We've already looked at the iris dataset, which consists of four features and one output variable, namely the species variable. Having the output variable available for all the observations in the training data is the defining characteristic of the supervised learning setting, which represents the most frequent scenario encountered. In a nutshell, the advantage of training a model under the supervised learning setting is that we have the correct answer that we should be predicting for the data points in our training data. As we saw in the previous section, kNN is a model that uses supervised learning, because the model makes its prediction for an input point by combining the values of the output variable for a small number of neighbors to that point. In this book, we will primarily focus on supervised learning.

Using the availability of the value of the output variable as a way to discriminate between different models, we can also envisage a second scenario in which the output variable is not specified. This is known as the unsupervised learning setting. An unsupervised version of the iris dataset would consist of only the four features. If we don't have the species output variable available to us, then we clearly have no idea as to which species each observation refers to. Indeed, we won't know how many species of flower are represented in the dataset, or how many observations belong to each species. At first glance, it would seem that without this information, no useful predictive task could be carried out. In fact, what we can do is examine the data and create groups of observations based on how similar they are to each other, using the four features available to us. This process is known as clustering. One benefit of clustering is that we can discover natural groups of data points in our data; for example, we might be able to discover that the flower samples in an unsupervised version of our iris set form three distinct groups that correspond to three different species.

Between unsupervised and supervised methods, which are two absolutes in terms of the availability of the output variable, reside the semi-supervised and reinforcement learning settings. Semi-supervised models are built using data for which a (typically quite small) fraction contains the values for the output variable, while the rest of the data is completely unlabeled. Many such models first use the labeled portion of the dataset in order to train the model coarsely, then incorporate the unlabeled data by projecting labels predicted by the model trained up this point.

In a reinforcement learning setting the output variable is not available, but other information that is directly linked with the output variable is provided. One example is predicting the next best move to win a chess game, based on data from complete chess games. Individual chess moves do not have output values in the training data, but for every game, the collective sequence of moves for each player resulted in either a win or a loss. Due to space constraints, semi-supervised and reinforcement settings aren't covered in this book.

In a previous section, we noted how most of the models we will encounter are parametric models, and we saw an example of a simple linear model. Parametric models have the characteristic that they tend to define a functional form. This means that they reduce the problem of selecting between all possible functions for the target function to a particular family of functions that form a parameter set. Selecting the specific function that will define the model essentially involves selecting precise values for the parameters. So, returning to our example of a three-feature linear model, we can see that we have the two following possible choices of parameters (the choices are infinite, of course; here we just demonstrate two specific ones):

Here, we have used a subscript on the output Y variable to denote the two different possible models. Which of these might be a better choice? The answer is that it depends on the data. If we apply each of our models on the observations in our dataset, we will get the predicted output for every observation. With supervised learning, every observation in our training data is labeled with the correct value of the output variable. To assess our model's goodness of fit, we can define an error function that measures the degree to which our predicted outputs differ from the correct outputs. We then use this to pick between our two candidate models in this case, but more generally to iteratively improve a model by moving through a sequence of progressively better candidate models.

Some parametric models are more flexible than linear models, meaning that they can be used to capture a greater variety of possible functions. Linear models, which require that the output be a linearly weighted combination of the input features, are considered strict. We can intuitively see that a more flexible model is more likely to allow us to approximate our input data with greater accuracy; however, when we look at overfitting, we'll see that this is not always a good thing. Models that are more flexible also tend to be more complex and, thus, training them often proves to be harder than training less flexible models.

Models are not necessarily parameterized, in fact, the class of models that have no parameters is known (unsurprisingly) as nonparametric models. Nonparametric models generally make no assumptions on the particular form of the output function. There are different ways of constructing a target function without parameters. Splines are a common example of a nonparametric model. The key idea behind splines is that we envisage the output function, whose form is unknown to us, as being defined exactly at the points that correspond to all the observations in our training data. Between the points, the function is locally interpolated using smooth polynomial functions. Essentially, the output function is built in a piecewise manner in the space between the points in our training data. Unlike most scenarios, splines will guarantee 100% accuracy on the training data, whereas it is perfectly normal to have some errors in our training data. Another good example of a nonparametric model is the k-nearest neighbor algorithm that we've already seen.

