Re: [Scikit-learn-general] sparse_encode implementation

2012-01-09 Thread Alexandre Gramfort
what is implemented in the scikit matches the algorithms implemented in SPAMS. SPAMS implements more like positivity constraints for example. A real comparison in terms of speed and results has however not been done. Note that for the positivity constraint we just need to modify LassoLARS and Lass

Re: [Scikit-learn-general] Export gram matrix

2012-01-09 Thread Olivier Grisel
2012/1/9 Mathias Verbeke : > Dear all, > > In the documentation of the SVM module, I saw that it was possible to pass > your own Gram matrix to the kernel. I was wondering if it was also possible > to do the reverse, i.e. to export the calculated Gram matrix (that gives the > similarity between the

[Scikit-learn-general] Export gram matrix

2012-01-09 Thread Mathias Verbeke
Dear all, In the documentation of the SVM module, I saw that it was possible to pass your own Gram matrix to the kernel. I was wondering if it was also possible to do the reverse, i.e. to export the calculated Gram matrix (that gives the similarity between the train and test instances)? Best and

Re: [Scikit-learn-general] sparse_encode implementation

2012-01-09 Thread Vlad Niculae
Short answer, no. sparse_encode is just a wrapper for funcionality that existed in the scikit already (lasso, omp), with support for parallelization. We couldn't embed SPAMS anyway, because of the license IIRC. A benchmark would be interesting indeed. Vlad On 09.01.2012, at 18:02, Ian Goodfell

[Scikit-learn-general] sparse_encode implementation

2012-01-09 Thread Ian Goodfellow
Is decomposition.sparse_encode implemented using SPAMS ( http://www.di.ens.fr/~mairal/software_eng.php ) ? If not, does anyone know how the two implementations compare? Thanks, Ian -- Ridiculously easy VDI. With Citrix VDI

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Lars Buitinck
2012/1/9 Olivier Grisel : > That would work. Alternatively we could have: > > algorithm="csvm" or algorithm="nusvm" as already used elsewhere > (e.g. neighbors, pls, dict_learning and manifold). +1. -- Lars Buitinck Scientific programmer, ILPS University of Amsterdam ---

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Andreas
On 01/09/2012 12:19 PM, Mathieu Blondel wrote: > On Mon, Jan 9, 2012 at 7:40 PM, Gael Varoquaux > wrote: > > >> Can it be that if nu is None C is used, or do you thihnk that this is >> confusing? >> > That wouldn't work for NuSVR, which uses both C and nu (I know, it's > confusing). >

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Gael Varoquaux
On Mon, Jan 09, 2012 at 08:19:33PM +0900, Mathieu Blondel wrote: > > Can it be that if nu is None C is used, or do you thihnk that this is > > confusing? > That wouldn't work for NuSVR, which uses both C and nu (I know, it's > confusing). That's exactly what I had in mind: I was proposing nu to b

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Mathieu Blondel
On Mon, Jan 9, 2012 at 7:40 PM, Gael Varoquaux wrote: > Can it be that if nu is None C is used, or do you thihnk that this is > confusing? That wouldn't work for NuSVR, which uses both C and nu (I know, it's confusing). If we merge C-SVM and nu-SVM classes, users may think that they can obtain

Re: [Scikit-learn-general] Publishing the HTML doc on github

2012-01-09 Thread Olivier Grisel
2012/1/9 Fabian Pedregosa : > On Mon, Jan 9, 2012 at 2:00 AM, Olivier Grisel > wrote: >> Hi all, >> >> As discussed earlier, here is a new tool to publish the doc on github >> rather than sourceforge. >> >> The result is available here: >> >>  https://github.com/scikit-learn/scikit-learn.org (the

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Olivier Grisel
2012/1/9 Gael Varoquaux : > On Mon, Jan 09, 2012 at 11:11:29AM +0100, Lars Buitinck wrote: >> 2012/1/9 Fabian Pedregosa : >> > I'm OK with the idea of having one class for classification and one >> > for regression. It's conceptually easier and simplifies the docs. +1 > >> What should the parameter

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Gael Varoquaux
On Mon, Jan 09, 2012 at 11:11:29AM +0100, Lars Buitinck wrote: > 2012/1/9 Fabian Pedregosa : > > I'm OK with the idea of having one class for classification and one > > for regression. It's conceptually easier and simplifies the docs. +1 > What should the parameter be called that chooses nu vs. C?

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Lars Buitinck
2012/1/9 Fabian Pedregosa : > I'm OK with the idea of having one class for classification and one > for regression. It's conceptually easier and simplifies the docs. +1 What should the parameter be called that chooses nu vs. C? -- Lars Buitinck Scientific programmer, ILPS University of Amsterdam

Re: [Scikit-learn-general] test time performance and sparse - dense dot products

2012-01-09 Thread Mathieu Blondel
On Mon, Jan 9, 2012 at 4:08 PM, Peter Prettenhofer wrote: > ``ravel`` is only used in the binary case so it is not responsible for > the copy. I was referring to ravel() in https://github.com/scipy/scipy/blob/master/scipy/sparse/compressed.py#L264, not in scikit-learn. Mathieu

Re: [Scikit-learn-general] Publishing the HTML doc on github

2012-01-09 Thread Fabian Pedregosa
On Mon, Jan 9, 2012 at 10:56 AM, Olivier Grisel wrote: > Thanks :) > > Can someone switch the DNS? I think you'll have to ask Stefan van der Walt -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a compl

Re: [Scikit-learn-general] Publishing the HTML doc on github

2012-01-09 Thread Olivier Grisel
Thanks :) Can someone switch the DNS? -- Olivier -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. W

Re: [Scikit-learn-general] Putting SVC and NuSVC into the same class

2012-01-09 Thread Fabian Pedregosa
On Sun, Jan 8, 2012 at 11:06 PM, Andreas wrote: > Hey everybody. > @larsmans (my personal hero for the day) started refactoring the SVM > class structure here: > https://github.com/larsmans/scikit-learn/commits/refactor-svm > after some discussion here: > https://github.com/scikit-learn/scikit-lea

Re: [Scikit-learn-general] Publishing the HTML doc on github

2012-01-09 Thread Fabian Pedregosa
On Mon, Jan 9, 2012 at 2:00 AM, Olivier Grisel wrote: > Hi all, > > As discussed earlier, here is a new tool to publish the doc on github > rather than sourceforge. > > The result is available here: > >  https://github.com/scikit-learn/scikit-learn.org (the repo for the > tool, basically a README.

Re: [Scikit-learn-general] test time performance and sparse - dense dot products

2012-01-09 Thread Peter Prettenhofer
I've just sent a PR which implements Oliviers solution - The overhead (converting to f-style) only applies to multi-class classification so I think its ok to do it this way. SGDClassifier currently does not support `partial_fit` only via the `init_coef` and `init_intercept` arguments, they are auto