# Earthmover Distance

Problem: Compute distance between points with uncertain locations (given by samples, or differing observations, or clusters).

For example, if I have the following three “points” in the plane, as indicated by their colors, which is closer, blue to green, or blue to red?

It’s not obvious, and there are multiple factors at work: the red points have fewer samples, but we can be more certain about the position; the blue points are less certain, but the closest non-blue point to a blue point is green; and the green points are equally plausibly “close to red” and “close to blue.” The centers of masses of the three sample sets are close to an equilateral triangle. In our example the “points” don’t overlap, but of course they could. And in particular, there should probably be a nonzero distance between two points whose sample sets have the same center of mass, as below. The distance quantifies the uncertainty.

All this is to say that it’s not obvious how to define a distance measure that is consistent with perceptual ideas of what geometry and distance should be.

Solution (Earthmover distance): Treat each sample set $A$ corresponding to a “point” as a discrete probability distribution, so that each sample $x \in A$ has probability mass $p_x = 1 / |A|$. The distance between $A$ and $B$ is the optional solution to the following linear program.

Each $x \in A$ corresponds to a pile of dirt of height $p_x$, and each $y \in B$ corresponds to a hole of depth $p_y$. The cost of moving a unit of dirt from $x$ to $y$ is the Euclidean distance $d(x, y)$ between the points (or whatever hipster metric you want to use).

Let $z_{x, y}$ be a real variable corresponding to an amount of dirt to move from $x \in A$ to $y \in B$, with cost $d(x, y)$. Then the constraints are:

• Each $z_{x, y} \geq 0$, so dirt only moves from $x$ to $y$.
• Every pile $x \in A$ must vanish, i.e. for each fixed $x \in A$, $\sum_{y \in B} z_{x,y} = p_x$.
• Likewise, every hole $y \in B$ must be completely filled, i.e. $\sum_{y \in B} z_{x,y} = p_y$.

The objective is to minimize the cost of doing this: $\sum_{x, y \in A \times B} d(x, y) z_{x, y}$.

In python, using the ortools library (and leaving out a few docstrings and standard import statements, full code on Github):

from ortools.linear_solver import pywraplp

def earthmover_distance(p1, p2):
dist1 = {x: count / len(p1) for (x, count) in Counter(p1).items()}
dist2 = {x: count / len(p2) for (x, count) in Counter(p2).items()}
solver = pywraplp.Solver('earthmover_distance', pywraplp.Solver.GLOP_LINEAR_PROGRAMMING)

variables = dict()

# for each pile in dist1, the constraint that says all the dirt must leave this pile
dirt_leaving_constraints = defaultdict(lambda: 0)

# for each hole in dist2, the constraint that says this hole must be filled
dirt_filling_constraints = defaultdict(lambda: 0)

# the objective
objective = solver.Objective()
objective.SetMinimization()

for (x, dirt_at_x) in dist1.items():
for (y, capacity_of_y) in dist2.items():
amount_to_move_x_y = solver.NumVar(0, solver.infinity(), 'z_{%s, %s}' % (x, y))
variables[(x, y)] = amount_to_move_x_y
dirt_leaving_constraints[x] += amount_to_move_x_y
dirt_filling_constraints[y] += amount_to_move_x_y
objective.SetCoefficient(amount_to_move_x_y, euclidean_distance(x, y))

for x, linear_combination in dirt_leaving_constraints.items():

for y, linear_combination in dirt_filling_constraints.items():

status = solver.Solve()
if status not in [solver.OPTIMAL, solver.FEASIBLE]:
raise Exception('Unable to find feasible solution')

return objective.Value()


Discussion: I’ve heard about this metric many times as a way to compare probability distributions. For example, it shows up in an influential paper about fairness in machine learning, and a few other CS theory papers related to distribution testing.

One might ask: why not use other measures of dissimilarity for probability distributions (Chi-squared statistic, Kullback-Leibler divergence, etc.)? One answer is that these other measures only give useful information for pairs of distributions with the same support. An example from a talk of Justin Solomon succinctly clarifies what Earthmover distance achieves

Also, why not just model the samples using, say, a normal distribution, and then compute the distance based on the parameters of the distributions? That is possible, and in fact makes for a potentially more efficient technique, but you lose some information by doing this. Ignoring that your data might not be approximately normal (it might have some curvature), with Earthmover distance, you get point-by-point details about how each data point affects the outcome.

This kind of attention to detail can be very important in certain situations. One that I’ve been paying close attention to recently is the problem of studying gerrymandering from a mathematical perspective. Justin Solomon of MIT is a champion of the Earthmover distance (see his fascinating talk here for more, with slides) which is just one topic in a field called “optimal transport.”

This has the potential to be useful in redistricting because of the nature of the redistricting problem. As I wrote previously, discussions of redistricting are chock-full of geometry—or at least geometric-sounding language—and people are very concerned with the apparent “compactness” of a districting plan. But the underlying data used to perform redistricting isn’t very accurate. The people who build the maps don’t have precise data on voting habits, or even locations where people live. Census tracts might not be perfectly aligned, and data can just plain have errors and uncertainty in other respects. So the data that district-map-drawers care about is uncertain much like our point clouds. With a theory of geometry that accounts for uncertainty (and the Earthmover distance is the “distance” part of that), one can come up with more robust, better tools for redistricting.

Solomon’s website has a ton of resources about this, under the names of “optimal transport” and “Wasserstein metric,” and his work extends from computing distances to computing important geometric values like the barycenter, computational advantages like parallelism.

Others in the field have come up with transparency techniques to make it clearer how the Earthmover distance relates to the geometry of the underlying space. This one is particularly fun because the explanations result in a path traveled from the start to the finish, and by setting up the underlying metric in just such a way, you can watch the distribution navigate a maze to get to its target. I like to imagine tiny ants carrying all that dirt.

Finally, work of Shirdhonkar and Jacobs provide approximation algorithms that allow linear-time computation, instead of the worst-case-cubic runtime of a linear solver.

# Bayesian Ranking for Rated Items

Problem: You have a catalog of items with discrete ratings (thumbs up/thumbs down, or 5-star ratings, etc.), and you want to display them in the “right” order.

Solution: In Python

'''
score: [int], [int], [float] -&gt; float

Return the expected value of the rating for an item with known
ratings specified by ratings, prior belief specified by
rating_prior, and a utility function specified by rating_utility,
assuming the ratings are a multinomial distribution and the prior
belief is a Dirichlet distribution.
'''
def score(self, ratings, rating_prior, rating_utility):
ratings = [r + p for (r, p) in zip(ratings, rating_prior)]
score = sum(r * u for (r, u) in zip(ratings, rating_utility))
return score / sum(ratings)


Discussion: This deceptively short solution can lead you on a long and winding path into the depths of statistics. I will do my best to give a short, clear version of the story.

As a working example I chose merely because I recently listened to a related podcast, say you’re selling mass-market romance novels—which, by all accounts, is a predictable genre. You have a list of books, each of which has been rated on a scale of 0-5 stars by some number of users. You want to display the top books first, so that time-constrained readers can experience the most titillating novels first, and newbies to the genre can get the best first time experience and be incentivized to buy more.

The setup required to arrive at the above code is the following, which I’ll phrase as a story.

Users’ feelings about a book, and subsequent votes, are independent draws from a known distribution (with unknown parameters). I will just call these distributions “discrete” distributions. So given a book and user, there is some unknown list $(p_0, p_1, p_2, p_3, p_4, p_5)$ of probabilities ($\sum_i p_i = 1$) for each possible rating a user could give for that book.

But how do users get these probabilities? In this story, the probabilities are the output of a randomized procedure that generates distributions. That modeling assumption is called a “Dirichlet prior,” with Dirichlet meaning it generates discrete distributions, and prior meaning it encodes domain-specific information (such as the fraction of 4-star ratings for a typical romance novel).

So the story is you have a book, and that book gets a Dirichlet distribution (unknown to us), and then when a user comes along they sample from the Dirichlet distribution to get a discrete distribution, which they then draw from to choose a rating. We observe the ratings, and we need to find the book’s underlying Dirichlet. We start by assigning it some default Dirichlet (the prior) and update that Dirichlet as we observe new ratings. Some other assumptions:

1. Books are indistinguishable except in the parameters of their Dirichlet distribution.
2. The parameters of a book’s Dirichlet distribution don’t change over time, and inherently reflect the book’s value.

So a Dirichlet distribution is a process that produces discrete distributions. For simplicity, in this post we will say a Dirichlet distribution is parameterized by a list of six integers $(n_0, \dots, n_5)$, one for each possible star rating. These values represent our belief in the “typical” distribution of votes for a new book. We’ll discuss more about how to set the values later. Sampling a value (a book’s list of probabilities) from the Dirichlet distribution is not trivial, but we don’t need to do that for this program. Rather, we need to be able to interpret a fixed Dirichlet distribution, and update it given some observed votes.

The interpretation we use for a Dirichlet distribution is its expected value, which, recall, is the parameters of a discrete distribution. In particular if $n = \sum_i n_i$, then the expected value is a discrete distribution whose probabilities are

$\displaystyle \left ( \frac{n_0}{n}, \frac{n_1}{n}, \dots, \frac{n_5}{n} \right )$

So you can think of each integer in the specification of a Dirichlet as “ghost ratings,” sometimes called pseudocounts, and we’re saying the probability is proportional to the count.

This is great, because if we knew the true Dirichlet distribution for a book, we could compute its ranking without a second thought. The ranking would simply be the expected star rating:

def simple_score(distribution):
return sum(i * p for (i, p) in enumerate(distribution))


Putting books with the highest score on top would maximize the expected happiness of a user visiting the site, provided that happiness matches the user’s voting behavior, since the simple_score is just the expected vote.

