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models.py
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605 lines (489 loc) · 22.8 KB
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import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
#from scipy.special import expit
from sklearn.metrics import silhouette_score
from tensorflow.keras.layers import *
from tensorflow.keras import backend as K
from tensorflow.keras.models import Model
from tensorflow.keras.losses import mse
from tensorflow.keras.layers import MultiHeadAttention, LayerNormalization, Add
import os
import pandas as pd
#from glob import glob
from tensorflow.keras.regularizers import l2
def sampling(args):
z_mean, z_log_var = args
batch = K.shape(z_mean)[0]
dim = K.int_shape(z_mean)[1]
# by default, random_normal has mean=0 and std=1.0
epsilon = K.random_normal(shape=(batch, dim))
return z_mean + K.exp(0.5 * z_log_var) * epsilon
def get_MRI_VAE_3D(
# input_shape=(119,143,103,1),
input_shape=(64,64,64,1),
latent_dim=2,
batch_size = 32,
disentangle=False,
gamma=1,
kernel_size = 3,
filters = 32,
intermediate_dim = 128,
nlayers = 2,
bias=True):
image_size, _, _, channels = input_shape
inputs = Input(shape=input_shape, name='encoder_input')
x = inputs
for i in range(nlayers):
filters *= 2
x = Conv3D(filters=filters,
kernel_size=kernel_size,
activation='relu',
strides=2,
padding='same',use_bias=bias)(x)
# shape info needed to build decoder model
shape = K.int_shape(--x)
# generate latent vector Q(z|X)
x = Flatten()(x)
x = Dense(intermediate_dim, activation='relu',use_bias=bias)(x)
z_mean = Dense(latent_dim, name='vae_mean',use_bias=bias)(x)
z_log_var = Dense(latent_dim, name='vae_log_var',use_bias=bias)(x)
# use reparameterization trick to push the sampling out as input
# note that "output_shape" isn't necessary with the TensorFlow backend
z = Lambda(sampling, output_shape=(latent_dim,), name='vae')([z_mean, z_log_var])
# instantiate encoder model
encoder = Model(inputs, [z_mean, z_log_var, z], name='encoder')
# build decoder model
latent_inputs = Input(shape=(latent_dim,), name='vae_sampling')
x = Dense(intermediate_dim, activation='relu',use_bias=bias)(latent_inputs)
x = Dense(shape[1] * shape[2] * shape[3] * shape[4], activation='relu',use_bias=bias)(x)
x = Reshape((shape[1], shape[2], shape[3],shape[4]))(x)
for i in range(nlayers):
x = Conv3DTranspose(filters=filters,
kernel_size=kernel_size,
activation='relu',
strides=2,
padding='same',
use_bias=bias)(x)
filters //= 2
outputs = Conv3DTranspose(filters=1,
kernel_size=kernel_size,
activation='sigmoid',
padding='same',
name='decoder_output',
use_bias=bias)(x)
# instantiate decoder model
decoder = Model(latent_inputs, outputs, name='decoder')
# decoder.summary()
# instantiate VAE model
outputs = decoder(encoder(inputs)[2])
vae = Model(inputs, outputs, name='vae')
if disentangle:
discriminator = Dense(1, activation='sigmoid')
z1 = Lambda(lambda x: x[:int(batch_size/2),:int(latent_dim/2)])(z)
z2 = Lambda(lambda x: x[int(batch_size/2):,:int(latent_dim/2)])(z)
s1 = Lambda(lambda x: x[:int(batch_size/2),int(latent_dim/2):])(z)
s2 = Lambda(lambda x: x[int(batch_size/2):,int(latent_dim/2):])(z)
q_bar = tf.keras.layers.concatenate(
[tf.keras.layers.concatenate([s1, z2], axis=1),
tf.keras.layers.concatenate([s2, z1], axis=1)],
axis=0)
q = tf.keras.layers.concatenate(
[tf.keras.layers.concatenate([s1, z1], axis=1),
tf.keras.layers.concatenate([s2, z2], axis=1)],
axis=0)
q_bar_score = (discriminator(q_bar)+.1) *.85 # +.1 * .85 so that it's 0<x<1