The distinction between regression and classification models has to do with the type of output we are trying to predict, and is generally relevant to supervised learning. Regression models try to predict a numerical or quantitative value, such as the stock market index, the amount of rainfall, or the cost of a project. Classification models try to predict a value from a finite (though still possibly large) set of classes or categories. Examples of this include predicting the topic of a website, the next word that will be typed by a user, a person's gender, or whether a patient has a particular disease given a series of symptoms. The majority of models that we will study in this book fall quite neatly into one of these two categories, although a few, such as neural networks, can be adapted to solve both types of problem. It is important to stress here that the distinction made is on the output only, and not on whether the feature values that are used to predict the output are quantitative or qualitative themselves. In general, features can be encoded in a way that allows both qualitative and quantitative features to be used in regression and classification models alike. Earlier, when we built a kNN model to predict the species of iris based on measurements of flower samples, we were solving a classification problem as our species output variable could take only one of three distinct labels.

The kNN approach can also be used in a regression setting; in this case, the model combines the numerical values of the output variable for the selected nearest neighbors by taking the mean or median in order to make its final prediction. Thus, kNN is also a model that can be used in both regression and classification settings.

Predictive models can use real-time machine learning or they can involve batch learning. The term real-time machine learning can refer to two different scenarios, although it certainly does not refer to the idea that real-time machine learning involves making a prediction in real time, that is, within a predefined time limit that is typically small. For example, once trained, a neural network model can produce its prediction of the output using only a few computations (depending on the number of inputs and network layers). This is not, however, what we mean when we talk about real-time machine learning.

A good example of a model that uses real-time machine learning is a weather predictor that uses a stream of incoming readings from various meteorological instruments. Here, the real-time aspect of the model refers to the fact that we are taking only a recent window of readings in order to predict the weather. The further we go back in time, the less relevant the readings will be and we can, thus, choose to use only the latest information in order to make our prediction. Of course, models that are to be used in a real-time setting must also be able to compute their predictions quickly—it is not of much use if it takes hours for a system taking measurements in the morning to compute a prediction for the evening, as by the time the computation ends, the prediction won't be of much value.

When talking about models that take into account information obtained over a recent time frame to make a prediction, we generally refer to models that have been trained on data that is assumed to be representative of all the data for which the model will be asked to make a prediction in the future. A second interpretation of real-time machine learning arises when we describe models that detect that the properties of the process being modeled have shifted in some way. We will focus on examples of the first kind in this book when we look at time series models.

In a nutshell, the first step of every project is to figure out precisely what the desired outcome is, as this will help steer us to make good decisions throughout the course of the project. In a predictive analytics project, this question involves drilling into the type of prediction that we want to make and understanding the task in detail. For example, suppose we are trying to build a model that predicts employee churn for a company. We first need to define this task precisely, while trying to avoid making the problem overly broad or overly specific. We could measure churn as the percentage of new full time hires that defect from the company within their first six months. Notice that once we properly define the problem, we have already made some progress in thinking about what data we will have to work with. For example, we won't have to collect data from part-time contractors or interns. This task also means that we should collect data from our own company only, but at the same time recognize that our model might not necessarily be applicable to make predictions for the workforce of a different company. If we are only interested in churn, it also means that we won't need to make predictions about employee performance or sick days (although it wouldn't hurt to ask the person for whom we are building the model, to avoid surprises in the future).

Once we have a precise enough idea of the model we want to build, the next logical question to ask is what sort of performance we are interested in achieving, and how we will measure this. That is to say, we need to define a performance metric for our model and then a minimum threshold of acceptable performance. We will go into substantial detail on how to assess the performance of models in this book. For now, we want to emphasize that, although it is not unusual to talk about assessing the performance of a model after we have trained it on some data, in practice it is important to remember that defining the expectations and performance target for our model is something that a predictive modeler should discuss with the stakeholders of a project at the very beginning. Models are never perfect and it is easy to spiral into a mode of forever trying to improve performance. Clear performance goals are not only useful in guiding us to decide which methods to use, but also in knowing when our model is good enough.

Finally, we also need to think about the data that will be available to us when the time comes to collect it, and the context in which the model will be used. For example, suppose we know that our employee churn model will be used as one of the factors that determine whether a new applicant in our company will be hired. In this context, we should only collect data from our existing employees who were available before they were hired. We cannot use the result of their first performance review, as this data won't be available for a prospective applicant.

Training a model to make predictions is often a data-intensive venture, and if there is one thing that you can never have too much of in this business, it is data. Collecting the data can often be the most time- and resource-consuming part of the entire process, which is why it is so critical that the first step of defining the task and identifying the right data to be collected is done properly. When we learn about how a model such as logistic regression works we often do this by way of an example dataset and this is largely the approach we'll follow in this book. Unfortunately, we don't have a way to simulate the process of collecting the data, and it may seem that most of the effort is spent on training and refining a model. When learning about models using existing datasets, we should bear in mind that a lot of effort has usually gone into collecting, curating, and preprocessing the data. We will look at data preprocessing more closely in a subsequent section.

