Fixed Win64 build problems with help of Sameh Khamis
[libdai.git] / ChangeLog
1 git master
2 ----------
3 * Added VC10 build files, kindly provided by Sameh Khamis
4 * Fixed several Win64 related bugs (found by Sameh Khamis):
5 - define NAN
6 - add some necessary casts of size_t to BigInt
7 - replaced occurrence of __PRETTY_FUNCTION__ with FUNCTION_NAME that was forgotten in a previous fix
8 This means that libDAI now builds successfully also on 64-bit Windows systems.
9 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
10 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION (Visual Studio) or __func__ (other compilers)
11 * Fixed bug (found by cax): when building MatLab MEX files, GMP libraries were not linked
12 * [Arman Aksoy] Added Makefile.MACOSX64
13 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)
14 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions
15 * Optimized ClusterGraph( const FactorGraph&, bool) constructor
16 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers
17 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()
18 * Fixed memory leak in CBP::run()
19 * Fixed typo in Priya's name
20
21
22 libDAI-0.3.0 (2011-07-12)
23 -------------------------
24
25 New license:
26 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)
27
28 Miscellaneous improvements:
29 * Improved Exception class
30 (it now stores more information and doesn't print to stderr by default)
31 * Added builtinInfAlgs() and builtinInfAlgNames()
32
33 Bug fixes:
34 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()
35 and maxDiff() implementations
36 * Now uses GMP big integer type to represent linear states and the number of
37 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya
38 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now
39 no longer works out-of-the-box.
40 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
41 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
42 instead of returning a MAP state with zero joint probability
43 (reported by Hynek Urban)
44 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
45 (the random seed needs to be an unsigned int on some platforms)
46 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
47 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
48 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)
49 * Replaced all Name members by name() virtual functions and removed global variable DAINames
50 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
51
52
53 libDAI-0.2.7 (2010-08-19)
54 -------------------------
55
56 * Removed interfaces deprecated in 0.2.6.
57 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
58 if one or more variables had a MAP belief with more than one maximum, an
59 incorrect MAP state could result.
60
61
62 libDAI-0.2.6 (2010-08-05)
63 -------------------------
64
65 New features:
66 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
67 * Added source code for one of the winning solvers of the
68 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
69 * Added support for reading files in the UAI Approximate Inference Challenge
70 format, supporting both the 2006/2008 evidence file format and the 2010
71 evidence file format (io.h/cpp).
72
73 Miscellaneous improvements:
74 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
75 for setting an upper limit on execution time.
76 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
77 * SmallSet:
78 - Added SmallSet::erase( const T& t ).
79 * VarSet:
80 - nrStates() now returns a long double instead of a size_t.
81 * Permute:
82 - Added ranges() accessor.
83 - Added inverse() method.
84 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
85 * Factor:
86 - Added createFactorDelta( const VarSet& vs, size_t state ).
87 * ClusterGraph:
88 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
89 - Added findCluster( const VarSet& cl ).
90 - Added elimVar( size_t i ).
91 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
92 * FactorGraph:
93 - Added isMaximal(size_t).
94 - Added maximalFactor(size_t).
95 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
96 * Gibbs:
97 - Added 'restart' property.
98 - Added Gibbs::findMaximum() for MAP inference.
99 * HAK:
100 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
101 * examples/examples_imagesegmentation.cpp:
102 - [Peter Rockett] Improved Makefiles for image segmentation example.
103 - Added build flag to specify the CImg version.
104 * util.h/cpp:
105 - Added fromString<>( const std::string& x ).
106
107 Interface changes (the old interface is marked obsolete and will be removed in the next release):
108 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
109 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
110 and replaced them by a globally defined Neighbor structure
111 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
112 and replaced them by a globally defined Neighbors type
113 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
114 and replaced them by a globally defined Edge type
115 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
116 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
117 variable is not found.
118 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
119 and replaced it with an improved version
120 'vector<string> tokenizeString( const string&, bool, const string& )'
121 * Removed interfaces deprecated in 0.2.5.
122
123 Bug fixes:
124 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
125 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
126 which have problems when comparing const_reverse_iterator with
127 reverse_iterator.
128 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
129 (segfault if factors depending on 0 variables were passed to MatLab)
130
131
132 libDAI-0.2.5 (2010-05-09)
133 -------------------------
134
135 New features:
136 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
137 weightedgraph, enum, util, exceptions, properties, index, prob,
138 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
139 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
140 * Added utils/uai2fg, a utility to convert the UAI inference competition file
141 formats to the libDAI factor graph file format
142 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
143 * Added examples/example_imagesegmentation
144
145 Miscellaneous improvements:
146 * TRWBP:
147 - Added initialization of TRWBP weights by sampling spanning trees
148 * MF:
149 - Added an "init" option that allows to initialize randomly
150 - Added an "updates" option that allows to choose between standard
151 mean field and "hard-spin" mean field
152 * MR:
153 - rewrote response propagation implementation with help of BBP
154 - now uses GraphAL to represent the Markov graph
155 - miscellaneous smaller cleanups
156 * TreeEP:
157 - Now also supports disconnected factor graphs
158 * JTree:
159 - Now also supports disconnected factor graphs
160 * ExactInf:
161 - Added findMaximum()
162 * RegionGraph:
163 - Added error checking code
164 - Changed the way a RegionGraph is streamed to an std::ostream.
