How to Automate Data Cleaning in Python?
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How to Automate Data Cleaning in Python?
In Data Science and Machine Learning, Data Cleaning plays an essential role. Data Cleaning is the process of retaining only the crucial information from the output so that only relevant features are sent as input to the machine learning model. It is a very crucial step in data science and it helps in getting better results as all the noise is already removed.
But, have you wondered that such a process can be time taking and coding a pipeline for every new dataset can be quite tiresome? Hence, it is a good idea to automate the whole process by creating a set pipeline for the process and then using it on every piece of data that one needs to clean. Such a pipeline can make the work easier as well as more refined. One will not have to worry about missing a step and all that is needed is to use that same pipeline again.
In this article, we will be working on creating a complete pipeline using multiple libraries, modules, and functions in Python to clean a CSV file.
How to Automate Data Cleaning in Python?
To understand the process of automating data cleaning by creating a pipeline in Python, we should start by understanding the whole point of data cleaning in a machine-learning task. The user information or any raw data contained a lot of noise (unwanted parts) in it. Such data sent to the model directly can lead to a lot of confusion and henceforth can lead to unsatisfactory results. Hence, removing all the unwanted and unnecessary data from the original data can help the model perform better. This is the reason that data cleaning is an essential step in most of the Machine Learning tasks.
In reference to data cleaning, automating the process, essentially means creating a set of rules (function in terms of code) that align and organize the whole process of data cleaning and make it easier for us to run the same pipeline as per the requirement on different sets of data.
Automating data cleaning in Python means creating a set of rules(function in terms of code) that align and organize the whole process of data cleaning.
The data cleaning process can be done using various libraries and the following are some most popular ones:
1. Text Data Cleaning Using Regular Expressions
Regular Expressions are simple sequences of characters that one matches in a given text. Furthermore, these identified sequences can be removed or extracted from the text using a simple Python module called Regex imported in the code as re.
Here’s a sample code for using regular expressions in Python:
- Python
import re# Read text# Remove all non-alphanumeric charactersclean_text = re.sub(r'[^a-zA-Z0-9\s]', '', text)# Find all email addresses in textemails = re.findall(r'\b[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Z|a-z]{2,}\b', text)# Replace all phone numbers with "PHONE NUMBER"clean_text = re.sub(r'\d{3}[-.\s]??\d{3}[-.\s]??\d{4}', 'PHONE NUMBER', clean_text)# Write cleaned text to output fileprint(clean_text)print("Emails found:", emails) |
Output:
Read the data from httpswwwgfgorg posted by gfggmailcom Emails found: ['[email protected]']
Here are some examples of the data cleaning tasks that can be done using regular expressions:
- Extract specific patterns from text data, such as email addresses, phone numbers, or dates.
- Remove unwanted characters or substrings from text data.
- Replace specific patterns or substrings with new values.
- Standardize text data by converting all characters to lowercase or uppercase.
- Identify and remove duplicates based on text data.
- Split text data into separate columns or rows based on delimiters or patterns.
2. Read the Dataset Using Pandas
Pandas is an extremely popular, well-known, and one of the libraries used in almost all Machine Learning tasks. Pandas are essentially a package of Python used to deal majorly with data frames and manipulate them as per the need. While working on the data cleaning process of a data frame pandas can prove to be a very helpful library.
Below is a sample code for using Pandas in Python for data cleaning:
- Python
import pandas as pd# Read in CSV filedf = pd.read_csv('input.csv')# Drop duplicatesdf = df.drop_duplicates()# Fill missing values with meandf = df.fillna(df.mean())# Convert data typesdf['date'] = pd.to_datetime(df['date'])df['amount'] = df['amount'].astype(float)# Define custom cleaning functiondef clean_name(name):return name.strip().title()# Apply custom function to 'name' columndf['name'] = df['name'].apply(clean_name)# Write cleaned data to CSV filedf.to_csv('output.csv', index=False) |
Here are some things you can do with Pandas to automate the data-cleaning process:
| Task | Function Used | Description |
|---|---|---|
| Remove duplicates | drop_duplicates() | Remove duplicate rows from a dataframe. |
| Drop missing values | dropna() | Remove rows or columns with missing values. |
| Impute missing values | fillna() | Fill in missing values in a dataframe with a specified value or method. |
| Convert data types | astype() | Convert the data type of a column in a dataframe. |
| Rename columns | rename() | Rename columns in a dataframe. |
| Group and aggregate data | groupby(), agg(), apply() | Group and aggregate data in a dataframe. |
| Filter data | query(), loc[], iloc[] | Filter data in a dataframe using various methods |
| Apply functions to data | apply() | Apply a function to a column or row in a dataframe |
| Merge data | merge(), join(), concat() | Merge data from multiple dataframes |
| Pivot data | pivot_table() | The method allows for more advanced features such as multi-index and custom aggregation. |
By using these functions and methods, you can create a powerful data-cleaning pipeline in Pandas to automate the data-cleaning process.
