From Coin Flipping to k-Means Clustering

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From the course by University of California San Diego

Genomic Data Science and Clustering (Bioinformatics V)

86 ratings

University of California San Diego

Genomic Data Science and Clustering (Bioinformatics V)

86 ratings

Course 5 of 7 in the Specialization Bioinformatics

How do we infer which genes orchestrate various processes in the cell? How did humans migrate out of Africa and spread around the world? In this class, we will see that these two seemingly different questions can be addressed using similar algorithmic and machine learning techniques arising from the general problem of dividing data points into distinct clusters. In the first half of the course, we will introduce algorithms for clustering a group of objects into a collection of clusters based on their similarity, a classic problem in data science, and see how these algorithms can be applied to gene expression data. In the second half of the course, we will introduce another classic tool in data science called principal components analysis that can be used to preprocess multidimensional data before clustering in an effort to greatly reduce the number dimensions without losing much of the "signal" in the data. Finally, you will learn how to apply popular bioinformatics software tools to solve a real problem in clustering.

From the lesson

Week 2: Advanced Clustering Techniques

<p>Welcome to week 2 of class!</p> <p>This week, we will see how we can move from a "hard" assignment of points to clusters toward a "soft" assignment that allows the boundaries of the clusters to blend. We will also see how to adapt the Lloyd algorithm that we encountered in the first week in order to produce an algorithm for soft clustering. We will also see another clustering algorithm called "hierarchical clustering" that groups objects into larger and larger clusters.</p>

From Hard to Soft Clustering 11:34

From Coin Flipping to k-Means Clustering 4:35

Expectation Maximization 7:33

Soft k-Means Clustering 3:26

Hierarchical Clustering 7:48

Meet the Instructors

Pavel Pevzner
Professor
Department of Computer Science and Engineering
Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering

I know you're wondering,

what coin flipping has to do with this k-means clustering.

I promise, I will explain in this section.

And in the previous section, we learned that if hidden vector is known

that we can derive parameters through but

in reality, neither hidden vector or parameters are known and

therefore it is unclear how to derive the basis of the coin.

Lets start from a simple problem.

Lets imagine for a second that parameters are actually known.

Lets start from this example.

The parameters are 0.35 for the blue coin, 0.80 for the green coin.

Can we derive the hidden vector?

Well, let's say what is the most likely coin to generate

the first sequence of flip where the fraction of heads is 0.4.

Well, we can compute the probability that the first sequence

as generated by the blue coin.

And this probability turned out to be 0.00113.

We can also compute the probabilities that was generated by the green coin and

it turned out to be a much smaller number 0.00003.

Which coin is more likely?

Of course the blue coin is more likely to generate the first sequence.

Which coin is more likely to generate the second sequence where we have nine heads?

Well, we do the same calculation.

It turn out that the probability of the second

series of flips to be generated by the blue coin is much smaller

than the probability of it being generated by the green coin, and therefore,

the most likely coin for the second series of flips is green.

By continuing this way, we can derive the hiddenvector.

It brings us to the following idea.

Yes, we do not know Parameters or

HiddenVector when we start evaluating the biases of coin.

But let's start from randomly chosen parameters.

As soon as parameters are chosen, we can derive the HiddenVector.

As soon as the HiddenVector is derived,

we question our wisdom in selecting the initial parameters and

estimate the parameters using data and hidden vector as I described.

Before through the [INAUDIBLE] product.

In this way we will arrive to the new parameters.

As soon as the new parameters are derived,

we once again evaluate the hidden vector and iterate.

We came up with an approximation algorithm for

evaluating parameters for the coin flip.

And let me show you how this algorithm work.

We start from randomly selected parameters.

As soon as parameters selected, we do form a HiddenVector, so

we assign each series of flips to either blue coin or red coin.

As soon as HiddenVector is derived,

we can use this HiddenVector to derive new parameters.

Soon as this new parameter is derived, we construct new HiddenVector and

we iterate until convergence.

Does this algorithm remind you of something?

Of course, it is the k-means algorithm or

something very similar to the Lloyd algorithm in disguise,

whereas data, hidden vector and parameters in k-means clustering.

Well, data is a set of datapoints.

Well, what are the parameters?

Parameters are of course, the positions of the centers.

And what is the HiddenVector?

HiddenVector is simply assignment of data points to k centers,

where each is an (n-dimensional vector with coordinates from 1 to k).

This assignment HiddenVector is shown below by green coordinates.

So we figure out how to solve the coin flipping problem and

what relationship it has to k-means clustering.

And now we'll talk about a more general

approach called Expectation Maximization.

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