[SciPy-Dev] Faster implementation of cluster.hierarchy

Travis Oliphant oliphant@enthought....
Wed Oct 12 09:18:00 CDT 2011


This looks very cool.  If we can get the BSD license then it would be perfect for integration into SciPy

It would be best of you could use Cython for the integration work.  

You can fork the SciPy project on github and start making your changes using another package's setup.py as an example. 

Thanks for your contributions.

Best,

Travis 

--
Travis Oliphant
(on a mobile)
512-826-7480


On Oct 12, 2011, at 6:12 AM, Conrad Lee <conradlee@gmail.com> wrote:

> A mathematician at Stanford named Daniel Müllner recently came up with a package that implements the hierarchical clustering methods found in scipy.cluster.hierarchy.  His implementation is in C++, but includes a python API that uses the same interface as scipy.cluster.hierarchy.
> 
> Müllner has posted benchmarks as well as algorithmic explanations of why his implementation is faster in a paper on arXiv.  He also has a webpage that describes the package here.
> 
> Because the results of the benchmarks look good, I am interested in getting the scikit-learn package to use this implementation for the hierarchical clustering provided by that package.  Rather than integrate the code in scikit-learn, it seems more appropriate to integrate it upstream in scipy.cluster.hierarchy.  Is there anyone who is interested in this integration?  I am inexperienced with integrating C++ code and python code, and also with how things work in the scipy project, so I'm not sure how to proceed.
> 
> Note: Although Müllner's code is currently under a GPL license, he has stated to me in e-mail that he would be willing to put it under the BSD-2 license it somebody put the time to integrate it into scipy.
> 
> Best regards,
> 
> Conrad Lee
> 
> 
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