1 git master HEAD

2 ---------------

4 * Made all "verbose" properties optional

5 * Unit tests should now also work on WINDOWS

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

7 * Fixed some bugs in the MatLab interface build system

8 * Fixed a bug in utils/fginfo.cpp

9 * Improved treeep.h/cpp:

10 - changed TreeEP::construct( const RootedTree& ) into

11 TreeEP::construct( const FactorGraph&, const RootedTree& )

12 * Improved jtree.h/cpp:

13 - changed JTree::construct( const std::vector<VarSet>&, bool ) into

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

15 - changed JTree::GenerateJT( const std::vector<VarSet> & )

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

17 * Improved regiongraph.h/cpp:

18 - Made (previously public) members RegionGraph::G, RegionGraph::ORs,

19 RegionGraph::IRs and RegionGraph::fac2OR protected.

20 - Removed partial constructor RegionGraph::RegionGraph( const FactorGraph& fg )

21 - Added some error checking code

22 - Renamed RegionGraph::calcCountingNumbers() into

23 RegionGraph::calcCVMCountingNumbers() and made it protected, because

24 exposing it to the world serves no purpose.

25 - Added RegionGraph::DAG() accessor which returns a reference to the

26 region graph DAG structure (currently implemented as a BipartiteGraph)

27 - Made RegionGraph::RecomputeORs(), RegionGraph::RecomputeORs( const VarSet& )

28 and RegionGraph::RecomputeOR( size_t ) protected and renamed them by changing

29 the "Recompute" into "recompute", because exposing them to the world serves no

30 purpose.

31 - RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )

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

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

34 NOT_IMPLEMENTED exception.

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

36 * Improved clustergraph.h/cpp:

37 - Made (previously public) members ClusterGraph::G, ClusterGraph::vars and

38 ClusterGraph::clusters private and added ClusterGraph::bipGraph(),

39 ClusterGraph::vars() and ClusterGraph::clusters() methods which offer

40 read-only access to these members.

41 - Deprecated ClusterGraph::toVector()

42 - Added ClusterGraph::nrVars() method

43 - Renamed ClusterGraph::size() method into ClusterGraph::nrClusters()

44 - Added ClusterGraph::var( size_t ) method

45 - Added ClusterGraph::cluster( size_t ) method

46 * Improved factorgraph.h/cpp:

47 - FactorGraph::clamped() now contains a delta factor for the clamped variable

48 - Renamed FactorGraph::Cliques() into FactorGraph::maximalFactorDomains()

49 - Added FactorGraph::MarkovGraph()

50 - Fixed bug in FactorGraph::clone()

51 - FactorGraph::findVars( const VarSet& ) now returns a SmallSet<size_t>

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

53 - Made (previously public) member FactorGraph::G private and added the

54 FactorGraph::bipGraph() method, which offers read-only access to it.

55 - Deprecated the iterator interface:

56 o FactorGraph::iterator typedef

57 o FactorGraph::const_iterator typedef

58 o FactorGraph::begin() members

59 o FactorGraph::end() members

60 - Deprecated FactorGraph::factor(size_t) which offered write access to a factor

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

62 as the outer regions are not automatically recomputed.

63 * Improved factor.h/cpp:

64 - Fixed bug in min( const TFactor<T> &, const TFactor<T> & )

65 - Fixed bug in max( const TFactor<T> &, const TFactor<T> & )

66 - Added TFactor<T>::takeAbs()

67 - Added TFactor<T>::takeExp()

68 - Added TFactor<T>::takeLog( bool )

69 - Added TFactor<T>::operator-() const

70 - Added TFactor<T>::sumAbs() const

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

72 - Renamed TFactor<T>::states() into TFactor<T>::nrStates()

73 - Added TFactor<T>::get(size_t) and TFactor<T>::set(size_t,T) operators;

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

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

76 * Improved prob.h/cpp:

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

78 constructor: the sizeHint argument no longer defaults to 0

79 - Deprecated TProb::accumulate( T init, binOp op1, unOp op2 );

80 instead, TProb::accumulateSum( T init, unOp op ) and

81 TProb::accumulateMax( T init, unOp op, bool minimize ) should be used.

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

83 ProbNormType and ProbDistType should be used instead.

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

85 - TProb<T>::accumulate() now also applies op2 to init

86 - Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()

