Joris Mooij [Thu, 12 Nov 2009 09:52:51 +0000 (10:52 +0100)]
Documented all exceptions and did some general cleanups
Joris Mooij [Wed, 11 Nov 2009 19:56:26 +0000 (20:56 +0100)]
Improved 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
Joris Mooij [Wed, 11 Nov 2009 13:49:39 +0000 (14:49 +0100)]
Improved error messages of Evidence::addEvidenceTabFile
Joris Mooij [Wed, 11 Nov 2009 13:38:26 +0000 (14:38 +0100)]
Improved documentation of include/dai/evidence.h
Joris Mooij [Tue, 10 Nov 2009 17:43:47 +0000 (18:43 +0100)]
Improved documentation of include/dai/cbp.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
Joris Mooij [Tue, 10 Nov 2009 11:03:10 +0000 (12:03 +0100)]
Improved documentation of include/dai/bp_dual.h
Joris Mooij [Tue, 10 Nov 2009 10:41:49 +0000 (11:41 +0100)]
Improved documentation of include/dai/gibbs.h
Joris Mooij [Tue, 10 Nov 2009 10:13:39 +0000 (11:13 +0100)]
Improved documentation of include/dai/mr.h
Joris Mooij [Tue, 10 Nov 2009 09:22:51 +0000 (10:22 +0100)]
Improved documentation of include/dai/lc.h
Joris Mooij [Mon, 9 Nov 2009 14:04:02 +0000 (15:04 +0100)]
Improved documentation of include/dai/treeep.h
Joris Mooij [Mon, 9 Nov 2009 10:27:44 +0000 (11:27 +0100)]
Added GPL license text to doxygen documentation
Joris Mooij [Mon, 9 Nov 2009 10:12:40 +0000 (11:12 +0100)]
Improved documentation of include/dai/hak.h
Joris Mooij [Thu, 5 Nov 2009 16:20:44 +0000 (17:20 +0100)]
Improved documentation of include/dai/jtree.h and did some cleanups
Joris Mooij [Thu, 5 Nov 2009 13:10:00 +0000 (14:10 +0100)]
Improved documentation of include/dai/bp.h
Joris Mooij [Tue, 3 Nov 2009 18:10:31 +0000 (19:10 +0100)]
Extended InfAlg interface with setProperties(), getProperties() and printProperties()
Joris Mooij [Tue, 3 Nov 2009 17:39:16 +0000 (18:39 +0100)]
Improved documentation of include/dai/mf.h
Joris Mooij [Tue, 3 Nov 2009 17:20:31 +0000 (18:20 +0100)]
Improved documentation of include/dai/exactinf.h
Joris Mooij [Tue, 3 Nov 2009 16:40:12 +0000 (17:40 +0100)]
Fixed regressions in SWIG code
Joris Mooij [Tue, 3 Nov 2009 16:15:50 +0000 (17:15 +0100)]
Declared class Diffs as obsolete
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
Joris Mooij [Tue, 3 Nov 2009 10:12:49 +0000 (11:12 +0100)]
Little additional improvement of 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
Joris Mooij [Mon, 2 Nov 2009 15:41:49 +0000 (16:41 +0100)]
Fixed tests/testall.bat
Joris Mooij [Fri, 30 Oct 2009 15:10:02 +0000 (16:10 +0100)]
Some cleanups of include/dai/prob.h
Joris Mooij [Thu, 29 Oct 2009 16:03:15 +0000 (17:03 +0100)]
Cleanup of include/dai/factor.h
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()
Joris Mooij [Wed, 28 Oct 2009 11:56:55 +0000 (12:56 +0100)]
Improved documentation of include/dai/properties.h
Joris Mooij [Tue, 27 Oct 2009 16:04:31 +0000 (17:04 +0100)]
Fixed const qualifiers in VarSet
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> & )
Joris Mooij [Mon, 26 Oct 2009 13:35:10 +0000 (14:35 +0100)]
Improved documentation of include/dai/regiongraph.h and did some cleanups
