Principal Components Analysis

Some datasets are naturally redundant. Loosely speaking, each element of the set contains “more information than necessary”. For example, imagine that the dataset you’re collecting has, in one column, daily temperatures in degrees Fahrenheit, and in another column, daily temperatures in degrees Celsius. In this case, all of the “signal” in these two columns actually happens in a lower-dimensional portion of the original space.

And since we tend to prefer simpler versions of the dataset, we would like to find out how to transform the original dataset to a representation with smaller dimension, but still much (or, in the extreme example above, all) of the signal. Principal Components Analysis is one the most fundamental tools to find such transformations.

In order to make things concrete, let’s assume that the dataset has $m$ elements, each containing $n$ attributes, and that we lay these out in a matrix $X$ that has $m$ rows and $n$ columns: $X \in R^{m,n}$.

PCA will return two things that are both useful. First, PCA gives us back a smaller version of the dataset: instead of having $n$ attributes, we will have $k$ attributes, and we will generally choose $k$ to be much smaller than $n$. Second, PCA will give us the transformation that takes any value in the input space into a value in the output space. In addition, this transformation is linear: a matrix that takes vectors from $n$-dimensional space to $k$-dimensional space.

Two ways to PCA

If you’ve read about PCA before, you might remember something like “the principal components are the eigenvectors of the covariance matrix”. This statement is true, but it doesn’t actually help you understand what the PCA is doing. Instead, we will look at the PCA in two ways.

PCA through the covariance matrix

Given a dataset represented as above, we can define the covariance between any two attributes of the dataset. If we think of each column of the matrix $ X_{*i} = [ x_{0,i}, x_{1,i}, \cdots, x_{n-1,i} ] $ as a vector (storing the values of these attributes), then the covariance between any two attributes is given by

\[\Cov[X_{*i}, X_{*j}] = E[(X_{*i} - E[X_{*i}])(X_{*j} - E[X_{*j}])]\]

To make our analysis easier, let’s work with a slightly different version of the dataset, $\tilde{X}$, where we will subtract the average column value from each column:

\[\tilde{X}_{i,j} = X_{i,j} - E[X_{*i}],\]

and so

\[E[\tilde{X}_{*i}] = 0.\]

Now, it’s easy to see that the covariance matrix of $\tilde{X}$ has a simpler expression:

\[\begin{align}\Cov[\tilde{X}_{*i}, \tilde{X}_{*j}] &=& E[(\tilde{X}_{*i} - E[\tilde{X}_{*i}])(\tilde{X}_{*j} - E[\tilde{X}_{*j}])]\\\Cov[\tilde{X}_{*i}, \tilde{X}_{*j}] &=& E[\tilde{X}_{*i} \tilde{X}_{*j}]\\m \Cov[\tilde{X}_{*i}, \tilde{X}_{*j}] &=& m \tilde{X}^T \tilde{X}\end{align}\]

$\tilde{X}^T \tilde{X}$ is a symmetric, $n \times n$ matrix.

Now let’s consider the expression $v^T \tilde{X}^T \tilde{X} v$: this is equal to $\langle \tilde{X} v, \tilde{X}v \rangle$, and so equal to $|| \tilde{X} v ||^2$, which is never a negative value. This means $\tilde{X}^T \tilde{X}$ cannot have a negative eigenvalue. It also means that we can then write $\tilde{X}^T \tilde{X}$ as

\[\tilde{X}^T \tilde{X} = U \Lambda U^T,\]

where $U$ is an orthogonal matrix (a rotation), and $\Lambda$ is a diagonal matrix of non-negative values, sorted from largest to smallest 1. This, in turn, yields:

\[\tilde{X}^T \tilde{X} = U \Lambda^{1/2} \Lambda^{1/2} U^T,\]

Now consider the expression $\tilde{X} U$. This expression rotates all of the vectors in $\tilde{X}$ (so that doesn’t change the lengths of each row vector). But now notice that the above equation leads to

\[\begin{align}U^T \tilde{X}^T \tilde{X} U &=& U^T U \Lambda U^T U\\ U^T \tilde{X}^T \tilde{X} U &=& \Lambda.\end{align}\]

So if we rotate the rows of $\tilde{X}$ by U, its covariance matrix is diagonal! That means that after rotating $\tilde{X}$ the attribute vectors (ie. the columns) are orthogonal to each other.

Now imagine if we created a matrix $\hat{U}$ equal to $U$, except that it lacks the very last column. $\hat{U}$ is a projection matrix: roughly speaking, it sends vectors from $R^n$ to $R^{n-1}$ in such a way that no vector increases in length. In that case $\tilde{X} \hat{U}$ will be an $m \times (n-1)$ matrix.

