62789e72d25eac4d3f83e5e5063ce503385c46c1
[libdai.git] / ChangeLog
1 git HEAD
2 --------
3
4
5 libDAI-0.3.2 (2015-07-17)
6 -------------------------
7
8 Miscellaneous improvements:
9 * [Charles Vaske] Various improvements to EM code, including interface changes
10 * Added 'inclusive' argument to DAG::ancestors() and DAG::descendants()
11 * [Julien Rebetez] added FactorGraph::printDot() to SWIG interface
12 * Extended SWIG python interface (inspired by Kyle Ellrott): inference is possible in Python now!
13 * Added toString() formatting functions to the classes that had an output streaming operator<<
14 * Merged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh
15
16 Build system improvements:
17 * Build system: optional compilation targets are now set in include/dai/dai_config.h instead of Makefile.ALL
18
19 Bug fixes:
20 * Disabled debugging output in src/cobwebgraph.cpp to fix compilation issue under OSX
21 * [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)
22 * Fixed regression in SWIG interface caused by new build system (thanks to Benjamin Mumm for reporting this)
23 * 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
24 * Removed conversion script FastInf->libDAI because it is buggy (uses wrong permutation of factor entries)
25 * Replaced all occurrences of std::size_t by size_t to avoid SWIG problems
26 * Fixed division-by-zero issue in pow() which caused problems for GLC+ with sparse factors
27 * Fixed bugs in unit test prob_test.cpp: replaced all occurences of
28 BOOST_CHECK_CLOSE(...,(Real)0.0,tol) with BOOST_CHECK_SMALL(...,tol)
29
30
31 libDAI-0.3.1 (2012-09-17)
32 -------------------------
33
34 Miscellaneous improvements:
35 * Full 64-bit support on all supported platforms (Linux, OSX, Windows)
36 * Added special MatLab interface for junction tree algorithm (dai_jtree)
37 * Optimized ClusterGraph( const FactorGraph&, bool) constructor
38
39 Build system improvements:
40 * Added Makefile.WINDOWS64, kindly provided by Lin Ming
41 * [Arman Aksoy] Added Makefile.MACOSX64
42 * Added VC10 build files, kindly provided by Sameh Khamis
43
44 Bug fixes:
45 * Fixed bug (found by Sameh Khamis): define NAN (Windows)
46 * Fixed bug (found by Sameh Khamis): add some necessary casts of size_t to BigInt (Windows)
47 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION__ (Visual Studio) or __func__ (other compilers)
48 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
49 * Fixed bug (found by cax): when building MatLab MEX files, GMP/MPIR libraries were not linked
50 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)
51 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions
52 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers
53 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()
54 * Fixed memory leak in CBP::run()
55 * Fixed typo in Priya's name
56
57
58 libDAI-0.3.0 (2011-07-12)
59 -------------------------
60
61 New license:
62 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)
63
64 Miscellaneous improvements:
65 * Improved Exception class
66 (it now stores more information and doesn't print to stderr by default)
67 * Added builtinInfAlgs() and builtinInfAlgNames()
68
69 Bug fixes:
70 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()
71 and maxDiff() implementations
72 * Now uses GMP big integer type to represent linear states and the number of
73 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya
74 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now
75 no longer works out-of-the-box.
76 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
77 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
78 instead of returning a MAP state with zero joint probability
79 (reported by Hynek Urban)
80 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
81 (the random seed needs to be an unsigned int on some platforms)
82 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
83 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
84 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)
85 * Replaced all Name members by name() virtual functions and removed global variable DAINames
86 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
87
88
89 libDAI-0.2.7 (2010-08-19)
90 -------------------------
91
92 * Removed interfaces deprecated in 0.2.6.
93 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
94 if one or more variables had a MAP belief with more than one maximum, an
95 incorrect MAP state could result.
96
97
98 libDAI-0.2.6 (2010-08-05)
99 -------------------------
100
101 New features:
102 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
103 * Added source code for one of the winning solvers of the
104 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
105 * Added support for reading files in the UAI Approximate Inference Challenge
106 format, supporting both the 2006/2008 evidence file format and the 2010
107 evidence file format (io.h/cpp).
108
109 Miscellaneous improvements:
110 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
111 for setting an upper limit on execution time.
112 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
113 * SmallSet:
114 - Added SmallSet::erase( const T& t ).
115 * VarSet:
116 - nrStates() now returns a long double instead of a size_t.
117 * Permute:
118 - Added ranges() accessor.
119 - Added inverse() method.
120 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
121 * Factor:
122 - Added createFactorDelta( const VarSet& vs, size_t state ).
123 * ClusterGraph:
124 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
125 - Added findCluster( const VarSet& cl ).
126 - Added elimVar( size_t i ).
127 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
128 * FactorGraph:
129 - Added isMaximal(size_t).
130 - Added maximalFactor(size_t).
131 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
132 * Gibbs:
133 - Added 'restart' property.
134 - Added Gibbs::findMaximum() for MAP inference.
