Re: [Scikit-learn-general] Pull requests: WIP/MRG convention

2011-12-19 Thread Robert Layton
On 19 December 2011 04:16, Fernando Perez wrote: > On Sun, Dec 18, 2011 at 4:08 AM, Gael Varoquaux > wrote: > > I suggest that we use the following conventions: > > Great idea. I really hope github adds soon support for proper labels > and milestones to PRs (I've filed a ticket asking for it al

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Jieyun Fu
I see. Makes sense. Thanks guys. On Mon, Dec 19, 2011 at 6:21 PM, Gael Varoquaux < gael.varoqu...@normalesup.org> wrote: > On Mon, Dec 19, 2011 at 10:24:18AM -0500, josef.p...@gmail.com wrote: > > On Mon, Dec 19, 2011 at 10:19 AM, Jieyun Fu wrote: > > > It's Wald's Z test in here. Search for Wal

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Gael Varoquaux
On Mon, Dec 19, 2011 at 10:24:18AM -0500, josef.p...@gmail.com wrote: > On Mon, Dec 19, 2011 at 10:19 AM, Jieyun Fu wrote: > > It's Wald's Z test in here. Search for Wald Test in > > http://userwww.sfsu.edu/~efc/classes/biol710/logistic/logisticreg.htm > > In ordinary linear regression they like

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread Lars Buitinck
2011/12/19 Olivier Grisel : > Maybe we could move the fast_svd into the future > sklearn.random_projection package and the graph_shortest_path in a > sklearn.graph package that would also host the kneighbors_graph func? I'm not sure if we should be developing a "machine learning & graph algorithms

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread Jacob VanderPlas
Good I think for now I'll keep everything in sklearn/utils, but just clean things up and write some documentation. I sent a message out to scipy-dev floating the idea of adding graph_shortest_path to scipy: we'll see where that goes. Jake Olivier Grisel wrote: > I think I am overall +1 but I

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread Olivier Grisel
I think I am overall +1 but I don't really like the sklearn.enhancements package name. What functions would go in such package? - fast_svd - graph_shortest_path - what else? Maybe we could move the fast_svd into the future sklearn.random_projection package and the graph_shortest_path in a sklearn

[Scikit-learn-general] Documentation file size and images

2011-12-19 Thread Andreas Müller
Someone suggested saving the figures in the examples as jpg to save room. As far as I see it, this is not possible. The pylab docstring says: *format*: One of the file extensions supported by the active backend. Most backends support png, pdf, ps, eps and svg And when I try

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread josef . pktd
On Mon, Dec 19, 2011 at 10:19 AM, Jieyun Fu wrote: > It's Wald's Z test in here. Search for Wald Test in > > http://userwww.sfsu.edu/~efc/classes/biol710/logistic/logisticreg.htm > > In ordinary linear regression they like to call it t-statistics. I guess > it's just a terminology thing. Since t

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Jieyun Fu
It's Wald's Z test in here. Search for Wald Test in http://userwww.sfsu.edu/~efc/classes/biol710/logistic/logisticreg.htm In ordinary linear regression they like to call it t-statistics. I guess it's just a terminology thing. Thanks again, On Mon, Dec 19, 2011 at 10:14 AM, Alexandre Gramfort <

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Alexandre Gramfort
what is : \hat{ beta } / std.err ? given a fitted model that gives clf.coef_ for the estimated coef? Alex On Mon, Dec 19, 2011 at 4:08 PM, Jieyun Fu wrote: > Hi Alex, > > I am sorry to bother you again, but it doesn't look like that > > univariate_selection.f_classif > > gives me the t-statisti

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Jieyun Fu
Hi Alex, I am sorry to bother you again, but it doesn't look like that univariate_selection.f_classif gives me the t-statistics of linear regression or logistic regression. It gives F-value, but what I am looking for is \hat{ beta } / std.err Thank you so much! On Mon, Dec 19, 2011 at 9:47 AM,

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Alexandre Gramfort
> I haven't found your example. Can you post a link? look at the docstring of cross_val_score > I was looking > at http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics > > By the way, Is there a built-in method to calculate t-stat ? I couldn't find > that even for ordinary l

Re: [Scikit-learn-general] t-statistics from LogisticRegression

2011-12-19 Thread Jieyun Fu
Hi Alex, I haven't found your example. Can you post a link? I was looking at http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics By the way, Is there a built-in method to calculate t-stat ? I couldn't find that even for ordinary linear regression. I wouldn't mind writing m

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread Virgile Fritsch
OK, but if basics methods are likely to become more efficient than already existing ones, they should be included in more general packages at some point (i.e. fast_svd may end into scipy.linalg). -- Virgile Fritsch On Mon, Dec 19, 2011 at 1:57 PM, xinfan meng wrote: > Good points. Sometimes pe

[Scikit-learn-general] A ref on Bayesian regularization for GMMs

2011-12-19 Thread bthirion
For those interested, I think that one might be helpful (I alluded to it) http://www.stat.washington.edu/raftery/Research/PDF/Fraley2007JClass.pdf Bertrand -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread xinfan meng
Good points. Sometimes people just want to use the nuts and bolts instead of a full-fledge machine. On Mon, Dec 19, 2011 at 6:35 PM, Jacob VanderPlas < vanderp...@astro.washington.edu> wrote: > Hi all, > I think we should re-think our utils model. Currently, it's a mish-mash > of tools for devel

Re: [Scikit-learn-general] Utils upgrade

2011-12-19 Thread Andreas Müller
+1 - Ursprüngliche Mail - Von: "Jacob VanderPlas" An: scikit-learn-general@lists.sourceforge.net Gesendet: Montag, 19. Dezember 2011 11:35:23 Betreff: [Scikit-learn-general] Utils upgrade Hi all, I think we should re-think our utils model. Currently, it's a mish-mash of tools for devel

[Scikit-learn-general] Utils upgrade

2011-12-19 Thread Jacob VanderPlas
Hi all, I think we should re-think our utils model. Currently, it's a mish-mash of tools for development (e.g. array2d, logsum, etc.) and performance code that's better than many other available python implementations (e.g. fast_svd, graph_shortest_path, etc.). As far as I can tell, none of t

Re: [Scikit-learn-general] RuntimeError: Factor is exactly singular

2011-12-19 Thread Jacob VanderPlas
Timmy, I'm taking a closer look at your problem now. There's something very strange in your adjacency matrix: a small set of points are the nearest neighbors of virtually every other point. I think this is leading to the singular weight matrices which cause the error. I visualized it like th