libdai.git
10 years agoCleaned up some code in TreeEP and JTree
Joris Mooij [Wed, 13 Jan 2010 12:52:53 +0000 (13:52 +0100)]
Cleaned up some code in TreeEP and JTree

10 years agoAdded BETHE method for GBP/HAK cluster choice
Joris Mooij [Wed, 13 Jan 2010 10:57:03 +0000 (11:57 +0100)]
Added BETHE method for GBP/HAK cluster choice

10 years agoRenamed some functions of BipartiteGraph
Joris Mooij [Tue, 12 Jan 2010 17:21:43 +0000 (18:21 +0100)]
Renamed some functions of BipartiteGraph

10 years agoAdded examples example_sprinkler_gibbs and example_sprinkler_em
Joris Mooij [Tue, 12 Jan 2010 16:39:33 +0000 (17:39 +0100)]
Added examples example_sprinkler_gibbs and example_sprinkler_em

10 years agoOptimized BipartiteGraph::isConnected() by using Boost Graph Library implementation
Joris Mooij [Tue, 12 Jan 2010 12:45:41 +0000 (13:45 +0100)]
Optimized BipartiteGraph::isConnected() by using Boost Graph Library implementation

10 years agoStrengthened convergence criteria of various algorithms
Joris Mooij [Tue, 12 Jan 2010 11:12:09 +0000 (12:12 +0100)]
Strengthened convergence criteria of various algorithms

10 years agoImproved README
Joris Mooij [Mon, 11 Jan 2010 20:30:38 +0000 (21:30 +0100)]
Improved README

10 years agoImplemented FBP::logZ()
Joris Mooij [Fri, 8 Jan 2010 11:02:16 +0000 (12:02 +0100)]
Implemented FBP::logZ()

10 years agoFixed typo in doxygen FBP update equation, and removed FBP::_scale_var stuff
Joris Mooij [Sun, 3 Jan 2010 20:06:05 +0000 (21:06 +0100)]
Fixed typo in doxygen FBP update equation, and removed FBP::_scale_var stuff

10 years agoFixed bug in HAK and changed tests/testdai "marginals" option
Joris Mooij [Wed, 30 Dec 2009 11:49:45 +0000 (12:49 +0100)]
Fixed bug in HAK and changed tests/testdai "marginals" option

10 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Mon, 21 Dec 2009 10:35:42 +0000 (11:35 +0100)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

Conflicts:
ChangeLog

10 years ago[Frederik Eaton] Added Fractional Belief Propagation
Joris Mooij [Mon, 21 Dec 2009 10:34:26 +0000 (11:34 +0100)]
[Frederik Eaton] Added Fractional Belief Propagation

10 years ago[Alexander Gerhard Schwing] Fixed error in BP that occured with damping and using...
Joris Mooij [Sun, 20 Dec 2009 17:20:06 +0000 (18:20 +0100)]
[Alexander Gerhard Schwing] Fixed error in BP that occured with damping and using log-domain updates

10 years agoFixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
Joris Mooij [Thu, 10 Dec 2009 15:39:06 +0000 (16:39 +0100)]
Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)

10 years ago[Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
Joris Mooij [Sun, 6 Dec 2009 17:27:58 +0000 (18:27 +0100)]
[Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp

10 years agoFixed regression in scripts/regenerate-properties
Joris Mooij [Fri, 27 Nov 2009 22:42:01 +0000 (23:42 +0100)]
Fixed regression in scripts/regenerate-properties
(now all errors are gathered before throwing the exception, as used to be the case)

10 years ago[Frederik Eaton] Added constructors for BBPCostFunction
Joris Mooij [Fri, 27 Nov 2009 21:23:18 +0000 (22:23 +0100)]
[Frederik Eaton] Added constructors for BBPCostFunction

10 years ago[Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
Joris Mooij [Fri, 27 Nov 2009 21:18:18 +0000 (22:18 +0100)]
[Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>

10 years ago[Frederik Eaton] Added unary minus to TProb<>
Joris Mooij [Fri, 27 Nov 2009 21:12:07 +0000 (22:12 +0100)]
[Frederik Eaton] Added unary minus to TProb<>

