Mathias Brandewinder on .NET, F#, VSTO and Excel development, and quantitative analysis / machine learning.
12. April 2014 11:05

A lightweight post this week. One of my favorite F# type providers is the World Bank type provider, which enables ridiculously easy access to a boatload of socio-economic data for every country in the world. However, numbers are cold – wouldn’t it be nice to visualize them using a map? Turns out it’s pretty easy to do, using another of my favorites, the R type provider. The rworldmap R package, as its name suggests, is all about world maps, and is a perfect fit with the World Bank data.

The video below shows you the results in action; I also added the code below, for good measure. The only caveat relates to the integration between the Deedle data frame library and R. I had to manually copy the Deedle.dll and Deedle.RProvider.Plugin.dll into packages\RProvider.1.0.5\lib for the R Provider to properly convert Deedle data frames into R data frames. Enjoy!

Here is the script I used:

#I @"..\packages\"
#r @"R.NET.1.5.5\lib\net40\RDotNet.dll"
#r @"RProvider.1.0.5\lib\RProvider.dll"
#r @"FSharp.Data.2.0.5\lib\net40\FSharp.Data.dll"
#r @"Deedle.0.9.12\lib\net40\Deedle.dll"
#r @"Deedle.RPlugin.0.9.12\lib\net40\Deedle.RProvider.Plugin.dll"

open FSharp.Data
open RProvider
open RProvider.base
open Deedle
open Deedle.RPlugin
open RProviderConverters

let wb = WorldBankData.GetDataContext()
wb.Countries.France.CapitalCity
wb.Countries.France.Indicators.Population (Total).[2000]

let countries = wb.Countries

let pop2000 = series [ for c in countries -> c.Code => c.Indicators.Population (Total).[2000]]
let pop2010 = series [ for c in countries -> c.Code => c.Indicators.Population (Total).[2010]]
let surface = series [ for c in countries -> c.Code => c.Indicators.Surface area (sq. km).[2010]]

let df = frame [ "Pop2000" => pop2000; "Pop2010" => pop2010; "Surface" => surface ]
df?Codes <- df.RowKeys

open RProvider.rworldmap

let map = R.joinCountryData2Map(df,"ISO3","Codes")
R.mapCountryData(map,"Pop2000")

df?Density <- df?Pop2010 / df?Surface
df?Growth <- (df?Pop2010 - df?Pop2000) / df?Pop2000

let map2 = R.joinCountryData2Map(df,"ISO3","Codes")
R.mapCountryData(map2,"Density")
R.mapCountryData(map2,"Growth")

Have a great week-end, everybody! And big thanks to Tomas for helping me figure out a couple of things about Deedle.

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...

2. February 2014 08:08

tl/dr: Community for F# has a brand-new page at www.c4fsharp.net – with links to a ton of recorded F# presentations, as well as F# hands-on Dojos and material. Check it out, and let us know on Twitter what you think, and what you want us to do next… and spread the word!

If you are into F# and don’t know Community for F#, you are missing out! Community for F#, aka C4FSharp, is the brainchild of Ryan Riley. Ryan has been running C4FSharp tirelessly for years, making great content available online for the F# community.

The idea of C4FSharp is particularly appealing to me, because in my opinion, it serves a very important role. The F# community is amazingly active and friendly, but has an interesting challenge: it is highly geographically dispersed. As a result, it is often difficult to attend presentations locally, or, if you organize Meetups, to find speakers.

Ryan has been doing a phenomenal job addressing that issue, by regularly organizing online live presentations, and making them available offline as well, so that no matter where you are, you can access all that great content. The most visible result is an amazing treasure trove of F# videos on Vimeo, going back all the way to 2010. While I am giving credit where credit is due, special hats off to Rick Minerich, who has been recording the NYC meetings since forever, and making them available on Vimeo as well – and also has been lending a helping hand when C4FSharp needed assistance. Long story short, Rick is just an all-around fantastic guy, so… thanks, Rick!

In any case, the question of how to help grow the F# community has been on my mind quite a bit recently, so I was very excited when Ryan accepted to try working on this as a team, and put our ideas together. The direction I am particularly interested in is to provide support for local groups to grow. Online is great, but nothing comes close to having a good old fashioned meeting with like-minded friends to discuss and learn. So one thing I would like to see happen is for C4FSharp to become a place where you can find resources to help you guys start and run your own local group. While running a Meetup group does take a bit of effort, it’s not nearly as complicated as what people think it is, and it is very fun and rewarding. So if you want to see F# meetings in your area, just start a Meetup group!

In that frame, Ryan has put together a brand-new web page at www.c4fsharp.net, where we started listing resources. The existing videos, of course, but also a repository of hands-on Dojos and presentation/workshop material. The hands-on Dojos is something we started doing in San Francisco last year with www.sfsharp.org, and  has been working really well. Instead of a classic presentation, the idea is to create a fun coding problem, sit down in groups and work on it, learn from each other, and share. It’s extremely fun, and, from a practical standpoint, it’s also very convenient, because you don’t need to fly in a speaker to present. Just grab the repository from GitHub, look at the instructions, and run with it!

Just to whet your appetite, here is a small selection of the amazing images that came out of running the Fractal Forest Dojo in Nashville and San Francisco this month:

… and special mention goes to @Luketopia, for his FunScript Fractal Generator!

What’s next? We have a ton of ideas on what we could do. We will obviously add more resources as we go – but we would really like to hear from you guys. So help us make Community for F# the resource you would like to have! Here is what we would like from you:

• Contact us on Twitter at @c4fsharp, and let us know what you like and don’t like, and want to see!
• Take a look at the Dojos, and let us know how to make them better! Pull requests are highly appreciated. We have more Dojos and presentation material coming up, stay tuned! And if you have Dojo ideas you want to contribute, we’d love to hear about it.
• If you are organizing a Presentation, talking at a user group or a conference, ping us on Twitter, and we’ll let the Community know about your event!
• If you want to broadcast a presentation live, contact us, we would love to help out and make it available to the broader community.
• If you like what we are doing, please spread the word!

In short – we intend to make C4FSharp the best resource we can make it for local F# communities, and we would love your input and help on how to make that happen!

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!