[bip] Announcing PEBL (and asking for assistance)

[Bruce Southey]

Abhik Shah wrote:
> Hi Titus,
>     Fine, so you want a tutorial that actually teaches rather than
> something quick that lets me claim I have a tutorial?!?
>
> I've created a bug report
> (http://code.google.com/p/pebl-project/issues/detail?id=16) for this
> and I've updated the tutorial using an example from a real dataset
> (Spellman cell cycle) and better explanation about the process and
> results.
>
> Updated docs at: http://ano.malo.us/pebl/docs/
> Updated tutorial:  http://ano.malo.us/pebl/docs/tutorial.html
>
> The explanation for the results is still weak but a screencast might
> be a better solution.
>
> Thanks,
> Abhik.
>
>
> On Tue, Jun 17, 2008 at 8:19 PM, C. Titus Brown <ctb at msu.edu> wrote:
>   
>> On Tue, Jun 17, 2008 at 05:34:41PM -0400, Abhik Shah wrote:
>> -> Hi,
>> ->   I've been working on pebl (Python Environment for Bayesian Learning)
>> -> for the past couple of years.  It's a python library for structure
>> -> learning of Bayesian networks from data and prior knowledge.  I've
>> -> implemented all features for a 1.0 release and have finalized the API.
>> ->  It has many unique features not found in any other package (python or
>> -> not), including:
>> ->
>> -> * ability to handle interventional data
>> -> * exact and heuristic methods for handling missing values and hidden variables
>> -> * nice AJAX-y html reports
>> -> * almost-transparent parallel processing on multiple platforms (XGrid,
>> -> IPython1 and Amazon EC2)
>> ->     * this is useful when dealing with many hidden variable
>> ->
>> -> Pebl includes sphinx-generated documentation and 200+ unittests.  I
>> -> think it's ready for prime time but would appreciate an informal code
>> -> review (or just comments) from this group.  Installation is currently
>> -> a bit painful but I'm working on improving that. Same goes for the
>> -> quality of the documentation.
>>
>> Hi, Abhik,
>>
>> the tutorial is cute, but completely uninformative!  What format is the
>> data in, for example? What does the analysis actually do??  What is the
>> output?  Can it solve real problems (and what would be an example of
>> one, and wouldn't that be a great tutorial instead?)
>>
>> However, to find out the answer to these questions I would be happy to
>> have you come give a presentation at MSU, if you're interested.  E-mail
>> me off-list if so.
>>
>> cheers,
>> --titus
>> --
>> C. Titus Brown, ctb at msu.edu
>>     
[This is meant to be critical but not negative]

Please indicate the license in the documentation because I should not 
have to download/install it to find it. One reason is that simply by 
just downloading the package can imply acceptance of the terms. Only by 
going to the project home do I see the license type (MIT) but not the 
ACTUAL license (link is to the general license and does not contain the 
author or authors of PEBL).

How is this different from say OpenBayes (http://www.openbayes.org/) , 
BNT (http://www.cs.ubc.ca/~murphyk/Software/BNT/bnt.html), or, more 
importantly, the SciKit on BNT: 
http://scipy.org/scipy/scikits/wiki/BayesNet ?
(Note that your project is linked there.)
It would be nice to have a single package for this (yes, I can guess 
what is involved).

What is the latest version of PEBL?
What operating systems are supported and known to work under? If you 
assume Linux or Windows just say so!
What version of Python is required and supported? Is it 2.5 specific or 
not (NumPy 1.1 and support Python 2.3 or higher; NumPy 1.2 will support 
Python 2.4 or higher)?
What version of NumPy is required and supported?

What software versions were used in creating the tutorial and 
installation documentation? These should be listed at the start of the 
tutorial.

Finally, if you want code review, why do you not provide the code?
Actually I can get via the main project page (but the egg seems to be 
very old) but not a tarball.

Bruce