f92ed710aac68d5df322966e3153e032666ac3cd
[libdai.git] / ChangeLog
1 libDAI-0.3.1 (2012-09-17)
2 -------------------------
3
4 Miscellaneous improvements:
5 * Full 64-bit support on all supported platforms (Linux, OSX, Windows)
6 * Added special MatLab interface for junction tree algorithm (dai_jtree)
7 * Optimized ClusterGraph( const FactorGraph&, bool) constructor
8
9 Build system improvements:
10 * Added Makefile.WINDOWS64, kindly provided by Lin Ming
11 * [Arman Aksoy] Added Makefile.MACOSX64
12 * Added VC10 build files, kindly provided by Sameh Khamis
13
14 Bug fixes:
15 * Fixed bug (found by Sameh Khamis): define NAN (Windows)
16 * Fixed bug (found by Same Khamis): add some necessary casts of size_t to BigInt (Windows)
17 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION__ (Visual Studio) or __func__ (other compilers)
18 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile
19 * Fixed bug (found by cax): when building MatLab MEX files, GMP/MPIR libraries were not linked
20 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)
21 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions
22 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers
23 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()
24 * Fixed memory leak in CBP::run()
25 * Fixed typo in Priya's name
26
27
28 libDAI-0.3.0 (2011-07-12)
29 -------------------------
30
31 New license:
32 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)
33
34 Miscellaneous improvements:
35 * Improved Exception class
36 (it now stores more information and doesn't print to stderr by default)
37 * Added builtinInfAlgs() and builtinInfAlgNames()
38
39 Bug fixes:
40 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()
41 and maxDiff() implementations
42 * Now uses GMP big integer type to represent linear states and the number of
43 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya
44 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now
45 no longer works out-of-the-box.
46 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)
47 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,
48 instead of returning a MAP state with zero joint probability
49 (reported by Hynek Urban)
50 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)
51 (the random seed needs to be an unsigned int on some platforms)
52 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)
53 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()
54 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)
55 * Replaced all Name members by name() virtual functions and removed global variable DAINames
56 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
57
58
59 libDAI-0.2.7 (2010-08-19)
60 -------------------------
61
62 * Removed interfaces deprecated in 0.2.6.
63 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
64 if one or more variables had a MAP belief with more than one maximum, an
65 incorrect MAP state could result.
66
67
68 libDAI-0.2.6 (2010-08-05)
69 -------------------------
70
71 New features:
72 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
73 * Added source code for one of the winning solvers of the
74 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
75 * Added support for reading files in the UAI Approximate Inference Challenge
76 format, supporting both the 2006/2008 evidence file format and the 2010
77 evidence file format (io.h/cpp).
78
79 Miscellaneous improvements:
80 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
81 for setting an upper limit on execution time.
82 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
83 * SmallSet:
84 - Added SmallSet::erase( const T& t ).
85 * VarSet:
86 - nrStates() now returns a long double instead of a size_t.
87 * Permute:
88 - Added ranges() accessor.
89 - Added inverse() method.
90 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
91 * Factor:
92 - Added createFactorDelta( const VarSet& vs, size_t state ).
93 * ClusterGraph:
94 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
95 - Added findCluster( const VarSet& cl ).
96 - Added elimVar( size_t i ).
97 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
98 * FactorGraph:
99 - Added isMaximal(size_t).
100 - Added maximalFactor(size_t).
101 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
102 * Gibbs:
103 - Added 'restart' property.
104 - Added Gibbs::findMaximum() for MAP inference.
105 * HAK:
106 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
107 * examples/examples_imagesegmentation.cpp:
108 - [Peter Rockett] Improved Makefiles for image segmentation example.
109 - Added build flag to specify the CImg version.
110 * util.h/cpp:
111 - Added fromString<>( const std::string& x ).
112
113 Interface changes (the old interface is marked obsolete and will be removed in the next release):
114 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
115 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
116 and replaced them by a globally defined Neighbor structure
117 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
118 and replaced them by a globally defined Neighbors type
119 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
120 and replaced them by a globally defined Edge type
121 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
122 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
123 variable is not found.
124 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
125 and replaced it with an improved version
126 'vector<string> tokenizeString( const string&, bool, const string& )'
127 * Removed interfaces deprecated in 0.2.5.
128
129 Bug fixes:
130 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
131 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
132 which have problems when comparing const_reverse_iterator with
133 reverse_iterator.