10 years ago[Frederik Eaton] Added Hellinger distance to TProb<>::DistType
Joris Mooij [Fri, 27 Nov 2009 21:05:58 +0000 (22:05 +0100)]
[Frederik Eaton] Added Hellinger distance to TProb<>::DistType

10 years agoSome small modifications to AUTHORS and main page of documentation
Joris Mooij [Tue, 17 Nov 2009 11:11:35 +0000 (12:11 +0100)]
Some small modifications to AUTHORS and main page of documentation

10 years agoForgot to update version and date in last commit
Joris Mooij [Tue, 17 Nov 2009 08:13:28 +0000 (09:13 +0100)]
Forgot to update version and date in last commit

10 years agoRemoved obsolete/deprecated stuff
Joris Mooij [Mon, 16 Nov 2009 20:09:46 +0000 (21:09 +0100)]
Removed obsolete/deprecated stuff

10 years agolibDAI version 0.2.3 v0.2.3
Joris Mooij [Mon, 16 Nov 2009 19:42:21 +0000 (20:42 +0100)]
libDAI version 0.2.3

10 years agoFixed compilation problem in BBP under gcc 3.4
Joris Mooij [Mon, 16 Nov 2009 19:15:37 +0000 (20:15 +0100)]
Fixed compilation problem in BBP under gcc 3.4

10 years agoSome small bug fixes
Joris Mooij [Mon, 16 Nov 2009 15:47:49 +0000 (16:47 +0100)]
Some small bug fixes

10 years agoUpdated ChangeLog and added some backwards compatibility stuff
Joris Mooij [Mon, 16 Nov 2009 13:46:31 +0000 (14:46 +0100)]
Updated ChangeLog and added some backwards compatibility stuff

10 years agoReplaced VarSet::calcState(),VarSet::calcStates() by non-members calcLinearState...
Joris Mooij [Mon, 16 Nov 2009 12:14:56 +0000 (13:14 +0100)]
Replaced VarSet::calcState(),VarSet::calcStates() by non-members calcLinearState(),calcState()

10 years agoImproved documentation
Joris Mooij [Mon, 16 Nov 2009 11:42:06 +0000 (12:42 +0100)]
Improved documentation

10 years agoSome documentation improvements
Joris Mooij [Sun, 15 Nov 2009 18:10:39 +0000 (19:10 +0100)]
Some documentation improvements

10 years agoSeveral improvements:
Joris Mooij [Thu, 12 Nov 2009 15:36:54 +0000 (16:36 +0100)]
Several improvements:
- Improved documentation in include/dai/doc.h
- README is now created automatically from doxygen documentation
- Makefile macros DAI_VERSION and DAI_DATE have been introduced,
  in order to store this information in a central place
- Renamed "ConditionalProbEstimation" into "CondProbEstimation"
- Variable labels are now nonnegative (of type size_t)
- Tiny change to .tab file format (added empty line after header)
- Other cleanups

10 years agoDocumented all exceptions and did some general cleanups
Joris Mooij [Thu, 12 Nov 2009 09:52:51 +0000 (10:52 +0100)]
Documented all exceptions and did some general cleanups

10 years agoImproved documentation of include/dai/emalg.h
Joris Mooij [Wed, 11 Nov 2009 19:56:26 +0000 (20:56 +0100)]
Improved documentation of include/dai/emalg.h

10 years agoWorking on documentation of include/dai/emalg.h
Joris Mooij [Wed, 11 Nov 2009 18:38:34 +0000 (19:38 +0100)]
Working on documentation of include/dai/emalg.h

10 years agoImproved error messages of Evidence::addEvidenceTabFile
Joris Mooij [Wed, 11 Nov 2009 13:49:39 +0000 (14:49 +0100)]
Improved error messages of Evidence::addEvidenceTabFile

10 years agoImproved documentation of include/dai/evidence.h
Joris Mooij [Wed, 11 Nov 2009 13:38:26 +0000 (14:38 +0100)]
Improved documentation of include/dai/evidence.h

10 years agoImproved documentation of include/dai/cbp.h
Joris Mooij [Tue, 10 Nov 2009 17:43:47 +0000 (18:43 +0100)]
Improved documentation of include/dai/cbp.h

10 years agoCleaned up BBP and improved documentation of include/dai/bbp.h
Joris Mooij [Tue, 10 Nov 2009 15:51:03 +0000 (16:51 +0100)]
Cleaned up BBP and improved documentation of include/dai/bbp.h

10 years agoImproved documentation of include/dai/bp_dual.h
Joris Mooij [Tue, 10 Nov 2009 11:03:10 +0000 (12:03 +0100)]
Improved documentation of include/dai/bp_dual.h

10 years agoImproved documentation of include/dai/gibbs.h
Joris Mooij [Tue, 10 Nov 2009 10:41:49 +0000 (11:41 +0100)]
Improved documentation of include/dai/gibbs.h

10 years agoImproved documentation of include/dai/mr.h
Joris Mooij [Tue, 10 Nov 2009 10:13:39 +0000 (11:13 +0100)]
Improved documentation of include/dai/mr.h

10 years agoImproved documentation of include/dai/lc.h
Joris Mooij [Tue, 10 Nov 2009 09:22:51 +0000 (10:22 +0100)]
Improved documentation of include/dai/lc.h

10 years agoImproved documentation of include/dai/treeep.h
Joris Mooij [Mon, 9 Nov 2009 14:04:02 +0000 (15:04 +0100)]
Improved documentation of include/dai/treeep.h

10 years agoAdded GPL license text to doxygen documentation
Joris Mooij [Mon, 9 Nov 2009 10:27:44 +0000 (11:27 +0100)]
Added GPL license text to doxygen documentation

10 years agoImproved documentation of include/dai/hak.h
Joris Mooij [Mon, 9 Nov 2009 10:12:40 +0000 (11:12 +0100)]
Improved documentation of include/dai/hak.h

10 years agoImproved documentation of include/dai/jtree.h and did some cleanups
Joris Mooij [Thu, 5 Nov 2009 16:20:44 +0000 (17:20 +0100)]
Improved documentation of include/dai/jtree.h and did some cleanups

10 years agoImproved documentation of include/dai/bp.h
Joris Mooij [Thu, 5 Nov 2009 13:10:00 +0000 (14:10 +0100)]
Improved documentation of include/dai/bp.h

10 years agoExtended InfAlg interface with setProperties(), getProperties() and printProperties()
Joris Mooij [Tue, 3 Nov 2009 18:10:31 +0000 (19:10 +0100)]
Extended InfAlg interface with setProperties(), getProperties() and printProperties()

10 years agoImproved documentation of include/dai/mf.h
Joris Mooij [Tue, 3 Nov 2009 17:39:16 +0000 (18:39 +0100)]
Improved documentation of include/dai/mf.h

10 years agoImproved documentation of include/dai/exactinf.h
Joris Mooij [Tue, 3 Nov 2009 17:20:31 +0000 (18:20 +0100)]
Improved documentation of include/dai/exactinf.h

10 years agoFixed regressions in SWIG code
Joris Mooij [Tue, 3 Nov 2009 16:40:12 +0000 (17:40 +0100)]
Fixed regressions in SWIG code

10 years agoDeclared class Diffs as obsolete
Joris Mooij [Tue, 3 Nov 2009 16:15:50 +0000 (17:15 +0100)]
Declared class Diffs as obsolete

10 years agoImproved documentation of include/dai/alldai.h and daialg.h, and
Joris Mooij [Tue, 3 Nov 2009 15:08:26 +0000 (16:08 +0100)]
Improved documentation of include/dai/alldai.h and daialg.h, and
declared calcPairBeliefsNew() and calcMarginal2ndO() as obsolete

10 years agoLittle additional improvement of documentation of include/dai/util.h
Joris Mooij [Tue, 3 Nov 2009 10:12:49 +0000 (11:12 +0100)]
Little additional improvement of documentation of include/dai/util.h

10 years agoRemoved DAI_ACCMUT macro and improved documentation of include/dai/util.h
Joris Mooij [Tue, 3 Nov 2009 10:04:16 +0000 (11:04 +0100)]
Removed DAI_ACCMUT macro and improved documentation of include/dai/util.h

10 years agoFixed tests/testall.bat
Joris Mooij [Mon, 2 Nov 2009 15:41:49 +0000 (16:41 +0100)]
Fixed tests/testall.bat

10 years agoSome cleanups of include/dai/prob.h
Joris Mooij [Fri, 30 Oct 2009 15:10:02 +0000 (16:10 +0100)]
Some cleanups of include/dai/prob.h

10 years agoCleanup of include/dai/factor.h
Joris Mooij [Thu, 29 Oct 2009 16:03:15 +0000 (17:03 +0100)]
Cleanup of include/dai/factor.h

10 years agoCleaned up TProb<T> and some misc other stuff, improved State class, and
Joris Mooij [Thu, 29 Oct 2009 13:10:19 +0000 (14:10 +0100)]
Cleaned up TProb<T> and some misc other stuff, improved State class, and
renamed PropertySet::allKeys() into PropertySet::keys()

10 years agoImproved documentation of include/dai/properties.h
Joris Mooij [Wed, 28 Oct 2009 11:56:55 +0000 (12:56 +0100)]
Improved documentation of include/dai/properties.h

10 years agoFixed const qualifiers in VarSet
Joris Mooij [Tue, 27 Oct 2009 16:04:31 +0000 (17:04 +0100)]
Fixed const qualifiers in VarSet

10 years agoReplaced doubles by Reals, fixed two bugs
Joris Mooij [Tue, 27 Oct 2009 13:00:56 +0000 (14:00 +0100)]
Replaced doubles by Reals, fixed two bugs

* Replaced all doubles by Reals where necessary
* Replaced constructor
    TFactor<T>::TFactor( const VarSet& vars, TIterator begin )
  by two constructors
    TFactor<T>::TFactor( const VarSet& vars, const T* p )
    TFactor<T>::TFactor( const VarSet& vars, const std::vector<S> &x )
* Fixed bugs (min and max were reversed) in
    TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
    TFactor<T> max( const TFactor<T> &, const TFactor<T> & )

10 years agoImproved documentation of include/dai/regiongraph.h and did some cleanups
Joris Mooij [Mon, 26 Oct 2009 13:35:10 +0000 (14:35 +0100)]
Improved documentation of include/dai/regiongraph.h and did some cleanups

10 years agoImproved documentation of include/dai/clustergraph.h
Joris Mooij [Mon, 26 Oct 2009 10:47:43 +0000 (11:47 +0100)]
Improved documentation of include/dai/clustergraph.h

10 years agoFixed regression introduced by previous commit
Joris Mooij [Mon, 26 Oct 2009 10:19:56 +0000 (11:19 +0100)]
Fixed regression introduced by previous commit

10 years agoAdded EXACT to aliases/aliases.conf
Joris Mooij [Mon, 26 Oct 2009 10:00:26 +0000 (11:00 +0100)]
Added EXACT to aliases/aliases.conf

10 years agoImproved documentation of include/dai/factorgraph.h
Joris Mooij [Thu, 22 Oct 2009 15:53:35 +0000 (17:53 +0200)]
Improved documentation of include/dai/factorgraph.h

10 years agoImproved documentation of include/dai/weightedgraph.h
Joris Mooij [Wed, 21 Oct 2009 16:08:49 +0000 (18:08 +0200)]
Improved documentation of include/dai/weightedgraph.h

10 years agoImproved documentation of factor.h
Joris Mooij [Tue, 20 Oct 2009 13:31:36 +0000 (15:31 +0200)]
Improved documentation of factor.h

10 years agoImproved documentation of include/dai/index.h
Joris Mooij [Mon, 19 Oct 2009 19:53:11 +0000 (21:53 +0200)]
Improved documentation of include/dai/index.h

10 years agoDocumentation improvement, interface changes and new example:
Joris Mooij [Mon, 19 Oct 2009 16:03:04 +0000 (18:03 +0200)]
Documentation improvement, interface changes and new example:
* Renamed Permute::convert_linear_index into Permute::convertLinearIndex
  (and provided an alias for backwards compatibility)
* Added examples/example_permute.cpp
* Improved documentation of include/dai/index.h

10 years agoRestored TProb<T>::makeZero, TProb<T>::makePositive, TFactor<T>::makeZero, TFactor...
Joris Mooij [Mon, 19 Oct 2009 11:47:50 +0000 (13:47 +0200)]
Restored TProb<T>::makeZero, TProb<T>::makePositive, TFactor<T>::makeZero, TFactor<T>::makePositive but marked them obsolete

10 years agoUpdated ChangeLog and added TODO
Joris Mooij [Mon, 19 Oct 2009 11:03:15 +0000 (13:03 +0200)]
Updated ChangeLog and added TODO

10 years agoVarious cleanups and documentation improvements for SmallSet and Prob
Joris Mooij [Mon, 19 Oct 2009 10:57:02 +0000 (12:57 +0200)]
Various cleanups and documentation improvements for SmallSet and Prob

10 years agoFixed bug in BipartiteGraph::eraseEdge and improved documentation
Joris Mooij [Fri, 16 Oct 2009 16:56:31 +0000 (18:56 +0200)]
Fixed bug in BipartiteGraph::eraseEdge and improved documentation

10 years agoFixed SWIG octave wrappers and added octave port of example_sprinkler
Joris Mooij [Wed, 14 Oct 2009 09:26:28 +0000 (11:26 +0200)]
Fixed SWIG octave wrappers and added octave port of example_sprinkler

10 years agoMerge branch 'pletscher'
Joris Mooij [Tue, 13 Oct 2009 15:12:07 +0000 (17:12 +0200)]
Merge branch 'pletscher'

Conflicts:

Makefile.CYGWIN
Makefile.LINUX
Makefile.MACOSX
Makefile.WINDOWS

10 years agoRenamed directory python into swig
Joris Mooij [Tue, 13 Oct 2009 15:09:59 +0000 (17:09 +0200)]
Renamed directory python into swig

10 years agoAdded octave target and a README to SWIG wrappers
Joris Mooij [Tue, 13 Oct 2009 15:09:19 +0000 (17:09 +0200)]
Added octave target and a README to SWIG wrappers

10 years agoAdded example_sprinkler.py, a python port of examples/example_sprinkler.cpp and added...
Joris Mooij [Tue, 13 Oct 2009 14:39:41 +0000 (16:39 +0200)]
Added example_sprinkler.py, a python port of examples/example_sprinkler.cpp and added copyright headers

10 years agoAdded init parameter to HAK/GBP to allow for random initialization
Joris Mooij [Fri, 9 Oct 2009 15:56:05 +0000 (17:56 +0200)]
Added init parameter to HAK/GBP to allow for random initialization

10 years agoReplaced the standard assert() macro by DAI_ASSERT
Joris Mooij [Thu, 24 Sep 2009 16:09:11 +0000 (18:09 +0200)]
Replaced the standard assert() macro by DAI_ASSERT

10 years agoIntroduced CCNODEBUGFLAGS in Makefile and added a constructor to TProb<T>
Joris Mooij [Thu, 24 Sep 2009 10:08:46 +0000 (12:08 +0200)]
Introduced CCNODEBUGFLAGS in Makefile and added a constructor to TProb<T>

10 years ago[Patrick Pletscher] Added experimental SWIG Python wrapper code
Joris Mooij [Tue, 22 Sep 2009 13:27:08 +0000 (15:27 +0200)]
[Patrick Pletscher] Added experimental SWIG Python wrapper code

10 years agoUpdated copyright headers
Joris Mooij [Wed, 16 Sep 2009 13:47:09 +0000 (15:47 +0200)]
Updated copyright headers