q_score = (discriminator(q)+.1) *.85
tc_loss = K.log(q_score / (1 - q_score))
discriminator_loss = - K.log(q_score) - K.log(1 - q_bar_score)
reconstruction_loss = mse(K.flatten(inputs), K.flatten(outputs))
reconstruction_loss *= image_size * image_size
kl_loss = 1 + z_log_var - K.square(z_mean) - K.exp(z_log_var)
kl_loss = K.sum(kl_loss, axis=-1)
kl_loss *= -0.5
if disentangle:
vae_loss = K.mean(reconstruction_loss) + K.mean(kl_loss) + gamma * K.mean(tc_loss) + K.mean(discriminator_loss)
else:
vae_loss = K.mean(reconstruction_loss) + K.mean(kl_loss)
vae.add_loss(vae_loss)
opt = tf.keras.optimizers.Adam(learning_rate=0.001,beta_1=0.9,beta_2=0.999,epsilon=1e-07,amsgrad=False,name='Adam')
vae.compile(optimizer=opt)
if disentangle:
vae.metrics_tensors = [reconstruction_loss, kl_loss, tc_loss, discriminator_loss]
return encoder, decoder, vae
def DECODE_SZ(input_shape=(64,64,64,1), latent_dim=16, beta=1, disentangle=False, gamma=1, bias=True, batch_size = 64):
image_size, _, _, channels = input_shape
kernel_size = 3
filters = 32
intermediate_dim = 128
nlayers = 2
# build encoder model
tg_inputs = Input(shape=input_shape, name='sz_inputs')
bg_inputs = Input(shape=input_shape, name='cm_inputs')
c_conv1 = Conv3D(filters=filters*2,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
c_conv2 = Conv3D(filters=filters*4,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
c_conv3 = Conv3D(filters=filters*8,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
c_bn = BatchNormalization()
# generate latent vector Q(z|X)
c_h_layer = Dense(intermediate_dim, activation='relu', use_bias=bias)
c_mean_layer = Dense(latent_dim, name='c_mean', use_bias=bias)
c_log_var_layer = Dense(latent_dim, name='c_log_var', use_bias=bias)
c_layer = Lambda(sampling, output_shape=(latent_dim,), name='c')
def c_encoder_func(inputs):
c_h = inputs
c_h = c_conv1(c_h)
c_h = c_conv2(c_h)
c_h = c_conv3(c_h)
c_h = c_bn(c_h)
shape = K.int_shape(c_h)
c_h = Flatten()(c_h)
c_h = c_h_layer(c_h)
c_mean = c_mean_layer(c_h)
c_log_var = c_log_var_layer(c_h)
c = c_mean
c = c_layer([c_mean, c_log_var])
return c_mean, c_log_var, c, shape
tg_c_mean, tg_c_log_var, tg_c, shape_c = c_encoder_func(tg_inputs)
########################################################################################################################
s_conv1 = Conv3D(filters=filters*2,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
s_conv2 = Conv3D(filters=filters*4,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
s_conv3 = Conv3D(filters=filters*8,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')
s_bn = BatchNormalization()
# generate latent vector Q(z|X)
s_h_layer = Dense(intermediate_dim, activation='relu', use_bias=bias)
s_mean_layer = Dense(latent_dim, name='s_mean', use_bias=bias)
s_log_var_layer = Dense(latent_dim, name='s_log_var', use_bias=bias)
s_layer = Lambda(sampling, output_shape=(latent_dim,), name='s')
def s_encoder_func(inputs):
s_h = inputs
s_h = s_conv1(s_h)
s_h = s_conv2(s_h)
s_h = s_conv3(s_h)
s_h = s_bn(s_h)
shape = K.int_shape(s_h)
s_h = Flatten()(s_h)
s_h = s_h_layer(s_h)
s_mean = s_mean_layer(s_h)
s_log_var = s_log_var_layer(s_h)
s = s_mean
s = s_layer([s_mean, s_log_var])
return s_mean, s_log_var, s, shape
tg_s_mean, tg_s_log_var, tg_s, shape_s = s_encoder_func(tg_inputs)
bg_c_mean, bg_c_log_var, bg_c, _ = c_encoder_func(bg_inputs)
# instantiate encoder models
c_encoder = tf.keras.models.Model(tg_inputs, [tg_c_mean, tg_c_log_var, tg_c], name='c_encoder')
