scala-glm: Regression modelling in Scala

Introduction

As discussed in the previous post, I’ve recently constructed and delivered a short course on statistical computing with Scala. Much of the course is concerned with writing statistical algorithms in Scala, typically making use of the scientific and numerical computing library, Breeze. Breeze has all of the essential tools necessary for building statistical algorithms, but doesn’t contain any higher level modelling functionality. As part of the course, I walked through how to build a small library for regression modelling on top of Breeze, including all of the usual regression diagnostics (such as standard errors, t-statistics, p-values, F-statistics, etc.). While preparing the course materials it occurred to me that it would be useful to package and document this code properly for general use. In advance of the course I packaged the code up into a bare-bones library, but since then I’ve fleshed it out, tidied it up and documented it properly, so it’s now ready for people to use.

The library covers PCA, linear regression modelling and simple one-parameter GLMs (including logistic and Poisson regression). The underlying algorithms are fairly efficient and numerically stable (eg. linear regression uses the QR decomposition of the model matrix, and the GLM fitting uses QR within each IRLS step), though they are optimised more for clarity than speed. The library also includes a few utility functions and procedures, including a pairs plot (scatter-plot matrix).

A linear regression example

Plenty of documentation is available from the scala-glm github repo which I won’t repeat here. But to give a rough idea of how things work, I’ll run through an interactive session for the linear regression example.

First, download a dataset from the UCI ML Repository to disk for subsequent analysis (caching the file on disk is good practice, as it avoids unnecessary load on the UCI server, and allows running the code off-line):

import scalaglm._
import breeze.linalg._

val url = "http://archive.ics.uci.edu/ml/machine-learning-databases/00291/airfoil_self_noise.dat"
val fileName = "self-noise.csv"

// download the file to disk if it hasn't been already
val file = new java.io.File(fileName)
if (!file.exists) {
  val s = new java.io.PrintWriter(file)
  val data = scala.io.Source.fromURL(url).getLines
  data.foreach(l => s.write(l.trim.
    split('\t').filter(_ != "").
    mkString("", ",", "\n")))
  s.close
}

Once we have a CSV file on disk, we can load it up and look at it.

val mat = csvread(new java.io.File(fileName))
// mat: breeze.linalg.DenseMatrix[Double] =
// 800.0    0.0  0.3048  71.3  0.00266337  126.201
// 1000.0   0.0  0.3048  71.3  0.00266337  125.201
// 1250.0   0.0  0.3048  71.3  0.00266337  125.951
// ...
println("Dim: " + mat.rows + " " + mat.cols)
// Dim: 1503 6
val figp = Utils.pairs(mat, List("Freq", "Angle", "Chord", "Velo", "Thick", "Sound"))
// figp: breeze.plot.Figure = breeze.plot.Figure@37718125

We can then regress the response in the final column on the other variables.

val y = mat(::, 5) // response is the final column
// y: DenseVector[Double] = DenseVector(126.201, 125.201, ...
val X = mat(::, 0 to 4)
// X: breeze.linalg.DenseMatrix[Double] =
// 800.0    0.0  0.3048  71.3  0.00266337
// 1000.0   0.0  0.3048  71.3  0.00266337
// 1250.0   0.0  0.3048  71.3  0.00266337
// ...
val mod = Lm(y, X, List("Freq", "Angle", "Chord", "Velo", "Thick"))
// mod: scalaglm.Lm =
// Lm(DenseVector(126.201, 125.201, ...
mod.summary
// Estimate	 S.E.	 t-stat	p-value		Variable
// ---------------------------------------------------------
// 132.8338	 0.545	243.866	0.0000 *	(Intercept)
//  -0.0013	 0.000	-30.452	0.0000 *	Freq
//  -0.4219	 0.039	-10.847	0.0000 *	Angle
// -35.6880	 1.630	-21.889	0.0000 *	Chord
//   0.0999	 0.008	12.279	0.0000 *	Velo
// -147.3005	15.015	-9.810	0.0000 *	Thick
// Residual standard error:   4.8089 on 1497 degrees of freedom
// Multiple R-squared: 0.5157, Adjusted R-squared: 0.5141
// F-statistic: 318.8243 on 5 and 1497 DF, p-value: 0.00000
val fig = mod.plots
// fig: breeze.plot.Figure = breeze.plot.Figure@60d7ebb0

There is a .predict method for generating point predictions (and standard errors) given a new model matrix, and fitting GLMs is very similar – these things are covered in the quickstart guide for the library.

Summary

scala-glm is a small Scala library built on top of the Breeze numerical library which enables simple and convenient regression modelling in Scala. It is reasonably well documented and usable in its current form, but I intend to gradually add additional features according to demand as time permits.

Scala for Data Science [book review]

This post will review the book:

Disclaimer: This book review has not been solicited by the publisher (or anyone else) in any way. I purchased the review copy of this book myself. I have not received any benefit from the writing of this review.

Introduction

On this blog I previously reviewed the (terrible) book, Scala for machine learning by the same publisher. I was therefore rather wary of buying this book. But the topic coverage looked good, so I decided to buy it, and wasn’t disappointed. Scala for Data Science is my top recommendation for getting started with statistical computing and data science applications using Scala.

Overview

The book assumes a basic familiarity with programming in Scala, at around the level of someone who has completed the Functional Programming Principles in Scala Coursera course. That is, it (quite sensibly) doesn’t attempt to teach the reader how to program in Scala, but rather how to approach the development of data science applications using Scala. It introduces more advanced Scala idioms gradually (eg. typeclasses don’t appear until Chapter 5), so it is relatively approachable for those who aren’t yet Scala experts. The book does cover Apache Spark, but Spark isn’t introduced until Chapter 10, so it isn’t “just another Spark book”. Most of the book is about developing data science applications in Scala, completely independently of Spark. That said, it also provides one of the better introductions to Spark, so doubles up as a pretty good introductory Spark book, in addition to being a good introduction to the development of data science applications with Scala. It should probably be emphasised that the book is very much focused on data science, rather than statistical computing, but there is plenty of material of relevance to those who are more interested in statistical computing than applied data science.

