1 git HEAD

2 --------

3 * Extended SWIG python interface (inspired by Kyle Ellrott): inference is possible in Python now!

4 * Added toString() formatting functions to the classes that had an output streaming operator<<

5 * Replaced all occurrences of std::size_t by size_t to avoid SWIG problems

6 * Fixed division-by-zero issue in pow() which caused problems for GLC+ with sparse factors

7 * Fixed bugs in unit test prob_test.cpp: replaced all occurences of

8 BOOST_CHECK_CLOSE(...,(Real)0.0,tol) with BOOST_CHECK_SMALL(...,tol)

9 * Merged Generalized Loop Correction code kindly provided by Siamak Ravanbakhsh

12 libDAI-0.3.1 (2012-09-17)

13 -------------------------

15 Miscellaneous improvements:

16 * Full 64-bit support on all supported platforms (Linux, OSX, Windows)

17 * Added special MatLab interface for junction tree algorithm (dai_jtree)

18 * Optimized ClusterGraph( const FactorGraph&, bool) constructor

20 Build system improvements:

21 * Added Makefile.WINDOWS64, kindly provided by Lin Ming

22 * [Arman Aksoy] Added Makefile.MACOSX64

23 * Added VC10 build files, kindly provided by Sameh Khamis

25 Bug fixes:

26 * Fixed bug (found by Sameh Khamis): define NAN (Windows)

27 * Fixed bug (found by Sameh Khamis): add some necessary casts of size_t to BigInt (Windows)

28 * Fixed bug (found by Yan): replaced GNU extension __PRETTY_FUNCTION__ by __FUNCTION__ (Visual Studio) or __func__ (other compilers)

29 * Fixed bug (found by Andy Mueller): added GMP library invocations to swig Makefile

30 * Fixed bug (found by cax): when building MatLab MEX files, GMP/MPIR libraries were not linked

31 * Fixed bug in findMaximum (it only considered a single connected component of the factor graph)

32 * [Benjamin Piwowarski] Renamed "foreach" macro into "bforeach" to avoid conflicts with newer Boost library versions

33 * Fixed "typename" bug in src/alldai.cpp which resulted in FTBFS with older g++ compilers

34 * Fixed memory leak in alldai.cpp and removed the function builtinInfAlgs()

35 * Fixed memory leak in CBP::run()

36 * Fixed typo in Priya's name

39 libDAI-0.3.0 (2011-07-12)

40 -------------------------

42 New license:

43 * Changed license from GPL v2+ to FreeBSD (BSD 2-clause)

45 Miscellaneous improvements:

46 * Improved Exception class

47 (it now stores more information and doesn't print to stderr by default)

48 * Added builtinInfAlgs() and builtinInfAlgNames()

50 Bug fixes:

51 * [Laurens van der Maaten] src/matlab/dai.cpp now correctly handles missing logZ()

52 and maxDiff() implementations

53 * Now uses GMP big integer type to represent linear states and the number of

54 states of VarSets (in some cases). This fixes a bug Jerome Maye and Priya

55 found in the State class. Unfortunately, the supplied Makefile.WINDOWS now

56 no longer works out-of-the-box.

57 * Fixed numerical issues in MF, FBP and TRWBP (discovered in sparse branch)

58 * Fixed bug in findMaximum(): inconsistent max-beliefs are now detected,

59 instead of returning a MAP state with zero joint probability

60 (reported by Hynek Urban)

61 * Fixed a Boost-related bug in src/util.cpp (reported by Avneesh Saluja)

62 (the random seed needs to be an unsigned int on some platforms)

63 * Fixed two bugs in examples/example_sprinkler_gibbs (reported by Priya)

64 * Fixed bug in tokenizeString() and Evidence::addEvidenceTabFile()

65 (a tab character at the end of a line was incorrectly discarded - bug reported by Priya)

66 * Replaced all Name members by name() virtual functions and removed global variable DAINames

67 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)

70 libDAI-0.2.7 (2010-08-19)

71 -------------------------

73 * Removed interfaces deprecated in 0.2.6.

74 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):

75 if one or more variables had a MAP belief with more than one maximum, an

76 incorrect MAP state could result.

79 libDAI-0.2.6 (2010-08-05)

80 -------------------------

82 New features:

83 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).

84 * Added source code for one of the winning solvers of the

85 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).

86 * Added support for reading files in the UAI Approximate Inference Challenge

87 format, supporting both the 2006/2008 evidence file format and the 2010

88 evidence file format (io.h/cpp).

90 Miscellaneous improvements:

91 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)

92 for setting an upper limit on execution time.

93 * 'maxmem' property added to JTree for setting an upper limit on memory usage.

94 * SmallSet:

95 - Added SmallSet::erase( const T& t ).

96 * VarSet:

97 - nrStates() now returns a long double instead of a size_t.

98 * Permute:

99 - Added ranges() accessor.

100 - Added inverse() method.

101 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.

102 * Factor:

103 - Added createFactorDelta( const VarSet& vs, size_t state ).

104 * ClusterGraph:

105 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.

106 - Added findCluster( const VarSet& cl ).

107 - Added elimVar( size_t i ).

108 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).

109 * FactorGraph:

110 - Added isMaximal(size_t).

111 - Added maximalFactor(size_t).

112 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).

113 * Gibbs:

114 - Added 'restart' property.

