Handling Missing Values in Machine Learning with Python
Handling missing values is a crucial step in preparing data for machine learning. This tutorial provides examples of how to manage missing values using Python, focusing on the Pandas library. We'll import the necessary libraries, read the data, and explore various methods to handle missing values.
You can check the full code in the Jupyter Notebook
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Importing Libraries
We begin by importing the necessary libraries for our data manipulation and analysis tasks.
import numpy as np
import pandas as pd- NumPy: A fundamental package for scientific computing in Python. It provides support for arrays, matrices, and numerous mathematical functions.
- Pandas: A powerful data manipulation and analysis library that provides data structures and functions needed to work with structured data seamlessly.
References:
Reading the Data
We read the CSV file containing the NFL play-by-play data.
data = pd.read_csv("./NFLPlayByPlay2009-2017_v4.csv")You can download the dataset from the Kaggle website
During the import, a warning indicates that some columns have mixed data types. This can be addressed by specifying the dtype option or setting low_memory=False.
Output:
/tmp/ipykernel_23803/1150844578.py:1: DtypeWarning: Columns (25,51) have mixed types. Specify dtype option on import or set low_memory=False.
data = pd.read_csv("./NFLPlayByPlay2009-2017_v4.csv")References:
Inspecting the Data
To get an overview of the data format, we inspect the first few rows of the dataframe.
data.head()Output:
Date GameID Drive qtr down time TimeUnder TimeSecs PlayTimeDiff SideofField ... yacEPA Home_WP_pre Away_WP_pre Home_WP_post Away_WP_post Win_Prob WPA airWPA yacWPA Season
0 2009-09-10 2009091000 1 1 NaN 15:00 15 3600 0.0 TEN ... NaN 0.485675 0.514325 0.546433 0.453567 0.485675 0.060758 NaN NaN 2009
1 2009-09-10 2009091000 1 1 1.0 14:53 15 3593 7.0 PIT ... 1.146076 0.546433 0.453567 0.551088 0.448912 0.546433 0.004655 -0.032244 0.036899 2009
2 2009-09-10 2009091000 1 1 2.0 14:16 15 3556 37.0 PIT ... NaN 0.551088 0.448912 0.510793 0.489207 0.551088 -0.040295 NaN NaN 2009
3 2009-09-10 2009091000 1 1 3.0 13:35 14 3515 41.0 PIT ... -5.031425 0.510793 0.489207 0.461217 0.538783 0.510793 -0.049576 0.106663 -0.156239 2009
4 2009-09-10 2009091000 1 1 4.0 13:27 14 3507 8.0 PIT ... NaN 0.461217 0.538783 0.558929 0.441071 0.461217 0.097712 NaN NaN 2009Counting Missing Values
We calculate the number of missing values in each column.
missing_values_per_column = data.isnull().sum()
missing_values_per_column[0:10] # taking the first ten columnsOutput:
Date 0
GameID 0
Drive 0
qtr 0
down 61154
time 224
TimeUnder 0
TimeSecs 224
PlayTimeDiff 444
SideofField 528
dtype: int64Total Missing Values
To understand the proportion of missing data, we calculate the total number of cells and the percentage of missing values.
total_cells = np.product(data.shape)
total_missing = missing_values_per_column.sum()
print('total_missing', total_missing)
print('total_cells', total_cells)
print('percentage missing', (total_missing / total_cells) * 100)Output:
total_missing 11505187
total_cells 41584176
percentage missing 27.66722370547874Counting Non-Missing Values
We can also count the non-missing values in each column.
data[:].count()Output:
Date 407688
GameID 407688
Drive 407688
qtr 407688
down 346534
...
Win_Prob 382679
WPA 402147
airWPA 159187
yacWPA 158926
Season 407688
Length: 102, dtype: int64Removing Rows with Missing Values
While not recommended, one way to handle missing values is to remove rows that contain them.