165 * ClusterGraph:
166 - Added nrVars() method
167 - Added var( size_t ) method
168 - Added cluster( size_t ) method
169 * FactorGraph:
170 - clamped() now contains a delta factor for the clamped variable
171 - Added MarkovGraph()
172 * TFactor:
173 - Added takeAbs()
174 - Added takeExp()
175 - Added takeLog( bool )
176 - Added operator-() const
177 - Added sumAbs() const
178 - Added operator==( const TFactor<T> &y )
179 - Added get(size_t), set(size_t,T)
180 * TProb:
181 - Added operator==( const TProb<T> &q )
182 - accumulate() now also applies op2 to init
183 - operator/= (T x) now yields 0 when dividing by 0
184 - Added resize(size_t)
185 - Added get(size_t) and set(size_t,T)
186 - Changed format of TProb<T> when streamed to an ostream
187 * multifor:
188 - Added reset()
189 * PropertySet:
190 - Added size()
191 - Added clear()
192 - Added erase()
193 * util.h/cpp:
194 - Added std::string toString( const T& x )
195 * weightedgraph.h/cpp:
196 - Added option to MaxSpanningTree and MinSpanningTree for
197 choosing between Prim's algorithm and Kruskal's algorithm
198 - Better error checking in RootedTree constructor
199 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
200 * BipartiteGraph:
201 - Added hasEdge()
202 - Added findNb1()
203 - Added findNb2()
204 - Added nb1Set()
205 - Added nb2Set()
206 - Added operator==( const BipartiteGraph& )
207 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
208 - Added operator<<( std::ostream&, const BipartiteGraph& )
209 * GraphAL:
210 - Added hasEdge(size_t,size_t)
211 - Added nbSet(size_t)
212 - Added operator==( const GraphAL& )
213 - Added operator<<( std::ostream&, const GraphAL& )
214 * SmallSet:
215 - Added insert( const T& t ) method
216 * Improved regression test
217 * Made all "verbose" properties optional
218 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
219 'ISING' factor type has been renamed to 'ISINGGAUSS'
220 * tests/testdai option "marginals" now has five possible values: NONE
221 outputs no marginals, VAR only variable marginals, FAC only factor
222 marginals, VARFAC both types of marginals, and ALL outputs all
223 marginals calculated by the algorithm.
224 * Compressed Makefile
225
226 Interface changes (the old interface is marked obsolete and will be removed in the next release):
227 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
228 * TreeEP:
229 - Changed construct( const RootedTree& ) into
230 construct( const FactorGraph&, const RootedTree& )
231 * JTree:
232 - Changed construct( const std::vector<VarSet>&, bool ) into
233 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
234 - Changed GenerateJT( const std::vector<VarSet> & )
235 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
236 * RegionGraph:
237 - Made (previously public) members G, ORs, IRs and fac2OR protected and
238 added DAG() accessor which returns a reference to the region graph DAG
239 structure (currently implemented as a BipartiteGraph).
240 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
241 protected, because exposing it to the world serves no purpose.
242 - Removed partial constructor RegionGraph( const FactorGraph& fg )
243 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
244 protected and renamed them by changing the "Recompute" into "recompute",
245 because exposing them to the world serves no purpose.
246 * ClusterGraph:
247 - Made (previously public) members G, vars and clusters private and added
248 bipGraph(), vars() and clusters() methods which offer read-only access
249 to these members.
250 - Deprecated toVector()
251 - Renamed size() into nrClusters()
252 * FactorGraph:
253 - Renamed Cliques() into maximalFactorDomains() and made it faster
254 - findVars( const VarSet& ) now returns a SmallSet<size_t>
255 and its argument now has a const-qualifier (which fixes a small bug).
256 - Made (previously public) member G private and added the
257 bipGraph() method, which offers read-only access to it.
258 - Deprecated the iterator interface:
259 o FactorGraph::iterator typedef
260 o FactorGraph::const_iterator typedef
261 o FactorGraph::begin() members
262 o FactorGraph::end() members
263 - Deprecated factor(size_t) which offered write access to a factor
264 because using this functionality in the descendant RegionGraph is dangerous,
265 as the outer regions are not automatically recomputed.