Chapter by chapter

  1. Scala and Data Science – motivation for using Scala in preference to certain other languages I could mention…
  2. Manipulating data with BreezeBreeze is the standard Scala library for scientific and statistical computing. It’s pretty good, but documentation is rather lacking. This Chapter provides a good tutorial introduction to Breeze, which should be enough to get people going sufficiently to be able to make some sense of the available on-line documentation.
  3. Plotting with breeze-viz – Breeze has some support for plotting and visualisation of data. It’s somewhat limited when compared to what is available in R, but is fine for interactive exploratory analysis. However, the available on-line documentation for breeze-viz is almost non-existent. This Chapter is the best introduction to breeze-viz that I have seen.
  4. Parallel collections and futures – the Scala standard library has built-in support for parallel and concurrent programming based on functional programming concepts such as parallel (monadic) collections and Futures. Again, this Chapter provides an excellent introduction to these powerful concepts, allowing the reader to start developing parallel algorithms for multi-core hardware with minimal fuss.
  5. Scala and SQL through JDBC – this Chapter looks at connecting to databases using standard JVM mechanisms such as JDBC. However, it gradually introduces more functional ways of interfacing with databases using typeclasses, motivating:
  6. Slick – a functional interface for SQL – an introduction to the Slick library for a more Scala-esque way of database interfacing.
  7. Web APIs – the practicalities of talking to web APIs. eg. authenticated HTTP requests and parsing of JSON responses.
  8. Scala and MongoDB – working with a NoSQL database from Scala
  9. Concurrency with Akka – Akka is the canonical implementation of the actor model in Scala, for building large concurrent applications. It is the foundation on which Spark is built.
  10. Distributed batch processing with Spark – a tutorial introduction to Apache Spark. Spark is a big data analytics framework built on top of Scala and Akka. It is arguably the best available framework for big data analytics on computing clusters in the cloud, and hence there is a lot of interest in it. Indeed, Spark is driving some of the interest in Scala.
  11. Spark SQL and DataFrames – interfacing with databases using Spark, and more importantly, an introduction to Spark’s DataFrame abstraction, which is now fundamental to developing machine learning pipelines in Spark.
  12. Distributed machine learning with MLLib – MLLib is the machine learning library for Spark. It is worth emphasising that unlike many early books on Spark, this chapter covers the newer DataFrame-based pipeline API, in addition to the original RDD-based API. Together, Chapters 10, 11 and 12 provide a pretty good tutorial introduction to Spark. After working through these, it should be easy to engage with the official on-line Spark documentation.
  13. Web APIs with Play – is concerned with developing a web API at the end of a data science pipeline.
  14. Visualisation with D3 and the Play framework – is concerned with integrating visualisation into a data science web application.

Summary

This book provides a good tutorial introduction to a large number of topics relevant to statisticians and data scientists interested in developing data science applications using Scala. After working through this book, readers should be well-placed to augment their knowledge with readily searchable on-line documentation.

In a follow-up post I will give a quick overview of some other books relevant to getting started with Scala for statistical computing and data science.

Calling R from Scala sbt projects

[Update: The jvmr package has been replaced by the rscala package. There is a new version of this post which replaces this one.]

Overview

In previous posts I’ve shown how the jvmr CRAN R package can be used to call Scala sbt projects from R and inline Scala Breeze code in R. In this post I will show how to call to R from a Scala sbt project. This requires that R and the jvmr CRAN R package are installed on your system, as described in the previous posts. Since I’m focusing here on Scala sbt projects, I’m also assuming that sbt is installed.

The only “trick” required for calling back to R from Scala is telling sbt where the jvmr jar file is located. You can find the location from the R console as illustrated by the following session:

> library(jvmr)
> .jvmr.jar
[1] "/home/ndjw1/R/x86_64-pc-linux-gnu-library/3.1/jvmr/java/jvmr_2.11-2.11.2.1.jar"

This location (which will obviously be different for you) can then be added in to your sbt classpath by adding the following line to your build.sbt file:

unmanagedJars in Compile += file("/home/ndjw1/R/x86_64-pc-linux-gnu-library/3.1/jvmr/java/jvmr_2.11-2.11.2.1.jar")

Once this is done, calling out to R from your Scala sbt project can be carried out as described in the jvmr documentation. For completeness, a working example is given below.

Example

In this example I will use Scala to simulate some data consistent with a Poisson regression model, and then push the data to R to fit it using the R function glm(), and then pull back the fitted regression coefficients into Scala. This is obviously a very artificial example, but the point is to show how it is possible to call back to R for some statistical procedure that may be “missing” from Scala.

The dependencies for this project are described in the file build.sbt

name := "jvmr test"

version := "0.1"

scalacOptions ++= Seq("-unchecked", "-deprecation", "-feature")

libraryDependencies  ++= Seq(
            "org.scalanlp" %% "breeze" % "0.10",
            "org.scalanlp" %% "breeze-natives" % "0.10"
)

resolvers ++= Seq(
            "Sonatype Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots/",
            "Sonatype Releases" at "https://oss.sonatype.org/content/repositories/releases/"
)

unmanagedJars in Compile += file("/home/ndjw1/R/x86_64-pc-linux-gnu-library/3.1/jvmr/java/jvmr_2.11-2.11.2.1.jar")

scalaVersion := "2.11.2"

The complete Scala program is contained in the file PoisReg.scala

import org.ddahl.jvmr.RInScala
import breeze.stats.distributions._
import breeze.linalg._

object ScalaToRTest {

  def main(args: Array[String]) = {

    // first simulate some data consistent with a Poisson regression model
    val x = Uniform(50,60).sample(1000)
    val eta = x map { xi => (xi * 0.1) - 3 }
    val mu = eta map { math.exp(_) }
    val y = mu map { Poisson(_).draw }
    
    // call to R to fit the Poission regression model
    val R = RInScala() // initialise an R interpreter
    R.x=x.toArray // send x to R
    R.y=y.toArray // send y to R
    R.eval("mod <- glm(y~x,family=poisson())") // fit the model in R
    // pull the fitted coefficents back into scala
    val beta = DenseVector[Double](R.toVector[Double]("mod$coefficients"))

    // print the fitted coefficents
    println(beta)

  }

}

If these two files are put in an empty directory, the code can be compiled and run by typing sbt run from the command prompt in the relevant directory. The commented code should be self-explanatory, but see the jvmr documentation for further details.