135 * HAK:
136 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
137 * examples/examples_imagesegmentation.cpp:
138 - [Peter Rockett] Improved Makefiles for image segmentation example.
139 - Added build flag to specify the CImg version.
140 * util.h/cpp:
141 - Added fromString<>( const std::string& x ).
142
143 Interface changes (the old interface is marked obsolete and will be removed in the next release):
144 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
145 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
146 and replaced them by a globally defined Neighbor structure
147 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
148 and replaced them by a globally defined Neighbors type
149 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
150 and replaced them by a globally defined Edge type
151 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
152 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
153 variable is not found.
154 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
155 and replaced it with an improved version
156 'vector<string> tokenizeString( const string&, bool, const string& )'
157 * Removed interfaces deprecated in 0.2.5.
158
159 Bug fixes:
160 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
161 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
162 which have problems when comparing const_reverse_iterator with
163 reverse_iterator.
164 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
165 (segfault if factors depending on 0 variables were passed to MatLab)
166
167
168 libDAI-0.2.5 (2010-05-09)
169 -------------------------
170
171 New features:
172 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
173 weightedgraph, enum, util, exceptions, properties, index, prob,
174 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
175 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
176 * Added utils/uai2fg, a utility to convert the UAI inference competition file
177 formats to the libDAI factor graph file format
178 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
179 * Added examples/example_imagesegmentation
180
181 Miscellaneous improvements:
182 * TRWBP:
183 - Added initialization of TRWBP weights by sampling spanning trees
184 * MF:
185 - Added an "init" option that allows to initialize randomly
186 - Added an "updates" option that allows to choose between standard
187 mean field and "hard-spin" mean field
188 * MR:
189 - rewrote response propagation implementation with help of BBP
190 - now uses GraphAL to represent the Markov graph
191 - miscellaneous smaller cleanups
192 * TreeEP:
193 - Now also supports disconnected factor graphs
194 * JTree:
195 - Now also supports disconnected factor graphs
196 * ExactInf:
197 - Added findMaximum()
198 * RegionGraph:
199 - Added error checking code
200 - Changed the way a RegionGraph is streamed to an std::ostream.
201 * ClusterGraph:
202 - Added nrVars() method
203 - Added var( size_t ) method
204 - Added cluster( size_t ) method
205 * FactorGraph:
206 - clamped() now contains a delta factor for the clamped variable
207 - Added MarkovGraph()
208 * TFactor:
209 - Added takeAbs()
210 - Added takeExp()
211 - Added takeLog( bool )
212 - Added operator-() const
213 - Added sumAbs() const
214 - Added operator==( const TFactor<T> &y )
215 - Added get(size_t), set(size_t,T)
216 * TProb:
217 - Added operator==( const TProb<T> &q )
218 - accumulate() now also applies op2 to init
219 - operator/= (T x) now yields 0 when dividing by 0
220 - Added resize(size_t)
221 - Added get(size_t) and set(size_t,T)
222 - Changed format of TProb<T> when streamed to an ostream
223 * multifor:
224 - Added reset()
225 * PropertySet:
226 - Added size()
227 - Added clear()
228 - Added erase()
229 * util.h/cpp:
230 - Added std::string toString( const T& x )
231 * weightedgraph.h/cpp:
232 - Added option to MaxSpanningTree and MinSpanningTree for
233 choosing between Prim's algorithm and Kruskal's algorithm
234 - Better error checking in RootedTree constructor
235 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
236 * BipartiteGraph:
237 - Added hasEdge()
238 - Added findNb1()
239 - Added findNb2()
240 - Added nb1Set()
241 - Added nb2Set()
242 - Added operator==( const BipartiteGraph& )
243 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
244 - Added operator<<( std::ostream&, const BipartiteGraph& )
245 * GraphAL:
246 - Added hasEdge(size_t,size_t)
247 - Added nbSet(size_t)
248 - Added operator==( const GraphAL& )
249 - Added operator<<( std::ostream&, const GraphAL& )
250 * SmallSet:
251 - Added insert( const T& t ) method
252 * Improved regression test
253 * Made all "verbose" properties optional
254 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
255 'ISING' factor type has been renamed to 'ISINGGAUSS'
256 * tests/testdai option "marginals" now has five possible values: NONE
257 outputs no marginals, VAR only variable marginals, FAC only factor
258 marginals, VARFAC both types of marginals, and ALL outputs all
259 marginals calculated by the algorithm.
260 * Compressed Makefile
261
262 Interface changes (the old interface is marked obsolete and will be removed in the next release):
263 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
264 * TreeEP:
265 - Changed construct( const RootedTree& ) into
266 construct( const FactorGraph&, const RootedTree& )
267 * JTree:
268 - Changed construct( const std::vector<VarSet>&, bool ) into
269 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
270 - Changed GenerateJT( const std::vector<VarSet> & )
271 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
272 * RegionGraph:
273 - Made (previously public) members G, ORs, IRs and fac2OR protected and
274 added DAG() accessor which returns a reference to the region graph DAG
275 structure (currently implemented as a BipartiteGraph).
