Pandas for Machine Learning

Data manipulation using the Pandas library.

Goku Mohandas

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Set up

First we'll import the NumPy and Pandas libraries and set seeds for reproducibility. We'll also download the dataset we'll be working with to disk.

import numpy as np
import pandas as pd

# Set seed for reproducibility
np.random.seed(seed=1234)

Load data

We're going to work with the Titanic dataset which has data on the people who embarked the RMS Titanic in 1912 and whether they survived the expedition or not. It's a very common and rich dataset which makes it very apt for exploratory data analysis with Pandas.

Let's load the data from the CSV file into a Pandas dataframe. The header=0 signifies that the first row (0th index) is a header row which contains the names of each column in our dataset.

# Read from CSV to Pandas DataFrame
url = "https://raw.githubusercontent.com/GokuMohandas/Made-With-ML/main/datasets/titanic.csv"
df = pd.read_csv(url, header=0)

# First few items
df.head(3)

	pclass	name	sex	age	sibsp	parch	ticket	fare	cabin	embarked	survived
0	1	Allen, Miss. Elisabeth Walton	female	29.0000	0	0	24160	211.3375	B5	S	1
1	1	Allison, Master. Hudson Trevor	male	0.9167	1	2	113781	151.5500	C22 C26	S	1
2	1	Allison, Miss. Helen Loraine	female	2.0000	1	2	113781	151.5500	C22 C26	S	0

These are the different features:

class: class of travel
name: full name of the passenger
sex: gender
age: numerical age
sibsp: # of siblings/spouse aboard
parch: number of parents/child aboard
ticket: ticket number
fare: cost of the ticket
cabin: location of room
embarked: port that the passenger embarked at
survived: survival metric (0 - died, 1 - survived)

Exploratory data analysis (EDA)

Now that we loaded our data, we're ready to start exploring it to find interesting information.

Be sure to check out our entire lesson focused on EDA in our MLOps course.

import matplotlib.pyplot as plt

We can use .describe() to extract some standard details about our numerical features.

# Describe features
df.describe()

	pclass	age	sibsp	parch	fare	survived
count	1309.000000	1046.000000	1309.000000	1309.000000	1308.000000	1309.000000
mean	2.294882	29.881135	0.498854	0.385027	33.295479	0.381971
std	0.837836	14.413500	1.041658	0.865560	51.758668	0.486055
min	1.000000	0.166700	0.000000	0.000000	0.000000	0.000000
25%	2.000000	21.000000	0.000000	0.000000	7.895800	0.000000
50%	3.000000	28.000000	0.000000	0.000000	14.454200	0.000000
75%	3.000000	39.000000	1.000000	0.000000	31.275000	1.000000
max	3.000000	80.000000	8.000000	9.000000	512.329200	1.000000

# Correlation matrix
plt.matshow(df.corr())
continuous_features = df.describe().columns
plt.xticks(range(len(continuous_features)), continuous_features, rotation="45")
plt.yticks(range(len(continuous_features)), continuous_features, rotation="45")
plt.colorbar()
plt.show()

We can also use .hist() to view the histogram of values for each feature.

# Histograms
df["age"].hist()

# Unique values
df["embarked"].unique()

array(['S', 'C', nan, 'Q'], dtype=object)

Filtering

We can filter our data by features and even by specific values (or value ranges) within specific features.

# Selecting data by feature
df["name"].head()

0                      Allen, Miss. Elisabeth Walton
1                     Allison, Master. Hudson Trevor
2                       Allison, Miss. Helen Loraine
3               Allison, Mr. Hudson Joshua Creighton
4    Allison, Mrs. Hudson J C (Bessie Waldo Daniels)
Name: name, dtype: object

