- Cyber Train

# 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:

Data cleaning and formatting

Exploratory data analysis

Feature engineering and selection

Compare several machine learning models on a performance metric

Perform hyperparameter tuning on the best model

Evaluate the best model on the testing set

Interpret the model results

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 wrangle__it 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**
**data**.head()

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 __dataframe.info__()method:

`# See the `**column** data **types** **and** non-missing **values**
__data.____info__()

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**
**plt**.style.use('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
sns.kdeplot(subset['score'].dropna(),
**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:

There are several strong negative correlations between the features and the target with the most negative the different categories of EUI (these measures vary slightly in how they are calculated). The __EUI — Energy Use Intensity__ — is the amount of energy used by a building divided by the square footage of the buildings. It is meant to be a measure of the efficiency of a building with a lower score being better. Intuitively, these correlations make sense: as the EUI increases, the Energy Star Score tends to decrease.

**Two-Variable Plots**

#### To visualize relationships between two continuous variables, we use scatterplots. We can include additional information, such as a categorical variable, in the color of the points. For example, the following plot shows the Energy Star Score vs. Site EUI colored by the building type:

This plot lets us visualize what a correlation coefficient of -0.7 looks like. As the Site EUI decreases, the Energy Star Score increases, a relationship that holds steady across the building types.

The final exploratory plot we will make is known as the __Pairs Plot. This is a great exploration tool__ because it lets us see relationships between multiple pairs of variables as well as distributions of single variables. Here we are using the seaborn visualization library and the PairGrid function to create a Pairs Plot with scatterplots on the upper triangle, histograms on the diagonal, and 2D kernel density plots and correlation coefficients on the lower triangle.

`# Extract the `**columns** **to** plot
plot_data = features[['score', 'Site EUI (kBtu/ft²)',
'Weather Normalized Source EUI (kBtu/ft²)',
'log_Total GHG Emissions (Metric Tons CO2e)']]
# Replace the inf **with** **nan**
plot_data = plot_data.replace({np.inf: np.**nan**, -np.inf: np.**nan**})
# **Rename** **columns**
plot_data = plot_data.**rename**(**columns** = {'Site EUI (kBtu/ft²)': 'Site EUI',
'Weather Normalized Source EUI (kBtu/ft²)': 'Weather Norm EUI',
'log_Total GHG Emissions (Metric Tons CO2e)': 'log GHG Emissions'})
# **Drop** na **values**
plot_data = plot_data.dropna()
# **Function** **to** calculate correlation coefficient **between** two **columns**
def corr_func(x, y, **kwargs):
r = np.corrcoef(x, y)[0][1]
ax = plt.gca()
ax.annotate("r = {:.2f}".format(r),
xy=(.2, .8), xycoords=ax.transAxes,
size = 20)
# **Create** the pairgrid **object**
grid = sns.PairGrid(data = plot_data, size = 3)
# Upper **is** a scatter plot
grid.map_upper(plt.scatter, color = 'red', alpha = 0.6)
# Diagonal **is** a histogram
grid.map_diag(plt.hist, color = 'red', edgecolor = 'black')
# Bottom **is** correlation **and** density plot
grid.map_lower(corr_func);
grid.map_lower(sns.kdeplot, cmap = plt.cm.Reds)
# Title **for** entire plot
plt.suptitle('Pairs Plot of Energy Data', size = 36, y = 1.02);

To see interactions between variables, we look for where a row intersects with a column. For example, to see the correlation of Weather Norm EUI with score, we look in the Weather Norm EUI row and the score column and see a correlation coefficient of -0.67. In addition to looking cool, plots such as these can help us decide which variables to include in modeling.

**Feature Engineering and Selection**

__Feature engineering and selection__ often provide the greatest return on time invested in a machine learning problem. First of all, let’s define what these two tasks are:

__Feature engineering:__The process of taking raw data and extracting or creating new features. This might mean taking transformations of variables, such as a natural log and square root, or one-hot encoding categorical variables so they can be used in a model. Generally, I think of feature engineering as creating additional features from the raw data.__selection:__The process of choosing the most relevant features in the data. In feature selection, we remove features to help the model generalize better to new data and create a more interpretable model. Generally, I think of feature selection as subtracting features so we are left with only those that are most important.

A machine learning model can only learn from the data we provide it, so ensuring that data includes all the relevant information for our task is crucial. If we don’t feed a model the correct data, then we are setting it up to fail and we should not expect it to learn!

For this project, we will take the following feature engineering steps:

One-hot encode categorical variables (borough and property use type)

Add in the natural log transformation of the numerical variables

__One-hot encoding__ is necessary to include categorical variables in a model. A machine learning algorithm cannot understand a building type of “office”, so we have to record it as a 1 if the building is an office and a 0 otherwise.