While we are collecting data, we should always keep in mind whether we are collecting the right kind of data. Many of the sanity checks that we perform on data during preprocessing also apply during collection, in order for us to spot whether we have made a mistake early on in the process. For example, we should always check that we measure features correctly and in the right units. We should also make sure that we collect data from sources that are sufficiently recent, reliable, and relevant to the task at hand. In the employee churn model we described in the previous section, as we collect information about past employees we should ensure that we are consistent in measuring our features. For example, when measuring how many days a person has been working in our company, we should consistently use either calendar days or business days. We must also check that when collecting dates, such as when a person joined or left the company, we invariably either use the US format (month followed by day) or the European format (day followed by month) and do not mix the two, otherwise a date like 03/05/2014 will be ambiguous. We should also try to get information from as broad a sample as possible and not introduce a hidden bias in our data collection. For example, if we wanted a general model for employee churn, we would not want to collect data from only female employees or employees from a single department.

How do we know when we have collected enough data? Early on when we are collecting the data and have not built and tested any model, it is impossible to tell how much data we will eventually need, and there aren't any simple rules of thumb that we can follow. We can, however, anticipate that certain characteristics of our problem will require more data. For example, when building a classifier that will learn to predict from one of three classes, we may want to check whether we have enough observations representative of each class.

The greater the number of output classes we have, the more data we will need to collect. Similarly, for regression models, it is also useful to check that the range of the output variable in the training data corresponds to the range that we would like to predict. If we are building a regression model that covers a large output range, we will also need to collect more data compared to a regression model that covers a smaller output range under the same accuracy requirements.

Another important factor to help us estimate how much data we will need, is the desired model performance. Intuitively, the higher the accuracy that we need for our model, the more data we should collect. We should also be aware that improving model performance is not a linear process. Getting from 90 to 95% accuracy can often require more effort and a lot more data, compared to making the leap from 70 to 90%. Models that have fewer parameters or are simpler in their design, such as linear regression models, often tend to need less data than more complex models such as neural networks. Finally, the greater the number of features that we want to incorporate into our model, the greater the amount of data we should collect. In addition, we should be aware of the fact that this requirement for additional data is also not going to be linear. That is to say, building a model with twice the number of features often requires much more than twice the amount of original data. This should be readily apparent, if we think of the number of different combinations of inputs our model will be required to handle. Adding twice the number of dimensions results in far more than twice the number of possible input combinations. To understand this, suppose we have a model with three input features, each of which takes 10 possible values. We have 10³ = 1000 possible input combinations. Adding a single extra feature that also takes 10 values raises this to 10,000 possible combinations, which is much more than twice the number of our initial input combinations.

There have been attempts to obtain a more quantifiable view of whether we have enough data for a particular dataset, but we will not have time to cover them in this book. A good place to start learning more about this area of predictive modeling is to study learning curves. In a nutshell, with this approach we build consecutive models on the same dataset by starting off with a small portion of the data and successively adding more. The idea is that if throughout this process the predictive accuracy on testing data always improves without tapering off, we probably could benefit from obtaining more data. As a final note for the data collection phase, even if we think we have enough data, we should always consider how much it would cost us (in terms of time and resources) in order to get more data, before making the choice to stop collecting and begin modeling.

Once we are clear on the prediction task, and we have the right kind of data, the next step is to pick our first model. To begin with, there is no best model overall, not even a best model using a few rules of thumb. In most cases, it makes sense to start off with a simple model, such as a Naïve Bayes model or a logistic regression in the case of a classification task, or a linear model in the case of regression. A simple model will give us a starting baseline performance, which we can then strive to improve. A simple model to start off with might also help in answering useful questions, such as how each feature contributes to the result, that is, how important is each feature and is the relationship with the output positively or negatively correlated. Sometimes, this kind of analysis itself warrants the production of a simple model first, followed by a more complex one, which will be used for the final prediction.

Sometimes a simple model might give us enough accuracy for the task at hand so that we won't need to invest more effort in order to give us a little bit extra. On the other hand, a simple model will often end up being inadequate for the task, requiring us to pick something more complicated. Choosing a more complex model over a simpler one is not always a straightforward decision, even if we can see that the accuracy of the complex model will be much better. Certain constraints, such as the number of features we have or the availability of data, may prevent us from moving to a more complex model. Knowing how to choose a model involves understanding the various strengths and limitations of the models in our toolkit. For every model we encounter in this book, we will pay particular attention to learning these points. In a real-world project, to help guide our decision, we often go back to the task requirements and ask a few questions, such as:

In practice, even if our first analysis points towards a particular model, we will most likely want to try out a number of options before making our final decision.

Before we can use our data to train our model, we typically need to preprocess it. In this section, we will discuss a number of common preprocessing steps that we usually perform. Some of these are necessary in order to detect and resolve problems in our data, while others are useful in order to transform our data and make them applicable to the model we have chosen.

