1 git HEAD

2 --------

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

4 UAI 2010 Approximate Inference Challenge

5 * Improved VarSet

6 - nrStates() now returns a double instead of a size_t

7 * Improved ClusterGraph

8 - added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor

9 - findVar( const Var& n ) no longer throws an exception if the variable is

10 not found

11 - added findCluster( const VarSet& cl )

12 - added elimVar( size_t i )

13 - added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 )

14 * Improved JTree (added 'maxmem' property)

15 * Improved HAK (added 'maxtime' property)

16 * Improved TreeEP (added 'maxtime' property)

17 * Added FactorGraph::logScore( const std::vector<size_t>& statevec )

18 * Improved Gibbs

19 - renamed 'iters' property into 'maxiter'

20 - added 'maxtime' property

21 - added 'restart' property

22 - added Gibbs::findMaximum()

23 * Improved BP (added 'maxtime' property)

24 * Added fromString<>( const std::string& x )

25 * Added SmallSet::erase( const T& t )

26 * Added DECMAP algorithm.

27 * Added createFactorDelta( const VarSet& vs, size_t state )

28 * [Peter Rockett] Improved Makefiles for image segmentation example.

29 * Removed deprecated interfaces.

30 * Added FactorGraph::isMaximal(size_t) and FactorGraph::maximalFactor(size_t).

31 * Added optional reverse argument to Permute::Permute( const std::vector<Var>& )

32 constructor.

33 * Added Permute::ranges() accessor.

34 * Added Permute::inverse() method.

35 * Optimized region graph construction for HAK/GBP with clusters=BETHE.

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

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

38 which have problems when comparing const_reverse_iterator with

39 reverse_iterator.

42 libDAI-0.2.5 (2010-05-09)

43 -------------------------

45 New features:

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

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

48 factor, factorgraph, clustergraph, regiongraph, daialg, alldai

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

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

51 formats to the libDAI factor graph file format

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

53 * Added examples/example_imagesegmentation

55 Miscellaneous improvements:

56 * TRWBP:

57 - Added initialization of TRWBP weights by sampling spanning trees

58 * MF:

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

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

61 mean field and "hard-spin" mean field

62 * MR:

63 - rewrote response propagation implementation with help of BBP

64 - now uses GraphAL to represent the Markov graph

65 - miscellaneous smaller cleanups

66 * TreeEP:

67 - Now also supports disconnected factor graphs

68 * JTree:

69 - Now also supports disconnected factor graphs

70 * ExactInf:

71 - Added findMaximum()

72 * RegionGraph:

73 - Added error checking code

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

75 * ClusterGraph:

76 - Added nrVars() method

77 - Added var( size_t ) method

78 - Added cluster( size_t ) method

79 * FactorGraph:

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

81 - Added MarkovGraph()

82 * TFactor:

83 - Added takeAbs()

84 - Added takeExp()

85 - Added takeLog( bool )

86 - Added operator-() const

87 - Added sumAbs() const

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

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

90 * TProb:

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

92 - accumulate() now also applies op2 to init

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

94 - Added resize(size_t)

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

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

97 * multifor:

98 - Added reset()

99 * PropertySet:

100 - Added size()

101 - Added clear()

102 - Added erase()

103 * util.h/cpp:

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

105 * weightedgraph.h/cpp:

106 - Added option to MaxSpanningTree and MinSpanningTree for

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

108 - Better error checking in RootedTree constructor

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

110 * BipartiteGraph:

111 - Added hasEdge()

112 - Added findNb1()

113 - Added findNb2()

114 - Added nb1Set()

115 - Added nb2Set()

116 - Added operator==( const BipartiteGraph& )

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

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

119 * GraphAL:

120 - Added hasEdge(size_t,size_t)

121 - Added nbSet(size_t)

122 - Added operator==( const GraphAL& )

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

124 * SmallSet:

125 - Added insert( const T& t ) method

126 * Improved regression test

127 * Made all "verbose" properties optional

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

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

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

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

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

133 marginals calculated by the algorithm.

134 * Compressed Makefile

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

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

138 * TreeEP:

139 - Changed construct( const RootedTree& ) into

140 construct( const FactorGraph&, const RootedTree& )

141 * JTree:

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

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

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

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

146 * RegionGraph:

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

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

149 structure (currently implemented as a BipartiteGraph).

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

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

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

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

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

155 because exposing them to the world serves no purpose.

156 * ClusterGraph:

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

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

159 to these members.

160 - Deprecated toVector()

161 - Renamed size() into nrClusters()

162 * FactorGraph:

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

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

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

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

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

168 - Deprecated the iterator interface:

169 o FactorGraph::iterator typedef

170 o FactorGraph::const_iterator typedef

171 o FactorGraph::begin() members

172 o FactorGraph::end() members

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

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

175 as the outer regions are not automatically recomputed.

176 * TFactor:

177 - Renamed states() into nrStates()

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

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

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

181 * TProb:

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

183 constructor: the sizeHint argument no longer defaults to 0

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

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

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

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

188 ProbNormType and ProbDistType should be used instead.

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

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

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

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

193 * PropertySet:

194 - Renamed Set() -> set()

195 - Renamed Get() -> get()

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

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

198 * util.h/cpp:

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

200 * weightedgraph.h/cpp:

201 - Renamed MaxSpanningTreePrims into MaxSpanningTree

202 - Renamed MinSpanningTreePrims into MinSpanningTree

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

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

205 * BipartiteGraph:

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

207 * SmallSet:

208 - The sizeHint argument of the iterator constructor

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

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

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

212 constructor.

214 Bug fixes:

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

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

217 * Fixed some bugs in the MatLab interface build system

218 * Fixed a bug in utils/fginfo.cpp

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

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

221 assignment from happening

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

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

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

225 NOT_IMPLEMENTED exception.

226 * Fixed bug in FactorGraph::clone()

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

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

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

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

231 * Fixed a bug in rnd_seed()

232 * BipartiteGraph:

233 - Fixed bug in eraseNode1()

234 - Fixed bug in eraseNode2()

235 - Fixed bug in isTree()

236 * GraphAL:

237 - Fixed bug in nrEdges()

238 - Fixed bug in addEdge()

239 - Fixed bug in isTree()

240 - Fixed bug in eraseNode()

241 - Fixed bug in printDot()

242 * Fixed bug in createGraphGrid3D()

243 * Fixed bug in createGraphRegular()

246 libDAI-0.2.4 (2010-02-11)

247 -------------------------

249 New features:

250 * Implemented Tree-Reweighted BP

251 * [Frederik Eaton] Implemented Fractional Belief Propagation

253 Miscellaneous improvements:

254 * Improved documentation

255 * [Frederik Eaton] Added constructors for BBPCostFunction

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

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

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

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

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

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

262 marginals calculated by the algorithm.

263 * Strengthened convergence criteria of various algorithms

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

265 similar to (but simpler than) BipartiteGraph

266 * Added some functionality to create various standard factors

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

268 * Added examples example_sprinkler_gibbs and example_sprinkler_em

269 * Implemented various heuristics for choosing a variable elimination sequence

270 in JTree

271 * Added BETHE method for GBP/HAK cluster choice

272 * Made alias support official part of the library

274 Build system:

275 * Moved platform independent build options into Makefile.ALL

276 * Windows platform now needs Boost 1.37 or higher

278 Code cleanup:

279 * Cleaned up utils/createfg and tests/testdai

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

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

283 * Removed obsolete/deprecated stuff

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

285 * Renamed some functions of BipartiteGraph:

286 add1() -> addNode1()

287 erase1() -> eraseNode1()

288 nr1() -> nrNodes1()

289 add2() -> addNode2()

290 erase2() -> eraseNode2()

291 nr2() -> nrNodes2()

292 * Renamed some functions in ClusterGraph:

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

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

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

296 * Changed interface of one RegionGraph constructor

297 * Renamed "Clamped BP" into "Conditioned BP"

299 Bug fixes:

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

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

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

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

304 and using log-domain updates

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

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

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

310 libDAI-0.2.3 (2009-11-16)

311 -------------------------

313 New features:

314 * Complete doxygen documentation (although more detailed documentation still

315 has to be written)

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

317 Expectation Maximization

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

319 octave interfaces

320 * Added Max-Product functionality to JTree

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

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

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

325 Code cleanup:

326 * Updated copyright headers

327 * Cleaned up error handling by introducing the DAI_THROWE macro

328 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern

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

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

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

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

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

335 Miscellaneous improvements:

336 * BipartiteGraph:

337 - Added eraseEdge( size_t n1, size_t n2 )

338 - [Frederik Eaton] Improved documentation of Neighbor

339 * TProb<T>:

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

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

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

343 - [Frederik Eaton] Added setUniform()

344 - [Frederik Eaton] Added sumAbs()

345 - [Frederik Eaton] Added argmax()

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

347 * TFactor<T>:

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

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

350 which reorders variables to canonical ordering before storing the table

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

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

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

354 * State:

355 - [Giuseppe Passino] Added prefix ++ operator

356 * Permute:

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

358 * FactorGraph:

359 - [Frederik Eaton] Added clampVar()

360 - [Frederik Eaton] Added clampFactor()

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

362 * PropertySet:

363 - Added keys(), for getting all keys

364 - [Frederik Eaton] Added default constructor

365 - [Frederik Eaton] Added constructor from string

366 * InfAlg:

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

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

369 * ExactInf:

370 - Added calcMarginal(const VarSet &)

371 * HAK:

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

373 * BP:

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

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

376 * JTree:

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

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

379 * MatLab interface:

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

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

382 (only for BP and JTree)

383 * README is now created automatically from doxygen documentation

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

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

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

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

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

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

390 alias substitutions

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

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

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

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

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

396 variables with the same labels

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

398 * Exception objects now remember their error code

399 * Examples:

400 - Moved example.cpp to examples/

401 - Added examples/example_bipgraph.cpp

402 - Added examples/example_varset.cpp

403 - Added examples/example_sprinkler.cpp

404 - Added examples/example_permute.cpp

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

407 Build system:

408 * Improved Makefile:

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

410 - Macros DAI_VERSION and DAI_DATE have been introduced,

411 in order to store this information in a central place

412 - Introduced CCNODEBUGFLAGS in Makefile

413 - Switched Makefile.win to GNU Make syntax

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

415 * Compatibility:

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

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

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

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

421 * Var:

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

423 * VarSet:

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

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

426 * Permute:

427 - Renamed convert_linear_index into convertLinearIndex

428 * TProb<>:

429 - Replaced log0() by log(true)

430 - Replaced takeLog0() by takeLog(true)

431 - Removed hasNonPositives()

432 - Renamed minVal() to min()

433 - Renamed maxVal() to max()

434 - Renamed totalSum() to sum()

435 * TFactor<>:

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

437 - Removed divided_by, use operator/ instead

438 - Removed divide, use operator/= instead

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

440 - Renamed minVal() to min()

441 - Renamed maxVal() to max()

442 - Renamed totalSum() to sum()

443 * FactorGraph:

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

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

446 * RegionGraph:

447 - Renamed Check_Counting_Numbers into checkCountingNumbers

448 - Renamed Calc_Counting_Numbers into calcCountingNumbers

449 * Miscellaneous:

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

451 - Replaced UEdgeVec by Graph

452 - Replaced DEdgeVec by new RootedTree class

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

454 - Merged calcPairBeliefsNew() into calcPairBeliefs()

455 - Removed calcMarginal2ndO()

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

457 - Removed class Diffs

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

459 BipartiteGraph and FactorGraph (which will be obsoleted soon)

461 Bug fixes:

462 * Fixed reversal of min and max in

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

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

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

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

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

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

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

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

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

472 for reporting this)

475 libDAI-0.2.2 (2008-09-30)

476 -------------------------

478 New features:

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

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

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

482 * Added ExactInf class for brute force exact inference.

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

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

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

486 of a double is too small.

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

488 * Improved documentation.

490 Improved architecture:

491 * Added Exceptions framework.

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

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

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

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

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

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

498 made easy by using boost::foreach.

499 * Added conditional compilation of inference methods.

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

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

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

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

504 specialization with T = Var.

505 * Improved ClusterGraph implementation, yielding significant speedups

506 for the JunctionTree algorithm on large factorgraphs.

508 Code cleanup:

509 * Moved everything into namespace "dai".

510 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

512 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

514 * Improved index.h:

515 - Renamed Index -> IndexFor

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

517 25% speedup of testregression

518 - Replaced multind by Permute

519 - Added MultiFor

520 - Added State

521 * New funcstionality of factor.h.

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

523 inference algorithm, because the Properties framework was not as

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

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

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

527 entangled) code.

528 * Removed x2x.

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

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

532 Miscellaneous improvements:

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

534 GCC under Cygwin.

535 * Contributions by Peter Gober:

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

537 * Misc contributions by Giuseppe Passino:

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

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

540 - changed #ifndefs to GNU style;

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

542 - dai::TProb:

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

544 o implementation of some methods via STL algorithms;

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

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

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

548 * Misc contributions by Christian Wojek:

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

550 and variables;

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

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

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

554 normtype is now Prob::NORMPROB by default.

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

557 Interface changes:

558 * VarSet::

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

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

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

562 - removed bool operator||

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

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

565 * FactorGraph::

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

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

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

569 - vars() -> vars

570 - factors() -> factors

571 - removed MakeFactorCavity(size_t)

572 - removed ExactMarginal(const VarSet &)

573 - removed ExactlogZ()

574 - removed updatedFactor(size_t)

575 - removed _normtype and NormType()

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

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

578 - undoProb(size_t) -> restoreFactor(size_t)

579 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

584 - removed hasNegatives()

585 * RegionGraph::

586 - nr_ORs() -> nrORs()

587 - nr_IRs() -> nrIRs()

588 - ORs() -> ORs

589 - IRs() -> IRs

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

591 * Renamed Index -> IndexFor

592 * Diffs:

593 - max() -> maxDiff()

594 - max_size() -> maxSize()

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

596 * Factor::

597 - max() -> maxVal()

598 - part_sum() -> partSum()

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

600 * VarSet::operator&&

601 * Properties -> PropertySet

604 libDAI-0.2.1 (2008-05-26)

605 -------------------------

607 Bugfix release.

608 * added missing cstdio header in util.h

609 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

610 * added description of the factor graph fileformat

611 * improved Makefile

614 libDAI-0.2.0 (2006-11-30)

615 -------------------------

617 First public release.

620 0.1.5 (2006-11-30)

621 ------------------

623 Regressions

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

626 - EXACT method does not work anymore.

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

628 costs involved; inner loops should be optimized.

630 General framework

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

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

634 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

641 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

649 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

658 command line (test) interface.

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

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

661 amount of code for handling enum parameters.

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

663 work for all approximate inference methods.

665 Bugfixes

667 - Fixed GBP free energy.

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

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

670 the logical NOT of what they should return).

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

672 - Fixed bug in utils/create_dreg_fg:

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

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

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

676 that consists of one outer region only.

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

678 - Fixed MaxDiffs flow (except for MR).

680 New functionality

682 - HAK supports several default cluster choices:

683 minimal (only factors)

684 delta (Markov blankets)

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

686 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

698 It supports different initialization methods (the original RESPPROP,

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

700 (FULL and LINEAR).

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

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

703 marginals.

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

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

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

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

708 random factor graphs.

709 - Wrote utility to visualize factor graphs using graphviz.

710 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

718 - Added Martijn's x2x

720 Improvements of existing code

722 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

726 outer regions from the factors.

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

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

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

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

731 timing and convergence criteria.

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

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

734 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

742 marginal functions to approximate cavity marginals.

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

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

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

746 arguments, randomize(), RemoveFirstOrderInteractions) and similar

747 operations to Prob

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

749 (tests/test is done).

750 - Renamed some FactorGraph methods:

751 nr_vars -> nrVars

752 nr_factors -> nrFactors

753 varind -> findVar

754 factorind -> findFactor

755 makeFacCavity -> makeFactorCavity

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

757 - Implemented RandomDRegularGraph

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

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

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

761 disconnected factor graphs).

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

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

764 - Removed calcCavityDist and calcCavityDist2ndO

765 - No longer depends on GSL.

766 - Increased portability by combining platform dependant utility functions

767 in util.{h,cpp}.

768 - Wrote *.m files providing help

770 Testing framework

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

773 functionality from the command line.

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

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

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

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

778 errors, relative logZ error and MaxDiff().

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

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

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

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

783 allow for easy visualization of the results using PyX.

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

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

786 regression testing).

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

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

789 results stored in tests/testfast.out

791 Miscellaneous

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

794 - Experimental MATLAB code added for StarEP approximation on cavity

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

796 - Renamed JunctionTree to JTree.

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

798 - Improved README

801 revision 252

802 ------------

804 Functionality

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

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

807 RegionGraph.

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

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

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

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

812 and when not.

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

814 it does not automatically merge factors anymore.

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

816 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

821 Implementation / code

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

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

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

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

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

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

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

829 multiple inheritance and polymorphism.

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

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

832 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

846 instead of initial pancakes.

848 Minor changes

849 - Started writing DoxyGen documentation

850 - Renamed lcptab2fg.m matlab/ai_writefg.m

851 - Moved all matlab stuff to matlab/

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

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

854 - Improved testing suite.

855 - Removed logreal support.

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

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

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

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

860 - Added FactorGraph::WriteToDotFile

863 0.1.4 (2006-04-13)

864 ------------------

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

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

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

868 handle (partially) negative factors.

869 - Added test suite.

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

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

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

873 Now uses precalculated indices for optimization.

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

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

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

877 _parallel_ updates).

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

879 original single variable beliefs, for all AI methods.

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

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

882 (see ai.h).

885 0.1.3 (2006-03-22)

886 --------------------

887 - All AI methods now return maxdiff

888 - ai.cpp:

889 o Now returns maxdiffinner and maxdiffouter

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

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

892 - bp.cpp:

893 o New CavityDist2ndO which estimates 2nd order cavity interactions

894 - Makefile:

895 o Bugfix: removed dependencies on algwim.*

898 0.1.2 (2006-02-28)

899 --------------------

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

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

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

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

904 the output arguments Q, Q0 of ai).

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

908 0.1.1 (2006-02-28)

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

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

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

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

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

914 of BipGraph checks for the existence of short loops.

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

916 description in the help).

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

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

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

922 0.1.0 (2006-02-28)

923 --------------------

924 First version worthy of a version number.