[英]How to implement a CNN-LSTM using Keras
我正在嘗試實現一個 CNN-LSTM,該 CNN-LSTM 對代表帕金森病/健康控制患者的語音的梅爾譜圖圖像進行分類。 我正在嘗試使用 LSTM model 實現預先存在的 model (DenseNet-169),但是我遇到了以下錯誤: ValueError: Input 0 of layer zero_padding2d is incompatible with the layer: expected ndim=4, found ndim=3. Full shape received: [None, 216, 1].
ValueError: Input 0 of layer zero_padding2d is incompatible with the layer: expected ndim=4, found ndim=3. Full shape received: [None, 216, 1].
誰能告訴我哪里出錯了?
import librosa
import os
import glob
import IPython.display as ipd
from pathlib import Path
import timeit
import time, sys
%matplotlib inline
import matplotlib.pyplot as plt
import librosa.display
import pandas as pd
from sklearn import datasets, linear_model
from sklearn.model_selection import train_test_split
from matplotlib import pyplot as plt
import numpy as np
import cv2
import seaborn as sns
%tensorflow_version 1.x #version 1 works without problems
import tensorflow
from tensorflow.keras import models
from sklearn.preprocessing import LabelEncoder
from tensorflow.keras.utils import to_categorical
from tensorflow.keras.layers import TimeDistributed
import keras
from tensorflow.keras.models import Sequential
from tensorflow.keras.callbacks import EarlyStopping
from sklearn.metrics import confusion_matrix, plot_confusion_matrix
from tensorflow.keras.layers import Conv2D, MaxPooling2D, Flatten, Dropout, Dense, BatchNormalization, Activation, GaussianNoise, LSTM
from sklearn.metrics import accuracy_score
DATA_DIR = Path('/content/drive/MyDrive/PhD_Project_Experiments/Spontaneous_Dialogue_PD_Dataset')
diagnosis = [x.name for x in DATA_DIR.glob('*') if x.is_dir()]
diagnosis
def create_paths_ds(paths: Path, label: str) -> list:
EXTENSION_TYPE = '.wav'
return [(x, label) for x in paths.glob('*' + EXTENSION_TYPE)]
from collections import Counter
categories_to_use = [
'Parkinsons_Disease',
'Healthy_Control',
]
NUM_CLASSES = len(categories_to_use)
print(f'Number of classes: {NUM_CLASSES}')
paths_all_labels = []
for cat in categories_to_use:
paths_all_labels += create_paths_ds(DATA_DIR / cat, cat)
X_train, X_test = train_test_split(paths_all_labels,test_size=0.1, stratify = [paths_all_labels[y][1] for y in range(len(paths_all_labels))] ) #fix stratified sampling for test data
X_train, X_val = train_test_split(X_train, test_size=0.2, stratify = [X_train[y][1] for y in range(len(X_train))] )
for i in categories_to_use:
print('Number of train samples for '+i+': '+ str([X_train[y][1] for y in range(len(X_train))].count(i))) #checks whether train samples are equally divided
print('Number of test samples for '+i+': '+ str([X_test[y][1] for y in range(len(X_test))].count(i))) #checks whether test samples are equally divided
print('Number of validation samples for '+i+': '+ str([X_val[y][1] for y in range(len(X_val))].count(i))) #checks whether val samples are equally divided
print(f'Train length: {len(X_train)}')
print(f'Validation length: {len(X_val)}')
print(f'Test length: {len(X_test)}')
def load_and_preprocess_lstm(dataset, SAMPLE_SIZE = 30):
IMG_SIZE = (216,128)
progress=0
data = []
labels = []
for (path, label) in dataset:
audio, sr = librosa.load(path)
dur = librosa.get_duration(audio, sr = sr)
sampleNum = int(dur / SAMPLE_SIZE)
offset = (dur % SAMPLE_SIZE) / 2
for i in range(sampleNum):
audio, sr = librosa.load(path, offset= offset+i, duration=SAMPLE_SIZE)
sample = librosa.feature.melspectrogram(audio, sr=sr)
# print(sample.shape)
sample = cv2.resize(sample, dsize=IMG_SIZE)
sample = np.expand_dims(sample,-1)
print(sample.shape)
data += [(sample, label)]
labels += [label]
progress +=1
print('\r Progress: '+str(round(100*progress/len(dataset))) + '%', end='')
return data, labels
def retrieve_samples(sample_size, model_type):
if model_type == 'cnn':
print("\nLoading train samples")
X_train_samples, train_labels = load_and_preprocess_cnn(X_train,sample_size)
print("\nLoading test samples")
X_test_samples, test_labels = load_and_preprocess_cnn(X_test,sample_size)