134 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
135 (segfault if factors depending on 0 variables were passed to MatLab)
136
137
138 libDAI-0.2.5 (2010-05-09)
139 -------------------------
140
141 New features:
142 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
143 weightedgraph, enum, util, exceptions, properties, index, prob,
144 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
145 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
146 * Added utils/uai2fg, a utility to convert the UAI inference competition file
147 formats to the libDAI factor graph file format
148 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
149 * Added examples/example_imagesegmentation
150
151 Miscellaneous improvements:
152 * TRWBP:
153 - Added initialization of TRWBP weights by sampling spanning trees
154 * MF:
155 - Added an "init" option that allows to initialize randomly
156 - Added an "updates" option that allows to choose between standard
157 mean field and "hard-spin" mean field
158 * MR:
159 - rewrote response propagation implementation with help of BBP
160 - now uses GraphAL to represent the Markov graph
161 - miscellaneous smaller cleanups
162 * TreeEP:
163 - Now also supports disconnected factor graphs
164 * JTree:
165 - Now also supports disconnected factor graphs
166 * ExactInf:
167 - Added findMaximum()
168 * RegionGraph:
169 - Added error checking code
170 - Changed the way a RegionGraph is streamed to an std::ostream.
171 * ClusterGraph:
172 - Added nrVars() method
173 - Added var( size_t ) method
174 - Added cluster( size_t ) method
175 * FactorGraph:
176 - clamped() now contains a delta factor for the clamped variable
177 - Added MarkovGraph()
178 * TFactor:
179 - Added takeAbs()
180 - Added takeExp()
181 - Added takeLog( bool )
182 - Added operator-() const
183 - Added sumAbs() const
184 - Added operator==( const TFactor<T> &y )
185 - Added get(size_t), set(size_t,T)
186 * TProb:
187 - Added operator==( const TProb<T> &q )
188 - accumulate() now also applies op2 to init
189 - operator/= (T x) now yields 0 when dividing by 0
190 - Added resize(size_t)
191 - Added get(size_t) and set(size_t,T)
192 - Changed format of TProb<T> when streamed to an ostream
193 * multifor:
194 - Added reset()
195 * PropertySet:
196 - Added size()
197 - Added clear()
198 - Added erase()
199 * util.h/cpp:
200 - Added std::string toString( const T& x )
201 * weightedgraph.h/cpp:
202 - Added option to MaxSpanningTree and MinSpanningTree for
203 choosing between Prim's algorithm and Kruskal's algorithm
204 - Better error checking in RootedTree constructor
205 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
206 * BipartiteGraph:
207 - Added hasEdge()
208 - Added findNb1()
209 - Added findNb2()
210 - Added nb1Set()
211 - Added nb2Set()
212 - Added operator==( const BipartiteGraph& )
213 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
214 - Added operator<<( std::ostream&, const BipartiteGraph& )
215 * GraphAL:
216 - Added hasEdge(size_t,size_t)
217 - Added nbSet(size_t)
218 - Added operator==( const GraphAL& )
219 - Added operator<<( std::ostream&, const GraphAL& )
220 * SmallSet:
221 - Added insert( const T& t ) method
222 * Improved regression test
223 * Made all "verbose" properties optional
224 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
225 'ISING' factor type has been renamed to 'ISINGGAUSS'
226 * tests/testdai option "marginals" now has five possible values: NONE
227 outputs no marginals, VAR only variable marginals, FAC only factor
228 marginals, VARFAC both types of marginals, and ALL outputs all
229 marginals calculated by the algorithm.
230 * Compressed Makefile
231
232 Interface changes (the old interface is marked obsolete and will be removed in the next release):
233 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
234 * TreeEP:
235 - Changed construct( const RootedTree& ) into
236 construct( const FactorGraph&, const RootedTree& )
237 * JTree:
238 - Changed construct( const std::vector<VarSet>&, bool ) into
239 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
240 - Changed GenerateJT( const std::vector<VarSet> & )
241 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
242 * RegionGraph:
243 - Made (previously public) members G, ORs, IRs and fac2OR protected and
244 added DAG() accessor which returns a reference to the region graph DAG
245 structure (currently implemented as a BipartiteGraph).
246 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
247 protected, because exposing it to the world serves no purpose.
248 - Removed partial constructor RegionGraph( const FactorGraph& fg )
249 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
250 protected and renamed them by changing the "Recompute" into "recompute",
251 because exposing them to the world serves no purpose.
252 * ClusterGraph:
253 - Made (previously public) members G, vars and clusters private and added
254 bipGraph(), vars() and clusters() methods which offer read-only access
255 to these members.
256 - Deprecated toVector()
257 - Renamed size() into nrClusters()
258 * FactorGraph:
259 - Renamed Cliques() into maximalFactorDomains() and made it faster
260 - findVars( const VarSet& ) now returns a SmallSet<size_t>
261 and its argument now has a const-qualifier (which fixes a small bug).
262 - Made (previously public) member G private and added the
263 bipGraph() method, which offers read-only access to it.
264 - Deprecated the iterator interface:
265 o FactorGraph::iterator typedef
266 o FactorGraph::const_iterator typedef
267 o FactorGraph::begin() members
268 o FactorGraph::end() members
269 - Deprecated factor(size_t) which offered write access to a factor
270 because using this functionality in the descendant RegionGraph is dangerous,
271 as the outer regions are not automatically recomputed.