115 - Added Gibbs::findMaximum() for MAP inference.

116 * HAK:

117 - Optimized region graph construction for HAK/GBP with clusters=BETHE.

118 * examples/examples_imagesegmentation.cpp:

119 - [Peter Rockett] Improved Makefiles for image segmentation example.

120 - Added build flag to specify the CImg version.

121 * util.h/cpp:

122 - Added fromString<>( const std::string& x ).

124 Interface changes (the old interface is marked obsolete and will be removed in the next release):

125 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.

126 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor

127 and replaced them by a globally defined Neighbor structure

128 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors

129 and replaced them by a globally defined Neighbors type

130 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge

131 and replaced them by a globally defined Edge type

132 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.

133 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the

134 variable is not found.

135 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'

136 and replaced it with an improved version

137 'vector<string> tokenizeString( const string&, bool, const string& )'

138 * Removed interfaces deprecated in 0.2.5.

140 Bug fixes:

141 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.

142 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)

143 which have problems when comparing const_reverse_iterator with

144 reverse_iterator.

145 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp

146 (segfault if factors depending on 0 variables were passed to MatLab)

149 libDAI-0.2.5 (2010-05-09)

150 -------------------------

152 New features:

153 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,

154 weightedgraph, enum, util, exceptions, properties, index, prob,

155 factor, factorgraph, clustergraph, regiongraph, daialg, alldai

156 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format

157 * Added utils/uai2fg, a utility to convert the UAI inference competition file

158 formats to the libDAI factor graph file format

159 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs

160 * Added examples/example_imagesegmentation

162 Miscellaneous improvements:

163 * TRWBP:

164 - Added initialization of TRWBP weights by sampling spanning trees

165 * MF:

166 - Added an "init" option that allows to initialize randomly

167 - Added an "updates" option that allows to choose between standard

168 mean field and "hard-spin" mean field

169 * MR:

170 - rewrote response propagation implementation with help of BBP

171 - now uses GraphAL to represent the Markov graph

172 - miscellaneous smaller cleanups

173 * TreeEP:

174 - Now also supports disconnected factor graphs

175 * JTree:

176 - Now also supports disconnected factor graphs

177 * ExactInf:

178 - Added findMaximum()

179 * RegionGraph:

180 - Added error checking code

181 - Changed the way a RegionGraph is streamed to an std::ostream.

182 * ClusterGraph:

183 - Added nrVars() method

184 - Added var( size_t ) method

185 - Added cluster( size_t ) method

186 * FactorGraph:

187 - clamped() now contains a delta factor for the clamped variable

188 - Added MarkovGraph()

189 * TFactor:

190 - Added takeAbs()

191 - Added takeExp()

192 - Added takeLog( bool )

193 - Added operator-() const

194 - Added sumAbs() const

195 - Added operator==( const TFactor<T> &y )

196 - Added get(size_t), set(size_t,T)

197 * TProb:

198 - Added operator==( const TProb<T> &q )

199 - accumulate() now also applies op2 to init

200 - operator/= (T x) now yields 0 when dividing by 0

201 - Added resize(size_t)

202 - Added get(size_t) and set(size_t,T)

203 - Changed format of TProb<T> when streamed to an ostream

204 * multifor:

205 - Added reset()

206 * PropertySet:

207 - Added size()

208 - Added clear()

209 - Added erase()

210 * util.h/cpp:

211 - Added std::string toString( const T& x )

212 * weightedgraph.h/cpp:

213 - Added option to MaxSpanningTree and MinSpanningTree for

214 choosing between Prim's algorithm and Kruskal's algorithm

215 - Better error checking in RootedTree constructor

216 - Added GraphEL::GraphEL( const GraphAL& G ) constructor

217 * BipartiteGraph:

218 - Added hasEdge()

219 - Added findNb1()

220 - Added findNb2()

221 - Added nb1Set()

222 - Added nb2Set()

223 - Added operator==( const BipartiteGraph& )

224 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor

225 - Added operator<<( std::ostream&, const BipartiteGraph& )

226 * GraphAL:

227 - Added hasEdge(size_t,size_t)

228 - Added nbSet(size_t)

229 - Added operator==( const GraphAL& )

230 - Added operator<<( std::ostream&, const GraphAL& )

231 * SmallSet:

232 - Added insert( const T& t ) method

233 * Improved regression test

234 * Made all "verbose" properties optional

235 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old

236 'ISING' factor type has been renamed to 'ISINGGAUSS'

237 * tests/testdai option "marginals" now has five possible values: NONE

238 outputs no marginals, VAR only variable marginals, FAC only factor

239 marginals, VARFAC both types of marginals, and ALL outputs all

240 marginals calculated by the algorithm.

241 * Compressed Makefile

243 Interface changes (the old interface is marked obsolete and will be removed in the next release):

244 * Removed RandomDRegularGraph(), please use createGraphRegular() instead

245 * TreeEP:

246 - Changed construct( const RootedTree& ) into

247 construct( const FactorGraph&, const RootedTree& )

248 * JTree:

249 - Changed construct( const std::vector<VarSet>&, bool ) into

250 construct( const FactorGraph&, const std::vector<VarSet>&, bool )

251 - Changed GenerateJT( const std::vector<VarSet> & )

252 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )

253 * RegionGraph:

254 - Made (previously public) members G, ORs, IRs and fac2OR protected and

255 added DAG() accessor which returns a reference to the region graph DAG

256 structure (currently implemented as a BipartiteGraph).