3. Mathematical Operations Using NumPy
NumPy is another popular library in Python for numerical computing. As its name suggests, it stands for Numerical Python. It provides a powerful array data structure that can be used for efficient data processing and analysis. NumPy has several functions for cleaning data, such as filtering, sorting, and aggregating data.
Here is an example code for using NumPy to filter and sort data:
- Python
import numpy as np# create a numpy arraydata = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])# filter the array to keep only values greater than 5filtered_data = data[data > 5]# sort the filtered data in descending ordersorted_data = np.sort(filtered_data)[::-1]print(sorted_data) |
Output:
[10 9 8 7 6]
Here are some things you can do with Pandas to automate the data-cleaning process:
| Task | Function Used | Description |
|---|---|---|
| Replace missing values | numpy.nan_to_num() | Replaces NaN values with zeros or a specified value |
| Identify missing values | numpy.isnan() | Returns a boolean array indicating where NaN values are found |
| Replace outliers | numpy.clip() | Clips values to a specified range to remove outliers |
| Normalize data | numpy.linalg.norm() | Computes the norm (magnitude) of a vector or matrix |
| Standardize data | numpy.std(), numpy.mean() | Computes the standard deviation and mean of a dataset |
| Scale data | numpy.interp() | Scales a dataset to a specified range |
| Remove duplicate values | numpy.unique() | Removes duplicate values from an array |
| Filter data based on a condition | numpy.where() | Returns values from one array if a condition in another array is met |
| Split data into chunks | numpy.array_split() | Splits an array into equally-sized subarrays |
Creating a Basic Data Cleaning Pipeline in Python
Now that we have discussed some of the popular libraries for automating data cleaning in Python, let’s dive into some of the techniques for using these libraries to clean data. Following is a structure of a basic data-cleaning pipeline that covers the most essential steps:
- Loading the CSV file: The CSV file is loaded as a data frame using the pandas module in Python.
- Preprocessing the Data: The data has multiple attributes and mostly these are not in a format that Machine Learning modules can understand. Hence following key preprocessing steps can be applied:
- Removing duplicates: Duplicate rows in a dataset can cause errors or bias in analysis, so it’s important to remove them.
- Correcting inconsistent data: Inconsistent data can arise due to errors in data entry or data integration.
- Handling outliers: Outliers can skew analysis, so it’s important to handle them appropriately.
- Formatting data: Data may need to be formatted to meet the requirements of the analysis.
- Handling missing values: Missing values can cause problems with analysis, so it’s important to handle them appropriately. Here’s an example of how to handle missing values using the pandas library in Python:
The above steps include some of the significant and key ones, but, as per the requirement, one can add or remove functions and clean the data using the updated pipeline.
Implementing the Pipeline
The final pipeline can be implemented as follows using Python. Here the implemented code is tested on a custom-generated dataset as well to see the effect of the data-cleaning process.
