Various EM code improvements by Charles Vaske and Andy Nguyen
[libdai.git] / ChangeLog
1 git HEAD
2 --------
3 * [Charles Vaske] Various improvements to EM code, including interface changes
4 * Fixed regression in SWIG interface caused by new build system (thanks to Benjamin Mumm for reporting this)
5 * Added 'inclusive' argument to DAG::ancestors() and DAG::descendants()
6 * [Julien Rebetez] added FactorGraph::printDot() to SWIG interface
7 * Build system: optional compilation targets are now set in include/dai/dai_config.h instead of Makefile.ALL
8 * 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
9 * Removed conversion script FastInf->libDAI because it is buggy (uses wrong permutation of factor entries)
10 * Extended SWIG python interface (inspired by Kyle Ellrott): inference is possible in Python now!
11 * Added toString() formatting functions to the classes that had an output streaming operator<<
12 * Replaced all occurrences of std::size_t by size_t to avoid SWIG problems
13 * Fixed division-by-zero issue in pow() which caused problems for GLC+ with sparse factors
14 * Fixed bugs in unit test prob_test.cpp: replaced all occurences of
15 BOOST_CHECK_CLOSE(...,(Real)0.0,tol) with BOOST_CHECK_SMALL(...,tol)
16 * Merged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh
17
18
19 libDAI-0.3.1 (2012-09-17)
20 -------------------------
21
22 Miscellaneous improvements:
23 * Full 64-bit support on all supported platforms (Linux, OSX, Windows)
24 * Added special MatLab interface for junction tree algorithm (dai_jtree)
25 * Optimized ClusterGraph( const FactorGraph&, bool) constructor
26
27 Build system improvements:
28 * Added Makefile.WINDOWS64, kindly provided by Lin Ming
29 * [Arman Aksoy] Added Makefile.MACOSX64
30 * Added VC10 build files, kindly provided by Sameh Khamis
31
32 Bug fixes:
33 * Fixed bug (found by Sameh Khamis): define NAN (Windows)
34 * Fixed bug (found by Sameh Khamis): add some necessary casts of size_t to BigInt (Windows)
35 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION__ (Visual Studio) or __func__ (other compilers)
36 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
37 * Fixed bug (found by cax): when building MatLab MEX files, GMP/MPIR libraries were not linked
38 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)
39 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions
40 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers
41 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()
42 * Fixed memory leak in CBP::run()
43 * Fixed typo in Priya's name
44
45
46 libDAI-0.3.0 (2011-07-12)
47 -------------------------
48
49 New license:
50 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)
51
52 Miscellaneous improvements:
53 * Improved Exception class
54 (it now stores more information and doesn't print to stderr by default)
55 * Added builtinInfAlgs() and builtinInfAlgNames()
56
57 Bug fixes:
58 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()
59 and maxDiff() implementations
60 * Now uses GMP big integer type to represent linear states and the number of
61 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya
62 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now
63 no longer works out-of-the-box.
64 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
65 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
66 instead of returning a MAP state with zero joint probability
67 (reported by Hynek Urban)
68 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
69 (the random seed needs to be an unsigned int on some platforms)
70 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
71 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
72 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)
73 * Replaced all Name members by name() virtual functions and removed global variable DAINames
74 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
75
76
77 libDAI-0.2.7 (2010-08-19)
78 -------------------------
79
80 * Removed interfaces deprecated in 0.2.6.
81 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
82 if one or more variables had a MAP belief with more than one maximum, an
83 incorrect MAP state could result.
84
85
86 libDAI-0.2.6 (2010-08-05)
87 -------------------------
88
89 New features:
90 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
91 * Added source code for one of the winning solvers of the
92 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
93 * Added support for reading files in the UAI Approximate Inference Challenge
94 format, supporting both the 2006/2008 evidence file format and the 2010
95 evidence file format (io.h/cpp).
96
97 Miscellaneous improvements:
98 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
99 for setting an upper limit on execution time.
100 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
101 * SmallSet:
102 - Added SmallSet::erase( const T& t ).
103 * VarSet:
104 - nrStates() now returns a long double instead of a size_t.
105 * Permute:
106 - Added ranges() accessor.
107 - Added inverse() method.
108 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
109 * Factor:
110 - Added createFactorDelta( const VarSet& vs, size_t state ).
111 * ClusterGraph:
112 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
113 - Added findCluster( const VarSet& cl ).
114 - Added elimVar( size_t i ).
115 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
116 * FactorGraph:
117 - Added isMaximal(size_t).
118 - Added maximalFactor(size_t).
119 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
120 * Gibbs:
121 - Added 'restart' property.
122 - Added Gibbs::findMaximum() for MAP inference.
123 * HAK:
124 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
125 * examples/examples_imagesegmentation.cpp:
126 - [Peter Rockett] Improved Makefiles for image segmentation example.
127 - Added build flag to specify the CImg version.
128 * util.h/cpp:
129 - Added fromString<>( const std::string& x ).