257 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it

258 protected, because exposing it to the world serves no purpose.

259 - Removed partial constructor RegionGraph( const FactorGraph& fg )

260 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )

261 protected and renamed them by changing the "Recompute" into "recompute",

262 because exposing them to the world serves no purpose.

263 * ClusterGraph:

264 - Made (previously public) members G, vars and clusters private and added

265 bipGraph(), vars() and clusters() methods which offer read-only access

266 to these members.

267 - Deprecated toVector()

268 - Renamed size() into nrClusters()

269 * FactorGraph:

270 - Renamed Cliques() into maximalFactorDomains() and made it faster

271 - findVars( const VarSet& ) now returns a SmallSet<size_t>

272 and its argument now has a const-qualifier (which fixes a small bug).

273 - Made (previously public) member G private and added the

274 bipGraph() method, which offers read-only access to it.

275 - Deprecated the iterator interface:

276 o FactorGraph::iterator typedef

277 o FactorGraph::const_iterator typedef

278 o FactorGraph::begin() members

279 o FactorGraph::end() members

280 - Deprecated factor(size_t) which offered write access to a factor

281 because using this functionality in the descendant RegionGraph is dangerous,

282 as the outer regions are not automatically recomputed.

283 * TFactor:

284 - Renamed states() into nrStates()

285 - Added get(size_t) and set(size_t,T) operators;

286 get() is equivalent to "operator[](size_t) const" and set() should

287 be used instead of the non-const operator[], which has been deprecated

288 * TProb:

289 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )

290 constructor: the sizeHint argument no longer defaults to 0

291 - Deprecated accumulate( T init, binOp op1, unOp op2 );

292 instead, accumulateSum( T init, unOp op ) and

293 accumulateMax( T init, unOp op, bool minimize ) should be used.

294 - Deprecated TProb::NormType and TProb::DistType;

295 ProbNormType and ProbDistType should be used instead.

296 - Fixed bug by renaming operator<=() to operator<()

297 - Added get(size_t) and set(size_t,T) operators;

298 get() is equivalent to "operator[](size_t) const" and set() should

299 be used instead of the non-const operator[], which has been deprecated

300 * PropertySet:

301 - Renamed Set() -> set()

302 - Renamed Get() -> get()

303 - Renamed GetAs<T>() -> getAs<T>()

304 - Renamed ConvertTo<T>() -> convertTo<T>()

305 * util.h/cpp:

306 - Removed max( const std::vector<Real> &v )

307 * weightedgraph.h/cpp:

308 - Renamed MaxSpanningTreePrims into MaxSpanningTree

309 - Renamed MinSpanningTreePrims into MinSpanningTree

310 - The vertices in DEdge and UEdge are now named "first" and "second"

311 for compatibility with a std::pair<size_t,size_t>

312 * BipartiteGraph:

313 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>

314 * SmallSet:

315 - The sizeHint argument of the iterator constructor

316 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )

317 no longer has a default value in order to avoid confusion with the

318 SmallSet::SmallSet( const T &t1, const T &t2 )

319 constructor.

321 Bug fixes:

322 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()

323 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]

324 * Fixed some bugs in the MatLab interface build system

325 * Fixed a bug in utils/fginfo.cpp

326 * Fixed a bug in JTree::findMaximum() and simplified the code

327 * Fixed bug in BBPCostFunction::operator=() which prevented the desired

328 assignment from happening

329 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )

330 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective

331 FactorGraph ancestor methods; this has been corrected by letting them throw a

332 NOT_IMPLEMENTED exception.

333 * Fixed bug in FactorGraph::clone()

334 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )

335 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )

336 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()

337 * Fixed bug in PropertySet::setAsString<T>()

338 * Fixed a bug in rnd_seed()

339 * BipartiteGraph:

340 - Fixed bug in eraseNode1()

341 - Fixed bug in eraseNode2()

342 - Fixed bug in isTree()

343 * GraphAL:

344 - Fixed bug in nrEdges()

345 - Fixed bug in addEdge()

346 - Fixed bug in isTree()

347 - Fixed bug in eraseNode()

348 - Fixed bug in printDot()

349 * Fixed bug in createGraphGrid3D()

350 * Fixed bug in createGraphRegular()

353 libDAI-0.2.4 (2010-02-11)

354 -------------------------

356 New features:

357 * Implemented Tree-Reweighted BP

358 * [Frederik Eaton] Implemented Fractional Belief Propagation

360 Miscellaneous improvements:

361 * Improved documentation

362 * [Frederik Eaton] Added constructors for BBPCostFunction

363 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>

364 * [Frederik Eaton] Added unary minus to TProb<>

365 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType

366 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp

367 * tests/testdai option "marginals" now has three possible values: NONE

368 outputs no marginals, VAR only variable marginals, and ALL outputs all

369 marginals calculated by the algorithm.