Inlining Scala Breeze code in R using jvmr and sbt

[Update: The CRAN package “jvmr” has been replaced by a new package “rscala”. Rather than completely re-write this post, I’ve just created a github gist containing a new function, breezeInterpreter(), which works similarly to the function breezeInit() in this post. Usage information is given at the top of the gist.]

Introduction

In the previous post I showed how to call Scala code from R using sbt and jvmr. The approach described in that post is the one I would recommend for any non-trivial piece of Scala code – mixing up code from different languages in the same source code file is not a good strategy in general. That said, for very small snippets of code, it can sometimes be convenient to inline Scala code directly into an R source code file. The canonical example of this is a computationally intensive algorithm being prototyped in R which has a slow inner loop. If the inner loop can be recoded in a few lines of Scala, it would be nice to just inline this directly into the R code without having to create a separate Scala project. The CRAN package jvmr provides a very simple and straightforward way to do this. However, as discussed in the last post, most Scala code for statistical computing (even short and simple code) is likely to rely on Breeze for special functions, probability distributions, non-uniform random number generation, numerical linear algebra, etc. In this post we will see how to use sbt in order to make sure that the Breeze library and all of its dependencies are downloaded and cached, and to provide a correct classpath with which to initialise a jvmr scalaInterpreter session.

Setting up

Configuring your system to be able to inline Scala Breeze code is very easy. You just need to install Java, R and sbt. Then install the CRAN R package jvmr. At this point you have everything you need except for the R function breezeInit, given at the end of this post. I’ve deferred the function to the end of the post as it is a bit ugly, and the details of it are not important. All it does is get sbt to ensure that Breeze is correctly downloaded and cached and then starts a scalaInterpreter with Breeze on the classpath. With this function available, we can use it within an R session as the following R session illustrates:

> b=breezeInit()
> b['import breeze.stats.distributions._']
NULL
> b['Poisson(10).sample(20).toArray']
 [1] 13 14 13 10  7  6 15 14  5 10 14 11 15  8 11 12  6  7  5  7
> summary(b['Gamma(3,2).sample(10000).toArray'])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.2124  3.4630  5.3310  5.9910  7.8390 28.5200 
> 

So we see that Scala Breeze code can be inlined directly into an R session, and if we are careful about return types, have the results of Scala expressions automatically unpack back into convenient R data structures.

Summary

In this post I have shown how easy it is to inline Scala Breeze code into R using sbt in conjunction with the CRAN package jvmr. This has many potential applications, with the most obvious being the desire to recode slow inner loops from R to Scala. This should give performance quite comparable with alternatives such as Rcpp, with the advantage being that you get to write beautiful, elegant, functional Scala code instead of horrible, ugly, imperative C++ code! 😉

The breezeInit function

The actual breezeInit() function is given below. It is a little ugly, but very simple. It is obviously easy to customise for different libraries and library versions as required. All of the hard work is done by sbt which must be installed and on the default system path in order for this function to work.

breezeInit<-function()
{
  library(jvmr)
  sbtStr="name := \"tmp\"

version := \"0.1\"

libraryDependencies  ++= Seq(
            \"org.scalanlp\" %% \"breeze\" % \"0.10\",
            \"org.scalanlp\" %% \"breeze-natives\" % \"0.10\"
)

resolvers ++= Seq(
            \"Sonatype Snapshots\" at \"https://oss.sonatype.org/content/repositories/snapshots/\",
            \"Sonatype Releases\" at \"https://oss.sonatype.org/content/repositories/releases/\"
)

scalaVersion := \"2.11.2\"

lazy val printClasspath = taskKey[Unit](\"Dump classpath\")

printClasspath := {
  (fullClasspath in Runtime value) foreach {
    e => print(e.data+\"!\")
  }
}
"
  tmps=file(file.path(tempdir(),"build.sbt"),"w")
  cat(sbtStr,file=tmps)
  close(tmps)
  owd=getwd()
  setwd(tempdir())
  cpstr=system2("sbt","printClasspath",stdout=TRUE)
  cpst=cpstr[length(cpstr)]
  cpsp=strsplit(cpst,"!")[[1]]
  cp=cpsp[2:(length(cpsp)-1)]
  si=scalaInterpreter(cp,use.jvmr.class.path=FALSE)
  setwd(owd)
  si
}

Calling Scala code from R using jvmr

[Update: the jvmr package has been replaced by a new package called rscala. I have a new post which explains it.]

Introduction

In previous posts I have explained why I think that Scala is a good language to use for statistical computing and data science. Despite this, R is very convenient for simple exploratory data analysis and visualisation – currently more convenient than Scala. I explained in my recent talk at the RSS what (relatively straightforward) things would need to be developed for Scala in order to make R completely redundant, but for the short term at least, it seems likely that I will need to use both R and Scala for my day-to-day work.

Since I use both Scala and R for statistical computing, it is very convenient to have a degree of interoperability between the two languages. I could call R from Scala code or Scala from R code, or both. Fortunately, some software tools have been developed recently which make this much simpler than it used to be. The software is jvmr, and as explained at the website, it enables calling Java and Scala from R and calling R from Java and Scala. I have previously discussed calling Java from R using the R CRAN package rJava. In this post I will focus on calling Scala from R using the CRAN package jvmr, which depends on rJava. I may examine calling R from Scala in a future post.

On a system with Java installed, it should be possible to install the jvmr R package with a simple

install.packages("jvmr")

from the R command prompt. The package has the usual documentation associated with it, but the draft paper describing the package is the best way to get an overview of its capabilities and a walk-through of simple usage.