272 * TFactor:
273 - Renamed states() into nrStates()
274 - Added get(size_t) and set(size_t,T) operators;
275 get() is equivalent to "operator[](size_t) const" and set() should
276 be used instead of the non-const operator[], which has been deprecated
277 * TProb:
278 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
279 constructor: the sizeHint argument no longer defaults to 0
280 - Deprecated accumulate( T init, binOp op1, unOp op2 );
281 instead, accumulateSum( T init, unOp op ) and
282 accumulateMax( T init, unOp op, bool minimize ) should be used.
283 - Deprecated TProb::NormType and TProb::DistType;
284 ProbNormType and ProbDistType should be used instead.
285 - Fixed bug by renaming operator<=() to operator<()
286 - Added get(size_t) and set(size_t,T) operators;
287 get() is equivalent to "operator[](size_t) const" and set() should
288 be used instead of the non-const operator[], which has been deprecated
289 * PropertySet:
290 - Renamed Set() -> set()
291 - Renamed Get() -> get()
292 - Renamed GetAs<T>() -> getAs<T>()
293 - Renamed ConvertTo<T>() -> convertTo<T>()
294 * util.h/cpp:
295 - Removed max( const std::vector<Real> &v )
296 * weightedgraph.h/cpp:
297 - Renamed MaxSpanningTreePrims into MaxSpanningTree
298 - Renamed MinSpanningTreePrims into MinSpanningTree
299 - The vertices in DEdge and UEdge are now named "first" and "second"
300 for compatibility with a std::pair<size_t,size_t>
301 * BipartiteGraph:
302 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
303 * SmallSet:
304 - The sizeHint argument of the iterator constructor
305 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
306 no longer has a default value in order to avoid confusion with the
307 SmallSet::SmallSet( const T &t1, const T &t2 )
308 constructor.
309
310 Bug fixes:
311 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
312 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
313 * Fixed some bugs in the MatLab interface build system
314 * Fixed a bug in utils/fginfo.cpp
315 * Fixed a bug in JTree::findMaximum() and simplified the code
316 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
317 assignment from happening
318 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
319 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
320 FactorGraph ancestor methods; this has been corrected by letting them throw a
321 NOT_IMPLEMENTED exception.
322 * Fixed bug in FactorGraph::clone()
323 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
324 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
325 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
326 * Fixed bug in PropertySet::setAsString<T>()
327 * Fixed a bug in rnd_seed()
328 * BipartiteGraph:
329 - Fixed bug in eraseNode1()
330 - Fixed bug in eraseNode2()
331 - Fixed bug in isTree()
332 * GraphAL:
333 - Fixed bug in nrEdges()
334 - Fixed bug in addEdge()
335 - Fixed bug in isTree()
336 - Fixed bug in eraseNode()
337 - Fixed bug in printDot()
338 * Fixed bug in createGraphGrid3D()
339 * Fixed bug in createGraphRegular()
340
341
342 libDAI-0.2.4 (2010-02-11)
343 -------------------------
344
345 New features:
346 * Implemented Tree-Reweighted BP
347 * [Frederik Eaton] Implemented Fractional Belief Propagation
348
349 Miscellaneous improvements:
350 * Improved documentation
351 * [Frederik Eaton] Added constructors for BBPCostFunction
352 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
353 * [Frederik Eaton] Added unary minus to TProb<>
354 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
355 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
356 * tests/testdai option "marginals" now has three possible values: NONE
357 outputs no marginals, VAR only variable marginals, and ALL outputs all
358 marginals calculated by the algorithm.
359 * Strengthened convergence criteria of various algorithms
360 * Added GraphAL, an adjacency list implementation for graphs,
361 similar to (but simpler than) BipartiteGraph
362 * Added some functionality to create various standard factors
363 (the functions whose names start with "createFactor")
364 * Added examples example_sprinkler_gibbs and example_sprinkler_em
365 * Implemented various heuristics for choosing a variable elimination sequence
366 in JTree
367 * Added BETHE method for GBP/HAK cluster choice
368 * Made alias support official part of the library
369
370 Build system:
371 * Moved platform independent build options into Makefile.ALL
372 * Windows platform now needs Boost 1.37 or higher
373
374 Code cleanup:
375 * Cleaned up utils/createfg and tests/testdai
376 * Cleanup of some duplicate code in BP, FBP, TRWBP
377
378 Interface changes (the old interface is marked obsolete and will be removed in the next release):
379 * Removed obsolete/deprecated stuff
380 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
381 * Renamed some functions of BipartiteGraph:
382 add1() -> addNode1()
383 erase1() -> eraseNode1()
384 nr1() -> nrNodes1()
385 add2() -> addNode2()
386 erase2() -> eraseNode2()
387 nr2() -> nrNodes2()
388 * Renamed some functions in ClusterGraph:
389 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
390 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
391 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
392 * Changed interface of one RegionGraph constructor
393 * Renamed "Clamped BP" into "Conditioned BP"
394
395 Bug fixes:
396 * Fixed regression in scripts/regenerate-properties (now all errors are
397 gathered before throwing the exception, as used to be the case)
398 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
399 * [Alexander Schwing] Fixed error in BP that occured with damping
400 and using log-domain updates
401 * Fixed bug in HAK for trivial region graphs (with only one outer region
402 and no inner regions), reported by Alejandro Lage.
