Mathias Brandewinder on .NET, F#, VSTO and Excel development, and quantitative analysis / machine learning.
8. August 2015 12:42

A couple of weeks ago, I came across this blog post by Steve Shogren, which looks at various programming languages, and attempts to define a “language safety score”, by taking into account a list of language criteria (Are nulls allowed? Can variables be mutated? And so on), aggregating them into an overall safety score – and finally looking for whether the resulting score was a reasonable predictor for the observed bug rate across various projects.

I thought this was an interesting idea. However, I also had reservations on the methodology. Picking a somewhat arbitrary list of criteria, giving them indiscriminately the same weight, and summing them up, didn’t seem to me like the most effective approach – especially given that Steve had already collected a nice dataset. If the goal is to identify which language features best predict how buggy the code will be, why not start from there, and build a model which attempts to predict the bug rate based on language features?

So I decided to give it a shot, and build a quick-and-dirty logistic regression model. In a nutshell, logistic regression attempts to model the probability of observing an event, based on a set of criteria / features. A prototypical application would be in medicine, trying to predict, for instance, the chances of developing a disease, given patient characteristics. In our case, the disease is a bug, and the patient a code base. We’ll use the criteria listed by Steve as potential predictors, and, as a nice side-product of logistic regression, we will get a quantification of how important each of the criteria is in predicting the bug rate.

I’ll discuss later some potential issues with the approach; for now, let’s build a model, and see where that leads us. I lifted the data from Steve’s post (hopefully without typos), with one minor modification: instead of scoring criteria as 1, 0 or –1, I just retained 1 or 0 (it’s there or it’s not there), and prepared an F# script, using the Accord framework to run my logistic regression.

Note: the entire script is here as a Gist.

#I @"../packages"
#r @"Accord.3.0.1-alpha\lib\net45\Accord.dll"
#r @"Accord.MachineLearning.3.0.1-alpha\lib\net45\Accord.MachineLearning.dll"
#r @"Accord.Math.3.0.1-alpha\lib\net45\Accord.Math.dll"
#r @"Accord.Statistics.3.0.1-alpha\lib\net45\Accord.Statistics.dll"

let language, bugrate, criteria =
[|  "F#",           0.023486288,    [|1.;1.;1.;0.;1.;1.;1.;0.;0.;0.;1.;1.;1.;0.|]
"Javascript",   0.039445132,    [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|]
"CoffeeScript", 0.047242288,    [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|]
"Clojure",      0.011503478,    [|0.;1.;0.;0.;0.;0.;1.;0.;1.;1.;1.;0.;0.;0.|]
"C#",           0.03261284,     [|0.;0.;1.;0.;0.;1.;1.;0.;0.;0.;1.;0.;1.;0.|]
"Python",       0.02531419,     [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|]
"Java",         0.032567736,    [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|]
"Ruby",         0.020303702,    [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|]
"Scala",        0.01904762,     [|1.;1.;1.;0.;1.;1.;1.;0.;0.;0.;1.;0.;0.;0.|]
"Go",           0.024698375,    [|0.;0.;1.;0.;0.;1.;1.;0.;0.;0.;1.;0.;1.;0.|]
"PHP",          0.031669293,    [|0.;0.;0.;0.;0.;0.;0.;0.;0.;0.;1.;0.;1.;0.|] |]
|> Array.unzip3

open Accord.Statistics.Models.Regression
open Accord.Statistics.Models.Regression.Fitting

let features = 14
let model = LogisticRegression(features)

let rec learn () =
let delta = learner.Run(criteria, bugrate)
if delta > 0.0001
then learn ()
else ignore ()

learn () |> ignore

And we are done – we have trained a model to predict the bug rate, based on our 14 criteria. How is this working? Let’s find out:

for i in 0 .. (language.Length - 1) do
let lang = language.[i]
let predicted = model.Compute(criteria.[i])
let real = bugrate.[i]
printfn "%16s Real: %.3f Pred: %.3f" lang real predicted

>
F# Real: 0.023 Pred: 0.023
Javascript Real: 0.039 Pred: 0.033
CoffeeScript Real: 0.047 Pred: 0.033
Clojure Real: 0.012 Pred: 0.011
C# Real: 0.033 Pred: 0.029
Python Real: 0.025 Pred: 0.033
Java Real: 0.033 Pred: 0.033
Ruby Real: 0.020 Pred: 0.033
Scala Real: 0.019 Pred: 0.020
Go Real: 0.025 Pred: 0.029
PHP Real: 0.032 Pred: 0.033