print("\nLoading val samples")
X_val_samples, val_labels = load_and_preprocess_cnn(X_val,sample_size)
print('\n')
elif model_type == 'lstm':
print("\nLoading train samples")
X_train_samples, train_labels = load_and_preprocess_lstm(X_train,sample_size)
print("\nLoading test samples")
X_test_samples, test_labels = load_and_preprocess_lstm(X_test,sample_size)
print("\nLoading val samples")
X_val_samples, val_labels = load_and_preprocess_lstm(X_val,sample_size)
print('\n')
elif model_type == "cnnlstm":
print("\nLoading train samples")
X_train_samples, train_labels = load_and_preprocess_lstm(X_train,sample_size)
print("\nLoading test samples")
X_test_samples, test_labels = load_and_preprocess_lstm(X_test,sample_size)
print("\nLoading val samples")
X_val_samples, val_labels = load_and_preprocess_lstm(X_val,sample_size)
print('\n')
print("shape: " + str(X_train_samples[0][0].shape))
print("number of training samples: "+ str(len(X_train_samples)))
print("number of validation samples: "+ str(len(X_val_samples)))
print("number of test samples: "+ str(len(X_test_samples)))
return X_train_samples, X_test_samples, X_val_samples
def create_cnn_lstm_model(input_shape):
model = Sequential()
cnn = tensorflow.keras.applications.DenseNet169(include_top=True, weights=None, input_tensor=None, input_shape=input_shape, pooling=None, classes=2)
# define LSTM model
model.add(tensorflow.keras.layers.TimeDistributed(cnn, input_shape=input_shape))
model.add(LSTM(units = 512, dropout=0.5, recurrent_dropout=0.3, return_sequences = True, input_shape = input_shape))
model.add(LSTM(units = 512, dropout=0.5, recurrent_dropout=0.3, return_sequences = False))
model.add(Dense(units=NUM_CLASSES, activation='sigmoid'))#Compile
model.compile(loss=tensorflow.keras.losses.binary_crossentropy, optimizer='adam', metrics=['accuracy'])
print(model.summary())
return model
def create_model_data_and_labels(X_train_samples, X_val_samples, X_test_samples):
#Prepare samples to work for training the model
labelizer = LabelEncoder()
#prepare training data and labels
x_train = np.array([x[0] for x in X_train_samples])
y_train = np.array([x[1] for x in X_train_samples])
y_train = labelizer.fit_transform(y_train)
y_train = to_categorical(y_train)
#prepare validation data and labels
x_val = np.array([x[0] for x in X_val_samples])
y_val = np.array([x[1] for x in X_val_samples])
y_val = labelizer.transform(y_val)
y_val = to_categorical(y_val)
#prepare test data and labels
x_test = np.array([x[0] for x in X_test_samples])
y_test = np.array([x[1] for x in X_test_samples])
y_test = labelizer.transform(y_test)
y_test = to_categorical(y_test)
return x_train, y_train, x_val, y_val, x_test, y_test, labelizer
#Main loop for testing multiple sample sizes
#choose model type: 'cnn' or 'lstm'
model_type = 'cnnlstm'
n_epochs = 20
patience= 20
es = EarlyStopping(patience=20)
fragment_sizes = [5,10]
start = timeit.default_timer()
ModelData = pd.DataFrame(columns = ['Model Type','Fragment size (s)', 'Time to Compute (s)', 'Early Stopping epoch', 'Training accuracy', 'Validation accuracy', 'Test Accuracy']) #create a DataFrame for storing the results
conf_matrix_data = []
for i in fragment_sizes:
start_per_size = timeit.default_timer()
print(f'\n---------- Model trained on fragments of size: {i} seconds ----------------')
X_train_samples, X_test_samples, X_val_samples = retrieve_samples(i,model_type)
x_train, y_train, x_val, y_val, x_test, y_test, labelizer = create_model_data_and_labels(X_train_samples, X_val_samples, X_test_samples)
if model_type == 'cnn':
model = create_cnn_model(X_train_samples[0][0].shape)
elif model_type == 'lstm':
model = create_lstm_model(X_train_samples[0][0].shape)
elif model_type == 'cnnlstm':
model = create_cnn_lstm_model(X_train_samples[0][0].shape)
history = model.fit(x_train, y_train,
batch_size = 8,
epochs=n_epochs,
verbose=1,
callbacks=[es],
validation_data=(x_val, y_val))
print('Finished training')
