libdai.git
4 years agoNew git HEAD version master
Joris Mooij [Fri, 17 Jul 2015 14:02:06 +0000 (16:02 +0200)]
New git HEAD version

4 years agolibDAI version 0.3.2 v0.3.2
Joris Mooij [Fri, 17 Jul 2015 13:33:42 +0000 (15:33 +0200)]
libDAI version 0.3.2

4 years agoUpdated ChangeLog
Joris Mooij [Fri, 2 Jan 2015 09:56:24 +0000 (10:56 +0100)]
Updated ChangeLog

4 years agoChanged testregression such that it doesn't fail on platform-dependent numerical...
Joris Mooij [Thu, 1 Jan 2015 16:24:54 +0000 (17:24 +0100)]
Changed testregression such that it doesn't fail on platform-dependent numerical rounding issues

4 years agoVarious fixes to make libDAI build successfully under modern OSX versions
Joris Mooij [Thu, 1 Jan 2015 15:46:21 +0000 (16:46 +0100)]
Various fixes to make libDAI build successfully under modern OSX versions

5 years agoVarious EM code improvements by Charles Vaske and Andy Nguyen
Joris Mooij [Tue, 29 Apr 2014 14:13:35 +0000 (16:13 +0200)]
Various EM code improvements by Charles Vaske and Andy Nguyen

5 years agoFixed regression in SWIG interface (thanks to Benjamin Mumm for reporting this) and...
Joris Mooij [Wed, 27 Nov 2013 13:25:37 +0000 (14:25 +0100)]
Fixed regression in SWIG interface (thanks to Benjamin Mumm for reporting this) and extended DAG::ancestors() and DAG::descendants()

6 years ago[Julien Rebetez] added FactorGraph::printDot() to SWIG interface
Joris Mooij [Thu, 31 Oct 2013 11:14:48 +0000 (12:14 +0100)]
[Julien Rebetez] added FactorGraph::printDot() to SWIG interface

6 years agoMultiple changes: changes in build system, one workaround and one bug fix
Joris Mooij [Tue, 29 Oct 2013 12:02:34 +0000 (13:02 +0100)]
Multiple changes: changes in build system, one workaround and one bug fix
- Optional compilation targets are now set in include/dai/dai_config.h instead of Makefile.ALL
- Workaround for bug in Boost Graph Library version 1.54 ("The graph may not contain an edge with negative weight") by not using Prim's minimum spanning tree algorithm anymore
- Small fix in swig/dai.i

6 years agoRemoved conversion script FastInf->libDAI because it is buggy (uses wrong permutation...
Joris Mooij [Mon, 24 Dec 2012 13:27:02 +0000 (14:27 +0100)]
Removed conversion script FastInf->libDAI because it is buggy (uses wrong permutation of factor entries)

6 years agoExtended SWIG python interface (inspired by Kyle Ellrott): inference is possible...
Joris Mooij [Thu, 22 Nov 2012 16:20:48 +0000 (17:20 +0100)]
Extended SWIG python interface (inspired by Kyle Ellrott): inference is possible in Python now!

7 years agoFixed division-by-zero issue in pow() which caused problems for GLC+ with sparse...
Joris Mooij [Tue, 13 Nov 2012 18:01:20 +0000 (19:01 +0100)]
Fixed division-by-zero issue in pow() which caused problems for GLC+ with sparse factors

7 years agoFixed some more BOOST_CHECK_CLOSE misuse
Joris Mooij [Tue, 30 Oct 2012 20:59:47 +0000 (21:59 +0100)]
Fixed some more BOOST_CHECK_CLOSE misuse

7 years agoFixed bugs in unit test prob_test.cpp
Joris Mooij [Tue, 30 Oct 2012 15:44:11 +0000 (16:44 +0100)]
Fixed bugs in unit test prob_test.cpp

