Data Analysis · Data Mining · NumPy · Pandas · Python · SciKit-Learn

Numpy vs Pandas Performance

Hi guys!

In the last post, I wrote about how to deal with missing values in a dataset. Honestly, that post is related to my PhD project. I will not explain the detail of my project but I need to replace a certain of percentage (10,20,…90 %) of my dataset to NaN then impute all those NaN values. In that post, I did experiment using Boston dataset, a quite small dataset (13 dimensions and 506 rows/tuples).

I got problems when I did experiments with a bigger dataset, for instance, Flights dataset. This dataset consists of 11 dimensions and almost one million rows (tuples) which is a quite large number. Let see Figure below:

To replace 80% values to NaN in Flight dataset using Pandas operation, it takes around 469 seconds. It’s really slow. Moreover, in this case, I only work on 8 dimensions (only numerical attributes).

I guess there are some reasons, why it has a slow performance: 1) because of the code itself; 2) due to using Pandas for large number operations, or 3) due to both reasons.

I was trying to find the answer and I found two posts about comparison performance between Numpy and Pandas including when we should use Numpy and Pandas: ([1], [2])

After reading those posts, I decided to use Numpy instead of Pandas in my operation due to my dataset has a large number of tuples (almost one million tuples).

This is how I implement. This function below is a function for replacing values to NaN:

def dropout(a, percent):
    # create a copy
    mat = a.copy()
    # number of values to replace
    prop = int(mat.size * percent)
    # indices to mask
    mask = random.sample(range(mat.size), prop)
    # replace with NaN
    np.put(mat, mask, [np.NaN]*len(mask))
    return mat

The code below is for missing values imputation. The code below is based on scikit learn example (scikit-learn has a function for imputing missing values). I imputed all numerical missing values with mean and all categorical missing values with the most frequent values:

from sklearn.base import TransformerMixin

class DataFrameImputer(TransformerMixin):
    def __init__(self):
        """Impute missing values.
        Columns of dtype object are imputed with the most frequent value 
        in column.
        Columns of other types are imputed with mean of column.
    def fit(self, X, y=None):
        self.fill = pd.Series([X[c].value_counts().index[0]
            if X[c].dtype == np.dtype('O') else X[c].mean() for c in X],
        return self
    def transform(self, X, y=None):
        return X.fillna(self.fill)

Here the results:

In Figure above, it can be seen that I converted Pandas data frame to numpy array. Just use this command

data = df.values

, your data frame will be converted to numpy array. Then I run the dropout function when all data in the form of numpy array. In the end, I re-converted again the data to Pandas dataframe after the operations finished.

Using Numpy operation to replace 80% data to NaN including imputing all NaN with most frequent values only takes 4 seconds. Moreover, in this case, I work on 11 dimensions (categorical and numerical attributes).

From this post, I just want to share to you that your choice matters. When we want to deal with a large number of tuples, we may consider choosing numpy instead of pandas. However, another important thing is no one can write optimized code!!

See you again in the next post!

Data Analysis · Data Mining · Pandas · Python · SciKit-Learn

Impute NaN values with mean of column Pandas Python

Incomplete data or a missing value is a common issue in data analysis. Systems or humans often collect data with missing values. Actually, we can do data analysis on data with missing values, it means we do not aware of the quality of data. However, it may produce the wrong results because of those missing values. The common approach to deal with missing value is dropping all tuples that have missing values. The problem with this dropping approach is it may generate bias results especially if the rows that contain NaN values are large, while in the end, we have to drop a large number of tuples. This way can be used if the data has a small number of missing values. In the case of data with a large number of missing values, we have to repair those missing values.

There are a lot of proposed imputation methods for repairing missing values. The simplest one is to repair missing values with the mean, median, or mode. It can be the mean of whole data or mean of each column in the data frame.

In this experiment, we will use Boston housing dataset. The Boston data frame has 506 rows and 14 columns. This dataset was taken from the StatLib library which is maintained at Carnegie Mellon University. The Boston house-price data has been used in many machine learning papers that address regression problems. MEDV attribute is the target (dependent variable), where others are independent variables. This dataset is available in the scikit-learn library, so we can just import it directly.  As usual, in this experiment, I am going to use Python Jupyter notebook. If you are not familiar with Jupyter Notebook, Pandas, Numpy, and other python libraries, I have a couple of old posts that may useful for you: 1) setup anaconda 2) understand python libraries for data science.

Let’s get started…

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.datasets import load_boston

boston_bunch = load_boston()
dfx = pd.DataFrame(, columns = boston_bunch.feature_names) #independent variables
dfy = pd.DataFrame(, columns = ['target']) #dependent variables
boston = dfx.join(dfy)

We can use command boston.head() to see the data, and boston.shape to see the dimension of the data. The next step is check the number of Na in boston dataset using command below.