403 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
404
405
406 libDAI-0.2.3 (2009-11-16)
407 -------------------------
408
409 New features:
410 * Complete doxygen documentation (although more detailed documentation still
411 has to be written)
412 * [Charles Vaske] Added parameter learning for conditional probabilities by
413 Expectation Maximization
414 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
415 octave interfaces
416 * Added Max-Product functionality to JTree
417 * [Frederik Eaton] Added Back-Belief-Propagation
418 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
419 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
420
421 Code cleanup:
422 * Updated copyright headers
423 * Cleaned up error handling by introducing the DAI_THROWE macro
424 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
425 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
426 dai::Exception and is even active if NDEBUG is defined
427 * Removed all the virtual default constructors *::create(), as they are not used
428 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
429 * [Frederik Eaton] Change cout to cerr in warnings and error messages
430
431 Miscellaneous improvements:
432 * BipartiteGraph:
433 - Added eraseEdge( size_t n1, size_t n2 )
434 - [Frederik Eaton] Improved documentation of Neighbor
435 * TProb<T>:
436 - Added divided_by(const TProb<T>&) const
437 - Added constructor TProb<T>( const std::vector<S> &v )
438 - Added size_t draw(), which draws a random index
439 - [Frederik Eaton] Added setUniform()
440 - [Frederik Eaton] Added sumAbs()
441 - [Frederik Eaton] Added argmax()
442 - [Giuseppe Passino] Added begin(), end()
443 * TFactor<T>:
444 - [Giuseppe Passino] Added begin(), end()
445 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
446 which reorders variables to canonical ordering before storing the table
447 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
448 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
449 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
450 * State:
451 - [Giuseppe Passino] Added prefix ++ operator
452 * Permute:
453 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
454 * FactorGraph:
455 - [Frederik Eaton] Added clampVar()
456 - [Frederik Eaton] Added clampFactor()
457 - [Giuseppe Passino] Added begin(), end()
458 * PropertySet:
459 - Added keys(), for getting all keys
460 - [Frederik Eaton] Added default constructor
461 - [Frederik Eaton] Added constructor from string
462 * InfAlg:
463 - Added setProperties(), getProperties() and printProperties()
464 - [Frederik Eaton] Added beliefV(), beliefF()
465 * ExactInf:
466 - Added calcMarginal(const VarSet &)
467 * HAK:
468 - Added "init" parameter to allow for random initialization
469 * BP:
470 - [Giuseppe Passino] Added findMaximum(), which can be used after running
471 max-product BP to construct a global state with maximum probability
472 * JTree:
473 - Added findMaximum(), which can be used after running
474 max-product JTree to construct a global state with maximum probability
475 * MatLab interface:
476 - MEX file dai now also returns variable and factor beliefs
477 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
478 (only for BP and JTree)
479 * README is now created automatically from doxygen documentation
480 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
481 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
482 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
483 and functions (concat(),rnd()) to util.h
484 * Changed output stream operator<< for Var and VarSet
485 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
486 alias substitutions
487 * [Frederik Eaton] Added useful aliases to aliases.conf
488 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
489 set instead of the linear search (which can yield enormous speedups - a
490 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
491 * Added debug assertions to Var which check for inconsistent dimensions of
492 variables with the same labels
493 * toc() now returns POSIX system time with maximum accuracy of microseconds
494 * Exception objects now remember their error code
495 * Examples:
496 - Moved example.cpp to examples/
497 - Added examples/example_bipgraph.cpp
498 - Added examples/example_varset.cpp
499 - Added examples/example_sprinkler.cpp
500 - Added examples/example_permute.cpp
501 - Added python and octave ports for examples/example_sprinkler.cpp
502
503 Build system:
504 * Improved Makefile:
505 - Merged Makefile.win and Makefile.shared into Makefile
506 - Macros DAI_VERSION and DAI_DATE have been introduced,
507 in order to store this information in a central place
508 - Introduced CCNODEBUGFLAGS in Makefile
509 - Switched Makefile.win to GNU Make syntax
510 - [Frederik Eaton] Added TAGS, lib targets to Makefile
511 * Compatibility:
512 - [Peter Gober] libDAI can now be built on Cygwin
513 - [Dan Preston] libDAI can now be built on Mac OS X
514 - Changed regression test so that it also works under Windows
515
516 Interface changes (the old interface is marked obsolete and will be removed in the next release):
517 * Var:
518 - Variable labels are now nonnegative (of type size_t)
519 * VarSet:
520 - Replaced calcState() by non-member calcLinearState()
521 - Replaced calcStates() by non-member calcState()
522 * Permute:
523 - Renamed convert_linear_index into convertLinearIndex
524 * TProb<>:
525 - Replaced log0() by log(true)
526 - Replaced takeLog0() by takeLog(true)
527 - Removed hasNonPositives()
528 - Renamed minVal() to min()
529 - Renamed maxVal() to max()
530 - Renamed totalSum() to sum()
531 * TFactor<>:
532 - Replaced log0() by TFactor<T>::log(true)
533 - Removed divided_by, use operator/ instead
534 - Removed divide, use operator/= instead
535 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
536 - Renamed minVal() to min()
537 - Renamed maxVal() to max()
538 - Renamed totalSum() to sum()
539 * FactorGraph:
540 - Changed clamp and clamp interfaces (the variable to be
541 clamped is now indicated by its index, not as a Var)
542 * RegionGraph:
543 - Renamed Check_Counting_Numbers into checkCountingNumbers
544 - Renamed Calc_Counting_Numbers into calcCountingNumbers
545 * Miscellaneous:
546 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
547 - Replaced UEdgeVec by Graph
548 - Replaced DEdgeVec by new RootedTree class
549 - Moved functionality of GrowRootedTree() into constructor of RootedTree
550 - Merged calcPairBeliefsNew() into calcPairBeliefs()
551 - Removed calcMarginal2ndO()
552 - Renamed smallSet<T> to SmallSet<T>
553 - Removed class Diffs
554 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
555 BipartiteGraph and FactorGraph (which will be obsoleted soon)
556
557 Bug fixes:
558 * Fixed reversal of min and max in
559 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
560 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
561 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
562 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
563 before typeid(std::string) (this fixes a strange bug for empty string property)
564 * Added work-around for bug in Boost Graph Library
565 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
566 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
567 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
568 for reporting this)
569
570
571 libDAI-0.2.2 (2008-09-30)
572 -------------------------
573
574 New features:
575 * Approximate inference methods now report the number of iterations needed.
576 * Added damping to various algorithms to improve convergence properties.
577 * Added more features to utils/createfg for creating factor graphs.
578 * Added ExactInf class for brute force exact inference.
579 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
580 whether calculations are done in the log-domain or in the linear domain;
581 doing calculations in the log-domain may help if the numerical range
582 of a double is too small.
583 * [Claudio Lima] Added Max-Product functionality to BP.
584 * Improved documentation.
585
586 Improved architecture:
587 * Added Exceptions framework.
588 * Pervasive change of BipartiteGraph implementation (based on an idea by
589 Giuseppe Passino). BipartiteGraph no longer stores the node properties
590 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
591 nor an edge list. Instead, it stores the graph structure as lists of
592 neighboring nodes. This yields a significant memory/speed improvement for
593 large factor graphs, and is more elegant as well. Iterating over neighbors is
594 made easy by using boost::foreach.
595 * Added conditional compilation of inference methods.
596 * VarSet is now implemented using a std::vector<Var> instead of a
597 std::set<Var>, which yields a significant speed improvement. Furthermore,
598 the implementation has been generalized, resulting in the small_set<T> class
599 which can be used to represent sets of small cardinality; VarSet is the
600 specialization with T = Var.
601 * Improved ClusterGraph implementation, yielding significant speedups
602 for the JunctionTree algorithm on large factorgraphs.
603
604 Code cleanup:
605 * Moved everything into namespace "dai".
606 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
607 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
608 * Removed utils/remove_short_loops and matlab/remove_short_loops.
609 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
610 * Improved index.h:
611 - Renamed Index -> IndexFor
612 - Added some .reserve()'s to IndexFor methods which yields a
613 25% speedup of testregression
614 - Replaced multind by Permute
615 - Added MultiFor
616 - Added State
617 * New funcstionality of factor.h.
618 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
619 inference algorithm, because the Properties framework was not as
620 convenient as I hoped, and not every inference algorithm needs a maxdiff
621 variable. Also, replaced some FactorGraph functionality in InfAlg by a
622 function that returns the FactorGraph. The result is cleaner (less
623 entangled) code.
624 * Removed x2x.
625 * Replaced Complex with real numbers (negative potentials are just too rare
626 to warrant the additional "complexity" :)).
627
628 Miscellaneous improvements:
629 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
630 GCC under Cygwin.
631 * Contributions by Peter Gober:
632 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
633 * Misc contributions by Giuseppe Passino:
634 - removed "using namespace std;" from header files - bad practice;
635 - moved header files in include/dai and sources in src;
636 - changed #ifndefs to GNU style;
637 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
638 - dai::TProb:
639 o removed copy constructor and assignment operators (redundant);
640 o implementation of some methods via STL algorithms;
641 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
642 o explicit constructor (prevents implicit conversion from size_t to TProb);
643 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
644 * Misc contributions by Christian Wojek:
645 - New FactorGraph constructor that constructs from given ranges of factors
646 and variables;
647 - Optimization of FactorGraph constructors using tr1::unordered_map.
