Everyone uses it but here's the thing. It doesn't actually do data reduction

Principal component analysis is the idea of trying to find a different view for our data in which we can separate it better

And I'll show an example piece of paper

And the idea is that what we want to try and do is reframe our data

Maybe move it around so that we can better separate things out better cluster things perhaps it's better for machine learning

Now as a side effect of this

in PCA, we also order our

Axes by the most to least useful in some sense. So then we can perform a separate data reduction

Technique later by taking the slightly less useful axes away by or in this case

Dimensions or attributes of our data PCA is commonly pitched as a data reduction technique. Actually. It's a data transformation technique

It just makes our data and meaning able to production later

So let's imagine we have some attributes and we we know that some are correlated some are not correlated

The problem is that maybe we don't want to just delete some of the attributes may be

0.65 correlation is I mean

It's it's good

But it's not it doesn't mean we definitely want to delete attribute two and keep only attribute one on the other hand maybe

We do need to reduce some of the number of dimensions we've got or maybe we just want to try and make our data

More amenable to things like clustering. So let's look at a quick example

Typically PCA is done over many dimensions when we've got lots and lots of attributes

I'm just going to show two because obviously I starts to break down when I try and draw that many on the page

So if we have two attributes

And what we want to try and do is work out what the contribution of each of these is to our data set

Which of these is useful which of these is not useful and now obviously if we had many dimensions, you know

Seven hundred ten thousand we can still apply the same technique. So maybe we have some data that's like this

We have some datasets over here and perhaps we have a little gap and maybe some data over here and in general

Our data is kind of increasing like this. So this means that attribute one and attribute two are positively correlated to some extent

but maybe the correlation is not so strong that we just wanted elite attribute to what we want to try and do is

Transform our data into a way where these are more useful imagine that you've got some data but looks a bit like this

But if we rotate our data

We take a different view we can see there's actually two

objects and then we can separate them out and maybe if you were to take them again you could see there was four objects and

So on this is the idea what PCA is going to do is find new axes for this data

That separate it better for PCA to work. What we would start by doing is standardizing our data

So all of our dimensions attribute one attribute to all of the attributes are going to be centered around zero

And they're going to have a standard deviation of one

PCA will not work really at all. If you have widely different scales for your data

So what we want to try and do is find a direction or an axis through these two attributes

That separates out our data better than individual attributes

Do let's see how this data looks just from attribute one

If we trace down this way

you can see that it's sort of got this amount of spread in actually Bute one and they kind of

Dotted around like this and they sort of should go all the way along like this so you can't really see anything on here

Meaningful about these two groups, right?

And of course the more dimensions you have the more this could be a problem

Similarly about tribute to if we trace along here it goes from this range to this range

This is the variance of attribute - like the range and we can see that roughly speaking

The data is as spread out in attribute one as it is in attribute to that spread is about the same and both of them

are kind of useful for looking of a data but not really because again,

We have an equal distribution of point all the way along here. So that's not hugely useful

All right. So if we look at just attribute one, that's not hugely helpful

If we look at just attribute two, that's not hugely helpful either. So what can we do?

well

what we want to try and do is find a new axis like some new attribute that fits through this data like this and can

Really separate everything out because the spread of this data is actually diagonally in some sense not this way or this way

So what principal component analysis is going to do is find this principal component miss axis through our data like this

Such that when we look at the spread of a data, it's maximized, right?

So the data is as spread out as we can find it

And this is going to happen over any number of attributes

So actually one here

attribute to attribute three attribute for all the way to attribute n when we've got maybe 700 or 800 or

$1000 so at the moment which is fitting one principal component, this is one line through our two-dimensional data

There's going to be more principal components later, right?

But what we want to do is we want to pick the direction through this data

However, many attributes it has that has the most spread. So how do we measure this?

There's really two goals which were exactly the same one is to maximize the variance

So we find a direction for this line such that these points at the very edge are farthest apart

The other one is that we minimize the error

so we take this error from here this distance this distance from all these points to our new axes and we minimize it so

You can imagine if we do this for all our points we can get the sum of the squared

distances from these points to this line and then as we move this line around

Sometimes if it's going to be better

Sometimes it's not if we have a line that goes like this

Some of these lines are going to be very large like this and that's going to be a higher amount of error

So what we'll find is that if we do this our first principal component will sit through whichever direction in the data

minimizes these distances and by definition

Maximizes this spread which makes this axis super useful if we use this axis now as our new X and we rotate this whole page

All our data is lovely and separated. And actually we have two distinct clusters in this data set, right?

