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Hands-On Guide to Datatable Library For Faster EDA

Hands-On Guide to Datatable Library For Faster EDA

Jayita Bhattacharyya
Datatable

Working with tabular data in data science we always use the Pandas library in Python. This is widely used for data exploration, analysis, munging and manipulation. These are the primary steps for understanding the data well and making it ready for the model to fit. The only disadvantage of using pandas is its time consuming when there’s a large amount of data(big data).

Datatable overcomes the limitations of pandas and speeds up the process of EDA(exploratory data analysis). Datatable has been built by H20.ai, one of the leading AI ML companies in the world. Datatable is pretty similar to pandas and R data.table libraries. Datatable has proper documentation. Works with Python version 3.6+.

Advantages of Datatable

  • Supports null values, date-time and categorical types.
  • Efficient algorithms for sorting/grouping/joining.
  • Minimal data copying by using “rowindex” views in filtering/sorting/grouping/joining 
  • operators to avoid unnecessary data copying.Faster data accessing than pandas 
  • Easily convert to another data-processing framework.

In this article, I’ll be discussing the implementation of the datatable library with a large dataset.

Installing datatable

pip install datatable



DatasetCredit Card Fraud Detection

The dataset contains transactions that have been made by credit cards in September 2013 by European cardholders. This dataset shows transactions that occurred in two days, where we have 492 frauds out of 284,807 transactions. A total of 31 features are time, class, amount and  V1 to V28.

Reading files

With pandas:

import pandas as pd
start = time.time()
pandas_df = pd.read_csv('../input/creditcardfraud/creditcard.csv')
end = time.time()
print(end - start)

3.0183897018432617


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With datatable:

import datatable as dt
import time
start = time.time()
df = dt.fread('../input/creditcardfraud/creditcard.csv')end = time.time()
print(end - start)

0.30858349800109863

Clearly, datatable performs much better than pandas. Datatable takes 30 milliseconds to fetch the data whereas pandas take more than 3 seconds. 

fread() -> datatable parser for text(csv) 

  • Automatically detects column types, quoting rules, separators, headers, etc.
  • Reads from the file, raw text, archives, glob, URL, shell.
  • Provides multithreaded file reading facility.
  • Includes a progress indicator while reading large files.

Dataset size:

print(df.shape) 

(284807, 31)

Feature Column names

print(df.names)

(‘Time’, ‘V1’, ‘V2’, ‘V3’, ‘V4’, ‘V5’, ‘V6’, ‘V7’, ‘V8’, ‘V9’, ‘V10’, ‘V11’, ‘V12’, ‘V13’, ‘V14’, ‘V15’, ‘V16’, ‘V17’, ‘V18’, ‘V19’, ‘V20’, ‘V21’, ‘V22’, ‘V23’, ‘V24’, ‘V25’, ‘V26’, ‘V27’, ‘V28’, ‘Amount’, ‘Class’)

df.head() -> displays the first 10 rows of the dataset in a compact mode as shown below.

Column Types

print(df.stypes) 

(stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.float64, stype.bool8)

Convert to numpy array

np_arr = df.to_numpy()

Convert to pandas 

df_pd = df.to_pandas()

Convert to python list object

py_obj = df.to_list()

Statistical functions

df.sum()- returns sum of all values in specified column
df.max()- returns maximum value in specified column
df.min()- returns minimum value in specified column
df.mean()- returns mean(average) of values from a column
df.sd()- returns standard deviation of a column
df.mode()- return mode from a column

Sorting Frame -> sort() function sorts the row by the column defined in ascending order.

With pandas:

start = time.time()
pandas_df.sort_values(by="Amount")
end = time.time()
print(end - start)

0.14470458030700684

With datatable:

start = time.time()
df.sort("Amount")
end = time.time()
print(end - start)

0.03646421432495117

See Also

GroupBy

Let us get the mean amount for each V1 feature. In datatable, operations of a Frame can be represented as dt[i,j,…] where i is row selector, j is column selector and .. are other modifiers. Derived from matrix notations.

start = time.time()
for i in range(500):
    pandas_df.groupby("V1")["Amount"].sum()
end = time.time()
print(end - start)

48.4233283996582

start = time.time()
for i in range(10):
    df[:, dt.sum(dt.f.Amount), dt.by(dt.f.V1)]
end = time.time()
print(end - start)

16.062947988510132

.f in dt.f means frame proxy referring to currently calling frame.

Here Datatable takes 1/4th the time of pandas.

Appending rows/columns to Frames:

cbind() for binding columns and rbind() for binding rows to existing Frame.

df.cbind(col1, col2)
df.rbind(rowname, force=True)

Deleting a column

del df[:, 'V27']

Saving Frames

Saving Frame in disk as binary format and opening it later instantly

df.to_jay("out.jay")
df_dt = dt.open("out.jay")

Write the Frame

df.to_csv(“out.csv”)

Conclusion

Datatable has a similar syntax to pandas and provides predominantly better performance speed for all operations. Datatable covers almost all types of text and tabular data formats.

Highly efficient when working with large amounts of data(having 100GB in RAM). Active contributions and development is going onto datatable as in some advanced functionalities it lacks as compared to pandas. 

The complete code of the above implementation is available at the AIM’s GitHub repository. Please visit this link to find the notebook of this code.

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