removed_rows_empty_data = data.dropna()
print(removed_rows_empty_data)Output:
Empty DataFrame
Columns: [Date, GameID, Drive, qtr, down, time, TimeUnder, TimeSecs, PlayTimeDiff, SideofField, yrdln, yrdline100, ydstogo, ydsnet, GoalToGo, FirstDown, posteam, DefensiveTeam, desc, PlayAttempted, Yards.Gained, sp, Touchdown, ExPointResult, TwoPointConv, DefTwoPoint, Safety, Onsidekick, PuntResult, PlayType, Passer, Passer_ID, PassAttempt, PassOutcome, PassLength, AirYards, YardsAfterCatch, QBHit, PassLocation, InterceptionThrown, Interceptor, Rusher, Rusher_ID, RushAttempt, RunLocation, RunGap, Receiver, Receiver_ID, Reception, ReturnResult, Returner, BlockingPlayer, Tackler1, Tackler2, FieldGoalResult, FieldGoalDistance, Fumble, RecFumbTeam, RecFumbPlayer, Sack, Challenge.Replay, ChalReplayResult, Accepted.Penalty, PenalizedTeam, PenaltyType, PenalizedPlayer, Penalty.Yards, PosTeamScore, DefTeamScore, ScoreDiff, AbsScoreDiff, HomeTeam, AwayTeam, Timeout_Indicator, Timeout_Team, posteam_timeouts_pre, HomeTimeouts_Remaining_Pre, AwayTimeouts_Remaining_Pre, HomeTimeouts_Remaining_Post, AwayTimeouts_Remaining_Post, No_Score_Prob, Opp_Field_Goal_Prob, Opp_Safety_Prob, Opp_Touchdown_Prob, Field_Goal_Prob, Safety_Prob, Touchdown_Prob, ExPoint_Prob, TwoPoint_Prob, ExpPts, EPA, airEPA, yacEPA, Home_WP_pre, Away_WP_pre, Home_WP_post, Away_WP_post, Win_Prob, WPA, airWPA, yacWPA, ...]
Index: []
[0 rows x 102 columns]Removing Columns with Missing Values
A more common approach is to remove columns that contain missing values.
removed_columns_empty_data = data.dropna(axis=1)
print(removed_columns_empty_data)Output:
Date GameID Drive qtr TimeUnder ydstogo ydsnet PlayAttempted Yards.Gained sp ... AwayTeam Timeout_Indicator posteam_timeouts_pre HomeTimeouts_Remaining_Pre AwayTimeouts_Remaining_Pre HomeTimeouts_Remaining_Post AwayTimeouts_Remaining_Post ExPoint_Prob TwoPoint_Prob Season
0 2009-09-10 2009091000 1 1 15 0 0 1 39 0 ... TEN 0 3 3 3 3 3 0.0 0.0 2009
1 2009-09-10 2009091000 1 1 15 10 5
1 5 0 ... TEN 0 3 3 3 3 3 0.0 0.0 2009
2 2009-09-10 2009091000 1 1 15 5 2 1 -3 0 ... TEN 0 3 3 3 3 3 0.0 0.0 2009
3 2009-09-10 2009091000 1 1 14 8 2 1 0 0 ... TEN 0 3 3 3 3 3 0.0 0.0 2009
4 2009-09-10 2009091000 1 1 14 8 2 1 0 0 ... TEN 0 3 3 3 3 3 0.0 0.0 2009
... ... ... ... ... ... ... ... ... ... .. ... ... ... ... ... ... ... ... ... ... ...
407683 2017-12-31 2017123101 29 4 1 0 -4 1 0 0 ... CIN 1 0 3 0 2 0 0.0 0.0 2017
407684 2017-12-31 2017123101 29 4 1 14 -4 1 0 0 ... CIN 0 2 2 0 2 0 0.0 0.0 2017
407685 2017-12-31 2017123101 29 4 1 14 9 1 13 0 ... CIN 0 2 2 0 2 0 0.0 0.0 2017
407686 2017-12-31 2017123101 30 4 1 10 -1 1 -1 0 ... CIN 0 0 2 0 2 0 0.0 0.0 2017
407687 2017-12-31 2017123101 30 4 0 0 -1 1 0 0 ... CIN 0 0 2 0 2 0 0.0 0.0 2017
[407688 rows x 37 columns]We then calculate the impact of this operation by comparing the number of columns before and after.
print("original columns: %d \n" % data.shape[1])
print("cleaned columns: %d \n" % removed_columns_empty_data.shape[1])Output:
original columns: 102
cleaned columns: 37Subsetting the Data
To focus on a smaller portion of the dataset, we can create a subset.
subset_nfl_data = data.loc[:, 'EPA':'Season'].head()
subset_nfl_dataOutput:
EPA airEPA yacEPA Home_WP_pre Away_WP_pre Home_WP_post Away_WP_post Win_Prob WPA airWPA yacWPA Season
0 2.014474 NaN NaN 0.485675 0.514325 0.546433 0.453567 0.485675 0.060758 NaN NaN 2009
1 0.077907 -1.068169 1.146076 0.546433 0.453567 0.551088 0.448912 0.546433 0.004655 -0.032244 0.036899 2009
2 -1.402760 NaN NaN 0.551088 0.448912 0.510793 0.489207 0.551088 -0.040295 NaN NaN 2009
3 -1.712583 3.318841 -5.031425 0.510793 0.489207 0.461217 0.538783 0.510793 -0.049576 0.106663 -0.156239 2009
4 2.097796 NaN NaN 0.461217 0.538783 0.558929 0.441071 0.461217 0.097712 NaN NaN 2009Basic Filling of Missing Values
A straightforward method for handling missing values is to fill them with a specific value, such as zero.