Adding transformed features can help our model learn non-linear relationships within the data. __Taking the square root, natural log, or various powers of features__ is common practice in data science and can be based on domain knowledge or what works best in practice. Here we will include the natural log of all numerical features.

The following code selects the numeric features, takes log transformations of these features, selects the two categorical features, one-hot encodes these features, and joins the two sets together. This seems like a lot of work, but it is relatively straightforward in Pandas!

*# Copy the original data*
features = data.copy()
*# Select the numeric columns*
numeric_subset = data.select_dtypes('number')
*# Create columns **with** log **of** numeric columns*
for col in numeric_subset.columns:
*# Skip the Energy Star Score column*
if col == 'score':
next
**else**:
numeric_subset['log_' + col] = np.log(numeric_subset[col])
*# Select the categorical columns*
categorical_subset = data[['Borough', 'Largest Property Use Type']]
*# One hot encode*
categorical_subset = pd.get_dummies(categorical_subset)
*# Join the two dataframes using concat*
*# Make sure to use axis **=** **1** to perform a column bind*
features = pd.concat([numeric_subset, categorical_subset], axis = 1)

After this process we have over 11,000 observations (buildings) with 110 columns (features). Not all of these features are likely to be useful for predicting the Energy Star Score, so now we will turn to feature selection to remove some of the variables. After this process we have over 11,000 observations (buildings) with 110 columns (features). Not all of these features are likely to be useful for predicting the Energy Star Score, so now we will turn to feature selection to remove some of the variables.

**Feature Selection**

#### Many of the 110 features we have in our data are redundant because they are highly correlated with one another. For example, here is a plot of Site EUI vs Weather Normalized Site EUI which have a correlation coefficient of 0.997.

Features that are strongly correlated with each other are known as __collinear__ and removing one of the variables in these pairs of features can often help a __machine learning model generalize and be more interpretable__. (I should point out we are talking about correlations of features with other features, not correlations with the target, which help our model!)

There are a number of methods to calculate collinearity between features, with one of the most common the __variance inflation factor__. In this project, we will use thebcorrelation coefficient to identify and remove collinear features. We will drop one of a pair of features if the correlation coefficient between them is greater than 0.6. For the implementation, take a look at the notebook (and __this Stack Overflow answer__)

While this value may seem arbitrary, I tried several different thresholds, and this choice yielded the best model. Machine learning is an __empirical field__ and is often about experimenting and finding what performs best! After feature selection, we are left with 64 total features and 1 target.

```
# Remove any columns with all na values
features = features.dropna(axis=1, how = 'all')
print(features.shape)
(11319, 65)
```

**Establishing a Baseline**

We have now completed data cleaning, exploratory data analysis, and feature engineering. The final step to take before getting started with modeling is establishing a naive baseline. This is essentially a guess against which we can compare our results. If the machine learning models do not beat this guess, then we might have to conclude that machine learning is not acceptable for the task or we might need to try a different approach.

For regression problems, a reasonable naive baseline is to guess the median value of the target on the training set for all the examples in the test set. This sets a relatively low bar for any model to surpass.

The metric we will use is __mean absolute error____ (mae)__ which measures the average absolute error on the predictions. There are many metrics for regression, but I like __Andrew Ng’s advice__ to pick a single metric and then stick to it when evaluating models. The mean absolute error is easy to calculate and is interpretable.

Before calculating the baseline, we need to split our data into a training and a testing set:

The training set of features is what we provide to our model during training along with the answers. The goal is for the model to learn a mapping between the features and the target.

The testing set of features is used to evaluate the trained model. The model is not allowed to see the answers for the testing set and must make predictions using only the features. We know the answers for the test set so we can compare the test predictions to the answers.

We will use 70% of the data for training and 30% for testing:

`# Split into 70% training `**and** 30% testing **set**
X, X_test, y, y_test = train_test_split(features, targets,
test_size = 0.3,
random_state = 42)

Now we can calculate the naive baseline performance:

`# Function to calculate `**mean** absolute **error**
def mae(y_true, y_pred):
**return** np.**mean**(abs(y_true - y_pred))
baseline_guess = np.**median**(y)
**print**('The baseline guess is a **score** of %0.2f' % baseline_guess)
**print**("Baseline Performance on the test set: MAE = %0.4f" % mae(y_test, baseline_guess))
The baseline guess is a **score** of 66.00

`Baseline Performance `**on** the **test** **set**: MAE = 24.5164

The naive estimate is off by about 25 points on the test set. The score ranges from 1–100, so this represents an error of 25%, quite a low bar to surpass!

