2009/6/8 Gael Varoquaux gael.varoqu...@normalesup.org:
On Mon, Jun 08, 2009 at 12:29:08AM -0400, David Warde-Farley wrote:
On 7-Jun-09, at 6:12 AM, Gael Varoquaux wrote:
Well, I do bootstrapping of PCAs, that is SVDs. I can tell you, it
makes
a big difference, especially since I have 8
On Sun, Jun 7, 2009 at 6:19 AM, Bruce Southeybsout...@gmail.com wrote:
On Sun, Jun 7, 2009 at 3:37 AM, Fernando Perezfperez@gmail.com wrote:
One more question. For these *_indices() functions, would you want an
interface that accepts *either*
diag_indices(size,ndim)
As I indicated
On 8-Jun-09, at 1:17 AM, David Cournapeau wrote:
I would not be surprised if David had this paper in mind :)
http://www.cs.toronto.edu/~roweis/papers/empca.pdf
Right you are :)
There is a slight trick to it, though, in that it won't produce an
orthogonal basis on its own, just something
On Mon, Jun 08, 2009 at 08:58:29AM +0200, Matthieu Brucher wrote:
Given the number of PCs, I think you may just be measuring noise.
As said in several manifold reduction publications (as the ones by
Torbjorn Vik who published on robust PCA for medical imaging), you
cannot expect to have more
2009/6/8 Gael Varoquaux gael.varoqu...@normalesup.org:
On Mon, Jun 08, 2009 at 08:58:29AM +0200, Matthieu Brucher wrote:
Given the number of PCs, I think you may just be measuring noise.
As said in several manifold reduction publications (as the ones by
Torbjorn Vik who published on robust PCA
2009/6/8 David Warde-Farley d...@cs.toronto.edu:
On 8-Jun-09, at 1:17 AM, David Cournapeau wrote:
I would not be surprised if David had this paper in mind :)
http://www.cs.toronto.edu/~roweis/papers/empca.pdf
Right you are :)
There is a slight trick to it, though, in that it won't
2009/6/8 Matthieu Brucher matthieu.bruc...@gmail.com:
I'm trying to compile it with ICC 10.1.018, and it fails :|
icc: scipy/special/cephes/const.c
scipy/special/cephes/const.c(94): error: floating-point operation
result is out of range
double INFINITY = 1.0/0.0; /* 99e999; */
I'm trying to compile it with ICC 10.1.018, and it fails :|
icc: scipy/special/cephes/const.c
scipy/special/cephes/const.c(94): error: floating-point operation
result is out of range
double INFINITY = 1.0/0.0; /* 99e999; */
^
scipy/special/cephes/const.c(99): error:
Matthieu Brucher wrote:
I'm trying to compile it with ICC 10.1.018, and it fails :|
icc: scipy/special/cephes/const.c
scipy/special/cephes/const.c(94): error: floating-point operation
result is out of range
double INFINITY = 1.0/0.0; /* 99e999; */
^
2009/6/8 David Cournapeau da...@ar.media.kyoto-u.ac.jp:
Matthieu Brucher wrote:
I'm trying to compile it with ICC 10.1.018, and it fails :|
icc: scipy/special/cephes/const.c
scipy/special/cephes/const.c(94): error: floating-point operation
result is out of range
double INFINITY = 1.0/0.0;
Hi Josef,
thanks for the summary! I am responding below, later I will make an
enhancement ticket.
josef.p...@gmail.com wrote:
On Sat, Jun 6, 2009 at 4:42 AM, Neil Crighton neilcrigh...@gmail.com wrote:
Robert Cimrman cimrman3 at ntc.zcu.cz writes:
Anne Archibald wrote:
1. add a keyword
On Mon, Jun 8, 2009 at 8:45 PM, Matthieu
Bruchermatthieu.bruc...@gmail.com wrote:
2009/6/8 David Cournapeau da...@ar.media.kyoto-u.ac.jp:
Matthieu Brucher wrote:
I'm trying to compile it with ICC 10.1.018, and it fails :|
icc: scipy/special/cephes/const.c
scipy/special/cephes/const.c(94):
Good luck with fixing this then :|
I've tried to build scipy with the MKL and ATLAS, and I have in both
cases a segmentation fault. With the MKL, it is the same as in a
previous mail, and for ATLAS it is there:
Regression test for #946. ... Segmentation fault
A bad ATLAS compilation?