Looks pretty good. Let’s confirm that with a chart, using FSharp.Charting:

#load "FSharp.Charting.0.90.12\FSharp.Charting.fsx"
open FSharp.Charting

let last = language.Length - 1

Chart.Combine [
Chart.Line ([ for i in 0 .. last -> bugrate.[i]], "Real", Labels=language)
Chart.Line ([ for i in 0 .. last -> model.Compute(criteria.[i])], "Pred") ]
|> Chart.WithLegend()

What criteria did our model identify as predictors for bugs? Let’s find out.

let criteriaNames = [|
"Null Variable Usage"
"Null List Iteration"
"Prevent Variable Reuse"
"Ensure List Element Exists"
"Safe Type Casting"
"Passing Wrong Type"
"Misspelled Method"
"Missing Enum Value"
"Variable Mutation"
"Memory Deallocation"
"Tail Call Optimization"
"Guaranteed Code Evaluation"
"Functional Purity" |]

for i in 0 .. (features - 1) do
let name = criteriaNames.[i]
let wald = model.GetWaldTest(i)
let odds = model.GetOddsRatio(i)
(printfn "%28s odds: %4.2f significant: %b" name odds wald.Significant)

>
Null Variable Usage odds:  0.22 significant: true
Null List Iteration odds:  0.86 significant: true
Prevent Variable Reuse odds:  0.64 significant: true
Ensure List Element Exists odds:  1.05 significant: true
Safe Type Casting odds:  1.00 significant: false
Passing Wrong Type odds:  0.86 significant: true
Misspelled Method odds:  1.05 significant: true
Missing Enum Value odds:  0.78 significant: true
Variable Mutation odds:  0.86 significant: true
Prevent Deadlocks odds:  0.64 significant: true
Memory Deallocation odds:  0.74 significant: true
Tail Call Optimization odds:  0.22 significant: true
Guaranteed Code Evaluation odds:  1.71 significant: true
Functional Purity odds:  0.69 significant: true

How should you read this? The first output, the odds ratio, describes how much more likely it is to observe success than failure when that criterion is active. In our case, success means “having a bug”, so for instance, if your language prevents using nulls, you’d expect 1.0 / 0.22 = 4.5 times less chances to write bugs. In other words, if the odds are close to 1.0, the criterion doesn’t make much of a difference. The closer to zero it is, the lower the predicted bug count, and vice-versa.

## Conclusions and caveats

The 3 most significant predictors of a low bug rate are, in order, no nulls, tail calls optimization, and (to a much lesser degree) lazy evaluation. After that, we have honorable scores for avoiding variable reuse, preventing deadlocks, and functional purity.

So… what’s the bottom line? First off, just based on the bug rates alone, it seems that using functional languages would be a safer bet than Javascript (and CoffeeScript) to avoid bugs.

Then, now would be a good time to reiterate that this is a quick-and-dirty analysis. Specifically, there are some clear issues with the dataset. First, we are fitting 12 languages on 14 criteria – that’s not much to go on. On top of that, there is some data redundancy. None of the languages in our sample has “ensure list element exists” (4th column is filled with zeroes), and all of them guarantee memory de-allocation (11th column filled with ones). I suspect there is some additional redundancy, because of the similarity between the columns.

Note: another interesting discussion would be whether the selected criteria properly cover the differences between languages. I chose to not go into that, and focus strictly on using the data as-is.

I ran the model again, dropping the 2 columns that contain no information; while this doesn’t change the predictions of the model, it does impact a bit the weight of each criterion. The results, while similar, do show some differences:

("Null Variable Usage", 0.0743885639)
("Functional Purity", 0.4565632287)
("Prevent Variable Reuse", 0.5367456237)
("Tail Call Optimization", 0.7028982809)
("Missing Enum Value", 0.7539575884)
("Null List Iteration", 0.7636177784)
("Passing Wrong Type", 0.7636177784)
("Variable Mutation", 0.7646027916)
("Safe Type Casting", 1.072641105)
("Misspelled Method", 1.072641105)
("Guaranteed Code Evaluation", 2.518831684)

Another piece of information I didn’t use is how many commits were taken into consideration. This matters, because the information gathered for PHP is across 10 times more commits than F#, for instance. It wouldn’t be very hard to do – instead of regressing against the bug rate, we could count the clean and buggy commits per language, and proceed along the lines of the last example described here.