Also note that all the rating system needs to make this work is that the rating options are linearly ordered. So a thumbs up/down (heaving bosom/flaccid member?) would work, too. We don’t need to know how happy it makes them to see a 5-star vs 4-star book. However, because as we’ll see next we have to approximate the distribution, and hence have uncertainty for scores of books with only a few ratings, it helps to incorporate numerical utility values (we’ll see this at the end).

Next, to update a given Dirichlet distribution with the results of some observed ratings, we have to dig a bit deeper into Bayes rule and the formulas for sampling from a Dirichlet distribution. Rather than do that, I’ll point you to this nice writeup by Jonathan Huang, where the core of the derivation is in Section 2.3 (page 4), and remark that the rule for updating for a new observation is to just add it to the existing counts.

Theorem: Given a Dirichlet distribution with parameters $(n_1, \dots, n_k)$ and a new observation of outcome $i$, the updated Dirichlet distribution has parameters $(n_1, \dots, n_{i-1}, n_i + 1, n_{i+1}, \dots, n_k)$. That is, you just update the $i$-th entry by adding $1$ to it.

This particular arithmetic to do the update is a mathematical consequence (derived in the link above) of the philosophical assumption that Bayes rule is how you should model your beliefs about uncertainty, coupled with the assumption that the Dirichlet process is how the users actually arrive at their votes.

The initial values $(n_0, \dots, n_5)$ for star ratings should be picked so that they represent the average rating distribution among all prior books, since this is used as the default voting distribution for a new, unknown book. If you have more information about whether a book is likely to be popular, you can use a different prior. For example, if JK Rowling wrote a Harry Potter Romance novel that was part of the canon, you could pretty much guarantee it would be popular, and set $n_5$ high compared to $n_0$. Of course, if it were actually popular you could just wait for the good ratings to stream in, so tinkering with these values on a per-book basis might not help much. On the other hand, most books by unknown authors are bad, and $n_5$ should be close to zero. Selecting a prior dictates how influential ratings of new items are compared to ratings of items with many votes. The more pseudocounts you add to the prior, the less new votes count.

This gets us to the following code for star ratings.

def score(self, ratings, rating_prior):
ratings = [r + p for (r, p) in zip(ratings, rating_prior)]
score = sum(i * u for (i, u) in enumerate(ratings))
return score / sum(ratings)


The only thing missing from the solution at the beginning is the utilities. The utilities are useful for two reasons. First, because books with few ratings encode a lot of uncertainty, having an idea about how extreme a feeling is implied by a specific rating allows one to give better rankings of new books.

Second, for many services, such as taxi rides on Lyft, the default star rating tends to be a 5-star, and 4-star or lower mean something went wrong. For books, 3-4 stars is a default while 5-star means you were very happy.

The utilities parameter allows you to weight rating outcomes appropriately. So if you are in a Lyft-like scenario, you might specify utilities like [-10, -5, -3, -2, 1] to denote that a 4-star rating has the same negative impact as two 5-star ratings would positively contribute. On the other hand, for books the gap between 4-star and 5-star is much less than the gap between 3-star and 4-star. The utilities simply allow you to calibrate how the votes should be valued in comparison to each other, instead of using their literal star counts.

# Singular Value Decomposition Part 2: Theorem, Proof, Algorithm

I’m just going to jump right into the definitions and rigor, so if you haven’t read the previous post motivating the singular value decomposition, go back and do that first. This post will be theorem, proof, algorithm, data. The data set we test on is a thousand-story CNN news data set. All of the data, code, and examples used in this post is in a github repository, as usual.

We start with the best-approximating $k$-dimensional linear subspace.

Definition: Let $X = \{ x_1, \dots, x_m \}$ be a set of $m$ points in $\mathbb{R}^n$. The best approximating $k$-dimensional linear subspace of $X$ is the $k$-dimensional linear subspace $V \subset \mathbb{R}^n$ which minimizes the sum of the squared distances from the points in $X$ to $V$.

Let me clarify what I mean by minimizing the sum of squared distances. First we’ll start with the simple case: we have a vector $x \in X$, and a candidate line $L$ (a 1-dimensional subspace) that is the span of a unit vector $v$. The squared distance from $x$ to the line spanned by $v$ is the squared length of $x$ minus the squared length of the projection of $x$ onto $v$. Here’s a picture.

I’m saying that the pink vector $z$ in the picture is the difference of the black and green vectors $x-y$, and that the “distance” from $x$ to $v$ is the length of the pink vector. The reason is just the Pythagorean theorem: the vector $x$ is the hypotenuse of a right triangle whose other two sides are the projected vector $y$ and the difference vector $z$.

Let’s throw down some notation. I’ll call $\textup{proj}_v: \mathbb{R}^n \to \mathbb{R}^n$ the linear map that takes as input a vector $x$ and produces as output the projection of $x$ onto $v$. In fact we have a brief formula for this when $v$ is a unit vector. If we call $x \cdot v$ the usual dot product, then $\textup{proj}_v(x) = (x \cdot v)v$. That’s $v$ scaled by the inner product of $x$ and $v$. In the picture above, since the line $L$ is the span of the vector $v$, that means that $y = \textup{proj}_v(x)$ and $z = x -\textup{proj}_v(x) = x-y$.

The dot-product formula is useful for us because it allows us to compute the squared length of the projection by taking a dot product $|x \cdot v|^2$. So then a formula for the distance of $x$ from the line spanned by the unit vector $v$ is

$\displaystyle (\textup{dist}_v(x))^2 = \left ( \sum_{i=1}^n x_i^2 \right ) - |x \cdot v|^2$

This formula is just a restatement of the Pythagorean theorem for perpendicular vectors.

$\displaystyle \sum_{i} x_i^2 = (\textup{proj}_v(x))^2 + (\textup{dist}_v(x))^2$

In particular, the difference vector we originally called $z$ has squared length $\textup{dist}_v(x)^2$. The vector $y$, which is perpendicular to $z$ and is also the projection of $x$ onto $L$, it’s squared length is $(\textup{proj}_v(x))^2$. And the Pythagorean theorem tells us that summing those two squared lengths gives you the squared length of the hypotenuse $x$.

If we were trying to find the best approximating 1-dimensional subspace for a set of data points $X$, then we’d want to minimize the sum of the squared distances for every point $x \in X$. Namely, we want the $v$ that solves $\min_{|v|=1} \sum_{x \in X} (\textup{dist}_v(x))^2$.

With some slight algebra we can make our life easier. The short version: minimizing the sum of squared distances is the same thing as maximizing the sum of squared lengths of the projections. The longer version: let’s go back to a single point $x$ and the line spanned by $v$. The Pythagorean theorem told us that

$\displaystyle \sum_{i} x_i^2 = (\textup{proj}_v(x))^2 + (\textup{dist}_v(x))^2$

The squared length of $x$ is constant. It’s an input to the algorithm and it doesn’t change through a run of the algorithm. So we get the squared distance by subtracting $(\textup{proj}_v(x))^2$ from a constant number,

$\displaystyle \sum_{i} x_i^2 - (\textup{proj}_v(x))^2 = (\textup{dist}_v(x))^2$

which means if we want to minimize the squared distance, we can instead maximize the squared projection. Maximizing the subtracted thing minimizes the whole expression.

It works the same way if you’re summing over all the data points in $X$. In fact, we can say it much more compactly this way. If the rows of $A$ are your data points, then $Av$ contains as each entry the (signed) dot products $x_i \cdot v$. And the squared norm of this vector, $|Av|^2$, is exactly the sum of the squared lengths of the projections of the data onto the line spanned by $v$. The last thing is that maximizing a square is the same as maximizing its square root, so we can switch freely between saying our objective is to find the unit vector $v$ that maximizes $|Av|$ and that which maximizes $|Av|^2$.

At this point you should be thinking,

Great, we have written down an optimization problem: $\max_{v : |v|=1} |Av|$. If we could solve this, we’d have the best 1-dimensional linear approximation to the data contained in the rows of $A$. But (1) how do we solve that problem? And (2) you promised a $k$-dimensional approximating subspace. I feel betrayed! Swindled! Bamboozled!

Here’s the fantastic thing. We can solve the 1-dimensional optimization problem efficiently (we’ll do it later in this post), and (2) is answered by the following theorem.

The SVD Theorem: Computing the best $k$-dimensional subspace reduces to $k$ applications of the one-dimensional problem.

We will prove this after we introduce the terms “singular value” and “singular vector.”

## Singular values and vectors

As I just said, we can get the best $k$-dimensional approximating linear subspace by solving the one-dimensional maximization problem $k$ times. The singular vectors of $A$ are defined recursively as the solutions to these sub-problems. That is, I’ll call $v_1$ the first singular vector of $A$, and it is:

$\displaystyle v_1 = \arg \max_{v, |v|=1} |Av|$

And the corresponding first singular value, denoted $\sigma_1(A)$, is the maximal value of the optimization objective, i.e. $|Av_1|$. (I will use this term frequently, that $|Av|$ is the “objective” of the optimization problem.) Informally speaking, $(\sigma_1(A))^2$ represents how much of the data was captured by the first singular vector. Meaning, how close the vectors are to lying on the line spanned by $v_1$. Larger values imply the approximation is better. In fact, if all the data points lie on a line, then $(\sigma_1(A))^2$ is the sum of the squared norms of the rows of $A$.

Now here is where we see the reduction from the $k$-dimensional case to the 1-dimensional case. To find the best 2-dimensional subspace, you first find the best one-dimensional subspace (spanned by $v_1$), and then find the best 1-dimensional subspace, but only considering those subspaces that are the spans of unit vectors perpendicular to $v_1$. The notation for “vectors $v$ perpendicular to $v_1$” is $v \perp v_1$. Restating, the second singular vector $v _2$ is defined as

$\displaystyle v_2 = \arg \max_{v \perp v_1, |v| = 1} |Av|$

And the SVD theorem implies the subspace spanned by $\{ v_1, v_2 \}$ is the best 2-dimensional linear approximation to the data. Likewise $\sigma_2(A) = |Av_2|$ is the second singular value. Its squared magnitude tells us how much of the data that was not “captured” by $v_1$ is captured by $v_2$. Again, if the data lies in a 2-dimensional subspace, then the span of $\{ v_1, v_2 \}$ will be that subspace.