7 years agoFixed GLC::CalcFactorBelief (now uses geometric averaging) and GLC::belief
Joris Mooij [Tue, 9 Oct 2012 09:34:23 +0000 (11:34 +0200)]
Fixed GLC::CalcFactorBelief (now uses geometric averaging) and GLC::belief

7 years agoMerged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh
Joris Mooij [Fri, 5 Oct 2012 11:03:34 +0000 (13:03 +0200)]
Merged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh

7 years agoRelease libDAI 0.3.1 v0.3.1
Joris Mooij [Mon, 17 Sep 2012 10:33:50 +0000 (12:33 +0200)]
Release libDAI 0.3.1

7 years agoOops, forgot a file in the last commit...
Joris Mooij [Mon, 17 Sep 2012 10:11:54 +0000 (12:11 +0200)]
Oops, forgot a file in the last commit...

7 years agoAdded Makefile.WINDOWS64, kindly provided by Lin Ming
Joris Mooij [Mon, 17 Sep 2012 10:10:57 +0000 (12:10 +0200)]
Added Makefile.WINDOWS64, kindly provided by Lin Ming

7 years agoAdded special MatLab interface for junction tree algorithm (dai_jtree)
Joris Mooij [Mon, 17 Sep 2012 10:10:21 +0000 (12:10 +0200)]
Added special MatLab interface for junction tree algorithm (dai_jtree)

7 years agoFixed Win64 build problems with help of Sameh Khamis
Joris Mooij [Thu, 2 Aug 2012 08:25:57 +0000 (10:25 +0200)]
Fixed Win64 build problems with help of Sameh Khamis

* Added VC10 build files, kindly provided by Sameh Khamis
* Fixed several Win64 related bugs (found by Sameh Khamis):
  - define NAN
  - add some necessary casts of size_t to BigInt
  - replaced occurrence of __PRETTY_FUNCTION__ with FUNCTION_NAME that was forgotten in a previous fix

7 years agoFixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
Joris Mooij [Wed, 16 May 2012 13:50:19 +0000 (15:50 +0200)]
Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile

7 years agoFixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION...
Joris Mooij [Tue, 8 May 2012 14:44:35 +0000 (16:44 +0200)]
Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION (Visual Studio) or __func__ (other compilers)

7 years agoFixed bug (found by cax): when building MatLab MEX files, GMP libraries were not...
Joris Mooij [Fri, 16 Mar 2012 11:55:44 +0000 (12:55 +0100)]
Fixed bug (found by cax): when building MatLab MEX files, GMP libraries were not linked

7 years ago[Arman Aksoy] Added Makefile.MACOSX64
Joris Mooij [Wed, 7 Mar 2012 12:24:24 +0000 (13:24 +0100)]
[Arman Aksoy] Added Makefile.MACOSX64

7 years agoFixed bug in findMaximum (it only considered a single connected component of the...
Joris Mooij [Sat, 11 Feb 2012 19:19:19 +0000 (20:19 +0100)]
Fixed bug in findMaximum (it only considered a single connected component of the factor graph)

7 years ago[Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts...
Joris Mooij [Sat, 11 Feb 2012 14:31:17 +0000 (15:31 +0100)]
[Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions

8 years agoForgot to commit ChangeLog in last commit
Joris Mooij [Tue, 26 Jul 2011 08:54:21 +0000 (10:54 +0200)]
Forgot to commit ChangeLog in last commit

8 years agoOptimized ClusterGraph( const FactorGraph&, bool) constructor
Joris Mooij [Tue, 26 Jul 2011 08:53:42 +0000 (10:53 +0200)]
Optimized ClusterGraph( const FactorGraph&, bool) constructor

8 years ago* Fixed "typename" bug in src/alldai.cpp and fixed a memory leak
Joris Mooij [Wed, 20 Jul 2011 15:53:11 +0000 (17:53 +0200)]
* Fixed "typename" bug in src/alldai.cpp and fixed a memory leak

- Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS for older g++ compilers
- Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()

8 years agoFixed memory leak in CBP::run()
Joris Mooij [Wed, 20 Jul 2011 15:36:31 +0000 (17:36 +0200)]
Fixed memory leak in CBP::run()

8 years agoFixed typo in Priya's name
Joris Mooij [Wed, 20 Jul 2011 15:35:44 +0000 (17:35 +0200)]
Fixed typo in Priya's name

8 years agoRelease: libDAI version 0.3.0 v0.3.0
Joris Mooij [Tue, 12 Jul 2011 14:24:40 +0000 (16:24 +0200)]
Release: libDAI version 0.3.0

8 years ago[Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()...
Joris Mooij [Tue, 12 Jul 2011 13:22:33 +0000 (15:22 +0200)]
[Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ() and maxDiff() implementations

8 years agoForgot to update ChangeLog in last commit
Joris Mooij [Tue, 12 Jul 2011 13:10:08 +0000 (15:10 +0200)]
Forgot to update ChangeLog in last commit

8 years agoImproved dai::Exception object (it now stores more information and doesn't print...
Joris Mooij [Tue, 12 Jul 2011 13:09:22 +0000 (15:09 +0200)]
Improved dai::Exception object (it now stores more information and doesn't print to stderr by default)

8 years agoAdded builtinInfAlgs() and builtinInfAlgNames()
Joris Mooij [Mon, 11 Jul 2011 15:43:22 +0000 (17:43 +0200)]
Added builtinInfAlgs() and builtinInfAlgNames()

8 years agoNow uses GMP big integers to represent linear states / total number of states
Joris Mooij [Mon, 11 Jul 2011 10:21:40 +0000 (12:21 +0200)]
Now uses GMP big integers to represent linear states / total number of states

8 years agoChanged license from GPL v2+ to FreeBSD (aka BSD 2-clause) license
Joris Mooij [Thu, 7 Jul 2011 10:35:58 +0000 (12:35 +0200)]
Changed license from GPL v2+ to FreeBSD (aka BSD 2-clause) license

8 years agoFixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
Joris Mooij [Wed, 6 Jul 2011 19:04:26 +0000 (21:04 +0200)]
Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)

8 years agoSmall change
Joris Mooij [Mon, 6 Jun 2011 18:58:34 +0000 (20:58 +0200)]
Small change

8 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Mon, 6 Jun 2011 18:58:15 +0000 (20:58 +0200)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

8 years agoA few small changes
Joris Mooij [Mon, 6 Jun 2011 18:57:49 +0000 (20:57 +0200)]
A few small changes

8 years agoSmall change in src/factorgraph.cpp
Joris Mooij [Wed, 18 May 2011 12:12:33 +0000 (14:12 +0200)]
Small change in src/factorgraph.cpp

8 years agoUpdated examples/example.cpp
Joris Mooij [Wed, 18 May 2011 09:36:21 +0000 (11:36 +0200)]
Updated examples/example.cpp

8 years agoOops, something went wrong in the last commit... restoring examples/example.cpp
Joris Mooij [Wed, 18 May 2011 09:34:56 +0000 (11:34 +0200)]
Oops, something went wrong in the last commit... restoring examples/example.cpp

8 years agoImplemented workaround for bug in State() class found by Jerome Maye
Joris Mooij [Wed, 18 May 2011 09:33:08 +0000 (11:33 +0200)]
Implemented workaround for bug in State() class found by Jerome Maye

8 years agoFixed bug in findMaximum(): inconsistent max-beliefs are now detected,
Joris Mooij [Mon, 9 May 2011 10:59:32 +0000 (12:59 +0200)]
Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
instead of returning a MAP state with zero joint probability
(reported by Hynek Urban)

8 years agoFixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
Joris Mooij [Wed, 30 Mar 2011 07:47:00 +0000 (09:47 +0200)]
Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
The random seed needs to be an unsigned int on some platforms