# Filtering
df[df["sex"]=="female"].head() # only the female data appear

	pclass	name	sex	age	sibsp	parch	ticket	fare	cabin	embarked	survived
0	1	Allen, Miss. Elisabeth Walton	female	29.0	0	0	24160	211.3375	B5	S	1
2	1	Allison, Miss. Helen Loraine	female	2.0	1	2	113781	151.5500	C22 C26	S	0
4	1	Allison, Mrs. Hudson J C (Bessie Waldo Daniels)	female	25.0	1	2	113781	151.5500	C22 C26	S	0
6	1	Andrews, Miss. Kornelia Theodosia	female	63.0	1	0	13502	77.9583	D7	S	1
8	1	Appleton, Mrs. Edward Dale (Charlotte Lamson)	female	53.0	2	0	11769	51.4792	C101	S	1

Sorting

We can also sort our features in ascending or descending order.

# Sorting
df.sort_values("age", ascending=False).head()

	pclass	name	sex	age	sibsp	ticket	fare	cabin	embarked	survived
14	1	Barkworth, Mr. Algernon Henry Wilson	male	80.0	0	27042	30.0000	A23	S	1
61	1	Cavendish, Mrs. Tyrell William (Julia Florence...	female	76.0	1	19877	78.8500	C46	S	1
1235	3	Svensson, Mr. Johan	male	74.0	0	347060	7.7750	NaN	S	0
135	1	Goldschmidt, Mr. George B	male	71.0	0	PC 17754	34.6542	A5	C	0
9	1	Artagaveytia, Mr. Ramon	male	71.0	0	PC 17609	49.5042	NaN	C	0

Grouping

We can also get statistics across our features for certain groups. Here we wan to see the average of our continuous features based on whether the passenger survived or not.

# Grouping
survived_group = df.groupby("survived")
survived_group.mean()

survived	pclass	age	sibsp	parch	fare
0	2.500618	30.545369	0.521632	0.328801	23.353831
1	1.962000	28.918228	0.462000	0.476000	49.361184

Indexing

We can use iloc to get rows or columns at particular positions in the dataframe.

# Selecting row 0
df.iloc[0, :]

pclass                                  1
name        Allen, Miss. Elisabeth Walton
sex                                female
age                                    29
sibsp                                   0
parch                                   0
ticket                              24160
fare                              211.338
cabin                                  B5
embarked                                S
survived                                1
Name: 0, dtype: object

# Selecting a specific value
df.iloc[0, 1]

'Allen, Miss. Elisabeth Walton'

Preprocessing

After exploring, we can clean and preprocess our dataset.

Be sure to check out our entire lesson focused on preprocessing in our MLOps course.

# Rows with at least one NaN value
df[pd.isnull(df).any(axis=1)].head()

	pclass	name	sex	age	ticket	fare	cabin	embarked	survived
9	1	Artagaveytia, Mr. Ramon	male	71.0	PC 17609	49.5042	NaN	C	0
13	1	Barber, Miss. Ellen "Nellie"	female	26.0	19877	78.8500	NaN	S	1
15	1	Baumann, Mr. John D	male	NaN	PC 17318	25.9250	NaN	S	0
23	1	Bidois, Miss. Rosalie	female	42.0	PC 17757	227.5250	NaN	C	1
25	1	Birnbaum, Mr. Jakob	male	25.0	13905	26.0000	NaN	C	0

# Drop rows with Nan values
df = df.dropna() # removes rows with any NaN values
df = df.reset_index() # reset's row indexes in case any rows were dropped
df.head()

	index	pclass	name	sex	age	sibsp	parch	ticket	fare	cabin	embarked	survived
0	0	1	Allen, Miss. Elisabeth Walton	female	29.0000	0	0	24160	211.3375	B5	S	1
1	1	1	Allison, Master. Hudson Trevor	male	0.9167	1	2	113781	151.5500	C22 C26	S	1
2	2	1	Allison, Miss. Helen Loraine	female	2.0000	1	2	113781	151.5500	C22 C26	S	0
3	3	1	Allison, Mr. Hudson Joshua Creighton	male	30.0000	1	2	113781	151.5500	C22 C26	S	0
4	4	1	Allison, Mrs. Hudson J C (Bessie Waldo Daniels)	female	25.0000	1	2	113781	151.5500	C22 C26	S	0