In spite of these issues, I think this constitutes a better base to construct a language score index. Rather than picking criteria by hand and giving them arbitrary weights, let the data speak. Measure how well each of them explains defects, and use that as a basis to determine their relative importance.

That’s it for today! Big thanks to Steve Shogren for a stimulating post, and for making the data available. And again, you can find the script here as a Gist. If you have comments or questions, ping me on Twitter!

1. March 2014 14:32

During some recent meanderings through the confines of the internet, I ended up discovering the Winnow Algorithm. The simplicity of the approach intrigued me, so I thought it would be interesting to try and implement it in F# and see how well it worked.

The purpose of the algorithm is to train a binary classifier, based on binary features. In other words, the goal is to predict one of two states, using a collection of features which are all binary. The prediction model assigns weights to each feature; to predict the state of an observation, it checks all the features that are “active” (true), and sums up the weights assigned to these features. If the total is above a certain threshold, the result is true, otherwise it’s false. Dead simple – and so is the corresponding F# code:

type Observation = bool []
type Label = bool
type Example = Label * Observation
type Weights = float []

let predict (theta:float) (w:Weights) (obs:Observation) =
(obs,w) ||> Seq.zip
|> Seq.filter fst
|> Seq.sumBy snd
|> ((<) theta)

We create some type aliases for convenience, and write a predict function which takes in theta (the threshold), weights and and observation; we zip together the features and the weights, exclude the pairs where the feature is not active, sum the weights, check whether the threshold is lower that the total, and we are done.

In a nutshell, the learning process feeds examples (observations with known label), and progressively updates the weights when the model makes mistakes. If the current model predicts the output correctly, don’t change anything. If it predicts true but should predict false, it is over-shooting, so weights that were used in the prediction (i.e. the weights attached to active features) are reduced. Conversely, if the prediction is false but the correct result should be true, the active features are not used enough to reach the threshold, so they should be bumped up.

And that’s pretty much it – the algorithm starts with arbitrary initial weights of 1 for every feature, and either doubles or halves them based on the mistakes. Again, the F# implementation is completely straightforward. The weights update can be written as follows:

let update (theta:float) (alpha:float) (w:Weights) (ex:Example) =
let real,obs = ex
match (real,predict theta w obs) with
| (true,false) -> w |> Array.mapi (fun i x -> if obs.[i] then alpha * x else x)
| (false,true) -> w |> Array.mapi (fun i x -> if obs.[i] then x / alpha else x)
| _ -> w

Let’s check that the update mechanism works:

> update 0.5 2. [|1.;1.;|] (false,[|false;true;|]);;
val it : float [] = [|1.0; 0.5|]

The threshold is 0.5, the adjustment multiplier is 2, and each feature is currently weighted at 1. The state of our example is [| false; true; |], so only the second feature is active, which means that the predicted value will be 1. (the weight of that feature). This is above the threshold 0.5, so the predicted value is true. However, because the correct value attached to that example is false, our prediction is incorrect, and the weight of the second feature is reduced, while the first one, which was not active, remains unchanged.

Let’s wrap this up in a convenience function which will learn from a sequence of examples, and give us directly a function that will classify observations:

let learn (theta:float) (alpha:float) (fs:int) (xs:Example seq) =
let updater = update theta alpha
let w0 = [| for f in 1 .. fs -> 1. |]
let w = Seq.fold (fun w x -> updater w x) w0 xs
fun (obs:Observation) -> predict theta w obs

We pass in the number of features, fs, to initialize the weights at the correct size, and use a fold to update the weights for each example in the sequence. Finally, we create and return a function that, given an observation, will predict the label, based on the weights we just learnt.

And that’s it – in 20 lines of code, we are done, the Winnow is implemented.

More...

15. February 2014 12:51

My favorite column in MSDN Magazine is Test Run; it was originally focused on testing, but the author, James McCaffrey, has been focusing lately on topics revolving around numeric optimization and machine learning, presenting a variety of methods and approaches. I quite enjoy his work, with one minor gripe –his examples are all coded in C#, which in my opinion is really too bad, because the algorithms would gain much clarity if written in F# instead.

Back in June 2013, he published a piece on Amoeba Method Optimization using C#. I hadn’t seen that approach before, and found it intriguing. I also found the C# code a bit too hairy for my feeble brain to follow, so I decided to rewrite it in F#.