Joris Mooij [Mon, 26 Oct 2009 10:47:43 +0000 (11:47 +0100)]
Improved documentation of include/dai/clustergraph.h
Joris Mooij [Mon, 26 Oct 2009 10:19:56 +0000 (11:19 +0100)]
Fixed regression introduced by previous commit
Joris Mooij [Mon, 26 Oct 2009 10:00:26 +0000 (11:00 +0100)]
Added EXACT to aliases/aliases.conf
Joris Mooij [Thu, 22 Oct 2009 15:53:35 +0000 (17:53 +0200)]
Improved documentation of include/dai/factorgraph.h
Joris Mooij [Wed, 21 Oct 2009 16:08:49 +0000 (18:08 +0200)]
Improved documentation of include/dai/weightedgraph.h
Joris Mooij [Tue, 20 Oct 2009 13:31:36 +0000 (15:31 +0200)]
Improved documentation of factor.h
Joris Mooij [Mon, 19 Oct 2009 19:53:11 +0000 (21:53 +0200)]
Improved documentation of include/dai/index.h
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
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
Joris Mooij [Mon, 19 Oct 2009 11:03:15 +0000 (13:03 +0200)]
Updated ChangeLog and added TODO
Joris Mooij [Mon, 19 Oct 2009 10:57:02 +0000 (12:57 +0200)]
Various cleanups and documentation improvements for SmallSet and Prob
Joris Mooij [Fri, 16 Oct 2009 16:56:31 +0000 (18:56 +0200)]
Fixed bug in BipartiteGraph::eraseEdge and improved documentation
Joris Mooij [Wed, 14 Oct 2009 09:26:28 +0000 (11:26 +0200)]
Fixed SWIG octave wrappers and added octave port of example_sprinkler
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
Joris Mooij [Tue, 13 Oct 2009 15:09:59 +0000 (17:09 +0200)]
Renamed directory python into swig
Joris Mooij [Tue, 13 Oct 2009 15:09:19 +0000 (17:09 +0200)]
Added octave target and a README to SWIG wrappers
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
Joris Mooij [Fri, 9 Oct 2009 15:56:05 +0000 (17:56 +0200)]
Added init parameter to HAK/GBP to allow for random initialization
Joris Mooij [Thu, 24 Sep 2009 16:09:11 +0000 (18:09 +0200)]
Replaced the standard assert() macro by DAI_ASSERT
Joris Mooij [Thu, 24 Sep 2009 10:08:46 +0000 (12:08 +0200)]
Introduced CCNODEBUGFLAGS in Makefile and added a constructor to TProb<T>
Joris Mooij [Tue, 22 Sep 2009 13:27:08 +0000 (15:27 +0200)]
[Patrick Pletscher] Added experimental SWIG Python wrapper code
Joris Mooij [Wed, 16 Sep 2009 13:47:09 +0000 (15:47 +0200)]
Updated copyright headers
Joris Mooij [Tue, 15 Sep 2009 10:47:21 +0000 (12:47 +0200)]
Added max-product functionality to JTree
Joris Mooij [Mon, 14 Sep 2009 11:35:14 +0000 (13:35 +0200)]
Fixed two regressions
Joris Mooij [Tue, 8 Sep 2009 09:18:33 +0000 (11:18 +0200)]
Fixed tabs and trailing whitespaces
Joris Mooij [Tue, 8 Sep 2009 08:40:20 +0000 (10:40 +0200)]
Fixed regression in TProb<T>
Joris Mooij [Tue, 8 Sep 2009 08:39:22 +0000 (10:39 +0200)]
Improved coding style of recent changes by Charlie Vaske
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
Joris Mooij [Tue, 8 Sep 2009 07:52:09 +0000 (09:52 +0200)]
Small documentation improvements
Joris Mooij [Mon, 7 Sep 2009 14:30:51 +0000 (16:30 +0200)]
Various fixes
Joris Mooij [Mon, 7 Sep 2009 13:44:13 +0000 (15:44 +0200)]
Cleaned up error handling by introducing the DAI_THROWE macro.
Joris Mooij [Fri, 4 Sep 2009 15:08:21 +0000 (17:08 +0200)]
Introduced DAI_DEBASSERT macro to abbreviate a common pattern
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
Joris Mooij [Sun, 16 Aug 2009 16:12:35 +0000 (18:12 +0200)]
[Patrick Pletscher] Fixed performance issue in FactorGraph::clamp and FactorGraph::clampVar
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
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)
Joris Mooij [Mon, 10 Aug 2009 19:59:05 +0000 (21:59 +0200)]
[Sebastian Nowozin] Fixed memory leak in MatLab interface (dai.cpp)
Joris Mooij [Thu, 6 Aug 2009 12:20:45 +0000 (14:20 +0200)]
Fixed clean_updates bug in BBP by commenting out this feature
Joris Mooij [Tue, 4 Aug 2009 15:37:38 +0000 (17:37 +0200)]
Updated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 15:35:49 +0000 (17:35 +0200)]
Merge branch 'eaton'
Conflicts:
ChangeLog
Makefile
include/dai/daialg.h
Joris Mooij [Tue, 4 Aug 2009 15:33:02 +0000 (17:33 +0200)]
Updated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 15:10:35 +0000 (17:10 +0200)]
Added CBP to README and to doxygen front page.
Joris Mooij [Tue, 4 Aug 2009 14:57:22 +0000 (16:57 +0200)]
Updated ChangeLog
Joris Mooij [Tue, 4 Aug 2009 14:39:13 +0000 (16:39 +0200)]
Cleanup of CBP code
Joris Mooij [Tue, 4 Aug 2009 13:36:37 +0000 (15:36 +0200)]
Even more cleanup of BBP code
Joris Mooij [Mon, 3 Aug 2009 15:44:14 +0000 (17:44 +0200)]
Cleanup of BBP code
Joris Mooij [Fri, 31 Jul 2009 15:25:21 +0000 (17:25 +0200)]
Cleanup of BP_dual code
Joris Mooij [Fri, 31 Jul 2009 14:22:12 +0000 (16:22 +0200)]
Marked the backwards compatibility edge interface of BipartiteGraph as obsolete
Joris Mooij [Fri, 31 Jul 2009 14:11:30 +0000 (16:11 +0200)]
Various cleanups
Joris Mooij [Fri, 31 Jul 2009 13:30:17 +0000 (15:30 +0200)]
MEX file dai now also returns variable and factor beliefs.
Joris Mooij [Fri, 31 Jul 2009 09:34:09 +0000 (11:34 +0200)]
Added MatLab Quickstart to the README
Joris Mooij [Wed, 29 Jul 2009 14:21:51 +0000 (16:21 +0200)]
Added Charlie Vaske to the list of contributors
Joris Mooij [Wed, 29 Jul 2009 14:13:16 +0000 (16:13 +0200)]
Merge branch 'vaske'
Joris Mooij [Wed, 29 Jul 2009 14:07:52 +0000 (16:07 +0200)]
Improved documentation and coding style of EM code
Joris Mooij [Tue, 28 Jul 2009 15:34:09 +0000 (17:34 +0200)]
Fixed bug in MaxSpanningTree
Joris Mooij [Tue, 28 Jul 2009 15:33:13 +0000 (17:33 +0200)]
Small cleanup of EM code
Joris Mooij [Tue, 28 Jul 2009 14:20:52 +0000 (16:20 +0200)]
Polished EM code
Joris Mooij [Tue, 21 Jul 2009 11:35:19 +0000 (13:35 +0200)]
Fixed testem failure caused by rounding error
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.
Joris Mooij [Mon, 20 Jul 2009 13:23:35 +0000 (15:23 +0200)]
Added BipartiteGraph::eraseEdge and some small cleanup
Joris Mooij [Fri, 17 Jul 2009 19:57:43 +0000 (21:57 +0200)]
Cleaned up part of BP code
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)
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>
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)
Charlie Vaske [Tue, 30 Jun 2009 02:00:48 +0000 (19:00 -0700)]
Full command line inference and tests
Charlie Vaske [Mon, 29 Jun 2009 02:07:49 +0000 (19:07 -0700)]
First working version of EM
Joris Mooij [Mon, 8 Jun 2009 15:57:49 +0000 (17:57 +0200)]
Fixed FTBFS bug on Windows
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)