s_encoder = tf.keras.models.Model(tg_inputs, [tg_s_mean, tg_s_log_var, tg_s], name='s_encoder')
###############################################################################################################################
# build decoder model
latent_inputs = Input(shape=(2*latent_dim,), name='sc_sampling')
x = Dense(intermediate_dim, activation='relu', use_bias=bias, kernel_regularizer=l2(0.01))(latent_inputs)
x = Dense(shape_c[1] * shape_c[2] * shape_c[3] * shape_c[4], activation='relu', use_bias=bias)(x)
x = Reshape((shape_c[1], shape_c[2], shape_c[3],shape_c[4]))(x)
x = Conv3DTranspose(filters=filters*8,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')(x)
x = BatchNormalization()(x)
for i in range(nlayers):
x = Conv3DTranspose(filters=filters,
kernel_size=kernel_size,
activation='relu',
strides=2,
use_bias=bias,
padding='same')(x)
x = BatchNormalization()(x)
filters //= 2
outputs = Conv3DTranspose(filters=1,
kernel_size=kernel_size,
activation='sigmoid',
padding='same',
use_bias=bias,
name='decoder_output')(x)
# instantiate decoder model
decode_sz_decoder = Model(latent_inputs, outputs, name='decoder')
def zeros_like(x):
return tf.zeros_like(x)
tg_outputs = decode_sz_decoder(tf.keras.layers.concatenate([tg_c, tg_s], -1))#患者数据时,同时走两个encoder
zeros = tf.keras.layers.Lambda(zeros_like)(tg_c)
bg_outputs = decode_sz_decoder(tf.keras.layers.concatenate([bg_c, zeros], -1))#正常人数据时,只走z_encoder,另外一部分用0向量代替
decode_sz = tf.keras.models.Model(inputs=[tg_inputs, bg_inputs],
outputs=[tg_outputs, bg_outputs],
name='contrastive_vae')
if disentangle:
discriminator = Dense(1, activation='sigmoid')
c1 = Lambda(lambda x: x[:int(batch_size/2),:])(tg_c)
c2 = Lambda(lambda x: x[int(batch_size/2):,:])(tg_c)
s1 = Lambda(lambda x: x[:int(batch_size/2),:])(tg_s)
s2 = Lambda(lambda x: x[int(batch_size/2):,:])(tg_s)
q_bar = tf.keras.layers.concatenate(
[tf.keras.layers.concatenate([s1, c2], axis=1),
tf.keras.layers.concatenate([s2, c1], axis=1)],
axis=0)
q = tf.keras.layers.concatenate(
[tf.keras.layers.concatenate([s1, c1], axis=1),
tf.keras.layers.concatenate([s2, c2], axis=1)],
axis=0)
q_bar_score = (discriminator(q_bar)+.1) *.85
q_score = (discriminator(q)+.1) *.85
tc_loss = K.log(q_score / (1 - q_score))
discriminator_loss = - K.log(q_score) - K.log(1 - q_bar_score)
else:
tc_loss = 0
discriminator_loss = 0
reconstruction_loss = tf.keras.losses.mse(K.flatten(tg_inputs), K.flatten(tg_outputs))
reconstruction_loss += tf.keras.losses.mse(K.flatten(bg_inputs), K.flatten(bg_outputs))
reconstruction_loss *= input_shape[0] * input_shape[1] * input_shape[2] * input_shape[3]
kl_loss = 1 + tg_c_log_var - tf.keras.backend.square(tg_c_mean) - tf.keras.backend.exp(tg_c_log_var)
kl_loss += 1 + tg_s_log_var - tf.keras.backend.square(tg_s_mean) - tf.keras.backend.exp(tg_s_log_var)
kl_loss += 1 + bg_c_log_var - tf.keras.backend.square(bg_c_mean) - tf.keras.backend.exp(bg_c_log_var)
kl_loss = tf.keras.backend.sum(kl_loss, axis=-1)
kl_loss *= -0.5
decode_sz_loss = tf.keras.backend.mean(reconstruction_loss + beta*kl_loss + gamma*tc_loss + discriminator_loss)
decode_sz.add_loss(decode_sz_loss)
opt = tf.keras.optimizers.Adam(learning_rate=0.001,beta_1=0.9,beta_2=0.999,epsilon=1e-07,amsgrad=False,name='Adam')
decode_sz.compile(optimizer=opt,run_eagerly=True)
return decode_sz, c_encoder, s_encoder, decode_sz_decoder
