libdai.git
9 years agoWorking on BipGraph unit tests
Joris Mooij [Mon, 22 Mar 2010 16:11:24 +0000 (17:11 +0100)]
Working on BipGraph unit tests

9 years agoAdded GraphAL unit tests, fixed 6 bugs in GraphAL and added functionality:
Joris Mooij [Mon, 22 Mar 2010 12:51:57 +0000 (13:51 +0100)]
Added GraphAL unit tests, fixed 6 bugs in GraphAL and added functionality:

  - Fixed bug in GraphAL::nrEdges()
  - Fixed bug in GraphAL::addEdge()
  - Fixed bug in GraphAL::isTree()
  - Fixed bug in GraphAL::printDot()
  - Fixed bug in createGraphGrid3D()
  - Fixed bug in createGraphRegular()
  - Added GraphAL::hasEdge(size_t,size_t)
  - Removed RandomDRegularGraph()

9 years agoAdded unit tests for VarSet
Joris Mooij [Sat, 20 Mar 2010 11:57:34 +0000 (12:57 +0100)]
Added unit tests for VarSet

9 years agoCompressed Makefile and added unit tests for SmallSet
Joris Mooij [Fri, 19 Mar 2010 16:39:43 +0000 (17:39 +0100)]
Compressed Makefile and added unit tests for SmallSet

9 years agoAdded unit tests for Var
Joris Mooij [Fri, 19 Mar 2010 12:38:04 +0000 (13:38 +0100)]
Added unit tests for Var

9 years agoAdded unit testing framework
Joris Mooij [Thu, 18 Mar 2010 09:35:07 +0000 (10:35 +0100)]
Added unit testing framework

9 years agoAdded initialization of TRWBP weights by sampling spanning trees
Joris Mooij [Wed, 17 Mar 2010 12:29:07 +0000 (13:29 +0100)]
Added initialization of TRWBP weights by sampling spanning trees

9 years agoCleaned up MR code
Joris Mooij [Mon, 1 Mar 2010 20:08:11 +0000 (21:08 +0100)]
Cleaned up MR code

9 years agoRewrote implementation of response propagation in MR
Joris Mooij [Mon, 1 Mar 2010 15:21:03 +0000 (16:21 +0100)]
Rewrote implementation of response propagation in MR

9 years agoFixed bug in BBPCostFunction::operator=() which prevented desired assignment from...
Joris Mooij [Mon, 1 Mar 2010 11:55:39 +0000 (12:55 +0100)]
Fixed bug in BBPCostFunction::operator=() which prevented desired assignment from happening

10 years ago[Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
Joris Mooij [Mon, 22 Feb 2010 19:22:16 +0000 (20:22 +0100)]
[Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]

10 years agoRemoved deprecated interfaces
Joris Mooij [Thu, 11 Feb 2010 18:35:26 +0000 (19:35 +0100)]
Removed deprecated interfaces

10 years agoFinished release 0.2.4 v0.2.4
Joris Mooij [Thu, 11 Feb 2010 11:12:10 +0000 (12:12 +0100)]
Finished release 0.2.4

10 years agoVarious changes:
Joris Mooij [Wed, 10 Feb 2010 15:45:20 +0000 (16:45 +0100)]
Various changes:

* Added GraphAL, an adjacency list implementation for graphs,
  similar to (but simpler than) BipartiteGraph
* Renamed Graph into GraphEL (for Graph, implemented as Edge List)
* Documented and cleaned up utils/createfg
* Renamed some of the factor creating functions introduced in the
  previous commit (now their names start with the prefix 'createFactor')

10 years agoAdded some functionality to create various standard factors and renamed "Clamped...
Joris Mooij [Wed, 10 Feb 2010 08:50:48 +0000 (09:50 +0100)]
Added some functionality to create various standard factors and renamed "Clamped BP" into "Conditioned BP"

10 years agoAdded Makefile.ALL (which I forgot to do at the last commit) and improved documentation
Joris Mooij [Sun, 7 Feb 2010 16:22:35 +0000 (17:22 +0100)]
Added Makefile.ALL (which I forgot to do at the last commit) and improved documentation

10 years agoMoved platform independent build options into Makefile.ALL and documented tests/testdai
Joris Mooij [Thu, 4 Feb 2010 12:53:34 +0000 (13:53 +0100)]
Moved platform independent build options into Makefile.ALL and documented tests/testdai

10 years agoWindows platform now needs boost 1.37 or higher
Joris Mooij [Wed, 3 Feb 2010 15:38:00 +0000 (16:38 +0100)]
Windows platform now needs boost 1.37 or higher

10 years agoMerged duplicate code (in calcBeliefF() and calcNewMessage()) in BP,FBP,TRWBP
Joris Mooij [Wed, 3 Feb 2010 13:22:58 +0000 (14:22 +0100)]
Merged duplicate code (in calcBeliefF() and calcNewMessage()) in BP,FBP,TRWBP

10 years agoFixed regression FBP and bugs in TRWBP
Joris Mooij [Fri, 22 Jan 2010 15:20:39 +0000 (16:20 +0100)]
Fixed regression FBP and bugs in TRWBP

10 years agoMerge branch 'master' of git.tuebingen.mpg.de:libdai
Joris Mooij [Fri, 22 Jan 2010 13:09:11 +0000 (14:09 +0100)]
Merge branch 'master' of git.tuebingen.mpg.de:libdai

Conflicts:
include/dai/doc.h

10 years agoImplementing TRWBP
Joris Mooij [Fri, 22 Jan 2010 12:41:14 +0000 (13:41 +0100)]
Implementing TRWBP

10 years agoImplemented various heuristics for choosing a variable elimination sequence in JTree
Joris Mooij [Mon, 18 Jan 2010 16:03:16 +0000 (17:03 +0100)]
Implemented various heuristics for choosing a variable elimination sequence in JTree

10 years agoMade alias support official part of the library
Joris Mooij [Fri, 15 Jan 2010 11:42:14 +0000 (12:42 +0100)]
Made alias support official part of the library

10 years agoMoved alias code from tests/testdai.cpp to src/alldai.cpp
Joris Mooij [Fri, 15 Jan 2010 10:39:20 +0000 (11:39 +0100)]
Moved alias code from tests/testdai.cpp to src/alldai.cpp

10 years agoFixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
Joris Mooij [Thu, 14 Jan 2010 20:18:29 +0000 (21:18 +0100)]
Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)

10 years agoMiscellaneous smaller improvements
Joris Mooij [Thu, 14 Jan 2010 12:59:47 +0000 (13:59 +0100)]
Miscellaneous smaller improvements

10 years agoCleaned up variable elimination code in ClusterGraph
Joris Mooij [Wed, 13 Jan 2010 17:36:52 +0000 (18:36 +0100)]
Cleaned up variable elimination code in ClusterGraph

10 years agoReverted BipartiteGraph::isConnected to old implementation
Joris Mooij [Wed, 13 Jan 2010 16:11:02 +0000 (17:11 +0100)]
Reverted BipartiteGraph::isConnected to old implementation
(because it the BGL implementation turned out to be slower)

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