.T.shape)]) + return probabilities, probabilities.shape + + @classmethod + def cost(cls, y, y_hat, y_mask, y_hat_mask, blank_symbol): + y_hat_mask_len = tensor.sum(y_hat_mask, axis=0, dtype='int32') + y_mask_len = tensor.sum(y_mask, axis=0, dtype='int32') + probabilities, sth = cls.path_probabs(y, y_hat, + y_mask, y_hat_mask, + blank_symbol) + batch_size = probabilities.shape[1] + labels_probab = (probabilities[y_hat_mask_len - 1, + tensor.arange(batch_size), + y_mask_len - 1] + + probabilities[y_hat_mask_len - 1, + tensor.arange(batch_size), + y_mask_len - 2]) + avg_cost = tensor.mean(-tensor.log(labels_probab)) + return avg_cost, sth + + @staticmethod + def _epslog(x): + return tensor.cast(tensor.log(tensor.clip(x, 1E-12, 1E12)), + theano.config.floatX) + + @staticmethod + def log_add(a, b): + max_ = tensor.maximum(a, b) + return (max_ + tensor.log1p(tensor.exp(a + b - 2 * max_))) + + @staticmethod + def log_dot_matrix(x, z): + inf = 1E12 + log_dot = tensor.dot(x, z) + zeros_to_minus_inf = (z.max(axis=0) - 1) * inf + return log_dot + zeros_to_minus_inf + + @staticmethod + def log_dot_tensor(x, z): + inf = 1E12 + log_dot = (x.dimshuffle(1, 'x', 0) * z).sum(axis=0).T + zeros_to_minus_inf = (z.max(axis=0) - 1) * inf + return log_dot + zeros_to_minus_inf.T + + @classmethod + def log_path_probabs(cls, y, y_hat, y_mask, y_hat_mask, blank_symbol): + pred_y = cls.class_batch_to_labeling_batch(y, y_hat, y_hat_mask) + r2, r3 = cls.recurrence_relation(y, y_mask, blank_symbol) + + def step(log_p_curr, log_p_prev): + p1 = log_p_prev + p2 = cls.log_dot_matrix(p1, r2) + p3 = cls.log_dot_tensor(p1, r3) + p123 = cls.log_add(p3, cls.log_add(p1, p2)) + + return (log_p_curr.T + + p123 + + cls._epslog(y_mask.T)) + + log_probabilities, _ = theano.scan( + step, + sequences=[cls._epslog(pred_y)], + outputs_info=[cls._epslog(tensor.eye(y.shape[0])[0] * + tensor.ones(y.T.shape))]) + return log_probabilities + + @classmethod + def log_cost(cls, y, y_hat, y_mask, y_hat_mask, blank_symbol): + y_hat_mask_len = tensor.sum(y_hat_mask, axis=0, dtype='int32') + y_mask_len = tensor.sum(y_mask, axis=0, dtype='int32') + log_probabs = cls.log_path_probabs(y, y_hat, + y_mask, y_hat_mask, + blank_symbol) + batch_size = log_probabs.shape[1] + labels_probab = cls.log_add( + log_probabs[y_hat_mask_len - 1, + tensor.arange(batch_size), + y_mask_len - 1], + log_probabs[y_hat_mask_len - 1, + tensor.arange(batch_size), + y_mask_len - 2]) + avg_cost = tensor.mean(-labels_probab) + return avg_cost + + @classmethod + def apply(cls, y, y_hat, y_mask, y_hat_mask, scale='log_scale'): + y_hat = y_hat.dimshuffle(0, 2, 1) + num_classes = y_hat.shape[1] - 1 + blanked_y, blanked_y_mask = cls.add_blanks( + y=y, + blank_symbol=num_classes.astype(floatX), + y_mask=y_mask) + if scale == 'log_scale': + final_cost = cls.log_cost(blanked_y, y_hat, + blanked_y_mask, y_hat_mask, + num_classes) + else: + final_cost, sth = cls.cost(blanked_y, y_hat, + blanked_y_mask, y_hat_mask, + num_classes) + return final_cost diff --git a/mohammad/ctc_test_data.pkl b/mohammad/ctc_test_data.pkl Binary files differnew file mode 100644 index 0000000..2833c1b --- /dev/null +++ b/mohammad/ctc_test_data.pkl diff --git a/mohammad/test_ctc.py b/mohammad/test_ctc.py new file mode 100644 index 0000000..a24d634 --- /dev/null +++ b/mohammad/test_ctc.py @@ -0,0 +1,135 @@ +import theano +import numpy +from theano import tensor +from blocks.model import Model +from blocks.bricks import Linear, Tanh +from ctc_cost import CTC +from blocks.initialization import