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