Making pandas Operations Faster

Jul 8, 2017  

pandas is one of the most commonly used Python library in data analysis and machine learning. It is versatile and can be used to handle many different types of data. Before feeding a model with training data, one would most probably pre-process the data and perform feature extraction on data stored as pandas DataFrame. I have been using pandas extensively in my work, and have recently discovered that the time required to manipulate data stored in a DataFrame can vary hugely depending on the method you used.

Numerical Operations

To demonstrate the differences, let’s generate some random data first. The following block of code will generate a DataFrame with 5,000 rows and 3 columns (A, B and C) with values ranging from -10 to 10.

In [1]: import pandas as pd
In [2]: import numpy as np
In [3]: data = np.random.randint(-10, 10, (5000, 3))
In [4]: df = pd.DataFrame(data=data, columns=["A", "B", "C"], index=None)

To track the time required to finish an operation, we can make use of the IPython magic function %timeit to measure the time required to execute a line in Python.

To start with, let’s consider a simple task of creating a new column in the DataFrame, whose values depend on whether the sum of the values in other columns are greater than zero. First, let’s try using the apply function of the DataFrame:

In [5]: %timeit df["D"] = df.apply(lambda x: 1 if x["A"] + x["B"] + x["C"] > 0 else 0, axis=1)
134 ms ± 1.59 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)

It takes about 134ms to finish the operation, which seems quite fast. However, if we take another approach by using numpy’s where() function, we can actually be much faster:

In [6]: %timeit df["E"] = np.where(df["A"] + df["B"] + df["C"] > 0, 1, 0)
757 µs ± 38.8 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

This is ~170 times faster! We can verified that the two methods actually give the same results as follows. (np.any checks if any of the values in a list is True).

In [7]: np.any(df["D"] != df["E"])
False

String Operations

As another example, let’s try searching substrings in a column. Firstly, let’s generate some random text data in a new column:

In [8]: df["F"] = np.random.choice(["apple", "banana", "orange", "pear"], 5000)

Let’s say we want to create a new column, whose values depend on whether Column F contains the substring an. Firstly, let’s try the apply function:

In [9]: %timeit df["G"] = df.apply(lambda x: 1 if "an" in x["F"] else 0, axis=1)
61.1 ms ± 685 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

Now, if we use the second approach:

In [10]: %timeit df["H"] = np.where(df["F"].str.contains("an"), 1, 0)
2.65 ms ± 40.9 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

which is ~30 times faster.

The conclusion is that whenever we can operate on the whole column, we should avoid using apply, which is looping over every row of the DataFrame, and is not able to take advantage of numpy vectorization when performing the calculation.