276 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
277 protected, because exposing it to the world serves no purpose.
278 - Removed partial constructor RegionGraph( const FactorGraph& fg )
279 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
280 protected and renamed them by changing the "Recompute" into "recompute",
281 because exposing them to the world serves no purpose.
282 * ClusterGraph:
283 - Made (previously public) members G, vars and clusters private and added
284 bipGraph(), vars() and clusters() methods which offer read-only access
285 to these members.
286 - Deprecated toVector()
287 - Renamed size() into nrClusters()
288 * FactorGraph:
289 - Renamed Cliques() into maximalFactorDomains() and made it faster
290 - findVars( const VarSet& ) now returns a SmallSet<size_t>
291 and its argument now has a const-qualifier (which fixes a small bug).
292 - Made (previously public) member G private and added the
293 bipGraph() method, which offers read-only access to it.
294 - Deprecated the iterator interface:
295 o FactorGraph::iterator typedef
296 o FactorGraph::const_iterator typedef
297 o FactorGraph::begin() members
298 o FactorGraph::end() members
299 - Deprecated factor(size_t) which offered write access to a factor
300 because using this functionality in the descendant RegionGraph is dangerous,
301 as the outer regions are not automatically recomputed.
302 * TFactor:
303 - Renamed states() into nrStates()
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 * TProb:
308 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
309 constructor: the sizeHint argument no longer defaults to 0
310 - Deprecated accumulate( T init, binOp op1, unOp op2 );
311 instead, accumulateSum( T init, unOp op ) and
312 accumulateMax( T init, unOp op, bool minimize ) should be used.
313 - Deprecated TProb::NormType and TProb::DistType;
314 ProbNormType and ProbDistType should be used instead.
315 - Fixed bug by renaming operator<=() to operator<()
316 - Added get(size_t) and set(size_t,T) operators;
317 get() is equivalent to "operator[](size_t) const" and set() should
318 be used instead of the non-const operator[], which has been deprecated
319 * PropertySet:
320 - Renamed Set() -> set()
321 - Renamed Get() -> get()
322 - Renamed GetAs<T>() -> getAs<T>()
323 - Renamed ConvertTo<T>() -> convertTo<T>()
324 * util.h/cpp:
325 - Removed max( const std::vector<Real> &v )
326 * weightedgraph.h/cpp:
327 - Renamed MaxSpanningTreePrims into MaxSpanningTree
328 - Renamed MinSpanningTreePrims into MinSpanningTree
329 - The vertices in DEdge and UEdge are now named "first" and "second"
330 for compatibility with a std::pair<size_t,size_t>
331 * BipartiteGraph:
332 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
333 * SmallSet:
334 - The sizeHint argument of the iterator constructor
335 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
336 no longer has a default value in order to avoid confusion with the
337 SmallSet::SmallSet( const T &t1, const T &t2 )
338 constructor.
339
340 Bug fixes:
341 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
342 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
343 * Fixed some bugs in the MatLab interface build system
344 * Fixed a bug in utils/fginfo.cpp
345 * Fixed a bug in JTree::findMaximum() and simplified the code
346 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
347 assignment from happening
348 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
349 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
350 FactorGraph ancestor methods; this has been corrected by letting them throw a
351 NOT_IMPLEMENTED exception.
352 * Fixed bug in FactorGraph::clone()
353 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
354 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
355 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
356 * Fixed bug in PropertySet::setAsString<T>()
357 * Fixed a bug in rnd_seed()
358 * BipartiteGraph:
359 - Fixed bug in eraseNode1()
360 - Fixed bug in eraseNode2()
361 - Fixed bug in isTree()
362 * GraphAL:
363 - Fixed bug in nrEdges()
364 - Fixed bug in addEdge()
365 - Fixed bug in isTree()
366 - Fixed bug in eraseNode()
367 - Fixed bug in printDot()
368 * Fixed bug in createGraphGrid3D()
369 * Fixed bug in createGraphRegular()
370
371
372 libDAI-0.2.4 (2010-02-11)
373 -------------------------
374
375 New features:
376 * Implemented Tree-Reweighted BP
377 * [Frederik Eaton] Implemented Fractional Belief Propagation
378
379 Miscellaneous improvements:
380 * Improved documentation
381 * [Frederik Eaton] Added constructors for BBPCostFunction
382 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
383 * [Frederik Eaton] Added unary minus to TProb<>
384 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
385 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
386 * tests/testdai option "marginals" now has three possible values: NONE
387 outputs no marginals, VAR only variable marginals, and ALL outputs all
388 marginals calculated by the algorithm.