**Conclusions**

In this article we walked through the first three steps of a machine learning problem. After defining the question, we:

Cleaned and formatted the raw data

Performed an exploratory data analysis to learn about the dataset

Developed a set of features that we will use for our models

Finally, we also completed the crucial step of establishing a baseline against which we can judge our machine learning algorithms.

**A Complete Machine Learning Walk-Through in Python (Part Two): Model Selection, Hyperparameter Tuning, and Evaluation**

**Model Evaluation and Selection**

As a reminder, we are working on a supervised regression task: __using New York City building energy data__, we want to develop a model that can predict the __Energy Star Score__ of a building. Our focus is on both accuracy of the predictions and interpretability of the model.

There are a __ton of machine learning models__ to choose from and deciding where to start can be intimidating. While there are __some charts__ that try to show you which algorithm to use, I prefer to just try out several and see which one works best! Machine learning is still a field driven primarily by __empirical (experimental) rather than theoretical results__, and it’s almost impossible to __know ahead of time which model will do the best__.

Generally, it’s a good idea to start out with simple, interpretable models such as linear regression, and if the performance is not adequate, move on to more complex, but usually more accurate methods. The following chart shows a (highly unscientific) version of the accuracy vs interpretability trade-off:

We will evaluate five different models covering the complexity spectrum:

**Linear Regression****K-Nearest Neighbors Regression****Random Forest Regression****Gradient Boosted Regression****Support Vector Machine Regression**

In this post we will focus on implementing these methods rather than the theory behind them. For anyone interesting in learning the background, I highly recommend __An Introduction to Statistical Learning__ (available free online) or __Hands-On Machine Learning with Scikit-Learn and TensorFlow__. Both of these textbooks do a great job of explaining the theory and showing how to effectively use the methods in R and Python respectively.

**Imputing Missing Values**

While we dropped the columns with more than 50% missing values when we cleaned the data, there are still quite a few missing observations. Machine learning models cannot deal with any absent values, so we have to fill them in, a __process known as imputation__.

First, we’ll read in all the data and remind ourselves what it looks like:

```
import pandas as pd
import numpy as np
# Read in data into dataframes
train_features = pd.read_csv('data/training_features.csv')
test_features = pd.read_csv('data/testing_features.csv')
train_labels = pd.read_csv('data/training_labels.csv')
test_labels = pd.read_csv('data/testing_labels.csv')
Training Feature Size: (6622, 64)
```**Testing **Feature Size: (2839, 64)
Training Labels Size: (6622, 1)
**Testing **Labels Size: (2839, 1)

Every value that is NaN represents a missing observation. While there are a __number of ways to fill in missing data__, we will use a relatively simple method, median imputation. This replaces all the missing values in a column with the median value of the column.

In the following code, we create a __Scikit-Learn__ Imputer object with the strategy set to median. We then train this object on the training data (using imputer.fit) and use it to fill in the missing values in both the training and testing data (using imputer.transform). This means missing values in the *test data* are filled in with the corresponding median value from the *training data*.

(We have to do imputation this way rather than training on all the data to avoid the problem of __test data leakage__, where information from the testing dataset spills over into the training data.)

`# `**Create** an imputer **object** **with** a median filling strategy
imputer = Imputer(strategy='median')
# Train **on** the training features
imputer.fit(train_features)
# Transform both training data **and** testing data
X = imputer.transform(train_features)
X_test = imputer.transform(test_features)
Missing **values** **in** training features: 0
Missing **values** **in** testing features: 0

All of the features now have real, finite values with no missing examples.

**Feature Scaling**

__Scaling__ refers to the general process of changing the range of a feature. __This is necessary__because features are measured in different units, and therefore cover different ranges. Methods such as __support vector machines__ and K-nearest neighbors that take into account distance measures between observations are significantly affected by the range of the features and scaling allows them to learn. While methods such as __Linear Regression and Random Forest__ do not actually require feature scaling, it is still best practice to take this step when we are comparing multiple algorithms.

We will scale the features by putting each one in a range between 0 and 1. This is done by taking each value of a feature, subtracting the minimum value of the feature, and dividing by the maximum minus the minimum (the range). This specific version of scaling is often called __normalization and the other main version is known as standardization__.

While this process would be easy to implement by hand, we can do it using a MinMaxScalerobject in Scikit-Learn. The code for this method is identical to that for imputation except with a scaler instead of imputer! Again, we make sure to train only using training data and then transform all the data.

*# Create the scaler object **with** a range **of** **0**-**1*
scaler = MinMaxScaler(feature_range=(0, 1))
*# Fit on the training data*
scaler.fit(X)
*# Transform both the training and testing data*
X = scaler.transform(X)
X_test = scaler.transform(X_test)

Every feature now has a minimum value of 0 and a maximum value of 1. Missing value imputation and feature scaling are two steps required in nearly any machine learning pipeline so it’s a good idea to understand how they work!

