Shlomi Schwartz Shlomi Schwartz - 2 years ago 403
Python Question

Keras - Save image embedding of the mnist data set

I've written the following simple MLP network for the


from __future__ import print_function

import keras
from keras.datasets import mnist
from keras.models import Sequential
from keras.layers import Dense, Dropout
from keras import callbacks

batch_size = 100
num_classes = 10
epochs = 20

tb = callbacks.TensorBoard(log_dir='/Users/shlomi.shwartz/tensorflow/notebooks/logs/minist', histogram_freq=10, batch_size=32,
write_graph=True, write_grads=True, write_images=True,
embeddings_freq=10, embeddings_layer_names=None,

early_stop = callbacks.EarlyStopping(monitor='val_loss', min_delta=0,
patience=3, verbose=1, mode='auto')

# the data, shuffled and split between train and test sets
(x_train, y_train), (x_test, y_test) = mnist.load_data()

x_train = x_train.reshape(60000, 784)
x_test = x_test.reshape(10000, 784)
x_train = x_train.astype('float32')
x_test = x_test.astype('float32')
x_train /= 255
x_test /= 255
print(x_train.shape[0], 'train samples')
print(x_test.shape[0], 'test samples')

# convert class vectors to binary class matrices
y_train = keras.utils.to_categorical(y_train, num_classes)
y_test = keras.utils.to_categorical(y_test, num_classes)

model = Sequential()
model.add(Dense(200, activation='relu', input_shape=(784,)))
model.add(Dense(100, activation='relu'))
model.add(Dense(60, activation='relu'))
model.add(Dense(30, activation='relu'))
model.add(Dense(10, activation='softmax'))



history =, y_train,
validation_data=(x_test, y_test))
score = model.evaluate(x_test, y_test, verbose=0)
print('Test loss:', score[0])
print('Test accuracy:', score[1])

The model ran fine, and I could see the scalars info on TensorBoard. However when I've changed embeddings_freq=10 to try and visualize the images (Like seen here) I got the following error:

Traceback (most recent call last):
File "/Users/shlomi.shwartz/IdeaProjects/TF/src/", line 65, in <module>
validation_data=(x_test, y_test))
File "/Users/shlomi.shwartz/tensorflow/lib/python3.6/site-packages/keras/", line 870, in fit
File "/Users/shlomi.shwartz/tensorflow/lib/python3.6/site-packages/keras/engine/", line 1507, in fit
File "/Users/shlomi.shwartz/tensorflow/lib/python3.6/site-packages/keras/engine/", line 1117, in _fit_loop
File "/Users/shlomi.shwartz/tensorflow/lib/python3.6/site-packages/keras/", line 52, in set_model
File "/Users/shlomi.shwartz/tensorflow/lib/python3.6/site-packages/keras/", line 719, in set_model
self.saver = tf.train.Saver(list(embeddings.values()))
File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/tensorflow/python/training/", line 1139, in __init__
File "/usr/local/Cellar/python3/3.6.1/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/tensorflow/python/training/", line 1161, in build
raise ValueError("No variables to save")
ValueError: No variables to save

Q: What am I missing? is that the right way of doing it in Keras?

Update: I understand there is some prerequisite in order to use embedding projection, however I haven't found a good tutorial for doing so in Keras, any help would be appreciated.

Answer Source

What is called "embedding" here in callbacks.TensorBoard is, in a broad sense, any layer weight. According to Keras documentation:

embeddings_layer_names: a list of names of layers to keep eye on. If None or empty list all the embedding layer will be watched.

So by default, it's going to monitor the Embedding layers, but you don't really need a Embedding layer to use this visualization tool.

In your provided MLP example, what's missing is the embeddings_layer_names argument. You have to figure out which layers you're going to visualize. Suppose you want to visualize the weights (or, kernel in Keras) of all Dense layers, you can specify embeddings_layer_names like this:

model = Sequential()
model.add(Dense(200, activation='relu', input_shape=(784,)))
model.add(Dense(100, activation='relu'))
model.add(Dense(60, activation='relu'))
model.add(Dense(30, activation='relu'))
model.add(Dense(10, activation='softmax'))

embedding_layer_names = set(
                            for layer in model.layers

tb = callbacks.TensorBoard(log_dir='temp', histogram_freq=10, batch_size=32,
                           write_graph=True, write_grads=True, write_images=True,
                           embeddings_freq=10, embeddings_metadata=None,


Then, you can see something like this in TensorBoard: tensorboard

You can see the relevant lines in Keras source if you want to figure out what's happening regarding embeddings_layer_names.


