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This is a lecture a lecture about

preprossings, preprocessing covariants with principal components analysis.

The idea is that often you have multiple quantitative

variables and sometimes they'll be highly correlated with each other.

In other words, they'll be very similar to being the almost the exact same variable.

In this case, it's not necessarily useful to include every variable in the model.

You might want to include some summary that

captures most of the information in those quantitative variables.

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So, as an example I'm going to use the spam data set again.

So I've loaded the caret package here, and I've loaded

the kernel app package, and loaded the spam data set.

I again, create a training and test set and I'm going to

perform only the operations on the training set that I'm doing here.

So that all exploration and model creation and

feature building has to happen in the training set.

The first thing that I do is that I

leave out just the 58th column of this training set.

Which in this case is the outcome.

So I'm looking at all the other predictor variables.

And I calculate the correlation between all those columns.

The correlation between all predictor variables.

And I take its absolute value.

So I'm looking for all the predictor variables that that have

a very high correlation or are very similar to each other.

Every variable has a correlation of 1 with itself.

So I'm not interested in those variable.

You know, removing variables that have high

correlations with themselves, since they all do.

So I set the diagonal of those matrix, that comes out to be equal to 0.

That's basically just setting the correlation

between variables with itself, equal to 0.

And then I look, which of these variables have a high correlation with each other?

In other words, which of the variables have a correlation greater than 0.8?

So it turns out two variables have a very high correlation with each other.

They are the num415 and num857.

So it's how, if the number 415 and

857 appears in the email and frequently appears together.

This is likely because there's a phone number that has similar variables there.

1:51

So, if I look at the spam dataset, at the columns 34

and 32, which I got from getting that from the previous correlation variable.

I see that it's these two variables, these

two columns that are highly correlated with each other.

And if I plot those two columns against each other, I see exactly what I'd expect.

So, the frequency of four 415 and 857 is incredibly highly

correlated, this basically lie perfectly on a line with each other.

So, as the number of 415 appears more frequently, so does the number 857.

So the idea is, including both of these predictors

in the model might not necessarily be very useful.

And so, the basic idea is, how can we take those variables

and turn them into, say, a single variable that might be better?

And one idea is to think about it as a weighted

combination of those predictors that explains most of what's going on.

So the idea is to pick the

combination that captures the most information possible.

And the benefits here are, you're reducing the number

of predictors you need to include in your model.

So that's nice.

And you're also reducing noise.

In other words, you're averaging or combining

variables together, so you might reduce them together.

So you do this in a clever way, you

actually gain quite a bit by doing principal component analysis.

So one idea to think about is just.

Basically what you're trying to do is figure out a

combination of these variables that explain close to the variability.

So just as an example, here's a combination I could do.

I could say I could take 0.71 times the 415 variable plus 0.71 times 857 variable.

And create a new variable called x.

Which is basically the sum of those two variables.

Then I could take the difference of those two variables.

By basically doing 0.71 times 415 minus 0.71 times 857.

So this is basically adding, x is adding the

two variables together, y is subtracting the two variables.

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So then if I plot those variables versus each other, when I add

them up, that's the x-axis, and when I take the difference, that's the y-axis.

And so you can see most of the variability is happening in the x-axis.

In other words there's lots of points all spread out across the x-axis,

but most of the points are clustered right here at 0 on the y-axis.

So that almost all of these points have a y value of 0.

So, the adding the two variables together captures most of the

information in those two variables and

subtracting the variables takes less information.

So the idea here is we might want to

use the sum of the two variables as a predictor.

That will reduce the number predicted that we will

have to use and renew some of the noise.

So there are two related problems to how you do this in a more general sense.

And so the ideas are find a new set of variables based on the variables

that you have that are uncorrelated and explain as much variability as possible.

In other words from the previous plot, we're looking for

the x variable which has lots of variation in it.

And not the y variable which is almost always 0.

So if you put the variables together in

one matrix, create the best matrix with fewer variables.

In other words this is lower rank if

you're talking mathematically that explains the original data.

These two problems are very closely related to each other.

And they're both the idea that, can we use

fewer variables to explain almost everything that's going on.

The first goal is a statistical goal and

the second goal is a data compression goal.

But they're also, they're both very useful for machine learning.

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So there's two related solutions and they're very similar to each other.

So if x is a matrix with a variable in each column, and an

observation in each row, like a data in frame you usually have in R.

Then the singular value decomposition is a matrix decomposition.

So it takes that data frame X, and breaks it up into

three matrices, a U matrix, and D matrix, and a B matrix.

And the V, the columns of U are called the left singular vectors.

And the columns of B are called the right singular vectors.

And D is a diagonal matrix.

Those are called the singular values.

5:44

You will learn about this in getting data

or exploratory data analysis if you've taken those classes.

The principle components are equal to the right singular

vectors if you scale the data in the same way.

In other words, the solution to both of those problems that I talked

about on the previous slide is the same if you do the right scaling.

So the idea here is, these variables in V are

constructed to explain the maximum amount of variation in the data.

So, just to show you how this works in

a real example, suppose we take that spam data set.

And we just take those two variables that were highly correlated with each other.

Variables 34 and 32.

So then we do principal components.

Same as the singular value decomposition on the, on that

small data set that just consists of those two variables.

If we plot the first principle component versus the second principle component.

We see a plot that is very similar to the one that I showed you earlier.

Where the first principal component looks like adding the two variables together.

And the second principal component looks a lot

like subtracting the two variables from each other.

So why would we do principal components, instead of just adding and subtracting?

Well, principal components allows you to perform this operation,

even if you have more than just two variables.