10 years agoAdded max-product functionality to JTree
Joris Mooij [Tue, 15 Sep 2009 10:47:21 +0000 (12:47 +0200)]
Added max-product functionality to JTree

10 years agoFixed two regressions
Joris Mooij [Mon, 14 Sep 2009 11:35:14 +0000 (13:35 +0200)]
Fixed two regressions

10 years agoFixed tabs and trailing whitespaces
Joris Mooij [Tue, 8 Sep 2009 09:18:33 +0000 (11:18 +0200)]
Fixed tabs and trailing whitespaces

10 years agoFixed regression in TProb<T>
Joris Mooij [Tue, 8 Sep 2009 08:40:20 +0000 (10:40 +0200)]
Fixed regression in TProb<T>

10 years agoImproved coding style of recent changes by Charlie Vaske
Joris Mooij [Tue, 8 Sep 2009 08:39:22 +0000 (10:39 +0200)]
Improved coding style of recent changes by Charlie Vaske

10 years agoMerge branch 'vaskeEmFix' of git://disco.cse.ucsc.edu/libDAI into mergeVaskeEmFix
Joris Mooij [Tue, 8 Sep 2009 07:57:19 +0000 (09:57 +0200)]
Merge branch 'vaskeEmFix' of git://disco.cse.ucsc.edu/libDAI into mergeVaskeEmFix

10 years agoSmall documentation improvements
Joris Mooij [Tue, 8 Sep 2009 07:52:09 +0000 (09:52 +0200)]
Small documentation improvements

10 years agoVarious fixes
Joris Mooij [Mon, 7 Sep 2009 14:30:51 +0000 (16:30 +0200)]
Various fixes

10 years agoCleaned up error handling by introducing the DAI_THROWE macro.
Joris Mooij [Mon, 7 Sep 2009 13:44:13 +0000 (15:44 +0200)]
Cleaned up error handling by introducing the DAI_THROWE macro.

10 years agoIntroduced DAI_DEBASSERT macro to abbreviate a common pattern
Joris Mooij [Fri, 4 Sep 2009 15:08:21 +0000 (17:08 +0200)]
Introduced DAI_DEBASSERT macro to abbreviate a common pattern

10 years agoChanged FactorGraph::clamp and DAIAlg::clamp interfaces
Joris Mooij [Wed, 2 Sep 2009 14:55:59 +0000 (16:55 +0200)]
Changed FactorGraph::clamp and DAIAlg::clamp interfaces

The variable to be clamped is now indicated by its index, not as a Var.
The old interface is marked obsolete

10 years ago[Patrick Pletscher] Fixed performance issue in FactorGraph::clamp and FactorGraph...
Joris Mooij [Sun, 16 Aug 2009 16:12:35 +0000 (18:12 +0200)]
[Patrick Pletscher] Fixed performance issue in FactorGraph::clamp and FactorGraph::clampVar

10 years agoEM bugfix. Convenience methods in Factor, Permute, Properties, EM.
Charles Vaske [Sat, 15 Aug 2009 18:27:51 +0000 (11:27 -0700)]
EM bugfix. Convenience methods in Factor, Permute, Properties, EM.

 -- Bugfix: was using abs() instead of fabs() in determining EM termination,
    which caused a loss of precision.
 -- New constructor in Permute for canonical variable ordering
 -- New constructor in Factor that reorders variables to canonical ordering
 -- New accessor in Properties for getting all keys
 -- New function for getting inferred parameters

10 years ago[Sebastian Nowozin] MEX file dai now also optionally returns the MAP state (only...
Joris Mooij [Tue, 11 Aug 2009 08:47:25 +0000 (10:47 +0200)]
[Sebastian Nowozin] MEX file dai now also optionally returns the MAP state (only for BP)

10 years ago[Sebastian Nowozin] Fixed memory leak in MatLab interface (dai.cpp)
Joris Mooij [Mon, 10 Aug 2009 19:59:05 +0000 (21:59 +0200)]
[Sebastian Nowozin] Fixed memory leak in MatLab interface (dai.cpp)