8 years agoFixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
Joris Mooij [Tue, 30 Nov 2010 21:49:26 +0000 (22:49 +0100)]
Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)

8 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Tue, 30 Nov 2010 21:17:26 +0000 (22:17 +0100)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

Conflicts:
ChangeLog

8 years agoFixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
Joris Mooij [Tue, 30 Nov 2010 21:15:55 +0000 (22:15 +0100)]
Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()

9 years ago[Frederik Eaton] Fixed some random number seed issues
Joris Mooij [Fri, 5 Nov 2010 11:16:09 +0000 (12:16 +0100)]
[Frederik Eaton] Fixed some random number seed issues

9 years agoImproved code in matlab/dai.cpp that tests whether findMaximum is supported
Joris Mooij [Fri, 22 Oct 2010 07:21:59 +0000 (09:21 +0200)]
Improved code in matlab/dai.cpp that tests whether findMaximum is supported

9 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Wed, 6 Oct 2010 08:59:33 +0000 (10:59 +0200)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

9 years agoUpdated bibliography details of libDAI JMLR paper
Joris Mooij [Wed, 6 Oct 2010 08:59:00 +0000 (10:59 +0200)]
Updated bibliography details of libDAI JMLR paper

9 years agoReplaced Name members by name() virtual functions (fixing a bug in matlab/dai.cpp)
Joris Mooij [Mon, 4 Oct 2010 08:40:52 +0000 (10:40 +0200)]
Replaced Name members by name() virtual functions (fixing a bug in matlab/dai.cpp)

9 years agoFinished a new release: libDAI 0.2.7. v0.2.7
Joris Mooij [Thu, 19 Aug 2010 12:01:05 +0000 (14:01 +0200)]
Finished a new release: libDAI 0.2.7.

9 years agoRemoved interfaces deprecated in 0.2.6
Joris Mooij [Tue, 17 Aug 2010 10:12:43 +0000 (12:12 +0200)]
Removed interfaces deprecated in 0.2.6

9 years agoFixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
Joris Mooij [Wed, 11 Aug 2010 07:16:10 +0000 (09:16 +0200)]
Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
if one or more variables had a MAP belief with more than one maximum, an
incorrect MAP state could result.

9 years agoFinished a new release: libDAI v0.2.6 v0.2.6
Joris Mooij [Thu, 5 Aug 2010 17:18:58 +0000 (19:18 +0200)]
Finished a new release: libDAI v0.2.6

9 years agoFixed example_imagesegmentation by adding InfAlg::setMaxIter(size_t)
Joris Mooij [Thu, 5 Aug 2010 15:28:30 +0000 (17:28 +0200)]
Fixed example_imagesegmentation by adding InfAlg::setMaxIter(size_t)

9 years agoImage segmentation example now has a build flag for the version of CImg
Joris Mooij [Thu, 5 Aug 2010 14:24:17 +0000 (16:24 +0200)]
Image segmentation example now has a build flag for the version of CImg

9 years agoMade members Neighbor, Neighbors and Edge of Graph, BipartiteGraph and DAG global
Joris Mooij [Thu, 5 Aug 2010 12:58:18 +0000 (14:58 +0200)]
Made members Neighbor, Neighbors and Edge of Graph, BipartiteGraph and DAG global

9 years agoAdded functionality for reading files in the UAI approximate inference challenge...
Joris Mooij [Thu, 5 Aug 2010 10:53:22 +0000 (12:53 +0200)]
Added functionality for reading files in the UAI approximate inference challenge format

9 years agoImproved tokenizeString
Joris Mooij [Thu, 5 Aug 2010 09:58:54 +0000 (11:58 +0200)]
Improved tokenizeString

9 years agoRemoved "optimized" code from ClusterGraph
Joris Mooij [Thu, 5 Aug 2010 07:40:50 +0000 (09:40 +0200)]
Removed "optimized" code from ClusterGraph

