Win-Vector Blog

It occurred to us recently that we don’t have any articles about Bayesian approaches to statistics here. I’m not going to get into the “Bayesian versus Frequentist” war; in my opinion, which style of approach to use is less about philosophy, and more about figuring out the best way to answer a question. Once you have the right question, then the right approach will naturally suggest itself to you. It could be a frequentist approach, it could be a bayesian one, it could be both — even while solving the same problem.

Let’s take the example that Bayesians love to hate: significance testing, especially in clinical trial style experiments. Clinical trial experiments are designed to answer questions of the form “Does treatment X have a discernible effect on condition Y, on average?” To be specific, let’s use the question “Does drugX reduce hypertension, on average?” Assuming that your experiment does show a positive effect, the statistical significance tests that you run should check for the sorts of problems that John discussed in our previous article, Worry about correctness and repeatability, not p-values: What are the chances that an ineffective drug could produce the results that I saw? How likely is it that another researcher could replicate my results with the same size trial?

We can argue about whether or not the question we are answering is the correct question — but given that it is the question, the procedure to answer it and to verify the statistical validity of the results is perfectly appropriate.

So what is the correct question? From your family doctor’s viewpoint, a clinical trial answers the question “If I prescribe drugX to all my hypertensive patients, will their blood pressure improve, on average?” That isn’t the question (hopefully) that your doctor actually asks, though possibly your insurance company does. Your doctor should be asking “If I prescribe drugX to this patient, the one sitting in my examination room, will the patient’s blood pressure improve?” There is only one patient, so there is no such thing as “on average.”

If your doctor has a masters degree in statistics, the question might be phrased as “If I prescribe drugX to this patient, what is the posterior probability that the patient’s blood pressure will improve?” And that’s a bayesian question. Read more…

Related posts:

1. Statistics to English Translation, Part 2a: ’Significant’ Doesn’t Always Mean ’Important’
2. Worry about correctness and repeatability, not p-values
3. Statistics to English Translation, Part 2b: Calculating Significance
4. “I don’t think that means what you think it means;” Statistics to English Translation, Part 1: Accuracy Measures
5. How to test XCOM “dice rolls” for fairness

A fair complaint when seeing yet another “data science” article is to say: “this is just medical statistics” or “this is already part of bioinformatics.” We certainly label many articles as “data science” on this blog. Probably the complaint is slightly cleaner if phrased as “this is already known statistics.” But the essence of the complaint is a feeling of claiming novelty in putting old wine in new bottles. Rob Tibshirani nailed this type of distinction in is famous machine learning versus statistics glossary.

I’ve written about statistics v.s. machine learning , but I would like to explain why we (the authors of this blog) often use the term data science. Nina Zumel explained being a data scientist very well, I am going to take a swipe at explaining data science.

We (the authors on this blog) label many of our articles as being about data science because we want to emphasize that the various techniques we write about are only meaningful when considered parts of a larger end to end process. The process we are interested in is the deployment of useful data driven models into production. The important components are learning the true business needs (often by extensive partnership with customers), enabling the collection of data, managing data, applying modeling techniques and applying statistics criticisms. The pre-existing term I have found that is closest to describing this whole project system is data science, so that is the term I use. I tend to use it a lot, because while I love the tools and techniques our true loyalty is to the whole process (and I want to emphasize this to our readers).

The phrase “data science” as in use it today is a fairly new term (made popular by William S. Cleveland, DJ Patil, and Jeff Hammerbacher). I myself worked in a “computational sciences” group in the mid 1990′s (this group emphasized simulation based modeling of small molecules and their biological interactions, the naming was an attempt to emphasize computation over computers). So for me “data science” seems like a good term when your work is driven by data (versus driven from computer simulations). For some people data science is considered a new calling and for others it is a faddish misrepresentation of work that has already been done. I think there are enough substantial differences in approach between traditional statistics, machine learning, data mining, predictive analytics, and data science to justify at least this much nomenclature. In this article I will try to describe (but not fully defend) my opinion. Read more…

Related posts:

1. A Personal Perspective on Machine Learning
2. Setting expectations in data science projects
3. The differing perspectives of statistics and machine learning
4. Data science project planning
5. On Being a Data Scientist

In data science work you often run into cryptic sentences like the following:

Age adjusted death rates per 10,000 person years across incremental thirds of muscular strength were 38.9, 25.9, and 26.6 for all causes; 12.1, 7.6, and 6.6 for cardiovascular disease; and 6.1, 4.9, and 4.2 for cancer (all P < 0.01 for linear trend).

(From “Association between muscular strength and mortality in men: prospective cohort study,” Ruiz et. al. BMJ 2008;337:a439.)

