[Biopython-dev] Thoughts on NN module

[Peter Cock]

We seem to be in agreement (Adil replied to me directly, I've asked
him to re-send that to the list for the public record).

Who would like to prepare a pull request adding the deprecation
warning and suggesting scikit-learn as an alternative? See:

http://biopython.org/wiki/Deprecation_policy

Peter

On Fri, Jun 9, 2017 at 9:49 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> I would be in favor of removing Bio.NeuralNetwork. It was useful in the
> past, but nowadays it seems out of scope for Biopython, and if scikit-learn
> offers a better solution then we don't need this module in Biopython.
>
> Best,
> -Michiel
>
>
> On Thursday, June 8, 2017 1:36 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>
> Hi Adil,
>
> So you'd be in favour of us deprecating and later removing
> Bio.NeuralNetwork which the original author Brad suggested
> on the other thread?
>
> http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021719.html
>
> Regards,
>
> Peter
>
> On Wed, Jun 7, 2017 at 5:18 PM, Adil Iqbal <aiqbal85 at gmail.com> wrote:
>> Hey guys,
>>
>> I wanted to try and save the machine learning module somehow, but based on
>> the varied applications of machine learning in bioinformatics, really the
>> best package to use is scikit-learn. It covers everything from Bayesian
>> networks, hierarchical clustering, decision trees, etc.
>>
>> I suppose biopython could offer pre-built, easily modified networks for
>> the
>> most common use-cases, that is, protein folding and gene pattern
>> recognition. Though we would need to use scikit-learn (or other machine
>> learning package) as a dependency.
>>
>> Another option would be to scrap the machine learning suite and focus more
>> on data management.
>>
>> Best,
>> Adil
>>
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>
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