**Implementing Machine Learning Models in Scikit-Learn**

After all the work we spent cleaning and formatting the data, actually creating, training, and predicting with the models is relatively simple. We will use the __Scikit-Learn library__ in Python, which has great documentation and a consistent model building syntax. Once you know how to make one model in Scikit-Learn, you can quickly implement a diverse range of algorithms.

We can illustrate one example of model creation, training (using .fit ) and testing (using .predict ) with the Gradient Boosting Regressor:

**from** sklearn.ensemble import GradientBoostingRegressor
*# Create the model*
gradient_boosted = GradientBoostingRegressor()
*# Fit the model on the training data*
gradient_boosted.fit(X, y)
*# Make predictions on the test data*
predictions = gradient_boosted.predict(X_test)
*# Evaluate the model*
mae = np.mean(abs(predictions - y_test))
print('Gradient Boosted Performance **on** **the** test **set**: MAE = %0.4f' % mae)
Gradient Boosted Performance **on** **the** test **set**: MAE = 10.0132

Model creation, training, and testing are each one line! To build the other models, we use the same syntax, with the only change the name of the algorithm. The results are presented below:

To put these figures in perspective, the naive baseline calculated using the median value of the target was 24.5. Clearly, machine learning is applicable to our problem because of the significant improvement over the baseline!

The __gradient boosted regressor__ (MAE = 10.013) slightly beats out the random forest (10.014 MAE). These results aren’t entirely fair because we are mostly using the default values for the hyperparameters. __Especially in models such as the support vector machine__, the performance is highly dependent on these settings. Nonetheless, from these results we will select the gradient boosted regressor for model optimization.

**Hyperparameter Tuning for Model Optimization**

In machine learning, after we have selected a model, we can optimize it for our problem by tuning the model hyperparameters.

First off, what are __hyperparameters and how do they differ from parameters__?

Model

**hyperparameters**are best thought of as settings for a machine learning algorithm that are set by the data scientist before training. Examples would be the number of trees in a random forest or the number of neighbors used in K-nearest neighbors algorithm.Model

**parameters**are what the model learns during training, such as weights in a linear regression.

Controlling the hyperparameters affects the model performance by altering the balance between __underfitting and overfitting__ in a model. Underfitting is when our model is not complex enough (it does not have enough degrees of freedom) to learn the mapping from features to target. An underfit model has __high bias__, which we can correct by making our model more complex.

Overfitting is when our model essentially memorizes the training data. An overfit model has __high variance__, which we can correct by limiting the complexity of the model through regularization. Both an underfit and an overfit model will not be able to generalize well to the testing data.

The problem with choosing the right hyperparameters is that the optimal set will be different for every machine learning problem! Therefore, the only way to find the best settings is to try out a number of them on each new dataset. Luckily, Scikit-Learn has a number of methods to allow us to efficiently evaluate hyperparameters. Moreover, projects such as __TPOT by Epistasis Lab__are trying to optimize the hyperparameter search using methods like __genetic programming__. In this project, we will stick to doing this with Scikit-Learn, but stayed tuned for more work on the auto-ML scene!

**Random Search with Cross Validation**

The particular hyperparameter tuning method we will implement is called random search with cross validation:

refers to the technique we will use to select hyperparameters. We define a grid and then randomly sample different combinations, rather than grid search where we exhaustively try out every single combination. (Surprisingly,__Random Search____random search performs nearly as well as grid search__with a drastic reduction in run time.)is the technique we use to evaluate a selected combination of hyperparameters. Rather than splitting the training set up into separate training and validation sets, which reduces the amount of training data we can use, we use K-Fold Cross Validation. This involves dividing the training data into K number of folds, and then going through an iterative process where we first train on K-1 of the folds and then evaluate performance on the Kth fold. We repeat this process K times and at the end of K-fold cross validation, we take the average error on each of the K iterations as the final performance measure.__Cross Validation__

The idea of K-Fold cross validation with K = 5 is shown below:

The entire process of performing random search with cross validation is:

Set up a grid of hyperparameters to evaluate

Randomly sample a combination of hyperparameters

Create a model with the selected combination

Evaluate the model using K-fold cross validation

Decide which hyperparameters worked the best

Of course, we don’t do actually do this manually, but rather let Scikit-Learn’s RandomizedSearchCV handle all the work!

**Slight Diversion:** __Gradient Boosted Methods__

__Gradient Boosted Methods__

Since we will be using the Gradient Boosted Regression model, I should give at least a little background! This model is an ensemble method, meaning that it is built out of many weak learners, in this case individual decision trees. While a __bagging algorithm such as random forest__ trains the weak learners in parallel and has them vote to make a prediction, a __boosting method__ like Gradient Boosting, trains the learners in sequence, with each learner “concentrating” on the mistakes made by the previous ones.