Feature transformations

Often, we'll find that our numerical features are measured on scales that are completely different from each other. For example, we might measure a person's body temperature in degrees Celsius, so the numerical values will typically be in the range of 36-38. At the same time, we might also measure a person's white blood cell count per microliter of blood. This feature generally takes values in the thousands. If we are to use these features as an input to an algorithm, such as kNN, we'd find that the large values of the white blood cell count feature dominate the Euclidean distance calculation. We could have several features in our input that are important and useful for classification, but if they were measured on scales that produce numerical values much smaller than one thousand, we'd essentially be picking our nearest neighbors mostly on the basis of a single feature, namely the white blood cell count. This problem comes up often and applies to many models, not just kNN. We handle this by transforming (also referred to as scaling) our input features before using them in our model.

We'll discuss three popular options for feature scaling. When we know that our input features are close to being normally distributed, one possible transformation to use is Z-score normalization, which works by subtracting the mean and dividing it by the standard deviation:

E(x) is the expectation or mean of x, and the standard deviation is the square root of the variance of x, written as Var(x). Notice that as a result of this transformation, the new feature will be centered on a mean of zero and will have unit variance. Another possible transformation, which is better when the input is uniformly distributed, is to scale all the features and outputs so that they lie within a single interval, typically the unit interval [0,1]:

A third option is known as the Box-Cox transformation. This is often applied when our input features are highly skewed (asymmetric) and our model requires the input features to be normally distributed or symmetrical at the very least:

As λ is in the denominator, it must take a value other than zero. The transformation is actually defined for a zero-valued λ: in this case, it is given by the natural logarithm of the input feature, ln(x). Notice that this is a parameterized transform and so there is a need to specify a concrete value of λ. There are various ways to estimate an appropriate value for λ from the data itself. Indicatively, we'll mention a technique to do this, known as cross-validation, which we will encounter later on in this book in Chapter 5, Support Vector Machines.

Note

The original reference for the Box-Cox transformation is a paper published in 1964 by the Journal of the Royal Statistical Society, titled An analysis of Transformations and authored by G. E. P. Box and D. R. Cox.

To get a feel for how these transformations work in practice, we'll try them out on the Sepal.Length feature from our iris dataset. Before we do this, however, we'll introduce the first R package that we will be working with, caret.

The caret package is a very useful package that has a number of goals. It provides a number of helpful functions that are commonly used in the process of predictive modeling, from data preprocessing and visualization, to feature selection and resampling techniques. It also features a unified interface for many predictive modeling functions and provides functionalities for parallel processing.

Note

The definitive reference for predictive modeling using the caret package is a book called Applied Predictive Modeling, written by Max Kuhn and Kjell Johnson and published by Springer. Max Kuhn is the principal author of the caret package itself. The book also comes with a companion website at http://appliedpredictivemodeling.com.

When we transform our input features on the data we use to train our model, we must remember that we will need to apply the same transformation to the features of later inputs that we will use at prediction time. For this reason, transforming data using the caret package is done in two steps. In the first step, we use the preProcess() function that stores the parameters of the transformations to be applied to the data, and in the second step, we use the predict() function to actually compute the transformation. We tend to use the preProcess() function only once, and then the predict() function every time we need to apply the same transformation to some data. The preProcess() function takes a data frame with some numerical values as its first input, and we will also specify a vector containing the names of the transformations to be applied to the method parameter. The predict() function then takes the output of the previous function along with the data we want to transform, which in the case of the training data itself may well be the same data frame. Let's see all this in action:

> library("caret")
> iris_numeric <- iris[1:4]
> pp_unit <- preProcess(iris_numeric, method = c("range"))
> iris_numeric_unit <- predict(pp_unit, iris_numeric)
> pp_zscore <- preProcess(iris_numeric, method = c("center", "scale"))
> iris_numeric_zscore <- predict(pp_zscore, iris_numeric)
> pp_boxcox <- preProcess(iris_numeric, method = c("BoxCox"))
> iris_numeric_boxcox <- predict(pp_boxcox, iris_numeric)

Tip

Downloading the example code:

You can download the example code files from your account at http://www.packtpub.com for all the Packt Publishing books you have purchased. If you purchased this book elsewhere, you can visit http://www.packtpub.com/support and register to have the files e-mailed directly to you.

We've created three new versions of the numerical features of the iris data, with the difference being that in each case we used a different transformation. We can visualize the effects of our transformations by plotting the density of the Sepal.Length feature for each scaled data frame using the density() function and plotting the results, as shown here:

Notice that the Z-score and unit interval transformations preserve the overall shape of the density while shifting and scaling the values, whereas the Box-Cox transformation also changes the overall shape, resulting in a density that is less skewed than the original.

