[Biojava-dev] bits of information

[Lachlan Coin]

Yeah sure - good idea to have both methods.  It seems like calling either
method 'information' would be confusing, so we should rename the current
method entropy, and add a new method but not call it information either.

Lachlan


On Tue, 3 Jun 2003, Francois Pepin wrote:

> I think that the name is misleading.
>
> It's obviously a measure of information, but it gives back the entropy.
>
> Just saying that something returns the information content is not quite
> correct in this case as it returns the entropy.
>
> The documentation should definitely be cleared up to make that clear.
>
> I think that adding the method in question would be a good idea as well.
>
> Francois
>
> -----Original Message-----
> From: biojava-dev-bounces at biojava.org
> [mailto:biojava-dev-bounces at biojava.org] On Behalf Of Lachlan Coin
> Sent: 3 juin, 2003 10:40
> To: Francois Pepin
> Cc: biojava-dev at biojava.org; 'Schreiber, Mark'
> Subject: RE: [Biojava-dev] bits of information
>
>
> The definitions are formal, and we all agree with the definition of
> entropy.
>
> Shannon's first coding theorem, tells us that
> the entropy of an information source is equal to the minimum average
> number of bits per symbol that must (and can in the limit) be used to
> encode source outputs.  So, if I try to communicate to you (using binary
> uniquely decipherable code) the outcome of sampling from a source X
> which has  entropy H(X), then I must use at least H(X) bits per symbol
> (if I am not to lose any information) and in the limit of transmiting
> N-> infinity symbols, I can achieve an average H(X) bits per code.
>
> Thus, H(X) - the entropy  - is a natural measure of the information
> content of a distribution.  This is what the method is returning at the
> moment.
>
> Lachlan
>
>

-------------------------------------------------------------
Lachlan Coin
Wellcome Trust Sanger Institute		Magdalene College
Cambridge  CB10 1SA			Cambridge CB30AG
Ph: +44 1223 494 820
Fax: +44 1223 494 919
------------------------------------------------------------