389 * Strengthened convergence criteria of various algorithms
390 * Added GraphAL, an adjacency list implementation for graphs,
391 similar to (but simpler than) BipartiteGraph
392 * Added some functionality to create various standard factors
393 (the functions whose names start with "createFactor")
394 * Added examples example_sprinkler_gibbs and example_sprinkler_em
395 * Implemented various heuristics for choosing a variable elimination sequence
396 in JTree
397 * Added BETHE method for GBP/HAK cluster choice
398 * Made alias support official part of the library
399
400 Build system:
401 * Moved platform independent build options into Makefile.ALL
402 * Windows platform now needs Boost 1.37 or higher
403
404 Code cleanup:
405 * Cleaned up utils/createfg and tests/testdai
406 * Cleanup of some duplicate code in BP, FBP, TRWBP
407
408 Interface changes (the old interface is marked obsolete and will be removed in the next release):
409 * Removed obsolete/deprecated stuff
410 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
411 * Renamed some functions of BipartiteGraph:
412 add1() -> addNode1()
413 erase1() -> eraseNode1()
414 nr1() -> nrNodes1()
415 add2() -> addNode2()
416 erase2() -> eraseNode2()
417 nr2() -> nrNodes2()
418 * Renamed some functions in ClusterGraph:
419 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
420 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
421 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
422 * Changed interface of one RegionGraph constructor
423 * Renamed "Clamped BP" into "Conditioned BP"
424
425 Bug fixes:
426 * Fixed regression in scripts/regenerate-properties (now all errors are
427 gathered before throwing the exception, as used to be the case)
428 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
429 * [Alexander Schwing] Fixed error in BP that occured with damping
430 and using log-domain updates
431 * Fixed bug in HAK for trivial region graphs (with only one outer region
432 and no inner regions), reported by Alejandro Lage.
433 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
434
435
436 libDAI-0.2.3 (2009-11-16)
437 -------------------------
438
439 New features:
440 * Complete doxygen documentation (although more detailed documentation still
441 has to be written)
442 * [Charles Vaske] Added parameter learning for conditional probabilities by
443 Expectation Maximization
444 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
445 octave interfaces
446 * Added Max-Product functionality to JTree
447 * [Frederik Eaton] Added Back-Belief-Propagation
448 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
449 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
450
451 Code cleanup:
452 * Updated copyright headers
453 * Cleaned up error handling by introducing the DAI_THROWE macro
454 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
455 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
456 dai::Exception and is even active if NDEBUG is defined
457 * Removed all the virtual default constructors *::create(), as they are not used
458 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
459 * [Frederik Eaton] Change cout to cerr in warnings and error messages
460
461 Miscellaneous improvements:
462 * BipartiteGraph:
463 - Added eraseEdge( size_t n1, size_t n2 )
464 - [Frederik Eaton] Improved documentation of Neighbor
465 * TProb<T>:
466 - Added divided_by(const TProb<T>&) const
467 - Added constructor TProb<T>( const std::vector<S> &v )
468 - Added size_t draw(), which draws a random index
469 - [Frederik Eaton] Added setUniform()
470 - [Frederik Eaton] Added sumAbs()
471 - [Frederik Eaton] Added argmax()
472 - [Giuseppe Passino] Added begin(), end()
473 * TFactor<T>:
474 - [Giuseppe Passino] Added begin(), end()
475 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
476 which reorders variables to canonical ordering before storing the table
477 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
478 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
479 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
480 * State:
481 - [Giuseppe Passino] Added prefix ++ operator
482 * Permute:
483 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
484 * FactorGraph:
485 - [Frederik Eaton] Added clampVar()
486 - [Frederik Eaton] Added clampFactor()
487 - [Giuseppe Passino] Added begin(), end()
488 * PropertySet:
489 - Added keys(), for getting all keys
490 - [Frederik Eaton] Added default constructor
491 - [Frederik Eaton] Added constructor from string
492 * InfAlg:
493 - Added setProperties(), getProperties() and printProperties()
494 - [Frederik Eaton] Added beliefV(), beliefF()
495 * ExactInf:
496 - Added calcMarginal(const VarSet &)
497 * HAK:
498 - Added "init" parameter to allow for random initialization
499 * BP:
500 - [Giuseppe Passino] Added findMaximum(), which can be used after running
501 max-product BP to construct a global state with maximum probability
502 * JTree:
503 - Added findMaximum(), which can be used after running
504 max-product JTree to construct a global state with maximum probability
505 * MatLab interface:
506 - MEX file dai now also returns variable and factor beliefs
507 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
508 (only for BP and JTree)
509 * README is now created automatically from doxygen documentation
510 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
511 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
512 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
513 and functions (concat(),rnd()) to util.h
514 * Changed output stream operator<< for Var and VarSet
515 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
516 alias substitutions
517 * [Frederik Eaton] Added useful aliases to aliases.conf
518 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
519 set instead of the linear search (which can yield enormous speedups - a
520 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
521 * Added debug assertions to Var which check for inconsistent dimensions of
522 variables with the same labels
523 * toc() now returns POSIX system time with maximum accuracy of microseconds