The accepted procedure is to recognize “p” or “p-value” as shorthand for “significance,” keep your mouth shut and hope the paper explains what is actually claimed somewhere later on. We know the writer is claiming significance, but despite the technical terminology they have not actually said which test they actually ran (lm(), glm(), contingency table, normal test, t-test, f-test, g-test, chi-sq, permutation test, exact test and so on). I am going to go out on a limb here and say these type of sentences are gibberish and nobody actually understands them. From experience we know generally what to expect, but it isn’t until we read further we can precisely pin down what is actually being claimed. This isn’t the authors’ fault, they are likely good scientists, good statisticians, and good writers; but this incantation is required by publishing tradition and reviewers.

We argue you should worry about the correctness of your results (how likely a bad result could look like yours, the subject of frequentist significance) and repeatability (how much variance is in your estimation procedure, as measured by procedures like the bootstrap). p-values and significance are important in how they help structure the above questions.

The legitimate purpose of technical jargon is to make conversations quicker and more precise. However, saying “p” is not much shorter than saying “significance” and there are many different procedures that return p-values (so saying “p” does not limit you down to exactly one procedure like a good acronym might). At best the savings in time would be from having to spend 10 minutes thinking which interpretation of significance is most approbate to the actual problem at hand versus needing a mere 30 seconds to read about the “p.” However, if you don’t have 10 minutes to consider if the entire result a paper is likely an observation artifact due to chance or noise (the subject of significance) then you really don’t care much about the paper.

In our opinion “p-values” have degenerated from a useful jargon into a secretive argot. We are going to discuss thinking about significance as “worrying about correctness” (a fundamental concern) instead of as a cut and dried statistical procedure you should automate out of view (uncritically copying reported p’s from fitters). Yes “p”s are significances, but there is no reason to not just say what sort of error you are claiming is unlikely. Read more…

Related posts:

1. Level fit summaries can be tricky in R
2. How to test XCOM “dice rolls” for fairness
3. A bit more on sample size
4. Statistics to English Translation, Part 2a: ’Significant’ Doesn’t Always Mean ’Important’
5. What does a generalized linear model do?

Using correlation to track model performance is “a mistake that nobody would ever make” combined with a vague “what would be wrong if I did do that” feeling. I hope after reading this feel a least a small urge to double check your work and presentations to make sure you have not reported correlation where R-squared, likelihood or root mean square error (RMSE) would have been more appropriate.

It is tempting (but wrong) to use correlation to track the performance of model predictions. The temptation arises because we often (correctly) use correlation to evaluate possible model inputs. And the correlation function is often a convenient built-in function. Read more…

Related posts:

1. Correlation and R-Squared
2. Level fit summaries can be tricky in R
3. Modeling Trick: Masked Variables
4. Your Data is Never the Right Shape
5. What does a generalized linear model do?

Recently Heroku was accused of using random queue routing while claiming to supply something similar to shortest queue routing (see: James Somers – Heroku’s Ugly Secret and more discussion at hacker news: Heroku’s Ugly Secret). If this is true it is pretty bad. I like randomized algorithms and I like queueing theory, but you need to work through proofs or at least simulations when playing with queues. You don’t want to pick an arbitrary algorithm and claim it works “due to randomness.” We will show a very quick example where randomized routing is very bad with near certainty. Just because things are “random” doesn’t mean you can’t or shouldn’t characterize them. Read more…

Related posts:

1. Six Fundamental Methods to Generate a Random Variable
2. Ergodic Theory for Interested Computer Scientists
3. Volunteers in Large Clubs: The Theorist’s View
4. Postel’s Law: Not Sure Who To Be Angry With
5. I am done with 32 bit machines

Check out Nina Zumel’s latest article: On Balance.

Related posts:

1. Public Service Article: JSTOR and other Useful Research Archives
2. YAYGDA (Yet Another Yahoo Google Deal Article)
3. Automatic Detection of Potential Deadlock
4. Something I don’t get about business and bailouts
5. Win-Vector’s Nina Zumel: “I Write, Therefore I Think”

XCOM: Enemy Unknown is a turn based video game where the player choses among actions (for example shooting an alien) that are labeled with a declared probability of success.

Image copyright Firaxis Games

A lot of gamers, after missing a 80% chance of success shot, start asking if the game’s pseudo random number generator is fair. Is the game really rolling the dice as stated, or is it cheating? Of course the matching question is: are player memories at all fair; would they remember the other 4 out of 5 times they made such a shot?