87 - TProb<T>& operator/= (T x) now yields 0 when dividing by 0

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

89 - Added TProb<T>::get(size_t) and TProb<T>::set(size_t,T) operators;

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

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

92 - Added TProb<T>::resize(size_t)

93 * Improved index.h/cpp:

94 - Added multifor::reset()

95 * Improved properties.h/cpp:

96 - Renamed PropertySet::Set() -> PropertySet::set()

97 - Renamed PropertySet::Get() -> PropertySet::get()

98 - Renamed PropertySet::GetAs<T>() -> PropertySet::getAs<T>()

99 - Renamed PropertySet::ConvertTo<T>() -> PropertySet::convertTo<T>()

100 - Added PropertySet::size()

101 - Added PropertySet::clear()

102 - Added PropertySet::erase()

103 - Fixed bug in PropertySet::setAsString<T>()

104 * Improved util.h/cpp:

105 - Fixed a bug in rnd_seed()

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

107 * Improved weightedgraph.h/cpp:

108 - Renamed MaxSpanningTreePrims into MaxSpanningTree

109 - Renamed MinSpanningTreePrims into MinSpanningTree

110 - Added option to MaxSpanningTree and MinSpanningTree for

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

112 - Better error checking in RootedTree constructor

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

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

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

116 * Improved bipgraph.h/cpp:

117 - Fixed bug in BipartiteGraph::eraseNode1()

118 - Fixed bug in BipartiteGraph::eraseNode2()

119 - Fixed bug in BipartiteGraph::isTree()

120 - Added BipartiteGraph::hasEdge()

121 - Added BipartiteGraph::findNb1()

122 - Added BipartiteGraph::findNb2()

123 - BipartiteGraph::delta1() and BipartiteGraph::delta2() now

124 return a SmallSet<size_t> instead of a vector<size_t>

125 - Added BipartiteGraph::operator==( const BipartiteGraph& )

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

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

128 * Improved graph.h/cpp:

129 - Fixed bug in GraphAL::nrEdges()

130 - Fixed bug in GraphAL::addEdge()

131 - Fixed bug in GraphAL::isTree()

132 - Fixed bug in GraphAL::eraseNode()

133 - Fixed bug in GraphAL::printDot()

134 - Fixed bug in createGraphGrid3D()

135 - Fixed bug in createGraphRegular()

136 - Added GraphAL::hasEdge(size_t,size_t)

137 - Added GraphAL::operator==( const GraphAL& )

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

139 * Improved smallset.h/cpp:

140 - The sizeHint argument of the iterator constructor

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

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

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

144 constructor.

145 - Added SmallSet::insert( const T& t ) method

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

147 * Compressed Makefile

148 * Added unit tests for var, smallset, varset, graph, bipgraph,

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

150 factor, factorgraph, clustergraph, regiongraph, daialg, alldai

151 * Added unit testing framework

152 * Added initialization of TRWBP weights by sampling spanning trees

153 * Cleaned up MR code:

154 - rewrote response propagation implementation with help of BBP

155 - now uses GraphAL to represent the Markov graph

156 - miscellaneous smaller cleanups

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

158 assignment from happening

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

160 * Removed deprecated functionality

161 * Updated ChangeLog for libDAI-0.2.4 (forgot a few entries)

164 libDAI-0.2.4 (2010-02-11)

165 -------------------------

167 New features:

168 * Implemented Tree-Reweighted BP

169 * [Frederik Eaton] Implemented Fractional Belief Propagation

171 Miscellaneous improvements:

172 * Improved documentation

173 * [Frederik Eaton] Added constructors for BBPCostFunction

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

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

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

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

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

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

180 marginals calculated by the algorithm.