9 years agoFixed a bug (introduced in commit 64db6bc3...) and another one in Factors2mx
Joris Mooij [Wed, 4 Aug 2010 15:10:07 +0000 (17:10 +0200)]
Fixed a bug (introduced in commit 64db6bc3...) and another one in Factors2mx

9 years agoSome small documentation updates
Joris Mooij [Wed, 4 Aug 2010 12:51:21 +0000 (14:51 +0200)]
Some small documentation updates

9 years agoAdded source code for one of the winning solvers of the UAI 2010 Approximate Inferenc...
Joris Mooij [Wed, 4 Aug 2010 12:16:01 +0000 (14:16 +0200)]
Added source code for one of the winning solvers of the UAI 2010 Approximate Inference Challenge

9 years agoImproved VarSet and the GIBBS alias
Joris Mooij [Wed, 4 Aug 2010 12:13:04 +0000 (14:13 +0200)]
Improved VarSet and the GIBBS alias

9 years agoFixed bug in BP (introduced in commit b8f96214...) and added regression test for...
Joris Mooij [Wed, 4 Aug 2010 09:21:57 +0000 (11:21 +0200)]
Fixed bug in BP (introduced in commit b8f96214...) and added regression test for DECMAP

9 years agoImproved ClusterGraph and JTree (added 'maxmem' property)
Joris Mooij [Wed, 4 Aug 2010 08:37:03 +0000 (10:37 +0200)]
Improved ClusterGraph and JTree (added 'maxmem' property)

9 years agoImproved HAK (added 'maxtime' property)
Joris Mooij [Tue, 3 Aug 2010 14:38:07 +0000 (16:38 +0200)]
Improved HAK (added 'maxtime' property)

9 years agoImproved TreeEP (added 'maxtime' property)
Joris Mooij [Tue, 3 Aug 2010 14:31:29 +0000 (16:31 +0200)]
Improved TreeEP (added 'maxtime' property)

9 years agoImproved Gibbs and added FactorGraph::logScore( const std::vector<size_t>& statevec )
Joris Mooij [Tue, 3 Aug 2010 14:29:43 +0000 (16:29 +0200)]
Improved Gibbs and added FactorGraph::logScore( const std::vector<size_t>& statevec )

9 years agoImproved BP (added 'maxtime' property)
Joris Mooij [Tue, 3 Aug 2010 13:41:26 +0000 (15:41 +0200)]
Improved BP (added 'maxtime' property)

9 years agoAdded some unit tests that I forgot earlier
Joris Mooij [Tue, 3 Aug 2010 13:23:19 +0000 (15:23 +0200)]
Added some unit tests that I forgot earlier

9 years agoAdded fromString<>( const std::string& x )
Joris Mooij [Tue, 3 Aug 2010 13:10:46 +0000 (15:10 +0200)]
Added fromString<>( const std::string& x )

9 years agoAdded SmallSet::erase( const T& t )
Joris Mooij [Tue, 3 Aug 2010 12:52:30 +0000 (14:52 +0200)]
Added SmallSet::erase( const T& t )

9 years agoAdded decimation algorithm DECMAP
Joris Mooij [Tue, 3 Aug 2010 12:38:15 +0000 (14:38 +0200)]
Added decimation algorithm DECMAP

9 years ago[Peter Rockett] Improved Makefiles for image segmentation example.
Joris Mooij [Mon, 2 Aug 2010 14:47:01 +0000 (16:47 +0200)]
[Peter Rockett] Improved Makefiles for image segmentation example.