Boosting methods have become popular in recent years and frequently win machine learning competitions. The __Gradient Boosting Method__ is one particular implementation that uses Gradient Descent to minimize the cost function by sequentially training learners on the residuals of previous ones. The Scikit-Learn implementation of Gradient Boosting is generally regarded as less efficient than other libraries such as __XGBoost __, but it will work well enough for our small dataset and is quite accurate.

**Back to Hyperparameter Tuning**

There are many hyperparameters to tune in a Gradient Boosted Regressor and you can look at the __Scikit-Learn documentation__ for the details. We will optimize the following hyperparameters:

loss: the loss function to minimize

n_estimators: the number of weak learners (decision trees) to use

max_depth: the maximum depth of each decision tree

min_samples_leaf: the minimum number of examples required at a leaf node of the decision tree

min_samples_split: the minimum number of examples required to split a node of the decision tree

max_features: the maximum number of features to use for splitting nodes

I’m not sure if there is anyone who truly understands how all of these interact, and the only way to find the best combination is to try them out!

In the following code, we build a hyperparameter grid, create a RandomizedSearchCV object, and perform hyperparameter search using 4-fold cross validation over 25 different combinations of hyperparameters:

`# Loss `**function** **to** be optimized
loss = ['ls', 'lad', 'huber']
# Number **of** trees used **in** the boosting process
n_estimators = [100, 500, 900, 1100, 1500]
# Maximum depth **of** **each** tree
max_depth = [2, 3, 5, 10, 15]
# Minimum number **of** samples per leaf
min_samples_leaf = [1, 2, 4, 6, 8]
# Minimum number **of** samples **to** split a node
min_samples_split = [2, 4, 6, 10]
# Maximum number **of** features **to** consider **for** making splits
max_features = ['auto', 'sqrt', 'log2', **None**]
# Define the grid **of** hyperparameters **to** **search**
hyperparameter_grid = {'loss': loss,
'n_estimators': n_estimators,
'max_depth': max_depth,
'min_samples_leaf': min_samples_leaf,
'min_samples_split': min_samples_split,
'max_features': max_features}
# **Create** the model **to** use **for** hyperparameter tuning
model = GradientBoostingRegressor(random_state = 42)
# **Set** up the random **search** **with** 4-fold **cross** validation
random_cv = RandomizedSearchCV(estimator=model,
param_distributions=hyperparameter_grid,
cv=4, n_iter=25,
scoring = 'neg_mean_absolute_error',
n_jobs = -1, **verbose** = 1,
return_train_score = **True**,
random_state=42)
# Fit **on** the training data
random_cv.fit(X, y)

After performing the search, we can inspect the RandomizedSearchCV object to find the best model:

*# Find the best combination **of** settings*
random_cv.best_estimator_
GradientBoostingRegressor(loss='lad', max_depth=5,
max_features=None,
min_samples_leaf=6,
min_samples_split=6,
n_estimators=500)

We can then use these results to perform grid search by choosing parameters for our grid that are close to these optimal values. However, further tuning is unlikely to significant improve our model. As a general rule, proper feature engineering will have a much larger impact on model performance than even the most extensive hyperparameter tuning. It’s the __law of diminishing returns applied to machine learning__: feature engineering gets you most of the way there, and hyperparameter tuning generally only provides a small benefit.

One experiment we can try is to change the number of estimators (decision trees) while holding the rest of the hyperparameters steady. This directly lets us observe the effect of this particular setting. See the __notebook for the implementation__, but here are the results:

As the number of trees used by the model increases, both the training and the testing error decrease. However, the training error decreases much more rapidly than the testing error and we can see that our model is overfitting: it performs very well on the training data, but is not able to achieve that same performance on the testing set.

We always expect at least some decrease in performance on the testing set (after all, the model can see the true answers for the training set), but a significant gap __indicates overfitting__. We can address overfitting by getting more training data, or decreasing the __complexity of our model through the hyerparameters__. In this case, we will leave the hyperparameters where they are, but I encourage anyone to try and reduce the overfitting.

For the final model, we will use 800 estimators because that resulted in the lowest error in cross validation. Now, time to test out this model!

**Evaluating on the Test Set**

As responsible machine learning engineers, we made sure to not let our model see the test set at any point of training. Therefore, we can use the __test set performance as an indicator__ of how well our model would perform when deployed in the real world.