181 * Strengthened convergence criteria of various algorithms

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

183 similar to (but simpler than) BipartiteGraph

184 * Added some functionality to create various standard factors

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

186 * Added examples example_sprinkler_gibbs and example_sprinkler_em

187 * Implemented various heuristics for choosing a variable elimination sequence

188 in JTree

189 * Added BETHE method for GBP/HAK cluster choice

190 * Made alias support official part of the library

192 Build system:

193 * Moved platform independent build options into Makefile.ALL

194 * Windows platform now needs Boost 1.37 or higher

196 Code cleanup:

197 * Cleaned up utils/createfg and tests/testdai

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

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

201 * Removed obsolete/deprecated stuff

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

203 * Renamed some functions of BipartiteGraph:

204 add1() -> addNode1()

205 erase1() -> eraseNode1()

206 nr1() -> nrNodes1()

207 add2() -> addNode2()

208 erase2() -> eraseNode2()

209 nr2() -> nrNodes2()

210 * Renamed some functions in ClusterGraph:

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

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

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

214 * Changed interface of one RegionGraph constructor

215 * Renamed "Clamped BP" into "Conditioned BP"

217 Bug fixes:

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

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

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

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

222 and using log-domain updates

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

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

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

228 libDAI-0.2.3 (2009-11-16)

229 -------------------------

231 New features:

232 * Complete doxygen documentation (although more detailed documentation still

233 has to be written)

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

235 Expectation Maximization

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

237 octave interfaces

238 * Added Max-Product functionality to JTree

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

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

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

243 Code cleanup:

244 * Updated copyright headers

245 * Cleaned up error handling by introducing the DAI_THROWE macro

246 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern

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

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

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

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

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

253 Miscellaneous improvements:

254 * BipartiteGraph:

255 - Added eraseEdge( size_t n1, size_t n2 )

256 - [Frederik Eaton] Improved documentation of Neighbor

257 * TProb<T>:

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

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

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

261 - [Frederik Eaton] Added setUniform()

262 - [Frederik Eaton] Added sumAbs()

263 - [Frederik Eaton] Added argmax()

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

265 * TFactor<T>:

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

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

268 which reorders variables to canonical ordering before storing the table

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

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

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

272 * State:

273 - [Giuseppe Passino] Added prefix ++ operator

274 * Permute:

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

276 * FactorGraph:

277 - [Frederik Eaton] Added clampVar()

278 - [Frederik Eaton] Added clampFactor()

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

280 * PropertySet:

281 - Added keys(), for getting all keys

282 - [Frederik Eaton] Added default constructor

283 - [Frederik Eaton] Added constructor from string

284 * InfAlg:

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

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

287 * ExactInf:

288 - Added calcMarginal(const VarSet &)

289 * HAK:

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

291 * BP:

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

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

294 * JTree:

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

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

297 * MatLab interface:

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

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

300 (only for BP and JTree)

301 * README is now created automatically from doxygen documentation

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

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

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

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

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

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

308 alias substitutions

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

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

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

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

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

314 variables with the same labels

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

316 * Exception objects now remember their error code

317 * Examples:

318 - Moved example.cpp to examples/

319 - Added examples/example_bipgraph.cpp

320 - Added examples/example_varset.cpp

321 - Added examples/example_sprinkler.cpp

322 - Added examples/example_permute.cpp

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

325 Build system:

326 * Improved Makefile:

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

328 - Macros DAI_VERSION and DAI_DATE have been introduced,

329 in order to store this information in a central place

330 - Introduced CCNODEBUGFLAGS in Makefile

331 - Switched Makefile.win to GNU Make syntax

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

333 * Compatibility:

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

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

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

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

339 * Var:

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

341 * VarSet:

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

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

344 * Permute:

345 - Renamed convert_linear_index into convertLinearIndex

346 * TProb<>:

347 - Replaced log0() by log(true)

348 - Replaced takeLog0() by takeLog(true)

349 - Removed hasNonPositives()

350 - Renamed minVal() to min()

351 - Renamed maxVal() to max()

352 - Renamed totalSum() to sum()

353 * TFactor<>:

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

355 - Removed divided_by, use operator/ instead

356 - Removed divide, use operator/= instead

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

358 - Renamed minVal() to min()

359 - Renamed maxVal() to max()

360 - Renamed totalSum() to sum()

361 * FactorGraph:

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

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

364 * RegionGraph:

365 - Renamed Check_Counting_Numbers into checkCountingNumbers

366 - Renamed Calc_Counting_Numbers into calcCountingNumbers

367 * Miscellaneous:

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

369 - Replaced UEdgeVec by Graph

370 - Replaced DEdgeVec by new RootedTree class

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

372 - Merged calcPairBeliefsNew() into calcPairBeliefs()

373 - Removed calcMarginal2ndO()

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

375 - Removed class Diffs

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

377 BipartiteGraph and FactorGraph (which will be obsoleted soon)

379 Bug fixes:

380 * Fixed reversal of min and max in

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

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

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

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

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

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

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

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

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

390 for reporting this)

393 libDAI-0.2.2 (2008-09-30)

394 -------------------------

396 New features:

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

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

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

400 * Added ExactInf class for brute force exact inference.