Now, let’s think of the sum of squared lengths of the rows (“sums of squares” for short, or SS) in $\tilde{X}\hat{U}$, and compare to the SS of $\tilde{X}$ (which is itself equal to the sum of squares of entries in each value in the matrix).

The remarkable feature of $\hat{U}$ is that, among all projection matrices from $R^n$ to $R^{n-1}$, $\hat{U}$ is such that the SS of $\tilde{X}\hat{U}$ is as close as possible to the SS of $\tilde{X}$ itself. This happens, essentially, because the SS of $\tilde{X}U$ is equal to that of $\Lambda^{1/2}$. Remember that $U$ is a rotation, so it doesn’t change the squared lengths of the rows: a right-multiplication by $U$ doesn’t change the SS of $\tilde{X}$!

In other words: among all possible projections which drop a column from $\tilde{X}$, we need to pick one that makes the SS of the projected matrix equivalent to dropping the smallest value from $\Lambda^{1/2}$ — if we don’t, then we could have picked a better projection! In the same way, if we wanted a projection to one-dimensional space, then we would pick the first column of $U$, because that would corresponds to the largest value in $\Lambda^{1/2}$, and so would be the “best” single one-dimensional projection (in the sense of preserving sums of squared lengths of the dataset).

The $i$-th column of $U$ is known as the $i$-th principal direction, and the attributes found by multiplying $\tilde{X}$ by these columns are the principal components of $X$.

The algorithm to compute the principal components of a dataset is, then:

  1. Let $X$ be a $m \times n$-dimensional matrix, where each row is an entry from the dataset.
  2. Let $\tilde{X}$ be the matrix where we subtract the column means from each column.
  3. Let $M = \tilde{X}^T \tilde{X}$ be the matrix $M = (m_{ij})$ of covariances between the $i$-th and $j$-th column of $\tilde{X}$. $M$ is an $n \times n$ matrix.
  4. Let $U$ be the matrix such that $M = U \Lambda U^T$, where $U$ is orthogonal, and $\Lambda$ has diagonal entries ordered from largest to smallest.
  5. The principal components of the dataset are (in order) the columns of $\tilde{X} U$.

PCA through a matrix of inner products

Now, let’s consider this seemingly different approach:

  1. Let $X$ be a $m \times n$-dimensional matrix, where each row is an entry from the dataset.
  2. Let $\tilde{X}$ be the matrix where we subtract the column means from each column.
  3. Let $M = \tilde{X} \tilde{X}^T$ be the matrix $M = (m_{ij})$ of inner products between the $i$-th and $j$-th rows of $\tilde{X}$. $M$ is an $m \times m$ matrix.
  4. Let $U$ be the matrix such that $M = U \Lambda U^T$, where $U$ is orthogonal, and $\Lambda$ has diagonal entries ordered from largest to smallest.
  5. The principal components of the dataset are (in order) the columns of $U \Lambda^{1/2}$.

Say what? How can these two things be the same?

PCA via the SVD.

The easiest way to see that these two approaches are identical is to consider the singular value decomposition (SVD) of $M$. The SVD of a matrix is a bit like the eigendecomposition, but it is more general: the SVD exists for any matrix, rectangular or square, symmetric or not. Concretely, the SVD of a $m \times n$ matrix $M$ is

\[M = U \Sigma V^T,\]

or a set of three matrices: $U$ is an orthogonal $m \times m$ matrix (whose columns are known as the left singular vectors); $\Sigma$ is a diagonal, rectangular $m \times n$ matrix with non-negative, non-increasing values in the diagonal (known as the singular values), and $V^T$ is an $n \times n$ orthogonal matrix (whose rows are known as the right singular vectors). Like the eigendecomposition, the SVD has two orthogonal matrices and a diagonal matrix. Unlike the eigendecomposition, the orthogonal matrices in the SVD are different from each other’s transpose, and they might even have different dimensions. The entries of the diagonal matrix of the SVD are never negative, unlike eigendecomposition. Finally, the SVD of any matrix always exists, but even some square matrices lack an eigendecomposition.