early_stopping_epoch = len(history.history['accuracy'])
training_accuracy = history.history['accuracy'][early_stopping_epoch-1-patience]
validation_accuracy = history.history['val_accuracy'][early_stopping_epoch-1-patience]
plot_data(history, i)
predictions = model.predict(x_test)
score = accuracy_score(labelizer.inverse_transform(y_test.argmax(axis=1)), labelizer.inverse_transform(predictions.argmax(axis=1)))
print('Fragment size = ' + str(i) + ' seconds')
print('Accuracy on test samples: ' + str(score))
conf_matrix_data += [(predictions, y_test, i)]
stop_per_size = timeit.default_timer()
time_to_compute = round(stop_per_size - start_per_size)
print ('Time to compute: '+str(time_to_compute))
ModelData.loc[len(ModelData)] = [model_type, i, time_to_compute, early_stopping_epoch, training_accuracy, validation_accuracy, score] #store particular settings configuration, early stoppping epoch and accuracies in dataframe
stop = timeit.default_timer()
print ('\ntime to compute: '+str(stop-start))
我相信 input_shape 是 (128, 216, 1)
這里的問題是您沒有時間軸來時間分布您的 CNN (DenseNet169) 層。
在這一步 -
tensorflow.keras.layers.TimeDistributed(cnn, input_shape=(128,216,1)))
您將 128 維軸作為時間軸傳遞。 這意味着每個 CNN (DenseNet169) 的輸入形狀為(216,1)
,這不是圖像,因此會引發錯誤,因為它期望 3D 張量(圖像)而不是 2D 張量。
您的輸入形狀需要是 4D 張量,例如 - (10, 128, 216, 1)
,因此10
成為時間軸(用於時間分布),並且(128, 216, 1)
成為圖像輸入CNN (DenseNet169)。
IIUC,您的數據包含 n 個音頻文件,每個文件包含可變數量的梅爾譜圖圖像。
tf.raggedtensors
才能使用可變張量形狀作為 model 的輸入ragged=True
None
作為時間分布軸形狀讓我們從一個示例數據集開始 -
import tensorflow as tf
from tensorflow.keras import layers, Model, utils, applications
#Assuming there are 5 audio files
num_audio = 5
data = []
#Create a random number of mel-spectrograms for each audio file
for i in range(num_audio):
n_images = np.random.randint(4,10)
data.append(np.random.random((n_images,128,216,1)))
print([i.shape for i in data])
[(5, 128, 216, 1),
(5, 128, 216, 1),
(9, 128, 216, 1),
(6, 128, 216, 1),
(4, 128, 216, 1)]
因此,您的數據應該看起來像這樣。 在這里,我有一個包含 5 個音頻文件的虛擬數據集,第一個有 5 個形狀(128,216,1)
的圖像,而最后一個有 4 個相同形狀的圖像。
接下來,讓我們轉換並存儲這些參差不齊的張量。 參差不齊的張量允許存儲可變長度的對象,在這種情況下,可以存儲可變數量的圖像。 在此處閱讀有關它們的更多信息。
#Convert each set of images (for each audio) to tensors and then a ragged tensor
tensors = [tensorflow.convert_to_tensor(i) for i in data]
X_train = tensorflow.ragged.stack(tensors).to_tensor()
#Creating dummy y_train, one for each audio files
y_train = tensorflow.convert_to_tensor(np.random.randint(0,2,(5,2)))
我正在使用functional API
,因為我發現它更具可讀性並且與顯式輸入層配合得更好,但是您也可以在Sequential API
中使用輸入層。 隨意將其轉換為您的偏好。
請注意,我使用(None,128,216,1)
作為輸入形狀。 這將創建 5 個通道(第一個用於批次的隱式通道)作為 - (Batch, audio_files, h, w, channels)
我有一個虛擬 LSTM 層來展示架構的工作原理,隨意堆疊更多層。 另外,請注意,您的DenseNet169
僅返回 2 個特征。 因此,您的TimeDistributed
層返回(None, None, 2)
形狀的張量,其中第一個None
是音頻文件的數量,第二個None
是圖像的數量(時間軸)。 因此,請相應地選擇下一層,因為 512 個 LSTM 單元可能太多了:)
#Create model
inp = layers.Input((None,128,216,1), ragged=True)
cnn = tensorflow.keras.applications.DenseNet169(include_top=True,
weights=None,
input_tensor=None,
input_shape=(128,216,1), #<----- input shape for cnn is just the image
pooling=None, classes=2)
#Feel free to modify these layers!
x = layers.TimeDistributed(cnn)(inp)
x = layers.LSTM(8)(x)
out = layers.Dense(2)(x)
model = Model(inp, out)
model.compile(loss='binary_crossentropy',
optimizer='adam',
metrics='accuracy')
utils.plot_model(model, show_shapes=True, show_layer_names=False)
下一步就是簡單地訓練。 隨意添加您自己的參數。
model.fit(X_train, y_train, epochs=2)
Epoch 1/2
WARNING:tensorflow:5 out of the last 5 calls to <function Model.make_train_function.<locals>.train_function at 0x7f8e55b4fe50> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has experimental_relax_shapes=True option that relaxes argument shapes that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details.
1/1 [==============================] - 37s 37s/step - loss: 3.4057 - accuracy: 0.4000
Epoch 2/2
1/1 [==============================] - 16s 16s/step - loss: 3.3544 - accuracy: 0.4000
希望有幫助。
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