370 * Strengthened convergence criteria of various algorithms

371 * Added GraphAL, an adjacency list implementation for graphs,

372 similar to (but simpler than) BipartiteGraph

373 * Added some functionality to create various standard factors

374 (the functions whose names start with "createFactor")

375 * Added examples example_sprinkler_gibbs and example_sprinkler_em

376 * Implemented various heuristics for choosing a variable elimination sequence

377 in JTree

378 * Added BETHE method for GBP/HAK cluster choice

379 * Made alias support official part of the library

381 Build system:

382 * Moved platform independent build options into Makefile.ALL

383 * Windows platform now needs Boost 1.37 or higher

385 Code cleanup:

386 * Cleaned up utils/createfg and tests/testdai

387 * Cleanup of some duplicate code in BP, FBP, TRWBP

389 Interface changes (the old interface is marked obsolete and will be removed in the next release):

390 * Removed obsolete/deprecated stuff

391 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)

392 * Renamed some functions of BipartiteGraph:

393 add1() -> addNode1()

394 erase1() -> eraseNode1()

395 nr1() -> nrNodes1()

396 add2() -> addNode2()

397 erase2() -> eraseNode2()

398 nr2() -> nrNodes2()

399 * Renamed some functions in ClusterGraph:

400 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()

401 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )

402 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )

403 * Changed interface of one RegionGraph constructor

404 * Renamed "Clamped BP" into "Conditioned BP"

406 Bug fixes:

407 * Fixed regression in scripts/regenerate-properties (now all errors are

408 gathered before throwing the exception, as used to be the case)

409 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)

410 * [Alexander Schwing] Fixed error in BP that occured with damping

411 and using log-domain updates

412 * Fixed bug in HAK for trivial region graphs (with only one outer region

413 and no inner regions), reported by Alejandro Lage.

414 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)

417 libDAI-0.2.3 (2009-11-16)

418 -------------------------

420 New features:

421 * Complete doxygen documentation (although more detailed documentation still

422 has to be written)

423 * [Charles Vaske] Added parameter learning for conditional probabilities by

424 Expectation Maximization

425 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and

426 octave interfaces

427 * Added Max-Product functionality to JTree

428 * [Frederik Eaton] Added Back-Belief-Propagation

429 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"

430 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"

432 Code cleanup:

433 * Updated copyright headers

434 * Cleaned up error handling by introducing the DAI_THROWE macro

435 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern

436 * Replaced the standard assert() macro by DAI_ASSERT, which throws a

437 dai::Exception and is even active if NDEBUG is defined

438 * Removed all the virtual default constructors *::create(), as they are not used

439 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators

440 * [Frederik Eaton] Change cout to cerr in warnings and error messages

442 Miscellaneous improvements:

443 * BipartiteGraph:

444 - Added eraseEdge( size_t n1, size_t n2 )

445 - [Frederik Eaton] Improved documentation of Neighbor

446 * TProb<T>:

447 - Added divided_by(const TProb<T>&) const

448 - Added constructor TProb<T>( const std::vector<S> &v )

449 - Added size_t draw(), which draws a random index

450 - [Frederik Eaton] Added setUniform()

451 - [Frederik Eaton] Added sumAbs()

452 - [Frederik Eaton] Added argmax()

453 - [Giuseppe Passino] Added begin(), end()

454 * TFactor<T>:

455 - [Giuseppe Passino] Added begin(), end()

456 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),

457 which reorders variables to canonical ordering before storing the table

458 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )

459 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets

460 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)

461 * State:

462 - [Giuseppe Passino] Added prefix ++ operator

463 * Permute:

464 - [Charles Vaske] Added constructor in Permute for canonical variable ordering

465 * FactorGraph:

466 - [Frederik Eaton] Added clampVar()

467 - [Frederik Eaton] Added clampFactor()

468 - [Giuseppe Passino] Added begin(), end()

469 * PropertySet:

470 - Added keys(), for getting all keys

471 - [Frederik Eaton] Added default constructor

472 - [Frederik Eaton] Added constructor from string

473 * InfAlg:

474 - Added setProperties(), getProperties() and printProperties()

475 - [Frederik Eaton] Added beliefV(), beliefF()

476 * ExactInf:

477 - Added calcMarginal(const VarSet &)

478 * HAK:

479 - Added "init" parameter to allow for random initialization

480 * BP:

481 - [Giuseppe Passino] Added findMaximum(), which can be used after running

482 max-product BP to construct a global state with maximum probability

483 * JTree:

484 - Added findMaximum(), which can be used after running

485 max-product JTree to construct a global state with maximum probability

486 * MatLab interface:

487 - MEX file dai now also returns variable and factor beliefs

488 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state

489 (only for BP and JTree)

490 * README is now created automatically from doxygen documentation

491 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)

492 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp

493 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)

494 and functions (concat(),rnd()) to util.h

495 * Changed output stream operator<< for Var and VarSet

496 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive

497 alias substitutions

498 * [Frederik Eaton] Added useful aliases to aliases.conf

499 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered

500 set instead of the linear search (which can yield enormous speedups - a

501 factor 500 has been measured on a binary Ising grid with 128x128 variables!)

