Problem Statement: I have problem making the Entity Embedding of Categorical Variable works for a simple dataset. I have followed the original github, or paper, or other blogposts[1,2,or this 3], or this Kaggle kernel; still not working.

Data Part: I am using the Ames Housing dataset as was hosted in Kaggle. I'm loading it in pandas dataframe as:

url = 'http://www.amstat.org/publications/jse/v19n3/decock/AmesHousing.xls'
# Load the file into a Pandas DataFrame
data_df = pd.read_excel(url)

For simplicity, out of 81 independent features, I am ONLY taking the Neighborhood, which is categorical, and the Gr Liv Area, which is numerical. And SalePrice, which is our target. I also split the data into train, and test and normalize the numerical variables.

features = ['Neighborhood','Gr Liv Area']
target = ['SalePrice']
data_df=data_df[features + target]

X_train, y_train = data_df.iloc[:2000][features], data_df.iloc[:2000][target]
X_test = data_df.iloc[2000:][features]

X_train['Gr Liv Area']=StandardScaler().fit_transform(X_train['Gr Liv Area'].reshape(-1, 1)) 

Embedding Neural Net: Here is the block of code where I am building the Entity Embedding Neural Net including both the categorical and numerical variables. In Entity Embedding, there is a particular hyperparamter that defines the embedding size (as we have in NLP). Here I am using of the above-mentioned blogpost strategy to choose that.

numerics = ['int16', 'int32', 'int64', 'float16', 'float32', 'float64']

for categorical_var in X_train.select_dtypes(include=['object']):

  #Name of the categorical variable that will be used in the Keras Embedding layer
  cat_emb_name= categorical_var.replace(" ", "")+'_Embedding'

  # Define the embedding_size
  no_of_unique_cat  = X_train[categorical_var].nunique()
  embedding_size = int(min(np.ceil((no_of_unique_cat)/2), 50 ))
  vocab  = no_of_unique_cat+1

  #One Embedding Layer for each categorical variable
  input_model = Input(shape=(1,))
  output_model = Embedding(vocab, embedding_size, name=cat_emb_name)(input_model)
  output_model = Reshape(target_shape=(embedding_size,))(output_model)    

  #Appending all the categorical inputs

  #Appending all the embeddings

#Other non-categorical data columns (numerical). 
#I define single another network for the other columns and add them to our models list.
input_numeric = Input(shape=(len(X_train.select_dtypes(include=numerics).columns.tolist()),))
embedding_numeric = Dense(64)(input_numeric) 

#At the end we concatenate altogther and add other Dense layers
output = Concatenate()(output_embeddings)
output = Dense(500, kernel_initializer="uniform")(output)
output = Activation('relu')(output)
output = Dense(256, kernel_initializer="uniform")(output)
output = Activation('relu')(output)
output = Dense(1, activation='sigmoid')(output)

model = Model(inputs=input_models, outputs=output)
model.compile(loss='mean_squared_error', optimizer='Adam',metrics=['mse','mape'])

At the end, the model looks like this: enter image description here

This look OK to me, unless I'm missing sth. Anyway, when I'm training the model like below:

history  =  model.fit(X_train,y_train  , epochs =  200 , batch_size = 16, verbose= 2)

I get a rather usual keras error:

ValueError: Error when checking model input: the list of Numpy arrays that you are passing to your model is not the size the model expected. Expected to see 2 array(s), but instead got the following list of 1 arrays: [array([['NAmes', 0.31507361227175135],
       ['NAmes', -1.2242024755540366],
       ['NAmes', -0.3472201781480285],

Then I looked more carefully at the original github or that Kaggle kernel, I noticed one has to convert the data to list format to match the network structure (still I am not sure I fully understand WHY!, see the preproc function there). Anyway, I convert my data to the list format like:

X_train_list = []

for i,column in enumerate(X_train.columns.tolist()):
  X_train_list.append(X_train.values[..., [i]])

Now when trying to train once again this time using the list format of the data i.e. X_train_list:

history  =  model.fit(X_train_list,y_train  , epochs =  200 , batch_size = 16, verbose= 2)

This time it starts with the first Epoch, then immediately stops with the following error:

ValueError: could not convert string to float: 'Mitchel'

It is rather obvious that it complains about one of the categories of the only Neighborhood variable that I have not encoded! Sure I have not, I thought that was the whole purpose of the Entity Embedding that the networks initiates a random embedding weights and learn the best embedding of that categorical variable during optimization of the target. Super confused!! Any help is much appreciated.

  • 1
    $\begingroup$ very interesting topic! Have you been able to find a solution so far? $\endgroup$
    – Seymour
    Jan 26, 2019 at 23:08
  • 1
    $\begingroup$ It is indeed interesting. Yes I have managed to make it work a few days after posting this questions here, but totally forgot to put it together and close the questions. I just cleaned up my notebook, and documented it and push everything in in a repository (see the link in the answer!). $\endgroup$ Jan 27, 2019 at 11:51
  • $\begingroup$ that is great news :) did Entity Embeddings improve your solution to the problem you were facing? are you satisfied? $\endgroup$
    – Seymour
    Jan 27, 2019 at 11:55
  • 1
    $\begingroup$ Well, that requires more time to benchmark and compare. It may differ from one case to another. I guess it might be superior in datasets containing high-cardinal categorical features. What I like about this method, is that it is quite neat and simple, in contrast to the well-known one-hot encoding that has its complications. Let me know how it works for your case. $\endgroup$ Jan 27, 2019 at 12:03
  • $\begingroup$ I do not need to use it. I discovered its existence because a guy mentioned a medium article about this topic in the microsoft malware competition. I investigated a bit and it seemed a very cool tool. Hope one day it will come at hand :) $\endgroup$
    – Seymour
    Jan 27, 2019 at 12:06

1 Answer 1


For those who are interested, I've spent some time, finally figured out that the problem was the way one has to prepare the categorical encoding for the Entity Embedding suitable for a neural network architecture; unfortunately none of the examples provided in blogposts or Kaggle kernels were clear about this step!

Here is the link to the repository containing a Jupyter notebook demonstrating a step-by-step working example. Hope some may find it useful.

P.S.: I have borrowed some of the functions from other people's work, kernels, that need to be referenced properly. Hopefully I will manage to update the notebook soon adding those refs.

  • 1
    $\begingroup$ The fact is that you had to convert categories into a numerical features? So for example feature color = ["red", "blue", "green"] needs first to be converted into color_encoded = [0, 1, 2] ? $\endgroup$
    – Seymour
    Jan 27, 2019 at 12:03
  • 1
    $\begingroup$ What do you mean it had to convert categories into a numerical features? What you mentioned here to 0, 1, 2 is the standard method. Here we will have an embedding matrix with parameters let's say w that we will learn the encoding on the fly during backpropagation! $\endgroup$ Jan 27, 2019 at 12:24
  • $\begingroup$ Because while I was going through the repository of the paper I saw they did label encoding, so I was wondering. $\endgroup$
    – Seymour
    Jan 27, 2019 at 12:50
  • $\begingroup$ But can you also only obtain the embedding matrix from the NN but then use the embedding matrix as input for other models like logistic regression? $\endgroup$
    – Seymour
    Jan 27, 2019 at 12:50
  • 1
    $\begingroup$ That is a good point, and I am not sure. But even in target-based encoding method, nobody is concerned about data leakage! I believe here it is not data leakage, it is only to find a categorical-encoding representation that map the feature to target! Unless I am totally wrong here! ;-) $\endgroup$ Jan 28, 2019 at 21:25

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