[Biopython-dev] Bio.NeuralNetwork question and updates on 'testseq.'

[Peter Cock]

Hi Adil,

Replies below.

On Wed, Jun 7, 2017 at 6:50 AM, Adil Iqbal <aiqbal85 at gmail.com> wrote:

> ​Hello all,
>
> *TL:DR - Neural Network module is out of date. Also, I'm having an issue
> with the unit test for the "testseq" function. *
>
> Just a quick question about the Neural Network module. The module seems
> just a bit out of date. It only has one available activation function and
> it's located in *the BackPropagation.Layer module
> <http://biopython.org/DIST/docs/api/Bio.NeuralNetwork.BackPropagation.Layer-pysrc.html>*
> for some reason.
>
> [image: Inline image 2]
>
> Machine learning research is progressed pretty far, and no one is really
> using the logistic function as much anymore. The big thing now, especially
> for hidden layers is ReLU, or at the very least TanH, both of which are no
> where to be found in the code. That's not to say that the logistic function
> shouldn't be included, but it should definitely not be the only option. The
> binary step function should also definitely be included - if only for
> output layers.
>
> Really, there should be a module *just* for activation functions. *And it
> should include all of them.*
> <https://en.wikipedia.org/wiki/Activation_function#Comparison_of_activation_functions>
>
> It's not that difficult, its really just a matter of plugging an argument
> into a mathematical formula and returning the result. It might be prudent
> to have an "Activation" class with each of the activation formulas as a
> method of the class. Though, the backprop code would have to refactored to
> account for that.
>
> Anyways, just a thought. I'd love to participate on that project, though
> it would have to be a community effort.
>


Currently the Bio.NeuralNetwork module is not under active development, so
you could perhaps take over this role? Alternatively, if you are familiar
with the current state-of-the-art, there may be a much more mature Python
library in this area we could recommend instead, and deprecate and later
remove Bio.NeuralNetwork from Biopython?

https://github.com/biopython/biopython/tree/master/Bio/NeuralNetwork

Other than style and compatibility updates, it does not seem to have been
changed meaningfully from the first commit by Brad Chapman back in 2001,

https://github.com/biopython/biopython/commit/8641712c2c648dbb28230a08eab1f525f465d2e8

Brad - did you write this or was it a contribution from someone else? The
headers do not have any copyright statements.



>
> I've also written a *unit test for the testseq function
> <https://github.com/Adil-Iqbal/biopython/blob/master/Tests/test_testseq.py>*
> called test_testseq.py. However, it is failing the Travis CI tests because
> it is unable to import testseq.py from the Scripts directory. I attempted
> using both relative and absolute imports (*PEP328*
> <https://www.python.org/dev/peps/pep-0328/>) but that did not work. I am
> actively looking for a solution, though I would appreciate any advice you
> guys could give me. (A pull request might be more efficient way clue me in
> than actually explaining the concept.)
>
>

Right now none of the Scripts/*.py or Doc/examples/*.py are checked from
our main test suite. That is a project worth thinking about.

One solution could be to write Scripts/some_file.py with a __main__ if
statement so that it can be run and tested at the command line using:

$ python Scripts/some_file.py

If you do that, then your Tests/test_some_script.py could call this in a
similar way via subprocess?


> Also, I've finalized the code for testseq. The seeding worked perfectly,
> but it was acting too much like a method and not enough like an argument. I
> had some of my younger cousins use it and they were a bit confused by how
> the seeding worked. Since the folks who would use the code are most likely
> students, teachers, and presenters (not necessarily Python experts), I
> decided to revert to an earlier solution. In this case, it is fair to trade
> a bit of elegance for easier intuitiveness.
>
> Thanks again,
> Adil
>
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