502 * Added debug assertions to Var which check for inconsistent dimensions of

503 variables with the same labels

504 * toc() now returns POSIX system time with maximum accuracy of microseconds

505 * Exception objects now remember their error code

506 * Examples:

507 - Moved example.cpp to examples/

508 - Added examples/example_bipgraph.cpp

509 - Added examples/example_varset.cpp

510 - Added examples/example_sprinkler.cpp

511 - Added examples/example_permute.cpp

512 - Added python and octave ports for examples/example_sprinkler.cpp

514 Build system:

515 * Improved Makefile:

516 - Merged Makefile.win and Makefile.shared into Makefile

517 - Macros DAI_VERSION and DAI_DATE have been introduced,

518 in order to store this information in a central place

519 - Introduced CCNODEBUGFLAGS in Makefile

520 - Switched Makefile.win to GNU Make syntax

521 - [Frederik Eaton] Added TAGS, lib targets to Makefile

522 * Compatibility:

523 - [Peter Gober] libDAI can now be built on Cygwin

524 - [Dan Preston] libDAI can now be built on Mac OS X

525 - Changed regression test so that it also works under Windows

527 Interface changes (the old interface is marked obsolete and will be removed in the next release):

528 * Var:

529 - Variable labels are now nonnegative (of type size_t)

530 * VarSet:

531 - Replaced calcState() by non-member calcLinearState()

532 - Replaced calcStates() by non-member calcState()

533 * Permute:

534 - Renamed convert_linear_index into convertLinearIndex

535 * TProb<>:

536 - Replaced log0() by log(true)

537 - Replaced takeLog0() by takeLog(true)

538 - Removed hasNonPositives()

539 - Renamed minVal() to min()

540 - Renamed maxVal() to max()

541 - Renamed totalSum() to sum()

542 * TFactor<>:

543 - Replaced log0() by TFactor<T>::log(true)

544 - Removed divided_by, use operator/ instead

545 - Removed divide, use operator/= instead

546 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead

547 - Renamed minVal() to min()

548 - Renamed maxVal() to max()

549 - Renamed totalSum() to sum()

550 * FactorGraph:

551 - Changed clamp and clamp interfaces (the variable to be

552 clamped is now indicated by its index, not as a Var)

553 * RegionGraph:

554 - Renamed Check_Counting_Numbers into checkCountingNumbers

555 - Renamed Calc_Counting_Numbers into calcCountingNumbers

556 * Miscellaneous:

557 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)

558 - Replaced UEdgeVec by Graph

559 - Replaced DEdgeVec by new RootedTree class

560 - Moved functionality of GrowRootedTree() into constructor of RootedTree

561 - Merged calcPairBeliefsNew() into calcPairBeliefs()

562 - Removed calcMarginal2ndO()

563 - Renamed smallSet<T> to SmallSet<T>

564 - Removed class Diffs

565 - [Frederik Eaton] Added backwards compatibility layer for edge interface to

566 BipartiteGraph and FactorGraph (which will be obsoleted soon)

568 Bug fixes:

569 * Fixed reversal of min and max in

570 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )

571 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )

572 * [Sebastian Nowozin] Fixed memory leak in MEX file dai

573 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)

574 before typeid(std::string) (this fixes a strange bug for empty string property)

575 * Added work-around for bug in Boost Graph Library

576 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).

577 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability

578 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston

579 for reporting this)

582 libDAI-0.2.2 (2008-09-30)

583 -------------------------

585 New features:

586 * Approximate inference methods now report the number of iterations needed.

587 * Added damping to various algorithms to improve convergence properties.

588 * Added more features to utils/createfg for creating factor graphs.

589 * Added ExactInf class for brute force exact inference.

590 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls

591 whether calculations are done in the log-domain or in the linear domain;

592 doing calculations in the log-domain may help if the numerical range

593 of a double is too small.

594 * [Claudio Lima] Added Max-Product functionality to BP.

595 * Improved documentation.

597 Improved architecture:

598 * Added Exceptions framework.

599 * Pervasive change of BipartiteGraph implementation (based on an idea by

600 Giuseppe Passino). BipartiteGraph no longer stores the node properties

601 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,

602 nor an edge list. Instead, it stores the graph structure as lists of

603 neighboring nodes. This yields a significant memory/speed improvement for

604 large factor graphs, and is more elegant as well. Iterating over neighbors is

605 made easy by using boost::foreach.

606 * Added conditional compilation of inference methods.

607 * VarSet is now implemented using a std::vector<Var> instead of a

608 std::set<Var>, which yields a significant speed improvement. Furthermore,

609 the implementation has been generalized, resulting in the small_set<T> class

610 which can be used to represent sets of small cardinality; VarSet is the

611 specialization with T = Var.

612 * Improved ClusterGraph implementation, yielding significant speedups

613 for the JunctionTree algorithm on large factorgraphs.

615 Code cleanup:

616 * Moved everything into namespace "dai".

617 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

618 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.

619 * Removed utils/remove_short_loops and matlab/remove_short_loops.

620 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.

621 * Improved index.h:

622 - Renamed Index -> IndexFor

623 - Added some .reserve()'s to IndexFor methods which yields a

624 25% speedup of testregression

625 - Replaced multind by Permute

626 - Added MultiFor

627 - Added State

628 * New funcstionality of factor.h.

629 * Moved Properties and MaxDiff frameworks from InfAlg to each individual

630 inference algorithm, because the Properties framework was not as

631 convenient as I hoped, and not every inference algorithm needs a maxdiff

632 variable. Also, replaced some FactorGraph functionality in InfAlg by a

633 function that returns the FactorGraph. The result is cleaner (less

634 entangled) code.

635 * Removed x2x.

636 * Replaced Complex with real numbers (negative potentials are just too rare

637 to warrant the additional "complexity" :)).