We can continue this process. Recursively define $v_k$, the $k$-th singular vector, to be the vector which maximizes $|Av|$, when $v$ is considered only among the unit vectors which are perpendicular to $\textup{span} \{ v_1, \dots, v_{k-1} \}$. The corresponding singular value $\sigma_k(A)$ is the value of the optimization problem.

As a side note, because of the way we defined the singular values as the objective values of “nested” optimization problems, the singular values are decreasing, $\sigma_1(A) \geq \sigma_2(A) \geq \dots \geq \sigma_n(A) \geq 0$. This is obvious: you only pick $v_2$ in the second optimization problem because you already picked $v_1$ which gave a bigger singular value, so $v_2$‘s objective can’t be bigger.

If you keep doing this, one of two things happen. Either you reach $v_n$ and since the domain is $n$-dimensional there are no remaining vectors to choose from, the $v_i$ are an orthonormal basis of $\mathbb{R}^n$. This means that the data in $A$ contains a full-rank submatrix. The data does not lie in any smaller-dimensional subspace. This is what you’d expect from real data.

Alternatively, you could get to a stage $v_k$ with $k < n$ and when you try to solve the optimization problem you find that every perpendicular $v$ has $Av = 0$. In this case, the data actually does lie in a $k$-dimensional subspace, and the first-through-$k$-th singular vectors you computed span this subspace.

Let’s do a quick sanity check: how do we know that the singular vectors $v_i$ form a basis? Well formally they only span a basis of the row space of $A$, i.e. a basis of the subspace spanned by the data contained in the rows of $A$. But either way the point is that each $v_{i+1}$ spans a new dimension from the previous $v_1, \dots, v_i$ because we’re choosing $v_{i+1}$ to be orthogonal to all the previous $v_i$. So the answer to our sanity check is “by construction.”

Back to the singular vectors, the discussion from the last post tells us intuitively that the data is probably never in a small subspace.  You never expect the process of finding singular vectors to stop before step $n$, and if it does you take a step back and ask if something deeper is going on. Instead, in real life you specify how much of the data you want to capture, and you keep computing singular vectors until you’ve passed the threshold. Alternatively, you specify the amount of computing resources you’d like to spend by fixing the number of singular vectors you’ll compute ahead of time, and settle for however good the $k$-dimensional approximation is.

Before we get into any code or solve the 1-dimensional optimization problem, let’s prove the SVD theorem.

Proof of SVD theorem.

Recall we’re trying to prove that the first $k$ singular vectors provide a linear subspace $W$ which maximizes the squared-sum of the projections of the data onto $W$. For $k=1$ this is trivial, because we defined $v_1$ to be the solution to that optimization problem. The case of $k=2$ contains all the important features of the general inductive step. Let $W$ be any best-approximating 2-dimensional linear subspace for the rows of $A$. We’ll show that the subspace spanned by the two singular vectors $v_1, v_2$ is at least as good (and hence equally good).

Let $w_1, w_2$ be any orthonormal basis for $W$ and let $|Aw_1|^2 + |Aw_2|^2$ be the quantity that we’re trying to maximize (and which $W$ maximizes by assumption). Moreover, we can pick the basis vector $w_2$ to be perpendicular to $v_1$. To prove this we consider two cases: either $v_1$ is already perpendicular to $W$ in which case it’s trivial, or else $v_1$ isn’t perpendicular to $W$ and you can choose $w_1$ to be $\textup{proj}_W(v_1)$ and choose $w_2$ to be any unit vector perpendicular to $w_1$.

Now since $v_1$ maximizes $|Av|$, we have $|Av_1|^2 \geq |Aw_1|^2$. Moreover, since $w_2$ is perpendicular to $v_1$, the way we chose $v_2$ also makes $|Av_2|^2 \geq |Aw_2|^2$. Hence the objective $|Av_1|^2 + |Av_2|^2 \geq |Aw_1|^2 + |Aw_2|^2$, as desired.

For the general case of $k$, the inductive hypothesis tells us that the first $k$ terms of the objective for $k+1$ singular vectors is maximized, and we just have to pick any vector $w_{k+1}$ that is perpendicular to all $v_1, v_2, \dots, v_k$, and the rest of the proof is just like the 2-dimensional case.

$\square$

Now remember that in the last post we started with the definition of the SVD as a decomposition of a matrix $A = U\Sigma V^T$? And then we said that this is a certain kind of change of basis? Well the singular vectors $v_i$ together form the columns of the matrix $V$ (the rows of $V^T$), and the corresponding singular values $\sigma_i(A)$ are the diagonal entries of $\Sigma$. When $A$ is understood we’ll abbreviate the singular value as $\sigma_i$.

To reiterate with the thoughts from last post, the process of applying $A$ is exactly recovered by the process of first projecting onto the (full-rank space of) singular vectors $v_1, \dots, v_k$, scaling each coordinate of that projection according to the corresponding singular values, and then applying this $U$ thing we haven’t talked about yet.

So let’s determine what $U$ has to be. The way we picked $v_i$ to make $A$ diagonal gives us an immediate suggestion: use the $Av_i$ as the columns of $U$. Indeed, define $u_i = Av_i$, the images of the singular vectors under $A$. We can swiftly show the $u_i$ form a basis of the image of $A$. The reason is because if $v = \sum_i c_i v_i$ (using all $n$ of the singular vectors $v_i$), then by linearity $Av = \sum_{i} c_i Av_i = \sum_i c_i u_i$. It is also easy to see why the $u_i$ are orthogonal (prove it as an exercise). Let’s further make sure the $u_i$ are unit vectors and redefine them as $u_i = \frac{1}{\sigma_i}Av_i$

If you put these thoughts together, you can say exactly what $A$ does to any given vector $x$. Since the $v_i$ form an orthonormal basis, $x = \sum_i (x \cdot v_i) v_i$, and then applying $A$ gives

\displaystyle \begin{aligned}Ax &= A \left ( \sum_i (x \cdot v_i) v_i \right ) \\ &= \sum_i (x \cdot v_i) A_i v_i \\ &= \sum_i (x \cdot v_i) \sigma_i u_i \end{aligned}

If you’ve been closely reading this blog in the last few months, you’ll recognize a very nice way to write the last line of the above equation. It’s an outer product. So depending on your favorite symbols, you’d write this as either $A = \sum_{i} \sigma_i u_i \otimes v_i$ or $A = \sum_i \sigma_i u_i v_i^T$. Or, if you like expressing things as matrix factorizations, as $A = U\Sigma V^T$. All three are describing the same object.

Let’s move on to some code.

## A black box example

Before we implement SVD from scratch (an urge that commands me from the depths of my soul!), let’s see a black-box example that uses existing tools. For this we’ll use the numpy library.

Recall our movie-rating matrix from the last post:

The code to compute the svd of this matrix is as simple as it gets:

from numpy.linalg import svd

movieRatings = [
[2, 5, 3],
[1, 2, 1],
[4, 1, 1],
[3, 5, 2],
[5, 3, 1],
[4, 5, 5],
[2, 4, 2],
[2, 2, 5],
]

U, singularValues, V = svd(movieRatings)


Printing these values out gives

[[-0.39458526  0.23923575 -0.35445911 -0.38062172 -0.29836818 -0.49464816 -0.30703202 -0.29763321]
[-0.15830232  0.03054913 -0.15299759 -0.45334816  0.31122898  0.23892035 -0.37313346  0.67223457]
[-0.22155201 -0.52086121  0.39334917 -0.14974792 -0.65963979  0.00488292 -0.00783684  0.25934607]
[-0.39692635 -0.08649009 -0.41052882  0.74387448 -0.10629499  0.01372565 -0.17959298  0.26333462]
[-0.34630257 -0.64128825  0.07382859 -0.04494155  0.58000668 -0.25806239  0.00211823 -0.24154726]
[-0.53347449  0.19168874  0.19949342 -0.03942604  0.00424495  0.68715732 -0.06957561 -0.40033035]
[-0.31660464  0.06109826 -0.30599517 -0.19611823 -0.01334272  0.01446975  0.85185852  0.19463493]
[-0.32840223  0.45970413  0.62354764  0.1783041   0.17631186 -0.39879476  0.06065902  0.25771578]]
[ 15.09626916   4.30056855   3.40701739]
[[-0.54184808 -0.67070995 -0.50650649]
[-0.75152295  0.11680911  0.64928336]
[ 0.37631623 -0.73246419  0.56734672]]


Now this is a bit weird, because the matrices $U, V$ are the wrong shape! Remember, there are only supposed to be three vectors since the input matrix has rank three. So what gives? This is a distinction that goes by the name “full” versus “reduced” SVD. The idea goes back to our original statement that $U \Sigma V^T$ is a decomposition with $U, V^T$ both orthogonal and square matrices. But in the derivation we did in the last section, the $U$ and $V$ were not square. The singular vectors $v_i$ could potentially stop before even becoming full rank.

In order to get to square matrices, what people sometimes do is take the two bases $v_1, \dots, v_k$ and $u_1, \dots, u_k$ and arbitrarily choose ways to complete them to a full orthonormal basis of their respective vector spaces. In other words, they just make the matrix square by filling it with data for no reason other than that it’s sometimes nice to have a complete basis. We don’t care about this. To be honest, I think the only place this comes in useful is in the desire to be particularly tidy in a mathematical formulation of something.

We can still work with it programmatically. By fudging around a bit with numpy’s shapes to get a diagonal matrix, we can reconstruct the input rating matrix from the factors.