Encoding categorical features

Many models, from linear regression to neural networks, require all the inputs to be numerical, and so we often need a way to encode categorical fields on a numerical scale. For example, if we have a size feature that takes values in the set {small, medium, large}, we may want to represent this with the numerical values 1, 2, and 3, respectively. In the case of ordered categories, such as the size feature just described, this mapping probably makes sense.

The number 3 is the largest on this scale and this corresponds to the large category, which is further away from the small category, represented by the number 1 than it is from the medium category, represented by the value 2. Using this scale is only one possible mapping, and in particular, it forces the medium category to be equidistant from the large and small categories, which may or may not be appropriate based on our knowledge about the specific feature. In the case of unordered categories, such as brands or colors, we generally avoid mapping them onto a single numerical scale. For example, if we mapped the set {blue, green, white, red, orange} to the numbers one through five, respectively, then this scale is arbitrary and there is no reason why red is closer to white and far from blue. To overcome this, we create a series of indicator features, I_i, which take the following form:

We need as many indicator features as we have categories, so for our color example, we would create five indicator features. In this case, I₁, might be:

In this way, our original color feature will be mapped to five indicator features and for every observation, only one of these indicator features takes the value 1 and the rest will be 0 as each observation will involve one color value in our original feature. Indicator features are binary features as they only take on two values: 0 and 1.

Note

We may often encounter an alternative approach that uses only n-1 binary features to encode n levels of a factor. This is done by choosing one level to be the reference level and it is indicated where each one of the n-1 binary features takes the value 0. This can be more economical on the number of features and avoids introducing a linear dependence between them, but it violates the property that all features are equidistant from each other.

> cor(iris_numeric)
             Sepal.Length Sepal.Width Petal.Length Petal.Width
Sepal.Length    1.0000000  -0.1175698    0.8717538   0.8179411
Sepal.Width    -0.1175698   1.0000000   -0.4284401  -0.3661259
Petal.Length    0.8717538  -0.4284401    1.0000000   0.9628654
Petal.Width     0.8179411  -0.3661259    0.9628654   1.0000000

> iris_cor <- cor(iris_numeric)
> findCorrelation(iris_cor)
[1] 3
> findCorrelation(iris_cor, cutoff = 0.99)
integer(0)
> findCorrelation(iris_cor, cutoff = 0.80)
[1] 3 4

> new_iris <- iris_numeric
> new_iris$Cmb <- 6.7 * new_iris$Sepal.Length –
                  0.9 * new_iris$Petal.Width
> set.seed(68)
> new_iris$Cmb.N <- new_iris$Cmb +   
                    rnorm(nrow(new_iris), sd = 0.1)
> options(digits = 4)
> head(new_iris,n = 3)
  Sepal.Length Sepal.Width Petal.Length Petal.Width   Cmb Cmb.N
1          5.1         3.5          1.4         0.2 33.99 34.13
2          4.9         3.0          1.4         0.2 32.65 32.63
3          4.7         3.2          1.3         0.2 31.31 31.27

> findLinearCombos(new_iris)
$linearCombos
$linearCombos[[1]]
[1] 5 1 4

$remove
[1] 5

> newer_iris <- iris_numeric
> newer_iris$ZV <- 6.5
> newer_iris$Yellow <- ifelse(rownames(newer_iris) == 1, T, F
> head(newer_iris, n = 3)
  Sepal.Length Sepal.Width Petal.Length Petal.Width  ZV Yellow
1          5.1         3.5          1.4         0.2 6.5   TRUE
2          4.9         3.0          1.4         0.2 6.5  FALSE
3          4.7         3.2          1.3         0.2 6.5  FALSE

> nearZeroVar(newer_iris)
[1] 5 6
> nearZeroVar(newer_iris, saveMetrics = T)
             freqRatio percentUnique zeroVar   nzv
Sepal.Length     1.111       23.3333   FALSE FALSE
Sepal.Width      1.857       15.3333   FALSE FALSE
Petal.Length     1.000       28.6667   FALSE FALSE
Petal.Width      2.231       14.6667   FALSE FALSE
ZV               0.000        0.6667    TRUE  TRUE
Yellow         149.000        1.3333   FALSE  TRUE

The number and type of features that we use with a model is one of the most important decisions that we will make in the predictive modeling process. Having the right features for a model will ensure that we have sufficient evidence on which to base a prediction. On the flip side, the number of features that we work with is precisely the number of dimensions that the model has. A large number of dimensions can be the source of several complications. High dimensional problems often suffer from data sparsity, which means that because of the number of dimensions available, the range of possible combinations of values across all the features grows so large that it is unlikely that we will ever collect enough data in order to have enough representative examples for training. In a similar vein, we often talk about the curse of dimensionality. This describes the fact that, because of the overwhelmingly large space of possible inputs, data points that we have collected are likely to be far away from each other in the feature space. As a result, local methods, such as k-nearest neighbors, that make predictions using observations in the training data that are close to the point for which we are trying to make a prediction, will not work as well in high dimensions. A large feature set is also problematic in that it may significantly increase the time needed to train (and predict, in some cases) our model.

