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