A Gibbs sampler in Scala using Breeze

For illustration I’m going to use a Scala implementation of a Gibbs sampler which relies on the Breeze scientific library, and will be built using the simple build tool, sbt. Most non-trivial Scala projects depend on various versions of external libraries, and sbt is an easy way to build even very complex projects trivially on any system with Java installed. You don’t even need to have Scala installed in order to build and run projects using sbt. I give some simple complete worked examples of building and running Scala sbt projects in the github repo associated with my recent RSS talk. Installing sbt is trivial as explained in the repo READMEs.

For this post, the Scala code, gibbs.scala is given below:

package gibbs

object Gibbs {

    import scala.annotation.tailrec
    import scala.math.sqrt
    import breeze.stats.distributions.{Gamma,Gaussian}

    case class State(x: Double, y: Double) {
      override def toString: String = x.toString + " , " + y + "\n"
    }

    def nextIter(s: State): State = {
      val newX = Gamma(3.0, 1.0/((s.y)*(s.y)+4.0)).draw
      State(newX, Gaussian(1.0/(newX+1), 1.0/sqrt(2*newX+2)).draw)
    }

    @tailrec def nextThinnedIter(s: State,left: Int): State =
      if (left==0) s else nextThinnedIter(nextIter(s),left-1)

    def genIters(s: State, stop: Int, thin: Int): List[State] = {
      @tailrec def go(s: State, left: Int, acc: List[State]): List[State] =
        if (left>0)
          go(nextThinnedIter(s,thin), left-1, s::acc)
          else acc
      go(s,stop,Nil).reverse
    }

    def main(args: Array[String]) = {
      if (args.length != 3) {
        println("Usage: sbt \"run <outFile> <iters> <thin>\"")
        sys.exit(1)
      } else {
        val outF=args(0)
        val iters=args(1).toInt
        val thin=args(2).toInt
        val out = genIters(State(0.0,0.0),iters,thin)
        val s = new java.io.FileWriter(outF)
        s.write("x , y\n")
        out map { it => s.write(it.toString) }
        s.close
      }
    }

}

This code requires Scala and the Breeze scientific library in order to build. We can specify this in a sbt build file, which should be called build.sbt and placed in the same directory as the Scala code.

name := "gibbs"

version := "0.1"

scalacOptions ++= Seq("-unchecked", "-deprecation", "-feature")

libraryDependencies  ++= Seq(
            "org.scalanlp" %% "breeze" % "0.10",
            "org.scalanlp" %% "breeze-natives" % "0.10"
)

resolvers ++= Seq(
            "Sonatype Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots/",
            "Sonatype Releases" at "https://oss.sonatype.org/content/repositories/releases/"
)

scalaVersion := "2.11.2"

Now, from a system command prompt in the directory where the files are situated, it should be possible to download all dependencies and compile and run the code with a simple

sbt "run output.csv 50000 1000"

Calling via R system calls

Since this code takes a relatively long time to run, calling it from R via simple system calls isn’t a particularly terrible idea. For example, we can do this from the R command prompt with the following commands

system("sbt \"run output.csv 50000 1000\"")
out=read.csv("output.csv")
library(smfsb)
mcmcSummary(out,rows=2)

This works fine, but won’t work so well for code which needs to be called repeatedly. For this, tighter integration between R and Scala would be useful, which is where jvmr comes in.

Calling sbt-based Scala projects via jvmr

jvmr provides a very simple way to embed a Scala interpreter within an R session, to be able to execute Scala expressions from R and to have the results returned back to the R session for further processing. The main issue with using this in practice is managing dependencies on external libraries and setting the Scala classpath correctly. For an sbt project such as we are considering here, it is relatively easy to get sbt to provide us with all of the information we need in a fully automated way.

First, we need to add a new task to our sbt build instructions, which will output the full classpath in a way that is easy to parse from R. Just add the following to the end of the file build.sbt:

lazy val printClasspath = taskKey[Unit]("Dump classpath")

printClasspath := {
  (fullClasspath in Runtime value) foreach {
    e => print(e.data+"!")
  }
}

Be aware that blank lines are significant in sbt build files. Once we have this in our build file, we can write a small R function to get the classpath from sbt and then initialise a jvmr scalaInterpreter with the correct full classpath needed for the project. An R function which does this, sbtInit(), is given below

sbtInit<-function()
{
  library(jvmr)
  system2("sbt","compile")
  cpstr=system2("sbt","printClasspath",stdout=TRUE)
  cpst=cpstr[length(cpstr)]
  cpsp=strsplit(cpst,"!")[[1]]
  cp=cpsp[1:(length(cpsp)-1)]
  scalaInterpreter(cp,use.jvmr.class.path=FALSE)
}

With this function at our disposal, it becomes trivial to call our Scala code direct from the R interpreter, as the following code illustrates.

sc=sbtInit()
sc['import gibbs.Gibbs._']
out=sc['genIters(State(0.0,0.0),50000,1000).toArray.map{s=>Array(s.x,s.y)}']
library(smfsb)
mcmcSummary(out,rows=2)

Here we call the getIters function directly, rather than via the main method. This function returns an immutable List of States. Since R doesn’t understand this, we map it to an Array of Arrays, which R then unpacks into an R matrix for us to store in the matrix out.

Summary

The CRAN package jvmr makes it very easy to embed a Scala interpreter within an R session. However, for most non-trivial statistical computing problems, the Scala code will have dependence on external scientific libraries such as Breeze. The standard way to easily manage external dependencies in the Scala ecosystem is sbt. Given an sbt-based Scala project, it is easy to add a task to the sbt build file and a function to R in order to initialise the jvmr Scala interpreter with the full classpath needed to call arbitrary Scala functions. This provides very convenient inter-operability between R and Scala for many statistical computing applications.

Brief introduction to Scala and Breeze for statistical computing

Introduction

In the previous post I outlined why I think Scala is a good language for statistical computing and data science. In this post I want to give a quick taste of Scala and the Breeze numerical library to whet the appetite of the uninitiated. This post certainly won’t provide enough material to get started using Scala in anger – but I’ll try and provide a few pointers along the way. It also won’t be very interesting to anyone who knows Scala – I’m not introducing any of the very cool Scala stuff here – I think that some of the most powerful and interesting Scala language features can be a bit frightening for new users.

