Monday, June 29, 2015

What I Did This Year

My master’s thesis, which I spent most of this year working on with my supervisor, Chris Yau, contains 83 pages, 82 equations, and 13,000 lines of code, but because you are brilliant I am going to explain it here in 800 words (plus one 300-word note on what I learned from the project) and you are going to understand all of it.


The thesis develops better ways of performing two important statistical tasks on a widely used type of biological data. First I’ll explain the data, then I’ll explain the tasks, then I’ll explain what we did.


The data is called single-cell gene expression data. In a previous post I explained why we like gene expression data: it tells us how much RNA cells produce from their genes, which tells us which genes are important to the cell’s functions.


Before, we could only measure gene expression data by combining hundreds of cells: otherwise there wasn’t enough RNA to measure. But single-cell gene expression data lets us measure RNA levels within single cells. This is exciting because rather than pretending that all the cells in a tissue, or a tumor, are identical, we can look for groups of cells which are different in important ways. It’s like the difference between asking “What are Americans like on average?” and interviewing individual Americans. (We’re not all bad!)


These differences between cells matter because they have implications for how we treat disease. For example, single-cell analysis reveals that brain tumors which are classified as a single type in fact contain mixtures of multiple types of cells. And this diversity makes the tumors harder to treat: the more diverse the tumor is, the worse the patient’s prognosis, possibly because treatments that work on one group of cells don’t work well on the rest of the cells.


So people are writing papers saying single-cell data will “revolutionize” science. (I would write papers saying things like that, but no one pays attention to me.) Unfortunately, single-cell data is also hard for standard statistical models to deal with, because it has a lot of “zeros”: cells where we cannot detect any RNA produced from a gene. If you plot how much RNA is measured from a gene, it looks like this:
The spike at zero is bad because many statistical models assume data is Gaussian -- that is, it makes a nice blob, pictured below.


Obviously, the spike at zero in single-cell data makes the data very not Gaussian, and this makes it harder to perform many statistical tasks. Specifically, there are two things we often want to do with data -- cluster it, where we divide cells into groups so that similar cells are put into the same group, and reduce its dimension, where we plot cells in two (or more) dimensions such that similar cells appear close together [1]. Standard methods for performing these tasks assume the data is Gaussian.


In my thesis, we first develop a model for the patterns of zeros in single-cell data, and, based on this model, show that zeros really do hurt the performance of standard methods. We show, in several different datasets, that genes that are expressed at a higher level are less likely to be zero, and develop a model that describes this relationship. (I describe the mathematical details here [2].) Based on our model, we generate simulated data and show that the performance of standard statistical methods gets worse as we add zeros. Here’s a demo: move the slider to add zeros, and watch how the clusters (which are supposed to be separate) get mushed together. This is bad. We have an important new type of data; we have important statistical tasks that we often want to perform; standard methods for performing the tasks do not work well on the new data.


Diagnosing the problem is easy; how do we fix it? We develop two new models: a clustering model (ZIMM, for zero-inflated mixture model) and a dimensionality-reduction model (ZIFA, for zero-inflated factor analysis -- new statistical models are required to have a cool acronym). I give more details on how we developed the models in this footnote [3]. We show that our models do a better job than standard models on both simulated data and real biological data and put the code online so other people can use them. We are giving talks on the work at various venues, and a paper is under review. If you’re interested in using or extending these models, feel free to send me or Chris an email.


While we developed these models for single-cell data, they are potentially useful for lots of other datasets which have many zeros or missing datapoints. In the thesis we discuss several examples: recommendation datasets (how much will a person will like a product? -- see, for example, Netflix’s million dollar competition to predict movie ratings), usage datasets (how often a person will use a product?) and network datasets (how strongly are two nodes, eg airports, connected in a network?) Feel free to read the last chapter of the thesis and let me know if you have ideas for further applications (translation: do my homework for me).


Working on this project taught me about the role of luck in research. I often feel there’s a great deal of luck when you investigate some cool statistical hypothesis (“older women with cats are more likely to be single”). The hypothesis may or may not turn out to be true, but its truth doesn’t depend on how good a scientist you are. This luck evens out, though, because better scientists a) look at more things b) look at more interesting things c) look at them more rigorously.


You might think, though, that when you’re just doing math rather than observing the world, there’s no luck involved, only skill; equations are within your control. Still, my experience this year makes me feel there’s still luck involved, and I’ll draw an analogy to chess. Chess, in theory, is a game with no luck; there’s no dice, no drawn cards. But you will still hear chess players say “I got lucky” (or, more often, “I got unlucky”) because they calculated ten moves ahead, and on the eleventh move, their queen happened to be in the right place, and so they won, but they didn’t foresee it.


Similarly, my thesis involves about ten pages of algebra, at the end of which the math works out nicely. But I didn’t know this would happen when I began; this is what I mean by getting lucky.


Again, though, I feel the luck evens out here. I may occasionally beat a chessplayer who sees farther ahead than me because my pieces end up in the right place, but most of the time I’m going to lose. Similarly, I have met mathematicians who can see further down a proof tree than I can (and also have an eerie instinct for which branches will yield fruit) and they can prove trickier things than I can. In the case of my thesis, while we got “lucky” in the end, we also had to fix my screwups revise our approach several times; the final product feels like the result of a lot of blood, sweat, and tea [4]. Or maybe I’m just saying that so Oxford will let me graduate.


Notes:
[1] For each cell, we have data for tens of thousands of genes. It’s very hard to visualize or analyze data with ten thousand dimensions. So we want to reduce ten thousand to something more manageable, like two, in a way that preserves basic patterns in the data.
[2] Call the probability that a gene is zero p0, and the average expression of a gene when it’s not zero μ. Then, p0  = exp(-lambda*μ2), where exp is the exponential function and lambda is a parameter we fit to the data. Here are four different real biological datasets: the orange line is the actual data, and the red is our fitted model. You can see the orange line fits the red line pretty closely.


[3] Here’s a two-step procedure for developing statistical models:


  1. Write down (using math) the process you think generates the data. This is usually the straightforward part. In the case of ZIFA and ZIMM, our process is “generate data using a standard statistical model. Then, add zeros to that data”.
  2. Your model will have “parameters” -- numbers that affect the predictions it makes. For example, if your model is
    number_of_colleges_you_get_into = A*your_SAT_score + B*your_parents’_income
    then A and B are parameters of the model. Obviously, in order to calculate useful things with a model (in this case, how many colleges you are expected to get into) you need a way of figuring out the values of the parameters (for example, A = .01, B = .001). This is the hard part; it took me most of the winter.
[4] The British do not cry, or if they do, they cry Earl Grey.




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