But enough about the SVD: let’s put it to use. Specifically, let’s look at the SVD of $\tilde{X}$:

\[\begin{align}\tilde{X} &=& U \Sigma V^T \\ \tilde{X} \tilde{X}^T & = & U \Sigma V^T V \Sigma^T U^T \\ \tilde{X}^T \tilde{X} &=& V \Sigma^T U^T U \Sigma V^T \end{align}\]

Since $U$ and $V$ are orthogonal, a lot of terms cancel:

\[\begin{align} \tilde{X} \tilde{X}^T & = & U \Sigma_1^2 U^T \\ \tilde{X}^T \tilde{X} &=& V \Sigma_2^2 V^T \end{align}\]

(We use $\Sigma_1^2$ and $\Sigma_2^2$ to differentiate them since the former is $m \times m$, and the latter is $n \times n$.) From here, we can see that there are a lot of relationships between the SVD of $\tilde{X}$ and the eigendecompositions of $\tilde{X}\tilde{X}^T$, and that of $\tilde{X}^T\tilde{X}$. Specifically, the singular values of $\tilde{X}$ are equal to the square roots of the eigenvalues of both $\tilde{X}\tilde{X}^T$ and $\tilde{X}^T\tilde{X}$; the left singular vectors of $\tilde{X}$ are the eigenvectors of $\tilde{X}\tilde{X}^T$, and the right singular vectors are the eigenvectors of $\tilde{X}^T\tilde{X}$.

Putting all of these things together, and multiplying both sides of the SVD $\tilde{X} = U \Sigma V^T$ on the right by $V$, we get:

\[\begin{align} \tilde{X} V &=& U \Sigma V^T V \\ \tilde{X} V &=& U \Sigma \end{align}\]

Now the left side of the equation is the result of PCA by covariance-matrix algorithm, and the right side of the equation is the result of PCA by the inner-product algorithm! So they are truly the same thing.

But why

The computation of the PCA via eigenvectors of covariance matrices is much more intuitive, so why do we care about these two different approaches?

The reason is a little strange, but extremely practical. Sometimes, we don’t have access to the rows or columns of $X$, but we do have access to the inner products. It is extremely useful to know that in these scenarios we can still recover principal components! This is the central insight of classical multidimensional scaling.

Odds and ends

The Centering Matrix

The procedure we’ve used above to convert $X$ to $\tilde{X}$ can be represented by a matrix. This is sometimes useful to know, especially when the centering operation happens in the middle of other matrix manipulation. Specifically, if $H = (I - \vec{1}\vec{1}^T / m)$, where $m$ is the number of rows of $X$, and $\vec{1}$ is an $m$-dimensional vector of all ones $(1, 1, \cdots, 1)$, then

\[\tilde{X} = H X.\]

It is easy to see why this is the case. Expand the definition:

\[\begin{align}\tilde{X} &=& (I - \vec{1}\vec{1}^T / m) X \\ \tilde{X} &=& X - \vec{1}\vec{1}^T X / m,\end{align}\]

and now note that $\vec{1}^T X$ is a vector that stores the column sums of $X$, and so $\vec{1}^T X / m$ stores the column averages. In addition, $\vec{1} v$ creates a matrix with $m$ copies of $v$. Putting this back into the expression we see that the column averages are copied into a matrix of the same size as $X$, and then subtracted from $X$ itself.

An interesting feature of the centering matrix is that you can write it from the left side (in which case the vectors are as big as there are rows in $X$), and $HX$ will be centering the columns of X. But you can also write it from the right side, in which case the vectors are as big as there are columns in $X$, and $XH$ will then be centering the rows of X.


  1. You are given $M$, for which you know that $M = U \Lambda U^T$, where $U$ is orthogonal, and $\Lambda$ is diagonal. Show that the columns of $U$ are eigenvectors of $M$, and the entries in the diagonal of $\Lambda$ are the eigenvalues.

  2. Show that the sum of squared lengths of $\tilde{X}$ is exactly the total variance in the dataset, which is the sum of the squared distance from each point to the average value.

  3. We talked about a set of data, but used a matrix in our computations. Set elements are unordered, but matrix rows have a specific order. Show that the PCA of a dataset is independent of the choice of ordering of rows in the matrix $X$.

  4. Finish the argument that any matrix $M$ that can be written as $M = X^T X$ cannot have a negative eigenvalue.


Mingwei Li provided careful proofreading and exercise suggestions.


  1. The decomposition of a matrix $M$ into $M = U \Lambda U^T$, that is, into an orthogonal matrix, a diagonal matrix, and the inverse of the same orthogonal matrix is known as a “diagonalization” of a matrix. In this form, it should be easy to see that the columns of $U$ are the eigenvectors of $M$, and the diagonal entries of $\Lambda$ are the eigenvectors (so this is also often known as an “eigendecomposition”).