Matthieu
2009/6/8 David Cournapeau da...@ar.media.kyoto-u.ac.jp:
Matthieu Brucher wrote:
Good luck with fixing this then :|
I've tried to build scipy with the MKL and ATLAS, and I have in both
cases a segmentation fault. With the MKL, it is the same as in a
previous mail, and for ATLAS it is there:
Note that EM can be very slow to converge:
http://www.cs.toronto.edu/~roweis/papers/emecgicml03.pdf
EM is great for churning-out papers, not so great for getting real work
done. Conjugate gradient is a much better tool, at least in my (and
Salakhutdinov's) experience. Btw, have you considered
On Mon, Jun 08, 2009 at 08:33:11AM -0400, Jason Rennie wrote:
EM is great for churning-out papers, not so great for getting real work
done.�
That's just what I thought.
Btw, have you considered how much the Gaussianity assumption is
hurting you?
I have. And the answer is: not
On Mon, Jun 8, 2009 at 3:29 AM, Gael Varoquaux
gael.varoqu...@normalesup.org wrote:
On Mon, Jun 08, 2009 at 08:58:29AM +0200, Matthieu Brucher wrote:
Given the number of PCs, I think you may just be measuring noise.
As said in several manifold reduction publications (as the ones by
Torbjorn
Jason Rennie wrote:
Note that EM can be very slow to converge:
http://www.cs.toronto.edu/~roweis/papers/emecgicml03.pdf
http://www.cs.toronto.edu/%7Eroweis/papers/emecgicml03.pdf
EM is great for churning-out papers, not so great for getting real
work done.
I think it depends on what you
On Mon, Jun 08, 2009 at 09:02:12AM -0400, josef.p...@gmail.com wrote:
whats the actual shape of the array/data you run your PCA on.
50 000 dimensions, 820 datapoints.
Number of time periods, size of cross section at point in time?
I am not sure what the question means. The data is sampled at
2009/6/8 Gael Varoquaux gael.varoqu...@normalesup.org:
On Mon, Jun 08, 2009 at 09:02:12AM -0400, josef.p...@gmail.com wrote:
whats the actual shape of the array/data you run your PCA on.
50 000 dimensions, 820 datapoints.
You definitely can't expect to find 50 meaningfull PCs. It's
impossible
On Mon, Jun 8, 2009 at 6:17 AM, Gael Varoquaux
gael.varoqu...@normalesup.org wrote:
On Mon, Jun 08, 2009 at 09:02:12AM -0400, josef.p...@gmail.com wrote:
whats the actual shape of the array/data you run your PCA on.
50 000 dimensions, 820 datapoints.
Have you tried shuffling each time series,
On Mon, Jun 08, 2009 at 06:28:06AM -0700, Keith Goodman wrote:
On Mon, Jun 8, 2009 at 6:17 AM, Gael Varoquaux
gael.varoqu...@normalesup.org wrote:
On Mon, Jun 08, 2009 at 09:02:12AM -0400, josef.p...@gmail.com wrote:
whats the actual shape of the array/data you run your PCA on.
50 000
Robert Cimrman wrote:
Hi Josef,
thanks for the summary! I am responding below, later I will make an
enhancement ticket.
Done, see http://projects.scipy.org/numpy/ticket/1133
r.
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Numpy-discussion mailing list
Numpy-discussion@scipy.org
Robert Cimrman wrote:
Hi Neil,
Neil Crighton wrote:
Hi all,
I posted this message couple of days ago, but gmane grouped it with an old
thread and it hasn't shown up on the front page. So here it is again...
I'd really like to see the setmember1d_nu function in ticket 1036 get into
OK, I'm stuck with #946 with the MKL as well (finally managed to
compile and use it with only the static library safe for libguide).
I'm trying to download the trunk at the moment to check if the
segmentation fault is still there.
Matthieu
2009/6/8 Matthieu Brucher matthieu.bruc...@gmail.com:
Is this lack of associativity really *always* such a huge issue? I can
imagine many situations where it is not. One just want to compute A*B*C,
without any particular knowing of whether A*(B*C) or (A*B)*C is best.