266 * TFactor:
267 - Renamed states() into nrStates()
268 - Added get(size_t) and set(size_t,T) operators;
269 get() is equivalent to "operator[](size_t) const" and set() should
270 be used instead of the non-const operator[], which has been deprecated
271 * TProb:
272 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
273 constructor: the sizeHint argument no longer defaults to 0
274 - Deprecated accumulate( T init, binOp op1, unOp op2 );
275 instead, accumulateSum( T init, unOp op ) and
276 accumulateMax( T init, unOp op, bool minimize ) should be used.
277 - Deprecated TProb::NormType and TProb::DistType;
278 ProbNormType and ProbDistType should be used instead.
279 - Fixed bug by renaming operator<=() to operator<()
280 - Added get(size_t) and set(size_t,T) operators;
281 get() is equivalent to "operator[](size_t) const" and set() should
282 be used instead of the non-const operator[], which has been deprecated
283 * PropertySet:
284 - Renamed Set() -> set()
285 - Renamed Get() -> get()
286 - Renamed GetAs<T>() -> getAs<T>()
287 - Renamed ConvertTo<T>() -> convertTo<T>()
288 * util.h/cpp:
289 - Removed max( const std::vector<Real> &v )
290 * weightedgraph.h/cpp:
291 - Renamed MaxSpanningTreePrims into MaxSpanningTree
292 - Renamed MinSpanningTreePrims into MinSpanningTree
293 - The vertices in DEdge and UEdge are now named "first" and "second"
294 for compatibility with a std::pair<size_t,size_t>
295 * BipartiteGraph:
296 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
297 * SmallSet:
298 - The sizeHint argument of the iterator constructor
299 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
300 no longer has a default value in order to avoid confusion with the
301 SmallSet::SmallSet( const T &t1, const T &t2 )
302 constructor.
303
304 Bug fixes:
305 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
306 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
307 * Fixed some bugs in the MatLab interface build system
308 * Fixed a bug in utils/fginfo.cpp
309 * Fixed a bug in JTree::findMaximum() and simplified the code
310 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
311 assignment from happening
312 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
313 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
314 FactorGraph ancestor methods; this has been corrected by letting them throw a
315 NOT_IMPLEMENTED exception.
316 * Fixed bug in FactorGraph::clone()
317 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
318 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
319 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
320 * Fixed bug in PropertySet::setAsString<T>()
321 * Fixed a bug in rnd_seed()
322 * BipartiteGraph:
323 - Fixed bug in eraseNode1()
324 - Fixed bug in eraseNode2()
325 - Fixed bug in isTree()
326 * GraphAL:
327 - Fixed bug in nrEdges()
328 - Fixed bug in addEdge()
329 - Fixed bug in isTree()
330 - Fixed bug in eraseNode()
331 - Fixed bug in printDot()
332 * Fixed bug in createGraphGrid3D()
333 * Fixed bug in createGraphRegular()
334
335
336 libDAI-0.2.4 (2010-02-11)
337 -------------------------
338
339 New features:
340 * Implemented Tree-Reweighted BP
341 * [Frederik Eaton] Implemented Fractional Belief Propagation
342
343 Miscellaneous improvements:
344 * Improved documentation
345 * [Frederik Eaton] Added constructors for BBPCostFunction
346 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
347 * [Frederik Eaton] Added unary minus to TProb<>
348 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
349 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
350 * tests/testdai option "marginals" now has three possible values: NONE
351 outputs no marginals, VAR only variable marginals, and ALL outputs all
352 marginals calculated by the algorithm.
353 * Strengthened convergence criteria of various algorithms
354 * Added GraphAL, an adjacency list implementation for graphs,
355 similar to (but simpler than) BipartiteGraph
356 * Added some functionality to create various standard factors
357 (the functions whose names start with "createFactor")
358 * Added examples example_sprinkler_gibbs and example_sprinkler_em
359 * Implemented various heuristics for choosing a variable elimination sequence
360 in JTree
361 * Added BETHE method for GBP/HAK cluster choice
362 * Made alias support official part of the library
363
364 Build system:
365 * Moved platform independent build options into Makefile.ALL
366 * Windows platform now needs Boost 1.37 or higher
367
368 Code cleanup:
369 * Cleaned up utils/createfg and tests/testdai
370 * Cleanup of some duplicate code in BP, FBP, TRWBP
371
372 Interface changes (the old interface is marked obsolete and will be removed in the next release):
373 * Removed obsolete/deprecated stuff
374 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
375 * Renamed some functions of BipartiteGraph:
376 add1() -> addNode1()
377 erase1() -> eraseNode1()
378 nr1() -> nrNodes1()
379 add2() -> addNode2()
380 erase2() -> eraseNode2()
381 nr2() -> nrNodes2()
382 * Renamed some functions in ClusterGraph:
383 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
384 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
385 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
386 * Changed interface of one RegionGraph constructor
387 * Renamed "Clamped BP" into "Conditioned BP"
388
389 Bug fixes:
390 * Fixed regression in scripts/regenerate-properties (now all errors are
391 gathered before throwing the exception, as used to be the case)
392 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
393 * [Alexander Schwing] Fixed error in BP that occured with damping
394 and using log-domain updates
395 * Fixed bug in HAK for trivial region graphs (with only one outer region
396 and no inner regions), reported by Alejandro Lage.