524 * Exception objects now remember their error code
525 * Examples:
526 - Moved example.cpp to examples/
527 - Added examples/example_bipgraph.cpp
528 - Added examples/example_varset.cpp
529 - Added examples/example_sprinkler.cpp
530 - Added examples/example_permute.cpp
531 - Added python and octave ports for examples/example_sprinkler.cpp
532
533 Build system:
534 * Improved Makefile:
535 - Merged Makefile.win and Makefile.shared into Makefile
536 - Macros DAI_VERSION and DAI_DATE have been introduced,
537 in order to store this information in a central place
538 - Introduced CCNODEBUGFLAGS in Makefile
539 - Switched Makefile.win to GNU Make syntax
540 - [Frederik Eaton] Added TAGS, lib targets to Makefile
541 * Compatibility:
542 - [Peter Gober] libDAI can now be built on Cygwin
543 - [Dan Preston] libDAI can now be built on Mac OS X
544 - Changed regression test so that it also works under Windows
545
546 Interface changes (the old interface is marked obsolete and will be removed in the next release):
547 * Var:
548 - Variable labels are now nonnegative (of type size_t)
549 * VarSet:
550 - Replaced calcState() by non-member calcLinearState()
551 - Replaced calcStates() by non-member calcState()
552 * Permute:
553 - Renamed convert_linear_index into convertLinearIndex
554 * TProb<>:
555 - Replaced log0() by log(true)
556 - Replaced takeLog0() by takeLog(true)
557 - Removed hasNonPositives()
558 - Renamed minVal() to min()
559 - Renamed maxVal() to max()
560 - Renamed totalSum() to sum()
561 * TFactor<>:
562 - Replaced log0() by TFactor<T>::log(true)
563 - Removed divided_by, use operator/ instead
564 - Removed divide, use operator/= instead
565 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
566 - Renamed minVal() to min()
567 - Renamed maxVal() to max()
568 - Renamed totalSum() to sum()
569 * FactorGraph:
570 - Changed clamp and clamp interfaces (the variable to be
571 clamped is now indicated by its index, not as a Var)
572 * RegionGraph:
573 - Renamed Check_Counting_Numbers into checkCountingNumbers
574 - Renamed Calc_Counting_Numbers into calcCountingNumbers
575 * Miscellaneous:
576 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
577 - Replaced UEdgeVec by Graph
578 - Replaced DEdgeVec by new RootedTree class
579 - Moved functionality of GrowRootedTree() into constructor of RootedTree
580 - Merged calcPairBeliefsNew() into calcPairBeliefs()
581 - Removed calcMarginal2ndO()
582 - Renamed smallSet<T> to SmallSet<T>
583 - Removed class Diffs
584 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
585 BipartiteGraph and FactorGraph (which will be obsoleted soon)
586
587 Bug fixes:
588 * Fixed reversal of min and max in
589 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
590 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
591 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
592 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
593 before typeid(std::string) (this fixes a strange bug for empty string property)
594 * Added work-around for bug in Boost Graph Library
595 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
596 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
597 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
598 for reporting this)
599
600
601 libDAI-0.2.2 (2008-09-30)
602 -------------------------
603
604 New features:
605 * Approximate inference methods now report the number of iterations needed.
606 * Added damping to various algorithms to improve convergence properties.
607 * Added more features to utils/createfg for creating factor graphs.
608 * Added ExactInf class for brute force exact inference.
609 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
610 whether calculations are done in the log-domain or in the linear domain;
611 doing calculations in the log-domain may help if the numerical range
612 of a double is too small.
613 * [Claudio Lima] Added Max-Product functionality to BP.
614 * Improved documentation.
615
616 Improved architecture:
617 * Added Exceptions framework.
618 * Pervasive change of BipartiteGraph implementation (based on an idea by
619 Giuseppe Passino). BipartiteGraph no longer stores the node properties
620 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
621 nor an edge list. Instead, it stores the graph structure as lists of
622 neighboring nodes. This yields a significant memory/speed improvement for
623 large factor graphs, and is more elegant as well. Iterating over neighbors is
624 made easy by using boost::foreach.
625 * Added conditional compilation of inference methods.
626 * VarSet is now implemented using a std::vector<Var> instead of a
627 std::set<Var>, which yields a significant speed improvement. Furthermore,
628 the implementation has been generalized, resulting in the small_set<T> class
629 which can be used to represent sets of small cardinality; VarSet is the
630 specialization with T = Var.
631 * Improved ClusterGraph implementation, yielding significant speedups
632 for the JunctionTree algorithm on large factorgraphs.
633
634 Code cleanup:
635 * Moved everything into namespace "dai".
636 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
637 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
638 * Removed utils/remove_short_loops and matlab/remove_short_loops.
639 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
640 * Improved index.h:
641 - Renamed Index -> IndexFor
642 - Added some .reserve()'s to IndexFor methods which yields a
643 25% speedup of testregression
644 - Replaced multind by Permute
645 - Added MultiFor
646 - Added State
647 * New funcstionality of factor.h.
648 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
649 inference algorithm, because the Properties framework was not as
650 convenient as I hoped, and not every inference algorithm needs a maxdiff
651 variable. Also, replaced some FactorGraph functionality in InfAlg by a
652 function that returns the FactorGraph. The result is cleaner (less
653 entangled) code.
654 * Removed x2x.
655 * Replaced Complex with real numbers (negative potentials are just too rare
656 to warrant the additional "complexity" :)).