648 * FactorGraph constructors no longer check for short loops (huge speed
649 increase for large factor graphs), nor for negative entries. Also, the
650 normtype is now Prob::NORMPROB by default.
651 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
652
653 Interface changes:
654 * VarSet::
655 - VarSet::stateSpace() -> nrStates(const VarSet &)
656 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
657 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
658 - removed bool operator||
659 - operator&&(const VarSet&) -> intersects(const VarSet&)
660 - operator&&(const Var&) -> contains(const Var&)
661 * FactorGraph::
662 - delta(const Var &) -> delta(size_t)
663 - Delta(const Var &) -> Delta(size_t)
664 - makeCavity(const Var &) -> makeCavity(size_t)
665 - vars() -> vars
666 - factors() -> factors
667 - removed MakeFactorCavity(size_t)
668 - removed ExactMarginal(const VarSet &)
669 - removed ExactlogZ()
670 - removed updatedFactor(size_t)
671 - removed _normtype and NormType()
672 - removed hasShortLoops(...) and removeShortLoops(...)
673 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
674 - undoProb(size_t) -> restoreFactor(size_t)
675 - saveProb(size_t) -> backupFactor(size_t)
676 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
677 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
678 - ReadFromFile(const char*) returns void (throws on error)
679 - WriteToFile(const char*) returns void (throws on error)
680 - removed hasNegatives()
681 * RegionGraph::
682 - nr_ORs() -> nrORs()
683 - nr_IRs() -> nrIRs()
684 - ORs() -> ORs
685 - IRs() -> IRs
686 * *::Regenerate() -> *::construct()
687 * Renamed Index -> IndexFor
688 * Diffs:
689 - max() -> maxDiff()
690 - max_size() -> maxSize()
691 * Prob::max() -> Prob::maxVal()
692 * Factor::
693 - max() -> maxVal()
694 - part_sum() -> partSum()
695 * toc() in util.h now returns seconds as a double
696 * VarSet::operator&&
697 * Properties -> PropertySet
698
699
700 libDAI-0.2.1 (2008-05-26)
701 -------------------------
702
703 Bugfix release.
704 * added missing cstdio header in util.h
705 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
706 * added description of the factor graph fileformat
707 * improved Makefile
708
709
710 libDAI-0.2.0 (2006-11-30)
711 -------------------------
712
713 First public release.
714
715
716 0.1.5 (2006-11-30)
717 ------------------
718
719 Regressions
720
721 - tests/testlcbp and tests/testlcbp are broken.
722 - EXACT method does not work anymore.
723 - The Properties framework gives a speed penalty because of the lookup
724 costs involved; inner loops should be optimized.
725
726 General framework
727
728 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
729 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
730 functions to forward functionality from either FactorGraph or RegionGraph
731 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
732 and in RegionGraph and no explicit interface is needed in descendants.
733 - New abstract base class InfAlg added, representing an inference algorithm,
734 from which DAIAlg<T> inherits. This solves the incompatibility problems of
735 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
736 DAIAlg<RegionGraph>). More work is required to reduce code duplication
737 (make FactorGraph part of InfAlg).
738 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
739 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
740 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
741 one to save a few factors, modify them (e.g. clamp them), and then restore them
742 to their old values. Undo should also init the corresponding messages / beliefs.
743 This can be used if a given factor graph repeatedly needs to be clamped in
744 different ways and an approximation method is run for each clamping; using the
745 saveProbs/undoProbs can give a significant speed increase.
746 - Switched to a general Properties framework that handles the parameters of
747 all inference methods in a uniform manner. The Properties class is a map of
748 several properties in boost::any objects, indexed by their names (strings).
749 It can read from a stream and write to a stream. It is recursive, in the sense
750 that a Properties object can hold a variable of type Properties as well.
751 - Added a generic way of constructing inference algorithms from a factor graph,
752 name and properties object. Added the newInfAlg function which constructs
753 the requested object. This is used by LCBP, the Matlab interface and the
754 command line (test) interface.
755 - Added a generic enum framework for enum parameters. Although implemented as a
756 hack, it is quite useful in that it drastically simplifies and reduces the
757 amount of code for handling enum parameters.
758 - Provided generic functions for calculating marginals in different ways that
759 work for all approximate inference methods.
760
761 Bugfixes
762
763 - Fixed GBP free energy.
764 - Fixed bug in junctiontree (it didn't init the _vars variable).
765 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
766 the logical NOT of what they should return).
767 - Fixed bug in RegionGraph::RecomputeOR(s).
