I am trying to understand from both a conceptual and a Python code point of view, how to represent phrases that are present in a corpus (that is used to train a neural network to classify phrases) as vectors and how to do PCA with them.

Consider that I do not want to use Word2Vec embedding and that I want only to extract the vectors from the embedding layer of my neural network.

The example I chose to understand how to do this is the following:

import numpy as np
from keras.preprocessing.text import one_hot, Tokenizer
from keras.preprocessing.sequence import pad_sequences
from keras.models import Sequential
from keras.layers import Dense
from keras.layers import Flatten
from keras.layers.embeddings import Embedding
# define documents
docs = np.array(['Well done!',
        'Good work',
        'Great effort',
        'nice work',
        'Poor effort!',
        'not good',
        'poor work',
        'Could have done better.'])
# define class labels
labels = np.array([1,1,1,1,1,0,0,0,0,0])
# train the tokenizer
vocab_size = 15
tokenizer = Tokenizer(num_words=vocab_size)

# encode the sentences
encoded_docs = tokenizer.texts_to_sequences(docs)
# pad documents to a max length of 4 words
max_length = 4
padded_docs = pad_sequences(encoded_docs, maxlen=max_length, padding='post')
# define the model
model = Sequential()
model.add(Embedding(vocab_size, 2, input_length=max_length, name='embeddings'))
model.add(Dense(1, activation='sigmoid'))

# compile the model
model.compile(optimizer='adam', loss='binary_crossentropy', metrics=['accuracy'])

# fit the model
model.fit(padded_docs, labels, epochs=50, verbose=2)

It is a classifier MLP so I define the class labels corresponding to each sentence of the docs, I assign to each word an integer based on the tokenizer module, I prepare all my sequences of words to have all the same length because keras likes to work in this way, and then I finally define, compile and fit the model. After fitting the model, I can extract the weights of my embedding layer with the following line of code:

# save embeddings
embeddings = model.get_layer('embeddings').get_weights()[0]

That is a 2D array with 2 dimensional embedding space (as chosen by me):

array([[-0.02900218, -0.02272025],
       [-0.03750041,  0.08604637],
       [ 0.00261297,  0.06689994],
       [ 0.06822112, -0.07083904],
       [ 0.042956  ,  0.00642773],
       [-0.01934443, -0.03651911],
       [ 0.02451712,  0.02507548],
       [ 0.01995835,  0.03889224],
       [ 0.01348991,  0.01143651],
       [ 0.02176871,  0.01283678],
       [-0.04610137, -0.04942843],
       [-0.02342983, -0.07704163],
       [-0.08990634, -0.06908827],
       [ 0.07353339, -0.06115208],
       [-0.06146053,  0.09602208]], dtype=float32)

At this point, I have two huge difficulties:

  • How to represent each phrase of the corpus with the embedding weights and so as a vector: based on the nice answer to this question, I suppose that first of all I have to check which are the integers assigned to each word and I can do it with:

That gives me the following representation:

[[6, 2], [3, 1], [7, 4], [8, 1], [9], [10], [5, 4], [11, 3], [5, 1], [12, 13, 2, 14]]

Then I assign to each integer the embedding weights of the trained network printed before and so I obtain:

X=np.array([[[[ 0.02451712,  0.02507548], [ 0.00261297,  0.06689994]], [[ 0.06822112, -0.07083904], [-0.03750041,  0.08604637]], [[ 0.01995835,  0.03889224], [ 0.042956  ,  0.00642773]], [[ 0.01348991,  0.01143651], [-0.03750041,  0.08604637]],  [ 0.02176871,  0.01283678], [-0.04610137, -0.04942843], [[-0.01934443, -0.03651911], [ 0.042956  ,  0.00642773]], [[-0.02342983, -0.07704163],  [ 0.06822112, -0.07083904]], [[-0.01934443, -0.03651911], [-0.03750041,  0.08604637]], [[-0.08990634, -0.06908827], [ 0.07353339, -0.06115208], [ 0.00261297,  0.06689994], [-0.06146053,  0.09602208]]]])

Is it correct to say that X contain the vector representation of all the words of my docs? Furthermore, if yes or in any case is there a function in Python that allows you to get it ? Or one should implement it from scratch? Then, I ignored the fact that the sequences were padded with zeros. Should I add zeros and make all my vectors (of the 2D array) as 4 dimensional vectors in order to represent each word properly ?

  • Once I obtain my vector representation of each word in the docs, how do I do the PCA representation of the 2D array that I obtain? What are samples and what are variables? In theory, I should obtain a plot in which the data labeled as 1 cluster together and the data labeled as 0 cluster together thanks to the fact that they are now given by the weights which are obtained by training the classifier neural network.

I hope I'm not too out of the way with everything.