Consequently, there are two types of process that feature engineering involves. The first of these, which grows the feature space, is the design of new features based on features within our data. Sometimes, a new feature that is a product or ratio of two original features might work better. There are many ways to combine existing features into new ones, and often it is expert knowledge from the problem's particular application domain that might help guide us. In general though, this process takes experience and a lot of trial and error. Note that there is no guarantee that adding a new feature will not degrade performance. Sometimes, adding a feature that is very noisy or highly correlated with an existing feature may actually cause us to lose accuracy.

The second process in feature engineering is feature reduction or shrinkage, which reduces the size of the feature space. In the previous section on data preprocessing, we looked at how we can detect individual features that may be problematic for our model in some way. Feature selection refers to the process in which the subset of features that are the most informative for our target output is selected from the original pool of features. Some methods, such as tree-based models, have built-in feature selection, as we shall see in Chapter 6, Tree-based Methods. In Chapter 2, Linear Regression, we'll also explore methods to perform feature selection for linear models.

Another way to reduce the overall number of features, a concept known as dimensionality reduction, is to transform the entire set of features into a completely new set of features that are fewer in number. A classic example of this is Principal Component Analysis (PCA).

In a nutshell, PCA creates a new set of input features, known as principal components, all of which are linear combinations of the original input features. For the first principal component, the linear combination weights are chosen in order to capture the maximum amount of variation in the data. If we could visualize the first principal component as a line in the original feature space, this would be the line in which the data varies the most. It also happens to be the line that is closest to all the data points in the original feature space. Every subsequent principal component attempts to capture a line of maximum variation, but in such a way that the new principal component is uncorrelated with the previous ones already computed. Thus, the second principal component selects the linear combination of original input features that have the highest degree of variation in the data, while being uncorrelated with the first principal component.

The principal components are ordered naturally in descending order according to the amount of variation that they capture. This allows us to perform dimensionality reduction in a simple manner by keeping the first N components, where we choose N so that the components chosen incorporate a minimum amount of the variance from the original dataset. We won't go into the details of the underlying linear algebra necessary to compute the principal components.

Instead, we'll direct our attention to the fact that this process is sensitive to the variance and scale of the original features. For this reason, we often scale our features before carrying out this process. To visualize how useful PCA can be, we'll once again turn to our faithful iris dataset. We can use the caret package to carry out PCA. To do this, we specify pca in the method parameter of the preProcess() function. We can also use the thresh parameter, which specifies the minimum variance we must retain. We'll explicitly use the value 0.95 so that we retain 95% of the variance of the original data, but note that this is also the default value of this parameter:

> pp_pca <- preProcess(iris_numeric,  method = c("BoxCox", "center", "scale", "pca"), thresh = 0.95)
> iris_numeric_pca <- predict(pp_pca, iris_numeric)
> head(iris_numeric_pca, n = 3)
     PC1     PC2
1 -2.304 -0.4748
2 -2.151  0.6483
3 -2.461  0.3464

As a result of this transformation, we are now left with only two features, so we can conclude that the first two principal components of the numerical iris features incorporate over 95% of the variation in the data.

If we are interested in learning the weights that were used to compute the principal components, we can inspect the rotation attribute of the pp_pca object:

> options(digits = 2)
> pp_pca$rotation
               PC1    PC2
Sepal.Length  0.52 -0.386
Sepal.Width  -0.27 -0.920
Petal.Length  0.58 -0.049
Petal.Width   0.57 -0.037

This means that the first principal component, PC1, was computed as follows:

Sometimes, instead of directly specifying a threshold for the total variance captured by the principal components, we might want to examine a plot of each principal component and its variance. This is known as a scree plot, and we can build this by first performing PCA and indicating that we want to keep all the components. To do this, instead of specifying a variance threshold, we set the pcaComp parameter, which is the number of principal components we want to keep. We will set this to 4, which includes all of them, remembering that the total number of principal components is the same as the total number of original features or dimensions we started out with. We will then compute the variance and cumulative variance of these components and store it in a data frame. Finally, we will plot this in the figure that follows, noting that the numbers in brackets are cumulative percentages of variance captured:

> pp_pca_full <- preProcess(iris_numeric,  method = c("BoxCox", "center", "scale", "pca"), pcaComp = 4)
> iris_pca_full <- predict(pp_pca_full, iris_numeric)
> pp_pca_var <- apply(iris_pca_full, 2, var)
> iris_pca_var <- data.frame(Variance = round(100 * pp_pca_var / sum(pp_pca_var), 2), CumulativeVariance = round(100 * cumsum(pp_pca_var) / sum(pp_pca_var), 2))
> iris_pca_var
    Variance CumulativeVariance
PC1    73.45              73.45
PC2    22.82              96.27
PC3     3.20              99.47
PC4     0.53             100.00

As we can see, the first principal component accounts for 73.45% of the total variance in the iris dataset, while together with the second component, the total variance captured is 96.27%. PCA is an unsupervised method for dimensionality reduction that does not make use of the output variable even when it is available. Instead, it looks at the data geometrically in the feature space. This means that we cannot ensure that PCA will give us a new feature space that will perform well in our prediction problem, beyond the computational advantages of having fewer features. These advantages might make PCA a viable choice even when there is reduction in model accuracy as long as this reduction is small and acceptable for the specific task. As a final note, we should point out that weights of the principal components, often referred to as loadings, are unique within a sign flip as long as they have been normalized. In cases where we have perfectly correlated features or perfect linear combinations we will obtain a few principal components that are exactly zero.

In our earlier discussion of parametric models, we saw that they come with a procedure to train the model using a set of training data. Nonparametric models will typically either perform lazy learning, in which case there really isn't an actual training procedure at all beyond memorizing the training data, or, as in the case of splines, will perform local computations on the training data.

Either way, if we are to assess the performance of our model, we need to split our data into a training set and a test set. The key idea is that we want to assess our model based on how we expect it to perform on unseen future data. We do this by using the test set, which is a portion (typically 15-30%) of the data we collected and set aside for this purpose and haven't used during training. For example, one possible divide is to have a training set with 80% of the observations in our original data, and a test set with the remaining 20%. The reason why we need a test set is that we cannot use the training set to fairly assess our model performance, since we fit our model to the training data and it does not represent data that we haven't seen before. From a prediction standpoint, if our goal was to maximize performance on our training data alone, then the best thing to do would be to simply memorize the input data along with the desired output values and our model would thus be a simple look-up table!

A good question to ask would be. How do we decide how much data to use for training and testing? There is a trade-off that is involved here that makes the answer to this question nontrivial. On the one hand, we would like to use as much data as possible in our training set, so that the model has more examples from which to learn. On the other hand, we would like to have a large test set so that we can test our trained model using many examples in order to minimize the variance of our estimate of the model's predictive performance. If we only have a handful of observations in our test set, then we cannot really generalize about how our model performs on unseen data overall.

Another factor that comes into play is how much starting data we have collected. If we have very little data, we may have to use a larger amount in order to train our model, such as an 85-15 split. If we have enough data, then we might consider a 70-30 split so that we can get a more accurate prediction on our test set.

To split a dataset using the caret package, we can use the createDataPartition() function to create a sampling vector containing the indices of the rows we will use in our training set. These are selected by randomly sampling the rows until a specified proportion of the rows have been sampled, using the p parameter:

> set.seed(2412)
> iris_sampling_vector <- createDataPartition(iris$Species, p = 0.8, list = FALSE)

Using our sampling vector, which we created for the iris dataset, we can construct our training and test sets. We'll do this for a few versions of the iris dataset that we built earlier when we experimented with different feature transformations:

> iris_train     <- iris_numeric[iris_sampling_vector,]
> iris_train_z   <- iris_numeric_zscore[iris_sampling_vector,]
> iris_train_pca <- iris_numeric_pca[iris_sampling_vector,]
> iris_train_labels <- iris$Species[iris_sampling_vector]
>
> iris_test        <- iris_numeric[-iris_sampling_vector,]
> iris_test_z      <- iris_numeric_zscore[-iris_sampling_vector,]
> iris_test_pca    <- iris_numeric_pca[-iris_sampling_vector,]
> iris_test_labels <- iris$Species[-iris_sampling_vector]

We are now in a position to build and test three different models for the iris dataset. These are in turn, the unnormalized model, a model where the input features have been centered and scaled with a Z-score transformation, and the PCA model with two principal components. We could use our test set in order to measure the predictive performance of each of these models after we build them; however, this would mean that, in our final estimate of unseen accuracy, we will have used the test set in the model selection, thus producing a biased estimate. For this reason, we often maintain a separate split of the data, usually as large as the test set, known as the validation set. This is used to tune model parameters, such as k in kNN, and among different encodings and transformations of the input features before using the test set to predict unseen performance. In Chapter 5, Support Vector Machines, we'll discuss an alternative to this approach known as cross-validation.