To reproduce the examples, you need to install Scala and Breeze. This isn’t very tricky, but I don’t want to get bogged down with a detailed walk-through here – I want to concentrate on the Scala language and Breeze library. You just need to install a recent version of Java, then Scala, and then Breeze. You might also want SBT and/or the ScalaIDE, though neither of these are necessary. Then you need to run the Scala REPL with the Breeze library in the classpath. There are several ways one can do this. The most obvious is to just run scala with the path to Breeze manually specified (or specified in an environment variable). Alternatively, you could run a console from an sbt session with a Breeze dependency (which is what I actually did for this post), or you could use a Scala Worksheet from inside a ScalaIDE project with a Breeze dependency.

A Scala REPL session

A first glimpse of Scala

We’ll start with a few simple Scala concepts that are not dependent on Breeze. For further information, see the Scala documentation.

Welcome to Scala version 2.10.3 (OpenJDK 64-Bit Server VM, Java 1.7.0_25).
Type in expressions to have them evaluated.
Type :help for more information.

scala> val a = 5
a: Int = 5

scala> a
res0: Int = 5

So far, so good. Using the Scala REPL is much like using the Python or R command line, so will be very familiar to anyone used to these or similar languages. The first thing to note is that labels need to be declared on first use. We have declared a to be a val. These are immutable values, which can not be just re-assigned, as the following code illustrates.

scala> a = 6
<console>:8: error: reassignment to val
       a = 6
         ^
scala> a
res1: Int = 5

Immutability seems to baffle people unfamiliar with functional programming. But fear not, as Scala allows declaration of mutable variables as well:

scala> var b = 7
b: Int = 7

scala> b
res2: Int = 7

scala> b = 8
b: Int = 8

scala> b
res3: Int = 8

The Zen of functional programming is to realise that immutability is generally a good thing, but that really isn’t the point of this post. Scala has excellent support for both mutable and immutable collections as part of the standard library. See the API docs for more details. For example, it has immutable lists.

scala> val c = List(3,4,5,6)
c: List[Int] = List(3, 4, 5, 6)

scala> c(1)
res4: Int = 4

scala> c.sum
res5: Int = 18

scala> c.length
res6: Int = 4

scala> c.product
res7: Int = 360

Again, this should be pretty familiar stuff for anyone familiar with Python. Note that the sum and product methods are special cases of reduce operations, which are well supported in Scala. For example, we could compute the sum reduction using

scala> c.foldLeft(0)((x,y) => x+y)
res8: Int = 18

or the slightly more condensed form given below, and similarly for the product reduction.

scala> c.foldLeft(0)(_+_)
res9: Int = 18

scala> c.foldLeft(1)(_*_)
res10: Int = 360

Scala also has a nice immutable Vector class, which offers a range of constant time operations (but note that this has nothing to do with the mutable Vector class that is part of the Breeze library).

scala> val d = Vector(2,3,4,5,6,7,8,9)
d: scala.collection.immutable.Vector[Int] = Vector(2, 3, 4, 5, 6, 7, 8, 9)

scala> d
res11: scala.collection.immutable.Vector[Int] = Vector(2, 3, 4, 5, 6, 7, 8, 9)

scala> d.slice(3,6)
res12: scala.collection.immutable.Vector[Int] = Vector(5, 6, 7)

scala> val e = d.updated(3,0)
e: scala.collection.immutable.Vector[Int] = Vector(2, 3, 4, 0, 6, 7, 8, 9)

scala> d
res13: scala.collection.immutable.Vector[Int] = Vector(2, 3, 4, 5, 6, 7, 8, 9)

scala> e
res14: scala.collection.immutable.Vector[Int] = Vector(2, 3, 4, 0, 6, 7, 8, 9)

Note that when e is created as an updated version of d the whole of d is not copied – only the parts that have been updated. And we don’t have to worry that aspects of d and e point to the same information in memory, as they are both immutable… As should be clear by now, Scala has excellent support for functional programming techniques. In addition to the reduce operations mentioned already, maps and filters are also well covered.

scala> val f=(1 to 10).toList
f: List[Int] = List(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)

scala> f
res15: List[Int] = List(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)

scala> f.map(x => x*x)
res16: List[Int] = List(1, 4, 9, 16, 25, 36, 49, 64, 81, 100)

scala> f map {x => x*x}
res17: List[Int] = List(1, 4, 9, 16, 25, 36, 49, 64, 81, 100)

scala> f filter {_ > 4}
res18: List[Int] = List(5, 6, 7, 8, 9, 10)

Note how Scala allows methods with a single argument to be written as an infix operator, making for more readable code.

A first look at Breeze

The next part of the session requires the Breeze library – see the Breeze quickstart guide for further details. We begin by taking a quick look at everyone’s favourite topic of non-uniform random number generation. Let’s start by generating a couple of draws from a Poisson distribution with mean 3.

scala> import breeze.stats.distributions._
import breeze.stats.distributions._

scala> val poi = Poisson(3.0)
poi: breeze.stats.distributions.Poisson = Poisson(3.0)

scala> poi.draw
res19: Int = 2

scala> poi.draw
res20: Int = 3

If more than a single draw is required, an iid sample can be obtained.

scala> val x = poi.sample(10)
x: IndexedSeq[Int] = Vector(2, 3, 3, 4, 2, 2, 1, 2, 4, 2)

scala> x
res21: IndexedSeq[Int] = Vector(2, 3, 3, 4, 2, 2, 1, 2, 4, 2)

scala> x.sum
res22: Int = 25

scala> x.length
res23: Int = 10

scala> x.sum.toDouble/x.length
res24: Double = 2.5

Note that this Vector is mutable. The probability mass function (PMF) of the Poisson distribution is also available.