657
658 Miscellaneous improvements:
659 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
660 GCC under Cygwin.
661 * Contributions by Peter Gober:
662 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
663 * Misc contributions by Giuseppe Passino:
664 - removed "using namespace std;" from header files - bad practice;
665 - moved header files in include/dai and sources in src;
666 - changed #ifndefs to GNU style;
667 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
668 - dai::TProb:
669 o removed copy constructor and assignment operators (redundant);
670 o implementation of some methods via STL algorithms;
671 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
672 o explicit constructor (prevents implicit conversion from size_t to TProb);
673 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
674 * Misc contributions by Christian Wojek:
675 - New FactorGraph constructor that constructs from given ranges of factors
676 and variables;
677 - Optimization of FactorGraph constructors using tr1::unordered_map.
678 * FactorGraph constructors no longer check for short loops (huge speed
679 increase for large factor graphs), nor for negative entries. Also, the
680 normtype is now Prob::NORMPROB by default.
681 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
682
683 Interface changes:
684 * VarSet::
685 - VarSet::stateSpace() -> nrStates(const VarSet &)
686 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
687 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
688 - removed bool operator||
689 - operator&&(const VarSet&) -> intersects(const VarSet&)
690 - operator&&(const Var&) -> contains(const Var&)
691 * FactorGraph::
692 - delta(const Var &) -> delta(size_t)
693 - Delta(const Var &) -> Delta(size_t)
694 - makeCavity(const Var &) -> makeCavity(size_t)
695 - vars() -> vars
696 - factors() -> factors
697 - removed MakeFactorCavity(size_t)
698 - removed ExactMarginal(const VarSet &)
699 - removed ExactlogZ()
700 - removed updatedFactor(size_t)
701 - removed _normtype and NormType()
702 - removed hasShortLoops(...) and removeShortLoops(...)
703 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
704 - undoProb(size_t) -> restoreFactor(size_t)
705 - saveProb(size_t) -> backupFactor(size_t)
706 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
707 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
708 - ReadFromFile(const char*) returns void (throws on error)
709 - WriteToFile(const char*) returns void (throws on error)
710 - removed hasNegatives()
711 * RegionGraph::
712 - nr_ORs() -> nrORs()
713 - nr_IRs() -> nrIRs()
714 - ORs() -> ORs
715 - IRs() -> IRs
716 * *::Regenerate() -> *::construct()
717 * Renamed Index -> IndexFor
718 * Diffs:
719 - max() -> maxDiff()
720 - max_size() -> maxSize()
721 * Prob::max() -> Prob::maxVal()
722 * Factor::
723 - max() -> maxVal()
724 - part_sum() -> partSum()
725 * toc() in util.h now returns seconds as a double
726 * VarSet::operator&&
727 * Properties -> PropertySet
728
729
730 libDAI-0.2.1 (2008-05-26)
731 -------------------------
732
733 Bugfix release.
734 * added missing cstdio header in util.h
735 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
736 * added description of the factor graph fileformat
737 * improved Makefile
738
739
740 libDAI-0.2.0 (2006-11-30)
741 -------------------------
742
743 First public release.
744
745
746 0.1.5 (2006-11-30)
747 ------------------
748
749 Regressions
750
751 - tests/testlcbp and tests/testlcbp are broken.
752 - EXACT method does not work anymore.
753 - The Properties framework gives a speed penalty because of the lookup
754 costs involved; inner loops should be optimized.
755
756 General framework
757
758 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
759 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
760 functions to forward functionality from either FactorGraph or RegionGraph
761 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
762 and in RegionGraph and no explicit interface is needed in descendants.
763 - New abstract base class InfAlg added, representing an inference algorithm,
764 from which DAIAlg<T> inherits. This solves the incompatibility problems of
765 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
766 DAIAlg<RegionGraph>). More work is required to reduce code duplication
767 (make FactorGraph part of InfAlg).
768 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
769 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
770 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
771 one to save a few factors, modify them (e.g. clamp them), and then restore them
772 to their old values. Undo should also init the corresponding messages / beliefs.
773 This can be used if a given factor graph repeatedly needs to be clamped in
774 different ways and an approximation method is run for each clamping; using the
775 saveProbs/undoProbs can give a significant speed increase.
776 - Switched to a general Properties framework that handles the parameters of
777 all inference methods in a uniform manner. The Properties class is a map of
778 several properties in boost::any objects, indexed by their names (strings).
779 It can read from a stream and write to a stream. It is recursive, in the sense
780 that a Properties object can hold a variable of type Properties as well.
781 - Added a generic way of constructing inference algorithms from a factor graph,
782 name and properties object. Added the newInfAlg function which constructs
783 the requested object. This is used by LCBP, the Matlab interface and the
784 command line (test) interface.
785 - Added a generic enum framework for enum parameters. Although implemented as a
786 hack, it is quite useful in that it drastically simplifies and reduces the
787 amount of code for handling enum parameters.
788 - Provided generic functions for calculating marginals in different ways that
789 work for all approximate inference methods.