- Python
import pandas as pdfrom sklearn.preprocessing import LabelEncoderimport numpy as npdef drop_duplicates(df, subset_name):df.drop_duplicates(subset=[subset_name], inplace=True)return dfdef encode(df, column_to_encode):le = LabelEncoder()# fit and transform a column using the LabelEncoderdf[column_to_encode] = le.fit_transform(df[column_to_encode])return dfdef outlier_handling(df, column_with_outliers):q1 = df[column_with_outliers].quantile(0.25)q3 = df[column_with_outliers].quantile(0.75)iqr = q3 - q1# remove outliersdf = df[(df[column_with_outliers] > (q1 - 1.5 * iqr)) & (df[column_with_outliers] < (q3 + 1.5 * iqr))] return dfdef date_formatting(df, column_with_date):# format date columndf[column_with_date] = pd.to_datetime(df[column_with_date], format='%m/%d/%Y') return dfdef remove_missing_values(df):# Find missing valuesmissing_values = df.isnull().sum()# Remove rows with missing valuesdf = df.dropna()# Print number of missing values removedprint("Removed {} missing values".format(missing_values.sum()))return dfdef data_cleaning_pipeline(df_path,duplication_subset,column_to_encode,column_with_outliers, column_with_date):df = pd.read_csv(df_path)df_no_duplicates = drop_duplicates(df, duplication_subset)df_encoded = encode(df_no_duplicates , column_to_encode)df_no_outliers = outlier_handling(df_encoded, column_with_outliers)df_date_formatted = date_formatting(df_no_outliers, column_with_date)df_no_nulls = remove_missing_values(df_date_formatted)return df_no_nulls# Create a sample DataFramedata = {'Name': ['John', 'Jane', 'Bob', 'John', 'Alice'],'Age': [30, 25, 40, 30, np.NaN],'Gender': ['Male', 'Female', 'Male', 'Male', 'Female'],'Income': [50000, 60000, 70000, 45000, 80000],'Birthdate': ['01/01/1990', '02/14/1996', '03/15/1981','01/01/1990', '06/30/1986'],'Married': [True, False, True, False, True],'Children': [2, 0, 1, 0, 3]}df = pd.DataFrame(data)print('Before Preprocessing:\n',df)# Save DataFrame as CSV filedf.to_csv('my_data.csv', index=False)clean_df = data_cleaning_pipeline('my_data.csv','Name', 'Gender', 'Income','Birthdate')print('\nAfter preprocessing')clean_df.head() |
Output:
Before Preprocessing:
Name Age Gender Income Birthdate Married Children
0 John 30.0 Male 50000 01/01/1990 True 2
1 Jane 25.0 Female 60000 02/14/1996 False 0
2 Bob 40.0 Male 70000 03/15/1981 True 1
3 John 30.0 Male 45000 01/01/1990 False 0
4 Alice NaN Female 80000 06/30/1986 True 3
Removed 1 missing values
After preprocessing
Name Age Gender Income Birthdate Married Children
0 John 30.0 1 50000 1990-01-01 True 2
1 Jane 25.0 0 60000 1996-02-14 False 0
2 Bob 40.0 1 70000 1981-03-15 True 1
In the above code, a random dataset is created and then it is saved into a CSV file to pass it through the data cleaning pipeline. You can easily use the same pipeline by simply passing a different file path in the “data_cleaning_pipeline functions”.
Following is a snippet of the data before the cleaning process:
- Python3
df.head() |
Output:
Before Preprocessing
Following is a snippet of the data after the cleaning process:
- Python3
clean_df.head() |
Output:
Cleaned dataset
Automating the data cleaning process, includes, systematically creating all the required functions and using them to solve the purpose as per the need. Some of the key ones and their code is explained in this article and used in the pipeline.
Finally concluding, using a detailed pipeline and standardizing the data-cleaning process can help save time and increase the efficiency of the process. The standard functions can be used as per the requirement once a pipeline has been created leaving a lesser chance for an error.
Q1. What is Data Cleaning?
Answer:
Data Cleaning is the process of retaining only the crucial information from the output so that only relevant features are sent as input to the machine learning model.
Q2. Why is data cleaning important?
Answer:
Data cleaning is an important step to make sure that the data or information passed to a machine learning model or used for a data science task is cleaned and does not contain any unrequired information.
Q3. Can data cleaning be automated?
Answer:
Yes, data cleaning can be automated using programming languages like Python. This not only helps in aligning the process but also saves a tonne of time that is spent time and again in rewriting a cleaning script for every new piece of data.
Q4. What are some common techniques used for data cleaning?
Answer:
Some common techniques used for data cleaning include identifying and handling missing values, removing duplicates, correcting inconsistent values, and handling outliers.
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