# import tensorflow as tf
# from tensorflow.keras import Input, Model
# from tensorflow.keras.layers import (
# Conv3D, Conv3DTranspose,
# Dense, Flatten, Reshape, Lambda,
# BatchNormalization, Cropping3D
# )
# from tensorflow.keras.regularizers import l2
# from tensorflow.keras import backend as K
# def sampling(args):
# """Reparametrization trick"""
# c_mean, c_log_var = args
# batch = tf.shape(c_mean)[0]
# dim = tf.shape(c_mean)[1]
# epsilon = tf.keras.backend.random_normal(shape=(batch, dim))
# return c_mean + tf.exp(0.5 * c_log_var) * epsilon
# def DECODE_SZ_ORI(
# # 修改 input_shape 为 (119, 143, 100, 1)
# input_shape=(119, 143, 100, 1),
# latent_dim=16,
# beta=1,
# disentangle=False,
# gamma=1,
# bias=True,
# batch_size=64
# ):
# depth, height, width, channels = input_shape
# kernel_size = 3
# filters = 32
# intermediate_dim = 128
# nlayers = 2
# # -----------------------
# # 构造 Encoder
# # -----------------------
# tg_inputs = Input(shape=input_shape, name='sz_inputs')
# bg_inputs = Input(shape=input_shape, name='cm_inputs')
# # 定义三层 Conv3D 和一个 BatchNormalization
# c_conv1 = Conv3D(filters=filters * 2,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# c_conv2 = Conv3D(filters=filters * 4,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# c_conv3 = Conv3D(filters=filters * 8,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# c_bn = BatchNormalization()
# # 生成潜在变量所需的 Dense 层
# c_h_layer = Dense(intermediate_dim, activation='relu', use_bias=bias)
# c_mean_layer = Dense(latent_dim, name='c_mean', use_bias=bias)
# c_log_var_layer = Dense(latent_dim, name='c_log_var', use_bias=bias)
# c_layer = Lambda(sampling, output_shape=(latent_dim,), name='c')
# def c_encoder_func(inputs):
# c_h = inputs
# c_h = c_conv1(c_h) # (119 → 60, 143 → 72, 100 → 50) channels=64
# c_h = c_conv2(c_h) # (60 → 30, 72 → 36, 50 → 25) channels=128
# c_h = c_conv3(c_h) # (30 → 15, 36 → 18, 25 → 13) channels=256
# c_h = c_bn(c_h)
# shape = K.int_shape(c_h) # (None, 15, 18, 13, 256)
# c_h = Flatten()(c_h)
# c_h = c_h_layer(c_h)
# c_mean = c_mean_layer(c_h)
# c_log_var = c_log_var_layer(c_h)
# c = c_layer([c_mean, c_log_var])
# return c_mean, c_log_var, c, shape
# tg_c_mean, tg_c_log_var, tg_c, shape_c = c_encoder_func(tg_inputs)
# # 分类器(“s” branch)的 Conv3D
# s_conv1 = Conv3D(filters=filters * 2,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# s_conv2 = Conv3D(filters=filters * 4,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# s_conv3 = Conv3D(filters=filters * 8,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')
# s_bn = BatchNormalization()
# s_h_layer = Dense(intermediate_dim, activation='relu', use_bias=bias)
# s_mean_layer = Dense(latent_dim, name='s_mean', use_bias=bias)
# s_log_var_layer = Dense(latent_dim, name='s_log_var', use_bias=bias)
# s_layer = Lambda(sampling, output_shape=(latent_dim,), name='s')
# def s_encoder_func(inputs):
# s_h = inputs
# s_h = s_conv1(s_h) # (119 → 60, 143 → 72, 100 → 50)
# s_h = s_conv2(s_h) # (60 → 30, 72 → 36, 50 → 25)
# s_h = s_conv3(s_h) # (30 → 15, 36 → 18, 25 → 13)
# s_h = s_bn(s_h)
# shape = K.int_shape(s_h) # (None, 15, 18, 13, 256)
# s_h = Flatten()(s_h)
# s_h = s_h_layer(s_h)
# s_mean = s_mean_layer(s_h)
# s_log_var = s_log_var_layer(s_h)
# s = s_layer([s_mean, s_log_var])
# return s_mean, s_log_var, s, shape
# tg_s_mean, tg_s_log_var, tg_s, shape_s = s_encoder_func(tg_inputs)
# bg_c_mean, bg_c_log_var, bg_c, _ = c_encoder_func(bg_inputs)
# # 最终创建 encoder 模型
# c_encoder = Model(tg_inputs, [tg_c_mean, tg_c_log_var, tg_c], name='c_encoder')
# s_encoder = Model(tg_inputs, [tg_s_mean, tg_s_log_var, tg_s], name='s_encoder')
# # -----------------------
# # 构造 Decoder
# # -----------------------
# latent_inputs = Input(shape=(2 * latent_dim,), name='sc_sampling')
# x = Dense(intermediate_dim, activation='relu', use_bias=bias, kernel_regularizer=l2(0.01))(latent_inputs)
# # 用 shape_c 构造一个全连接变形
# d_c, h_c, w_c, f_c = shape_c[1], shape_c[2], shape_c[3], shape_c[4]
# x = Dense(d_c * h_c * w_c * f_c, activation='relu', use_bias=bias)(x)
# x = Reshape((d_c, h_c, w_c, f_c))(x) # (15, 18, 13, 256)
# # 与 encoder 中 Conv3D 层镜像,对应添加 Conv3DTranspose
# x = Conv3DTranspose(filters=filters * 8,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')(x)
# x = BatchNormalization()(x)
# # 由 (15 → 30, 18 → 36, 13 → 26)
# current_filters = filters # 此时 filters=32
# for i in range(nlayers):
# x = Conv3DTranspose(filters=current_filters,
# kernel_size=kernel_size,
# activation='relu',
# strides=2,
# use_bias=bias,
# padding='same')(x)
# x = BatchNormalization()(x)
# current_filters //= 2
# # 以上两层分别: (30 → 60, 36 → 72, 26 → 52); (60 → 120, 72 → 144, 52 → 104)
# outputs = Conv3DTranspose(filters=1,
# kernel_size=kernel_size,
# activation='sigmoid',
# padding='same',
# use_bias=bias,
# name='decoder_output')(x)
# # 此时 shape = (120, 144, 104, 1)
# # 用 Cropping3D 裁剪到 (119, 143, 100)
# outputs = Cropping3D(cropping=((0, 1), (0, 1), (0, 4)), name='decoder_crop')(outputs)
# # 最终 shape = (119, 143, 100, 1)
# decode_sz_decoder = Model(latent_inputs, outputs, name='decoder')
# tg_concat = tf.keras.layers.concatenate([tg_c, tg_s], axis=-1)
# tg_outputs = decode_sz_decoder(tg_concat)
# zeros = Lambda(lambda x: tf.zeros_like(x))(tg_c)
# bg_concat = tf.keras.layers.concatenate([bg_c, zeros], axis=-1)
# bg_outputs = decode_sz_decoder(bg_concat)
# decode_sz = Model(inputs=[tg_inputs, bg_inputs],
# outputs=[tg_outputs, bg_outputs],
# name='contrastive_vae')
# if disentangle:
# discriminator = Dense(1, activation='sigmoid')
# half_batch = batch_size // 2
# c1 = Lambda(lambda x: x[:half_batch, :])(tg_c)
# c2 = Lambda(lambda x: x[half_batch:, :])(tg_c)
# s1 = Lambda(lambda x: x[:half_batch, :])(tg_s)
# s2 = Lambda(lambda x: x[half_batch:, :])(tg_s)
# q_bar = tf.keras.layers.concatenate(
# [tf.keras.layers.concatenate([s1, c2], axis=1),
# tf.keras.layers.concatenate([s2, c1], axis=1)],
# axis=0
# )
# q = tf.keras.layers.concatenate(
# [tf.keras.layers.concatenate([s1, c1], axis=1),
# tf.keras.layers.concatenate([s2, c2], axis=1)],
# axis=0
# )
# q_bar_score = (discriminator(q_bar) + 0.1) * 0.85
# q_score = (discriminator(q) + 0.1) * 0.85
# tc_loss = K.log(q_score / (1 - q_score))
# discriminator_loss = -K.log(q_score) - K.log(1 - q_bar_score)
# else:
# tc_loss = 0
# discriminator_loss = 0
# # 重建损失:MSE(TG) + MSE(BG),并乘以体素总数
# reconstruction_loss = (
# tf.keras.losses.mse(K.flatten(tg_inputs), K.flatten(tg_outputs)) +
# tf.keras.losses.mse(K.flatten(bg_inputs), K.flatten(bg_outputs))
# )
# reconstruction_loss *= (depth * height * width * channels)
# # KL 损失:tg_c, tg_s, bg_c 三个分支
# kl_loss = (
# 1 + tg_c_log_var - K.square(tg_c_mean) - K.exp(tg_c_log_var) +
# 1 + tg_s_log_var - K.square(tg_s_mean) - K.exp(tg_s_log_var) +
# 1 + bg_c_log_var - K.square(bg_c_mean) - K.exp(bg_c_log_var)
# )
# kl_loss = K.sum(kl_loss, axis=-1) * -0.5
# decode_sz_loss = K.mean(reconstruction_loss + beta * kl_loss + gamma * tc_loss + discriminator_loss)
# decode_sz.add_loss(decode_sz_loss)
# opt = tf.keras.optimizers.Adam(learning_rate=0.0005,
# beta_1=0.9,
# beta_2=0.999,
# epsilon=1e-07,
# amsgrad=False,
# name='Adam')
# decode_sz.compile(optimizer=opt, run_eagerly=True)
# return decode_sz, c_encoder, s_encoder, decode_sz_decoder