Sigma = np.vstack([
np.diag(singularValues),
np.zeros((5, 3)),
])

print(np.round(movieRatings - np.dot(U, np.dot(Sigma, V)), decimals=10))


And the output is, as one expects, a matrix of all zeros. Meaning that we decomposed the movie rating matrix, and built it back up from the factors.

We can actually get the SVD as we defined it (with rectangular matrices) by passing a special flag to numpy’s svd.

U, singularValues, V = svd(movieRatings, full_matrices=False)
print(U)
print(singularValues)
print(V)

Sigma = np.diag(singularValues)
print(np.round(movieRatings - np.dot(U, np.dot(Sigma, V)), decimals=10))


And the result

[[-0.39458526  0.23923575 -0.35445911]
[-0.15830232  0.03054913 -0.15299759]
[-0.22155201 -0.52086121  0.39334917]
[-0.39692635 -0.08649009 -0.41052882]
[-0.34630257 -0.64128825  0.07382859]
[-0.53347449  0.19168874  0.19949342]
[-0.31660464  0.06109826 -0.30599517]
[-0.32840223  0.45970413  0.62354764]]
[ 15.09626916   4.30056855   3.40701739]
[[-0.54184808 -0.67070995 -0.50650649]
[-0.75152295  0.11680911  0.64928336]
[ 0.37631623 -0.73246419  0.56734672]]
[[-0. -0. -0.]
[-0. -0.  0.]
[ 0. -0.  0.]
[-0. -0. -0.]
[-0. -0. -0.]
[-0. -0. -0.]
[-0. -0. -0.]
[ 0. -0. -0.]]


This makes the reconstruction less messy, since we can just multiply everything without having to add extra rows of zeros to $\Sigma$.

What do the singular vectors and values tell us about the movie rating matrix? (Besides nothing, since it’s a contrived example) You’ll notice that the first singular vector $\sigma_1 > 15$ while the other two singular values are around $4$. This tells us that the first singular vector covers a large part of the structure of the matrix. I.e., a rank-1 matrix would be a pretty good approximation to the whole thing. As an exercise to the reader, write a program that evaluates this claim (how good is “good”?).

## The greedy optimization routine

Now we’re going to write SVD from scratch. We’ll first implement the greedy algorithm for the 1-d optimization problem, and then we’ll perform the inductive step to get a full algorithm. Then we’ll run it on the CNN data set.

The method we’ll use to solve the 1-dimensional problem isn’t necessarily industry strength (see this document for a hint of what industry strength looks like), but it is simple conceptually. It’s called the power method. Now that we have our decomposition of theorem, understanding how the power method works is quite easy.

Let’s work in the language of a matrix decomposition $A = U \Sigma V^T$, more for practice with that language than anything else (using outer products would give us the same result with slightly different computations). Then let’s observe $A^T A$, wherein we’ll use the fact that $U$ is orthonormal and so $U^TU$ is the identity matrix:

$\displaystyle A^TA = (U \Sigma V^T)^T(U \Sigma V^T) = V \Sigma U^TU \Sigma V^T = V \Sigma^2 V^T$

So we can completely eliminate $U$ from the discussion, and look at just $V \Sigma^2 V^T$. And what’s nice about this matrix is that we can compute its eigenvectors, and eigenvectors turn out to be exactly the singular vectors. The corresponding eigenvalues are the squared singular values. This should be clear from the above derivation. If you apply $(V \Sigma^2 V^T)$ to any $v_i$, the only parts of the product that aren’t zero are the ones involving $v_i$ with itself, and the scalar $\sigma_i^2$ factors in smoothly. It’s dead simple to check.

Theorem: Let $x$ be a random unit vector and let $B = A^TA = V \Sigma^2 V^T$. Then with high probability, $\lim_{s \to \infty} B^s x$ is in the span of the first singular vector $v_1$. If we normalize $B^s x$ to a unit vector at each $s$, then furthermore the limit is $v_1$.

Proof. Start with a random unit vector $x$, and write it in terms of the singular vectors $x = \sum_i c_i v_i$. That means $Bx = \sum_i c_i \sigma_i^2 v_i$. If you recursively apply this logic, you get $B^s x = \sum_i c_i \sigma_i^{2s} v_i$. In particular, the dot product of $(B^s x)$ with any $v_j$ is $c_i \sigma_j^{2s}$.

What this means is that so long as the first singular value $\sigma_1$ is sufficiently larger than the second one $\sigma_2$, and in turn all the other singular values, the part of $B^s x$  corresponding to $v_1$ will be much larger than the rest. Recall that if you expand a vector in terms of an orthonormal basis, in this case $B^s x$ expanded in the $v_i$, the coefficient of $B^s x$ on $v_j$ is exactly the dot product. So to say that $B^sx$ converges to being in the span of $v_1$ is the same as saying that the ratio of these coefficients, $|(B^s x \cdot v_1)| / |(B^s x \cdot v_j)| \to \infty$ for any $j$. In other words, the coefficient corresponding to the first singular vector dominates all of the others. And so if we normalize, the coefficient of $B^s x$ corresponding to $v_1$ tends to 1, while the rest tend to zero.

Indeed, this ratio is just $(\sigma_1 / \sigma_j)^{2s}$ and the base of this exponential is bigger than 1.

$\square$

If you want to be a little more precise and find bounds on the number of iterations required to converge, you can. The worry is that your random starting vector is “too close” to one of the smaller singular vectors $v_j$, so that if the ratio of $\sigma_1 / \sigma_j$ is small, then the “pull” of $v_1$ won’t outweigh the pull of $v_j$ fast enough. Choosing a random unit vector allows you to ensure with high probability that this doesn’t happen. And conditioned on it not happening (or measuring “how far the event is from happening” precisely), you can compute a precise number of iterations required to converge. The last two pages of these lecture notes have all the details.

We won’t compute a precise number of iterations. Instead we’ll just compute until the angle between $B^{s+1}x$ and $B^s x$ is very small. Here’s the algorithm

import numpy as np
from numpy.linalg import norm

from random import normalvariate
from math import sqrt

def randomUnitVector(n):
unnormalized = [normalvariate(0, 1) for _ in range(n)]
theNorm = sqrt(sum(x * x for x in unnormalized))
return [x / theNorm for x in unnormalized]

def svd_1d(A, epsilon=1e-10):
''' The one-dimensional SVD '''

n, m = A.shape
x = randomUnitVector(m)
lastV = None
currentV = x
B = np.dot(A.T, A)

iterations = 0
while True:
iterations += 1
lastV = currentV
currentV = np.dot(B, lastV)
currentV = currentV / norm(currentV)

if abs(np.dot(currentV, lastV)) > 1 - epsilon:
print("converged in {} iterations!".format(iterations))
return currentV


We start with a random unit vector $x$, and then loop computing $x_{t+1} = Bx_t$, renormalizing at each step. The condition for stopping is that the magnitude of the dot product between $x_t$ and $x_{t+1}$ (since they’re unit vectors, this is the cosine of the angle between them) is very close to 1.

And using it on our movie ratings example:

if __name__ == "__main__":
movieRatings = np.array([
[2, 5, 3],
[1, 2, 1],
[4, 1, 1],
[3, 5, 2],
[5, 3, 1],
[4, 5, 5],
[2, 4, 2],
[2, 2, 5],
], dtype='float64')

print(svd_1d(movieRatings))


With the result

converged in 6 iterations!
[-0.54184805 -0.67070993 -0.50650655]


Note that the sign of the vector may be different from numpy’s output because we start with a random vector to begin with.

The recursive step, getting from $v_1$ to the entire SVD, is equally straightforward. Say you start with the matrix $A$ and you compute $v_1$. You can use $v_1$ to compute $u_1$ and $\sigma_1(A)$. Then you want to ensure you’re ignoring all vectors in the span of $v_1$ for your next greedy optimization, and to do this you can simply subtract the rank 1 component of $A$ corresponding to $v_1$. I.e., set $A' = A - \sigma_1(A) u_1 v_1^T$. Then it’s easy to see that $\sigma_1(A') = \sigma_2(A)$ and basically all the singular vectors shift indices by 1 when going from $A$ to $A'$. Then you repeat.

If that’s not clear enough, here’s the code.

def svd(A, epsilon=1e-10):
n, m = A.shape
svdSoFar = []

for i in range(m):
matrixFor1D = A.copy()

for singularValue, u, v in svdSoFar[:i]:
matrixFor1D -= singularValue * np.outer(u, v)

v = svd_1d(matrixFor1D, epsilon=epsilon)  # next singular vector
u_unnormalized = np.dot(A, v)
sigma = norm(u_unnormalized)  # next singular value
u = u_unnormalized / sigma

svdSoFar.append((sigma, u, v))

# transform it into matrices of the right shape
singularValues, us, vs = [np.array(x) for x in zip(*svdSoFar)]

return singularValues, us.T, vs


And we can run this on our movie rating matrix to get the following

>>> theSVD = svd(movieRatings)
>>> theSVD[0]
array([ 15.09626916,   4.30056855,   3.40701739])
>>> theSVD[1]
array([[ 0.39458528, -0.23923093,  0.35446407],
[ 0.15830233, -0.03054705,  0.15299815],
[ 0.221552  ,  0.52085578, -0.39336072],
[ 0.39692636,  0.08649568,  0.41052666],
[ 0.34630257,  0.64128719, -0.07384286],
[ 0.53347448, -0.19169154, -0.19948959],
[ 0.31660465, -0.0610941 ,  0.30599629],
[ 0.32840221, -0.45971273, -0.62353781]])
>>> theSVD[2]
array([[ 0.54184805,  0.67071006,  0.50650638],
[ 0.75151641, -0.11679644, -0.64929321],
[-0.37632934,  0.73246611, -0.56733554]])


Checking this against our numpy output shows it’s within a reasonable level of precision (considering the power method took on the order of ten iterations!)