9 years agoUpdated documentation of dai.m (suggested by Kevin Murphy)
Joris Mooij [Tue, 29 Jun 2010 10:15:29 +0000 (12:15 +0200)]
Updated documentation of dai.m (suggested by Kevin Murphy)

9 years agoMerge branch 'master' of git@git.tuebingen.mpg.de:libdai
Joris Mooij [Mon, 28 Jun 2010 12:15:10 +0000 (14:15 +0200)]
Merge branch 'master' of git@git.tuebingen.mpg.de:libdai

9 years agoAdded backwards compatability code for example_imagesegmentation
Joris Mooij [Mon, 28 Jun 2010 12:14:05 +0000 (14:14 +0200)]
Added backwards compatability code for example_imagesegmentation

9 years agoImproved performance of TreeEP constructor
Joris Mooij [Thu, 17 Jun 2010 15:20:38 +0000 (17:20 +0200)]
Improved performance of TreeEP constructor

9 years agoRemoved deprecated interfaces
Joris Mooij [Mon, 17 May 2010 18:02:54 +0000 (20:02 +0200)]
Removed deprecated interfaces

9 years agoMiscellaneous improvements in FactorGraph, Permute, HAK
Joris Mooij [Sun, 16 May 2010 18:27:02 +0000 (20:27 +0200)]
Miscellaneous improvements in FactorGraph, Permute, HAK

* Added FactorGraph::isMaximal(size_t) and FactorGraph::maximalFactor(size_t)
* Added optional reverse argument to Permute::Permute( const std::vector<Var>& )
  constructor
* Added Permute::ranges() accessor
* Added Permute::inverse() method
* Optimized region graph construction for HAK/GBP with clusters=BETHE

9 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Thu, 13 May 2010 17:29:07 +0000 (19:29 +0200)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

9 years agoFixed three minor issues
Joris Mooij [Thu, 13 May 2010 17:28:42 +0000 (19:28 +0200)]
Fixed three minor issues

9 years agoFixed two problems related to g++ 4.0.0 on Darwin 9.8.0
Joris Mooij [Wed, 12 May 2010 09:49:28 +0000 (11:49 +0200)]
Fixed two problems related to g++ 4.0.0 on Darwin 9.8.0

- Moved isnan() into dai namespace
- Added workaround for standard library implementations that
  cannot compare const_reverse_iterator and reverse_iterator

9 years agoFixed wrong version number in documentation and README v0.2.5
Joris Mooij [Sun, 9 May 2010 14:49:35 +0000 (16:49 +0200)]
Fixed wrong version number in documentation and README

9 years agoFinished a new release: libDAI 0.2.5
Joris Mooij [Sun, 9 May 2010 13:40:50 +0000 (15:40 +0200)]
Finished a new release: libDAI 0.2.5

9 years agoAdded DAG class and various minor improvements
Joris Mooij [Wed, 5 May 2010 09:17:55 +0000 (11:17 +0200)]
Added DAG class and various minor improvements

9 years agoHopefully the final change to make the regression test reproducible!
Joris Mooij [Tue, 4 May 2010 10:07:11 +0000 (12:07 +0200)]
Hopefully the final change to make the regression test reproducible!

9 years agoImproved regression test (again) to make it reproducible
Joris Mooij [Tue, 4 May 2010 09:50:39 +0000 (11:50 +0200)]
Improved regression test (again) to make it reproducible

9 years agoImproved regression test
Joris Mooij [Tue, 4 May 2010 07:21:01 +0000 (09:21 +0200)]
Improved regression test

9 years agoBuild process now continues if compilation of example_imagesegmentation is not succesful
Joris Mooij [Mon, 3 May 2010 10:36:46 +0000 (12:36 +0200)]
Build process now continues if compilation of example_imagesegmentation is not succesful

9 years agoCleaned up example_imagesegmentation
Joris Mooij [Sun, 2 May 2010 19:08:44 +0000 (21:08 +0200)]
Cleaned up example_imagesegmentation

9 years agoChanged to newer CImg interface and fixed two regressions
Joris Mooij [Fri, 30 Apr 2010 16:55:36 +0000 (18:55 +0200)]
Changed to newer CImg interface and fixed two regressions