397 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
398
399
400 libDAI-0.2.3 (2009-11-16)
401 -------------------------
402
403 New features:
404 * Complete doxygen documentation (although more detailed documentation still
405 has to be written)
406 * [Charles Vaske] Added parameter learning for conditional probabilities by
407 Expectation Maximization
408 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
409 octave interfaces
410 * Added Max-Product functionality to JTree
411 * [Frederik Eaton] Added Back-Belief-Propagation
412 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
413 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
414
415 Code cleanup:
416 * Updated copyright headers
417 * Cleaned up error handling by introducing the DAI_THROWE macro
418 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
419 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
420 dai::Exception and is even active if NDEBUG is defined
421 * Removed all the virtual default constructors *::create(), as they are not used
422 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
423 * [Frederik Eaton] Change cout to cerr in warnings and error messages
424
425 Miscellaneous improvements:
426 * BipartiteGraph:
427 - Added eraseEdge( size_t n1, size_t n2 )
428 - [Frederik Eaton] Improved documentation of Neighbor
429 * TProb<T>:
430 - Added divided_by(const TProb<T>&) const
431 - Added constructor TProb<T>( const std::vector<S> &v )
432 - Added size_t draw(), which draws a random index
433 - [Frederik Eaton] Added setUniform()
434 - [Frederik Eaton] Added sumAbs()
435 - [Frederik Eaton] Added argmax()
436 - [Giuseppe Passino] Added begin(), end()
437 * TFactor<T>:
438 - [Giuseppe Passino] Added begin(), end()
439 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
440 which reorders variables to canonical ordering before storing the table
441 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
442 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
443 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
444 * State:
445 - [Giuseppe Passino] Added prefix ++ operator
446 * Permute:
447 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
448 * FactorGraph:
449 - [Frederik Eaton] Added clampVar()
450 - [Frederik Eaton] Added clampFactor()
451 - [Giuseppe Passino] Added begin(), end()
452 * PropertySet:
453 - Added keys(), for getting all keys
454 - [Frederik Eaton] Added default constructor
455 - [Frederik Eaton] Added constructor from string
456 * InfAlg:
457 - Added setProperties(), getProperties() and printProperties()
458 - [Frederik Eaton] Added beliefV(), beliefF()
459 * ExactInf:
460 - Added calcMarginal(const VarSet &)
461 * HAK:
462 - Added "init" parameter to allow for random initialization
463 * BP:
464 - [Giuseppe Passino] Added findMaximum(), which can be used after running
465 max-product BP to construct a global state with maximum probability
466 * JTree:
467 - Added findMaximum(), which can be used after running
468 max-product JTree to construct a global state with maximum probability
469 * MatLab interface:
470 - MEX file dai now also returns variable and factor beliefs
471 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
472 (only for BP and JTree)
473 * README is now created automatically from doxygen documentation
474 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
475 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
476 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
477 and functions (concat(),rnd()) to util.h
478 * Changed output stream operator<< for Var and VarSet
479 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
480 alias substitutions
481 * [Frederik Eaton] Added useful aliases to aliases.conf
482 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
483 set instead of the linear search (which can yield enormous speedups - a
484 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
485 * Added debug assertions to Var which check for inconsistent dimensions of
486 variables with the same labels
487 * toc() now returns POSIX system time with maximum accuracy of microseconds
488 * Exception objects now remember their error code
489 * Examples:
490 - Moved example.cpp to examples/
491 - Added examples/example_bipgraph.cpp
492 - Added examples/example_varset.cpp
493 - Added examples/example_sprinkler.cpp
494 - Added examples/example_permute.cpp
495 - Added python and octave ports for examples/example_sprinkler.cpp
496
497 Build system:
498 * Improved Makefile:
499 - Merged Makefile.win and Makefile.shared into Makefile
500 - Macros DAI_VERSION and DAI_DATE have been introduced,
501 in order to store this information in a central place
502 - Introduced CCNODEBUGFLAGS in Makefile
503 - Switched Makefile.win to GNU Make syntax
504 - [Frederik Eaton] Added TAGS, lib targets to Makefile
505 * Compatibility:
506 - [Peter Gober] libDAI can now be built on Cygwin
507 - [Dan Preston] libDAI can now be built on Mac OS X
508 - Changed regression test so that it also works under Windows
509
510 Interface changes (the old interface is marked obsolete and will be removed in the next release):
511 * Var:
512 - Variable labels are now nonnegative (of type size_t)
513 * VarSet:
514 - Replaced calcState() by non-member calcLinearState()
515 - Replaced calcStates() by non-member calcState()
516 * Permute:
517 - Renamed convert_linear_index into convertLinearIndex
518 * TProb<>:
519 - Replaced log0() by log(true)
520 - Replaced takeLog0() by takeLog(true)
521 - Removed hasNonPositives()
522 - Renamed minVal() to min()
523 - Renamed maxVal() to max()
524 - Renamed totalSum() to sum()
525 * TFactor<>:
526 - Replaced log0() by TFactor<T>::log(true)
527 - Removed divided_by, use operator/ instead
528 - Removed divide, use operator/= instead
529 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
530 - Renamed minVal() to min()
531 - Renamed maxVal() to max()
532 - Renamed totalSum() to sum()
533 * FactorGraph:
534 - Changed clamp and clamp interfaces (the variable to be
535 clamped is now indicated by its index, not as a Var)
536 * RegionGraph:
537 - Renamed Check_Counting_Numbers into checkCountingNumbers
538 - Renamed Calc_Counting_Numbers into calcCountingNumbers
539 * Miscellaneous:
540 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
541 - Replaced UEdgeVec by Graph
542 - Replaced DEdgeVec by new RootedTree class
543 - Moved functionality of GrowRootedTree() into constructor of RootedTree
544 - Merged calcPairBeliefsNew() into calcPairBeliefs()
545 - Removed calcMarginal2ndO()
546 - Renamed smallSet<T> to SmallSet<T>
547 - Removed class Diffs
548 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
549 BipartiteGraph and FactorGraph (which will be obsoleted soon)
550
551 Bug fixes:
552 * Fixed reversal of min and max in
553 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
554 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
555 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
556 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
557 before typeid(std::string) (this fixes a strange bug for empty string property)
558 * Added work-around for bug in Boost Graph Library
559 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
560 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
561 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
562 for reporting this)
563
564
565 libDAI-0.2.2 (2008-09-30)
566 -------------------------
567
568 New features:
569 * Approximate inference methods now report the number of iterations needed.
570 * Added damping to various algorithms to improve convergence properties.
571 * Added more features to utils/createfg for creating factor graphs.
572 * Added ExactInf class for brute force exact inference.
573 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
574 whether calculations are done in the log-domain or in the linear domain;
575 doing calculations in the log-domain may help if the numerical range
576 of a double is too small.
577 * [Claudio Lima] Added Max-Product functionality to BP.
578 * Improved documentation.
579
580 Improved architecture:
581 * Added Exceptions framework.
582 * Pervasive change of BipartiteGraph implementation (based on an idea by
583 Giuseppe Passino). BipartiteGraph no longer stores the node properties
584 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
585 nor an edge list. Instead, it stores the graph structure as lists of
586 neighboring nodes. This yields a significant memory/speed improvement for
587 large factor graphs, and is more elegant as well. Iterating over neighbors is
588 made easy by using boost::foreach.
589 * Added conditional compilation of inference methods.
590 * VarSet is now implemented using a std::vector<Var> instead of a
591 std::set<Var>, which yields a significant speed improvement. Furthermore,
592 the implementation has been generalized, resulting in the small_set<T> class
593 which can be used to represent sets of small cardinality; VarSet is the
594 specialization with T = Var.
595 * Improved ClusterGraph implementation, yielding significant speedups
596 for the JunctionTree algorithm on large factorgraphs.
597
598 Code cleanup:
599 * Moved everything into namespace "dai".
600 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
601 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
602 * Removed utils/remove_short_loops and matlab/remove_short_loops.
603 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
604 * Improved index.h:
605 - Renamed Index -> IndexFor
606 - Added some .reserve()'s to IndexFor methods which yields a
607 25% speedup of testregression
608 - Replaced multind by Permute
609 - Added MultiFor
610 - Added State
611 * New funcstionality of factor.h.
612 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
613 inference algorithm, because the Properties framework was not as
614 convenient as I hoped, and not every inference algorithm needs a maxdiff
615 variable. Also, replaced some FactorGraph functionality in InfAlg by a
616 function that returns the FactorGraph. The result is cleaner (less
617 entangled) code.
618 * Removed x2x.
619 * Replaced Complex with real numbers (negative potentials are just too rare
620 to warrant the additional "complexity" :)).
621
622 Miscellaneous improvements:
623 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
624 GCC under Cygwin.
625 * Contributions by Peter Gober:
626 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
627 * Misc contributions by Giuseppe Passino:
628 - removed "using namespace std;" from header files - bad practice;
629 - moved header files in include/dai and sources in src;
630 - changed #ifndefs to GNU style;
631 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
632 - dai::TProb:
633 o removed copy constructor and assignment operators (redundant);
634 o implementation of some methods via STL algorithms;
635 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
636 o explicit constructor (prevents implicit conversion from size_t to TProb);
637 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
638 * Misc contributions by Christian Wojek:
639 - New FactorGraph constructor that constructs from given ranges of factors
640 and variables;
641 - Optimization of FactorGraph constructors using tr1::unordered_map.