scala> poi.probabilityOf(2)
res25: Double = 0.22404180765538775

scala> x map {x => poi.probabilityOf(x)}
res26: IndexedSeq[Double] = Vector(0.22404180765538775, 0.22404180765538775, 0.22404180765538775, 0.16803135574154085, 0.22404180765538775, 0.22404180765538775, 0.14936120510359185, 0.22404180765538775, 0.16803135574154085, 0.22404180765538775)

scala> x map {poi.probabilityOf(_)}
res27: IndexedSeq[Double] = Vector(0.22404180765538775, 0.22404180765538775, 0.22404180765538775, 0.16803135574154085, 0.22404180765538775, 0.22404180765538775, 0.14936120510359185, 0.22404180765538775, 0.16803135574154085, 0.22404180765538775)

Obviously, Gaussian variables (and Gamma, and several others) are supported in a similar way.

scala> val gau=Gaussian(0.0,1.0)
gau: breeze.stats.distributions.Gaussian = Gaussian(0.0, 1.0)

scala> gau.draw
res28: Double = 1.606121255846881

scala> gau.draw
res29: Double = -0.1747896055492152

scala> val y=gau.sample(20)
y: IndexedSeq[Double] = Vector(-1.3758577012869702, -1.2148314970824652, -0.022501190144116855, 0.3244006323566883, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> y
res30: IndexedSeq[Double] = Vector(-1.3758577012869702, -1.2148314970824652, -0.022501190144116855, 0.3244006323566883, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> y.sum/y.length
res31: Double = -0.34064156102380994

scala> y map {gau.logPdf(_)}
res32: IndexedSeq[Double] = Vector(-1.8654307403000054, -1.6568463163564844, -0.9191916849836235, -0.9715564183413823, -0.9836614354155007, -1.3847302992371653, -1.0023094506890617, -0.9256472309869705, -1.3059361584943119, -0.975419259871957, -1.1669755840586733, -1.6444202843394145, -0.93783943912556, -0.9683690047171869, -0.9209315167224245, -2.090114759123421, -1.6843650876361744, -1.0915455053203147, -1.359378517654625, -1.1399116208702693)

scala> Gamma(2.0,3.0).sample(5)
res33: IndexedSeq[Double] = Vector(2.38436441278546, 2.125017198373521, 2.333118708811143, 5.880076392566909, 2.0901427084667503)

This is all good stuff for those of us who like to do Markov chain Monte Carlo. There are not masses of statistical data analysis routines built into Breeze, but a few basic tools are provided, including some basic summary statistics.

scala> import breeze.stats.DescriptiveStats._
import breeze.stats.DescriptiveStats._

scala> mean(y)
res34: Double = -0.34064156102380994

scala> variance(y)
res35: Double = 0.574257149387757

scala> meanAndVariance(y)
res36: (Double, Double) = (-0.34064156102380994,0.574257149387757)

Support for linear algebra is an important part of any scientific library. Here the Breeze developers have made the wise decision to provide a nice Scala interface to netlib-java. This in turn calls out to any native optimised BLAS or LAPACK libraries installed on the system, but will fall back to Java code if no optimised libraries are available. This means that linear algebra code using Scala and Breeze should run as fast as code written in any other language, including C, C++ and Fortran, provided that optimised libraries are installed on the system. For further details see the Breeze linear algebra guide. Let’s start by creating and messing with a dense vector.

scala> import breeze.linalg._
import breeze.linalg._

scala> val v=DenseVector(y.toArray)
v: breeze.linalg.DenseVector[Double] = DenseVector(-1.3758577012869702, -1.2148314970824652, -0.022501190144116855, 0.3244006323566883, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> v(1) = 0

scala> v
res38: breeze.linalg.DenseVector[Double] = DenseVector(-1.3758577012869702, 0.0, -0.022501190144116855, 0.3244006323566883, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> v(1 to 3) := 1.0
res39: breeze.linalg.DenseVector[Double] = DenseVector(1.0, 1.0, 1.0)

scala> v
res40: breeze.linalg.DenseVector[Double] = DenseVector(-1.3758577012869702, 1.0, 1.0, 1.0, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> v(1 to 3) := DenseVector(1.0,1.5,2.0)
res41: breeze.linalg.DenseVector[Double] = DenseVector(1.0, 1.5, 2.0)

scala> v
res42: breeze.linalg.DenseVector[Double] = DenseVector(-1.3758577012869702, 1.0, 1.5, 2.0, 0.35978577573558407, 0.9651857500320781, -0.40834034207848985, 0.11583348205331555, -0.8797699986810634, -0.33609738668214695, 0.7043252811790879, -1.2045594639823656, 0.19442688045065826, -0.31442160076087067, 0.06313451540562891, -1.5304745838587115, -1.2372764884467027, 0.5875490994217284, -0.9385520597707431, -0.6647903243363228)

scala> v :> 0.0
res43: breeze.linalg.BitVector = BitVector(1, 2, 3, 4, 5, 7, 10, 12, 14, 17)

scala> (v :> 0.0).toArray
res44: Array[Boolean] = Array(false, true, true, true, true, true, false, true, false, false, true, false, true, false, true, false, false, true, false, false)

Next let’s create and mess around with some dense matrices.

scala> val m = new DenseMatrix(5,4,linspace(1.0,20.0,20).toArray)
m: breeze.linalg.DenseMatrix[Double] = 
1.0  6.0   11.0  16.0  
2.0  7.0   12.0  17.0  
3.0  8.0   13.0  18.0  
4.0  9.0   14.0  19.0  
5.0  10.0  15.0  20.0  

scala> m
res45: breeze.linalg.DenseMatrix[Double] = 
1.0  6.0   11.0  16.0  
2.0  7.0   12.0  17.0  
3.0  8.0   13.0  18.0  
4.0  9.0   14.0  19.0  
5.0  10.0  15.0  20.0  

scala> m.rows
res46: Int = 5

scala> m.cols
res47: Int = 4

scala> m(::,1)
res48: breeze.linalg.DenseVector[Double] = DenseVector(6.0, 7.0, 8.0, 9.0, 10.0)

scala> m(1,::)
res49: breeze.linalg.DenseMatrix[Double] = 2.0  7.0  12.0  17.0  

scala> m(1,::) := linspace(1.0,2.0,4)
res50: breeze.linalg.DenseMatrix[Double] = 1.0  1.3333333333333333  1.6666666666666665  2.0  