Making predictions on the test set and calculating the performance is relatively straightforward. Here, we compare the performance of the default Gradient Boosted Regressor to the tuned model:

`# Make predictions `**on** the test **set** **using** **default** **and** **final** model
default_pred = default_model.predict(X_test)
final_pred = final_model.predict(X_test)
**Default** model performance **on** the test **set**: MAE = 10.0118.
**Final** model performance **on** the test **set**: MAE = 9.0446.

Hyperparameter tuning improved the accuracy of the model by about 10%. Depending on the use case, 10% could be a massive improvement, but it came at a significant time investment!

We can also time how long it takes to train the two models using the %timeit magic command in Jupyter Notebooks. First is the default model:

```
%%timeit -n 1 -r 5
default_model.fit(X, y)
1.09 s ± 153 ms per loop (mean ± std. dev. of 5 runs, 1 loop each)
```

1 second to train seems very reasonable. The final tuned model is not so fast:

```
%%timeit -n 1 -r 5
final_model.fit(X, y)
12.1 s ± 1.33 s per loop (mean ± std. dev. of 5 runs, 1 loop each)
```

This demonstrates a fundamental aspect of machine learning: it is __always a game of trade-offs__. We constantly have to balance accuracy vs interpretability, __bias vs variance__, accuracy vs run time, and so on. The right blend will ultimately depend on the problem. In our case, a 12 times increase in run-time is large in relative terms, but in absolute terms it’s not that significant.

Once we have the final predictions, we can investigate them to see if they exhibit any noticeable skew. On the left is a density plot of the predicted and actual values, and on the right is a histogram of the residuals:

The model predictions seem to follow the distribution of the actual values although the peak in the density occurs closer to the median value (66) on the training set than to the true peak in density (which is near 100). The residuals are nearly normally distribution, although we see a few large negative values where the model predictions were far below the true values.

**Conclusions**

In this article we covered several steps in the machine learning workflow:

Imputation of missing values and scaling of features

Evaluating and comparing several machine learning models

Hyperparameter tuning using random grid search and cross validation

Evaluating the best model on the test set

The results of this work showed us that machine learning is applicable to the task of predicting a building’s Energy Star Score using the available data. Using a gradient boosted regressor we were able to predict the scores on the test set to within 9.1 points of the true value. Moreover, we saw that hyperparameter tuning can increase the performance of a model at a significant cost in terms of time invested. This is one of many trade-offs we have to consider when developing a machine learning solution.

**A Complete Machine Learning Walk-Through in Python (Part Three): Interpreting a machine learning model and presenting results**

As a reminder, we are working through a supervised regression machine learning problem. Using __New York City building energy data__, we have developed a model which can predict the Energy Star Score of a building. The final model we built is a __Gradient Boosted Regressor__which is able to predict the Energy Star Score on the test data to within 9.1 points (on a 1–100 scale).

**Model Interpretation**

The gradient boosted regressor sits somewhere in the middle on the __scale of model interpretability__: the entire model is complex, but it is made up of hundreds of __decision trees__, which by themselves are quite understandable. We will look at three ways to understand how our model makes predictions:

Visualizing a single decision tree

The first two methods are specific to ensembles of trees, while the third — as you might have guessed from the name — can be applied to any machine learning model. LIME is a relatively new package and represents an exciting step in the ongoing effort to __explain machine learning predictions__.

**Feature Importances**

Feature importances attempt to show the relevance of each feature to the task of predicting the target. The technical details of feature importances are complex (they __measure the mean decrease impurity__, or the __reduction in error from including the feature__), but we can use the relative values to compare which features are the most relevant. In Scikit-Learn, we can __extract the feature importances__ from any ensemble of tree-based learners.

With model as our trained model, we can find the feature importances usingmodel.feature_importances_. Then we can put them into a pandas DataFrame and display or plot the top ten most important:

```
import pandas as pd
```*# model is the trained model*
importances = model.feature_importances_
*# train_features is the dataframe **of** training features*
feature_list = list(train_features.columns)
*# Extract the feature importances into a dataframe*
feature_results = pd.DataFrame({'feature': feature_list,
'importance': importances})
*# Show the top **10** most important*
feature_results = feature_results.sort_values('importance',
ascending = False).reset_index(drop=True)
feature_results.head(10)

The Site EUI(__Energy Use Intensity__) and the Weather Normalized Site Electricity Intensityare by far the most important features, accounting for over 66% of the total importance. After the top two features, the importance drops off significantly, which indicates we might not need to retain all 64 features in the data to achieve high performance. (In __the Jupyter notebook__, I take a look at using only the top 10 features and discover that the model is not quite as accurate.)

Based on these results, we can finally answer one of our initial questions: the most important indicators of a building’s Energy Star Score are the Site EUI and the Weather Normalized Site Electricity Intensity. While we do want __to be careful about reading too much into the feature importances__, they are a useful way to start to understand how the model makes its predictions.

