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model.py
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model.py
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from tensorflow.keras.layers import (
Input, Conv1D, MaxPooling1D, Dropout, BatchNormalization, Activation, Add, Flatten, Dense)
from tensorflow.keras.models import Model
import numpy as np
class ResidualUnit(object):
"""Residual unit block (unidimensional).
Parameters
----------
n_samples_out: int
Number of output samples.
n_filters_out: int
Number of output filters.
kernel_initializer: str, optional
Initializer for the weights matrices. See Keras initializers. By default it uses
'he_normal'.
dropout_keep_prob: float [0, 1), optional
Dropout rate used in all Dropout layers. Default is 0.8
kernel_size: int, optional
Kernel size for convolutional layers. Default is 17.
preactivation: bool, optional
When preactivation is true use full preactivation architecture proposed
in [1]. Otherwise, use architecture proposed in the original ResNet
paper [2]. By default it is true.
postactivation_bn: bool, optional
Defines if you use batch normalization before or after the activation layer (there
seems to be some advantages in some cases:
https://github.com/ducha-aiki/caffenet-benchmark/blob/master/batchnorm.md).
If true, the batch normalization is used before the activation
function, otherwise the activation comes first, as it is usually done.
By default it is false.
activation_function: string, optional
Keras activation function to be used. By default 'relu'.
References
----------
.. [1] K. He, X. Zhang, S. Ren, and J. Sun, "Identity Mappings in Deep Residual Networks,"
arXiv:1603.05027 [cs], Mar. 2016. https://arxiv.org/pdf/1603.05027.pdf.
.. [2] K. He, X. Zhang, S. Ren, and J. Sun, "Deep Residual Learning for Image Recognition," in 2016 IEEE Conference
on Computer Vision and Pattern Recognition (CVPR), 2016, pp. 770-778. https://arxiv.org/pdf/1512.03385.pdf
"""
def __init__(self, n_samples_out, n_filters_out, kernel_initializer='he_normal',
dropout_keep_prob=0.8, kernel_size=17, preactivation=True,
postactivation_bn=False, activation_function='relu'):
self.n_samples_out = n_samples_out
self.n_filters_out = n_filters_out
self.kernel_initializer = kernel_initializer
self.dropout_rate = 1 - dropout_keep_prob
self.kernel_size = kernel_size
self.preactivation = preactivation
self.postactivation_bn = postactivation_bn
self.activation_function = activation_function
def _skip_connection(self, y, downsample, n_filters_in):
"""Implement skip connection."""
# Deal with downsampling
if downsample > 1:
y = MaxPooling1D(downsample, strides=downsample, padding='same')(y)
elif downsample == 1:
y = y
else:
raise ValueError("Number of samples should always decrease.")
# Deal with n_filters dimension increase
if n_filters_in != self.n_filters_out:
# This is one of the two alternatives presented in ResNet paper
# Other option is to just fill the matrix with zeros.
y = Conv1D(self.n_filters_out, 1, padding='same',
use_bias=False, kernel_initializer=self.kernel_initializer)(y)
return y
def _batch_norm_plus_activation(self, x):
if self.postactivation_bn:
x = Activation(self.activation_function)(x)
x = BatchNormalization(center=False, scale=False)(x)
else:
x = BatchNormalization()(x)
x = Activation(self.activation_function)(x)
return x
def __call__(self, inputs):
"""Residual unit."""
x, y = inputs
n_samples_in = y.shape[1]
downsample = n_samples_in // self.n_samples_out
n_filters_in = y.shape[2]
y = self._skip_connection(y, downsample, n_filters_in)
# 1st layer
x = Conv1D(self.n_filters_out, self.kernel_size, padding='same',
use_bias=False, kernel_initializer=self.kernel_initializer)(x)
x = self._batch_norm_plus_activation(x)
if self.dropout_rate > 0:
x = Dropout(self.dropout_rate)(x)
# 2nd layer
x = Conv1D(self.n_filters_out, self.kernel_size, strides=downsample,
padding='same', use_bias=False,
kernel_initializer=self.kernel_initializer)(x)
if self.preactivation:
x = Add()([x, y]) # Sum skip connection and main connection
y = x
x = self._batch_norm_plus_activation(x)
if self.dropout_rate > 0:
x = Dropout(self.dropout_rate)(x)
else:
x = BatchNormalization()(x)
x = Add()([x, y]) # Sum skip connection and main connection
x = Activation(self.activation_function)(x)
if self.dropout_rate > 0:
x = Dropout(self.dropout_rate)(x)
y = x
return [x, y]
def get_model(n_classes, last_layer='sigmoid'):
kernel_size = 16
kernel_initializer = 'he_normal'
signal = Input(shape=(5000, 12), dtype=np.float32, name='signal')
x = signal
x = Conv1D(64, kernel_size, padding='same', use_bias=False,
kernel_initializer=kernel_initializer)(x)
x = BatchNormalization()(x)
x = Activation('relu')(x)
x, y = ResidualUnit(1024, 128, kernel_size=kernel_size,
kernel_initializer=kernel_initializer)([x, x])
x, y = ResidualUnit(256, 196, kernel_size=kernel_size,
kernel_initializer=kernel_initializer)([x, y])
x, y = ResidualUnit(64, 256, kernel_size=kernel_size,
kernel_initializer=kernel_initializer)([x, y])
x, _ = ResidualUnit(16, 320, kernel_size=kernel_size,
kernel_initializer=kernel_initializer)([x, y])
x = Flatten()(x)
diagn = Dense(n_classes, activation=last_layer, kernel_initializer=kernel_initializer)(x)
model = Model(signal, diagn)
return model
if __name__ == "__main__":
model = get_model(6)
model.summary()