Thank you in advance.

P.S.: please, if you downvote the question give me the reason of your downvoting. It's not a question I threw there but there was some research effort.

  • $\begingroup$ obtaining a vector out of a word, can be done in so many different ways imaginable, each of them capturing some part of what the word means. So it is not unique, using word2vec is simply one option. $\endgroup$
    – Nikos M.
    Nov 14, 2021 at 15:03
  • $\begingroup$ Ok... is my procedure correct ? @NikosM. $\endgroup$ Nov 14, 2021 at 16:25
  • $\begingroup$ Getting embeddings for phrases, is somewhat ambiguous. One can try approaches, a simple one is to simply consider each phrase as a distinct word and get word embeddings, which are now actually phrase embeddings. But phrases are more complex and some non-trivial NLP model might be more helpful $\endgroup$
    – Nikos M.
    Nov 15, 2021 at 15:46

2 Answers 2


We can use the below code to fetch the embeddings for each word

 words_embeddings = {w:embeddings[idx] for w, idx in tokenizer.word_index.items()}

res_vectors = np.empty((0, 2), float)
words = []
for k,v in words_embeddings.items():
  print(k,"-->", v)
  res_vectors = np.append(res_vectors, [v], axis=0)

Since each word is represented as a 2D vector, I have not reduced the dimensionality of the vector. With the below code we can get the word representations.

import matplotlib.pyplot as plt
plt.title("Word Embedding Space",size=20)
for i, word in enumerate(words):

enter image description here

To get better results, try to increase the vector dimensions of each word.

If we use a 100-dimensional vector for a word. We can make use of PCA as below.

from sklearn.decomposition import PCA
pca = PCA(n_components=2)
res_vectors = pca.fit_transform(res_vectors)

Word representations in this case. enter image description here

We can get the phrase embeddings as below:

doc_vecs = np.empty((0,2), float)
for i, doc in enumerate(padded_docs):
  vec = np.empty((0,2), float)
  for token in doc:  
    vec = np.append(vec, [embeddings[token]], axis=0)
  vec = vec.mean(axis=0)  
  print(docs[i], "-->", vec)
  doc_vecs = np.append(doc_vecs, [vec], axis=0)

Phrase Representation:

import matplotlib.pyplot as plt
plt.scatter(doc_vecs [:,0],doc_vecs [:,1],linewidths=10,color='blue')
plt.title("Phrase Embedding Space",size=20)
for i, doc in enumerate(docs):
  plt.annotate(doc,xy=(doc_vecs [i,0],doc_vecs [i,1]))

enter image description here

  • $\begingroup$ Thank you very much for the clear and the "practical" answer @Shirinidhi . Now many things are better in my mind but one last thing: as the title of my question post said, I was looking for the embedding and the PCA representation of the phrases of the docs and not of the single words. How can I obtain them ? $\endgroup$ Nov 15, 2021 at 14:15
  • $\begingroup$ Updated the answer to include phrase embeddings $\endgroup$ Nov 15, 2021 at 17:44
  • $\begingroup$ Thank you very much. One observation: you have copied the wrong code for plotting the phrase embedding space... I think you confused with the one written before for word embedding space. $\endgroup$ Nov 16, 2021 at 10:46
  • $\begingroup$ Variable name should have been updated $\endgroup$ Nov 16, 2021 at 10:54
  • $\begingroup$ So you simply concatenate the word vectors of each phrase to get the phrase vectors..? It is an option, although not the only one, neither the most appropriate for all cases $\endgroup$
    – Nikos M.
    Nov 20, 2021 at 12:11
  1. Your X contains representations of all the words in docs. Each doc(phrase) is represented as a 4x2 second order tensor(since you are padding with max length 4 and your word embeddings have 2 dimensions).

you can obtain such matrix by using embeddings(encoded_docs).Use of padding is dependent on the downstream task you are try to do with these embeddings.

  1. PCA is usually done to map vectors $R^d \rightarrow R^c$. Doc representations above are $R^{4*2}$, to perform PCA on these you'll have to either flatten your doc representations or use some of the recent tensor PCA techniques.

you can Flatten the representations similar to the way you've done above to get $R^8$ vectors for each doc, or you can additively combine each word in a phrase to get $R^2$ vectors. I would suggest the later option. First option requires you to pad the phrases while second option doesn't require the padding.

Post this you can use regular PCA to reduce dimensions and visualize the data and identify clusters. But with the data that you are using in this example might not result in meaningful representations or visualizations as it is too small.

  • $\begingroup$ Thank you @PavanKandru for the help, but it is still difficult for me to put in practice what you said. If you write a working Python code after each explanation you gave, I will be fully satisfied. $\endgroup$ Nov 15, 2021 at 10:17

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