>>> np.round(np.abs(npSVD[0]) - np.abs(theSVD[1]), decimals=5)
array([[ -0.00000000e+00,  -0.00000000e+00,   0.00000000e+00],
[  0.00000000e+00,  -0.00000000e+00,   0.00000000e+00],
[  0.00000000e+00,  -1.00000000e-05,   1.00000000e-05],
[  0.00000000e+00,   0.00000000e+00,  -0.00000000e+00],
[  0.00000000e+00,  -0.00000000e+00,   1.00000000e-05],
[ -0.00000000e+00,   0.00000000e+00,  -0.00000000e+00],
[  0.00000000e+00,  -0.00000000e+00,   0.00000000e+00],
[ -0.00000000e+00,   1.00000000e-05,  -1.00000000e-05]])
>>> np.round(np.abs(npSVD[2]) - np.abs(theSVD[2]), decimals=5)
array([[  0.00000000e+00,   0.00000000e+00,  -0.00000000e+00],
[ -1.00000000e-05,  -1.00000000e-05,   1.00000000e-05],
[  1.00000000e-05,   0.00000000e+00,  -1.00000000e-05]])
>>> np.round(np.abs(npSVD[1]) - np.abs(theSVD[0]), decimals=5)
array([ 0.,  0., -0.])


So there we have it. We added an extra little bit to the svd function, an argument $k$ which stops computing the svd after it reaches rank $k$.

## CNN stories

One interesting use of the SVD is in topic modeling. Topic modeling is the process of taking a bunch of documents (news stories, or emails, or movie scripts, whatever) and grouping them by topic, where the algorithm gets to choose what counts as a “topic.” Topic modeling is just the name that natural language processing folks use instead of clustering.

The SVD can help one model topics as follows. First you construct a matrix $A$ called a document-term matrix whose rows correspond to words in some fixed dictionary and whose columns correspond to documents. The $(i,j)$ entry of $A$ contains the number of times word $i$ shows up in document $j$. Or, more precisely, some quantity derived from that count, like a normalized count. See this table on wikipedia for a list of options related to that. We’ll just pick one arbitrarily for use in this post.

The point isn’t how we normalize the data, but what the SVD of $A = U \Sigma V^T$ means in this context. Recall that the domain of $A$, as a linear map, is a vector space whose dimension is the number of stories. We think of the vectors in this space as documents, or rather as an “embedding” of the abstract concept of a document using the counts of how often each word shows up in a document as a proxy for the semantic meaning of the document. Likewise, the codomain is the space of all words, and each word is embedded by which documents it occurs in. If we compare this to the movie rating example, it’s the same thing: a movie is the vector of ratings it receives from people, and a person is the vector of ratings of various movies.

Say you take a rank 3 approximation to $A$. Then you get three singular vectors $v_1, v_2, v_3$ which form a basis for a subspace of words, i.e., the “idealized” words. These idealized words are your topics, and you can compute where a “new word” falls by looking at which documents it appears in (writing it as a vector in the domain) and saying its “topic” is the closest of the $v_1, v_2, v_3$. The same process applies to new documents. You can use this to cluster existing documents as well.

The dataset we’ll use for this post is a relatively small corpus of a thousand CNN stories picked from 2012. Here’s an excerpt from one of them

\$ cat data/cnn-stories/story479.txt
3 things to watch on Super Tuesday
Here are three things to watch for: Romney's big day. He's been the off-and-on frontrunner throughout the race, but a big Super Tuesday could begin an end game toward a sometimes hesitant base coalescing behind former Massachusetts Gov. Mitt Romney. Romney should win his home state of Massachusetts, neighboring Vermont and Virginia, ...


So let’s first build this document-term matrix, with the normalized values, and then we’ll compute it’s SVD and see what the topics look like.

Step 1 is cleaning the data. We used a bunch of routines from the nltk library that boils down to this loop:

    for filename, documentText in documentDict.items():
tokens = tokenize(documentText)
tagged_tokens = pos_tag(tokens)
wnl = WordNetLemmatizer()
stemmedTokens = [wnl.lemmatize(word, wordnetPos(tag)).lower()
for word, tag in tagged_tokens]


This turns the Super Tuesday story into a list of words (with repetition):

["thing", "watch", "three", "thing", "watch", "big", ... ]


If you’ll notice the name Romney doesn’t show up in the list of words. I’m only keeping the words that show up in the top 100,000 most common English words, and then lemmatizing all of the words to their roots. It’s not a perfect data cleaning job, but it’s simple and good enough for our purposes.

Now we can create the document term matrix.

def makeDocumentTermMatrix(data):
words = allWords(data)  # get the set of all unique words

wordToIndex = dict((word, i) for i, word in enumerate(words))
indexToWord = dict(enumerate(words))
indexToDocument = dict(enumerate(data))

matrix = np.zeros((len(words), len(data)))
for docID, document in enumerate(data):
docWords = Counter(document['words'])
for word, count in docWords.items():
matrix[wordToIndex[word], docID] = count

return matrix, (indexToWord, indexToDocument)


This creates a matrix with the raw integer counts. But what we need is a normalized count. The idea is that a common word like “thing” shows up disproportionately more often than “election,” and we don’t want raw magnitude of a word count to outweigh its semantic contribution to the classification. This is the applied math part of the algorithm design. So what we’ll do (and this technique together with SVD is called latent semantic indexing) is normalize each entry so that it measures both the frequency of a term in a document and the relative frequency of a term compared to the global frequency of that term. There are many ways to do this, and we’ll just pick one. See the github repository if you’re interested.

So now lets compute a rank 10 decomposition and see how to cluster the results.

    data = load()
matrix, (indexToWord, indexToDocument) = makeDocumentTermMatrix(data)
matrix = normalize(matrix)
sigma, U, V = svd(matrix, k=10)


This uses our svd, not numpy’s. Though numpy’s routine is much faster, it’s fun to see things work with code written from scratch. The result is too large to display here, but I can report the singular values.

>>> sigma
array([ 42.85249098,  21.85641975,  19.15989197,  16.2403354 ,
15.40456779,  14.3172779 ,  13.47860033,  13.23795002,
12.98866537,  12.51307445])


Now we take our original inputs and project them onto the subspace spanned by the singular vectors. This is the part that represents each word (resp., document) in terms of the idealized words (resp., documents), the singular vectors. Then we can apply a simple k-means clustering algorithm to the result, and observe the resulting clusters as documents.

    projectedDocuments = np.dot(matrix.T, U)
projectedWords = np.dot(matrix, V.T)

documentCenters, documentClustering = cluster(projectedDocuments)
wordCenters, wordClustering = cluster(projectedWords)

wordClusters = [
[indexToWord[i] for (i, x) in enumerate(wordClustering) if x == j]
for j in range(len(set(wordClustering)))
]

documentClusters = [
[indexToDocument[i]['text']
for (i, x) in enumerate(documentClustering) if x == j]
for j in range(len(set(documentClustering)))
]


And now we can inspect individual clusters. Right off the bat we can tell the clusters aren’t quite right simply by looking at the sizes of each cluster.

>>> Counter(wordClustering)
Counter({1: 9689, 2: 1051, 8: 680, 5: 557, 3: 321, 7: 225, 4: 174, 6: 124, 9: 123})
>>> Counter(documentClustering)
Counter({7: 407, 6: 109, 0: 102, 5: 87, 9: 85, 2: 65, 8: 55, 4: 47, 3: 23, 1: 15})


What looks wrong to me is the size of the largest word cluster. If we could group words by topic, then this is saying there’s a topic with over nine thousand words associated with it! Inspecting it even closer, it includes words like “vegan,” “skunk,” and “pope.” On the other hand, some word clusters are spot on. Examine, for example, the fifth cluster which includes words very clearly associated with crime stories.

>>> wordClusters[4]
['account', 'accuse', 'act', 'affiliate', 'allegation', 'allege', 'altercation', 'anything', 'apartment', 'arrest', 'arrive', 'assault', 'attorney', 'authority', 'bag', 'black', 'blood', 'boy', 'brother', 'bullet', 'candy', 'car', 'carry', 'case', 'charge', 'chief', 'child', 'claim', 'client', 'commit', 'community', 'contact', 'convenience', 'court', 'crime', 'criminal', 'cry', 'dead', 'deadly', 'death', 'defense', 'department', 'describe', 'detail', 'determine', 'dispatcher', 'district', 'document', 'enforcement', 'evidence', 'extremely', 'family', 'father', 'fear', 'fiancee', 'file', 'five', 'foot', 'friend', 'front', 'gate', 'girl', 'girlfriend', 'grand', 'ground', 'guilty', 'gun', 'gunman', 'gunshot', 'hand', 'happen', 'harm', 'head', 'hear', 'heard', 'hoodie', 'hour', 'house', 'identify', 'immediately', 'incident', 'information', 'injury', 'investigate', 'investigation', 'investigator', 'involve', 'judge', 'jury', 'justice', 'kid', 'killing', 'lawyer', 'legal', 'letter', 'life', 'local', 'man', 'men', 'mile', 'morning', 'mother', 'murder', 'near', 'nearby', 'neighbor', 'newspaper', 'night', 'nothing', 'office', 'officer', 'online', 'outside', 'parent', 'person', 'phone', 'police', 'post', 'prison', 'profile', 'prosecute', 'prosecution', 'prosecutor', 'pull', 'racial', 'racist', 'release', 'responsible', 'return', 'review', 'role', 'saw', 'scene', 'school', 'scream', 'search', 'sentence', 'serve', 'several', 'shoot', 'shooter', 'shooting', 'shot', 'slur', 'someone', 'son', 'sound', 'spark', 'speak', 'staff', 'stand', 'store', 'story', 'student', 'surveillance', 'suspect', 'suspicious', 'tape', 'teacher', 'teen', 'teenager', 'told', 'tragedy', 'trial', 'vehicle', 'victim', 'video', 'walk', 'watch', 'wear', 'whether', 'white', 'witness', 'young']


As sad as it makes me to see that ‘black’ and ‘slur’ and ‘racial’ appear in this category, it’s a reminder that naively using the output of a machine learning algorithm can perpetuate racism.

