Category Archives: statistics

Small area estimates by others in PHM

Article alert
The following new article has just been published in Population Health Metrics

Small area synthetic estimates of smoking prevalence during pregnancy in England
Szatkowski L, Fahy S, Coleman T, Taylor J, Twigg L, Moon G, Leonardi-Bee J
Population Health Metrics 2015, 13 :34 (9 December 2015)


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Filed under global health, statistics

Laplace approximation in PyMC3, revisited

I found an even better example of the value of Laplace approximation, and its just a small tweak to the example I did a few weeks ago:

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MCMC in Python: Gaussian mixture model in PyMC3

PyMC3 is really coming along. I tried it out on a Gaussian mixture model that was the subject of some discussion on GitHub:

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Filed under MCMC, software engineering, statistics

Laplace approximation in Python: another cool trick with PyMC3

I admit that I’ve been skeptical of the complete rewrite of PyMC that underlies version 3. It seemed to me motivated by an interest in using unproven new step methods that require knowing the derivative of the posterior distribution. But, it is really coming together, and regardless of whether or not the Hamiltonian Monte Carlo stuff pays off, there are some cool tricks you can do when you can get derivatives without a hassle.

Exhibit 1: A Laplace approximation approach to fitting mixed effect models (as described in

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By no means unhelpful

Good advice from Density Estimation for Statistics and Data Analysis by Bernard. W. Silverman:



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Kish Stuff

A student came by interested in survey statistics and we go to talking about what an amazing person Leslie Kish must have been. We did some googling on it. Here are a few items we found:

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Non-parametric regression in Python: Gaussian Processes in sklearn (with a little PyMC)

I’ve got a fun class going this quarter, on “artificial intelligence for health metricians”, and the course content mixed with some of the student interest has got me looking at the options for doing Gaussian process regression in Python. `PyMC2` has some nice stuff, but the `sklearn` version fits with the rest of my course examples more naturally, so I’m using that instead.

But `sklearn` doesn’t have the fanciest of fancy covariance functions implemented, and at IHME we have been down the road of the Matern covariance function for over five years now. It’s in `PyMC`, so I took a crack at mash-up. (Took a mash at a mash-up?) There is some room for improvement, but it is a start. If you need to do non-parametric regression for something that is differentiable more than once, but less than infinity times, you could try starting here:

p.s. Chris Fonnesbeck has some great notes on doing stuff like this and much more here:

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Filed under statistics