639 Miscellaneous improvements:

640 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with

641 GCC under Cygwin.

642 * Contributions by Peter Gober:

643 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.

644 * Misc contributions by Giuseppe Passino:

645 - removed "using namespace std;" from header files - bad practice;

646 - moved header files in include/dai and sources in src;

647 - changed #ifndefs to GNU style;

648 - added extra warning checks (-W -Wextra) and fixed resulting warnings;

649 - dai::TProb:

650 o removed copy constructor and assignment operators (redundant);

651 o implementation of some methods via STL algorithms;

652 o added methods takeExp, takeLog, takeLog0 for transformation in-place;

653 o explicit constructor (prevents implicit conversion from size_t to TProb);

654 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);

655 * Misc contributions by Christian Wojek:

656 - New FactorGraph constructor that constructs from given ranges of factors

657 and variables;

658 - Optimization of FactorGraph constructors using tr1::unordered_map.

659 * FactorGraph constructors no longer check for short loops (huge speed

660 increase for large factor graphs), nor for negative entries. Also, the

661 normtype is now Prob::NORMPROB by default.

662 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).

664 Interface changes:

665 * VarSet::

666 - VarSet::stateSpace() -> nrStates(const VarSet &)

667 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )

668 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )

669 - removed bool operator||

670 - operator&&(const VarSet&) -> intersects(const VarSet&)

671 - operator&&(const Var&) -> contains(const Var&)

672 * FactorGraph::

673 - delta(const Var &) -> delta(size_t)

674 - Delta(const Var &) -> Delta(size_t)

675 - makeCavity(const Var &) -> makeCavity(size_t)

676 - vars() -> vars

677 - factors() -> factors

678 - removed MakeFactorCavity(size_t)

679 - removed ExactMarginal(const VarSet &)

680 - removed ExactlogZ()

681 - removed updatedFactor(size_t)

682 - removed _normtype and NormType()

683 - removed hasShortLoops(...) and removeShortLoops(...)

684 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )

685 - undoProb(size_t) -> restoreFactor(size_t)

686 - saveProb(size_t) -> backupFactor(size_t)

687 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)

688 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)

689 - ReadFromFile(const char*) returns void (throws on error)

690 - WriteToFile(const char*) returns void (throws on error)

691 - removed hasNegatives()

692 * RegionGraph::

693 - nr_ORs() -> nrORs()

694 - nr_IRs() -> nrIRs()

695 - ORs() -> ORs

696 - IRs() -> IRs

697 * *::Regenerate() -> *::construct()

698 * Renamed Index -> IndexFor

699 * Diffs:

700 - max() -> maxDiff()

701 - max_size() -> maxSize()

702 * Prob::max() -> Prob::maxVal()

703 * Factor::

704 - max() -> maxVal()

705 - part_sum() -> partSum()

706 * toc() in util.h now returns seconds as a double

707 * VarSet::operator&&

708 * Properties -> PropertySet

711 libDAI-0.2.1 (2008-05-26)

712 -------------------------

714 Bugfix release.

715 * added missing cstdio header in util.h

716 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

717 * added description of the factor graph fileformat

718 * improved Makefile

721 libDAI-0.2.0 (2006-11-30)

722 -------------------------

724 First public release.

727 0.1.5 (2006-11-30)

728 ------------------

730 Regressions

732 - tests/testlcbp and tests/testlcbp are broken.

733 - EXACT method does not work anymore.

734 - The Properties framework gives a speed penalty because of the lookup

735 costs involved; inner loops should be optimized.

737 General framework

739 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for

740 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"

741 functions to forward functionality from either FactorGraph or RegionGraph

742 to DAIAlg. Functionality like clamping can be implemented in FactorGraph

743 and in RegionGraph and no explicit interface is needed in descendants.

744 - New abstract base class InfAlg added, representing an inference algorithm,

745 from which DAIAlg<T> inherits. This solves the incompatibility problems of

746 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with

747 DAIAlg<RegionGraph>). More work is required to reduce code duplication

748 (make FactorGraph part of InfAlg).

749 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),

750 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.

751 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables

752 one to save a few factors, modify them (e.g. clamp them), and then restore them

753 to their old values. Undo should also init the corresponding messages / beliefs.

754 This can be used if a given factor graph repeatedly needs to be clamped in

755 different ways and an approximation method is run for each clamping; using the

756 saveProbs/undoProbs can give a significant speed increase.

757 - Switched to a general Properties framework that handles the parameters of

758 all inference methods in a uniform manner. The Properties class is a map of

759 several properties in boost::any objects, indexed by their names (strings).

760 It can read from a stream and write to a stream. It is recursive, in the sense

761 that a Properties object can hold a variable of type Properties as well.

762 - Added a generic way of constructing inference algorithms from a factor graph,

763 name and properties object. Added the newInfAlg function which constructs

764 the requested object. This is used by LCBP, the Matlab interface and the

765 command line (test) interface.

766 - Added a generic enum framework for enum parameters. Although implemented as a

767 hack, it is quite useful in that it drastically simplifies and reduces the

768 amount of code for handling enum parameters.

769 - Provided generic functions for calculating marginals in different ways that

770 work for all approximate inference methods.

772 Bugfixes

774 - Fixed GBP free energy.

775 - Fixed bug in junctiontree (it didn't init the _vars variable).

776 - Corrected two bugs in operator&& and operator|| in VarSet (they returned

777 the logical NOT of what they should return).

778 - Fixed bug in RegionGraph::RecomputeOR(s).

779 - Fixed bug in utils/create_dreg_fg:

780 graph structure was not random for given parameters (forgot to call srand()).

781 - TreeEP bug workaround: use the complete junction tree instead of a subtree.

782 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree

783 that consists of one outer region only.

784 - Fixed INIT bug in LCBP2::UpdatePancake().

785 - Fixed MaxDiffs flow (except for MR).

787 New functionality

789 - HAK supports several default cluster choices:

790 minimal (only factors)

791 delta (Markov blankets)

792 loop (all loops consisting of loops consisting of <loopdepth> or less variables)

793 Only the maximal clusters are used as outer clusters.

794 - Implemented TreeEP. It generalizes the heuristic method described in the

795 Minka & Qi paper for obtaining a tree with the most relevant interactions to

796 higher order interactions. Almost all optimizations described in the Minka & Qi

797 paper are used, except that evidence is passed over the whole tree instead of

798 relevant subsets (the latter is almost implemented but buggy). Also added

799 alternative (worst-case) algorithm that uses a maximum spanning tree on the

800 weighted graph where the weight between neighbours i and j is given by

801 N(psi,i,j), where psi is the product of all the factors involving both i and j

802 (which is an upper bound on the effective interaction between i and j).

803 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it

804 to be able to handle connectivities larger than 3 (in principle, up to 32).

805 It supports different initialization methods (the original RESPPROP,

806 the CLAMPING method and EXACT which uses JTree) and different update methods

807 (FULL and LINEAR).

808 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little

809 networks and uses some approximate inference method on them for calculating

810 marginals.

811 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);

812 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order

813 interactions and LCBPL is LCBPI improved for higher-order interactions.

814 - Wrote one single program utils/createfg for creating various types of

815 random factor graphs.

816 - Wrote utility to visualize factor graphs using graphviz.

817 (it uses the BOOST Program Options library)

818 - Added fginfo utility that displays some info about a .fg file.

819 - Implemented Factor::strength function that calculates the potential strength

820 N(psi,i,j) between variables i and j as described in cs.IT:0504030

821 - Wrote a general MatLab interface matlab/dai (similar to tests/test);

822 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.

823 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.

824 - Implemented a MATLAB interface ai_potstrength for Factor::strength

825 - Added Martijn's x2x

827 Improvements of existing code

829 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

830 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that

831 associates outer region indices to factor indices (no powers yet, this

832 is deemed superfluous) and provides functions to recompute (some of) the

833 outer regions from the factors.

834 - InfAlg descendants run() methods now stop immediately and return NAN in case

835 they detect NANs. Only BP does not do NAN checking for performance reasons.

836 - LCBP now works with factors containing zeroes (by defining x/0 = 0).

837 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,

838 timing and convergence criteria.

839 - Implemented logZ() for JTree. It does the calculation during message-passing.

840 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);

841 hopefully this will give more accurate approximations.

842 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality

843 for a faster way of calculating marginals, which does not require a call to init()

844 nor cloning the whole object for each clamping. This leads to a significant speedup.

845 - LCBP (and LCBP2) now have complete flexibility in the specification of the

846 inner method, i.e. the method used to generate the initial cavity approximations.

847 One can pass two strings, a name and a properties string, and LCBP simply invokes

848 newInfAlg to construct the corresponding inference algorithm and uses the generic

849 marginal functions to approximate cavity marginals.

850 - Replaced the global "method" variable by local properties and removed ai.h

851 - Added some methods to Factor (operators *, *=, /, /= with doubles as

852 second argument, operators -, +=, -= with other Factors as second

853 arguments, randomize(), RemoveFirstOrderInteractions) and similar

854 operations to Prob

855 - Moving towards boost::program_options for handling command line arguments

856 (tests/test is done).

857 - Renamed some FactorGraph methods:

858 nr_vars -> nrVars

859 nr_factors -> nrFactors

860 varind -> findVar

861 factorind -> findFactor

862 makeFacCavity -> makeFactorCavity

863 - LCBP_SEQMAXRES has been removed because it did strange things.

864 - Implemented RandomDRegularGraph

865 - Implemented JTree::calcMarginal for marginals that are not confined

866 within one cluster (using cut-set conditioning).

867 - Added isConnected() method to FactorGraph (some methods do not work with

868 disconnected factor graphs).

869 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs

870 - Removed single node interaction "correction" code from clamping methods

871 - Removed calcCavityDist and calcCavityDist2ndO

872 - No longer depends on GSL.

873 - Increased portability by combining platform dependant utility functions

874 in util.{h,cpp}.

875 - Wrote *.m files providing help

877 Testing framework

879 - Made a new and significantly improved testing framework that provides most

880 functionality from the command line.

881 - The basis is provided by tests/test, which uses the newInfAlg functionality

882 and enables the user to easily compare from the command line different

883 inference methods on a given factorgraph. All parameters can be specified.

884 Output consists of CPU time, average and maximum single variable marginal

885 errors, relative logZ error and MaxDiff().

886 - tests/aliases.conf contains aliases for standard combinations of methods

887 and their options (which can be used in tests/test).

888 - tests/large contains several bash/python scripts that create random factor

889 graphs, compare several approximate inference algorithms (using tests/test) and

890 allow for easy visualization of the results using PyX.

891 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions

892 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for

893 regression testing).

894 - Added a regression test to the Makefile which is included in the standard

895 target. It compares all inference methods on tests/testfast.fg with the

896 results stored in tests/testfast.out

898 Miscellaneous

900 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)

901 - Experimental MATLAB code added for StarEP approximation on cavity

902 - Renamed project to libDAI and changed directory name accordingly.

903 - Renamed JunctionTree to JTree.

904 - Fixed licensing (now it's officially GPL).

905 - Improved README

908 revision 252

909 ------------

911 Functionality

912 - Added RegionGraph, GBP, CVM and HAK (double-loop).

913 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a

914 RegionGraph.

915 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,

916 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the

917 RegionGraph constructors assign each Factor to a unique outer region instead of dividing

918 it over all subsuming outer regions. See README for when negative factors are known to work

919 and when not.

920 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,

921 it does not automatically merge factors anymore.

922 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)

923 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

924 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes

925 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented

926 such that it does not store the complete pancakes, but represents them as little factor graphs).

928 Implementation / code

929 - Made a seperate type WeightedGraph, which until now only implements Prim's

930 maximal spanning tree algorithm and is only used by the junction tree code. It might

931 be good to make it a class somewhere in the future and extend it's interface.

932 - Made a seperate class ClusterGraph, which is only used by the junction tree

933 code. It's main purpose is a graph-theoretical variable elimination algorithm.

934 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.

935 - Massive code cleanup, moving towards "generic" programming style, using

936 multiple inheritance and polymorphism.

937 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class

938 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp

939 that can be used by FactorGraph-based DAIAlgs.

940 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing

941 and VarSet) and provides functionality for it (which is used by TFactor<T>).

942 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.

943 I had to overload the insert methods of set<Var> so that they calculate the new statespace.

944 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.

945 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:

946 o using Prob's instead of Factor's;

947 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);

948 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).

949 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>

950 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method

951 that takes the cavitydists and multiplies them with the relevant factors. This

952 resulted in an API change in AI which now accepts and returns initial cavitydists

953 instead of initial pancakes.

955 Minor changes

956 - Started writing DoxyGen documentation

957 - Renamed lcptab2fg.m matlab/ai_writefg.m

958 - Moved all matlab stuff to matlab/

959 - More detailed reporting (also reports clocks used).

960 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.

961 - Improved testing suite.

962 - Removed logreal support.

963 - FactorGraph now also supports input streams and ignores comment lines in .fg files.

964 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create

965 full and periodic 2D Ising networks according to some command line parameters.

966 - Now logZ really returns logZ instead of -logZ.

967 - Added FactorGraph::WriteToDotFile

970 0.1.4 (2006-04-13)

971 ------------------

972 - Added file IO routines to read and write factorgraphs.

973 - Added L-infinity normalization for use with (partially) negative factors.

974 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to

975 handle (partially) negative factors.

976 - Added test suite.

977 - All probabilities are now represented using double instead of LogReal<double>.

978 - Combined Alg and Alg3 into LCBP. Several update schemes possible.

979 - Combined several variants of BP into doBP. Several update schemes possible.

980 Now uses precalculated indices for optimization.

981 - Renamed Node -> Var and Potential -> Factor.

982 - Extensive code cleanup. More use of OO techniques. Changed API.

983 - MaxIter now means maximum number of passes (corresponding to number of

984 _parallel_ updates).

985 - MaxDiff now means the maximum L-infinity distance between the updated and

986 original single variable beliefs, for all AI methods.

987 - Implemented RBP which converges faster than BP for difficult problems.

988 - Now uses method parameter which is a bitmask combining outmethod and inmethod

989 (see ai.h).

992 0.1.3 (2006-03-22)

993 --------------------

994 - All AI methods now return maxdiff

995 - ai.cpp:

996 o Now returns maxdiffinner and maxdiffouter

997 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)

998 o New InitCav outermethod (only create initial cavity distributions)

999 - bp.cpp:

1000 o New CavityDist2ndO which estimates 2nd order cavity interactions

1001 - Makefile:

1002 o Bugfix: removed dependencies on algwim.*

1005 0.1.2 (2006-02-28)

1006 --------------------

1007 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).

1008 - Added the possibility to provide initial cavity distributions as an input

1009 argument to ai (not much error checking is done, so be careful).

1010 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for

1011 the output arguments Q, Q0 of ai).

1012 - Removed algwim.* since it does not work.

1015 0.1.1 (2006-02-28)

1016 --------------------

1017 - The constructors of (Log)FactorGraph and LogFactorGraph from a

1018 vector<(Log)Potential> now merge potentials to prevent short loops (of length

1019 4) in the factor graph. These are used in ai to construct the factor graphs

1020 from the psi argument. If compiled with DEBUG defined, the method calc_nb()

1021 of BipGraph checks for the existence of short loops.

1022 - Changed calling syntax of ai (now the actual syntax *does* correspond to its

1023 description in the help).

1024 - ai does not hook cout anymore (which caused weird segfaults).

1025 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.

1026 - Removed network.* since it is not useful.

1029 0.1.0 (2006-02-28)

1030 --------------------

1031 First version worthy of a version number.