# Dropping multiple columns
df = df.drop(["name", "cabin", "ticket"], axis=1) # we won't use text features for our initial basic models
df.head()

	index	pclass	sex	age	sibsp	parch	fare	embarked	survived
0	0	1	female	29.0000	0	0	211.3375	S	1
1	1	1	male	0.9167	1	2	151.5500	S	1
2	2	1	female	2.0000	1	2	151.5500	S	0
3	3	1	male	30.0000	1	2	151.5500	S	0
4	4	1	female	25.0000	1	2	151.5500	S	0

# Map feature values
df["sex"] = df["sex"].map( {"female": 0, "male": 1} ).astype(int)
df["embarked"] = df["embarked"].dropna().map( {"S":0, "C":1, "Q":2} ).astype(int)
df.head()

	index	pclass	sex	age	sibsp	parch	fare	survived
0	0	1	0	29.0000	0	0	211.3375	1
1	1	1	1	0.9167	1	2	151.5500	1
2	2	1	0	2.0000	1	2	151.5500	0
3	3	1	1	30.0000	1	2	151.5500	0
4	4	1	0	25.0000	1	2	151.5500	0

Feature engineering

We're now going to use feature engineering to create a column called family_size. We'll first define a function called get_family_size that will determine the family size using the number of parents and siblings.

# Lambda expressions to create new features
def get_family_size(sibsp, parch):
    family_size = sibsp + parch
    return family_size

Once we define the function, we can use lambda to apply that function on each row (using the numbers of siblings and parents in each row to determine the family size for each row).

df["family_size"] = df[["sibsp", "parch"]].apply(lambda x: get_family_size(x["sibsp"], x["parch"]), axis=1)
df.head()

	index	pclass	sex	age	sibsp	parch	fare	survived	family_size
0	0	1	0	29.0000	0	0	211.3375	1	0
1	1	1	1	0.9167	1	2	151.5500	1	3
2	2	1	0	2.0000	1	2	151.5500	0	3
3	3	1	1	30.0000	1	2	151.5500	0	3
4	4	1	0	25.0000	1	2	151.5500	0	3

# Reorganize headers
df = df[["pclass", "sex", "age", "sibsp", "parch", "family_size", "fare", '"mbarked", "survived"]]
df.head()

	pclass	sex	age	sibsp	parch	family_size	fare	survived
0	1	0	29.0000	0	0	0	211.3375	1
1	1	1	0.9167	1	2	3	151.5500	1
2	1	0	2.0000	1	2	3	151.5500	0
3	1	1	30.0000	1	2	3	151.5500	0
4	1	0	25.0000	1	2	3	151.5500	0

Tip

Feature engineering can be done in collaboration with domain experts that can guide us on what features to engineer and use.

Save data

Finally, let's save our preprocessed data into a new CSV file to use later.

# Saving dataframe to CSV
df.to_csv("processed_titanic.csv", index=False)

# See the saved file
!ls -l

total 96
-rw-r--r-- 1 root root  6975 Dec  3 17:36 processed_titanic.csv
drwxr-xr-x 1 root root  4096 Nov 21 16:30 sample_data
-rw-r--r-- 1 root root 85153 Dec  3 17:36 titanic.csv

Scaling

When working with very large datasets, our Pandas DataFrames can become very large and it can be very slow or impossible to operate on them. This is where packages that can distribute workloads or run on more efficient hardware can come in handy.

Dask: parallel computing to scale packages like Numpy, Pandas and scikit-learn on one/multiple machines.
cuDF: efficient dataframe loading and computation on a GPU.

And, of course, we can combine these together (Dask-cuDF) to operate on partitions of a dataframe on the GPU.

To cite this content, please use:

@article{madewithml,
    author       = {Goku Mohandas},
    title        = { Pandas - Made With ML },
    howpublished = {\url{https://madewithml.com/}},
    year         = {2023}
}