The result shows that Boston dataset has no Na values. The question is how we create/change some values to NA? is that possible?

#Change some values (20%) to NAN randomly
# Change 10% Values to NA randomly
import collections
import random
df = boston
replaced = collections.defaultdict(set)
ix = [(row, col) for row in range(df.shape[0]) for col in range(df.shape[1])]
to_replace = int(round(.2*len(ix)))
for row, col in ix:
    if len(replaced[row]) < df.shape[1] - 1:
        df.iloc[row, col] = np.nan
        to_replace -= 1
        if to_replace == 0:

Using the code above, we can replace some values (20%) in Boston dataset to NA. We also can change the percentage of NA by changing the code above(see .2*). Na values are absolutely random with respect to the whole data. Then, now check again is there any missing values in our boston dataset?


The result shows that all columns have around 20% NaN values. Then how to replace all those missing values (impute those missing values) based on the mean of each column?

#fill NA with mean() of each column in boston dataset
df = df.apply(lambda x: x.fillna(x.mean()),axis=0)

Now, use command boston.head() to see the data. We have fixed missing values based on the mean of each column. We also can impute our missing values using median() or mode() by replacing the function mean().

This imputation method is the simplest one, there are a lot of sophisticated algorithms (e.g., regression, monte carlo, etc) out there that can be used for repairing missing values. Maybe I’ll post it next time.

All codes and results can be accessed through this link

Thank you, see you

Data Analysis · Data Mining · NumPy · Pandas · SciKit-Learn

Remove Duplicates from Correlation Matrix Python

Correlation is one of the most important things that usually used by the data analysts in their analytical workflow. By using correlation, we can understand the mutual relationship or association between two attributes. Let’s start with the example. For instance, I want to do an analysis of the “Boston housing dataset”, let see the example code below. If you are not familiar with Jupyter Notebook, Pandas, Numpy, and other python libraries, I have a couple of old posts that may useful for you: 1) setup anaconda 2) understand python libraries for data science.

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn import datasets

boston = datasets.load_boston() #Load Boston Housing dataset, this dataset is available on Scikit-learn
boston = pd.DataFrame(boston['data'], columns=boston['feature_names'])

We can use the command boston.head() to see the data, and boston.shape to see the dimension of the data. We can easily use this command below to get correlation value among all attributes in Boston housing dataset. (e.g., in this experiment I used Pearson correlation).

dataCorr = boston.corr(method='pearson')

After using this command, we will see the matrix of correlation like in Figure below:

The question is, how to remove duplicates from this matrix of correlation to make it more readable? I found a nice answer on stackoverflow, we can use this command:

dataCorr = dataCorr[abs(dataCorr) >= 0.01].stack().reset_index()
dataCorr = dataCorr[dataCorr['level_0'].astype(str)!=dataCorr['level_1'].astype(str)]

# filtering out lower/upper triangular duplicates 
dataCorr['ordered-cols'] = dataCorr.apply(lambda x: '-'.join(sorted([x['level_0'],x['level_1']])),axis=1)
dataCorr = dataCorr.drop_duplicates(['ordered-cols'])
dataCorr.drop(['ordered-cols'], axis=1, inplace=True)

dataCorr.sort_values(by=[0], ascending=False).head(10) #Get 10 highest correlation of pairwaise attributes

Finally, we get the table that consists of the pair of attributes and the correlation values, and the most important thing is we do not have any duplication.

I also found another way from a guy in Github who create a nice function to remove this duplication. Please see through this link.

Thank you and see you next time.

Bokeh · Data Analysis · Data Mining · Keras · Machine Learning · Matplotlib · NumPy · Pandas · Plotting in Python · Ploty · SciKit-Learn · SciPy · Seaborn

Python for Data Science








See ya next time

Brisbane, 24 November 2017

Bokeh · Data Mining · NumPy · Pandas · Plotting in Python

Python for Data Science Cheat Sheet

Berikut adalah Python for Data Science Cheat Sheet yang cukup membantu untuk merefresh ingatan kita atau bagi yang baru awal menggunakan Python untuk analisis data, mining data atau data science bisa dijadikan bahan bacaan.


Python Basic for Data Science

Berikut Cheat Sheet nya:
Python basic

Untuk file PDF dengan kualitas bagus bisa didownload di sini


Python NumPy Cheat Sheet

Berikut Cheat Sheet gambarnya:

Numpy Basic

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Python Pandas Cheat Sheet

Berikut Cheat Sheet gambarnya:

Pandas Basic

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Python Bokeh Interactive Visualization Cheat Sheet

Berikut Cheat Sheet gambarnya:


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Cheat Sheet di atas saya dapatkan dari DataCamp.

Semoga bermanfaat.