This article is intended as an introduction to the methods you would use to test such a question (be it in a video game, in science, or in a business application such as measuring advertisement conversion). There are already some interesting articles on collecting and analyzing XCOM data and finding and characterizing the actual pseudo random generator code in the game, and discussing the importance of repeatable pseudo-random results. But we want to add a discussion pointed a bit more at analysis technique in general. We emphasize methods that are efficient in their use of data. This is a statistical term meaning that a maximal amount of learning is gained from the data. In particular we do not recommend data binning as a first choice for analysis as it cuts down on sample size and thus is not the most efficient estimation technique. Read more…

Related posts:

1. Statistics to English Translation, Part 2a: ’Significant’ Doesn’t Always Mean ’Important’
2. Statistics to English Translation, Part 2b: Calculating Significance
3. Why you can not to use statistics to dispute magic
4. Level fit summaries can be tricky in R
5. The Simpler Derivation of Logistic Regression

We have been writing for a while about the convergence of Newton steps applied to a logistic regression (See: What does a generalized linear model do?, How robust is logistic regression? and Newton-Raphson can compute an average). This is all based on our principle of working examples for understanding. This eventually progressed to some writing on the nature of problem solving (a nice complement to our earlier writing on calculation). In the course of research we were directed to a very powerful technique called the MM algorithm (see: “The MM Algorithm” Kenneth Lang, 2007; “A Tutorial on MM Algorithms”, David R. Hunter, Kenneth Lange, Amer. Statistician 58:30–37, 2004; and “Monotonicity of Quadratic-Approximation Algorithms”, Dankmar Bohning, Bruce G. Lindsay, Ann. Inst. Statist. Math, Vol. 40, No. 4, pp 641-664, 1988). The MM algorithm introduces an essential idea: majorized functions (not to be confused with the majorized order on R^d). Majorization it is an interesting way to modify Newton methods to be reliable contractions (and therefore converge in a manner similar to EM algorithms).

Here we will work an example of the MM method. We will not work it in its most general form, but in a form that quickly reveals much of the beauty of the method. We also introduce a “collared Newton step” which guarantees convergence without resorting to line-search (essentially resolving the issues in solving a logistic regression by Newton style methods). Read more…

Related posts:

1. How robust is logistic regression?
2. Newton-Raphson can compute an average
3. The equivalence of logistic regression and maximum entropy models
4. The Mathematician’s Dilemma
5. The Simpler Derivation of Logistic Regression

This was originally posted at ninazumel.com. I’m re-blogging it here.

Photo: John Mount

I came across a post from Emily Willingham the other day: “Is a PhD required for Good Science Writing?”. As a science writer with a science PhD, her answer is: is it not required, and it can often be an impediment. I saw a similar sentiment echoed once by Lee Gutkind, the founder and editor of the journal Creative Nonfiction. I don’t remember exactly what he wrote, but it was something to the effect that scientists are exactly the wrong people to produce literary, accessible writing about matters scientific.

I don’t agree with Gutkind’s point, but I can see where it comes from. Academic writing has a reputation for being deliberately obscure and prolix, jargonistic. Very few people read journal papers for fun (well, except me, but I’m weird). On the other hand, a science writer with a PhD has been trained for critical thinking, and should have a nose for bullpucky, even outside their field of expertise. This can come in handy when writing about medical research or controversial new scientific findings. Any scientist — any person — is going to hype up their work. It’s the writer’s job to see through that hype.

I’m not a science writer in the sense that Dr. Willingham is. I write statistics and data science articles (blog posts) for non-statisticians. Generally, the audience that I write for is professionally interested in the topic, but aren’t necessarily experts at it. And as a writer, many of my concerns are the same as those of a popular science writer.

I want to cut through the bullpucky. I want you, the reader, to come away understanding something you thought you didn’t — or even couldn’t — understand. I want you, the analyst or data science practitioner, to understand your tools well enough to innovate, not just use them blindly. And if I’m writing about one of my innovations, I want you to understand it well enough to possibly use it, not just be awed at my supposed brilliance.

I don’t do these things perfectly; but in the process of trying, and of reading other writers with similar objectives, I’ve figured out a few things.

Read more…

Related posts:

1. What does a generalized linear model do?
2. Kernel Methods and Support Vector Machines de-Mystified
3. Public Service Article: JSTOR and other Useful Research Archives
4. A Personal Perspective on Machine Learning

Logistic Regression is a popular and effective technique for modeling categorical outcomes as a function of both continuous and categorical variables. The question is: how robust is it? Or: how robust are the common implementations? (note: we are using robust in a more standard English sense of performs well for all inputs, not in the technical statistical sense of immune to deviations from assumptions or outliers.)

Even a detailed reference such as “Categorical Data Analysis” (Alan Agresti, Wiley, 1990) leaves off with an empirical observation: “the convergence … for the Newton-Raphson method is usually fast” (chapter 4, section 4.7.3, page 117). This is a book that if there is a known proof that the estimation step is a contraction (one very strong guarantee of convergence) you would expect to see the proof reproduced. I always suspected there was some kind of Brouwer fixed-point theorem based folk-theorem proving absolute convergence of the Newton-Raphson method in for the special case of logistic regression. This can not be the case as the Newton-Raphson method can diverge even on trivial full-rank well-posed logistic regression problems. Read more…

Related posts:

1. The equivalence of logistic regression and maximum entropy models
2. Learn Logistic Regression (and beyond)
3. The Simpler Derivation of Logistic Regression
4. Newton-Raphson can compute an average
5. Large Data Logistic Regression (with example Hadoop code)