filled_basic_data = data.fillna(0)
filled_basic_data.head()Output:
Date GameID Drive qtr down time TimeUnder TimeSecs PlayTimeDiff SideofField ... yacEPA Home_WP_pre Away_WP_pre Home_WP_post Away_WP_post Win_Prob WPA airWPA yacWPA Season
0 2009-09-10 2009091000 1 1 0.0 15:00 15 3600 0.0 TEN ... 0.000000 0.485675 0.514325 0.546433 0.453567 0.485675 0.060758 0.000000 0.000000 2009
1 2009-09-10 2009091000 1 1 1.0 14:53 15 3593 7.0 PIT ... 1.146076 0.546433 0.453567 0.551088 0.448912 0.546433 0.004655 -0.032244 0.036899 2009
2 2009-09-10 2009091000 1 1 2.0 14:16 15 3556 37.0 PIT ... 0.000000 0.551088 0.448912 0.510793 0.489207 0.551088 -0.040295 0.000000 0.000000 2009
3 2009-09-10 2009091000 1 1 3.0 13:35 14 3515 41.0 PIT ... -5.031425 0.510793 0.489207 0.461217 0.538783 0.510793 -0.049576 0.106663 -0.156239 2009
4 2009-09-10 2009091000 1 1 4.0 13:27 14 3507 8.0 PIT ... 0.000000 0.461217 0.538783 0.558929 0.441071 0.461217 0.097712 0.000000 0.000000 2009Column-Based Filling
Another approach is to fill missing values based on the next valid observation in the column.
column_based_fill = data.bfill(axis=0).fillna(0)
column_based_fill.head()Output:
Date GameID Drive qtr down time TimeUnder TimeSecs PlayTimeDiff SideofField ... yacEPA Home_WP_pre Away_WP_pre Home_WP_post Away_WP_post Win_Prob WPA airWPA yacWPA Season
0 2009-09-10 2009091000 1 1 1.0 15:00 15 3600 0.0 TEN ... 1.146076 0.485675 0.514325 0.546433
0.453567 0.485675 0.060758 -0.032244 0.036899 2009
1 2009-09-10 2009091000 1 1 1.0 14:53 15 3593 7.0 PIT ... 1.146076 0.546433 0.453567 0.551088 0.448912 0.546433 0.004655 -0.032244 0.036899 2009
2 2009-09-10 2009091000 1 1 2.0 14:16 15 3556 37.0 PIT ... -5.031425 0.551088 0.448912 0.510793 0.489207 0.551088 -0.040295 0.106663 -0.156239 2009
3 2009-09-10 2009091000 1 1 3.0 13:35 14 3515 41.0 PIT ... -5.031425 0.510793 0.489207 0.461217 0.538783 0.510793 -0.049576 0.106663 -0.156239 2009
4 2009-09-10 2009091000 1 1 4.0 13:27 14 3507 8.0 PIT ... 0.163935 0.461217 0.538783 0.558929 0.441071 0.461217 0.097712 -0.010456 0.006029 2009References:
These steps provide a comprehensive guide to identifying and handling missing values in a dataset, ensuring the data is ready for analysis and modeling. Each method has its pros and cons, and the choice of method depends on the specific context and requirements of your analysis.
Extra exercise from kaggle
This notebook is an exercise in the Data Cleaning course. You can reference the tutorial at this link.
In this exercise, you'll apply what you learned in the Handling missing values tutorial.
1) Take a first look at the data
Run the next code cell to load in the libraries and dataset you'll use to complete the exercise.
# modules we'll use
import pandas as pd
import numpy as np
# read in all our data
sf_permits = pd.read_csv("./Building_Permits.csv")
# set seed for reproducibility
np.random.seed(0)
/tmp/ipykernel_33/3534875831.py:6: DtypeWarning: Columns (22,32) have mixed types. Specify dtype option on import or set low_memory=False. sf_permits = pd.read_csv("../input/building-permit-applications-data/Building_Permits.csv")
You can download the dataset from the Kaggle website.
Use the code cell below to print the first five rows of the sf_permits DataFrame.
# TODO: Your code here!
sf_permits.head()| Permit Number | Permit Type | Permit Type Definition | Permit Creation Date | Block | Lot | Street Number | Street Number Suffix | Street Name | Street Suffix | ... | Existing Construction Type | Existing Construction Type Description | Proposed Construction Type | Proposed Construction Type Description | Site Permit | Supervisor District | Neighborhoods - Analysis Boundaries | Zipcode | Location | Record ID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 201505065519 | 4 | sign - erect | 05/06/2015 | 0326 | 023 | 140 | NaN | Ellis | St | ... | 3.0 | constr type 3 | NaN | NaN | NaN | 3.0 | Tenderloin | 94102.0 | (37.785719256680785, -122.40852313194863) | 1380611233945 |
| 1 | 201604195146 | 4 | sign - erect | 04/19/2016 | 0306 | 007 | 440 | NaN | Geary | St | ... | 3.0 | constr type 3 | NaN | NaN | NaN | 3.0 | Tenderloin | 94102.0 | (37.78733980600732, -122.41063199757738) | 1420164406718 |
| 2 | 201605278609 | 3 | additions alterations or repairs | 05/27/2016 | 0595 | 203 | 1647 | NaN | Pacific | Av | ... | 1.0 | constr type 1 | 1.0 | constr type 1 | NaN | 3.0 | Russian Hill | 94109.0 | (37.7946573324287, -122.42232562979227) | 1424856504716 |
| 3 | 201611072166 | 8 | otc alterations permit | 11/07/2016 | 0156 | 011 | 1230 | NaN | Pacific | Av | ... | 5.0 | wood frame (5) | 5.0 | wood frame (5) | NaN | 3.0 | Nob Hill | 94109.0 | (37.79595867909168, -122.41557405519474) | 1443574295566 |
| 4 | 201611283529 | 6 | demolitions | 11/28/2016 | 0342 | 001 | 950 | NaN | Market | St | ... | 3.0 | constr type 3 | NaN | NaN | NaN | 6.0 | Tenderloin | 94102.0 | (37.78315261897309, -122.40950883997789) | 144548169992 |
5 rows × 43 columns
The first five rows of the data does show that several columns have missing values. You can see this in the "Street Number Suffix", "Proposed Construction Type" and "Site Permit" columns, among others.
2) How many missing data points do we have?
What percentage of the values in the dataset are missing? Your answer should be a number between 0 and 100. (If 1/4 of the values in the dataset are missing, the answer is 25.)
# TODO: Your code here!
total_cells = np.product(sf_permits.shape)
missing_values_count = sf_permits.isnull().sum();
total_missing_cells = missing_values_count.sum();
# print("shape", sf_permits.shape)
print('total cells', total_cells)
# print('total missing per column', missing_values_count)
print('total missing cells', total_missing_cells)
percent_missing = (total_missing_cells / total_cells) * 100
print('percent missing', percent_missing)
total cells 8552700 total missing cells 2245941 percent missing 26.26002315058403
Correct3) Figure out why the data is missing
Look at the columns "Street Number Suffix" and "Zipcode" from the San Francisco Building Permits dataset. Both of these contain missing values.
- Which, if either, are missing because they don't exist?
- Which, if either, are missing because they weren't recorded?
Once you have an answer, run the code cell below.
Correct:If a value in the "Street Number Suffix" column is missing, it is likely because it does not exist. If a value in the "Zipcode" column is missing, it was not recorded.
4) Drop missing values: rows
If you removed all of the rows of sf_permits with missing values, how many rows are left?
Note: Do not change the value of sf_permits when checking this.
# TODO: Your code here!
total_rows = sf_permits.shape[0]
total_rows_after_drop= sf_permits.dropna().shape[0]
print(total_rows)
print(total_rows_after_drop) # no rows198900 0
Correct:There are no rows remaining in the dataset!
5) Drop missing values: columns
Now try removing all the columns with empty values.
- Create a new DataFrame called
sf_permits_with_na_droppedthat has all of the columns with empty values removed. - How many columns were removed from the original
sf_permitsDataFrame? Use this number to set the value of thedropped_columnsvariable below.
sf_permits_with_na_dropped = sf_permits.dropna(axis=1)
dropped_columns = sf_permits.shape[1] - sf_permits_with_na_dropped.shape[1]6) Fill in missing values automatically
Try replacing all the NaN's in the sf_permits data with the one that comes directly after it and then replacing any remaining NaN's with 0. Set the result to a new DataFrame sf_permits_with_na_imputed.
sf_permits_with_na_imputed = sf_permits.bfill(axis=0).fillna(0)More practice
- Check out this noteboook on handling missing values using scikit-learn's imputer.
- Look back at the "Zipcode" column in the
sf_permitsdataset, which has some missing values. How would you go about figuring out what the actual zipcode of each address should be? (You might try using another dataset. You can search for datasets about San Fransisco on the Datasets listing.)