In a nutshell, the Amoeba approach is a heuristic to find the minimum of a function. Its proper respectable name is the Nelder-Nead method. The reason it is also called the Amoeba method is because of the way the algorithm works: in its simple form, it starts from a triangle, the “Amoeba”; at each step, the Amoeba “probes” the value of 3 points in its neighborhood, and moves based on how much better the new points are. As a result, the triangle is iteratively updated, and behaves a bit like an Amoeba moving on a surface.

Before going into the actual details of the algorithm, here is how my final result looks like. You can find the entire code here on GitHub, with some usage examples in the Sample.fsx script file. Let’s demo the code in action: in a script file, we load the Amoeba code, and use the same function the article does, the Rosenbrock function. We transform the function a bit, so that it takes a Point (an alias for an Array of floats, essentially a vector) as an input, and pass it to the solve function, with the domain where we want to search, in that case, [ –10.0; 10.0 ] for both x and y:

#load "Amoeba.fs"

open Amoeba
open Amoeba.Solver

let g (x:float) y =
100. * pown (y - x * x) 2 + pown (1. - x) 2

let testFunction (x:Point) =
g x.[0] x.[1]

solve Default [| (-10.,10.); (-10.,10.) |] testFunction 1000

Running this in the F# interactive window should produce the following:

val it : Solution = (0.0, [|1.0; 1.0|])
>

The algorithm properly identified that the minimum is 0, for a value of x = 1.0 and y = 1.0. Note that results may vary: this is a heuristic, which starts with a random initial amoeba, so each run could produce slightly different results, and might at times epically fail.

More...

18. January 2014 14:49

A couple of months ago, I started working on an F# decision tree & random forest library, and pushed a first draft out in July 2013. It was a very minimal implementation, but it was a start, and my plan was to keep refining and add features. And then life happened: I got really busy, I began a very poorly disciplined refactoring effort on the code base, I second and third guessed my design - and got nothing to show for a while. Finally in December, I took some time off in Europe, disappeared in the French country side, a perfect setup to roll up my sleeves and finally get some serious coding done.

And here we go - drum roll please, version 0.1 of Charon is out. You can find it on GitHub, or install it as a NuGet package.

As you can guess from the version number, this is alpha-release grade code. There will be breaking changes, there are probably bugs and obvious things to improve, but I thought it was worth releasing, because it is in a shape good enough to illustrate the direction I am taking, and hopefully get some feedback from the community.

But first, what does Charon do? Charon is a decision tree and random forest machine learning classifier. An example will probably illustrate best what it does - let's work through the classic Titanic example. Using the Titanic passenger list, we want to create a model that predicts whether a passenger is likely to survive the disaster – or meet a terrible fate. Here is how you would do that with Charon, in a couple of lines of F#.

First, we use the CSV type provider to extract passenger information from our data file:

open Charon
open FSharp.Data

type DataSet = CsvProvider<"""C:\Users\Mathias\Documents\GitHub\Charon\Charon\Charon.Examples\titanic.csv""",
SafeMode=true, PreferOptionals=true>

type Passenger = DataSet.Row

In order to define a model, Charon needs two pieces of information: what is it you are trying to predict (the label, in that case, whether the passenger survives or not), and what information Charon is allowed to use to produce predictions (the features, in that case whatever passenger information we think is relevant):

let training =
use data = new DataSet()
[| for passenger in data.Data ->
passenger, // label source
passenger |] // features source

let labels = "Survived", (fun (obs:Passenger) -> obs.Survived) |> Categorical

let features =
[
"Sex", (fun (o:Passenger) -> o.Sex) |> Categorical;
"Class", (fun (o:Passenger) -> o.Pclass) |> Categorical;
"Age", (fun (o:Passenger) -> o.Age) |> Numerical;
]

For each feature, we specify whether the feature is Categorical (a finite number of "states" is expected, for instance Sex) or Numerical (the feature is to be interpreted as a numeric value, such as Age).

