libdai.git
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)

10 years agoFixed clean_updates bug in BBP by commenting out this feature
Joris Mooij [Thu, 6 Aug 2009 12:20:45 +0000 (14:20 +0200)]
Fixed clean_updates bug in BBP by commenting out this feature

10 years agoUpdated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 15:37:38 +0000 (17:37 +0200)]
Updated ChangeLog

10 years agoMerge branch 'eaton'
Joris Mooij [Tue, 4 Aug 2009 15:35:49 +0000 (17:35 +0200)]
Merge branch 'eaton'

Conflicts:

ChangeLog
Makefile
include/dai/daialg.h

10 years agoUpdated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 15:33:02 +0000 (17:33 +0200)]
Updated ChangeLog

10 years agoAdded CBP to README and to doxygen front page.
Joris Mooij [Tue, 4 Aug 2009 15:10:35 +0000 (17:10 +0200)]
Added CBP to README and to doxygen front page.

10 years agoUpdated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 14:57:22 +0000 (16:57 +0200)]
Updated ChangeLog

10 years agoCleanup of CBP code
Joris Mooij [Tue, 4 Aug 2009 14:39:13 +0000 (16:39 +0200)]
Cleanup of CBP code

10 years agoEven more cleanup of BBP code
Joris Mooij [Tue, 4 Aug 2009 13:36:37 +0000 (15:36 +0200)]
Even more cleanup of BBP code

10 years agoCleanup of BBP code
Joris Mooij [Mon, 3 Aug 2009 15:44:14 +0000 (17:44 +0200)]
Cleanup of BBP code

10 years agoCleanup of BP_dual code
Joris Mooij [Fri, 31 Jul 2009 15:25:21 +0000 (17:25 +0200)]
Cleanup of BP_dual code

10 years agoMarked the backwards compatibility edge interface of BipartiteGraph as obsolete
Joris Mooij [Fri, 31 Jul 2009 14:22:12 +0000 (16:22 +0200)]
Marked the backwards compatibility edge interface of BipartiteGraph as obsolete

10 years agoVarious cleanups
Joris Mooij [Fri, 31 Jul 2009 14:11:30 +0000 (16:11 +0200)]
Various cleanups

10 years agoMEX file dai now also returns variable and factor beliefs.
Joris Mooij [Fri, 31 Jul 2009 13:30:17 +0000 (15:30 +0200)]
MEX file dai now also returns variable and factor beliefs.

10 years agoAdded MatLab Quickstart to the README
Joris Mooij [Fri, 31 Jul 2009 09:34:09 +0000 (11:34 +0200)]
Added MatLab Quickstart to the README

10 years agoAdded Charlie Vaske to the list of contributors
Joris Mooij [Wed, 29 Jul 2009 14:21:51 +0000 (16:21 +0200)]
Added Charlie Vaske to the list of contributors

10 years agoMerge branch 'vaske'
Joris Mooij [Wed, 29 Jul 2009 14:13:16 +0000 (16:13 +0200)]
Merge branch 'vaske'

10 years agoImproved documentation and coding style of EM code
Joris Mooij [Wed, 29 Jul 2009 14:07:52 +0000 (16:07 +0200)]
Improved documentation and coding style of EM code

10 years agoFixed bug in MaxSpanningTree
Joris Mooij [Tue, 28 Jul 2009 15:34:09 +0000 (17:34 +0200)]
Fixed bug in MaxSpanningTree

10 years agoSmall cleanup of EM code
Joris Mooij [Tue, 28 Jul 2009 15:33:13 +0000 (17:33 +0200)]
Small cleanup of EM code

10 years agoPolished EM code
Joris Mooij [Tue, 28 Jul 2009 14:20:52 +0000 (16:20 +0200)]
Polished EM code

10 years agoFixed testem failure caused by rounding error
Joris Mooij [Tue, 21 Jul 2009 11:35:19 +0000 (13:35 +0200)]
Fixed testem failure caused by rounding error

10 years agoRemoved all the virtual default constructors *::create(), as they are not used.
Joris Mooij [Mon, 20 Jul 2009 14:37:05 +0000 (16:37 +0200)]
Removed all the virtual default constructors *::create(), as they are not used.

10 years agoAdded BipartiteGraph::eraseEdge and some small cleanup
Joris Mooij [Mon, 20 Jul 2009 13:23:35 +0000 (15:23 +0200)]
Added BipartiteGraph::eraseEdge and some small cleanup

10 years agoCleaned up part of BP code
Joris Mooij [Fri, 17 Jul 2009 19:57:43 +0000 (21:57 +0200)]
Cleaned up part of BP code

10 years agoImprovements of TFactor<T>
Joris Mooij [Fri, 17 Jul 2009 16:55:48 +0000 (18:55 +0200)]
Improvements of TFactor<T>

- Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
- Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)

10 years agoRenamed SampleData->Observation, changed Observation and Evidence
Joris Mooij [Thu, 16 Jul 2009 07:25:38 +0000 (09:25 +0200)]
Renamed SampleData->Observation, changed Observation and Evidence
by removing Observation::_name and changing the Evidence::_samples
variable from map<string,Observation> to vector<Observation>

11 years agoAdded EM code by Charlie Vaske (and cleaned up the style a bit)
Joris Mooij [Mon, 13 Jul 2009 11:02:29 +0000 (13:02 +0200)]
Added EM code by Charlie Vaske (and cleaned up the style a bit)

11 years agoFull command line inference and tests
Charlie Vaske [Tue, 30 Jun 2009 02:00:48 +0000 (19:00 -0700)]
Full command line inference and tests

11 years agoFirst working version of EM
Charlie Vaske [Mon, 29 Jun 2009 02:07:49 +0000 (19:07 -0700)]
First working version of EM

11 years agoFixed FTBFS bug on Windows
Joris Mooij [Mon, 8 Jun 2009 15:57:49 +0000 (17:57 +0200)]
Fixed FTBFS bug on Windows

11 years agoFixed a Windows build issue
Joris Mooij [Sat, 6 Jun 2009 15:03:38 +0000 (17:03 +0200)]
Fixed a Windows build issue
(removed include <ext/hash_map> in include/dai/bbp.h)

11 years agoRemoved erroneous 'inline' directives in gibbs.cpp
Joris Mooij [Wed, 3 Jun 2009 15:20:35 +0000 (17:20 +0200)]
Removed erroneous 'inline' directives in gibbs.cpp

11 years ago[Frederik Eaton] CBP and BBP now use automatically generated properties (using script...
Joris Mooij [Mon, 1 Jun 2009 11:45:25 +0000 (13:45 +0200)]
[Frederik Eaton] CBP and BBP now use automatically generated properties (using scripts/regenerate-properties)

11 years ago[Frederik Eaton] Major cleanup of BBP and CBP code and documentation
Joris Mooij [Mon, 1 Jun 2009 10:52:42 +0000 (12:52 +0200)]
[Frederik Eaton] Major cleanup of BBP and CBP code and documentation

- BBP: change to use Neighbor interface
- tests/aliases.conf: updated with new CBP properties
- Add doxygen documentation to headers

11 years ago[Frederik Eaton] Improved bp_dual
Joris Mooij [Mon, 1 Jun 2009 10:14:56 +0000 (12:14 +0200)]
[Frederik Eaton] Improved bp_dual

BP_dual is no longer an InfAlg, but calculates dual messages from
the beliefs of an existing InfAlg

11 years ago[Frederik Eaton] Several small changes
Joris Mooij [Mon, 1 Jun 2009 09:54:40 +0000 (11:54 +0200)]
[Frederik Eaton] Several small changes

- Updated doxygen.conf to version 1.5.9
- Removed bp_dual from alldai.h/cpp
- Added newInfAlgFromString to alldai.h/cpp
- Added rnd to util.h
- Added FactorGraph::clampVar and FactorGraph::clampFactor
- Changed BP to be able to record order in which messages are sent (for use by BBP)

11 years ago[Frederik Eaton] Change doxygen.conf to expand DAI_ACCMUT macro
Joris Mooij [Wed, 27 May 2009 16:11:33 +0000 (18:11 +0200)]
[Frederik Eaton] Change doxygen.conf to expand DAI_ACCMUT macro

11 years ago[Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor
Joris Mooij [Mon, 25 May 2009 07:11:37 +0000 (09:11 +0200)]
[Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor

11 years ago- [Frederik Eaton]: Misc smaller changes
Joris Mooij [Mon, 25 May 2009 06:48:22 +0000 (08:48 +0200)]
- [Frederik Eaton]: Misc smaller changes
  * include/dai/daialg.h: (InfAlg)
      Add beliefV, beliefF; create sensible default for 'virtual create()'
  * include/dai/properties.h: (PropertySet)
      Add default constructor
      Allow construction from string
      Add method allKeys() to produce list of keys
      In getStringAs(), check for typeid(ValueType) before typeid(std::string)
        (fixes strange bug for empty string property)
  * include/dai/util.h:
      Added comments for macros
      Added function to concatenate two vectors

11 years agoAdded workaround for bug in Boost Graph Library
Joris Mooij [Mon, 4 May 2009 15:14:27 +0000 (17:14 +0200)]
Added workaround for bug in Boost Graph Library

11 years agoSmall improvement to testdai warning message of previous commit.
Joris Mooij [Wed, 11 Mar 2009 09:19:35 +0000 (10:19 +0100)]
Small improvement to testdai warning message of previous commit.

11 years ago[Frederik Eaton] Change testdai help message to warn if the user is running a debuggi...
Joris Mooij [Wed, 11 Mar 2009 09:18:28 +0000 (10:18 +0100)]
[Frederik Eaton] Change testdai help message to warn if the user is running a debugging build

11 years agoTwo tiny improvements
Joris Mooij [Mon, 9 Mar 2009 20:04:40 +0000 (21:04 +0100)]
Two tiny improvements

11 years agoImprovements to BP_dual code
Joris Mooij [Fri, 6 Mar 2009 16:32:56 +0000 (17:32 +0100)]
Improvements to BP_dual code

11 years agoSome improvements to the new BP_dual/BBP/CBP code to make it compile
Joris Mooij [Wed, 4 Mar 2009 11:21:57 +0000 (12:21 +0100)]
Some improvements to the new BP_dual/BBP/CBP code to make it compile