768 - Fixed bug in utils/create_dreg_fg:
769 graph structure was not random for given parameters (forgot to call srand()).
770 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
771 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
772 that consists of one outer region only.
773 - Fixed INIT bug in LCBP2::UpdatePancake().
774 - Fixed MaxDiffs flow (except for MR).
775
776 New functionality
777
778 - HAK supports several default cluster choices:
779 minimal (only factors)
780 delta (Markov blankets)
781 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
782 Only the maximal clusters are used as outer clusters.
783 - Implemented TreeEP. It generalizes the heuristic method described in the
784 Minka & Qi paper for obtaining a tree with the most relevant interactions to
785 higher order interactions. Almost all optimizations described in the Minka & Qi
786 paper are used, except that evidence is passed over the whole tree instead of
787 relevant subsets (the latter is almost implemented but buggy). Also added
788 alternative (worst-case) algorithm that uses a maximum spanning tree on the
789 weighted graph where the weight between neighbours i and j is given by
790 N(psi,i,j), where psi is the product of all the factors involving both i and j
791 (which is an upper bound on the effective interaction between i and j).
792 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
793 to be able to handle connectivities larger than 3 (in principle, up to 32).
794 It supports different initialization methods (the original RESPPROP,
795 the CLAMPING method and EXACT which uses JTree) and different update methods
796 (FULL and LINEAR).
797 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
798 networks and uses some approximate inference method on them for calculating
799 marginals.
800 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
801 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
802 interactions and LCBPL is LCBPI improved for higher-order interactions.
803 - Wrote one single program utils/createfg for creating various types of
804 random factor graphs.
805 - Wrote utility to visualize factor graphs using graphviz.
806 (it uses the BOOST Program Options library)
807 - Added fginfo utility that displays some info about a .fg file.
808 - Implemented Factor::strength function that calculates the potential strength
809 N(psi,i,j) between variables i and j as described in cs.IT:0504030
810 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
811 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
812 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
813 - Implemented a MATLAB interface ai_potstrength for Factor::strength
814 - Added Martijn's x2x
815
816 Improvements of existing code
817
818 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
819 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
820 associates outer region indices to factor indices (no powers yet, this
821 is deemed superfluous) and provides functions to recompute (some of) the
822 outer regions from the factors.
823 - InfAlg descendants run() methods now stop immediately and return NAN in case
824 they detect NANs. Only BP does not do NAN checking for performance reasons.
825 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
826 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
827 timing and convergence criteria.
828 - Implemented logZ() for JTree. It does the calculation during message-passing.
829 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
830 hopefully this will give more accurate approximations.
831 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
832 for a faster way of calculating marginals, which does not require a call to init()
833 nor cloning the whole object for each clamping. This leads to a significant speedup.
834 - LCBP (and LCBP2) now have complete flexibility in the specification of the
835 inner method, i.e. the method used to generate the initial cavity approximations.
836 One can pass two strings, a name and a properties string, and LCBP simply invokes
837 newInfAlg to construct the corresponding inference algorithm and uses the generic
838 marginal functions to approximate cavity marginals.
839 - Replaced the global "method" variable by local properties and removed ai.h
840 - Added some methods to Factor (operators *, *=, /, /= with doubles as
841 second argument, operators -, +=, -= with other Factors as second
842 arguments, randomize(), RemoveFirstOrderInteractions) and similar
843 operations to Prob
844 - Moving towards boost::program_options for handling command line arguments
845 (tests/test is done).
846 - Renamed some FactorGraph methods:
847 nr_vars -> nrVars
848 nr_factors -> nrFactors
849 varind -> findVar
850 factorind -> findFactor
851 makeFacCavity -> makeFactorCavity
852 - LCBP_SEQMAXRES has been removed because it did strange things.
853 - Implemented RandomDRegularGraph
854 - Implemented JTree::calcMarginal for marginals that are not confined
855 within one cluster (using cut-set conditioning).
856 - Added isConnected() method to FactorGraph (some methods do not work with
857 disconnected factor graphs).
858 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
859 - Removed single node interaction "correction" code from clamping methods
860 - Removed calcCavityDist and calcCavityDist2ndO
861 - No longer depends on GSL.
862 - Increased portability by combining platform dependant utility functions
863 in util.{h,cpp}.
864 - Wrote *.m files providing help
865
866 Testing framework
867
868 - Made a new and significantly improved testing framework that provides most
869 functionality from the command line.
870 - The basis is provided by tests/test, which uses the newInfAlg functionality
871 and enables the user to easily compare from the command line different
872 inference methods on a given factorgraph. All parameters can be specified.
873 Output consists of CPU time, average and maximum single variable marginal
874 errors, relative logZ error and MaxDiff().
875 - tests/aliases.conf contains aliases for standard combinations of methods
876 and their options (which can be used in tests/test).
