Monadic probabilistic programming in Scala with Rainier

Introduction

Rainier is an interesting new probabilistic programming library for Scala recently open-sourced by Stripe. Probabilistic programming languages provide a computational framework for building and fitting Bayesian models to data. There are many interesting probabilistic programming languages, and there is currently a lot of interesting innovation happening with probabilistic programming languages embedded in strongly typed functional programming languages such as Scala and Haskell. However, most such languages tend to be developed by people lacking expertise in statistics and numerics, leading to elegant, composable languages which work well for toy problems, but don’t scale well to the kinds of practical problems that applied statisticians are interested in. Conversely, there are a few well-known probabilistic programming languages developed by and for statisticians which have efficient inference engines, but are hampered by inflexible, inelegant languages and APIs. Rainier is interesting because it is an attempt to bridge the gap between these two worlds: it has a functional, composable, extensible, monadic API, yet is backed by a very efficient, high-performance scalable inference engine, using HMC and a static compute graph for reverse-mode AD. Clearly there will be some loss of generality associated with choosing an efficient inference algorithm (eg. for HMC, there needs to be a fixed number of parameters and they must all be continuous), but it still covers a large proportion of the class of hierarchical models commonly used in applied statistical modelling.

In this post I’ll give a quick introduction to Rainier using an interactive session requiring only that SBT is installed and the Rainier repo is downloaded or cloned.

Interactive session

To follow along with this post just clone, or download and unpack, the Rainier repo, and run SBT from the top-level Rainier directory and paste commands. First start a Scala REPL.

project rainierPlot
console

Before we start building models, we need some data. For this post we will focus on a simple logistic regression model, and so we will begin by simulating some synthetic data consistent with such a model.

val r = new scala.util.Random(0)
val N = 1000
val beta0 = 0.1
val beta1 = 0.3
val x = (1 to N) map { i =>
  3.0 * r.nextGaussian
}
val theta = x map { xi =>
  beta0 + beta1 * xi
}
def expit(x: Double): Double = 1.0 / (1.0 + math.exp(-x))
val p = theta map expit
val y = p map (pi => (r.nextDouble < pi))

Now we have some synthetic data, we can fit the model and see if we are able to recover the “true” parameters used to generate the synthetic data. In Rainier, we build models by declaring probabilistic programs for the model and the data, and then run an inference engine to generate samples from the posterior distribution.

Start with a bunch of Rainier imports:

import com.stripe.rainier.compute._
import com.stripe.rainier.core._
import com.stripe.rainier.sampler._
import com.stripe.rainier.repl._

Now we want to build a model. We do so by describing the joint distribution of parameters and data. Rainier has a few built-in distributions, and these can be combined using standard functional monadic combinators such as map, zip, flatMap, etc., to create a probabilistic program representing a probability monad for the model. Due to the monadic nature of such probabilistic programs, it is often most natural to declare them using a for-expression.

val model = for {
  beta0 <- Normal(0, 5).param
  beta1 <- Normal(0, 5).param
  _ <- Predictor.from{x: Double =>
      {
        val theta = beta0 + beta1 * x
        val p = Real(1.0) / (Real(1.0) + (Real(0.0) - theta).exp)
        Categorical.boolean(p)
      }
    }.fit(x zip y)
} yield Map("b0"->beta0, "b1"->beta1)

This kind of construction is very natural for anyone familiar with monadic programming in Scala, but will no doubt be a little mysterious otherwise. RandomVariable is the probability monad used for HMC sampling, and these can be constructed from Distributions using .param (for unobserved parameters) and .fit (for variables with associated observations). Predictor is just a convenience for observations corresponding to covariate information. model is therefore a RandomVariable over beta0 and beta1, the two unobserved parameters of interest. Note that I briefly discussed this kind of pure functional approach to describing probabilistic programs (using Rand from Breeze) in my post on MCMC as a stream.

Now we have our probabilistic program, we can sample from it using HMC as follows.

implicit val rng = ScalaRNG(3)
val its = 10000
val thin = 5
val out = model.sample(HMC(5), 10000, its*thin, thin)
println(out.take(10))

The argument to HMC() is the number of leapfrog steps to take per iteration.

Finally, we can use EvilPlot to look at the HMC output and check that we have managed to reasonably recover the true parameters associated with our synthetic data.

import com.cibo.evilplot.geometry.Extent
import com.stripe.rainier.plot.EvilTracePlot._

render(traces(out, truth = Map("b0" -> beta0, "b1" -> beta1)),
  "traceplots.png", Extent(1200, 1000))
render(pairs(out, truth = Map("b0" -> beta0, "b1" -> beta1)), "pairs.png")

Everything looks good, and the sampling is very fast!

Further reading

For further information, see the Rainier repo. In particular, start with the tour of Rainier’s core, which gives a more detailed introduction to how Rainier works than this post. Those interested in how the efficient AD works may want to read about the compute graph, and the implementation notes explain how it all fits together. There is some basic ScalaDoc for the core package, and also some examples (including this one), and there’s a gitter channel for asking questions. This is a very new project, so there are a few minor bugs and wrinkles in the initial release, but development is progressing rapidly, so I fully expect the library to get properly battle-hardened over the next few months.

For those unfamiliar with the monadic approach to probabilistic programming, then Ścibior et al (2015) is probably a good starting point.

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Published by

darrenjw

I am Professor of Stochastic Modelling within the School of Mathematics & Statistics at Newcastle University, UK. I am also a computational systems biologist.

2 thoughts on “Monadic probabilistic programming in Scala with Rainier”

  1. Hey Darren,

    This looks really nice. There is quite a lot of interest in probabilistic programming in the clojure community too, I’ve yet to try this out on Scala. I was hoping to pick your brains about the limitations of AD. It is my understanding that many AD libraries have difficulty when your likelihood involves a lot of linear algebra operatoins. For instance imagine a Gaussian process likelihood, where you would like to do inference on the variance and length scale of the GP. When the linear algebra operations concern matrices which are themselves functions of the hyper parameters, is it still possible for AD to compute the derivative? I don’t think many AD libraries can do this, but I also haven’t exhaustively tried them out. Do you have a feel for this?

  2. I’m afraid that I don’t have a good feel for this – I’m really not an AD expert. Of course, linear algebra operations are composed of elementary mathematical operations, so I don’t think there’s any fundamental reason why it can’t work. However, there are a number of different approaches one can take to developing AD frameworks, and it seems very likely that some will be much better suited to these kinds of problems than others. Also worth noting is that deep learning models involve lots of linear algebra operations, so looking at AD frameworks for DL may be informative. But hopefully there are some AD/HMC experts reading this who can offer further insight.

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