790
791 Bugfixes
792
793 - Fixed GBP free energy.
794 - Fixed bug in junctiontree (it didn't init the _vars variable).
795 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
796 the logical NOT of what they should return).
797 - Fixed bug in RegionGraph::RecomputeOR(s).
798 - Fixed bug in utils/create_dreg_fg:
799 graph structure was not random for given parameters (forgot to call srand()).
800 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
801 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
802 that consists of one outer region only.
803 - Fixed INIT bug in LCBP2::UpdatePancake().
804 - Fixed MaxDiffs flow (except for MR).
805
806 New functionality
807
808 - HAK supports several default cluster choices:
809 minimal (only factors)
810 delta (Markov blankets)
811 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
812 Only the maximal clusters are used as outer clusters.
813 - Implemented TreeEP. It generalizes the heuristic method described in the
814 Minka & Qi paper for obtaining a tree with the most relevant interactions to
815 higher order interactions. Almost all optimizations described in the Minka & Qi
816 paper are used, except that evidence is passed over the whole tree instead of
817 relevant subsets (the latter is almost implemented but buggy). Also added
818 alternative (worst-case) algorithm that uses a maximum spanning tree on the
819 weighted graph where the weight between neighbours i and j is given by
820 N(psi,i,j), where psi is the product of all the factors involving both i and j
821 (which is an upper bound on the effective interaction between i and j).
822 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
823 to be able to handle connectivities larger than 3 (in principle, up to 32).
824 It supports different initialization methods (the original RESPPROP,
825 the CLAMPING method and EXACT which uses JTree) and different update methods
826 (FULL and LINEAR).
827 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
828 networks and uses some approximate inference method on them for calculating
829 marginals.
830 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
831 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
832 interactions and LCBPL is LCBPI improved for higher-order interactions.
833 - Wrote one single program utils/createfg for creating various types of
834 random factor graphs.
835 - Wrote utility to visualize factor graphs using graphviz.
836 (it uses the BOOST Program Options library)
837 - Added fginfo utility that displays some info about a .fg file.
838 - Implemented Factor::strength function that calculates the potential strength
839 N(psi,i,j) between variables i and j as described in cs.IT:0504030
840 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
841 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
842 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
843 - Implemented a MATLAB interface ai_potstrength for Factor::strength
844 - Added Martijn's x2x
845
846 Improvements of existing code
847
848 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
849 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
850 associates outer region indices to factor indices (no powers yet, this
851 is deemed superfluous) and provides functions to recompute (some of) the
852 outer regions from the factors.
853 - InfAlg descendants run() methods now stop immediately and return NAN in case
854 they detect NANs. Only BP does not do NAN checking for performance reasons.
855 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
856 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
857 timing and convergence criteria.
858 - Implemented logZ() for JTree. It does the calculation during message-passing.
859 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
860 hopefully this will give more accurate approximations.
861 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
862 for a faster way of calculating marginals, which does not require a call to init()
863 nor cloning the whole object for each clamping. This leads to a significant speedup.
864 - LCBP (and LCBP2) now have complete flexibility in the specification of the
865 inner method, i.e. the method used to generate the initial cavity approximations.
866 One can pass two strings, a name and a properties string, and LCBP simply invokes
867 newInfAlg to construct the corresponding inference algorithm and uses the generic
868 marginal functions to approximate cavity marginals.
869 - Replaced the global "method" variable by local properties and removed ai.h
870 - Added some methods to Factor (operators *, *=, /, /= with doubles as
871 second argument, operators -, +=, -= with other Factors as second
872 arguments, randomize(), RemoveFirstOrderInteractions) and similar
873 operations to Prob
874 - Moving towards boost::program_options for handling command line arguments
875 (tests/test is done).
876 - Renamed some FactorGraph methods:
877 nr_vars -> nrVars
878 nr_factors -> nrFactors
879 varind -> findVar
880 factorind -> findFactor
881 makeFacCavity -> makeFactorCavity
882 - LCBP_SEQMAXRES has been removed because it did strange things.
883 - Implemented RandomDRegularGraph
884 - Implemented JTree::calcMarginal for marginals that are not confined
885 within one cluster (using cut-set conditioning).
886 - Added isConnected() method to FactorGraph (some methods do not work with
887 disconnected factor graphs).
888 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
889 - Removed single node interaction "correction" code from clamping methods
890 - Removed calcCavityDist and calcCavityDist2ndO
891 - No longer depends on GSL.
892 - Increased portability by combining platform dependant utility functions
893 in util.{h,cpp}.
894 - Wrote *.m files providing help
895
896 Testing framework
897
898 - Made a new and significantly improved testing framework that provides most
899 functionality from the command line.
900 - The basis is provided by tests/test, which uses the newInfAlg functionality
901 and enables the user to easily compare from the command line different
902 inference methods on a given factorgraph. All parameters can be specified.
903 Output consists of CPU time, average and maximum single variable marginal
904 errors, relative logZ error and MaxDiff().
905 - tests/aliases.conf contains aliases for standard combinations of methods
906 and their options (which can be used in tests/test).
