example calls of information-theory functions?

[Lee Spector]

I'd like to use some of the functions in http://liebke.github.io/incanter/branch-1.0.x/information-theory-api.html (mainly mutual-information), but I'm not completely clear about what the arguments should look like.

Does anyone have any example code that calls these, preferably for a simple example?

Thanks,

-Lee


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Lee Spector, Professor of Computer Science
Cognitive Science, Hampshire College
893 West Street, Amherst, MA 01002-3359
lspe...@hampshire.edu, http://hampshire.edu/lspector/
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[David Edgar Liebke]

Hi Lee,

The information-theory namespace was pulled out a while back and became part of the Infer library, http://github.com/aria42/infer.

But to your question, it appears, based on the source code, that the mutual information function takes a nested map of categories to counts, representing a joint distribution and a vector of two maps each representing the individual distributions.

(def X {:a 2, :b 1, :c 4, :d 3})
(def Y {:a 1 :b 4, :c 1, :d 2})

(def XY {:a {:a 0, :b 1, :1, :d 5}, :b {:a 4, :b 1, :c 1, :d 1}, :c {...}, :d {...}}) ;; top-level keys represent the X value.

(mutual-information XY [X Y])

I haven't actually tried it, but hopefully that will be enough to get you started.

David

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[Lee Spector]

Thanks David.

I found looking at the tests in infer's information_theory_test.clj to be useful as well.

Unfortunately, when I try to use infer.information-theory I get errors, starting with:

Exception in thread "main" java.lang.IllegalStateException: Can't dynamically bind non-dynamic var: clojure.contrib.macro-utils/protected-symbols, compiling:(clojure/contrib/monads.clj:195)

This is after adding [infer "1.0-SNAPSHOT"] to the project.clj and doing lein deps, which seems to work. It's in a new clojure 1.4.0 project.

Any ideas?

Thanks,

-Lee

[liebke]

Sorry, no idea. Infer hasn't been updated in a few years and is based
on a really old version of Clojure (1.2.0-master-SNAPSHOT) as well as
the old clojure-contrib/monads library (the source of your compiling
error), which has since migrated to https://github.com/clojure/algo.monads.
It might take some work to resuscitate the library.

David

On May 17, 10:27 am, Lee Spector <lspec...@hampshire.edu> wrote:
> Thanks David.
>
> I found looking at the tests in infer's information_theory_test.clj to be useful as well.
>
> Unfortunately, when I try to use infer.information-theory I get errors, starting with:
>
> Exception in thread "main" java.lang.IllegalStateException: Can't dynamically bind non-dynamic var: clojure.contrib.macro-utils/protected-symbols, compiling:(clojure/contrib/monads.clj:195)
>
> This is after adding [infer "1.0-SNAPSHOT"] to the project.clj and doing lein deps, which seems to work. It's in a new clojure 1.4.0 project.
>
> Any ideas?
>
> Thanks,
>
>  -Lee
>
> On May 16, 2013, at 9:34 AM, David Edgar Liebke wrote:
>
>
>
>
>
>
>
> > Hi Lee,
>

> > The information-theory namespace was pulled out a while back and became part of the Infer library,http://github.com/aria42/infer.

[Alex Ott]

Yep, it looks like it heavily relied on clojure-contrib, although I've got at least compilable version :-)

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[Alex Ott]

Lee, you can grab code from https://github.com/alexott/infer - it was fixed for work with clojure 1.5.1

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[Lee Spector]

Thanks Alex!

-Lee