Here’s another interesting cluster corresponding to economic words:

>>> wordClusters[6]
['agreement', 'aide', 'analyst', 'approval', 'approve', 'austerity', 'average', 'bailout', 'beneficiary', 'benefit', 'bill', 'billion', 'break', 'broadband', 'budget', 'class', 'combine', 'committee', 'compromise', 'conference', 'congressional', 'contribution', 'core', 'cost', 'currently', 'cut', 'deal', 'debt', 'defender', 'deficit', 'doc', 'drop', 'economic', 'economy', 'employee', 'employer', 'erode', 'eurozone', 'expire', 'extend', 'extension', 'fee', 'finance', 'fiscal', 'fix', 'fully', 'fund', 'funding', 'game', 'generally', 'gleefully', 'growth', 'hamper', 'highlight', 'hike', 'hire', 'holiday', 'increase', 'indifferent', 'insistence', 'insurance', 'job', 'juncture', 'latter', 'legislation', 'loser', 'low', 'lower', 'majority', 'maximum', 'measure', 'middle', 'negotiation', 'offset', 'oppose', 'package', 'pass', 'patient', 'pay', 'payment', 'payroll', 'pension', 'plight', 'portray', 'priority', 'proposal', 'provision', 'rate', 'recession', 'recovery', 'reduce', 'reduction', 'reluctance', 'repercussion', 'rest', 'revenue', 'rich', 'roughly', 'sale', 'saving', 'scientist', 'separate', 'sharp', 'showdown', 'sign', 'specialist', 'spectrum', 'spending', 'strength', 'tax', 'tea', 'tentative', 'term', 'test', 'top', 'trillion', 'turnaround', 'unemployed', 'unemployment', 'union', 'wage', 'welfare', 'worker', 'worth']


One can also inspect the stories, though the clusters are harder to print out here. Interestingly the first cluster of documents are stories exclusively about Trayvon Martin. The second cluster is mostly international military conflicts. The third cluster also appears to be about international conflict, but what distinguishes it from the first cluster is that every story in the second cluster discusses Syria.

>>> len([x for x in documentClusters[1] if 'Syria' in x]) / len(documentClusters[1])
0.05555555555555555
>>> len([x for x in documentClusters[2] if 'Syria' in x]) / len(documentClusters[2])
1.0


Anyway, you can explore the data more at your leisure (and tinker with the parameters to improve it!).

## Issues with the power method

Though I mentioned that the power method isn’t an industry strength algorithm I didn’t say why. Let’s revisit that before we finish. The problem is that the convergence rate of even the 1-dimensional problem depends on the ratio of the first and second singular values, $\sigma_1 / \sigma_2$. If that ratio is very close to 1, then the convergence will take a long time and need many many matrix-vector multiplications.

One way to alleviate that is to do the trick where, to compute a large power of a matrix, you iteratively square $B$. But that requires computing a matrix square (instead of a bunch of matrix-vector products), and that requires a lot of time and memory if the matrix isn’t sparse. When the matrix is sparse, you can actually do the power method quite quickly, from what I’ve heard and read.

But nevertheless, the industry standard methods involve computing a particular matrix decomposition that is not only faster than the power method, but also numerically stable. That means that the algorithm’s runtime and accuracy doesn’t depend on slight changes in the entries of the input matrix. Indeed, you can have two matrices where $\sigma_1 / \sigma_2$ is very close to 1, but changing a single entry will make that ratio much larger. The power method depends on this, so it’s not numerically stable. But the industry standard technique is not. This technique involves something called Householder reflections. So while the power method was great for a proof of concept, there’s much more work to do if you want true SVD power.

Until next time!

# Big Dimensions, and What You Can Do About It

Data is abundant, data is big, and big is a problem. Let me start with an example. Let’s say you have a list of movie titles and you want to learn their genre: romance, action, drama, etc. And maybe in this scenario IMDB doesn’t exist so you can’t scrape the answer. Well, the title alone is almost never enough information. One nice way to get more data is to do the following:

1. Pick a large dictionary of words, say the most common 100,000 non stop-words in the English language.
2. Crawl the web looking for documents that include the title of a film.
3. For each film, record the counts of all other words appearing in those documents.
4. Maybe remove instances of “movie” or “film,” etc.

After this process you have a length-100,000 vector of integers associated with each movie title. IMDB’s database has around 1.5 million listed movies, and if we have a 32-bit integer per vector entry, that’s 600 GB of data to get every movie.

One way to try to find genres is to cluster this (unlabeled) dataset of vectors, and then manually inspect the clusters and assign genres. With a really fast computer we could simply run an existing clustering algorithm on this dataset and be done. Of course, clustering 600 GB of data takes a long time, but there’s another problem. The geometric intuition that we use to design clustering algorithms degrades as the length of the vectors in the dataset grows. As a result, our algorithms perform poorly. This phenomenon is called the “curse of dimensionality” (“curse” isn’t a technical term), and we’ll return to the mathematical curiosities shortly.

A possible workaround is to try to come up with faster algorithms or be more patient. But a more interesting mathematical question is the following:

Is it possible to condense high-dimensional data into smaller dimensions and retain the important geometric properties of the data?

This goal is called dimension reduction. Indeed, all of the chatter on the internet is bound to encode redundant information, so for our movie title vectors it seems the answer should be “yes.” But the questions remain, how does one find a low-dimensional condensification? (Condensification isn’t a word, the right word is embedding, but embedding is overloaded so we’ll wait until we define it) And what mathematical guarantees can you prove about the resulting condensed data? After all, it stands to reason that different techniques preserve different aspects of the data. Only math will tell.

In this post we’ll explore this so-called “curse” of dimensionality, explain the formality of why it’s seen as a curse, and implement a wonderfully simple technique called “the random projection method” which preserves pairwise distances between points after the reduction. As usual, and all the code, data, and tests used in the making of this post are on Github.

## Some curious issues, and the “curse”

We start by exploring the curse of dimensionality with experiments on synthetic data.

In two dimensions, take a circle centered at the origin with radius 1 and its bounding square.

The circle fills up most of the area in the square, in fact it takes up exactly $\pi$ out of 4 which is about 78%. In three dimensions we have a sphere and a cube, and the ratio of sphere volume to cube volume is a bit smaller, $4 \pi /3$ out of a total of 8, which is just over 52%. What about in a thousand dimensions? Let’s try by simulation.

import random

def randUnitCube(n):
return [(random.random() - 0.5)*2 for _ in range(n)]

def sphereCubeRatio(n, numSamples):
randomSample = [randUnitCube(n) for _ in range(numSamples)]
return sum(1 for x in randomSample if sum(a**2 for a in x) <= 1) / numSamples 

The result is as we computed for small dimension,

 >>> sphereCubeRatio(2,10000)
0.7857
>>> sphereCubeRatio(3,10000)
0.5196


And much smaller for larger dimension

>>> sphereCubeRatio(20,100000) # 100k samples
0.0
>>> sphereCubeRatio(20,1000000) # 1M samples
0.0
>>> sphereCubeRatio(20,2000000)
5e-07


Forget a thousand dimensions, for even twenty dimensions, a million samples wasn’t enough to register a single random point inside the unit sphere. This illustrates one concern, that when we’re sampling random points in the $d$-dimensional unit cube, we need at least $2^d$ samples to ensure we’re getting a even distribution from the whole space. In high dimensions, this face basically rules out a naive Monte Carlo approximation, where you sample random points to estimate the probability of an event too complicated to sample from directly. A machine learning viewpoint of the same problem is that in dimension $d$, if your machine learning algorithm requires a representative sample of the input space in order to make a useful inference, then you require $2^d$ samples to learn.

Luckily, we can answer our original question because there is a known formula for the volume of a sphere in any dimension. Rather than give the closed form formula, which involves the gamma function and is incredibly hard to parse, we’ll state the recursive form. Call $V_i$ the volume of the unit sphere in dimension $i$. Then $V_0 = 1$ by convention, $V_1 = 2$ (it’s an interval), and $V_n = \frac{2 \pi V_{n-2}}{n}$. If you unpack this recursion you can see that the numerator looks like $(2\pi)^{n/2}$ and the denominator looks like a factorial, except it skips every other number. So an even dimension would look like $2 \cdot 4 \cdot \dots \cdot n$, and this grows larger than a fixed exponential. So in fact the total volume of the sphere vanishes as the dimension grows! (In addition to the ratio vanishing!)

def sphereVolume(n):
values = [0] * (n+1)
for i in range(n+1):
if i == 0:
values[i] = 1
elif i == 1:
values[i] = 2
else:
values[i] = 2*math.pi / i * values[i-2]

return values[-1]


This should be counterintuitive. I think most people would guess, when asked about how the volume of the unit sphere changes as the dimension grows, that it stays the same or gets bigger.  But at a hundred dimensions, the volume is already getting too small to fit in a float.

>>> sphereVolume(20)
0.025806891390014047
>>> sphereVolume(100)
2.3682021018828297e-40
>>> sphereVolume(1000)
0.0


The scary thing is not just that this value drops, but that it drops exponentially quickly. A consequence is that, if you’re trying to cluster data points by looking at points within a fixed distance $r$ of one point, you have to carefully measure how big $r$ needs to be to cover the same proportional volume as it would in low dimension.