877 - tests/large contains several bash/python scripts that create random factor
878 graphs, compare several approximate inference algorithms (using tests/test) and
879 allow for easy visualization of the results using PyX.
880 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
881 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
882 regression testing).
883 - Added a regression test to the Makefile which is included in the standard
884 target. It compares all inference methods on tests/testfast.fg with the
885 results stored in tests/testfast.out
886
887 Miscellaneous
888
889 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
890 - Experimental MATLAB code added for StarEP approximation on cavity
891 - Renamed project to libDAI and changed directory name accordingly.
892 - Renamed JunctionTree to JTree.
893 - Fixed licensing (now it's officially GPL).
894 - Improved README
895
896
897 revision 252
898 ------------
899
900 Functionality
901 - Added RegionGraph, GBP, CVM and HAK (double-loop).
902 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
903 RegionGraph.
904 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
905 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
906 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
907 it over all subsuming outer regions. See README for when negative factors are known to work
908 and when not.
909 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
910 it does not automatically merge factors anymore.
911 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
912 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
913 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
914 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
915 such that it does not store the complete pancakes, but represents them as little factor graphs).
916
917 Implementation / code
918 - Made a seperate type WeightedGraph, which until now only implements Prim's
919 maximal spanning tree algorithm and is only used by the junction tree code. It might
920 be good to make it a class somewhere in the future and extend it's interface.
921 - Made a seperate class ClusterGraph, which is only used by the junction tree
922 code. It's main purpose is a graph-theoretical variable elimination algorithm.
923 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
924 - Massive code cleanup, moving towards "generic" programming style, using
925 multiple inheritance and polymorphism.
926 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
927 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
928 that can be used by FactorGraph-based DAIAlgs.
929 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
930 and VarSet) and provides functionality for it (which is used by TFactor<T>).
931 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
932 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
933 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
934 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
935 o using Prob's instead of Factor's;
936 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
937 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
938 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
939 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
940 that takes the cavitydists and multiplies them with the relevant factors. This
941 resulted in an API change in AI which now accepts and returns initial cavitydists
942 instead of initial pancakes.
943
944 Minor changes
945 - Started writing DoxyGen documentation
946 - Renamed lcptab2fg.m matlab/ai_writefg.m
947 - Moved all matlab stuff to matlab/
948 - More detailed reporting (also reports clocks used).
949 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
950 - Improved testing suite.
951 - Removed logreal support.
952 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
953 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
954 full and periodic 2D Ising networks according to some command line parameters.
955 - Now logZ really returns logZ instead of -logZ.
956 - Added FactorGraph::WriteToDotFile
957
958
959 0.1.4 (2006-04-13)
960 ------------------
961 - Added file IO routines to read and write factorgraphs.
962 - Added L-infinity normalization for use with (partially) negative factors.
963 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
964 handle (partially) negative factors.
965 - Added test suite.
966 - All probabilities are now represented using double instead of LogReal<double>.
967 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
968 - Combined several variants of BP into doBP. Several update schemes possible.
969 Now uses precalculated indices for optimization.
970 - Renamed Node -> Var and Potential -> Factor.
971 - Extensive code cleanup. More use of OO techniques. Changed API.
972 - MaxIter now means maximum number of passes (corresponding to number of
973 _parallel_ updates).
974 - MaxDiff now means the maximum L-infinity distance between the updated and
975 original single variable beliefs, for all AI methods.
976 - Implemented RBP which converges faster than BP for difficult problems.
977 - Now uses method parameter which is a bitmask combining outmethod and inmethod
978 (see ai.h).
979
980
981 0.1.3 (2006-03-22)
982 --------------------
983 - All AI methods now return maxdiff
984 - ai.cpp:
985 o Now returns maxdiffinner and maxdiffouter
986 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
987 o New InitCav outermethod (only create initial cavity distributions)
988 - bp.cpp:
989 o New CavityDist2ndO which estimates 2nd order cavity interactions
990 - Makefile:
991 o Bugfix: removed dependencies on algwim.*
992
993
994 0.1.2 (2006-02-28)
995 --------------------
996 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
997 - Added the possibility to provide initial cavity distributions as an input
998 argument to ai (not much error checking is done, so be careful).
999 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
1000 the output arguments Q, Q0 of ai).
1001 - Removed algwim.* since it does not work.
1002
1003
1004 0.1.1 (2006-02-28)
1005 --------------------
1006 - The constructors of (Log)FactorGraph and LogFactorGraph from a
1007 vector<(Log)Potential> now merge potentials to prevent short loops (of length
1008 4) in the factor graph. These are used in ai to construct the factor graphs
1009 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
1010 of BipGraph checks for the existence of short loops.
1011 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
1012 description in the help).
1013 - ai does not hook cout anymore (which caused weird segfaults).
1014 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
1015 - Removed network.* since it is not useful.
1016
1017
1018 0.1.0 (2006-02-28)
1019 --------------------
1020 First version worthy of a version number.