The Model is now fully specified, and we can train it on our dataset, and retrieve the results:

let results = basicTree training (labels,features) { DefaultSettings with Holdout = 0.1 }

printfn "Quality, training: %.3f" (results.TrainingQuality |> Option.get)
printfn "Quality, holdout: %.3f" (results.HoldoutQuality |> Option.get)

printfn "Tree:"
printfn "%s" (results.Pretty)

… which generates the following output:

Quality, training: 0.796
Quality, holdout: 0.747
Tree:
├ Sex = male
│   ├ Class = 3 → Survived False
│   ├ Class = 1 → Survived False
│   └ Class = 2
│      ├ Age = <= 16.000 → Survived True
│      └ Age = >  16.000 → Survived False
└ Sex = female
├ Class = 3 → Survived False
├ Class = 1 → Survived True
└ Class = 2 → Survived True

Charon automatically figures out what features are most informative, and organizes them into a tree; in our example, it appears that being a lady was a much better idea than being a guy – and being a rich lady traveling first or second class an even better idea. Charon also automatically breaks down continuous variables into bins. For instance, second-class male passengers under 16 had apparently much better odds of surviving than other male passengers. Charon splits the sample into training and validation; in this example, while our model appears quite good on the training set, with nearly 80% correct calls, the performance on the validation set is much weaker, with under 75% correctly predicted, suggesting an over-fitting issue.

I won’t demonstrate the Random Forest here; the API is basically the same, with better results but less human-friendly output. While formal documentation is lacking for the moment, you can find code samples in the Charon.Examples project that illustrate usage on the Titanic and the Nursery datasets.

What I hope I conveyed with this small example is the design priorities for Charon: a lightweight API that permits quick iterations to experiment with features and refine a model, using the F# Interactive capabilities.

I will likely discuss in later posts some of the challenges I ran into while implementing support for continuous variables – I learnt a lot in the process. I will leave it at that for today – in the meanwhile, I would love to get feedback on the current direction, and what you may like or hate about it. If you have comments, feel free to hit me up on Twitter, or to open an Issue on GitHub!

6. September 2013 08:15

Recently, Cesar De Souza began moving his .NET machine learning library, Accord.NET, from Google Code to GitHub. The move is still in progress, but that motivated me to take a closer look at the library; given that it is built in C#, with an intended C# usage in mind, I wanted to see how usable it is from F#.

There is a lot in the library; as a starting point, I decided I would try out its Support Vector Machine (SVM), a classic machine learning algorithm, and run it on a classic problem, automatically recognizing hand-written digits. The dataset I will be using here is a subset of the Kaggle Digit Recognizer contest; each example in the dataset is a 28x28 grayscale pixels image, the result of scanning a number written down by a human, and what the actual number is. From that original dataset, I sampled 5,000 examples, which will be used to train the algorithm, and another 500 in a validation set, which we’ll use to evaluate the performance of the model on data it hasn’t “seen before”.

The full example is available as a gist on GitHub.

I’ll be working in a script file within a Library project, as I typically do when exploring data. First, we need to add references to Accord.NET via NuGet:

#r @"..\packages\Accord.2.8.1.0\lib\Accord.dll"
#r @"..\packages\Accord.Math.2.8.1.0\lib\Accord.Math.dll"
#r @"..\packages\Accord.Statistics.2.8.1.0\lib\Accord.Statistics.dll"
#r @"..\packages\Accord.MachineLearning.2.8.1.0\lib\Accord.MachineLearning.dll"

open System
open System.IO

open Accord.MachineLearning
open Accord.MachineLearning.VectorMachines
open Accord.MachineLearning.VectorMachines.Learning
open Accord.Statistics.Kernels


Note the added reference to the Accord.dll and Accord.Math.dll assemblies; while the code presented below doesn’t reference it explicitly, it looks like Accord.MachineLearning is trying to load the assembly, which fails miserably if they are not referenced.

Then, we need some data; once the training set and validation set have been downloaded to your local machine (see the gist for the datasets url), that’s fairly easy to do:

let training = @"C:/users/mathias/desktop/dojosample/trainingsample.csv"
let validation = @"C:/users/mathias/desktop/dojosample/validationsample.csv"

|> fun lines -> lines.[1..]
|> Array.map (fun line -> line.Split(','))
|> Array.map (fun line ->
(line.[0] |> Convert.ToInt32), (line.[1..] |> Array.map Convert.ToDouble))
|> Array.unzip

let labels, observations = readData training


We read every line of the CSV file into an array of strings, drop the headers with array slicing, keeping only items at or after index 1, split each line around commas (so that each line is now an array of strings), retrieve separately the first element of each line (what the number actually is), and all the pixels, which we transform into a float, and finally unzip the result, so that we get an array of integers (the actual numbers), and an array of arrays, the grayscale level of each pixel.

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