I am trying to build a decision tree model. After one-hot encoding, it seems somehow the data still has a problem. When I run the following code, I receive this error:

ValueError: Number of labels=172 does not match number of samples=540

import pandas as pd
import numpy as np

df = pd.read_csv("https://library.startlearninglabs.uw.edu/DATASCI420/Datasets/Bank%20Data.csv", sep=",")
df.columns=['age', 'sex', 'region', 'income', 'married', 'children', 'car',
       'save_act', 'current_act', 'mortgage', 'pep']

(nrows, ncols) = df.shape
colnames = list(df.columns.values)
string_encoding = {}
df_encoded = df.copy()
for i in range(ncols):
    levels = list(set(df.iloc[:, i]))
    num_levels = len(levels)
    string_encoding_i = dict(zip(levels, range(num_levels)))
    string_encoding[colnames[i]] = string_encoding_i
    for j in range(nrows):
        df_encoded.iloc[j, i] = string_encoding_i[df.iloc[j, i]]


# One Hot Encoding Categorial Variables
from sklearn import preprocessing
enc = preprocessing.OneHotEncoder()

non_categorial_features = ['age',

for categorical_feature in list(df.columns):
    if categorical_feature not in non_categorial_features:
        df[categorical_feature] = df[categorical_feature].astype('category')

df_with_dummies = pd.get_dummies(df, sparse=True)

df = pd.concat([df, df_with_dummies], axis=1)


df = df.drop(['sex', 'region', 'married', 'car',
       'save_act', 'current_act', 'mortgage', 'pep_NO', 'pep_YES'], axis=1)


from sklearn import tree
import numpy as np
from sklearn.model_selection import train_test_split 

# prepare for decision tree

title_names =['age', 'income', 'children', 'counts', 'age', 'income',
       'children', 'sex_FEMALE', 'sex_MALE', 'region_INNER_CITY',
       'region_RURAL', 'region_SUBURBAN', 'region_TOWN', 'married_NO',
       'married_YES', 'car_NO', 'car_YES', 'save_act_NO', 'save_act_YES',
       'current_act_NO', 'current_act_YES', 'mortgage_NO', 'mortgage_YES', 'pep']

df = df[title_names]

X = df.iloc[:,0:23]
Y = df.iloc[:, 23]
X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size = 0.1, random_state = 99)

# decision tree
from sklearn.tree import DecisionTreeClassifier 

# Use entropy = no limit on samples for split
model_ent = DecisionTreeClassifier(criterion='entropy').fit(X_train, y_train) 
y_ent_pred = model_ent.predict(X_test)

# Use information gain (default) limit min_samples to 4
model_gini = DecisionTreeClassifier(min_samples_leaf=5).fit(X_train, y_train)
y_gini_pred = model_gini.predict(X_test)
  • $\begingroup$ here is the error info: $\endgroup$
    – user633599
    Feb 10, 2019 at 19:00
  • $\begingroup$ ValueError: Number of labels=150 does not match number of samples=480 $\endgroup$
    – user633599
    Feb 10, 2019 at 19:01

1 Answer 1


It looks like Y is a SpareSeries as well as y_train and y_test. So when that is passed to the decision tree fit method, it only interprets those entries with label 1 as existing. According to the pandas documentation:

We have implemented “sparse” versions of Series and DataFrame. These are not sparse in the typical “mostly 0”. Rather, you can view these objects as being “compressed” where any data matching a specific value (NaN / missing value, though any value can be chosen) is omitted.

I'm not sure why it is a sparse data structure, but you can use the to_dense method to densify it:

Y = df.iloc[:, 23].to_dense()

Edit: Danny below mentions you could just remove Sparse=True from get_dummies.

  • 1
    $\begingroup$ I agree with you but since it's quite a small dataset, I'd recommend to get rid of the sparse = True. $\endgroup$
    – Danny
    Feb 11, 2019 at 15:14

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