Here’s a related issue. Say I take a bunch of points generated uniformly at random in the unit cube.

from itertools import combinations

def distancesRandomPoints(n, numSamples):
randomSample = [randUnitCube(n) for _ in range(numSamples)]
pairwiseDistances = [dist(x,y) for (x,y) in combinations(randomSample, 2)]
return pairwiseDistances


In two dimensions, the histogram of distances between points looks like this

However, as the dimension grows the distribution of distances changes. It evolves like the following animation, in which each frame is an increase in dimension from 2 to 100.

The shape of the distribution doesn’t appear to be changing all that much after the first few frames, but the center of the distribution tends to infinity (in fact, it grows like $\sqrt{n}$). The variance also appears to stay constant. This chart also becomes more variable as the dimension grows, again because we should be sampling exponentially many more points as the dimension grows (but we don’t). In other words, as the dimension grows the average distance grows and the tightness of the distribution stays the same. So at a thousand dimensions the average distance is about 26, tightly concentrated between 24 and 28. When the average is a thousand, the distribution is tight between 998 and 1002. If one were to normalize this data, it would appear that random points are all becoming equidistant from each other.

So in addition to the issues of runtime and sampling, the geometry of high-dimensional space looks different from what we expect. To get a better understanding of “big data,” we have to update our intuition from low-dimensional geometry with analysis and mathematical theorems that are much harder to visualize.

## The Johnson-Lindenstrauss Lemma

Now we turn to proving dimension reduction is possible. There are a few methods one might first think of, such as look for suitable subsets of coordinates, or sums of subsets, but these would all appear to take a long time or they simply don’t work.

Instead, the key technique is to take a random linear subspace of a certain dimension, and project every data point onto that subspace. No searching required. The fact that this works is called the Johnson-Lindenstrauss Lemma. To set up some notation, we’ll call $d(v,w)$ the usual distance between two points.

Lemma [Johnson-Lindenstrauss (1984)]: Given a set $X$ of $n$ points in $\mathbb{R}^d$, project the points in $X$ to a randomly chosen subspace of dimension $c$. Call the projection $\rho$. For any $\varepsilon > 0$, if $c$ is at least $\Omega(\log(n) / \varepsilon^2)$, then with probability at least 1/2 the distances between points in $X$ are preserved up to a factor of $(1+\varepsilon)$. That is, with good probability every pair $v,w \in X$ will satisfy

$\displaystyle \| v-w \|^2 (1-\varepsilon) \leq \| \rho(v) - \rho(w) \|^2 \leq \| v-w \|^2 (1+\varepsilon)$

Before we do the proof, which is quite short, it’s important to point out that the target dimension $c$ does not depend on the original dimension! It only depends on the number of points in the dataset, and logarithmically so. That makes this lemma seem like pure magic, that you can take data in an arbitrarily high dimension and put it in a much smaller dimension.

On the other hand, if you include all of the hidden constants in the bound on the dimension, it’s not that impressive. If your data have a million dimensions and you want to preserve the distances up to 1% ($\varepsilon = 0.01$), the bound is bigger than a million! If you decrease the preservation $\varepsilon$ to 10% (0.1), then you get down to about 12,000 dimensions, which is more reasonable. At 45% the bound drops to around 1,000 dimensions. Here’s a plot showing the theoretical bound on $c$ in terms of $\varepsilon$ for $n$ fixed to a million.

But keep in mind, this is just a theoretical bound for potentially misbehaving data. Later in this post we’ll see if the practical dimension can be reduced more than the theory allows. As we’ll see, an algorithm run on the projected data is still effective even if the projection goes well beyond the theoretical bound. Because the theorem is known to be tight in the worst case (see the notes at the end) this speaks more to the robustness of the typical algorithm than to the robustness of the projection method.

A second important note is that this technique does not necessarily avoid all the problems with the curse of dimensionality. We mentioned above that one potential problem is that “random points” are roughly equidistant in high dimensions. Johnson-Lindenstrauss actually preserves this problem because it preserves distances! As a consequence, you won’t see strictly better algorithm performance if you project (which we suggested is possible in the beginning of this post). But you will alleviate slow runtimes if the runtime depends exponentially on the dimension. Indeed, if you replace the dimension $d$ with the logarithm of the number of points $\log n$, then $2^d$ becomes linear in $n$, and $2^{O(d)}$ becomes polynomial.

## Proof of the J-L lemma

Let’s prove the lemma.

Proof. To start we make note that one can sample from the uniform distribution on dimension-$c$ linear subspaces of $\mathbb{R}^d$ by choosing the entries of a $c \times d$ matrix $A$ independently from a normal distribution with mean 0 and variance 1. Then, to project a vector $x$ by this matrix (call the projection $\rho$), we can compute

$\displaystyle \rho(x) = \frac{1}{\sqrt{c}}A x$

Now fix $\varepsilon > 0$ and fix two points in the dataset $x,y$. We want an upper bound on the probability that the following is false

$\displaystyle \| x-y \|^2 (1-\varepsilon) \leq \| \rho(x) - \rho(y) \|^2 \leq \| x-y \|^2 (1+\varepsilon)$

Since that expression is a pain to work with, let’s rearrange it by calling $u = x-y$, and rearranging (using the linearity of the projection) to get the equivalent statement.

$\left | \| \rho(u) \|^2 - \|u \|^2 \right | \leq \varepsilon \| u \|^2$

And so we want a bound on the probability that this event does not occur, meaning the inequality switches directions.

Once we get such a bound (it will depend on $c$ and $\varepsilon$) we need to ensure that this bound is true for every pair of points. The union bound allows us to do this, but it also requires that the probability of the bad thing happening tends to zero faster than $1/\binom{n}{2}$. That’s where the $\log(n)$ will come into the bound as stated in the theorem.

Continuing with our use of $u$ for notation, define $X$ to be the random variable $\frac{c}{\| u \|^2} \| \rho(u) \|^2$. By expanding the notation and using the linearity of expectation, you can show that the expected value of $X$ is $c$, meaning that in expectation, distances are preserved. We are on the right track, and just need to show that the distribution of $X$, and thus the possible deviations in distances, is tightly concentrated around $c$. In full rigor, we will show

$\displaystyle \Pr [X \geq (1+\varepsilon) c] < e^{-(\varepsilon^2 - \varepsilon^3) \frac{c}{4}}$

Let $A_i$ denote the $i$-th column of $A$. Define by $X_i$ the quantity $\langle A_i, u \rangle / \| u \|$. This is a weighted average of the entries of $A_i$ by the entries of $u$. But since we chose the entries of $A$ from the normal distribution, and since a weighted average of normally distributed random variables is also normally distributed (has the same distribution), $X_i$ is a $N(0,1)$ random variable. Moreover, each column is independent. This allows us to decompose $X$ as

$X = \frac{k}{\| u \|^2} \| \rho(u) \|^2 = \frac{\| Au \|^2}{\| u \|^2}$

Expanding further,

$X = \sum_{i=1}^c \frac{\| A_i u \|^2}{\|u\|^2} = \sum_{i=1}^c X_i^2$

Now the event $X \leq (1+\varepsilon) c$ can be expressed in terms of the nonegative variable $e^{\lambda X}$, where $0 < \lambda < 1/2$ is parameter, to get

$\displaystyle \Pr[X \geq (1+\varepsilon) c] = \Pr[e^{\lambda X} \geq e^{(1+\varepsilon)c \lambda}]$

This will become useful because the sum $X = \sum_i X_i^2$ will split into a product momentarily. First we apply Markov’s inequality, which says that for any nonnegative random variable $Y$, $\Pr[Y \geq t] \leq \mathbb{E}[Y] / t$. This lets us write

$\displaystyle \Pr[e^{\lambda X} \geq e^{(1+\varepsilon) c \lambda}] \leq \frac{\mathbb{E}[e^{\lambda X}]}{e^{(1+\varepsilon) c \lambda}}$

Now we can split up the exponent $\lambda X$ into $\sum_{i=1}^c \lambda X_i^2$, and using the i.i.d.-ness of the $X_i^2$ we can rewrite the RHS of the inequality as

$\left ( \frac{\mathbb{E}[e^{\lambda X_1^2}]}{e^{(1+\varepsilon)\lambda}} \right )^c$

A similar statement using $-\lambda$ is true for the $(1-\varepsilon)$ part, namely that

$\displaystyle \Pr[X \leq (1-\varepsilon)c] \leq \left ( \frac{\mathbb{E}[e^{-\lambda X_1^2}]}{e^{-(1-\varepsilon)\lambda}} \right )^c$

The last thing that’s needed is to bound $\mathbb{E}[e^{\lambda X_i^2}]$, but since $X_i^2 \sim N(0,1)$, we can use the known density function for a normal distribution, and integrate to get the exact value $\mathbb{E}[e^{\lambda X_1^2}] = \frac{1}{\sqrt{1-2\lambda}}$. Including this in the bound gives us a closed-form bound in terms of $\lambda, c, \varepsilon$. Using standard calculus the optimal $\lambda \in (0,1/2)$ is $\lambda = \varepsilon / 2(1+\varepsilon)$. This gives

$\displaystyle \Pr[X \geq (1+\varepsilon) c] \leq ((1+\varepsilon)e^{-\varepsilon})^{c/2}$

Using the Taylor series expansion for $e^x$, one can show the bound $1+\varepsilon < e^{\varepsilon - (\varepsilon^2 - \varepsilon^3)/2}$, which simplifies the final upper bound to $e^{-(\varepsilon^2 - \varepsilon^3) c/4}$.

Doing the same thing for the $(1-\varepsilon)$ version gives an equivalent bound, and so the total bound is doubled, i.e. $2e^{-(\varepsilon^2 - \varepsilon^3) c/4}$.

As we said at the beginning, applying the union bound means we need

$\displaystyle 2e^{-(\varepsilon^2 - \varepsilon^3) c/4} < \frac{1}{\binom{n}{2}}$

Solving this for $c$ gives $c \geq \frac{8 \log m}{\varepsilon^2 - \varepsilon^3}$, as desired.