So here's a dirty solution for visualizing layer outputs. Since the original TensorBoard callback does not support this, implementing a new callback seems inevitable.

Since it will take up a lot of page space to re-write the entire TensorBoard callback here, I'll just extend the original TensorBoard, and write out the parts that are different (which is already quite lengthy). But to avoid duplicated computations and model saving, re-writing the TensorBoard callback will be a better and cleaner way.

import tensorflow as tf
from tensorflow.contrib.tensorboard.plugins import projector
from keras import backend as K
from keras.models import Model
from keras.callbacks import TensorBoard

class TensorResponseBoard(TensorBoard):
    def __init__(self, val_size, img_path, img_size, **kwargs):
        super(TensorResponseBoard, self).__init__(**kwargs)
        self.val_size = val_size
        self.img_path = img_path
        self.img_size = img_size

    def set_model(self, model):
        super(TensorResponseBoard, self).set_model(model)

        if self.embeddings_freq and self.embeddings_layer_names:
            embeddings = {}
            for layer_name in self.embeddings_layer_names:
                # initialize tensors which will later be used in `on_epoch_end()` to
                # store the response values by feeding the val data through the model
                layer = self.model.get_layer(layer_name)
                output_dim = layer.output.shape[-1]
                response_tensor = tf.Variable(tf.zeros([self.val_size, output_dim]),
                                              name=layer_name + '_response')
                embeddings[layer_name] = response_tensor

            self.embeddings = embeddings
            self.saver = tf.train.Saver(list(self.embeddings.values()))

            response_outputs = [self.model.get_layer(layer_name).output
                                for layer_name in self.embeddings_layer_names]
            self.response_model = Model(self.model.inputs, response_outputs)

            config = projector.ProjectorConfig()
            embeddings_metadata = {layer_name: self.embeddings_metadata
                                   for layer_name in embeddings.keys()}

            for layer_name, response_tensor in self.embeddings.items():
                embedding = config.embeddings.add()
                embedding.tensor_name =

                # for coloring points by labels
                embedding.metadata_path = embeddings_metadata[layer_name]

                # for attaching images to the points
                embedding.sprite.image_path = self.img_path

            projector.visualize_embeddings(self.writer, config)

    def on_epoch_end(self, epoch, logs=None):
        super(TensorResponseBoard, self).on_epoch_end(epoch, logs)

        if self.embeddings_freq and self.embeddings_ckpt_path:
            if epoch % self.embeddings_freq == 0:
                # feeding the validation data through the model
                val_data = self.validation_data[0]
                response_values = self.response_model.predict(val_data)
                if len(self.embeddings_layer_names) == 1:
                    response_values = [response_values]

                # record the response at each layers we're monitoring
                response_tensors = []
                for layer_name in self.embeddings_layer_names:
                K.batch_set_value(list(zip(response_tensors, response_values)))

                # finally, save all tensors holding the layer responses
      , self.embeddings_ckpt_path, epoch)

To use it:

tb = TensorResponseBoard(log_dir=log_dir, histogram_freq=10, batch_size=10,
                         write_graph=True, write_grads=True, write_images=True,
                         val_size=len(x_test), img_path='images.jpg', img_size=[28, 28])

Before launching TensorBoard, you'll need to save the labels and images to log_dir for visualization:

from PIL import Image
img_array = x_test.reshape(100, 100, 28, 28)
img_array_flat = np.concatenate([np.concatenate([x for x in row], axis=1) for row in img_array])
img = Image.fromarray(np.uint8(255 * (1. - img_array_flat))), 'images.jpg'))
np.savetxt(os.path.join(log_dir, 'metadata.tsv'), np.where(y_test)[1], fmt='%d')

Here's the result:


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