**Visualizing a Single Decision Tree**

#### While the entire gradient boosting regressor may be difficult to understand, any one individual decision tree is quite intuitive. We can visualize any tree in the forest using the __Scikit-Learn function__ [export_graphviz](__http://scikit-learn.org/stable/modules/generated/sklearn.tree.export_graphviz.html)__. We first extract a tree from the ensemble then save it as a dot file:

```
from sklearn import tree
```**# Extract a single ****tree**** ****(****number ****105****)**
single*_tree **=** model**.**estimators_*[105][0]
**# Save the tree to a dot file**
tree.export*_graphviz**(**single_*tree, out_file = 'images/tree.dot',
feature*_names **=** feature_*list)

Using the __Graphviz visualization software__ we can convert the dot file to a png from the command line:

`dot -Tpng images/tree.dot -o images/tree.png`

The result is a complete decision tree:

This is a little overwhelming! Even though this tree only has a depth of 6 (the number of layers), it’s difficult to follow. We can modify the call to export_graphviz and limit our tree to a more reasonable depth of 2:

Each node (box) in the tree has four pieces of information:

The question asked about the value of one feature of the data point: this determines if we go right or left out of the node

The mse which is a measure of the error of the node

The samples which is the number of examples (data points) in the node

The value is the estimate of the target for all the samples in the node

(Leaf nodes only have 2.–4. because they represent the final estimate and do not have any children).

A decision tree makes a prediction for a data point by starting at the top node, called the root, and working its way down through the tree. At each node, a yes-or-no question is asked of the data point. For example, the question for the node above is: Does the building have a Site EUI less than or equal to 68.95? If the answer is yes, the building is placed in the right child node, and if the answer is no, the building goes to the left child node.

This process is repeated at each layer of the tree until the data point is placed in a leaf node, at the bottom of the tree (the leaf nodes are cropped from the small tree image). The prediction for all the data points in a leaf node is the value. If there are multiple data points ( samples ) in a leaf node, they all get the same prediction. As the depth of the tree is increased, the error on the training set will decrease because there are more leaf nodes and the examples can be more finely divided. However, a tree that is too deep will __overfit to the training data__ and will not be able to generalize to new testing data.

In the __second article__, we tuned a number of the model hyperparameters, which control aspects of each tree such as the maximum depth of the tree and the minimum number of samples required in a leaf node. These both have a significant impact on the balance of under vs over-fitting, and visualizing a single decision tree allows us to see how these settings work.

Although we cannot examine every tree in the model, looking at one lets us understand how each individual learner makes a prediction. This __flowchart-based__ method seems much like how a human makes decisions, answering one question about a single value at a time. __Decision-tree-based ensembles__ combine the predictions of many individual decision trees in order to create a more accurate model with less variance. __Ensembles of trees tend to be very accurate__, and also are intuitive to explain.

**Local Interpretable Model-Agnostic Explanations (LIME)**

The final tool we will explore for trying to understand how our model “thinks” is a new entry into the field of model explanations. __LIME aims to explain a single prediction from any machine learning model__ by creating a approximation of the model locally near the data point using a simple model such as linear regression (the __full details can be found in the paper__ ).

Here we will use LIME to examine a prediction the model gets completely wrong to see what it might tell us about why the model makes mistakes.

First we need to find the observation our model gets most wrong. We do this by training and predicting with the model and extracting the example on which the model has the greatest error:

```
from sklearn.ensemble import GradientBoostingRegressor
```*# Create the model **with** the best hyperparamters*
model = GradientBoostingRegressor(loss='lad', max_depth=5, max_features=None,
min_samples_leaf=6, min_samples_split=6,
n_estimators=800, random_state=42)
*# Fit and test on the features*
model.fit(X, y)
model_pred = model.predict(X_test)
*# Find the residuals*
residuals = abs(model_pred - y_test)
*# Extract the most wrong prediction*
wrong = X_test[np.argmax(residuals), :]
print('Prediction: %0.4f' % np.argmax(residuals))
print('Actual Value: %0.4f' % y_test[np.argmax(residuals)])
Prediction: 12.8615
Actual Value: 100.0000

Next, we create the LIME explainer object passing it our training data, the mode, the training labels, and the names of the features in our data. Finally, we ask the explainer object to explain the wrong prediction, passing it the observation and the prediction function.

```
import lime
```*# Create a lime explainer object*
explainer = lime.lime_tabular.LimeTabularExplainer(training_data = X,
mode = 'regression',
training_labels = y,
feature_names = feature_list)
*# Explanation **for** wrong prediction*
exp = explainer.explain_instance(data_row = wrong,
predict_fn = model.predict)
*# Plot the prediction explaination*
exp.as_pyplot_figure();

The plot explaining this prediction is below:

Here’s how to interpret the plot: Each entry on the y-axis indicates one value of a variable and the red and green bars show the effect this value has on the prediction. For example, the top entry says the Site EUI is greater than 95.90 which subtracts about 40 points from the prediction. The second entry says the Weather Normalized Site Electricity Intensity is less than 3.80 which adds about 10 points to the prediction. The final prediction is an intercept term plus the sum of each of these individual contributions.