$\square$

## Projecting in Practice

Let’s write a python program to actually perform the Johnson-Lindenstrauss dimension reduction scheme. This is sometimes called the Johnson-Lindenstrauss transform, or JLT.

First we define a random subspace by sampling an appropriately-sized matrix with normally distributed entries, and a function that performs the projection onto a given subspace (for testing).

import random
import math
import numpy

def randomSubspace(subspaceDimension, ambientDimension):
return numpy.random.normal(0, 1, size=(subspaceDimension, ambientDimension))

def project(v, subspace):
subspaceDimension = len(subspace)
return (1 / math.sqrt(subspaceDimension)) * subspace.dot(v)


We have a function that computes the theoretical bound on the optimal dimension to reduce to.

def theoreticalBound(n, epsilon):
return math.ceil(8*math.log(n) / (epsilon**2 - epsilon**3))


And then performing the JLT is simply matrix multiplication

def jlt(data, subspaceDimension):
ambientDimension = len(data[0])
A = randomSubspace(subspaceDimension, ambientDimension)
return (1 / math.sqrt(subspaceDimension)) * A.dot(data.T).T


The high-dimensional dataset we’ll use comes from a data mining competition called KDD Cup 2001. The dataset we used deals with drug design, and the goal is to determine whether an organic compound binds to something called thrombin. Thrombin has something to do with blood clotting, and I won’t pretend I’m an expert. The dataset, however, has over a hundred thousand features for about 2,000 compounds. Here are a few approximate target dimensions we can hope for as epsilon varies.

>>> [((1/x),theoreticalBound(n=2000, epsilon=1/x))
for x in [2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20]]
[('0.50', 487), ('0.33', 821), ('0.25', 1298), ('0.20', 1901),
('0.17', 2627), ('0.14', 3477), ('0.12', 4448), ('0.11', 5542),
('0.10', 6757), ('0.07', 14659), ('0.05', 25604)]


Going down from a hundred thousand dimensions to a few thousand is by any measure decreases the size of the dataset by about 95%. We can also observe how the distribution of overall distances varies as the size of the subspace we project to varies.

The animation proceeds from 5000 dimensions down to 2 (when the plot is at its bulkiest closer to zero).

The last three frames are for 10, 5, and 2 dimensions respectively. As you can see the histogram starts to beef up around zero. To be honest I was expecting something a bit more dramatic like a uniform-ish distribution. Of course, the distribution of distances is not all that matters. Another concern is the worst case change in distances between any two points before and after the projection. We can see that indeed when we project to the dimension specified in the theorem, that the distances are within the prescribed bounds.

def checkTheorem(oldData, newData, epsilon):

for (x,y), (x2,y2) in zip(combinations(oldData, 2), combinations(newData, 2)):
oldNorm = numpy.linalg.norm(x2-y2)**2
newNorm = numpy.linalg.norm(x-y)**2

if newNorm == 0 or oldNorm == 0:
continue

if abs(oldNorm / newNorm - 1) &gt; epsilon:

if __name__ == &quot;__main__&quot;
from data import thrombin

numPoints = len(train)
epsilon = 0.2
subspaceDim = theoreticalBound(numPoints, epsilon)
ambientDim = len(train[0])
newData = jlt(train, subspaceDim)

print(checkTheorem(train, newData, epsilon))


This program prints zero every time I try running it, which is the poor man’s way of saying it works “with high probability.” We can also plot statistics about the number of pairs of data points that are distorted by more than $\varepsilon$ as the subspace dimension shrinks. We ran this on the following set of subspace dimensions with $\varepsilon = 0.1$ and took average/standard deviation over twenty trials:

   dims = [1000, 750, 500, 250, 100, 75, 50, 25, 10, 5, 2]


The result is the following chart, whose x-axis is the dimension projected to (so the left hand is the most extreme projection to 2, 5, 10 dimensions), the y-axis is the number of distorted pairs, and the error bars represent a single standard deviation away from the mean.

This chart provides good news about this dataset because the standard deviations are low. It tells us something that mathematicians often ignore: the predictability of the tradeoff that occurs once you go past the theoretically perfect bound. In this case, the standard deviations tell us that it’s highly predictable. Moreover, since this tradeoff curve measures pairs of points, we might conjecture that the distortion is localized around a single set of points that got significantly “rattled” by the projection. This would be an interesting exercise to explore.

Now all of these charts are really playing with the JLT and confirming the correctness of our code (and hopefully our intuition). The real question is: how well does a machine learning algorithm perform on the original data when compared to the projected data? If the algorithm only “depends” on the pairwise distances between the points, then we should expect nearly identical accuracy in the unprojected and projected versions of the data. To show this we’ll use an easy learning algorithm, the k-nearest-neighbors clustering method. The problem, however, is that there are very few positive examples in this particular dataset. So looking for the majority label of the nearest $k$ neighbors for any $k > 2$ unilaterally results in the “all negative” classifier, which has 97% accuracy. This happens before and after projecting.

To compensate for this, we modify k-nearest-neighbors slightly by having the label of a predicted point be 1 if any label among its nearest neighbors is 1. So it’s not a majority vote, but rather a logical OR of the labels of nearby neighbors. Our point in this post is not to solve the problem well, but rather to show how an algorithm (even a not-so-good one) can degrade as one projects the data into smaller and smaller dimensions. Here is the code.

def nearestNeighborsAccuracy(data, labels, k=10):
from sklearn.neighbors import NearestNeighbors
trainData, trainLabels, testData, testLabels = randomSplit(data, labels) # cross validation
model = NearestNeighbors(n_neighbors=k).fit(trainData)
distances, indices = model.kneighbors(testData)
predictedLabels = []

for x in indices:
xLabels = [trainLabels[i] for i in x[1:]]
predictedLabel = max(xLabels)
predictedLabels.append(predictedLabel)

totalAccuracy = sum(x == y for (x,y) in zip(testLabels, predictedLabels)) / len(testLabels)
falsePositive = (sum(x == 0 and y == 1 for (x,y) in zip(testLabels, predictedLabels)) /
sum(x == 0 for x in testLabels))
falseNegative = (sum(x == 1 and y == 0 for (x,y) in zip(testLabels, predictedLabels)) /
sum(x == 1 for x in testLabels))



And here is the accuracy of this modified k-nearest-neighbors algorithm run on the thrombin dataset. The horizontal line represents the accuracy of the produced classifier on the unmodified data set. The x-axis represents the dimension projected to (left-hand side is the lowest), and the y-axis represents the accuracy. The mean accuracy over fifty trials was plotted, with error bars representing one standard deviation. The complete code to reproduce the plot is in the Github repository.

Likewise, we plot the proportion of false positive and false negatives for the output classifier. Note that a “positive” label made up only about 2% of the total data set. First the false positives

Then the false negatives

As we can see from these three charts, things don’t really change that much (for this dataset) even when we project down to around 200-300 dimensions. Note that for these parameters the “correct” theoretical choice for dimension was on the order of 5,000 dimensions, so this is a 95% savings from the naive approach, and 99.75% space savings from the original data. Not too shabby.

## Notes

The $\Omega(\log(n))$ worst-case dimension bound is asymptotically tight, though there is some small gap in the literature that depends on $\varepsilon$. This result is due to Noga Alon, the very last result (Section 9) of this paper. [Update: as djhsu points out in the comments, this gap is now closed thanks to Larsen and Nelson]

We did dimension reduction with respect to preserving the Euclidean distance between points. One might naturally wonder if you can achieve the same dimension reduction with a different metric, say the taxicab metric or a $p$-norm. In fact, you cannot achieve anything close to logarithmic dimension reduction for the taxicab ($l_1$) metric. This result is due to Brinkman-Charikar in 2004.

The code we used to compute the JLT is not particularly efficient. There are much more efficient methods. One of them, borrowing its namesake from the Fast Fourier Transform, is called the Fast Johnson-Lindenstrauss Transform. The technique is due to Ailon-Chazelle from 2009, and it involves something called “preconditioning a sparse projection matrix with a randomized Fourier transform.” I don’t know precisely what that means, but it would be neat to dive into that in a future post.

The central focus in this post was whether the JLT preserves distances between points, but one might be curious as to whether the points themselves are well approximated. The answer is an enthusiastic no. If the data were images, the projected points would look nothing like the original images. However, it appears the degradation tradeoff is measurable (by some accounts perhaps linear), and there appears to be some work (also this by the same author) when restricting to sparse vectors (like word-association vectors).

Note that the JLT is not the only method for dimensionality reduction. We previously saw principal component analysis (applied to face recognition), and in the future we will cover a related technique called the Singular Value Decomposition. It is worth noting that another common technique specific to nearest-neighbor is called “locality-sensitive hashing.” Here the goal is to project the points in such a way that “similar” points land very close to each other. Say, if you were to discretize the plane into bins, these bins would form the hash values and you’d want to maximize the probability that two points with the same label land in the same bin. Then you can do things like nearest-neighbors by comparing bins.

Another interesting note, if your data is linearly separable (like the examples we saw in our age-old post on Perceptrons), then you can use the JLT to make finding a linear separator easier. First project the data onto the dimension given in the theorem. With high probability the points will still be linearly separable. And then you can use a perceptron-type algorithm in the smaller dimension. If you want to find out which side a new point is on, you project and compare with the separator in the smaller dimension.

Beyond its interest for practical dimensionality reduction, the JLT has had many other interesting theoretical consequences. More generally, the idea of “randomly projecting” your data onto some small dimensional space has allowed mathematicians to get some of the best-known results on many optimization and learning problems, perhaps the most famous of which is called MAX-CUT; the result is by Goemans-Williamson and it led to a mathematical constant being named after them, $\alpha_{GW} =.878567 \dots$. If you’re interested in more about the theory, Santosh Vempala wrote a wonderful (and short!) treatise dedicated to this topic.