642 * FactorGraph constructors no longer check for short loops (huge speed
643 increase for large factor graphs), nor for negative entries. Also, the
644 normtype is now Prob::NORMPROB by default.
645 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
646
647 Interface changes:
648 * VarSet::
649 - VarSet::stateSpace() -> nrStates(const VarSet &)
650 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
651 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
652 - removed bool operator||
653 - operator&&(const VarSet&) -> intersects(const VarSet&)
654 - operator&&(const Var&) -> contains(const Var&)
655 * FactorGraph::
656 - delta(const Var &) -> delta(size_t)
657 - Delta(const Var &) -> Delta(size_t)
658 - makeCavity(const Var &) -> makeCavity(size_t)
659 - vars() -> vars
660 - factors() -> factors
661 - removed MakeFactorCavity(size_t)
662 - removed ExactMarginal(const VarSet &)
663 - removed ExactlogZ()
664 - removed updatedFactor(size_t)
665 - removed _normtype and NormType()
666 - removed hasShortLoops(...) and removeShortLoops(...)
667 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
668 - undoProb(size_t) -> restoreFactor(size_t)
669 - saveProb(size_t) -> backupFactor(size_t)
670 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
671 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
672 - ReadFromFile(const char*) returns void (throws on error)
673 - WriteToFile(const char*) returns void (throws on error)
674 - removed hasNegatives()
675 * RegionGraph::
676 - nr_ORs() -> nrORs()
677 - nr_IRs() -> nrIRs()
678 - ORs() -> ORs
679 - IRs() -> IRs
680 * *::Regenerate() -> *::construct()
681 * Renamed Index -> IndexFor
682 * Diffs:
683 - max() -> maxDiff()
684 - max_size() -> maxSize()
685 * Prob::max() -> Prob::maxVal()
686 * Factor::
687 - max() -> maxVal()
688 - part_sum() -> partSum()
689 * toc() in util.h now returns seconds as a double
690 * VarSet::operator&&
691 * Properties -> PropertySet
692
693
694 libDAI-0.2.1 (2008-05-26)
695 -------------------------
696
697 Bugfix release.
698 * added missing cstdio header in util.h
699 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
700 * added description of the factor graph fileformat
701 * improved Makefile
702
703
704 libDAI-0.2.0 (2006-11-30)
705 -------------------------
706
707 First public release.
708
709
710 0.1.5 (2006-11-30)
711 ------------------
712
713 Regressions
714
715 - tests/testlcbp and tests/testlcbp are broken.
716 - EXACT method does not work anymore.
717 - The Properties framework gives a speed penalty because of the lookup
718 costs involved; inner loops should be optimized.
719
720 General framework
721
722 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
723 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
724 functions to forward functionality from either FactorGraph or RegionGraph
725 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
726 and in RegionGraph and no explicit interface is needed in descendants.
727 - New abstract base class InfAlg added, representing an inference algorithm,
728 from which DAIAlg<T> inherits. This solves the incompatibility problems of
729 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
730 DAIAlg<RegionGraph>). More work is required to reduce code duplication
731 (make FactorGraph part of InfAlg).
732 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
733 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
734 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
735 one to save a few factors, modify them (e.g. clamp them), and then restore them
736 to their old values. Undo should also init the corresponding messages / beliefs.
737 This can be used if a given factor graph repeatedly needs to be clamped in
738 different ways and an approximation method is run for each clamping; using the
739 saveProbs/undoProbs can give a significant speed increase.
740 - Switched to a general Properties framework that handles the parameters of
741 all inference methods in a uniform manner. The Properties class is a map of
742 several properties in boost::any objects, indexed by their names (strings).
743 It can read from a stream and write to a stream. It is recursive, in the sense
744 that a Properties object can hold a variable of type Properties as well.
745 - Added a generic way of constructing inference algorithms from a factor graph,
746 name and properties object. Added the newInfAlg function which constructs
747 the requested object. This is used by LCBP, the Matlab interface and the
748 command line (test) interface.
749 - Added a generic enum framework for enum parameters. Although implemented as a
750 hack, it is quite useful in that it drastically simplifies and reduces the
751 amount of code for handling enum parameters.
752 - Provided generic functions for calculating marginals in different ways that
753 work for all approximate inference methods.
754
755 Bugfixes
756
757 - Fixed GBP free energy.
758 - Fixed bug in junctiontree (it didn't init the _vars variable).
759 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
760 the logical NOT of what they should return).
761 - Fixed bug in RegionGraph::RecomputeOR(s).
762 - Fixed bug in utils/create_dreg_fg:
763 graph structure was not random for given parameters (forgot to call srand()).