130
131 Interface changes (the old interface is marked obsolete and will be removed in the next release):
132 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
133 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
134 and replaced them by a globally defined Neighbor structure
135 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
136 and replaced them by a globally defined Neighbors type
137 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
138 and replaced them by a globally defined Edge type
139 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
140 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
141 variable is not found.
142 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
143 and replaced it with an improved version
144 'vector<string> tokenizeString( const string&, bool, const string& )'
145 * Removed interfaces deprecated in 0.2.5.
146
147 Bug fixes:
148 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
149 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
150 which have problems when comparing const_reverse_iterator with
151 reverse_iterator.
152 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
153 (segfault if factors depending on 0 variables were passed to MatLab)
154
155
156 libDAI-0.2.5 (2010-05-09)
157 -------------------------
158
159 New features:
160 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
161 weightedgraph, enum, util, exceptions, properties, index, prob,
162 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
163 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
164 * Added utils/uai2fg, a utility to convert the UAI inference competition file
165 formats to the libDAI factor graph file format
166 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
167 * Added examples/example_imagesegmentation
168
169 Miscellaneous improvements:
170 * TRWBP:
171 - Added initialization of TRWBP weights by sampling spanning trees
172 * MF:
173 - Added an "init" option that allows to initialize randomly
174 - Added an "updates" option that allows to choose between standard
175 mean field and "hard-spin" mean field
176 * MR:
177 - rewrote response propagation implementation with help of BBP
178 - now uses GraphAL to represent the Markov graph
179 - miscellaneous smaller cleanups
180 * TreeEP:
181 - Now also supports disconnected factor graphs
182 * JTree:
183 - Now also supports disconnected factor graphs
184 * ExactInf:
185 - Added findMaximum()
186 * RegionGraph:
187 - Added error checking code
188 - Changed the way a RegionGraph is streamed to an std::ostream.
189 * ClusterGraph:
190 - Added nrVars() method
191 - Added var( size_t ) method
192 - Added cluster( size_t ) method
193 * FactorGraph:
194 - clamped() now contains a delta factor for the clamped variable
195 - Added MarkovGraph()
196 * TFactor:
197 - Added takeAbs()
198 - Added takeExp()
199 - Added takeLog( bool )
200 - Added operator-() const
201 - Added sumAbs() const
202 - Added operator==( const TFactor<T> &y )
203 - Added get(size_t), set(size_t,T)
204 * TProb:
205 - Added operator==( const TProb<T> &q )
206 - accumulate() now also applies op2 to init
207 - operator/= (T x) now yields 0 when dividing by 0
208 - Added resize(size_t)
209 - Added get(size_t) and set(size_t,T)
210 - Changed format of TProb<T> when streamed to an ostream
211 * multifor:
212 - Added reset()
213 * PropertySet:
214 - Added size()
215 - Added clear()
216 - Added erase()
217 * util.h/cpp:
218 - Added std::string toString( const T& x )
219 * weightedgraph.h/cpp:
220 - Added option to MaxSpanningTree and MinSpanningTree for
221 choosing between Prim's algorithm and Kruskal's algorithm
222 - Better error checking in RootedTree constructor
223 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
224 * BipartiteGraph:
225 - Added hasEdge()
226 - Added findNb1()
227 - Added findNb2()
228 - Added nb1Set()
229 - Added nb2Set()
230 - Added operator==( const BipartiteGraph& )
231 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
232 - Added operator<<( std::ostream&, const BipartiteGraph& )
233 * GraphAL:
234 - Added hasEdge(size_t,size_t)
235 - Added nbSet(size_t)
236 - Added operator==( const GraphAL& )
237 - Added operator<<( std::ostream&, const GraphAL& )
238 * SmallSet:
239 - Added insert( const T& t ) method
240 * Improved regression test
241 * Made all "verbose" properties optional
242 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
243 'ISING' factor type has been renamed to 'ISINGGAUSS'
244 * tests/testdai option "marginals" now has five possible values: NONE
245 outputs no marginals, VAR only variable marginals, FAC only factor
246 marginals, VARFAC both types of marginals, and ALL outputs all
247 marginals calculated by the algorithm.
248 * Compressed Makefile
249
250 Interface changes (the old interface is marked obsolete and will be removed in the next release):
251 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
252 * TreeEP:
253 - Changed construct( const RootedTree& ) into
254 construct( const FactorGraph&, const RootedTree& )
255 * JTree:
256 - Changed construct( const std::vector<VarSet>&, bool ) into
257 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
258 - Changed GenerateJT( const std::vector<VarSet> & )
259 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
260 * RegionGraph:
261 - Made (previously public) members G, ORs, IRs and fac2OR protected and
262 added DAG() accessor which returns a reference to the region graph DAG
263 structure (currently implemented as a BipartiteGraph).
264 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
265 protected, because exposing it to the world serves no purpose.
266 - Removed partial constructor RegionGraph( const FactorGraph& fg )
267 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
268 protected and renamed them by changing the "Recompute" into "recompute",
269 because exposing them to the world serves no purpose.
270 * ClusterGraph:
271 - Made (previously public) members G, vars and clusters private and added
272 bipGraph(), vars() and clusters() methods which offer read-only access
273 to these members.
274 - Deprecated toVector()
275 - Renamed size() into nrClusters()
276 * FactorGraph:
277 - Renamed Cliques() into maximalFactorDomains() and made it faster
278 - findVars( const VarSet& ) now returns a SmallSet<size_t>
279 and its argument now has a const-qualifier (which fixes a small bug).
280 - Made (previously public) member G private and added the
281 bipGraph() method, which offers read-only access to it.
282 - Deprecated the iterator interface:
283 o FactorGraph::iterator typedef
284 o FactorGraph::const_iterator typedef
285 o FactorGraph::begin() members
286 o FactorGraph::end() members
287 - Deprecated factor(size_t) which offered write access to a factor
288 because using this functionality in the descendant RegionGraph is dangerous,
289 as the outer regions are not automatically recomputed.
290 * TFactor:
291 - Renamed states() into nrStates()
292 - Added get(size_t) and set(size_t,T) operators;
293 get() is equivalent to "operator[](size_t) const" and set() should
294 be used instead of the non-const operator[], which has been deprecated
295 * TProb:
296 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
297 constructor: the sizeHint argument no longer defaults to 0
298 - Deprecated accumulate( T init, binOp op1, unOp op2 );
299 instead, accumulateSum( T init, unOp op ) and
300 accumulateMax( T init, unOp op, bool minimize ) should be used.
301 - Deprecated TProb::NormType and TProb::DistType;
302 ProbNormType and ProbDistType should be used instead.
303 - Fixed bug by renaming operator<=() to operator<()
304 - Added get(size_t) and set(size_t,T) operators;
305 get() is equivalent to "operator[](size_t) const" and set() should
306 be used instead of the non-const operator[], which has been deprecated
307 * PropertySet:
308 - Renamed Set() -> set()
309 - Renamed Get() -> get()
310 - Renamed GetAs<T>() -> getAs<T>()
311 - Renamed ConvertTo<T>() -> convertTo<T>()
312 * util.h/cpp:
313 - Removed max( const std::vector<Real> &v )
314 * weightedgraph.h/cpp:
315 - Renamed MaxSpanningTreePrims into MaxSpanningTree
316 - Renamed MinSpanningTreePrims into MinSpanningTree
317 - The vertices in DEdge and UEdge are now named "first" and "second"
318 for compatibility with a std::pair<size_t,size_t>
319 * BipartiteGraph:
320 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
321 * SmallSet:
322 - The sizeHint argument of the iterator constructor
323 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
324 no longer has a default value in order to avoid confusion with the
325 SmallSet::SmallSet( const T &t1, const T &t2 )
326 constructor.
327
328 Bug fixes:
329 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
330 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
331 * Fixed some bugs in the MatLab interface build system
332 * Fixed a bug in utils/fginfo.cpp
333 * Fixed a bug in JTree::findMaximum() and simplified the code
334 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
335 assignment from happening
336 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
337 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
338 FactorGraph ancestor methods; this has been corrected by letting them throw a
339 NOT_IMPLEMENTED exception.
340 * Fixed bug in FactorGraph::clone()
341 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
342 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
343 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
344 * Fixed bug in PropertySet::setAsString<T>()
345 * Fixed a bug in rnd_seed()
346 * BipartiteGraph:
347 - Fixed bug in eraseNode1()
348 - Fixed bug in eraseNode2()
349 - Fixed bug in isTree()
350 * GraphAL:
351 - Fixed bug in nrEdges()
352 - Fixed bug in addEdge()
353 - Fixed bug in isTree()
354 - Fixed bug in eraseNode()
355 - Fixed bug in printDot()
356 * Fixed bug in createGraphGrid3D()
357 * Fixed bug in createGraphRegular()
358
359
360 libDAI-0.2.4 (2010-02-11)
361 -------------------------
362
363 New features:
364 * Implemented Tree-Reweighted BP
365 * [Frederik Eaton] Implemented Fractional Belief Propagation
366
367 Miscellaneous improvements:
368 * Improved documentation
369 * [Frederik Eaton] Added constructors for BBPCostFunction
370 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
371 * [Frederik Eaton] Added unary minus to TProb<>
372 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
373 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
374 * tests/testdai option "marginals" now has three possible values: NONE
375 outputs no marginals, VAR only variable marginals, and ALL outputs all
376 marginals calculated by the algorithm.
377 * Strengthened convergence criteria of various algorithms
378 * Added GraphAL, an adjacency list implementation for graphs,
379 similar to (but simpler than) BipartiteGraph
380 * Added some functionality to create various standard factors
381 (the functions whose names start with "createFactor")
382 * Added examples example_sprinkler_gibbs and example_sprinkler_em
383 * Implemented various heuristics for choosing a variable elimination sequence
384 in JTree
385 * Added BETHE method for GBP/HAK cluster choice
386 * Made alias support official part of the library
387
388 Build system:
389 * Moved platform independent build options into Makefile.ALL
390 * Windows platform now needs Boost 1.37 or higher
391
392 Code cleanup:
393 * Cleaned up utils/createfg and tests/testdai
394 * Cleanup of some duplicate code in BP, FBP, TRWBP
395
396 Interface changes (the old interface is marked obsolete and will be removed in the next release):
397 * Removed obsolete/deprecated stuff
398 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
399 * Renamed some functions of BipartiteGraph:
400 add1() -> addNode1()
401 erase1() -> eraseNode1()
402 nr1() -> nrNodes1()
403 add2() -> addNode2()
404 erase2() -> eraseNode2()
405 nr2() -> nrNodes2()
406 * Renamed some functions in ClusterGraph:
407 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
408 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
409 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
410 * Changed interface of one RegionGraph constructor
411 * Renamed "Clamped BP" into "Conditioned BP"
412
413 Bug fixes:
414 * Fixed regression in scripts/regenerate-properties (now all errors are
415 gathered before throwing the exception, as used to be the case)
416 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
417 * [Alexander Schwing] Fixed error in BP that occured with damping
418 and using log-domain updates
419 * Fixed bug in HAK for trivial region graphs (with only one outer region
420 and no inner regions), reported by Alejandro Lage.
421 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
422
423
424 libDAI-0.2.3 (2009-11-16)
425 -------------------------
426
427 New features:
428 * Complete doxygen documentation (although more detailed documentation still
429 has to be written)
430 * [Charles Vaske] Added parameter learning for conditional probabilities by
431 Expectation Maximization
432 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
433 octave interfaces
434 * Added Max-Product functionality to JTree
435 * [Frederik Eaton] Added Back-Belief-Propagation
436 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
437 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
438
439 Code cleanup:
440 * Updated copyright headers
441 * Cleaned up error handling by introducing the DAI_THROWE macro
442 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
443 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
444 dai::Exception and is even active if NDEBUG is defined
445 * Removed all the virtual default constructors *::create(), as they are not used
446 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
447 * [Frederik Eaton] Change cout to cerr in warnings and error messages
448
449 Miscellaneous improvements:
450 * BipartiteGraph:
451 - Added eraseEdge( size_t n1, size_t n2 )
452 - [Frederik Eaton] Improved documentation of Neighbor
453 * TProb<T>:
454 - Added divided_by(const TProb<T>&) const
455 - Added constructor TProb<T>( const std::vector<S> &v )
456 - Added size_t draw(), which draws a random index
457 - [Frederik Eaton] Added setUniform()
458 - [Frederik Eaton] Added sumAbs()
459 - [Frederik Eaton] Added argmax()
460 - [Giuseppe Passino] Added begin(), end()
461 * TFactor<T>:
462 - [Giuseppe Passino] Added begin(), end()
463 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
464 which reorders variables to canonical ordering before storing the table
465 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
466 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
467 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
468 * State:
469 - [Giuseppe Passino] Added prefix ++ operator
470 * Permute:
471 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
472 * FactorGraph:
473 - [Frederik Eaton] Added clampVar()
474 - [Frederik Eaton] Added clampFactor()
475 - [Giuseppe Passino] Added begin(), end()
476 * PropertySet:
477 - Added keys(), for getting all keys
478 - [Frederik Eaton] Added default constructor
479 - [Frederik Eaton] Added constructor from string
480 * InfAlg:
481 - Added setProperties(), getProperties() and printProperties()
482 - [Frederik Eaton] Added beliefV(), beliefF()
483 * ExactInf:
484 - Added calcMarginal(const VarSet &)
485 * HAK:
486 - Added "init" parameter to allow for random initialization
487 * BP:
488 - [Giuseppe Passino] Added findMaximum(), which can be used after running
489 max-product BP to construct a global state with maximum probability
490 * JTree:
491 - Added findMaximum(), which can be used after running
492 max-product JTree to construct a global state with maximum probability
493 * MatLab interface:
494 - MEX file dai now also returns variable and factor beliefs
495 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
496 (only for BP and JTree)
497 * README is now created automatically from doxygen documentation
498 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
499 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
500 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
501 and functions (concat(),rnd()) to util.h
502 * Changed output stream operator<< for Var and VarSet
503 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
504 alias substitutions
505 * [Frederik Eaton] Added useful aliases to aliases.conf
506 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
507 set instead of the linear search (which can yield enormous speedups - a
508 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
509 * Added debug assertions to Var which check for inconsistent dimensions of
510 variables with the same labels
511 * toc() now returns POSIX system time with maximum accuracy of microseconds
512 * Exception objects now remember their error code
513 * Examples:
514 - Moved example.cpp to examples/
515 - Added examples/example_bipgraph.cpp
516 - Added examples/example_varset.cpp
517 - Added examples/example_sprinkler.cpp
518 - Added examples/example_permute.cpp
519 - Added python and octave ports for examples/example_sprinkler.cpp
520
521 Build system:
522 * Improved Makefile:
523 - Merged Makefile.win and Makefile.shared into Makefile
524 - Macros DAI_VERSION and DAI_DATE have been introduced,
525 in order to store this information in a central place
526 - Introduced CCNODEBUGFLAGS in Makefile
527 - Switched Makefile.win to GNU Make syntax
528 - [Frederik Eaton] Added TAGS, lib targets to Makefile
529 * Compatibility:
530 - [Peter Gober] libDAI can now be built on Cygwin
531 - [Dan Preston] libDAI can now be built on Mac OS X
532 - Changed regression test so that it also works under Windows
533
534 Interface changes (the old interface is marked obsolete and will be removed in the next release):
535 * Var:
536 - Variable labels are now nonnegative (of type size_t)
537 * VarSet:
538 - Replaced calcState() by non-member calcLinearState()
539 - Replaced calcStates() by non-member calcState()
540 * Permute:
541 - Renamed convert_linear_index into convertLinearIndex
542 * TProb<>:
543 - Replaced log0() by log(true)
544 - Replaced takeLog0() by takeLog(true)
545 - Removed hasNonPositives()
546 - Renamed minVal() to min()
547 - Renamed maxVal() to max()
548 - Renamed totalSum() to sum()
549 * TFactor<>:
550 - Replaced log0() by TFactor<T>::log(true)
551 - Removed divided_by, use operator/ instead
552 - Removed divide, use operator/= instead
553 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
554 - Renamed minVal() to min()
555 - Renamed maxVal() to max()
556 - Renamed totalSum() to sum()
557 * FactorGraph:
558 - Changed clamp and clamp interfaces (the variable to be
559 clamped is now indicated by its index, not as a Var)
560 * RegionGraph:
561 - Renamed Check_Counting_Numbers into checkCountingNumbers
562 - Renamed Calc_Counting_Numbers into calcCountingNumbers
563 * Miscellaneous:
564 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
565 - Replaced UEdgeVec by Graph
566 - Replaced DEdgeVec by new RootedTree class
567 - Moved functionality of GrowRootedTree() into constructor of RootedTree
568 - Merged calcPairBeliefsNew() into calcPairBeliefs()
569 - Removed calcMarginal2ndO()
570 - Renamed smallSet<T> to SmallSet<T>
571 - Removed class Diffs
572 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
573 BipartiteGraph and FactorGraph (which will be obsoleted soon)
574
575 Bug fixes:
576 * Fixed reversal of min and max in
577 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
578 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
579 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
580 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
581 before typeid(std::string) (this fixes a strange bug for empty string property)
582 * Added work-around for bug in Boost Graph Library
583 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
584 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
585 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
586 for reporting this)
587
588
589 libDAI-0.2.2 (2008-09-30)
590 -------------------------
591
592 New features:
593 * Approximate inference methods now report the number of iterations needed.
594 * Added damping to various algorithms to improve convergence properties.
595 * Added more features to utils/createfg for creating factor graphs.
596 * Added ExactInf class for brute force exact inference.
597 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
598 whether calculations are done in the log-domain or in the linear domain;
599 doing calculations in the log-domain may help if the numerical range
600 of a double is too small.
601 * [Claudio Lima] Added Max-Product functionality to BP.
602 * Improved documentation.
603
604 Improved architecture:
605 * Added Exceptions framework.
606 * Pervasive change of BipartiteGraph implementation (based on an idea by
607 Giuseppe Passino). BipartiteGraph no longer stores the node properties
608 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
609 nor an edge list. Instead, it stores the graph structure as lists of
610 neighboring nodes. This yields a significant memory/speed improvement for
611 large factor graphs, and is more elegant as well. Iterating over neighbors is
612 made easy by using boost::foreach.
613 * Added conditional compilation of inference methods.
614 * VarSet is now implemented using a std::vector<Var> instead of a
615 std::set<Var>, which yields a significant speed improvement. Furthermore,
616 the implementation has been generalized, resulting in the small_set<T> class
617 which can be used to represent sets of small cardinality; VarSet is the
618 specialization with T = Var.
619 * Improved ClusterGraph implementation, yielding significant speedups
620 for the JunctionTree algorithm on large factorgraphs.
621
622 Code cleanup:
623 * Moved everything into namespace "dai".
624 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
625 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
626 * Removed utils/remove_short_loops and matlab/remove_short_loops.
627 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
628 * Improved index.h:
629 - Renamed Index -> IndexFor
630 - Added some .reserve()'s to IndexFor methods which yields a
631 25% speedup of testregression
632 - Replaced multind by Permute
633 - Added MultiFor
634 - Added State
635 * New funcstionality of factor.h.
636 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
637 inference algorithm, because the Properties framework was not as
638 convenient as I hoped, and not every inference algorithm needs a maxdiff
639 variable. Also, replaced some FactorGraph functionality in InfAlg by a
640 function that returns the FactorGraph. The result is cleaner (less
641 entangled) code.
642 * Removed x2x.
643 * Replaced Complex with real numbers (negative potentials are just too rare
644 to warrant the additional "complexity" :)).
645
646 Miscellaneous improvements:
647 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
648 GCC under Cygwin.
649 * Contributions by Peter Gober:
650 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
651 * Misc contributions by Giuseppe Passino:
652 - removed "using namespace std;" from header files - bad practice;
653 - moved header files in include/dai and sources in src;
654 - changed #ifndefs to GNU style;
655 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
656 - dai::TProb:
657 o removed copy constructor and assignment operators (redundant);
658 o implementation of some methods via STL algorithms;
659 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
660 o explicit constructor (prevents implicit conversion from size_t to TProb);
661 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
662 * Misc contributions by Christian Wojek:
663 - New FactorGraph constructor that constructs from given ranges of factors
664 and variables;
665 - Optimization of FactorGraph constructors using tr1::unordered_map.
666 * FactorGraph constructors no longer check for short loops (huge speed
667 increase for large factor graphs), nor for negative entries. Also, the
668 normtype is now Prob::NORMPROB by default.
669 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
670
671 Interface changes:
672 * VarSet::
673 - VarSet::stateSpace() -> nrStates(const VarSet &)
674 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
675 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
676 - removed bool operator||
677 - operator&&(const VarSet&) -> intersects(const VarSet&)
678 - operator&&(const Var&) -> contains(const Var&)
679 * FactorGraph::
680 - delta(const Var &) -> delta(size_t)
681 - Delta(const Var &) -> Delta(size_t)
682 - makeCavity(const Var &) -> makeCavity(size_t)
683 - vars() -> vars
684 - factors() -> factors
685 - removed MakeFactorCavity(size_t)
686 - removed ExactMarginal(const VarSet &)
687 - removed ExactlogZ()
688 - removed updatedFactor(size_t)
689 - removed _normtype and NormType()
690 - removed hasShortLoops(...) and removeShortLoops(...)
691 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
692 - undoProb(size_t) -> restoreFactor(size_t)
693 - saveProb(size_t) -> backupFactor(size_t)
694 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
695 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
696 - ReadFromFile(const char*) returns void (throws on error)
697 - WriteToFile(const char*) returns void (throws on error)
698 - removed hasNegatives()
699 * RegionGraph::
700 - nr_ORs() -> nrORs()
701 - nr_IRs() -> nrIRs()
702 - ORs() -> ORs
703 - IRs() -> IRs
704 * *::Regenerate() -> *::construct()
705 * Renamed Index -> IndexFor
706 * Diffs:
707 - max() -> maxDiff()
708 - max_size() -> maxSize()
709 * Prob::max() -> Prob::maxVal()
710 * Factor::
711 - max() -> maxVal()
712 - part_sum() -> partSum()
713 * toc() in util.h now returns seconds as a double
714 * VarSet::operator&&
715 * Properties -> PropertySet
716
717
718 libDAI-0.2.1 (2008-05-26)
719 -------------------------
720
721 Bugfix release.
722 * added missing cstdio header in util.h
723 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
724 * added description of the factor graph fileformat
725 * improved Makefile
726
727
728 libDAI-0.2.0 (2006-11-30)
729 -------------------------
730
731 First public release.
732
733
734 0.1.5 (2006-11-30)
735 ------------------
736
737 Regressions
738
739 - tests/testlcbp and tests/testlcbp are broken.
740 - EXACT method does not work anymore.
741 - The Properties framework gives a speed penalty because of the lookup
742 costs involved; inner loops should be optimized.
743
744 General framework
745
746 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
747 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
748 functions to forward functionality from either FactorGraph or RegionGraph
749 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
750 and in RegionGraph and no explicit interface is needed in descendants.
751 - New abstract base class InfAlg added, representing an inference algorithm,
752 from which DAIAlg<T> inherits. This solves the incompatibility problems of
753 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
754 DAIAlg<RegionGraph>). More work is required to reduce code duplication
755 (make FactorGraph part of InfAlg).
756 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
757 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
758 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
759 one to save a few factors, modify them (e.g. clamp them), and then restore them
760 to their old values. Undo should also init the corresponding messages / beliefs.
761 This can be used if a given factor graph repeatedly needs to be clamped in
762 different ways and an approximation method is run for each clamping; using the
763 saveProbs/undoProbs can give a significant speed increase.
764 - Switched to a general Properties framework that handles the parameters of
765 all inference methods in a uniform manner. The Properties class is a map of
766 several properties in boost::any objects, indexed by their names (strings).
767 It can read from a stream and write to a stream. It is recursive, in the sense
768 that a Properties object can hold a variable of type Properties as well.
769 - Added a generic way of constructing inference algorithms from a factor graph,
770 name and properties object. Added the newInfAlg function which constructs
771 the requested object. This is used by LCBP, the Matlab interface and the
772 command line (test) interface.
773 - Added a generic enum framework for enum parameters. Although implemented as a
774 hack, it is quite useful in that it drastically simplifies and reduces the
775 amount of code for handling enum parameters.
776 - Provided generic functions for calculating marginals in different ways that
777 work for all approximate inference methods.
778
779 Bugfixes
780
781 - Fixed GBP free energy.
782 - Fixed bug in junctiontree (it didn't init the _vars variable).
783 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
784 the logical NOT of what they should return).
785 - Fixed bug in RegionGraph::RecomputeOR(s).
786 - Fixed bug in utils/create_dreg_fg:
787 graph structure was not random for given parameters (forgot to call srand()).
788 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
789 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
790 that consists of one outer region only.
791 - Fixed INIT bug in LCBP2::UpdatePancake().
792 - Fixed MaxDiffs flow (except for MR).
793
794 New functionality
795
796 - HAK supports several default cluster choices:
797 minimal (only factors)
798 delta (Markov blankets)
799 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
800 Only the maximal clusters are used as outer clusters.
801 - Implemented TreeEP. It generalizes the heuristic method described in the
802 Minka & Qi paper for obtaining a tree with the most relevant interactions to
803 higher order interactions. Almost all optimizations described in the Minka & Qi
804 paper are used, except that evidence is passed over the whole tree instead of
805 relevant subsets (the latter is almost implemented but buggy). Also added
806 alternative (worst-case) algorithm that uses a maximum spanning tree on the
807 weighted graph where the weight between neighbours i and j is given by
808 N(psi,i,j), where psi is the product of all the factors involving both i and j
809 (which is an upper bound on the effective interaction between i and j).
810 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
811 to be able to handle connectivities larger than 3 (in principle, up to 32).
812 It supports different initialization methods (the original RESPPROP,
813 the CLAMPING method and EXACT which uses JTree) and different update methods
814 (FULL and LINEAR).
815 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
816 networks and uses some approximate inference method on them for calculating
817 marginals.
818 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
819 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
820 interactions and LCBPL is LCBPI improved for higher-order interactions.
821 - Wrote one single program utils/createfg for creating various types of
822 random factor graphs.
823 - Wrote utility to visualize factor graphs using graphviz.
824 (it uses the BOOST Program Options library)
825 - Added fginfo utility that displays some info about a .fg file.
826 - Implemented Factor::strength function that calculates the potential strength
827 N(psi,i,j) between variables i and j as described in cs.IT:0504030
828 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
829 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
830 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
831 - Implemented a MATLAB interface ai_potstrength for Factor::strength
832 - Added Martijn's x2x
833
834 Improvements of existing code
835
836 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
837 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
838 associates outer region indices to factor indices (no powers yet, this
839 is deemed superfluous) and provides functions to recompute (some of) the
840 outer regions from the factors.
841 - InfAlg descendants run() methods now stop immediately and return NAN in case
842 they detect NANs. Only BP does not do NAN checking for performance reasons.
843 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
844 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
845 timing and convergence criteria.
846 - Implemented logZ() for JTree. It does the calculation during message-passing.
847 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
848 hopefully this will give more accurate approximations.
849 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
850 for a faster way of calculating marginals, which does not require a call to init()
851 nor cloning the whole object for each clamping. This leads to a significant speedup.
852 - LCBP (and LCBP2) now have complete flexibility in the specification of the
853 inner method, i.e. the method used to generate the initial cavity approximations.
854 One can pass two strings, a name and a properties string, and LCBP simply invokes
855 newInfAlg to construct the corresponding inference algorithm and uses the generic
856 marginal functions to approximate cavity marginals.
857 - Replaced the global "method" variable by local properties and removed ai.h
858 - Added some methods to Factor (operators *, *=, /, /= with doubles as
859 second argument, operators -, +=, -= with other Factors as second
860 arguments, randomize(), RemoveFirstOrderInteractions) and similar
861 operations to Prob
862 - Moving towards boost::program_options for handling command line arguments
863 (tests/test is done).
864 - Renamed some FactorGraph methods:
865 nr_vars -> nrVars
866 nr_factors -> nrFactors
867 varind -> findVar
868 factorind -> findFactor
869 makeFacCavity -> makeFactorCavity
870 - LCBP_SEQMAXRES has been removed because it did strange things.
871 - Implemented RandomDRegularGraph
872 - Implemented JTree::calcMarginal for marginals that are not confined
873 within one cluster (using cut-set conditioning).
874 - Added isConnected() method to FactorGraph (some methods do not work with
875 disconnected factor graphs).
876 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
877 - Removed single node interaction "correction" code from clamping methods
878 - Removed calcCavityDist and calcCavityDist2ndO
879 - No longer depends on GSL.
880 - Increased portability by combining platform dependant utility functions
881 in util.{h,cpp}.
882 - Wrote *.m files providing help
883
884 Testing framework
885
886 - Made a new and significantly improved testing framework that provides most
887 functionality from the command line.
888 - The basis is provided by tests/test, which uses the newInfAlg functionality
889 and enables the user to easily compare from the command line different
890 inference methods on a given factorgraph. All parameters can be specified.
891 Output consists of CPU time, average and maximum single variable marginal
892 errors, relative logZ error and MaxDiff().
893 - tests/aliases.conf contains aliases for standard combinations of methods
894 and their options (which can be used in tests/test).