If the user is allowed to blindly use A*B*C, I don't really see why he
wouldn't be
David,
I've checked out the trunk, and the segmentation fault isn't there
anymore (the trunk is labeled 0.8.0 though)
Here is the log from the remaining errors with the MKL:
==
ERROR: Failure: ImportError
On Mon, Jun 8, 2009 at 8:55 AM, David Cournapeau
da...@ar.media.kyoto-u.ac.jp wrote:
I think it depends on what you are doing - EM is used for 'real' work
too, after all :)
Certainly, but EM is really just a mediocre gradient descent/hill climbing
algorithm that is relatively easy to
Matthieu Brucher wrote:
David,
I've checked out the trunk, and the segmentation fault isn't there
anymore (the trunk is labeled 0.8.0 though)
Yes, the upcoming 0.7.1 release has its code in the 0.7.x svn branch.
But the fix for #946 is a backport of 0.8.0, so in theory, it should be
fixed
2009/6/8 David Cournapeau da...@ar.media.kyoto-u.ac.jp:
Matthieu Brucher wrote:
David,
I've checked out the trunk, and the segmentation fault isn't there
anymore (the trunk is labeled 0.8.0 though)
Yes, the upcoming 0.7.1 release has its code in the 0.7.x svn branch.
But the fix for #946
Jason Rennie wrote:
I hung-out in the machine learning community appx. 1999-2007 and
thought the Salakhutdinov work was extremely refreshing to see after
listening to no end of papers applying EM to whatever was the hot
topic at the time. :)
Isn't it true for any general framework who enjoys
Matthieu Brucher wrote:
Concerning the other errors: did you compile with intel compilers or GNU
ones ?
Only Intel compilers. Maybe I should check the rc branch instead of the trunk?
I just wanted to confirm - I am actually rather surprised there are not
more errors :)
cheers,
Hi All,
I'm new to python and tools like matplotlib and Mayavi so I may be
missing something basic. I've been looking for a fairly lightweight
editor/interactive shell combo that allows me to create plots and
figures from a shell and play with them and kill them gracefully. The
Mayavi
On Mon, Jun 8, 2009 at 12:29 PM, Jonno jonnojohn...@gmail.com wrote:
Hi All,
I'm new to python and tools like matplotlib and Mayavi so I may be
missing something basic. I've been looking for a fairly lightweight
editor/interactive shell combo that allows me to create plots and
figures from a
Olivier Verdier wrote:
One
should realize that allowing dot(A,B,C) is just *better* than the
present situation where the user is forced into writing dot(dot(A,B),C)
or dot(A,dot(B,C)).
I'm lost now -- how is this better in any significant way?
Tom K. wrote:
But,
almost all experienced
On Mon, Jun 8, 2009 at 11:39 AM, josef.p...@gmail.com wrote:
I'm using now pydee as my main shell to try out new scripts and I
don't have any problems with the plots. I'm creating plots the
standard way
from matplotlib import pyplot as plt
plt.plot(x,y)
and I can close the poping up plot
On Mon, Jun 8, 2009 at 11:35 AM, Gökhan SEVERgokhanse...@gmail.com wrote:
Hello,
To me, IPython is the right way to follow. Try whos to see what's in your
namespace.
You may want see this instructional video (A Demonstration of the 'IPython'
Interactive Shell) to learn more about IPython's
2009/6/8 Christopher Barker chris.bar...@noaa.gov
Olivier Verdier wrote:
One
should realize that allowing dot(A,B,C) is just *better* than the
present situation where the user is forced into writing dot(dot(A,B),C)
or dot(A,dot(B,C)).
I'm lost now -- how is this better in any
On Mon, Jun 8, 2009 at 12:11 PM, Jonno jonnojohn...@gmail.com wrote:
On Mon, Jun 8, 2009 at 11:35 AM, Gökhan SEVERgokhanse...@gmail.com
wrote:
Hello,
To me, IPython is the right way to follow. Try whos to see what's in
your
namespace.
You may want see this instructional video (A
On Jun 8, 2009, at 12:26 PM, Gökhan SEVER wrote:
On Mon, Jun 8, 2009 at 12:11 PM, Jonno jonnojohn...@gmail.com wrote:
On Mon, Jun 8, 2009 at 11:35 AM, Gökhan SEVERgokhanse...@gmail.com
wrote:
Hello,
To me, IPython is the right way to follow. Try whos to see
what's in your
namespace.
Olivier Verdier wrote:
Well, allowing dot(A,B,C) does not remove any other possibility does it?
I won't fight for this though. I personally don't care but I think that
it would remove the last argument for matrices against arrays, namely
the fact that A*B*C is easier to write than
Going back to Alan Isaac's example:
1) beta = (X.T*X).I * X.T * Y
2) beta = np.dot(np.dot(la.inv(np.dot(X.T,X)),X.T),Y)
Robert Kern wrote:
4) beta = la.lstsq(X, Y)[0]
I really hate that example.
Remember, the example is a **teaching** example.
I actually use NumPy in a Master's level
Changing the site.cfg as you suggested did the trick!
For what its worth, setup.py build no longer fails as before at compilation
step (line 95),
(I'm still puzzled whether this earlier 'failure' was caused by some error
in my build process but I should probably let it go.)
and
On Mon, Jun 8, 2009 at 14:10, Alan G Isaacais...@american.edu wrote:
Going back to Alan Isaac's example:
1) beta = (X.T*X).I * X.T * Y
2) beta = np.dot(np.dot(la.inv(np.dot(X.T,X)),X.T),Y)
Robert Kern wrote:
4) beta = la.lstsq(X, Y)[0]
I really hate that example.
Remember, the
Hello,
I'm working on the new datetime64 and timedelta64 dtypes (as proposed
here:
http://projects.scipy.org/numpy/browser/trunk/doc/neps/datetime-proposal3.rst).
I'm looking through the C code in numpy core, and can't seem to find
much in the way of dtypes. Pierre suggested looking through the
On 8-Jun-09, at 8:33 AM, Jason Rennie wrote:Note that EM can be very slow to converge:That's absolutely true, but EM for PCA can be a life saver in cases where diagonalizing (or even computing) the full covariance matrix is not a realistic option. Diagonalization can be a lot of wasted effort if
On Mon, Jun 8, 2009 at 3:33 PM, Robert Kernrobert.k...@gmail.com wrote:
On Mon, Jun 8, 2009 at 14:10, Alan G Isaacais...@american.edu wrote:
Going back to Alan Isaac's example:
1) beta = (X.T*X).I * X.T * Y
2) beta = np.dot(np.dot(la.inv(np.dot(X.T,X)),X.T),Y)
Robert Kern wrote:
4) beta
Let's Finish Documenting SciPy!
Last year, we began the SciPy Documentation Marathon to write
reference pages (docstrings) for NumPy and SciPy. It was a huge
job, bigger than we first imagined, with NumPy alone having over 2,000
functions.
We created the doc wiki (now at
Gökhan SEVER wrote:
So far, IPython-Scite is the fastest that I can build my programs.
Experiment in Ipython and build pieces in Scite. I would like to know
what others use in this respect?
Peppy (http://peppy.flipturn.org/) + iPython
It would be nice to have those two integrated, though
2009/6/8 Robert Kern robert.k...@gmail.com:
Remember, the example is a **teaching** example.
I know. Honestly, I would prefer that teachers skip over the normal
equations entirely and move directly to decomposition approaches. If
you are going to make them implement least-squares from more
2009/6/8 Stéfan van der Walt ste...@sun.ac.za:
2009/6/8 Robert Kern robert.k...@gmail.com:
Remember, the example is a **teaching** example.
I know. Honestly, I would prefer that teachers skip over the normal
equations entirely and move directly to decomposition approaches. If
you are going
Travis Oliphant wrote:
You might take a look at EPDLab as well. Thanks to Gael Varoquaux, It
integrates IPython into an Envisage application and has a crude
name-space browser
I was wondering when you guys would get around to making one of those.
Nice start, the iPython shell is nice,
On Mon, Jun 8, 2009 at 15:21, josef.p...@gmail.com wrote:
2009/6/8 Stéfan van der Walt ste...@sun.ac.za:
2009/6/8 Robert Kern robert.k...@gmail.com:
Remember, the example is a **teaching** example.
I know. Honestly, I would prefer that teachers skip over the normal
equations entirely and
On Mon, Jun 8, 2009 at 15:34, Christopher Barkerchris.bar...@noaa.gov wrote:
Travis Oliphant wrote:
You might take a look at EPDLab as well. Thanks to Gael Varoquaux, It
integrates IPython into an Envisage application and has a crude
name-space browser
I was wondering when you guys would
On Mon, Jun 8, 2009 at 15:34, Robert Kernrobert.k...@gmail.com wrote:
On Mon, Jun 8, 2009 at 15:34, Christopher Barkerchris.bar...@noaa.gov wrote:
Travis Oliphant wrote:
You might take a look at EPDLab as well. Thanks to Gael Varoquaux, It
integrates IPython into an Envisage application and
On 8-Jun-09, at 12:58 PM, Jonno wrote:
Thanks Josef,
I shouldn't have included Matplotlib since Pydee does work well with
its plots. I had forgotten that. It really is just the Mayavi plots
(or scenes I guess) that don't play well.
I don't know how exactly matplotlib integration issues are
On Mon, Jun 08, 2009 at 05:19:11PM -0400, David Warde-Farley wrote:
On 8-Jun-09, at 12:58 PM, Jonno wrote:
Thanks Josef,
I shouldn't have included Matplotlib since Pydee does work well with
its plots. I had forgotten that. It really is just the Mayavi plots
(or scenes I guess) that
On Mon, Jun 08, 2009 at 12:54:25PM -0500, Travis Oliphant wrote:
You might take a look at EPDLab as well. Thanks to Gael Varoquaux, It
integrates IPython into an Envisage application and has a crude name-space
browser
And it integrates with editra to have an editor where you can
Hi, folks. Unable to find a printed reference for the definition we use to
compute the functions in the Subject line of this email, I posted a couple
queries for help in this regard in the Discussion for fv
(http://docs.scipy.org/numpy/docs/numpy.lib.financial.fv/#discussion-sec).
josef
Gael Varoquaux wrote:
Click in the menu: 'new file in remote browser', or something like this.
If you have editra installed, it will launch it, with a special plugin
allowing you to execute selected code in EPDLab.
very cool, thanks!
-Chris
--
Christopher Barker, Ph.D.
Oceanographer
On Mon, Jun 08, 2009 at 01:34:39PM -0700, Christopher Barker wrote:
Travis Oliphant wrote:
You might take a look at EPDLab as well. Thanks to Gael Varoquaux, It
integrates IPython into an Envisage application and has a crude
name-space browser
I was wondering when you guys would get
Hi all,
I'm new in numpy. Actually, I'm new in Python. In order to learn a bit, I
want to create a program to plot the Mandelbrot set. This program is quite
simple, and I have already programmed it. The problem is that I come from
fortran, so I use to think in for loops. I know that it is not the
Dear SciPy Community Members:
Hi! My name is David Goldsmith. I've been hired for the summer by Joe
Harrington to further progress on NumPy documentation and ultimately, pending
funding, SciPy documentation. Joe and I are reviving last summer’s enthusiasm
in the community for this
I look forward to an instructive reply: the Pythonic way to do it would be to
take advantage of the facts that Numpy is pre-vectorized and uses
broadcasting, but so far I haven't been able to figure out (though I haven't
yet really buckled down and tried real hard) how to broadcast a
On Mon, Jun 8, 2009 at 4:47 PM, Christopher Barker chris.bar...@noaa.govwrote:
Gael Varoquaux wrote:
Click in the menu: 'new file in remote browser', or something like this.
If you have editra installed, it will launch it, with a special plugin
allowing you to execute selected code in
On Mon, Jun 8, 2009 at 17:04, David Goldsmithd_l_goldsm...@yahoo.com wrote:
I look forward to an instructive reply: the Pythonic way to do it would be
to take advantage of the facts that Numpy is pre-vectorized and uses
broadcasting, but so far I haven't been able to figure out (though I
2009/6/8 Robert Kern robert.k...@gmail.com:
On Mon, Jun 8, 2009 at 17:04, David Goldsmithd_l_goldsm...@yahoo.com wrote:
I look forward to an instructive reply: the Pythonic way to do it would be
to take advantage of the facts that Numpy is pre-vectorized and uses
broadcasting, but so far I
Thanks, Robert!
DG
--- On Mon, 6/8/09, Robert Kern robert.k...@gmail.com wrote:
I haven't been able to figure out (though I haven't yet
really buckled down and tried real hard) how to broadcast a
conditionally-terminated iteration where the number of
iterations will vary among the array
--- On Mon, 6/8/09, Anne Archibald peridot.face...@gmail.com wrote:
You can't, really. What you can do is just keep
iterating with the
whole data set and ignore the parts that have already
converged. Here
is an example:
Well, yes and no. This is only worth doing if the number of
On Mon, Jun 8, 2009 at 18:01, David Goldsmithd_l_goldsm...@yahoo.com wrote:
--- On Mon, 6/8/09, Anne Archibald peridot.face...@gmail.com wrote:
You can't, really. What you can do is just keep
iterating with the
whole data set and ignore the parts that have already
converged. Here
is an
On Mon, Jun 8, 2009 at 5:44 PM, d_l_goldsm...@yahoo.com wrote:
Hi, folks. Unable to find a printed reference for the definition we use to
compute the functions in the Subject line of this email, I posted a couple
queries for help in this regard in the Discussion for fv
On 09/06/09 00:16, Gael Varoquaux wrote:
On Mon, Jun 08, 2009 at 05:14:27PM -0500, Gökhan SEVER wrote:
IPython's edit command works in a similar fashion, too.
edit test.py
The cool thing is that you can select text in the editor and execute in
EPDLab. On the other hand, I know
Hi Juan
2009/6/8 Juanjo Gomez Navarro juanjo.gomeznava...@gmail.com:
I'm new in numpy. Actually, I'm new in Python. In order to learn a bit, I
want to create a program to plot the Mandelbrot set. This program is quite
simple, and I have already programmed it. The problem is that I come from
Hi,
Just a heads-up on something they're talking about over at CorePy.
Regards
Stéfan
-- Forwarded message --
From: Andrew Friedley afrie...@osl.iu.edu
Date: 2009/6/8
Subject: [Corepy-devel] New ExtBuffer object
To: CorePy Development corepy-de...@osl.iu.edu
I wrote a new
--- On Mon, 6/8/09, Robert Kern robert.k...@gmail.com wrote:
Goldsmithd_l_goldsm...@yahoo.com
wrote:
The advantage of my implementation is that I didn't have to
think too
hard about it.
--
Robert Kern
Agreed. :-)
DG
___
--- On Mon, 6/8/09, Skipper Seabold jsseab...@gmail.com wrote:
There was a recent discussion about numpy.financial in this
thread
http://mail.scipy.org/pipermail/numpy-discussion/2009-May/042709.html.
Skipper
Thanks, Skipper. Having now read that thread (but not the arguments, provided
On 6/8/2009 11:18 PM David Goldsmith apparently wrote:
I formally move that numpy.financial (or at least that
subset of it consisting of functions which are commonly
subject to multiple definitions) be moved out of numpy.
My recollection is that Travis O. added this with the
explicit
So would we regard a hard-copy of the users guide or reference manual for such
a spreadsheet as sufficiently permanent to pass muster for use as a reference?
DG
--- On Mon, 6/8/09, Alan G Isaac ais...@american.edu wrote:
From: Alan G Isaac ais...@american.edu
Subject: Re: [Numpy-discussion]
On Tue, Jun 9, 2009 at 12:18 AM, Robert Kernrobert.k...@gmail.com wrote:
On Mon, Jun 8, 2009 at 22:54, David Goldsmithd_l_goldsm...@yahoo.com wrote:
So would we regard a hard-copy of the users guide or reference manual for
such a spreadsheet as sufficiently permanent to pass muster for use as
--- On Mon, 6/8/09, Skipper Seabold jsseab...@gmail.com wrote:
I forgot the last payment (which doesn't earn any
interest), so one more 100.
So in fact they're not in agreement?
pretty soon. I don't have a more permanent reference
for fv offhand,
but it should be in any corporate finance
On Tue, Jun 09, 2009 at 01:10:24PM +1200, Jochen Schroeder wrote:
On 09/06/09 00:16, Gael Varoquaux wrote:
On Mon, Jun 08, 2009 at 05:14:27PM -0500, Gökhan SEVER wrote:
IPython's edit command works in a similar fashion, too.
edit test.py
The cool thing is that you can select
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