We can get another look at the same information by calling the explainer .show_in_notebook()method:

*# Show the explanation **in** the Jupyter Notebook*
exp.show_in_notebook()

This shows the reasoning process of the model on the left by displaying the contributions of each variable to the prediction. The table on the right shows the actual values of the variables for the data point.

For this example, the model prediction was about 12 and the actual value was 100! While initially this prediction may be puzzling, looking at the explanation, we can see this was not an extreme guess, but a reasonable estimate given the values for the data point. The Site EUI was relatively high and we would expect the Energy Star Score to be low (because EUI is strongly negatively correlated with the score), a conclusion shared by our model. In this case, the logic was faulty because the building had a perfect score of 100.

It can be frustrating when a model is wrong, but explanations such as these help us to understand why the model is incorrect. Moreover, based on the explanation, we might want to investigate why the building has a perfect score despite such a high Site EUI. Perhaps we can learn something new about the problem that would have escaped us without investigating the model. Tools such as this are not perfect, but they go a long way towards helping us understand the model which in turn can allow us to make __better decisions__.

**Documenting Work and Reporting Results**

An often under-looked part of any technical project is documentation and reporting. We can do the best analysis in the world, but if we do not __clearly communicate the results__, then they will not have any impact!

When we document a data science project, we take all the versions of the data and code and package it so it our project can be reproduced or built on by other data scientists. It’s important to remember that code is read more often than it is written, and we want to make sure our work is understandable **both for others and for ourselves** if we come back to it a few months later. This means putting in helpful comments in the code and explaining your reasoning. I find __Jupyter Notebooks__ to be a great tool for documentation because they allow for explanations and code one after the other.

Jupyter Notebooks can also be a good platform for communicating findings to others. Using __notebook extensions__, we can __hide the code from our final report __, because although it’s hard to believe, not everyone wants to see a bunch of Python code in a document!

Personally, I struggle with succinctly summarizing my work because I like to go through all the details. However, it’s important to __understand your audience__ when you are presenting and __tailor the message accordingly__. With that in mind, here is my 30-second takeaway from the project:

Using the New York City energy data, it is possible to build a model that can predict the Energy Star Score of buildings to within 9.1 points.

The Site EUI and Weather Normalized Electricity Intensity are the most relevant factors for predicting the Energy Star Score.

Originally, I was given this project as a job-screening “assignment” by a start-up. For the final report, they wanted to see both my work and my conclusions, so I developed a Jupyter Notebook to turn in. However, instead of converting directly to PDF in Jupyter, I converted it to a __Latex__ .tex file that I then edited in __texStudio__ before rendering to a PDF for the __final version__. The default PDF output from Jupyter has a decent appearance, but it can be significantly improved with a few minutes of editing. Moreover, Latex is a powerful document preparation system and it’s good to know the basics.

At the end of the day, our work is only as valuable as the decisions it enables, and being able to present results is a crucial skill. Furthermore, by properly documenting work, we allow others to reproduce our results, give us feedback so we can become better data scientists, and build on our work for the future.

**Conclusions**

Throughout this series of posts, we’ve walked through a complete end-to-end machine learning project. We started by cleaning the data, moved into model building, and finally looked at how to interpret a machine learning model. As a reminder, the general structure of a machine learning project is below:

Data cleaning and formatting

Exploratory data analysis

Feature engineering and selection

Compare several machine learning models on a performance metric

Perform hyperparameter tuning on the best model

Evaluate the best model on the testing set

Interpret the model results to the extent possible

Draw conclusions and write a well-documented report

While the exact steps vary by project, and machine learning is often an __iterative rather than linear process__, this guide should serve you well as you tackle future machine learning projects. I hope this series has given you confidence to be able to implement your own machine learning solutions, but remember, **none of us do this by ourselves**! If you want any help, there are many incredibly supportive communities where you can look for advice.

A few resources I have found helpful throughout my learning process:

__Hands-On Machine Learning with Scikit-Learn and Tensorflow__(__Jupyter Notebooks for this book__are available online for free)!__Datacamp__: Good beginner tutorials for practicing data science coding__Coursera__: Free and paid courses in many subjects__Udacity__: Paid programming and data science courses