scala> m
res51: breeze.linalg.DenseMatrix[Double] = 
1.0  6.0                 11.0                16.0  
1.0  1.3333333333333333  1.6666666666666665  2.0   
3.0  8.0                 13.0                18.0  
4.0  9.0                 14.0                19.0  
5.0  10.0                15.0                20.0  

scala> 

scala> val n = m.t
n: breeze.linalg.DenseMatrix[Double] = 
1.0   1.0                 3.0   4.0   5.0   
6.0   1.3333333333333333  8.0   9.0   10.0  
11.0  1.6666666666666665  13.0  14.0  15.0  
16.0  2.0                 18.0  19.0  20.0  

scala> n
res52: breeze.linalg.DenseMatrix[Double] = 
1.0   1.0                 3.0   4.0   5.0   
6.0   1.3333333333333333  8.0   9.0   10.0  
11.0  1.6666666666666665  13.0  14.0  15.0  
16.0  2.0                 18.0  19.0  20.0  

scala> val o = m*n
o: breeze.linalg.DenseMatrix[Double] = 
414.0              59.33333333333333  482.0              516.0              550.0              
59.33333333333333  9.555555555555555  71.33333333333333  77.33333333333333  83.33333333333333  
482.0              71.33333333333333  566.0              608.0              650.0              
516.0              77.33333333333333  608.0              654.0              700.0              
550.0              83.33333333333333  650.0              700.0              750.0              

scala> o
res53: breeze.linalg.DenseMatrix[Double] = 
414.0              59.33333333333333  482.0              516.0              550.0              
59.33333333333333  9.555555555555555  71.33333333333333  77.33333333333333  83.33333333333333  
482.0              71.33333333333333  566.0              608.0              650.0              
516.0              77.33333333333333  608.0              654.0              700.0              
550.0              83.33333333333333  650.0              700.0              750.0              

scala> val p = n*m
p: breeze.linalg.DenseMatrix[Double] = 
52.0                117.33333333333333  182.66666666666666  248.0              
117.33333333333333  282.77777777777777  448.22222222222223  613.6666666666667  
182.66666666666666  448.22222222222223  713.7777777777778   979.3333333333334  
248.0               613.6666666666667   979.3333333333334   1345.0             

scala> p
res54: breeze.linalg.DenseMatrix[Double] = 
52.0                117.33333333333333  182.66666666666666  248.0              
117.33333333333333  282.77777777777777  448.22222222222223  613.6666666666667  
182.66666666666666  448.22222222222223  713.7777777777778   979.3333333333334  
248.0               613.6666666666667   979.3333333333334   1345.0             

So, messing around with vectors and matrices is more-or-less as convenient as in well-known dynamic and math languages. To conclude this section, let us see how to simulate some data from a regression model and then solve the least squares problem to obtain the estimated regression coefficients. We will simulate 1,000 observations from a model with 5 covariates.

scala> val X = new DenseMatrix(1000,5,gau.sample(5000).toArray)
X: breeze.linalg.DenseMatrix[Double] = 
-0.40186606934180685  0.9847148198711287    ... (5 total)
-0.4760404521336951   -0.833737041320742    ...
-0.3315199616926892   -0.19460446824586297  ...
-0.14764615494496836  -0.17947658245206904  ...
-0.8357372755800905   -2.456222113596015    ...
-0.44458309216683184  1.848007773944826     ...
0.060314034896221065  0.5254462055311016    ...
0.8637867740789016    -0.9712570453363925   ...
0.11620167261655819   -1.2231380938032232   ...
-0.3335514290842617   -0.7487303696662753   ...
-0.5598937433421866   0.11083382409013512   ...
-1.7213395389510568   1.1717491221846357    ...
-1.078873342208984    0.9386859686451607    ...
-0.7793854546738327   -0.9829373863442161   ...
-1.054275201631216    0.10100826507456745   ...
-0.6947188686537832   1.215...
scala> val b0 = linspace(1.0,2.0,5)
b0: breeze.linalg.DenseVector[Double] = DenseVector(1.0, 1.25, 1.5, 1.75, 2.0)

scala> val y0 = X * b0
y0: breeze.linalg.DenseVector[Double] = DenseVector(0.08200546839589107, -0.5992571365601228, -5.646398002309553, -7.346136663325798, -8.486423788193362, 1.451119214541837, -0.25792385841948406, 2.324936340609002, -1.2285599639827862, -4.030261316643863, -4.1732627416377674, -0.5077151099958077, -0.2087263741903591, 0.46678616461409383, 2.0244342278575975, 1.775756468177401, -4.799821190728213, -1.8518388060564481, 1.5892306875621767, -1.6528539564387008, 1.4064864330994125, -0.8734630221484178, -7.75470002781836, -0.2893619536998493, -5.972958583649336, -4.952666733286302, 0.5431255990489059, -2.477076684976403, -0.6473617571867107, -0.509338416957489, -1.5415350935719594, -0.47068802465681125, 2.546118380362026, -7.940401988804477, -1.037049442788122, -1.564016663370888, -3.3147087994...
scala> val y = y0 + DenseVector(gau.sample(1000).toArray)
y: breeze.linalg.DenseVector[Double] = DenseVector(-0.572127338358624, -0.16481167194161406, -4.213873268823003, -10.142015065601388, -7.893898543052863, 1.7881055848475076, -0.26987820512025357, 3.3289433195054148, -2.514141419925489, -4.643625974157769, -3.8061000214061886, 0.6462624993109218, 0.23603338389134149, 1.0211137806779267, 2.0061727641393317, 0.022624943149799348, -5.429601401989341, -1.836181225242386, 1.0265599173053048, -0.1673732536615371, 0.8418249443853956, -1.1547110533101967, -8.392100167478764, -1.1586377992526877, -6.400362975646245, -5.487018086963841, 0.3038055584347069, -1.2247410435868684, -0.06476921390724344, -1.5039074374120407, -1.0189111630970076, 1.307339668865724, 2.048320821568789, -8.769328824477714, -0.9104251029228555, -1.3533910178496698, -2.178788...
scala> val b = X \ y  // defaults to a QR-solve of the least squares problem
b: breeze.linalg.DenseVector[Double] = DenseVector(0.9952708232116663, 1.2344546192238952, 1.5543512339052412, 1.744091673457169, 1.9874158953720507)

So all of the most important building blocks for statistical computing are included in the Breeze library.