764 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
765 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
766 that consists of one outer region only.
767 - Fixed INIT bug in LCBP2::UpdatePancake().
768 - Fixed MaxDiffs flow (except for MR).
769
770 New functionality
771
772 - HAK supports several default cluster choices:
773 minimal (only factors)
774 delta (Markov blankets)
775 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
776 Only the maximal clusters are used as outer clusters.
777 - Implemented TreeEP. It generalizes the heuristic method described in the
778 Minka & Qi paper for obtaining a tree with the most relevant interactions to
779 higher order interactions. Almost all optimizations described in the Minka & Qi
780 paper are used, except that evidence is passed over the whole tree instead of
781 relevant subsets (the latter is almost implemented but buggy). Also added
782 alternative (worst-case) algorithm that uses a maximum spanning tree on the
783 weighted graph where the weight between neighbours i and j is given by
784 N(psi,i,j), where psi is the product of all the factors involving both i and j
785 (which is an upper bound on the effective interaction between i and j).
786 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
787 to be able to handle connectivities larger than 3 (in principle, up to 32).
788 It supports different initialization methods (the original RESPPROP,
789 the CLAMPING method and EXACT which uses JTree) and different update methods
790 (FULL and LINEAR).
791 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
792 networks and uses some approximate inference method on them for calculating
793 marginals.
794 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
795 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
796 interactions and LCBPL is LCBPI improved for higher-order interactions.
797 - Wrote one single program utils/createfg for creating various types of
798 random factor graphs.
799 - Wrote utility to visualize factor graphs using graphviz.
800 (it uses the BOOST Program Options library)
801 - Added fginfo utility that displays some info about a .fg file.
802 - Implemented Factor::strength function that calculates the potential strength
803 N(psi,i,j) between variables i and j as described in cs.IT:0504030
804 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
805 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
806 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
807 - Implemented a MATLAB interface ai_potstrength for Factor::strength
808 - Added Martijn's x2x
809
810 Improvements of existing code
811
812 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
813 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
814 associates outer region indices to factor indices (no powers yet, this
815 is deemed superfluous) and provides functions to recompute (some of) the
816 outer regions from the factors.
817 - InfAlg descendants run() methods now stop immediately and return NAN in case
818 they detect NANs. Only BP does not do NAN checking for performance reasons.
819 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
820 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
821 timing and convergence criteria.
822 - Implemented logZ() for JTree. It does the calculation during message-passing.
823 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
824 hopefully this will give more accurate approximations.
825 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
826 for a faster way of calculating marginals, which does not require a call to init()
827 nor cloning the whole object for each clamping. This leads to a significant speedup.
828 - LCBP (and LCBP2) now have complete flexibility in the specification of the
829 inner method, i.e. the method used to generate the initial cavity approximations.
830 One can pass two strings, a name and a properties string, and LCBP simply invokes
831 newInfAlg to construct the corresponding inference algorithm and uses the generic
832 marginal functions to approximate cavity marginals.
833 - Replaced the global "method" variable by local properties and removed ai.h
834 - Added some methods to Factor (operators *, *=, /, /= with doubles as
835 second argument, operators -, +=, -= with other Factors as second
836 arguments, randomize(), RemoveFirstOrderInteractions) and similar
837 operations to Prob
838 - Moving towards boost::program_options for handling command line arguments
839 (tests/test is done).
840 - Renamed some FactorGraph methods:
841 nr_vars -> nrVars
842 nr_factors -> nrFactors
843 varind -> findVar
844 factorind -> findFactor
845 makeFacCavity -> makeFactorCavity
846 - LCBP_SEQMAXRES has been removed because it did strange things.
847 - Implemented RandomDRegularGraph
848 - Implemented JTree::calcMarginal for marginals that are not confined
849 within one cluster (using cut-set conditioning).
850 - Added isConnected() method to FactorGraph (some methods do not work with
851 disconnected factor graphs).
852 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
853 - Removed single node interaction "correction" code from clamping methods
854 - Removed calcCavityDist and calcCavityDist2ndO
855 - No longer depends on GSL.
856 - Increased portability by combining platform dependant utility functions
857 in util.{h,cpp}.
858 - Wrote *.m files providing help
859
860 Testing framework
861
862 - Made a new and significantly improved testing framework that provides most
863 functionality from the command line.
864 - The basis is provided by tests/test, which uses the newInfAlg functionality
865 and enables the user to easily compare from the command line different
866 inference methods on a given factorgraph. All parameters can be specified.
867 Output consists of CPU time, average and maximum single variable marginal
868 errors, relative logZ error and MaxDiff().
869 - tests/aliases.conf contains aliases for standard combinations of methods
870 and their options (which can be used in tests/test).
871 - tests/large contains several bash/python scripts that create random factor
872 graphs, compare several approximate inference algorithms (using tests/test) and
873 allow for easy visualization of the results using PyX.