Once we have split our data, trained our model by following the relevant training procedure that it requires, and tuned our model parameters, we then have to assess its performance on the test set. Typically, we won't find the same performance on our test set as on our training set. Sometimes, we may even find that the performance we see when we deploy our model does not match what we expected to see, based on the performance on our training or test sets. There are a number of possible reasons for this disparity in performance. The first of these is that the data we may have collected may either not be representative of the process that we are modeling, or that there are certain combinations of feature inputs that we simply did not encounter in our training data. This could produce results that are inconsistent with our expectations. This situation can happen both in the real world, but also with our test set if it contains outliers, for example. Another common situation is the problem of model overfitting.

Overfitting is a problem in which some models, especially more flexible models, perform well on their training dataset, but perform significantly worse on an unseen test set. This occurs when a model matches the observations in the training data too closely and fails to generalize on unseen data. Put differently, the model is picking up on spurious details and variations in a training dataset, which are not representative of the underlying population as a whole. Overfitting is one of the key reasons why we do not choose our model based on its performance on the training data. Other sources of discrepancy between training and test data performance are model bias and variance. Together, these actually form a well-known trade-off in statistical modeling known as the bias-variance tradeoff.

The variance of a statistical model refers to how much the model's predicted function would change, should a differently chosen training set (but generated from the exact same process or system that we are trying to predict as the original) be used to train the model. A low variance is desired because essentially, we don't want to predict a very different function with a different training set that is generated from the same process. Model bias refers to the errors inherently introduced in the predicted function, as a result of the limitation as to what functional forms the specific model can learn. For example, linear models introduce bias when trying to approximate nonlinear functions because they can only learn linear functions. The ideal scenario for a good predictive model is to have both a low variance and a low bias. It is important for a predictive modeler to be aware of the fact that there is a bias-variance trade-off that arises from the choice of models. Models that are typically more complex because of the fact that they make fewer assumptions on the target function are prone to less bias, but higher variance than simpler but more restrictive models, such as linear models. This is because more complex models are able to approximate the training data more closely due to their flexibility, but as a result, they are more sensitive to changes in training data. This, of course, is also related to the problem of overfitting that complex models often exhibit.

We can actually see the effects of overfitting by first training some kNN models on our iris datasets. There are a number of packages that offer an implementation of the kNN algorithm, but we will use the knn3() function provided by the caret package with which we are familiar. To train a model using this function, all we have to do is provide it with a data frame that contains the numerical input features, a vector of output labels, and k, the number of nearest neighbors we want to use for the prediction:

> knn_model     <- knn3(iris_train, iris_train_labels, k = 5)
> knn_model_z   <- knn3(iris_train_z, iris_train_labels, k = 5)
> knn_model_pca <- knn3(iris_train_pca, iris_train_labels, k = 5)

To see the effect of different values of k, we will use the iris PCA model that is conveniently available in two dimensions for us to visualize and repeatedly train:

In the preceding plots, we have used different symbols to denote data points corresponding to different species. The lines shown in the plots correspond to the decision boundaries between the different species, which are the class labels of our output variable. Notice that using a low value of k, such as 1, captures local variations in the data very closely and, as a result, the decision boundaries are very irregular. A higher value of k uses many neighbors to create a prediction, resulting in a smoothing effect and smoother decision boundaries. Tuning k in kNN is an example of tuning a model parameter to balance the effect of overfitting.

We haven't mentioned any specific performance metrics in this section. There are different measures of model quality relevant to regression and classification, and we will address these after we wrap up our discussion on the predictive modeling process.

During the first iteration of this process (and this is very much an iterative process!), we usually arrive at this stage, having trained and assessed a simple model. Simple models usually allow us to get to a quick and dirty solution with minimum effort, thus giving us an early sense of how far away we are from a model that will make predictions with reasonable accuracy. Simple models are also great at giving us a baseline level of performance against which we can benchmark the performance of future models. As modelers, we often acquire a preference toward one method over others, but it is important to remember that it is generally well worth the effort to try out different approaches to a problem and use the data to help us decide which one we should end up using.

Before picking the final model, it is worth considering whether it might be a good idea to use more than one model to solve our problem. In Chapter 7, Ensemble Methods, we spend an entire chapter studying techniques that involve many models working together to boost the predictive accuracy of the overall system.

Once we have chosen the final model to use, we want to finalize its implementation so that the end users can use it reliably. Programmers refer to this process as deploying to production. This is where sound software engineering principles become extremely important. The following guidelines offer some useful advice: