libDAI version 0.3.2
[libdai.git] / ChangeLog
1 libDAI-0.3.2 (2015-07-17)
2 -------------------------
3
4 Miscellaneous improvements:
5 * [Charles Vaske] Various improvements to EM code, including interface changes
6 * Added 'inclusive' argument to DAG::ancestors() and DAG::descendants()
7 * [Julien Rebetez] added FactorGraph::printDot() to SWIG interface
8 * Extended SWIG python interface (inspired by Kyle Ellrott): inference is possible in Python now!
9 * Added toString() formatting functions to the classes that had an output streaming operator<<
10 * Merged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh
11
12 Build system improvements:
13 * Build system: optional compilation targets are now set in include/dai/dai_config.h instead of Makefile.ALL
14
15 Bug fixes:
16 * Disabled debugging output in src/cobwebgraph.cpp to fix compilation issue under OSX
17 * [Lee C Baker] patch in include/dai/enum.h to fix compilation issues on OSX related to std::wistream and std::wostream (another workaround would be to specify -std=c++11)
18 * Fixed regression in SWIG interface caused by new build system (thanks to Benjamin Mumm for reporting this)
19 * 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
20 * Removed conversion script FastInf->libDAI because it is buggy (uses wrong permutation of factor entries)
21 * Replaced all occurrences of std::size_t by size_t to avoid SWIG problems
22 * Fixed division-by-zero issue in pow() which caused problems for GLC+ with sparse factors
23 * Fixed bugs in unit test prob_test.cpp: replaced all occurences of
24 BOOST_CHECK_CLOSE(...,(Real)0.0,tol) with BOOST_CHECK_SMALL(...,tol)
25
26
27 libDAI-0.3.1 (2012-09-17)
28 -------------------------
29
30 Miscellaneous improvements:
31 * Full 64-bit support on all supported platforms (Linux, OSX, Windows)
32 * Added special MatLab interface for junction tree algorithm (dai_jtree)
33 * Optimized ClusterGraph( const FactorGraph&, bool) constructor
34
35 Build system improvements:
36 * Added Makefile.WINDOWS64, kindly provided by Lin Ming
37 * [Arman Aksoy] Added Makefile.MACOSX64
38 * Added VC10 build files, kindly provided by Sameh Khamis
39
40 Bug fixes:
41 * Fixed bug (found by Sameh Khamis): define NAN (Windows)
42 * Fixed bug (found by Sameh Khamis): add some necessary casts of size_t to BigInt (Windows)
43 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION__ (Visual Studio) or __func__ (other compilers)
44 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
45 * Fixed bug (found by cax): when building MatLab MEX files, GMP/MPIR libraries were not linked
46 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)
47 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions
48 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers
49 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()
50 * Fixed memory leak in CBP::run()
51 * Fixed typo in Priya's name
52
53
54 libDAI-0.3.0 (2011-07-12)
55 -------------------------
56
57 New license:
58 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)
59
60 Miscellaneous improvements:
61 * Improved Exception class
62 (it now stores more information and doesn't print to stderr by default)
63 * Added builtinInfAlgs() and builtinInfAlgNames()
64
65 Bug fixes:
66 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()
67 and maxDiff() implementations
68 * Now uses GMP big integer type to represent linear states and the number of
69 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya
70 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now
71 no longer works out-of-the-box.
72 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
73 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
74 instead of returning a MAP state with zero joint probability
75 (reported by Hynek Urban)
76 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
77 (the random seed needs to be an unsigned int on some platforms)
78 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
79 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
80 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)
81 * Replaced all Name members by name() virtual functions and removed global variable DAINames
82 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
83
84
85 libDAI-0.2.7 (2010-08-19)
86 -------------------------
87
88 * Removed interfaces deprecated in 0.2.6.
89 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
90 if one or more variables had a MAP belief with more than one maximum, an
91 incorrect MAP state could result.
92
93
94 libDAI-0.2.6 (2010-08-05)
95 -------------------------
96
97 New features:
98 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
99 * Added source code for one of the winning solvers of the
100 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
101 * Added support for reading files in the UAI Approximate Inference Challenge
102 format, supporting both the 2006/2008 evidence file format and the 2010
103 evidence file format (io.h/cpp).
104
105 Miscellaneous improvements:
106 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
107 for setting an upper limit on execution time.
108 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
109 * SmallSet:
110 - Added SmallSet::erase( const T& t ).
111 * VarSet:
112 - nrStates() now returns a long double instead of a size_t.
113 * Permute:
114 - Added ranges() accessor.
115 - Added inverse() method.
116 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
117 * Factor:
118 - Added createFactorDelta( const VarSet& vs, size_t state ).
119 * ClusterGraph:
120 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
121 - Added findCluster( const VarSet& cl ).
122 - Added elimVar( size_t i ).
123 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
124 * FactorGraph:
125 - Added isMaximal(size_t).
126 - Added maximalFactor(size_t).
127 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
128 * Gibbs:
129 - Added 'restart' property.
130 - Added Gibbs::findMaximum() for MAP inference.
131 * HAK:
132 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
133 * examples/examples_imagesegmentation.cpp:
134 - [Peter Rockett] Improved Makefiles for image segmentation example.
135 - Added build flag to specify the CImg version.
136 * util.h/cpp:
137 - Added fromString<>( const std::string& x ).
138
139 Interface changes (the old interface is marked obsolete and will be removed in the next release):
140 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
141 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
142 and replaced them by a globally defined Neighbor structure
143 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
144 and replaced them by a globally defined Neighbors type
145 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
146 and replaced them by a globally defined Edge type
147 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
148 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
149 variable is not found.
150 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
151 and replaced it with an improved version
152 'vector<string> tokenizeString( const string&, bool, const string& )'
153 * Removed interfaces deprecated in 0.2.5.
154
155 Bug fixes:
156 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
157 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
158 which have problems when comparing const_reverse_iterator with
159 reverse_iterator.
160 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
161 (segfault if factors depending on 0 variables were passed to MatLab)
162
163
164 libDAI-0.2.5 (2010-05-09)
165 -------------------------
166
167 New features:
168 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
169 weightedgraph, enum, util, exceptions, properties, index, prob,
170 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
171 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
172 * Added utils/uai2fg, a utility to convert the UAI inference competition file
173 formats to the libDAI factor graph file format
174 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
175 * Added examples/example_imagesegmentation
176
177 Miscellaneous improvements:
178 * TRWBP:
179 - Added initialization of TRWBP weights by sampling spanning trees
180 * MF:
181 - Added an "init" option that allows to initialize randomly
182 - Added an "updates" option that allows to choose between standard
183 mean field and "hard-spin" mean field
184 * MR:
185 - rewrote response propagation implementation with help of BBP
186 - now uses GraphAL to represent the Markov graph
187 - miscellaneous smaller cleanups
188 * TreeEP:
189 - Now also supports disconnected factor graphs
190 * JTree:
191 - Now also supports disconnected factor graphs
192 * ExactInf:
193 - Added findMaximum()
194 * RegionGraph:
195 - Added error checking code
196 - Changed the way a RegionGraph is streamed to an std::ostream.
197 * ClusterGraph:
198 - Added nrVars() method
199 - Added var( size_t ) method
200 - Added cluster( size_t ) method
201 * FactorGraph:
202 - clamped() now contains a delta factor for the clamped variable
203 - Added MarkovGraph()
204 * TFactor:
205 - Added takeAbs()
206 - Added takeExp()
207 - Added takeLog( bool )
208 - Added operator-() const
209 - Added sumAbs() const
210 - Added operator==( const TFactor<T> &y )
211 - Added get(size_t), set(size_t,T)
212 * TProb:
213 - Added operator==( const TProb<T> &q )
214 - accumulate() now also applies op2 to init
215 - operator/= (T x) now yields 0 when dividing by 0
216 - Added resize(size_t)
217 - Added get(size_t) and set(size_t,T)
218 - Changed format of TProb<T> when streamed to an ostream
219 * multifor:
220 - Added reset()
221 * PropertySet:
222 - Added size()
223 - Added clear()
224 - Added erase()
225 * util.h/cpp:
226 - Added std::string toString( const T& x )
227 * weightedgraph.h/cpp:
228 - Added option to MaxSpanningTree and MinSpanningTree for
229 choosing between Prim's algorithm and Kruskal's algorithm
230 - Better error checking in RootedTree constructor
231 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
232 * BipartiteGraph:
233 - Added hasEdge()
234 - Added findNb1()
235 - Added findNb2()
236 - Added nb1Set()
237 - Added nb2Set()
238 - Added operator==( const BipartiteGraph& )
239 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
240 - Added operator<<( std::ostream&, const BipartiteGraph& )
241 * GraphAL:
242 - Added hasEdge(size_t,size_t)
243 - Added nbSet(size_t)
244 - Added operator==( const GraphAL& )
245 - Added operator<<( std::ostream&, const GraphAL& )
246 * SmallSet:
247 - Added insert( const T& t ) method
248 * Improved regression test
249 * Made all "verbose" properties optional
250 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
251 'ISING' factor type has been renamed to 'ISINGGAUSS'
252 * tests/testdai option "marginals" now has five possible values: NONE
253 outputs no marginals, VAR only variable marginals, FAC only factor
254 marginals, VARFAC both types of marginals, and ALL outputs all
255 marginals calculated by the algorithm.
256 * Compressed Makefile
257
258 Interface changes (the old interface is marked obsolete and will be removed in the next release):
259 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
260 * TreeEP:
261 - Changed construct( const RootedTree& ) into
262 construct( const FactorGraph&, const RootedTree& )
263 * JTree:
264 - Changed construct( const std::vector<VarSet>&, bool ) into
265 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
266 - Changed GenerateJT( const std::vector<VarSet> & )
267 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
268 * RegionGraph:
269 - Made (previously public) members G, ORs, IRs and fac2OR protected and
270 added DAG() accessor which returns a reference to the region graph DAG
271 structure (currently implemented as a BipartiteGraph).
272 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
273 protected, because exposing it to the world serves no purpose.
274 - Removed partial constructor RegionGraph( const FactorGraph& fg )
275 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
276 protected and renamed them by changing the "Recompute" into "recompute",
277 because exposing them to the world serves no purpose.
278 * ClusterGraph:
279 - Made (previously public) members G, vars and clusters private and added
280 bipGraph(), vars() and clusters() methods which offer read-only access
281 to these members.
282 - Deprecated toVector()
283 - Renamed size() into nrClusters()
284 * FactorGraph:
285 - Renamed Cliques() into maximalFactorDomains() and made it faster
286 - findVars( const VarSet& ) now returns a SmallSet<size_t>
287 and its argument now has a const-qualifier (which fixes a small bug).
288 - Made (previously public) member G private and added the
289 bipGraph() method, which offers read-only access to it.
290 - Deprecated the iterator interface:
291 o FactorGraph::iterator typedef
292 o FactorGraph::const_iterator typedef
293 o FactorGraph::begin() members
294 o FactorGraph::end() members
295 - Deprecated factor(size_t) which offered write access to a factor
296 because using this functionality in the descendant RegionGraph is dangerous,
297 as the outer regions are not automatically recomputed.
298 * TFactor:
299 - Renamed states() into nrStates()
300 - Added get(size_t) and set(size_t,T) operators;
301 get() is equivalent to "operator[](size_t) const" and set() should
302 be used instead of the non-const operator[], which has been deprecated
303 * TProb:
304 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
305 constructor: the sizeHint argument no longer defaults to 0
306 - Deprecated accumulate( T init, binOp op1, unOp op2 );
307 instead, accumulateSum( T init, unOp op ) and
308 accumulateMax( T init, unOp op, bool minimize ) should be used.
309 - Deprecated TProb::NormType and TProb::DistType;
310 ProbNormType and ProbDistType should be used instead.
311 - Fixed bug by renaming operator<=() to operator<()
312 - Added get(size_t) and set(size_t,T) operators;
313 get() is equivalent to "operator[](size_t) const" and set() should
314 be used instead of the non-const operator[], which has been deprecated
315 * PropertySet:
316 - Renamed Set() -> set()
317 - Renamed Get() -> get()
318 - Renamed GetAs<T>() -> getAs<T>()
319 - Renamed ConvertTo<T>() -> convertTo<T>()
320 * util.h/cpp:
321 - Removed max( const std::vector<Real> &v )
322 * weightedgraph.h/cpp:
323 - Renamed MaxSpanningTreePrims into MaxSpanningTree
324 - Renamed MinSpanningTreePrims into MinSpanningTree
325 - The vertices in DEdge and UEdge are now named "first" and "second"
326 for compatibility with a std::pair<size_t,size_t>
327 * BipartiteGraph:
328 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
329 * SmallSet:
330 - The sizeHint argument of the iterator constructor
331 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
332 no longer has a default value in order to avoid confusion with the
333 SmallSet::SmallSet( const T &t1, const T &t2 )
334 constructor.
335
336 Bug fixes:
337 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
338 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
339 * Fixed some bugs in the MatLab interface build system
340 * Fixed a bug in utils/fginfo.cpp
341 * Fixed a bug in JTree::findMaximum() and simplified the code
342 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
343 assignment from happening
344 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
345 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
346 FactorGraph ancestor methods; this has been corrected by letting them throw a
347 NOT_IMPLEMENTED exception.
348 * Fixed bug in FactorGraph::clone()
349 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
350 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
351 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
352 * Fixed bug in PropertySet::setAsString<T>()
353 * Fixed a bug in rnd_seed()
354 * BipartiteGraph:
355 - Fixed bug in eraseNode1()
356 - Fixed bug in eraseNode2()
357 - Fixed bug in isTree()
358 * GraphAL:
359 - Fixed bug in nrEdges()
360 - Fixed bug in addEdge()
361 - Fixed bug in isTree()
362 - Fixed bug in eraseNode()
363 - Fixed bug in printDot()
364 * Fixed bug in createGraphGrid3D()
365 * Fixed bug in createGraphRegular()
366
367
368 libDAI-0.2.4 (2010-02-11)
369 -------------------------
370
371 New features:
372 * Implemented Tree-Reweighted BP
373 * [Frederik Eaton] Implemented Fractional Belief Propagation
374
375 Miscellaneous improvements:
376 * Improved documentation
377 * [Frederik Eaton] Added constructors for BBPCostFunction
378 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
379 * [Frederik Eaton] Added unary minus to TProb<>
380 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
381 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
382 * tests/testdai option "marginals" now has three possible values: NONE
383 outputs no marginals, VAR only variable marginals, and ALL outputs all
384 marginals calculated by the algorithm.
385 * Strengthened convergence criteria of various algorithms
386 * Added GraphAL, an adjacency list implementation for graphs,
387 similar to (but simpler than) BipartiteGraph
388 * Added some functionality to create various standard factors
389 (the functions whose names start with "createFactor")
390 * Added examples example_sprinkler_gibbs and example_sprinkler_em
391 * Implemented various heuristics for choosing a variable elimination sequence
392 in JTree
393 * Added BETHE method for GBP/HAK cluster choice
394 * Made alias support official part of the library
395
396 Build system:
397 * Moved platform independent build options into Makefile.ALL
398 * Windows platform now needs Boost 1.37 or higher
399
400 Code cleanup:
401 * Cleaned up utils/createfg and tests/testdai
402 * Cleanup of some duplicate code in BP, FBP, TRWBP
403
404 Interface changes (the old interface is marked obsolete and will be removed in the next release):
405 * Removed obsolete/deprecated stuff
406 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
407 * Renamed some functions of BipartiteGraph:
408 add1() -> addNode1()
409 erase1() -> eraseNode1()
410 nr1() -> nrNodes1()
411 add2() -> addNode2()
412 erase2() -> eraseNode2()
413 nr2() -> nrNodes2()
414 * Renamed some functions in ClusterGraph:
415 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
416 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
417 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
418 * Changed interface of one RegionGraph constructor
419 * Renamed "Clamped BP" into "Conditioned BP"
420
421 Bug fixes:
422 * Fixed regression in scripts/regenerate-properties (now all errors are
423 gathered before throwing the exception, as used to be the case)
424 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
425 * [Alexander Schwing] Fixed error in BP that occured with damping
426 and using log-domain updates
427 * Fixed bug in HAK for trivial region graphs (with only one outer region
428 and no inner regions), reported by Alejandro Lage.
429 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
430
431
432 libDAI-0.2.3 (2009-11-16)
433 -------------------------
434
435 New features:
436 * Complete doxygen documentation (although more detailed documentation still
437 has to be written)
438 * [Charles Vaske] Added parameter learning for conditional probabilities by
439 Expectation Maximization
440 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
441 octave interfaces
442 * Added Max-Product functionality to JTree
443 * [Frederik Eaton] Added Back-Belief-Propagation
444 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
445 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
446
447 Code cleanup:
448 * Updated copyright headers
449 * Cleaned up error handling by introducing the DAI_THROWE macro
450 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
451 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
452 dai::Exception and is even active if NDEBUG is defined
453 * Removed all the virtual default constructors *::create(), as they are not used
454 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
455 * [Frederik Eaton] Change cout to cerr in warnings and error messages
456
457 Miscellaneous improvements:
458 * BipartiteGraph:
459 - Added eraseEdge( size_t n1, size_t n2 )
460 - [Frederik Eaton] Improved documentation of Neighbor
461 * TProb<T>:
462 - Added divided_by(const TProb<T>&) const
463 - Added constructor TProb<T>( const std::vector<S> &v )
464 - Added size_t draw(), which draws a random index
465 - [Frederik Eaton] Added setUniform()
466 - [Frederik Eaton] Added sumAbs()
467 - [Frederik Eaton] Added argmax()
468 - [Giuseppe Passino] Added begin(), end()
469 * TFactor<T>:
470 - [Giuseppe Passino] Added begin(), end()
471 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
472 which reorders variables to canonical ordering before storing the table
473 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
474 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
475 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
476 * State:
477 - [Giuseppe Passino] Added prefix ++ operator
478 * Permute:
479 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
480 * FactorGraph:
481 - [Frederik Eaton] Added clampVar()
482 - [Frederik Eaton] Added clampFactor()
483 - [Giuseppe Passino] Added begin(), end()
484 * PropertySet:
485 - Added keys(), for getting all keys
486 - [Frederik Eaton] Added default constructor
487 - [Frederik Eaton] Added constructor from string
488 * InfAlg:
489 - Added setProperties(), getProperties() and printProperties()
490 - [Frederik Eaton] Added beliefV(), beliefF()
491 * ExactInf:
492 - Added calcMarginal(const VarSet &)
493 * HAK:
494 - Added "init" parameter to allow for random initialization
495 * BP:
496 - [Giuseppe Passino] Added findMaximum(), which can be used after running
497 max-product BP to construct a global state with maximum probability
498 * JTree:
499 - Added findMaximum(), which can be used after running
500 max-product JTree to construct a global state with maximum probability
501 * MatLab interface:
502 - MEX file dai now also returns variable and factor beliefs
503 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
504 (only for BP and JTree)
505 * README is now created automatically from doxygen documentation
506 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
507 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
508 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
509 and functions (concat(),rnd()) to util.h
510 * Changed output stream operator<< for Var and VarSet
511 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
512 alias substitutions
513 * [Frederik Eaton] Added useful aliases to aliases.conf
514 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
515 set instead of the linear search (which can yield enormous speedups - a
516 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
517 * Added debug assertions to Var which check for inconsistent dimensions of
518 variables with the same labels
519 * toc() now returns POSIX system time with maximum accuracy of microseconds
520 * Exception objects now remember their error code
521 * Examples:
522 - Moved example.cpp to examples/
523 - Added examples/example_bipgraph.cpp
524 - Added examples/example_varset.cpp
525 - Added examples/example_sprinkler.cpp
526 - Added examples/example_permute.cpp
527 - Added python and octave ports for examples/example_sprinkler.cpp
528
529 Build system:
530 * Improved Makefile:
531 - Merged Makefile.win and Makefile.shared into Makefile
532 - Macros DAI_VERSION and DAI_DATE have been introduced,
533 in order to store this information in a central place
534 - Introduced CCNODEBUGFLAGS in Makefile
535 - Switched Makefile.win to GNU Make syntax
536 - [Frederik Eaton] Added TAGS, lib targets to Makefile
537 * Compatibility:
538 - [Peter Gober] libDAI can now be built on Cygwin
539 - [Dan Preston] libDAI can now be built on Mac OS X
540 - Changed regression test so that it also works under Windows
541
542 Interface changes (the old interface is marked obsolete and will be removed in the next release):
543 * Var:
544 - Variable labels are now nonnegative (of type size_t)
545 * VarSet:
546 - Replaced calcState() by non-member calcLinearState()
547 - Replaced calcStates() by non-member calcState()
548 * Permute:
549 - Renamed convert_linear_index into convertLinearIndex
550 * TProb<>:
551 - Replaced log0() by log(true)
552 - Replaced takeLog0() by takeLog(true)
553 - Removed hasNonPositives()
554 - Renamed minVal() to min()
555 - Renamed maxVal() to max()
556 - Renamed totalSum() to sum()
557 * TFactor<>:
558 - Replaced log0() by TFactor<T>::log(true)
559 - Removed divided_by, use operator/ instead
560 - Removed divide, use operator/= instead
561 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
562 - Renamed minVal() to min()
563 - Renamed maxVal() to max()
564 - Renamed totalSum() to sum()
565 * FactorGraph:
566 - Changed clamp and clamp interfaces (the variable to be
567 clamped is now indicated by its index, not as a Var)
568 * RegionGraph:
569 - Renamed Check_Counting_Numbers into checkCountingNumbers
570 - Renamed Calc_Counting_Numbers into calcCountingNumbers
571 * Miscellaneous:
572 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
573 - Replaced UEdgeVec by Graph
574 - Replaced DEdgeVec by new RootedTree class
575 - Moved functionality of GrowRootedTree() into constructor of RootedTree
576 - Merged calcPairBeliefsNew() into calcPairBeliefs()
577 - Removed calcMarginal2ndO()
578 - Renamed smallSet<T> to SmallSet<T>
579 - Removed class Diffs
580 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
581 BipartiteGraph and FactorGraph (which will be obsoleted soon)
582
583 Bug fixes:
584 * Fixed reversal of min and max in
585 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
586 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
587 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
588 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
589 before typeid(std::string) (this fixes a strange bug for empty string property)
590 * Added work-around for bug in Boost Graph Library
591 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
592 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
593 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
594 for reporting this)
595
596
597 libDAI-0.2.2 (2008-09-30)
598 -------------------------
599
600 New features:
601 * Approximate inference methods now report the number of iterations needed.
602 * Added damping to various algorithms to improve convergence properties.
603 * Added more features to utils/createfg for creating factor graphs.
604 * Added ExactInf class for brute force exact inference.
605 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
606 whether calculations are done in the log-domain or in the linear domain;
607 doing calculations in the log-domain may help if the numerical range
608 of a double is too small.
609 * [Claudio Lima] Added Max-Product functionality to BP.
610 * Improved documentation.
611
612 Improved architecture:
613 * Added Exceptions framework.
614 * Pervasive change of BipartiteGraph implementation (based on an idea by
615 Giuseppe Passino). BipartiteGraph no longer stores the node properties
616 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
617 nor an edge list. Instead, it stores the graph structure as lists of
618 neighboring nodes. This yields a significant memory/speed improvement for
619 large factor graphs, and is more elegant as well. Iterating over neighbors is
620 made easy by using boost::foreach.
621 * Added conditional compilation of inference methods.
622 * VarSet is now implemented using a std::vector<Var> instead of a
623 std::set<Var>, which yields a significant speed improvement. Furthermore,
624 the implementation has been generalized, resulting in the small_set<T> class
625 which can be used to represent sets of small cardinality; VarSet is the
626 specialization with T = Var.
627 * Improved ClusterGraph implementation, yielding significant speedups
628 for the JunctionTree algorithm on large factorgraphs.
629
630 Code cleanup:
631 * Moved everything into namespace "dai".
632 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
633 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
634 * Removed utils/remove_short_loops and matlab/remove_short_loops.
635 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
636 * Improved index.h:
637 - Renamed Index -> IndexFor
638 - Added some .reserve()'s to IndexFor methods which yields a
639 25% speedup of testregression
640 - Replaced multind by Permute
641 - Added MultiFor
642 - Added State
643 * New funcstionality of factor.h.
644 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
645 inference algorithm, because the Properties framework was not as
646 convenient as I hoped, and not every inference algorithm needs a maxdiff
647 variable. Also, replaced some FactorGraph functionality in InfAlg by a
648 function that returns the FactorGraph. The result is cleaner (less
649 entangled) code.
650 * Removed x2x.
651 * Replaced Complex with real numbers (negative potentials are just too rare
652 to warrant the additional "complexity" :)).
653
654 Miscellaneous improvements:
655 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
656 GCC under Cygwin.
657 * Contributions by Peter Gober:
658 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
659 * Misc contributions by Giuseppe Passino:
660 - removed "using namespace std;" from header files - bad practice;
661 - moved header files in include/dai and sources in src;
662 - changed #ifndefs to GNU style;
663 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
664 - dai::TProb:
665 o removed copy constructor and assignment operators (redundant);
666 o implementation of some methods via STL algorithms;
667 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
668 o explicit constructor (prevents implicit conversion from size_t to TProb);
669 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
670 * Misc contributions by Christian Wojek:
671 - New FactorGraph constructor that constructs from given ranges of factors
672 and variables;
673 - Optimization of FactorGraph constructors using tr1::unordered_map.
674 * FactorGraph constructors no longer check for short loops (huge speed
675 increase for large factor graphs), nor for negative entries. Also, the
676 normtype is now Prob::NORMPROB by default.
677 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
678
679 Interface changes:
680 * VarSet::
681 - VarSet::stateSpace() -> nrStates(const VarSet &)
682 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
683 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
684 - removed bool operator||
685 - operator&&(const VarSet&) -> intersects(const VarSet&)
686 - operator&&(const Var&) -> contains(const Var&)
687 * FactorGraph::
688 - delta(const Var &) -> delta(size_t)
689 - Delta(const Var &) -> Delta(size_t)
690 - makeCavity(const Var &) -> makeCavity(size_t)
691 - vars() -> vars
692 - factors() -> factors
693 - removed MakeFactorCavity(size_t)
694 - removed ExactMarginal(const VarSet &)
695 - removed ExactlogZ()
696 - removed updatedFactor(size_t)
697 - removed _normtype and NormType()
698 - removed hasShortLoops(...) and removeShortLoops(...)
699 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
700 - undoProb(size_t) -> restoreFactor(size_t)
701 - saveProb(size_t) -> backupFactor(size_t)
702 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
703 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
704 - ReadFromFile(const char*) returns void (throws on error)
705 - WriteToFile(const char*) returns void (throws on error)
706 - removed hasNegatives()
707 * RegionGraph::
708 - nr_ORs() -> nrORs()
709 - nr_IRs() -> nrIRs()
710 - ORs() -> ORs
711 - IRs() -> IRs
712 * *::Regenerate() -> *::construct()
713 * Renamed Index -> IndexFor
714 * Diffs:
715 - max() -> maxDiff()
716 - max_size() -> maxSize()
717 * Prob::max() -> Prob::maxVal()
718 * Factor::
719 - max() -> maxVal()
720 - part_sum() -> partSum()
721 * toc() in util.h now returns seconds as a double
722 * VarSet::operator&&
723 * Properties -> PropertySet
724
725
726 libDAI-0.2.1 (2008-05-26)
727 -------------------------
728
729 Bugfix release.
730 * added missing cstdio header in util.h
731 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
732 * added description of the factor graph fileformat
733 * improved Makefile
734
735
736 libDAI-0.2.0 (2006-11-30)
737 -------------------------
738
739 First public release.
740
741
742 0.1.5 (2006-11-30)
743 ------------------
744
745 Regressions
746
747 - tests/testlcbp and tests/testlcbp are broken.
748 - EXACT method does not work anymore.
749 - The Properties framework gives a speed penalty because of the lookup
750 costs involved; inner loops should be optimized.
751
752 General framework
753
754 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
755 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
756 functions to forward functionality from either FactorGraph or RegionGraph
757 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
758 and in RegionGraph and no explicit interface is needed in descendants.
759 - New abstract base class InfAlg added, representing an inference algorithm,
760 from which DAIAlg<T> inherits. This solves the incompatibility problems of
761 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
762 DAIAlg<RegionGraph>). More work is required to reduce code duplication
763 (make FactorGraph part of InfAlg).
764 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
765 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
766 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
767 one to save a few factors, modify them (e.g. clamp them), and then restore them
768 to their old values. Undo should also init the corresponding messages / beliefs.
769 This can be used if a given factor graph repeatedly needs to be clamped in
770 different ways and an approximation method is run for each clamping; using the
771 saveProbs/undoProbs can give a significant speed increase.
772 - Switched to a general Properties framework that handles the parameters of
773 all inference methods in a uniform manner. The Properties class is a map of
774 several properties in boost::any objects, indexed by their names (strings).
775 It can read from a stream and write to a stream. It is recursive, in the sense
776 that a Properties object can hold a variable of type Properties as well.
777 - Added a generic way of constructing inference algorithms from a factor graph,
778 name and properties object. Added the newInfAlg function which constructs
779 the requested object. This is used by LCBP, the Matlab interface and the
780 command line (test) interface.
781 - Added a generic enum framework for enum parameters. Although implemented as a
782 hack, it is quite useful in that it drastically simplifies and reduces the
783 amount of code for handling enum parameters.
784 - Provided generic functions for calculating marginals in different ways that
785 work for all approximate inference methods.
786
787 Bugfixes
788
789 - Fixed GBP free energy.
790 - Fixed bug in junctiontree (it didn't init the _vars variable).
791 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
792 the logical NOT of what they should return).
793 - Fixed bug in RegionGraph::RecomputeOR(s).
794 - Fixed bug in utils/create_dreg_fg:
795 graph structure was not random for given parameters (forgot to call srand()).
796 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
797 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
798 that consists of one outer region only.
799 - Fixed INIT bug in LCBP2::UpdatePancake().
800 - Fixed MaxDiffs flow (except for MR).
801
802 New functionality
803
804 - HAK supports several default cluster choices:
805 minimal (only factors)
806 delta (Markov blankets)
807 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
808 Only the maximal clusters are used as outer clusters.
809 - Implemented TreeEP. It generalizes the heuristic method described in the
810 Minka & Qi paper for obtaining a tree with the most relevant interactions to
811 higher order interactions. Almost all optimizations described in the Minka & Qi
812 paper are used, except that evidence is passed over the whole tree instead of
813 relevant subsets (the latter is almost implemented but buggy). Also added
814 alternative (worst-case) algorithm that uses a maximum spanning tree on the
815 weighted graph where the weight between neighbours i and j is given by
816 N(psi,i,j), where psi is the product of all the factors involving both i and j
817 (which is an upper bound on the effective interaction between i and j).
818 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
819 to be able to handle connectivities larger than 3 (in principle, up to 32).
820 It supports different initialization methods (the original RESPPROP,
821 the CLAMPING method and EXACT which uses JTree) and different update methods
822 (FULL and LINEAR).
823 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
824 networks and uses some approximate inference method on them for calculating
825 marginals.
826 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
827 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
828 interactions and LCBPL is LCBPI improved for higher-order interactions.
829 - Wrote one single program utils/createfg for creating various types of
830 random factor graphs.
831 - Wrote utility to visualize factor graphs using graphviz.
832 (it uses the BOOST Program Options library)
833 - Added fginfo utility that displays some info about a .fg file.
834 - Implemented Factor::strength function that calculates the potential strength
835 N(psi,i,j) between variables i and j as described in cs.IT:0504030
836 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
837 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
838 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
839 - Implemented a MATLAB interface ai_potstrength for Factor::strength
840 - Added Martijn's x2x
841
842 Improvements of existing code
843
844 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
845 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
846 associates outer region indices to factor indices (no powers yet, this
847 is deemed superfluous) and provides functions to recompute (some of) the
848 outer regions from the factors.
849 - InfAlg descendants run() methods now stop immediately and return NAN in case
850 they detect NANs. Only BP does not do NAN checking for performance reasons.
851 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
852 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
853 timing and convergence criteria.
854 - Implemented logZ() for JTree. It does the calculation during message-passing.
855 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
856 hopefully this will give more accurate approximations.
857 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
858 for a faster way of calculating marginals, which does not require a call to init()
859 nor cloning the whole object for each clamping. This leads to a significant speedup.
860 - LCBP (and LCBP2) now have complete flexibility in the specification of the
861 inner method, i.e. the method used to generate the initial cavity approximations.
862 One can pass two strings, a name and a properties string, and LCBP simply invokes
863 newInfAlg to construct the corresponding inference algorithm and uses the generic
864 marginal functions to approximate cavity marginals.
865 - Replaced the global "method" variable by local properties and removed ai.h
866 - Added some methods to Factor (operators *, *=, /, /= with doubles as
867 second argument, operators -, +=, -= with other Factors as second
868 arguments, randomize(), RemoveFirstOrderInteractions) and similar
869 operations to Prob
870 - Moving towards boost::program_options for handling command line arguments
871 (tests/test is done).
872 - Renamed some FactorGraph methods:
873 nr_vars -> nrVars
874 nr_factors -> nrFactors
875 varind -> findVar
876 factorind -> findFactor
877 makeFacCavity -> makeFactorCavity
878 - LCBP_SEQMAXRES has been removed because it did strange things.
879 - Implemented RandomDRegularGraph
880 - Implemented JTree::calcMarginal for marginals that are not confined
881 within one cluster (using cut-set conditioning).
882 - Added isConnected() method to FactorGraph (some methods do not work with
883 disconnected factor graphs).
884 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
885 - Removed single node interaction "correction" code from clamping methods
886 - Removed calcCavityDist and calcCavityDist2ndO
887 - No longer depends on GSL.
888 - Increased portability by combining platform dependant utility functions
889 in util.{h,cpp}.
890 - Wrote *.m files providing help
891
892 Testing framework
893
894 - Made a new and significantly improved testing framework that provides most
895 functionality from the command line.
896 - The basis is provided by tests/test, which uses the newInfAlg functionality
897 and enables the user to easily compare from the command line different
898 inference methods on a given factorgraph. All parameters can be specified.
899 Output consists of CPU time, average and maximum single variable marginal
900 errors, relative logZ error and MaxDiff().
901 - tests/aliases.conf contains aliases for standard combinations of methods
902 and their options (which can be used in tests/test).
903 - tests/large contains several bash/python scripts that create random factor
904 graphs, compare several approximate inference algorithms (using tests/test) and
905 allow for easy visualization of the results using PyX.
906 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
907 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
908 regression testing).
909 - Added a regression test to the Makefile which is included in the standard
910 target. It compares all inference methods on tests/testfast.fg with the
911 results stored in tests/testfast.out
912
913 Miscellaneous
914
915 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
916 - Experimental MATLAB code added for StarEP approximation on cavity
917 - Renamed project to libDAI and changed directory name accordingly.
918 - Renamed JunctionTree to JTree.
919 - Fixed licensing (now it's officially GPL).
920 - Improved README
921
922
923 revision 252
924 ------------
925
926 Functionality
927 - Added RegionGraph, GBP, CVM and HAK (double-loop).
928 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
929 RegionGraph.
930 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
931 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
932 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
933 it over all subsuming outer regions. See README for when negative factors are known to work
934 and when not.
935 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
936 it does not automatically merge factors anymore.
937 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
938 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
939 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
940 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
941 such that it does not store the complete pancakes, but represents them as little factor graphs).
942
943 Implementation / code
944 - Made a seperate type WeightedGraph, which until now only implements Prim's
945 maximal spanning tree algorithm and is only used by the junction tree code. It might
946 be good to make it a class somewhere in the future and extend it's interface.
947 - Made a seperate class ClusterGraph, which is only used by the junction tree
948 code. It's main purpose is a graph-theoretical variable elimination algorithm.
949 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
950 - Massive code cleanup, moving towards "generic" programming style, using
951 multiple inheritance and polymorphism.
952 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
953 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
954 that can be used by FactorGraph-based DAIAlgs.
955 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
956 and VarSet) and provides functionality for it (which is used by TFactor<T>).
957 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
958 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
959 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
960 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
961 o using Prob's instead of Factor's;
962 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
963 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
964 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
965 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
966 that takes the cavitydists and multiplies them with the relevant factors. This
967 resulted in an API change in AI which now accepts and returns initial cavitydists
968 instead of initial pancakes.
969
970 Minor changes
971 - Started writing DoxyGen documentation
972 - Renamed lcptab2fg.m matlab/ai_writefg.m
973 - Moved all matlab stuff to matlab/
974 - More detailed reporting (also reports clocks used).
975 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
976 - Improved testing suite.
977 - Removed logreal support.
978 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
979 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
980 full and periodic 2D Ising networks according to some command line parameters.
981 - Now logZ really returns logZ instead of -logZ.
982 - Added FactorGraph::WriteToDotFile
983
984
985 0.1.4 (2006-04-13)
986 ------------------
987 - Added file IO routines to read and write factorgraphs.
988 - Added L-infinity normalization for use with (partially) negative factors.
989 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
990 handle (partially) negative factors.
991 - Added test suite.
992 - All probabilities are now represented using double instead of LogReal<double>.
993 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
994 - Combined several variants of BP into doBP. Several update schemes possible.
995 Now uses precalculated indices for optimization.
996 - Renamed Node -> Var and Potential -> Factor.
997 - Extensive code cleanup. More use of OO techniques. Changed API.
998 - MaxIter now means maximum number of passes (corresponding to number of
999 _parallel_ updates).
1000 - MaxDiff now means the maximum L-infinity distance between the updated and
1001 original single variable beliefs, for all AI methods.
1002 - Implemented RBP which converges faster than BP for difficult problems.
1003 - Now uses method parameter which is a bitmask combining outmethod and inmethod
1004 (see ai.h).
1005
1006
1007 0.1.3 (2006-03-22)
1008 --------------------
1009 - All AI methods now return maxdiff
1010 - ai.cpp:
1011 o Now returns maxdiffinner and maxdiffouter
1012 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
1013 o New InitCav outermethod (only create initial cavity distributions)
1014 - bp.cpp:
1015 o New CavityDist2ndO which estimates 2nd order cavity interactions
1016 - Makefile:
1017 o Bugfix: removed dependencies on algwim.*
1018
1019
1020 0.1.2 (2006-02-28)
1021 --------------------
1022 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
1023 - Added the possibility to provide initial cavity distributions as an input
1024 argument to ai (not much error checking is done, so be careful).
1025 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
1026 the output arguments Q, Q0 of ai).
1027 - Removed algwim.* since it does not work.
1028
1029
1030 0.1.1 (2006-02-28)
1031 --------------------
1032 - The constructors of (Log)FactorGraph and LogFactorGraph from a
1033 vector<(Log)Potential> now merge potentials to prevent short loops (of length
1034 4) in the factor graph. These are used in ai to construct the factor graphs
1035 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
1036 of BipGraph checks for the existence of short loops.
1037 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
1038 description in the help).
1039 - ai does not hook cout anymore (which caused weird segfaults).
1040 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
1041 - Removed network.* since it is not useful.
1042
1043
1044 0.1.0 (2006-02-28)
1045 --------------------
1046 First version worthy of a version number.