907 - tests/large contains several bash/python scripts that create random factor
908 graphs, compare several approximate inference algorithms (using tests/test) and
909 allow for easy visualization of the results using PyX.
910 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
911 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
912 regression testing).
913 - Added a regression test to the Makefile which is included in the standard
914 target. It compares all inference methods on tests/testfast.fg with the
915 results stored in tests/testfast.out
916
917 Miscellaneous
918
919 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
920 - Experimental MATLAB code added for StarEP approximation on cavity
921 - Renamed project to libDAI and changed directory name accordingly.
922 - Renamed JunctionTree to JTree.
923 - Fixed licensing (now it's officially GPL).
924 - Improved README
925
926
927 revision 252
928 ------------
929
930 Functionality
931 - Added RegionGraph, GBP, CVM and HAK (double-loop).
932 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
933 RegionGraph.
934 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
935 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
936 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
937 it over all subsuming outer regions. See README for when negative factors are known to work
938 and when not.
939 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
940 it does not automatically merge factors anymore.
941 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
942 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
943 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
944 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
945 such that it does not store the complete pancakes, but represents them as little factor graphs).
946
947 Implementation / code
948 - Made a seperate type WeightedGraph, which until now only implements Prim's
949 maximal spanning tree algorithm and is only used by the junction tree code. It might
950 be good to make it a class somewhere in the future and extend it's interface.
951 - Made a seperate class ClusterGraph, which is only used by the junction tree
952 code. It's main purpose is a graph-theoretical variable elimination algorithm.
953 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
954 - Massive code cleanup, moving towards "generic" programming style, using
955 multiple inheritance and polymorphism.
956 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
957 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
958 that can be used by FactorGraph-based DAIAlgs.
959 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
960 and VarSet) and provides functionality for it (which is used by TFactor<T>).
961 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
962 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
963 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
964 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
965 o using Prob's instead of Factor's;
966 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
967 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
968 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
969 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
970 that takes the cavitydists and multiplies them with the relevant factors. This
971 resulted in an API change in AI which now accepts and returns initial cavitydists
972 instead of initial pancakes.
973
974 Minor changes
975 - Started writing DoxyGen documentation
976 - Renamed lcptab2fg.m matlab/ai_writefg.m
977 - Moved all matlab stuff to matlab/
978 - More detailed reporting (also reports clocks used).
979 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
980 - Improved testing suite.
981 - Removed logreal support.
982 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
983 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
984 full and periodic 2D Ising networks according to some command line parameters.
985 - Now logZ really returns logZ instead of -logZ.
986 - Added FactorGraph::WriteToDotFile
987
988
989 0.1.4 (2006-04-13)
990 ------------------
991 - Added file IO routines to read and write factorgraphs.
992 - Added L-infinity normalization for use with (partially) negative factors.
993 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
994 handle (partially) negative factors.
995 - Added test suite.
996 - All probabilities are now represented using double instead of LogReal<double>.
997 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
998 - Combined several variants of BP into doBP. Several update schemes possible.
999 Now uses precalculated indices for optimization.
1000 - Renamed Node -> Var and Potential -> Factor.
1001 - Extensive code cleanup. More use of OO techniques. Changed API.
1002 - MaxIter now means maximum number of passes (corresponding to number of
1003 _parallel_ updates).
1004 - MaxDiff now means the maximum L-infinity distance between the updated and
1005 original single variable beliefs, for all AI methods.
1006 - Implemented RBP which converges faster than BP for difficult problems.
1007 - Now uses method parameter which is a bitmask combining outmethod and inmethod
1008 (see ai.h).
1009
1010
1011 0.1.3 (2006-03-22)
1012 --------------------
1013 - All AI methods now return maxdiff
1014 - ai.cpp:
1015 o Now returns maxdiffinner and maxdiffouter
1016 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
1017 o New InitCav outermethod (only create initial cavity distributions)
1018 - bp.cpp:
1019 o New CavityDist2ndO which estimates 2nd order cavity interactions
1020 - Makefile:
1021 o Bugfix: removed dependencies on algwim.*
1022
1023
1024 0.1.2 (2006-02-28)
1025 --------------------
1026 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
1027 - Added the possibility to provide initial cavity distributions as an input
1028 argument to ai (not much error checking is done, so be careful).
1029 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
1030 the output arguments Q, Q0 of ai).
1031 - Removed algwim.* since it does not work.
1032
1033
1034 0.1.1 (2006-02-28)
1035 --------------------
1036 - The constructors of (Log)FactorGraph and LogFactorGraph from a
1037 vector<(Log)Potential> now merge potentials to prevent short loops (of length
1038 4) in the factor graph. These are used in ai to construct the factor graphs
1039 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
1040 of BipGraph checks for the existence of short loops.
1041 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
1042 description in the help).
1043 - ai does not hook cout anymore (which caused weird segfaults).
1044 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
1045 - Removed network.* since it is not useful.
1046
1047
1048 0.1.0 (2006-02-28)
1049 --------------------
1050 First version worthy of a version number.