895 - tests/large contains several bash/python scripts that create random factor
896 graphs, compare several approximate inference algorithms (using tests/test) and
897 allow for easy visualization of the results using PyX.
898 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
899 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
900 regression testing).
901 - Added a regression test to the Makefile which is included in the standard
902 target. It compares all inference methods on tests/testfast.fg with the
903 results stored in tests/testfast.out
904
905 Miscellaneous
906
907 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
908 - Experimental MATLAB code added for StarEP approximation on cavity
909 - Renamed project to libDAI and changed directory name accordingly.
910 - Renamed JunctionTree to JTree.
911 - Fixed licensing (now it's officially GPL).
912 - Improved README
913
914
915 revision 252
916 ------------
917
918 Functionality
919 - Added RegionGraph, GBP, CVM and HAK (double-loop).
920 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
921 RegionGraph.
922 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
923 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
924 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
925 it over all subsuming outer regions. See README for when negative factors are known to work
926 and when not.
927 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
928 it does not automatically merge factors anymore.
929 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
930 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
931 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
932 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
933 such that it does not store the complete pancakes, but represents them as little factor graphs).
934
935 Implementation / code
936 - Made a seperate type WeightedGraph, which until now only implements Prim's
937 maximal spanning tree algorithm and is only used by the junction tree code. It might
938 be good to make it a class somewhere in the future and extend it's interface.
939 - Made a seperate class ClusterGraph, which is only used by the junction tree
940 code. It's main purpose is a graph-theoretical variable elimination algorithm.
941 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
942 - Massive code cleanup, moving towards "generic" programming style, using
943 multiple inheritance and polymorphism.
944 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
945 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
946 that can be used by FactorGraph-based DAIAlgs.
947 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
948 and VarSet) and provides functionality for it (which is used by TFactor<T>).
949 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
950 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
951 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
952 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
953 o using Prob's instead of Factor's;
954 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
955 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
956 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
957 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
958 that takes the cavitydists and multiplies them with the relevant factors. This
959 resulted in an API change in AI which now accepts and returns initial cavitydists
960 instead of initial pancakes.
961
962 Minor changes
963 - Started writing DoxyGen documentation
964 - Renamed lcptab2fg.m matlab/ai_writefg.m
965 - Moved all matlab stuff to matlab/
966 - More detailed reporting (also reports clocks used).
967 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
968 - Improved testing suite.
969 - Removed logreal support.
970 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
971 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
972 full and periodic 2D Ising networks according to some command line parameters.
973 - Now logZ really returns logZ instead of -logZ.
974 - Added FactorGraph::WriteToDotFile
975
976
977 0.1.4 (2006-04-13)
978 ------------------
979 - Added file IO routines to read and write factorgraphs.
980 - Added L-infinity normalization for use with (partially) negative factors.
981 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
982 handle (partially) negative factors.
983 - Added test suite.
984 - All probabilities are now represented using double instead of LogReal<double>.
985 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
986 - Combined several variants of BP into doBP. Several update schemes possible.
987 Now uses precalculated indices for optimization.
988 - Renamed Node -> Var and Potential -> Factor.
989 - Extensive code cleanup. More use of OO techniques. Changed API.
990 - MaxIter now means maximum number of passes (corresponding to number of
991 _parallel_ updates).
992 - MaxDiff now means the maximum L-infinity distance between the updated and
993 original single variable beliefs, for all AI methods.
994 - Implemented RBP which converges faster than BP for difficult problems.
995 - Now uses method parameter which is a bitmask combining outmethod and inmethod
996 (see ai.h).
997
998
999 0.1.3 (2006-03-22)
1000 --------------------
1001 - All AI methods now return maxdiff
1002 - ai.cpp:
1003 o Now returns maxdiffinner and maxdiffouter
1004 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
1005 o New InitCav outermethod (only create initial cavity distributions)
1006 - bp.cpp:
1007 o New CavityDist2ndO which estimates 2nd order cavity interactions
1008 - Makefile:
1009 o Bugfix: removed dependencies on algwim.*
1010
1011
1012 0.1.2 (2006-02-28)
1013 --------------------
1014 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
1015 - Added the possibility to provide initial cavity distributions as an input
1016 argument to ai (not much error checking is done, so be careful).
1017 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
1018 the output arguments Q, Q0 of ai).
1019 - Removed algwim.* since it does not work.
1020
1021
1022 0.1.1 (2006-02-28)
1023 --------------------
1024 - The constructors of (Log)FactorGraph and LogFactorGraph from a
1025 vector<(Log)Potential> now merge potentials to prevent short loops (of length
1026 4) in the factor graph. These are used in ai to construct the factor graphs
1027 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
1028 of BipGraph checks for the existence of short loops.
1029 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
1030 description in the help).
1031 - ai does not hook cout anymore (which caused weird segfaults).
1032 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
1033 - Removed network.* since it is not useful.
1034
1035
1036 0.1.0 (2006-02-28)
1037 --------------------
1038 First version worthy of a version number.