874 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
875 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
876 regression testing).
877 - Added a regression test to the Makefile which is included in the standard
878 target. It compares all inference methods on tests/testfast.fg with the
879 results stored in tests/testfast.out
880
881 Miscellaneous
882
883 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
884 - Experimental MATLAB code added for StarEP approximation on cavity
885 - Renamed project to libDAI and changed directory name accordingly.
886 - Renamed JunctionTree to JTree.
887 - Fixed licensing (now it's officially GPL).
888 - Improved README
889
890
891 revision 252
892 ------------
893
894 Functionality
895 - Added RegionGraph, GBP, CVM and HAK (double-loop).
896 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
897 RegionGraph.
898 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
899 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
900 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
901 it over all subsuming outer regions. See README for when negative factors are known to work
902 and when not.
903 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
904 it does not automatically merge factors anymore.
905 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
906 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
907 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
908 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
909 such that it does not store the complete pancakes, but represents them as little factor graphs).
910
911 Implementation / code
912 - Made a seperate type WeightedGraph, which until now only implements Prim's
913 maximal spanning tree algorithm and is only used by the junction tree code. It might
914 be good to make it a class somewhere in the future and extend it's interface.
915 - Made a seperate class ClusterGraph, which is only used by the junction tree
916 code. It's main purpose is a graph-theoretical variable elimination algorithm.
917 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
918 - Massive code cleanup, moving towards "generic" programming style, using
919 multiple inheritance and polymorphism.
920 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
921 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
922 that can be used by FactorGraph-based DAIAlgs.
923 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
924 and VarSet) and provides functionality for it (which is used by TFactor<T>).
925 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
926 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
927 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
928 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
929 o using Prob's instead of Factor's;
930 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
931 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
932 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
933 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
934 that takes the cavitydists and multiplies them with the relevant factors. This
935 resulted in an API change in AI which now accepts and returns initial cavitydists
936 instead of initial pancakes.
937
938 Minor changes
939 - Started writing DoxyGen documentation
940 - Renamed lcptab2fg.m matlab/ai_writefg.m
941 - Moved all matlab stuff to matlab/
942 - More detailed reporting (also reports clocks used).
943 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
944 - Improved testing suite.
945 - Removed logreal support.
946 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
947 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
948 full and periodic 2D Ising networks according to some command line parameters.
949 - Now logZ really returns logZ instead of -logZ.
950 - Added FactorGraph::WriteToDotFile
951
952
953 0.1.4 (2006-04-13)
954 ------------------
955 - Added file IO routines to read and write factorgraphs.
956 - Added L-infinity normalization for use with (partially) negative factors.
957 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
958 handle (partially) negative factors.
959 - Added test suite.
960 - All probabilities are now represented using double instead of LogReal<double>.
961 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
962 - Combined several variants of BP into doBP. Several update schemes possible.
963 Now uses precalculated indices for optimization.
964 - Renamed Node -> Var and Potential -> Factor.
965 - Extensive code cleanup. More use of OO techniques. Changed API.
966 - MaxIter now means maximum number of passes (corresponding to number of
967 _parallel_ updates).
968 - MaxDiff now means the maximum L-infinity distance between the updated and
969 original single variable beliefs, for all AI methods.
970 - Implemented RBP which converges faster than BP for difficult problems.
971 - Now uses method parameter which is a bitmask combining outmethod and inmethod
972 (see ai.h).
973
974
975 0.1.3 (2006-03-22)
976 --------------------
977 - All AI methods now return maxdiff
978 - ai.cpp:
979 o Now returns maxdiffinner and maxdiffouter
980 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
981 o New InitCav outermethod (only create initial cavity distributions)
982 - bp.cpp:
983 o New CavityDist2ndO which estimates 2nd order cavity interactions
984 - Makefile:
985 o Bugfix: removed dependencies on algwim.*
986
987
988 0.1.2 (2006-02-28)
989 --------------------
990 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
991 - Added the possibility to provide initial cavity distributions as an input
992 argument to ai (not much error checking is done, so be careful).
993 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
994 the output arguments Q, Q0 of ai).
995 - Removed algwim.* since it does not work.
996
997
998 0.1.1 (2006-02-28)
999 --------------------
1000 - The constructors of (Log)FactorGraph and LogFactorGraph from a
1001 vector<(Log)Potential> now merge potentials to prevent short loops (of length
1002 4) in the factor graph. These are used in ai to construct the factor graphs
1003 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
1004 of BipGraph checks for the existence of short loops.
1005 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
1006 description in the help).
1007 - ai does not hook cout anymore (which caused weird segfaults).
1008 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
1009 - Removed network.* since it is not useful.
1010
1011
1012 0.1.0 (2006-02-28)
1013 --------------------
1014 First version worthy of a version number.