IsotropicGaussian, Constant +from fuel.datasets import IterableDataset +from fuel.streams import DataStream +from blocks.algorithms import (GradientDescent, Scale, + StepClipping, CompositeRule) +from blocks.extensions.monitoring import TrainingDataMonitoring +from blocks.main_loop import MainLoop +from blocks.extensions import FinishAfter, Printing +from blocks.bricks.recurrent import SimpleRecurrent +from blocks.graph import ComputationGraph +try: + import cPickle as pickle +except: + import pickle + +floatX = theano.config.floatX + + +@theano.compile.ops.as_op(itypes=[tensor.lvector], + otypes=[tensor.lvector]) +def print_pred(y_hat): + blank_symbol = 4 + res = [] + for i, s in enumerate(y_hat): + if (s != blank_symbol) and (i == 0 or s != y_hat[i - 1]): + res += [s] + return numpy.asarray(res) + +n_epochs = 200 +x_dim = 4 +h_dim = 9 +num_classes = 4 + +with open("ctc_test_data.pkl", "rb") as pkl_file: + try: + data = pickle.load(pkl_file) + inputs = data['inputs'] + labels = data['labels'] + # from S x T x B x D to S x T x B + inputs_mask = numpy.max(data['mask_inputs'], axis=-1) + labels_mask = data['mask_labels'] + except: + data = pickle.load(pkl_file, encoding='bytes') + inputs = data[b'inputs'] + labels = data[b'labels'] + # from S x T x B x D to S x T x B + inputs_mask = numpy.max(data[b'mask_inputs'], axis=-1) + labels_mask = data[b'mask_labels'] + + + +print('Building model ...') +# T x B x F +x = tensor.tensor3('x', dtype=floatX) +# T x B +x_mask = tensor.matrix('x_mask', dtype=floatX) +# L x B +y = tensor.matrix('y', dtype=floatX) +# L x B +y_mask = tensor.matrix('y_mask', dtype=floatX) + +x_to_h = Linear(name='x_to_h', + input_dim=x_dim, + output_dim=h_dim) +x_transform = x_to_h.apply(x) +rnn = SimpleRecurrent(activation=Tanh(), + dim=h_dim, name="rnn") +h = rnn.apply(x_transform) +h_to_o = Linear(name='h_to_o', + input_dim=h_dim, + output_dim=num_classes + 1) +h_transform = h_to_o.apply(h) +# T x B x C+1 +y_hat = tensor.nnet.softmax( + h_transform.reshape((-1, num_classes + 1)) +).reshape((h.shape[0], h.shape[1], -1)) +y_hat.name = 'y_hat' + +y_hat_mask = x_mask +cost = CTC().apply(y, y_hat, y_mask, y_hat_mask, 'normal_scale') +cost.name = 'CTC' +# Initialization +for brick in (rnn, x_to_h, h_to_o): + brick.weights_init = IsotropicGaussian(0.01) + brick.biases_init = Constant(0) + brick.initialize() + +print('Bulding DataStream ...') +dataset = IterableDataset({'x': inputs, + 'x_mask': inputs_mask, + 'y': labels, + 'y_mask': labels_mask}) +stream = DataStream(dataset) + +print('Bulding training process...') +algorithm = GradientDescent(cost=cost, + parameters=ComputationGraph(cost).parameters, + step_rule=CompositeRule([StepClipping(10.0), + Scale(0.02)])) +monitor_cost = TrainingDataMonitoring([cost], + prefix="train", + after_epoch=True) + +# sample number to monitor +sample = 8 + +y_hat_max_path = print_pred(tensor.argmax(y_hat[:, sample, :], axis=1)) +y_hat_max_path.name = 'Viterbi' +monitor_output = TrainingDataMonitoring([y_hat_max_path], + prefix="y_hat", + every_n_epochs=1) + +length = tensor.sum(y_mask[:, sample]).astype('int32') +tar = y[:length, sample].astype('int32') +tar.name = '_Target_Seq' +monitor_target = TrainingDataMonitoring([tar], + prefix="y", + every_n_epochs=1) + +model = Model(cost) +main_loop = MainLoop(data_stream=stream, algorithm=algorithm, + extensions=[monitor_cost, monitor_output, + monitor_target, + FinishAfter(after_n_epochs=n_epochs), + Printing()], + model=model) + +print('Starting training ...') +main_loop.run() |