At this point it is really worth reminding yourself that Scala is actually a statically typed language, despite the fact that in this session we have not explicitly declared the type of anything at all! This is because Scala has type inference, which makes type declarations optional when it is straightforward for the compiler to figure out what the types must be. For example, for our very first expression, val a = 5, because the RHS is an Int, it is clear that the LHS must also be an Int, and so the compiler infers that the type of a must be an Int, and treats the code as if the type had been declared as val a: Int = 5. This type inference makes Scala feel very much like a dynamic language in general use. Typically, we carefully specify the types of function arguments (and often the return type of the function, too), but then for the main body of each function, just let the compiler figure out all of the types and write code as if the language were dynamic. To me, this seems like the best of all worlds. The convenience of dynamic languages with the safety of static typing.

Declaring the types of function arguments is not usually a big deal, as the following simple example demonstrates.

scala> def mean(arr: Array[Int]): Double = {
     |   arr.sum.toDouble/arr.length
     | }
mean: (arr: Array[Int])Double

scala> mean(Array(3,1,4,5))
res55: Double = 3.25

A complete Scala program

For completeness, I will finish this post with a very simple but complete Scala/Breeze program. In a previous post I discussed a simple Gibbs sampler in Scala, but in that post I used the Java COLT library for random number generation. Below is a version using Breeze instead.

object BreezeGibbs {

  import breeze.stats.distributions._
  import scala.math.sqrt

  class State(val x: Double, val y: Double)

  def nextIter(s: State): State = {
    val newX = Gamma(3.0, 1.0 / ((s.y) * (s.y) + 4.0)).draw()
    new State(newX, Gaussian(1.0 / (newX + 1), 1.0 / sqrt(2 * newX + 2)).draw())
  }

  def nextThinnedIter(s: State, left: Int): State = {
    if (left == 0) s
    else nextThinnedIter(nextIter(s), left - 1)
  }

  def genIters(s: State, current: Int, stop: Int, thin: Int): State = {
    if (!(current > stop)) {
      println(current + " " + s.x + " " + s.y)
      genIters(nextThinnedIter(s, thin), current + 1, stop, thin)
    } else s
  }

  def main(args: Array[String]) {
    println("Iter x y")
    genIters(new State(0.0, 0.0), 1, 50000, 1000)
  }

}

Summary

In this post I’ve tried to give a quick taste of the Scala language and the Breeze library for those used to dynamic languages for statistical computing. Hopefully I’ve illustrated that the basics don’t look too different, so there is no reason to fear Scala. It is perfectly possible to start using Scala as a better and faster Python or R. Once you’ve mastered the basics, you can then start exploring the full power of the language. There’s loads of introductory Scala material to be found on-line. It probably makes sense to start with the links I’ve highlighted above. After that, just start searching – there’s an interesting set of tutorials I noticed just the other day. A very time-efficient way to learn Scala quickly is to do the FP with Scala course on Coursera, but whether this makes sense will depend on when it is next running. For those who prefer real books, the book Programming in Scala is the standard reference, and I’ve also found Functional programming in Scala to be useful (free text of the first edition of the former and a draft of the latter can be found on-line).

REPL Script

Below is a copy of the complete REPL script, for reference.

// start with non-Breeze stuff

val a = 5
a
a = 6
a

var b = 7
b
b = 8
b

val c = List(3,4,5,6)
c(1)
c.sum
c.length
c.product
c.foldLeft(0)((x,y) => x+y)
c.foldLeft(0)(_+_)
c.foldLeft(1)(_*_)

val d = Vector(2,3,4,5,6,7,8,9)
d
d.slice(3,6)
val e = d.updated(3,0)
d
e

val f=(1 to 10).toList
f
f.map(x => x*x)
f map {x => x*x}
f filter {_ > 4}

// introduce breeze through random distributions
// https://github.com/scalanlp/breeze/wiki/Quickstart

import breeze.stats.distributions._
val poi = Poisson(3.0)
poi.draw
poi.draw
val x = poi.sample(10)
x
x.sum
x.length
x.sum.toDouble/x.length
poi.probabilityOf(2)
x map {x => poi.probabilityOf(x)}
x map {poi.probabilityOf(_)}

val gau=Gaussian(0.0,1.0)
gau.draw
gau.draw
val y=gau.sample(20)
y
y.sum/y.length
y map {gau.logPdf(_)}

Gamma(2.0,3.0).sample(5)

import breeze.stats.DescriptiveStats._
mean(y)
variance(y)
meanAndVariance(y)


// move on to linear algebra
// https://github.com/scalanlp/breeze/wiki/Breeze-Linear-Algebra

import breeze.linalg._
val v=DenseVector(y.toArray)
v(1) = 0
v
v(1 to 3) := 1.0
v
v(1 to 3) := DenseVector(1.0,1.5,2.0)
v
v :> 0.0
(v :> 0.0).toArray

val m = new DenseMatrix(5,4,linspace(1.0,20.0,20).toArray)
m
m.rows
m.cols
m(::,1)
m(1,::)
m(1,::) := linspace(1.0,2.0,4)
m

val n = m.t
n
val o = m*n
o
val p = n*m
p

// regression and QR solution

val X = new DenseMatrix(1000,5,gau.sample(5000).toArray)
val b0 = linspace(1.0,2.0,5)
val y0 = X * b0
val y = y0 + DenseVector(gau.sample(1000).toArray)
val b = X \ y  // defaults to a QR-solve of the least squares problem

// a simple function example

def mean(arr: Array[Int]): Double = {
  arr.sum.toDouble/arr.length
}

mean(Array(3,1,4,5))