So that's what we're going to do

Now as I mentioned PCA doesn't typically reduce the number of attributes from two to one just like that

We're going to have another principal component which represents the second amount of most variance orthogonal e so at ninety degrees

So that's going to be this one here

We find the first principal component which maximizes variance and then we find the next one along that maximizes events in the next direction

Now if there were multiple dimensions we'd keep applying this process

We keep finding new axes for our data that systematically show more and more of a spread of our data

But we're crucially we're ordering this by the amount of variance that they represent

So this is PC one or principal component one. This is principal component two and

Principal component one is always going to have the most

Varied data in it principal component to the next most three the next most all the way to the end with the least

so a natural

Side-effect of this process is that we're going to have new axes through our data

Which and we're going to have a same number of axes as there are original dimensions in our data

But they're going to get less and less useful in terms of the variance of our data as we go forward

So PC one is going to be the most important

most of our data is spread out across

Pc-1 pc2 a little bit less spread out PC three a little bit less still all the way down to PC n all the way

Down here if you wanted to perform dimensionality reduction because you felt you had too many dimensions to your data

you could just for example keep the first 10 principal components project your data into that space and

Still retain most of the information

we won't go into the mathematics of how to calculate these principal components because you can find out very easily online and all has a

Lovely function to do it for us

I wanted to focus on intuitively what PCA does but how we will actually project these points onto these new

axes and rotate the whole thing is

Each of these principal components is going to be a weighted sum of all the attributes

So for example PC one is going to be some amount of attribute one

Added to some amount of attribute two now in this case because it sort of goes off at sort of 45 degrees

It's going to be about the same but you could imagine if your data was like this

It'll be mostly attribute one and a little bit of attribute two if it was like this

It'll be mostly attribute to a little bit attribute one

All right. Now, of course the n-dimensional data or we have many more dimensions that I can't draw on the page

The principle is exactly the same some amount of attribute one attribute to attribute three and so on all the way to the end

Right and that's going to project our points straight onto this line through that data

So when we talk about minimizing the error you can imagine

Rotating this about the center of these points here like this

And as you do this these red lines are going to change in length

And it's going to settle on the very center line where these weights are minimized

Right and as it happens that also maximizes the variance of these points here because of the fact that this mathematics is based around

eigenvectors and eigenvalues

Pc2 is always going to come out or foggin all or in this case at 90 degrees to pc one now

This is true of however many dimensions. You've got every single new axis that appears or new vector

A new principal component is going to come out or foggin all to the ones before

Until you run out of dimensions and you can't do it anymore

We've already reached the most we can fit in on this two-dimensional plane

We've got one here and we've got another one orthogonal to it

There is no other lines I can draw for that to be true

Right, but obviously if we had more attributes, that would be the case

so the reason that it's so important to scare your data appropriately is that you're trying to find the direction for your data that

Maximizes the variance now, if one of your dimensions is much much bigger than the other of course

That one is the one that's going to maximize the variance

if you've got salary that's between naught and

10,000 and all your others are between naught and 1

Then your first principal component is going to be predominately salary because that's the most important thing as far as it know

If as it knows this is why it's so important to standardize your data first

We're going to continue to use our music data set for this video now for those of you

Forgotten this data set is a set of music files that are freely available online

Where we've got the metadata of a genres or titles for different tracks and then for those tracks

We've also calculated some features about the actual audio for example

Temporal features how loud they are?

How fast the music is how upbeat it is whether you could dance to it this kind of thing

Apparently dance ability is a measurable trait

Apparently these teachers have been generated by two different libraries once called Lib rosa

Which is freely available online and the other ways echo nests

Which are the features that a core of Spotify and how it does its music recommender system and its playlists

So let's load the data set

So I'm going to read it. It takes quite a long time to load

It'll probably be faster if it wasn't in a CSV, you've got to remember if your files are in CSV

You've got to actually pass the more than workout, whether they're numerical or text, you know for every cell. Okay, so we've got

13,000 instances or rows in our data and we've got

751 attributes or dimensions to our data? So these are going to include features from both liberals

ER and echo nest and the other metadata of these tracks

So we're going to select just the echo nest features for this part

Just be it's a little bit easier to have fewer dimensions to look at this would work just as well

On all the other features as long as they're numeric

So we're gonna select echo nest is equal to the music data frame all of the rows and just the echo nests columns

Which are 528 to the end and then we're going to standardize all this data now

So we're going to Center it around 0 a mean of 0 and a standard deviation of 1 using the scale function

now take a minute to finish and then we can just check to make sure that our

Variance and our mean or what we expected. So we're going to apply over dimension two

so that's over all the columns the

Variance function and find out what the variances are and you can see they're all one, which is exactly what we want

So let's have a look at the mean the mean should be centered about 0

It won't be exactly 0 just because of you know, floating point errors and so on. So there we go. So 1.5

10 to the minus 17 very very small right close enough to 0 perfectly fine

So the function we're going to use is the PPR comp function in R

This is going to perform principal component analysis for those of you who are interested in learning more

What it's going to do is create a covariance matrix, and then it's going to use singular value decomposition

To find the eigenvectors and the eigenvalues and those are the things that actually we want from a PCA