You may be able to reduce all of the variables down into a very small number

of combinations of sums and differences and weighted

sums and differences of the variables that you've observed.

So, using principal components can let you look at a

large number of quantitative variables and reduce it quite a bit.

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The one thing that you can also look at

it in this principal component object is the rotation matrix.

Which is basically how it's summing up the

two variable to get each of the principal components.

And so here you can see why I put 0.71

in the sum and the difference on the first slide.

So, principal component one is just 0.7081 times num14, 415, and 0.7061 times num857.

Principal component two is just the difference

again, by multiply by 0.7061, and minus 0.7081.

So basically, in this particular case the first principal component, the one

that explains the most variability is just adding the two variables up.

And the variable that explains the second most variability in these

two variables is the taking the difference between the two variables.

7:59

So in this spam data we can do, actually do

this for a more variables than just the two variables.

This is why principal components may be useful.

So here, I'm creating a variable that's just going to

be the color we're going to color our points by.

So it's color equal to black if you are not

a spam and color equal to red if you're a spam.

And this variable here, or this statement here

calculates the principal components on the entire data set.

So you'll notice that I've applied a function

of the data set, the log 10 transform.

And I've added one.

I've done this to make the data look a little bit more Gaussian.

Because some of the variables are normal

looking, because some of the variables are skewed.

And you often have to do that

for principal component analysis to look sensible.

So then I calculated the principal components of the entire data set.

So in this case I can now again

plot principal component one, versus principal component two.

Principle component one is no longer a very easy addition of two variables.

It might be some quite complicated combination

of all the variables in the data set.

But it's the combination that explains the most variation in the data.

Principle component two is the combination that explains the second most variation.

And principal component three explains the third most and so forth.

So if I plot principal component one.

That's just a variable that I've calculated.

Versus variable principal component two

that's another variable that I've calculated.

Then I color them by the spam indicator.

So, whether each point, so each of

these points corresponds to a single observation.

The red ones correspond to spam observations

and the black ones just ham observations.

You could see that in principal component

one space, or along the principal component one.

There's a little bit of separation of the ham messages from the spam messages.

In other words the spam messages tend to have

a little bit higher values than principal component one.

So this is a way to reduce the size of your data set while still

capturing a large amount of variation which

is a, a, the idea behind feature creation.

9:54

You can do this in caret as well.

So you can do it using the pre-process function.

So this is just using, basically doing

a similar type operation with a caret package.

You pass the pre-process function.

The same data set you did before.

You tell it what methods you use.

In this case you tell it to use principal component analysis or PCA.

You tell it the number of principal components to compute.

And then, what we can do is you can actually calculate the

values of each new principle compo, so the principle component are two variables.

There is principle component one, principle component two.

And they're basically a model that you fit to the data.

So the idea is that if you get a new observation you have

to predict what the principle component will look like for that new variable.

So we pass this pre-processed object and the data set,

to the predict function and that gives us the principle component.

If we plot them versus each other, you see spam pc

1, so that's principle component 1 versus principle component 2 here.

And again you see a little bit of separation.

Between the ham and the spam messages, in

both principle component one and principle component two.

You can do this, like I showed you before, by

doing preprocessing with the method PCA, using the preProcess function.

And then you can create training predictions by using the predict function.

And then, fitting a model that relates

the training variable to the principal component.

So here I haven't used the full training set as the data for fitting my model.

I've just [UNKNOWN] the principal components for the model fitting.

In the test data set you have to use the same principal

component that you calculated in the trained video set for the test variables.

So the idea here is we again pass at

the pre-process object that we calculated in the training set.

But now we pass at the new testing data.

So this predict function is going to take

the principle components we calculated from training.

And get the new values for the test data set on those same principle components.

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So then, what you can do, is you can predict.

The, using the modelFit on the original data using the test principal components.

And you can use the confusionMatrix argument in caret to get the accuracy.

And so, here we calculated a relatively small number of

principal components, but still have a relatively high accuracy in prediction.

So principal component analysis can reduce

the number of variables while maintaining accuracy.

12:18

So the other thing that you can do is you can

actually decide for this analysis to not use the predict function separately.

You can build it right into your training exercise.

So if you take the train function from the

caret package, and you pass it in a training set.

But you tell it to pre process with principal component analysis.

It will do that pre-processing as part of the training process.

And then when you do the prediction on the new data set you just pass

it a testing data set and will, it will actually calculate the PC's for you.

The reason why I showed you the more elaborate way

of calculating the PC's first and passing them to the model.

Is so that you can see what's going on under the hood.

When you pass a command like this, to the train function in the caret package.

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So this is most useful for linear type models.

This includes linear discriminant analysis, linear

and generalized linear regression, things like that.

It can make it a little bit harder to interpret the predictors.

In the case where I only had two variables, it was just the sum

and the difference of those variables, it was very easy to predict what that meant.

In general though, if you do principal

components on a large number of quantitative variables.

In each principal component might be quite a complex weighted sum of

the variables you've observed and so it could be very hard to interpret.

You have to watch out for outliers.

Outliers can really wreak havoc on calculating principal components.

So you do that by looking at

an exploratory analysis first and identifying outliers.

Doing transforms, like I did the log ten transform of

the data, you might do Box Cox transformations as well.

And again, plotting predictors to identify problems is the

key place to figure out where this is working out.

For more information, you can see the exploratory data analysis class

where we talk about principal component analysis and SVD in more detail.

And this book the Elements of Statistical Learning has

a quite nice, if a little bit technical overview.

Of how principal components work for machine learning.