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A Complete Machine Learning Project Walk-Through in Python

Updated: Jul 2, 2019

By Dylan Iqbal

A Complete Machine Learning Project Walk-Through in Python (Part One): Putting the machine learning pieces together

Reading through a data science book or taking a course, it can feel like you have the individual pieces, but don’t quite know how to put them together. Taking the next step and solving a complete machine learning problem can be daunting, but preserving and completing a first project will give you the confidence to tackle any data science problem. This series of articles will walk through a complete machine learning solution with a real-world dataset to let you see how all the pieces come together.

We’ll follow the general machine learning workflow step-by-step:

  1. Data cleaning and formatting

  2. Exploratory data analysis

  3. Feature engineering and selection

  4. Compare several machine learning models on a performance metric

  5. Perform hyperparameter tuning on the best model

  6. Evaluate the best model on the testing set

  7. Interpret the model results

  8. Draw conclusions and document work

Along the way, we’ll see how each step flows into the next and how to specifically implement each part in Python. The complete project is available on GitHub, with the first notebook here.

Problem Definition

The first step before we get coding is to understand the problem we are trying to solve and the available data. In this project, we will work with publicly available building energy data from New York City.

The objective is to use the energy data to build a model that can predict the Energy Star Score of a building and interpret the results to find the factors which influence the score.

The data includes the Energy Star Score, which makes this a supervised regression machine learning task:

  • Supervised: we have access to both the features and the target and our goal is to train a model that can learn a mapping between the two

  • Regression: The Energy Star score is a continuous variable

We want to develop a model that is both **accurate **— it can predict the Energy Star Score close to the true value — and interpretable — we can understand the model predictions. Once we know the goal, we can use it to guide our decisions as we dig into the data and build models.

Data Cleaning

Contrary to what most data science courses would have you believe, not every dataset is a perfectly curated group of observations with no missing values or anomalies (looking at you mtcars and iris datasets). Real-world data is messy which means we need to clean and wrangleit into an acceptable format before we can even start the analysis. Data cleaning is an un-glamorous, but necessary part of most actual data science problems.

First, we can load in the data as a Pandas DataFrame and take a look:

import pandas as pd
import numpy as np

# Read in data into a dataframe 
data = pd.read_csv('data/Energy_and_Water_Data_Disclosure_for_Local_Law_84_2017__Data_for_Calendar_Year_2016_.csv')

# Display top of dataframe

This is a subset of the full data which contains 60 columns. Already, we can see a couple issues: first, we know that we want to predict the ENERGY STAR Score but we don’t know what any of the columns mean. While this isn’t necessarily an issue — we can often make an accurate model without any knowledge of the variables — we want to focus on interpretability, and it might be important to understand at least some of the columns.

When I originally got the assignment from the start-up, I didn’t want to ask what all the column names meant, so I looked at the name of the file,

and decided to search for “Local Law 84”. That led me to this page which explains this is an NYC law requiring all buildings of a certain size to report their energy use. More searching brought me to all the definitions of the columns. Maybe looking at a file name is an obvious place to start, but for me this was a reminder to go slow so you don’t miss anything important!

We don’t need to study all of the columns, but we should at least understand the Energy Star Score, which is described as:

A 1-to-100 percentile ranking based on self-reported energy usage for the reporting year. The Energy Star score is a relative measure used for comparing the energy efficiency of buildings.

That clears up the first problem, but the second issue is that missing values are encoded as “Not Available”. This is a string in Python which means that even the columns with numbers will be stored as object datatypes because Pandas converts a column with any strings into a column of all strings. We can see the datatypes of the columns using the

# See the column data types and non-missing values

Sure enough, some of the columns that clearly contain numbers (such as ft²), are stored as objects. We can’t do numerical analysis on strings, so these will have to be converted to number (specifically float) data types!

Here’s a little Python code that replaces all the “Not Available” entries with not a number ( np.nan), which can be interpreted as numbers, and then converts the relevant columns to the float datatype:

# Replace all occurrences of Not Available with numpy not a number
data = data.replace({'Not Available': np.nan})

# Iterate through the columns
for col in list(data.columns):
    # Select columns that should be numeric
    if ('ft²' in col or 'kBtu' in col or 'Metric Tons CO2e' in col or 'kWh' in 
        col or 'therms' in col or 'gal' in col or 'Score' in col):
        # Convert the data type to float
data[col] = data[col].astype(float)

Once the correct columns are numbers, we can start to investigate the data.

Missing Data and Outliers

In addition to incorrect datatypes, another common problem when dealing with real-world data is missing values. These can arise for many reasons and have to be either filled in or removed before we train a machine learning model. First, let’s get a sense of how many missing values are in each column (see the notebook for code).

(To create this table, I used a function from this Stack Overflow Forum).

While we always want to be careful about removing information, if a column has a high percentage of missing values, then it probably will not be useful to our model. The threshold for removing columns should depend on the problem (here is a discussion), and for this project, we will remove any columns with more than 50% missing values.

  • At this point, we may also want to remove outliers. These can be due to typos in data entry, mistakes in units, or they could be legitimate but extreme values. For this project, we will remove anomalies based on the definition of extreme outliers: Below the first quartile − 3 ∗ Above the third quartile + 3 ∗ interquartile range

(For the code to remove the columns and the anomalies, see the notebook). At the end of the data cleaning and anomaly removal process, we are left with over 11,000 buildings and 49 features.

Exploratory Data Analysis

Now that the tedious — but necessary — step of data cleaning is complete, we can move on to exploring our data! Exploratory Data Analysis (EDA) is an open-ended process where we calculate statistics and make figures to find trends, anomalies, patterns, or relationships within the data.

In short, the goal of EDA is to learn what our data can tell us. It generally starts out with a high level overview, then narrows in to specific areas as we find interesting parts of the data. The findings may be interesting in their own right, or they can be used to inform our modeling choices, such as by helping us decide which features to use.

Single Variable Plots

The goal is to predict the Energy Star Score (renamed to score in our data) so a reasonable place to start is examining the distribution of this variable. A histogram is a simple yet effective way to visualize the distribution of a single variable and is easy to make using matplotlib.

import matplotlib.pyplot as plt

# Histogram of the Energy Star Score'fivethirtyeight')
plt.hist(data['score'].dropna(), bins = 100, edgecolor = 'k');
plt.xlabel('Score'); plt.ylabel('Number of Buildings'); 
plt.title('Energy Star Score Distribution');

This looks quite suspicious! The Energy Star score is a percentile rank, which means we would expect to see a uniform distribution, with each score assigned to the same number of buildings. However, a disproportionate number of buildings have either the highest, 100, or the lowest, 1, score (higher is better for the Energy Star score).

If we go back to the definition of the score, we see that it is based on “self-reported energy usage” which might explain the very high scores. Asking building owners to report their own energy usage is like asking students to report their own scores on a test! As a result, this probably is not the most objective measure of a building’s energy efficiency.

If we had an unlimited amount of time, we might want to investigate why so many buildings have very high and very low scores which we could by selecting these buildings and seeing what they have in common. However, our objective is only to predict the score and not to devise a better method of scoring buildings! We can make a note in our report that the scores have a suspect distribution, but our main focus in on predicting the score.

Looking for Relationships

A major part of EDA is searching for relationships between the features and the target. Variables that are correlated with the target are useful to a model because they can be used to predict the target. One way to examine the effect of a categorical variable (which takes on only a limited set of values) on the target is through a density plot using the seaborn library.

A density plot can be thought of as a smoothed histogram because it shows the distribution of a single variable. We can color a density plot by class to see how a categorical variable changes the distribution. The following code makes a density plot of the Energy Star Score colored by the the type of building (limited to building types with more than 100 data points):

# Create a list of buildings with more than 100 measurements
types = data.dropna(subset=['score'])
types = types['Largest Property Use Type'].value_counts()
types = list(types[types.values > 100].index)

# Plot of distribution of scores for building categories
figsize(12, 10)

# Plot each building
for b_type in types:
    # Select the building type
    subset = data[data['Largest Property Use Type'] == b_type]
    # Density plot of Energy Star scores
               label = b_type, shade = False, alpha = 0.8);
# label the plot
plt.xlabel('Energy Star Score', size = 20); plt.ylabel('Density', size = 20); 
plt.title('Density Plot of Energy Star Scores by Building Type', size = 28);

We can see that the building type has a significant impact on the Energy Star Score. Office buildings tend to have a higher score while Hotels have a lower score. This tells us that we should include the building type in our modeling because it does have an impact on the target. As a categorical variable, we will have to one-hot encode the building type.

A similar plot can be used to show the Energy Star Score by borough:

The borough does not seem to have as large of an impact on the score as the building type. Nonetheless, we might want to include it in our model because there are slight differences between the boroughs.

To quantify relationships between variables, we can use the Pearson Correlation Coefficient. This is a measure of the strength and direction of a linear relationship between two variables. A score of +1 is a perfectly linear positive relationship and a score of -1 is a perfectly negative linear relationship. Several values of the correlation coefficient are shown below:

While the correlation coefficient cannot capture non-linear relationships, it is a good way to start figuring out how variables are related. In Pandas, we can easily calculate the correlations between any columns in a dataframe:

# Find all correlations with the score and sort 
correlations_data = data.corr()['score'].sort_values()

The most negative (left) and positive (right) correlations with the target: