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License: MIT License
Automatically exported from code.google.com/p/pmtk3
License: MIT License
Probabilistic modeling toolkit version 3 See pmtk3.googlecode.com for details. Steps: 1. run initPmtk3.m (takes a few minutes) 2. run testPmtk3.m (takes under a minute) 3. run runDemos.m (takes about 1 hour) The code relies on various external toolboxes (in addition to those in pmtksupport), listed below: opt : Mathworks optimization toolbox stats : Mathworks statistics toolbox image : Mathworks image processing toolbox bio : Mathworks bioinformatics toolbox gviz: graphviz libdai: libdai glmnet: glmnet (Fortran library not available for maci64) libsvm: libsvm (Matlab inferface) UGM: Mark Schmidt's UGM package If some of these packages are missing and/or not compiled for your computer, some demos may be skipped.
What steps will reproduce the problem?
a=[1,2,3,4,5,6,1,2,3,4,5,6,6,5,4,3,2,1,1,2,3,31,31,2,32,12,4,5,60,0,2,1,3,4,5,81,32,2,1];
[model, loglikHist] = hmmFit(a, 2, 'discrete');
(This example is due to George Toderici)
What is the expected output? What do you see instead?
The penalizd log likelihood should go up, but instead it gives a warning that
it does not.
Please use labels and text to provide additional information.
The problem is that the data involves a non consecutive set of integers,
spanning 0 to 81. Internally this gets canonized to 1..12. However,there is
still some residual problem. Perhaps the log prior on the transmat is not being
added to the objective function.
Original issue reported on code.google.com by murphyk2
on 3 Apr 2011 at 2:12
What steps will reproduce the problem?
x=randn(100,20); y=randn(100,1); fit=glmnet(x,y);
What is the expected output? What do you see instead?
it shoudl return a struct. Instead it returns
> x=randn(100,20); y=randn(100,1); fit=glmnet(x,y);
??? Invalid MEX-file
'/Users/kpmurphy/pmtksupport/glmnet-matlab/glmnetMex.mexmaci64':
dlopen(/Users/kpmurphy/pmtksupport/glmnet-matlab/glmnetMex.mexmaci64, 1):
Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Users/kpmurphy/pmtksupport/glmnet-matlab/glmnetMex.mexmaci64
Reason: image not found.
Error in ==> glmnet at 254
[a0,ca,ia,nin,rsq,alm,nlp,jerr] = glmnetMex(parm,x,y,jd,vp,ne,nx,nlam,flmin,ulam,thresh,isd,weights,ka);
254 [a0,ca,ia,nin,rsq,alm,nlp,jerr] =
glmnetMex(parm,x,y,jd,vp,ne,nx,nlam,flmin,ulam,thresh,isd,weights,ka);
Please use labels and text to provide additional information.
it cannot find this fortran library:
/usr/local/lib/libgfortran.2.dylib
Original issue reported on code.google.com by murphyk2
on 28 Feb 2011 at 7:51
What steps will reproduce the problem?
1.x=[1 2 1 1 2; ...
2 2 2 2 1; ...
1 1 1 1 2 ]
2.model=markovFit(x);
What is the expected output? What do you see instead?
>> model.A
ans =
0.5714 0.4286
0.4000 0.6000
>> model.pi
ans =
0.6667 0.3333
===========================but we have
??? Error using ==> plus
Matrix dimensions must agree.
Error in ==> markovFit at 27
model.pi = rowvec(normalize(histc(X(:, 1), 1:nstates)) + rowvec(pseudoCountsPi
- 1));
What version / revision of the product are you using? On what operating
system?
PMTK (r2774), Matlab
Please provide any additional information below.
I think the simplest way is to change
model.pi = rowvec(normalize(histc(X(:, 1), 1:nstates)) + rowvec(pseudoCountsPi
- 1));
to
model.pi = rowvec(normalize(histc(X(:, 1)', 1:nstates)) + rowvec(pseudoCountsPi
- 1));
Original issue reported on code.google.com by RA.Dragun
on 19 Apr 2011 at 11:54
What steps will reproduce the problem?
1. Define a mrf using mrfCreate. I used a simple 5x5 grid graph and define
parameters nodePots and edgePots.
What is the expected output? What do you see instead?
I get an error saying
??? In an assignment A(I) = B, the number of elements in B and
I must be the same.
Error in ==> tabularFactorMultiply at 33
ns(Ti.domain) = Ti.sizes;
The error seems to be in tabularFactorMultiply.m
What version / revision of the product are you using? On what operating system?
Latest april 2 version on Matlab 7.4 on Windows 7.
Original issue reported on code.google.com by [email protected]
on 14 Apr 2011 at 4:51
What steps will reproduce the problem?
Edit dgmLogprobTest line 92 uncomment this line:
%assert(approxeq(logZ7, logZ1, tol));
Then run dgmLogproTest.
What is the expected output? What do you see instead?
When trial=2, so all nodes are clamped, the logprob can be computed
by multiplying all the CPDs together, since the model is fully visible.
This should give the same result as the normalization constant for
inference. However, the assertion is violated.
Please use labels and text to provide additional information.
Bayes net probability of the evidence computation is failing.
Pretty fundamental... (seems to work if libdai on path - not sure
what the connection is, the libdai should not need to be called
if the model is fully visible)
Original issue reported on code.google.com by murphyk2
on 28 Feb 2011 at 7:55
What steps will reproduce the problem?
1. Download the current version (pmtk3-23nov10.zip)
2. run initPmtk3
3. run testPmtk3
What is the expected output? What do you see instead?
Just downloaded pmtk3-23nov10.zip, and testPmtk3 produces:
parse error near line 53 of file
/home/jpate/git/prosodicParsing/pmt3k/pmtk3-23nov10/toolbox/SupervisedModels/log
reg/logregFit.m
syntax error
>>> [ weights ....
Changing the "...." to "..." fixes the error.
What version / revision of the product are you using? On what operating
system?
$ uname -a
Linux PURPLE-HAZE 2.6.36-ARCH #1 SMP PREEMPT Sat Jan 8 14:15:27 CET 2011 x86_64
Celeron(R) Dual-Core CPU T3000 @ 1.80GHz GenuineIntel GNU/Linux
$ octave -v
GNU Octave, version 3.2.4
Copyright (C) 2009 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.
Octave was configured for "x86_64-unknown-linux-gnu".
Additional information about Octave is available at http://www.octave.org.
Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html
Report bugs to <[email protected]> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).
Please provide any additional information below.
Although I'm using octave, this just seems to be a typo with an extra "."
(especially considering the output of svn diff -r2598
toolbox/SupervisedModels/logreg/logregFit.m)
Original issue reported on code.google.com by [email protected]
on 17 Jan 2011 at 12:01
What steps will reproduce the problem?
1. run hmmNbestDemo.m
2. Undefined function or variable "xi_summed".
Error in hmmFwdBackMaxProduct (line 39)
xi_summed = xi_summed + tmpXi./sum(tmpXi(:)); % inlined call to
normalize
Error in hmmNbestDemo (line 17)
[ff, logmaxprob] = hmmFwdBackMaxProduct(initDist, transmat, softev);
3.
What is the expected output? What do you see instead?
no error, xi_summed seems to be uninitiated, ff is not assigned in
hmmFwdBackMaxProduct.m
What version / revision of the product are you using? On what operating
system? pmtk3 2011dec15, windows 7, matlab 2012a
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 10 Jun 2012 at 7:10
What steps will reproduce the problem?
1. Download and install with initPmtk3
2. Evaluate [a b] = hmmFit({randn(1,50)}, 4, 'gauss')
What is the expected output? What do you see instead?
Expect no output. Instead, error obtained:
??? Invalid MEX-file
'C:\Users\fasiha\Documents\MATLAB\pmtk3-read-only\toolbox\LatentVariableModels\h
mm\sub\hmmFwdBack.mexw64':
Access is denied.
Error in ==> hmmFitEm>estep at 68
[gamma, alpha, beta, logp] = hmmFwdBack(pi, A, Bi);
Error in ==> emAlgo at 62
[ess, ll] = estep(model, data);
Error in ==> hmmFitEm at 46
[model, loglikHist] = emAlgo(model, data, initFn, @estep, @mstep, EMargs{:});
Error in ==> hmmFit at 69
[model, loglikHist] = hmmFitEm(data, nstates, type, varargin{:});
What version / revision of the product are you using? On what operating system?
SVN checkout r2778, Windows7, Matlab 2011a.
Please provide any additional information below.
I had Cygwin available, so in the directory
"pmtk3-read-only/toolbox/LatentVariableModels/hmm/sub", I ran "chmod 755
*.mex*" to add the execute bit on all mex files. This fixes the problem.
I am not sure how to do this without Cygwin, or if it affects anyone else on
Windows using a current checked out.
Original issue reported on code.google.com by wuzzyview
on 10 Oct 2011 at 2:37
What steps will reproduce the problem?
1. run hmmDiscreteTest.m
What is the expected output? What do you see instead?
syntax error [~,z] = max(pz,[],2)
What version / revision of the product are you using? On what operating
system?
pmtk3
Octave 3.2.4
Windows7
Original issue reported on code.google.com by [email protected]
on 24 Apr 2011 at 12:41
What steps will reproduce the problem?
1.initPmtk3
What is the expected output? What do you see instead?
-pmtkSupportRoot.m failed to download
What version / revision of the product are you using? On what operating
system?
-pmtk3-2april2011 , Windows7 64 bits, Matlab 7.11.0 (R2001b)
Please provide any additional information below.
downloading 39 packages to pmtk3/pmtksupportCopy from
pmtksupport.googlecode.com - this may take a few minutes
downloading GGM-GWishart.............done
downloading GPstuff-2.0..............done
downloading SPAMS-1.02...............done
downloading boostingDemo.............done
downloading bpca.....................done
downloading dpMixWood................done
downloading dpmixturesTeh07..........done
downloading ekfukf1.2................done
downloading export_fig...............done
downloading exportfig................done
downloading fastICA-2.5..............done
downloading fastfit..................done
downloading gaimc1.0-graphAlgo.......done
downloading glmnet-matlab............done
downloading gpml-matlab..............done
downloading graphViz4Matlab..........done
downloading l1ls.....................done
downloading lars.....................done
downloading libdai-0.2.6.............done
downloading liblinear-1.51...........done
downloading libsvm-mat-2.9.1.........done
downloading lightspeed2.3............done
downloading markSchmidt-9march2011...done
downloading matbugs..................done
downloading matlabRlink..............done
downloading maxBranching.............done
downloading mcmcdiag.................done
downloading mplp-1.0.................done
downloading netlab3.3................done
downloading onlineEM.................done
downloading pfColorTracker...........done
downloading pmtkSupportRoot.m........failed to download
downloading randraw..................done
downloading rbpfSlam.................done
downloading readme.txt...............failed to download
downloading rjmcmcRbf................done
downloading sparseBayes2.0...........done
downloading svmLightWindows..........done
downloading vblinlogreg..............done
Original issue reported on code.google.com by [email protected]
on 24 Sep 2011 at 2:48
What steps will reproduce the problem?
1. train separate models using positive discrete samples from different classes
2. cross-test for the highest likelihood using hmmLogprob
What is the expected output? What do you see instead?
hmmLogprob sometimes crashes when a model is tested on data that do not belong
to the same class
What version / revision of the product are you using? On what operating system?
pmtk3 nov 2010
Please provide any additional information below.
The problem is that the discretized positive samples in the training set might
not include all the possible observations for a class, but hmmFit estimates the
number of observations from the positive samples. So, if there are 8
observation symbols, but a class makes use of only the first 6, the trained
model also has 6 observation states, and cannot evaluate samples belonging to
other classes, a crucial step for classification.
Solution:
There should be an option to set the number of observations directly.
Original issue reported on code.google.com by [email protected]
on 16 Jan 2011 at 9:00
What steps will reproduce the problem?
1. pmtk3-3jan[[11]].zip
What is the expected output? What do you see instead?
It is 2012 now.
What version / revision of the product are you using? On what operating
system?
n/a
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 5 Jan 2012 at 2:31
dgmFit is supposed to handle missing local evidence, but currently crashes if
you pass it a ragged array.
Original issue reported on code.google.com by [email protected]
on 11 Aug 2010 at 1:55
What steps will reproduce the problem?
1. Set len to 101 in hmmDiscreteFitTest
2. Run the demo
From Nachi Sahoo:
hmmFitEM.m, line 207-209: it is relying on a hard clustering
assignment to initialize transition probability matrix. Sometimes the
initial clustering gets a fewer number of clusters than the number of
states in hmm. So, the transition probability matrix formed on line
209 is smaller than it should be. One way to fix it is to change line
209 from
A = accumarray([z(1:end-1), z(2:end)], 1);
to
A = accumarray([z(1:end-1), z(2:end)], 1, [nstates,
nstates]);
Since, we'd know the number of states at this point. It ensures that
we'd have the correct sized transition matrix.
Original issue reported on code.google.com by [email protected]
on 8 Aug 2010 at 4:08
What steps will reproduce the problem?
trainingData = data(:,4);
nHidStates = 4;
% Learn the model using EM with random restarts
nrestarts = 2;
modelEM = hmmFit(trainingData, nHidStates, 'discrete', ...
'convTol', 1e-5, 'nRandomRestarts', nrestarts, 'verbose', false);
What is the expected output? What do you see instead?
It should create an hmm model. Instead it returns the error:
??? Undefined function or method 'logsumexp' for input arguments of type
'double'.
Error in ==> normalizeLogspace at 12
L = logsumexp(x, 2);
What version / revision of the product are you using? On what operating system?
Matlab version R2010b on Windows XP running pmtk3.
Please provide any additional information below.
PMTK installation failed -- was unable to download during the installation
process -- proxy should have worked.
Original issue reported on code.google.com by [email protected]
on 19 Jul 2011 at 8:37
In revision 33 of pmtk3, util/setSeed.m and util/restoreSeed.m were
removed. However, these functions are still used by util/Kfold.m
Original issue reported on code.google.com by byronknoll
on 17 Jan 2010 at 9:24
What steps will reproduce the problem?
1. x = some_test_data
2. mixModel = mixGaussFit(x, 2, 'verbose', true, 'maxIter',
100,'nrandomRestarts',100);
What is the expected output? What do you see instead?
********** Random Restart 2 **********
initializing model for EM
??? Undefined function or variable 'd'.
Error in ==> mixGaussFit>initGauss at 41
mu = randn(d, nmix);
Error in ==> mixGaussFit>@(m,X,r)initGauss(m,X,r,initParams,prior) at 24
initFn = @(m, X, r)initGauss(m, X, r, initParams, prior);
Error in ==> emAlgo at 56
model = init(model, data, restartNum);
Error in ==> emAlgo at 38
[models{i}, llhists{i}] = emAlgo(model, data, init, estep,...
Error in ==> mixGaussFit at 25
[model, loglikHist] = emAlgo(model, data, initFn, @estep, @mstep , ...
What version / revision of the product are you using? On what operating
system?
PMTK (r2774)/Windows (Matlab)
Please provide any additional information below.
Failure in
function model = initGauss(model, X, restartNum, initParams, prior)
when restartNum ~= 1
mu = randn(d, nmix);
regularizer = 2;
Sigma = stackedRandpd(d, nmix, regularizer);
model.mixWeight = normalize(rand(1, nmix) + regularizer);
We need to define d from model or from data.
Original issue reported on code.google.com by RA.Dragun
on 20 Apr 2011 at 12:35
What steps will reproduce the problem?
1.initial installation of pmtk in matlab
2.
3.
What is the expected output? What do you see instead?
i get this error:
>> initPmtk3
initializing pmtk3
downloading 38 packages to pmtk3/pmtksupportCopy from
pmtksupport.googlecode.com - this may take a few minutes
downloading GGM-GWishart.............Error using perl (line 80)
System error: Can't locate LWP/Simple.pm in @INC (@INC contains: /etc/perl
/usr/local/lib/perl/5.14.2
/usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14
/usr/share/perl/5.14
/usr/local/lib/site_perl .) at
/home/pajrul/pmtk3-3jan11/pmtkTools/supportTools/fetchfile.pl line 4.
BEGIN failed--compilation aborted at
/home/pajrul/pmtk3-3jan11/pmtkTools/supportTools/fetchfile.pl line
4.
Command executed: perl
/home/pajrul/pmtk3-3jan11/pmtkTools/supportTools/fetchfile.pl "
http://pmtksupport.googlecode.com/svn/trunk/GGM-GWishart/GGM-GWishart.zip"
/home/pajrul/pmtk3-3jan11/pmtksupportCopy/GGM-GWishart.zip
Error in downloadFile (line 13)
status = perl(fetcher, source, dest);
Error in downloadAllSupport (line 21)
ok = downloadFile(source, dest);
Error in initPmtk3 (line 49)
downloadAllSupport();
What version / revision of the product are you using? On what operating
system?
on matlab r2011b running on ubuntu 12.04
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 21 May 2012 at 3:55
>> loadData('data45')
downloading http://pmtkdata.googlecode.com/svn/trunk/data45/data45.zip to
F:\matlab_scripts\toolboxes\pmtk3-2april2011\pmtkdataCopy\data45.zip
??? Error using ==> loadData at 79
Cannot find
http://pmtkdata.googlecode.com/svn/trunk/data45/data45.zip
Original issue reported on code.google.com by [email protected]
on 15 Dec 2011 at 1:18
What steps will reproduce the problem?
Simply try to use conversation matrix NSTATESxNSTATES and a vector as pi0 that is <> NSTATES (not 1xNSTATES). This results in an error in hmmFwdBack.*: Can't multiply pi0 * A by MATLAB.
Happened to me using isolatedWordClassificationWithHmmsDemo and changing nstates. Because pi0 is a fixed vector it wasn't and thus leads to the error.
What is the expected output? What do you see instead?
hmmFit should assert(pi0 * A) is possible and else report correct size needed.
What version / revision of the product are you using? On what operating
system?
pmtk3: 24 October and MATLAB 2009a
Original issue reported on code.google.com by [email protected]
on 3 Nov 2010 at 3:18
What steps will reproduce the problem?
1. Run the initialization
What is the expected output? What do you see instead?
Process: MATLAB [16789]
Path:
/Applications/MATLAB_R2012a_Student.app/Contents/MacOS/StartMATLAB
Identifier: com.mathworks.matlab
Version: R2012a [7.14.0] (7.14.0)
Code Type: X86-64 (Native)
Parent Process: launchd [394]
User ID: 501
Date/Time: 2012-10-22 02:59:08.805 +0100
OS Version: Mac OS X 10.8.2 (12C60)
Report Version: 10
Interval Since Last Report: 342359 sec
Crashes Since Last Report: 66
Per-App Interval Since Last Report: 74655 sec
Per-App Crashes Since Last Report: 30
Anonymous UUID: 4A31AB5A-7A61-775E-2132-0CD351D2D0EC
Crashed Thread: 3
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Dyld Error Message:
Symbol not found: __gfortran_allocate64_array
Referenced from: /Users/USER/*/glmnetMex.mexmaci64
Expected in: /Applications/MATLAB_R2012a_Student.app/sys/os/maci64/libgfortran.3.dylib
What version / revision of the product are you using? On what operating
system?
Matlab Student Version R2012a 64-bit (maci64) on Mac OS 10.8.2 (Mountain Lion)
Please provide any additional information below.
The problem appears at the last step of the initialization "Compile mex", after
pfColorTracker.
Original issue reported on code.google.com by [email protected]
on 22 Oct 2012 at 2:44
What steps will reproduce the problem?
1.Some functionality that uses function
path = viterbi_path(prior, transmat, obslik)
What is the expected output? What do you see instead?
What version / revision of the product are you using? On what operating
system?
pmtk r2776
Please provide any additional information below.
Replace normalise function with normalize one on lines: 53, 64
http://code.google.com/p/pmtk3/source/browse/trunk/toolbox/LatentVariableModels/
hmm/sub/viterbi_path.m#53
Original issue reported on code.google.com by RA.Dragun
on 28 Aug 2011 at 7:56
What steps will reproduce the problem?
1. > initPmtk3Octave
2. > plotMFCC
What is the expected output? What do you see instead?
The specgram function does not run and no plot is produced. I expected
'signalToolboxInstalled' to be true, but it is not.
What version / revision of the product are you using? On what operating system?
I'm using a copy off trunk at http://pmtk3.googlecode.com/svn/trunk with Octave
3.2.3 on Ubuntu 10.04.3 LTS.
Please provide any additional information below.
I investigated and found that the initPmtkOctave function unilaterally sets
*ToolboxInstalled variables to 0. Inspecting the normal init function, I
learned how I *thought* things should work and made modifications such that it
did. My patch for this assumes that if the folder named in 'toolbox' exists in
the path, then the toolbox must be installed. This may or may not be the
appropriate way to detect this in Octave. If it is not, I'd be happy to
improve the patch by making it more robust.
I also had make another change in order to get this to work correctly. It
seems restoredefaultpath() does not do what I expected, in that the signal
processing toolbox is omitted from the path after this function is called. But
upon further reading, it appears the correct behavior is to set the path to its
value /prior to any octaverc processing/
(http://octave.1599824.n4.nabble.com/octaverc-and-version-in-path-td1648598i20.h
tml). So, given the fact that the toolkit paths are added in
/etc/octave3.2.conf, I'm proposing restoredefaultpath() be removed. Would this
cause problems elsewhere? If so, perhaps there is a way to trigger the path
changes that come from the system-wide initialization file (and perhaps the
user initialization files as well), so that restoredefaultpath() can still be
used, but the add-on paths are included as well.
Original issue reported on code.google.com by [email protected]
on 10 Aug 2011 at 6:18
Attachments:
What steps will reproduce the problem?
1. have matlabroot not contain MATLAB: in all caps
2. run initPmtk3
3.
What is the expected output? What do you see instead?
Instead of a successful initialization, the output is
>> initPmtk3
initializing pmtk3
??? Error using ==> catdirs at 24
All arguments must be strings.
Error in ==> addpath at 64
p = catdirs(varargin{1:n});
Error in ==> initPmtk3 at 12
addpath(genpathPMTK(fullfile(thisDir, 'localUtil')));
What version / revision of the product are you using? On what operating
system?
Revision: 2135
Please provide any additional information below.
For the time being case insensitive search might work for most people. i.e.,
change line 13 in genpathPMTK.m from
if isempty(strfind(matlabroot, 'MATLAB'))
to
if isempty(strfind(upper(matlabroot), 'MATLAB'))
Original issue reported on code.google.com by [email protected]
on 16 Aug 2010 at 1:23
What steps will reproduce the problem?
1. Fully defined a HMM (hmmCreate)
2. Sampled training and test data (hmmSample)
3. Trained a HMM (hmmFit)
4. Tested HMM (hmmLogprob)
-> Got a log likelihood greater than zero.
Things that look weird:
The state-transition matrix A of the trained model is not normalized:
normalize(model.A)-model.A should be zero(..).
Could also be a numerical over-/underflow issue: I am using relative long
sequencces.
Or my sampling HMM could be crap:
%d=1
nstates = 7;
pi = [1 0 0 0 0 0 0];
A = normalize(diag(ones(nstates, 1)) + ...
diag(ones(nstates-1, 1), 1), 2);
sigma = [[0.05],[0.05],[0.05],[0.05],[0.05],[0.05],[0.05]];
mu = [0.7, 1.4, 2.1, 2.8, 3.5, 4.2, 4.9];
emission = condGaussCpdCreate(mu, sigma);
modelValid = hmmCreate('gauss', pi, A, emission);
What is the expected output? What do you see instead?
The log of a probality can't be greater than zero.
What version / revision of the product are you using? On what operating
system?
MATLAB 2009a
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 15 Nov 2010 at 9:46
Attachments:
What steps will reproduce the problem?
1. Follow the installation instruction:
http://code.google.com/p/pmtk3/wiki/installation
2. Macintosh; matlab 7.9.0.529 (R2009b)
3. testPmtk3 crashes.
What is the expected output? What do you see instead?
I expected the demos to run. Instead I get:
??? Undefined function or variable 'p'.
Error in ==> LogisticLossSimple at 16
Xw = X .* repmat(rowvec(weights), 1, p);
Sure enough, LogisticLossSimple refers to an undefined variable 'p'.
What version / revision of the product are you using? On what operating
system?
pmtk3-24October2010.zip
MacOS 10.6.5
Please provide any additional information below.
Here's the command history in matlab:
>> initPmtk3
initializing pmtk3
downloading GGM-GWishart.............done
downloading SPAMS-1.02...............failed
downloading bpca.....................done
downloading dpmixturesTeh07..........done
downloading ekfukf1.2................done
downloading export_fig...............done
downloading exportfig................done
downloading fastICA-2.5..............done
downloading fastfit..................done
downloading gaimc1.0-graphAlgo.......done
downloading glmnet-matlab............done
downloading gpml-matlab..............done
downloading graphViz4Matlab..........done
downloading l1ls.....................done
downloading lars.....................done
downloading libdai-0.2.6.............done
downloading liblinear-1.51...........done
downloading libsvm-mat-2.9.1.........done
downloading lightspeed2.3............done
downloading markSchmidt-21june2010...done
downloading matbugs..................done
downloading matlabRlink..............done
downloading mcmcdiag.................failed
downloading mplp-1.0.................done
downloading netlab3.3................done
downloading onlineEM.................done
downloading randraw..................done
downloading sparseBayes2.0...........done
downloading svmLightWindows..........done
downloading vblinlogreg..............done
welcome to pmtk3
>> testPmtk3
Checking for matlabTools.........PASSED
Checking initialization..........PASSED
Checking pmtkSupport packages....PASSED
Checking pmtkData................downloading
http://pmtkdata.googlecode.com/svn/trunk/crabs/crabs.zip to
/Users/don/Documents/MATLAB/MurphySimulator/pmtk3/data/crabs.zip
unzipped and loaded crabs.mat
PASSED
Checking for graphviz............Please install or upgrade graphViz
Please install or upgrade graphViz
Please install or upgrade graphViz
Please install or upgrade graphViz
Please install or upgrade graphViz
FAILED
Testing selected code............
nll =
6.9315
??? Undefined function or variable 'p'.
Error in ==> LogisticLossSimple at 16
Xw = X .* repmat(rowvec(weights), 1, p);
Error in ==> logregFit>@(w)LogisticLossSimple(w,X,y,weights) at 101
loss = @(w) LogisticLossSimple(w, X, y, weights);
Error in ==> penalizedL2 at 13
[nll,g] = gradFunc(w,varargin{:});
Error in ==> logregFit>@(w)penalizedL2(w,loss,lambdaVec(:)) at 133
penloss = @(w)penalizedL2(w, loss, lambdaVec(:));
Error in ==> minFunc at 303
[f,g] = funObj(x,varargin{:});
Error in ==> logregFit at 135
[w, opt.finalObj, opt.exitflag, opt.output] = ...
Error in ==> logregL2FitTest at 19
model1 = logregFit(X, y01, 'lambda', lambda, 'preproc', pp, 'fitOptions', opts);
Error in ==> testPmtk3 at 66
logregL2FitTest;
Original issue reported on code.google.com by [email protected]
on 23 Nov 2010 at 7:44
What steps will reproduce the problem?
1.modelEM = hmmFit(observed, nstates, 'discrete', ...
'maxIter', 1000, 'verbose', true, 'convTol', 1e-7, 'nRandomRestarts', 3);
2.
3.
What is the expected output? What do you see instead?
??? Error using ==> normalize
Too many input arguments.
Error in ==> discreteFit at 32
model.T = normalize(bsxfun(@plus, counts, colvec(alpha-1)), 1);
What version / revision of the product are you using? On what operating
system?
pmtk3-3jan11. Windows 7. Matlab R2010a
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 23 May 2012 at 12:05
What steps will reproduce the problem?
1.
2.
3.
What is the expected output? What do you see instead?
Attempted to access obsmat(:,3116); index out
of bounds because size(obsmat)=[2560,2560].
Error in ==> multinomial_prob at 19
B(:,t) = obsmat(:, data(t));
Error in ==> dhmm_em>compute_ess_dhmm at 103
obslik = multinomial_prob(obs, obsmat);
Error in ==> dhmm_em at 47
[loglik, exp_num_trans, exp_num_visits1,
exp_num_emit] = ...
Error in ==> Markov_Model at 72
[LL,prior_hat,A_hat,B_hat] = dhmm_em(signal+1,
prior,A1,B1, 'max_iter',4);
What version / revision of the product are you using? On what operating
system? Matlab R2011a, Windows 7
Please provide any additional information below.
I checked the multinomial_prob function from which the error seems to have been
generated and found
for t=1:T
B(:,t) = obsmat(:, data(t));
end
This doesn't make sense to me. Why does the observed value of my data have to
be less than the dimensions of my output matrix? (Thats the root of the problem
as far as I understand)
Original issue reported on code.google.com by [email protected]
on 31 May 2012 at 6:56
I had trouble downloading data, and got errors with isOctave after running
initPmtk3.m. The solution is to create the folders:
pmtk3-1nov12/pmtkTools/systemInfo
pmtk3-1nov12/pmtkdataCopy
pmtk3-1nov12/pmtkdataSmall
and then run initPmtk3
Original issue reported on code.google.com by [email protected]
on 6 Dec 2012 at 2:04
What steps will reproduce the problem?
1.>> cd C:\pmtk3
>> initPmtk3
What is the expected output? What do you see instead?
>> initPmtk3
initializing pmtk3
downloading 38 packages to pmtk3/pmtksupportCopy from
pmtksupport.googlecode.com - this may take a few minutes
downloading GGM-GWishart.............failed to download
downloading GPstuff-2.0..............failed to download
downloading SPAMS-1.02...............failed to download
downloading Sparsa...................failed to download
downloading boostingDemo.............failed to download
downloading bpca.....................failed to download
downloading dpMixWood................failed to download
downloading dpmixturesTeh07..........failed to download
downloading ekfukf1.2................failed to download
downloading export_fig...............failed to download
downloading exportfig................failed to download
downloading fastICA-2.5..............failed to download
downloading fastfit..................failed to download
downloading gaimc1.0-graphAlgo.......failed to download
downloading glmnet-matlab............failed to download
downloading gpml-matlab..............failed to download
downloading graphViz4Matlab..........failed to download
downloading l1ls.....................failed to download
downloading lars.....................failed to download
downloading libdai-0.2.6.............failed to download
downloading liblinear-1.51...........failed to download
downloading libsvm-mat-2.9.1.........failed to download
downloading lightspeed2.3............failed to download
downloading markSchmidt-9march2011...failed to download
downloading matbugs..................failed to download
downloading matlabRlink..............failed to download
downloading maxBranching.............failed to download
downloading mcmcdiag.................failed to download
downloading mplp-1.0.................failed to download
downloading netlab3.3................failed to download
downloading onlineEM.................failed to download
downloading pfColorTracker...........failed to download
downloading randraw..................failed to download
downloading rbpfSlam.................failed to download
downloading rjmcmcRbf................failed to download
downloading sparseBayes2.0...........failed to download
downloading svmLightWindows..........failed to download
downloading vblinlogreg..............failed to download
??? Error using ==> writeText at 31
could not open C:\pmtk3\pmtksupportCopy\pmtkSupportRoot.m
Error in ==> downloadAllSupport at 47
writeText(rootText, fullfile(destnRoot, 'pmtkSupportRoot.m'));
Error in ==> initPmtk3 at 49
downloadAllSupport();
>>
What version / revision of the product are you using? On what operating
system?
Matlab 7.9.0(R2009b)
Windows Vista
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 14 Sep 2012 at 7:48
What steps will reproduce the problem?
1. Follow the tutorial on:
http://pmtk3.googlecode.com/svn/trunk/docs/tutorial/html/tutFoundations.html
2. From this line on I get different outputs to the ones shown in the tutorial:
m2 = gaussFit(X(1:50,:)); cond(m2.Sigma)
3. Later, this crashes: L = gaussLogprob(m3, X);
Saying: ??? Error using ==> chol
Matrix must be positive definite.
What is the expected output? What do you see instead?
An output for L is expected. I get an error.
What version / revision of the product are you using? On what operating
system?
R2011a (64bit) on Windows 7 64bit system
Please provide any additional information below.
Looking inside the gaussLogprob function, it says:
% Full covariance case
if 0
logp2 = -0.5*sum((X/Sigma).*X, 2);
logZ2 = (d/2)*log(2*pi) + 0.5*logdet(Sigma);
logp2 = logp2 - logZ2;
end
% slightly faster version
R = chol(Sigma);
logp = -0.5*sum((X/R).^2, 2);
logZ = 0.5*d*log(2*pi) + sum(log(diag(R)));
logp = logp - logZ;
Maybe the 'if 0' should be replaced by a test for positive definiteness.
Original issue reported on code.google.com by [email protected]
on 5 Jul 2011 at 1:12
What steps will reproduce the problem?
1. > initPmtk3Octave
2. > isolatedWordClassificationWithHmmsDemo
3. /several errors occur/
What is the expected output? What do you see instead?
Output should match that shown in the tutorial. Three separate errors -- two
apparently related to Octave/Matlab compatibility issues and one typo --
prevent the demo from running to completion.
What version / revision of the product are you using? On what operating system?
I'm using a copy off trunk at http://pmtk3.googlecode.com/svn/trunk with Octave
3.2.3 on Ubuntu 10.04.3 LTS.
Please provide any additional information below.
The errors are:
* toolbox/LatentVariableModels/hmm/sub/hmmFitEm.m: Replace tilde (~)
used to ignore output parameter.
* toolbox/Algorithms/optimization/emAlgo.m: Delete extra '.' causing
syntax error.
* demos/isolatedWordClassificationWithHmmsDemo.m: Replaced call to
display() with disp().
The first fix is a known issue:
http://code.google.com/p/pmtk3/issues/detail?id=26
The third fix may not be the right thing to do. Octave /has/ a display()
function, and I can't imagine why it can't handle basic types. I can
demonstrate the error by entering
octave:3> d=3.14
d = 3.1400
octave:4> display(d)
error: display: not defined for class "double"
error: called from:
error: /usr/share/octave/3.2.3/m/general/display.m at line 36, column 3
Original issue reported on code.google.com by [email protected]
on 10 Aug 2011 at 6:19
Attachments:
Dear Sir / Madam,
I am using the matbugs interface you developed to run WinBugs from MatLab.
However, in the last days, it start not to work as it appears the following
image (in WinBugs) when i run it from MATLAB. I suppose the question is the way
both softwares are communicating but don’t know, exactly, where the erro ris.
Could you help me on that? I install WinBUGS in folder ‘C:/JCM/WinBugs14’,
then i run the matbugs.m, by running the schools example and the WinBugs
feedback is the one in atachment (MATLAB2009b and WINDOWS7).
Sincere regards,
Jose Matos
Original issue reported on code.google.com by [email protected]
on 17 Nov 2010 at 12:19
Attachments:
What steps will reproduce the problem?
1. dgmLogprobTest - the final assertion (commented out) fails
What is the expected output? What do you see instead?
Please use labels and text to provide additional information.
I changed dgmInferNodes and insertClampedBels to handle
the case that single marginals are not returned as cell arrays.
It's something to do with this.
Original issue reported on code.google.com by murphyk2
on 2 Apr 2011 at 10:38
What steps will reproduce the problem?
1.>> system('svn checkout http://pmtk3.googlecode.com/svn/trunk/ pmtk3')
Checked out revision 2659.
ans =
0
2.>> downloadAllSupport
downloading GGM-GWishart.............done
downloading SPAMS-1.02...............failed
downloading bpca.....................done
downloading dpmixturesTeh07..........done
downloading ekfukf1.2................done
downloading export_fig...............done
downloading exportfig................done
downloading fastICA-2.5..............done
downloading fastfit..................done
downloading gaimc1.0-graphAlgo.......done
downloading glmnet-matlab............done
downloading gpml-matlab..............done
downloading graphViz4Matlab..........done
downloading l1ls.....................done
downloading lars.....................done
downloading libdai-0.2.6.............done
downloading liblinear-1.51...........done
downloading libsvm-mat-2.9.1.........done
downloading lightspeed2.3............done
downloading markSchmidt-21june2010...done
downloading matbugs..................done
downloading matlabRlink..............done
downloading mcmcdiag.................failed
downloading mplp-1.0.................done
downloading netlab3.3................done
downloading onlineEM.................done
downloading randraw..................done
downloading sparseBayes2.0...........done
downloading svmLightWindows..........done
downloading vblinlogreg..............done
What is the expected output? What do you see instead?
downloading SPAMS-1.02...............failed
downloading mcmcdiag.................failed
What version / revision of the product are you using? On what operating
system?
revision 2659
Please provide any additional information below.
I think there are no ZIPped files on the paths
http://pmtksupport.googlecode.com/svn/trunk/SPAMS-1.02/
and
http://pmtksupport.googlecode.com/svn/trunk/mcmcdiag/
Thanks
Original issue reported on code.google.com by RA.Dragun
on 26 Nov 2010 at 7:33
What steps will reproduce the problem?
Run the initialization
What is the expected output? What do you see instead?
Matlab crashes gives this error message:
Process: MATLAB [3801]
Path: /Applications/MATLAB_R2012a.app/Contents/MacOS/StartMATLAB
Identifier: com.mathworks.matlab
Version: R2012a [7.14.0] (7.14.0)
Code Type: X86-64 (Native)
Parent Process: launchd [134]
Date/Time: 2012-09-16 00:31:51.371 -0400
OS Version: Mac OS X 10.7.4 (11E53)
Report Version: 9
Interval Since Last Report: 79014 sec
Crashes Since Last Report: 4
Per-App Interval Since Last Report: 575374 sec
Per-App Crashes Since Last Report: 4
Anonymous UUID: 6BFC8F52-6A0E-496B-9C3C-652CC662D37A
Crashed Thread: 3
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Application Specific Information:
objc[3801]: garbage collection is OFF
Dyld Error Message:
Symbol not found: __gfortran_allocate64_array
Referenced from: /Users/USER/Documents/*/glmnetMex.mexmaci64
Expected in: /Applications/MATLAB_R2012a.app/sys/os/maci64/libgfortran.3.dylib
What version / revision of the product are you using? On what operating
system?
Jan11 2012, version 3
Mac OS Lion (10.7.4)
Please provide any additional information below.
The problem seems to appear at the last step of the initialization "Compile
mex"
Original issue reported on code.google.com by [email protected]
on 16 Sep 2012 at 4:39
What steps will reproduce the problem?
1. Set a weight vector in glmnetSet() produced options struct
2. Run cvglmnetMulticlass() with above options
What is the expected output? What do you see instead?
Should train a glmnet model. Instead, error occurs in cvglmnetMulticlass() line
60 because the weight vector inside the CV loop has a different size w.r.t
target vector y.
What version / revision of the product are you using? On what operating
system?
pmtk3-3jan11/pmtk3-2april2011, Win7 64bit
Please provide any additional information below.
Proposed MATLAB code to replace lines 57-62 in cvglmnetMulticlass.m:
weights = options.weights;
for i=1:nfolds
which=foldid==i;
if verbose, disp(['Fitting fold # ' num2str(i) ' of ' num2str(nfolds)]);end
options.weights = weights(~which);
cvfit = glmnet(x(~which,:), y(~which),family, options);
predmat(which,:) = glmnetPredict(cvfit, type,x(which,:),options.lambda);
end
options.weights = weights;
Original issue reported on code.google.com by [email protected]
on 30 Jan 2012 at 2:43
What steps will reproduce the problem?
1. Fit a HMM model using MixGaussTied
2.
3.
What is the expected output? What do you see instead?
As the help describes, the model should output a matrix model.emission.M such
that M(j,k) = p(Mt = k| St=j) where Mt is the mixture. Therefore, truly M's
ROWS and not COLUMNS should sum to 1. This is necessary in order for the other
equation in the help to be true, that is
P(Xt |St =i) = Sum_m P(Mt = m |St =i) gauss(Xt |mu(m), Sigma(m) ).
Note then that in the above equation it is necessary for Sum_m P(Mt = m|St = i)
= 1, otherwise we aren't normalizing the probability correctly. But note that
this sum over index m, corresponds to summing ROW i of matrix M. However the
output of this algorithm is always a matrix M that has its COLUMNS summing to
1. But this makes no sense, because this is a sum over the mixture weight of
certain component across states. Instead what we truly want is to have a matrix
M, with each row telling us the mixing components of the mixture, and this
components should sum to 1 for each state (i.e. for each row).
What version / revision of the product are you using? On what operating
system?
Linux, version from 3Jan11.
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 19 Oct 2012 at 9:55
What steps will reproduce the problem?
1. model = mixexpFit(FGD,FGT,4);
2. >> yp=mixexpPredict(model,FGD);
What is the expected output? What do you see instead?
??? Reference to non-existent field 'Nclasses'.
Error in ==> mixexpPredict at 34
yhat_k = zeros(N, model.Nclasses, K);
What version / revision of the product are you using? On what operating
system?
PMTK (r2776)/Windows (Matlab)
Please provide any additional information below.
yhat_k = zeros(N, model.Nclasses, K);
replace with
yhat_k = zeros(N, model.nclasses, K);
Original issue reported on code.google.com by RA.Dragun
on 2 Jun 2011 at 6:28
What steps will reproduce the problem?
1.Fitting a HMM on observations and setting the nr of States higher than 2
2. This is a Gauss or GaussMixTied
3. It works normal with 1xT(i) sequences
What is the expected output? What do you see instead?
An error is generated at the next line with generativeClassifierFit. Chol
seems to be the problem in gaussLogprob at line 52
What version / revision of the product are you using? On what operating
system? Edition pmtk3 28feb 2011, Matlab R2007b, Ubuntu
Please provide any additional information below.
File is based on
http://pmtk3.googlecode.com/svn-history/r2517/trunk/docs/tutorial/html/tutGenCla
ssif.html
Original issue reported on code.google.com by [email protected]
on 14 Mar 2011 at 2:03
Attachments:
What steps will reproduce the problem?
N/A
What is the expected output? What do you see instead?
N/A
Please provide any additional information below.
The attached file is a simple utility for converting factor graphs to pairwise
MRF models (very similar to factorGraphToMrf2) due to mrfCreate not currently
supporting general clique potentials. Intended to help with importing from
formats external to pmtk3 (i.e. convert to factor graph representation and from
there to mrf or mrf2 in order to be able to call different inference routines).
Original issue reported on code.google.com by [email protected]
on 13 Sep 2012 at 7:28
Attachments:
What steps will reproduce the problem?
1. Download pmtk3-23nov10.zip or the current svn
2. run initPmtk3 then testPmtk3 in current Octave
What is the expected output? What do you see instead?
I expect to see the tests all pass. Instead, I receive the error message:
error: cov: x and y must have the same number of observations
error: called from:
error: /usr/share/octave/3.2.4/m/statistics/base/cov.m at line 56, column 7
error: evaluating argument list element number 1
error: evaluating argument list element number 1
error:
/home/jpate/git/prosodicParsing/pmt3k/pmtk3-23nov10/toolbox/LatentVariableModels
/ppca/sub/pcaPmtk.m at line 31, column 18
error:
/home/jpate/git/prosodicParsing/pmt3k/pmtk3-23nov10/demos/bookDemos/Latent_facto
r_models_for_continuous_data/pcaDemo2d.m at line 12, column 28
error: /home/jpate/git/prosodicParsing/pmt3k/pmtk3-23nov10/testPmtk3.m at
line 75, column
cov is different in octave and matlab, see:
http://www.mathworks.com/help/techdoc/ref/cov.html
http://octave.sourceforge.net/octave/function/cov.html
What version / revision of the product are you using? On what operating
system?
Again, this is with both a fresh svn clone and the .zip file in the Downloads
page.
$ uname -a
Linux PURPLE-HAZE 2.6.36-ARCH #1 SMP PREEMPT Sat Jan 8 14:15:27 CET 2011 x86_64
Celeron(R) Dual-Core CPU T3000 @ 1.80GHz GenuineIntel GNU/Linux
$ octave -v
GNU Octave, version 3.2.4
Copyright (C) 2009 John W. Eaton and others.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.
Octave was configured for "x86_64-unknown-linux-gnu".
Additional information about Octave is available at http://www.octave.org.
Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html
Report bugs to <[email protected]> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).
Please provide any additional information below.
We see that line 32 of testPmtk3.m is commented out and the offending line 31
is added in revision 2551 with
svn blame toolbox/LatentVariableModels/ppca/sub/pcaPmtk.m
but there is no commit message. I tried uncommenting 32 and commenting out line
31, and all tests from testPmtk3 pass.
Original issue reported on code.google.com by [email protected]
on 17 Jan 2011 at 12:30
plotDecisionBoundary.m is broken in the current revision (r187)
Original issue reported on code.google.com by [email protected]
on 4 Feb 2010 at 4:59
What steps will reproduce the problem?
1. Create a condDiscreteProdCPD by any means with d > 1.
2. Run mkSoftEvidence on it and some observations.
3. Compare output with the brute-force for-loop implementation.
What is the expected output? What do you see instead?
The computed values for logB will be different. In particular, L(:,:,i) will be
equal to zero for i not equal to d (the dimension of the observations).
What version / revision of the product are you using? On what operating
system?
The tarball from '23nov10'
Please provide any additional information below.
The exact error is clear: at line mkSoftEvidence.m, you'll see:
> L(:,:,d) = logT(:, Xobs(j, :), j);
Note that this is a for loop 'for j = 1:d', so the L(:,:,d) should instead be
'L(:,:,j)'. This change fixes the issue.
Original issue reported on code.google.com by [email protected]
on 1 Mar 2011 at 8:32
What steps will reproduce the problem?
1.Running the code on HMM with many states and sub-states.
What is the expected output? What do you see instead?
Expected: Positive transition and output matrix
Obtained: small negative values (~10-18) Can these be due to numerical
problems?
What version / revision of the product are you using? On what operating
system?
The 2005 MIT release
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 30 Jan 2012 at 5:01
What steps will reproduce the problem?
1. See attached file mrfToMrf2Issue.m
What is the expected output? What do you see instead?
The function testMisconceptionMRFtoMRF2() should generate the same output as
the testMisconceptionMRF(). Instead, the edge potentials in the mrf2 model
appear to be getting set up incorrectly.
What version / revision of the product are you using? On what operating
system?
pmtk3-3jan11.zip - uploaded january 2012.
Matlab r2011a, Win 32 bit.
Windows 7 64bit.
Please provide any additional information below.
The attached updated file factorGraphToMrf2.m contains a proposed fix for the
issue, which appears to be at line 34:
edgesWithPots = cell2mat(cellfuncell(@(f)f.domain, epots));
whereby a row vector is returned, which is inconsistent with edgeEnds - i.e. a
column vector - when compared at line 35.
The proposed fix is after line 32:
epots = fg.factors(edgeFacNdx);
to add the following:
if isrowvec(epots)
epots = epots';
end
Original issue reported on code.google.com by [email protected]
on 3 Sep 2012 at 9:22
Attachments:
What steps will reproduce the problem?
%% generate observation sequence and hidded state sequence using Matlab
%% HMM toolbox
TRANS = [.9 .1; .05 .95;];
EMIS = [1/6, 1/6, 1/6, 1/6, 1/6, 1/6;...
7/12, 1/12, 1/12, 1/12, 1/12, 1/12];
[seq,states] = hmmgenerate(10000,TRANS,EMIS);
%% test hmmFit function of pmtk3
[model, loglikHist] = hmmFit(seq, 2, 'discrete');
model.emission.T % good
model.A % good
%% test hmmFitFullyObs function of pmtk3
model = hmmFitFullyObs(states, seq, 'discrete');
model.emission.T % problem: all elements of this matrix are "1"
model.A % good
What is the expected output? What do you see instead?
All elements of model.emission.T generated by hmmFitFullyObs function are "1",
which I think is not correct.
What version / revision of the product are you using? On what operating
system?
pmtk3-23nov10, Matlab 2009b, Win XP sp3
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 10 Dec 2010 at 6:13
Attachments:
What steps will reproduce the problem?
1. Edit line 6 of mypath: p = tokenize(path, ';:'); so that it has a chance
of working on macosx
2. Run whoCallsMe
What is the expected output? What do you see instead?
seg violation
What version / revision of the product are you using? On what operating
system?
MaxOSX 10.6.5
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 20 Jan 2011 at 9:19
- libsvm-mat-2.9.1 does not have .mexmaci64 binaries, and running 'make'
does not create them
What steps will reproduce the problem?
x=randn(10,20); y=randn(10,1);
model = svmFit(x, y, 'C', 1,'kernelParam', 1, 'kernel', 'rbf');
What is the expected output? What do you see instead?
It should return a model struct.
Instead I get this message
??? Undefined function or method 'libsvmTrain' for input arguments of type
'double'.
Error in ==> svmlibFit at 89
model = libsvmTrain(y, X, options);
Error in ==> svmFit at 147
model = fitFn(X, y, C, kernelParam, kernel, fitOptions{:});
Please use labels and text to provide additional information.
svmFit chooses which svm solver to use: it could be libsvm,
svmlight (windows only), or pure matlab (needs opt toolbox).
Currently this choice is made based on expected speed of the method,
not based on the OS the user is using. This should be improved.
Original issue reported on code.google.com by murphyk2
on 28 Feb 2011 at 7:49
What steps will reproduce the problem?
1. Running MATLAB 2012A on win7.
2. call model = hmmFitEm(X, 25, 'gauss'); where X = 1x8,000 vector of values
between -3 and +3 on a grid with 0.25 spacing.
3. Following output seen:
Error using chol
Matrix must be positive definite.
Error in gaussLogprob (line 52)
R = chol(Sigma);
Error in mixGaussInferLatent (line 17)
logPz(:, k) = logMix(k) + gaussLogprob(mu(:, k), Sigma(:, :, k), X);
Error in mixGaussFit>estep (line 52)
[weights, ll] = mixGaussInferLatent(model, data);
Error in emAlgo (line 62)
[ess, ll] = estep(model, data);
Error in mixGaussFit (line 25)
[model, loglikHist] = emAlgo(model, data, initFn, @estep, @mstep , ...
Error in hmmFitEm>initWithMixModel (line 244)
mixModel = mixGaussFit(stackedData, nstates, 'verbose', false, 'maxIter', 10);
Error in hmmFitEm>initGauss (line 146)
model = initWithMixModel(model, data);
Error in hmmFitEm>@(m,X,r)initFn(m,X,r,emissionPrior) (line 45)
initFn = @(m, X, r)initFn(m, X, r, emissionPrior);
Error in emAlgo (line 56)
model = init(model, data, restartNum);
Error in hmmFitEm (line 46)
[model, loglikHist] = emAlgo(model, data, initFn, @estep, @mstep, EMargs{:});
model = hmmFitEm(X, config.K, 'gauss');
Original issue reported on code.google.com by [email protected]
on 14 Nov 2012 at 1:23
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