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

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

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

404 of a double is too small.

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

406 * Improved documentation.

408 Improved architecture:

409 * Added Exceptions framework.

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

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

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

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

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

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

416 made easy by using boost::foreach.

417 * Added conditional compilation of inference methods.

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

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

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

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

422 specialization with T = Var.

423 * Improved ClusterGraph implementation, yielding significant speedups

424 for the JunctionTree algorithm on large factorgraphs.

426 Code cleanup:

427 * Moved everything into namespace "dai".

428 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

430 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

432 * Improved index.h:

433 - Renamed Index -> IndexFor

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

435 25% speedup of testregression

436 - Replaced multind by Permute

437 - Added MultiFor

438 - Added State

439 * New funcstionality of factor.h.

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

441 inference algorithm, because the Properties framework was not as

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

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

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

445 entangled) code.

446 * Removed x2x.

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

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

450 Miscellaneous improvements:

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

452 GCC under cygwin.

453 * Contributions by Peter Gober:

454 - Renamed variable _N in mr.* for compatibility with g++ under cygwin.

455 * Misc contributions by Giuseppe Passino:

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

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

458 - changed #ifndefs to GNU style;

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

460 - dai::TProb:

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

462 o implementation of some methods via STL algorithms;

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

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

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

466 * Misc contributions by Christian Wojek:

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

468 and variables;

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

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

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

472 normtype is now Prob::NORMPROB by default.

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

475 Interface changes:

476 * VarSet::

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

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

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

480 - removed bool operator||

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

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

483 * FactorGraph::

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

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

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

487 - vars() -> vars

488 - factors() -> factors

489 - removed MakeFactorCavity(size_t)

490 - removed ExactMarginal(const VarSet &)

491 - removed ExactlogZ()

492 - removed updatedFactor(size_t)

493 - removed _normtype and NormType()

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

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

496 - undoProb(size_t) -> restoreFactor(size_t)

497 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

502 - removed hasNegatives()

503 * RegionGraph::

504 - nr_ORs() -> nrORs()

505 - nr_IRs() -> nrIRs()

506 - ORs() -> ORs

507 - IRs() -> IRs

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

509 * Renamed Index -> IndexFor

510 * Diffs:

511 - max() -> maxDiff()

512 - max_size() -> maxSize()

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

514 * Factor::

515 - max() -> maxVal()

516 - part_sum() -> partSum()

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

518 * VarSet::operator&&

519 * Properties -> PropertySet

522 libDAI-0.2.1 (2008-05-26)

523 -------------------------

525 Bugfix release.

526 * added missing cstdio header in util.h

527 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

528 * added description of the factor graph fileformat

529 * improved Makefile

532 libDAI-0.2.0 (2006-11-30)

533 -------------------------

535 First public release.

538 0.1.5 (2006-11-30)

539 ------------------

541 Regressions

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

544 - EXACT method does not work anymore.

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

546 costs involved; inner loops should be optimized.

548 General framework

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

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

552 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

559 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

567 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

576 command line (test) interface.

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

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

579 amount of code for handling enum parameters.

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

581 work for all approximate inference methods.

583 Bugfixes

585 - Fixed GBP free energy.

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

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

588 the logical NOT of what they should return).

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

590 - Fixed bug in utils/create_dreg_fg:

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

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

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

594 that consists of one outer region only.

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

596 - Fixed MaxDiffs flow (except for MR).

598 New functionality

600 - HAK supports several default cluster choices:

601 minimal (only factors)

602 delta (Markov blankets)

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

604 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

616 It supports different initialization methods (the original RESPPROP,

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

618 (FULL and LINEAR).

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

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

621 marginals.

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

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

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

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

626 random factor graphs.

627 - Wrote utility to visualize factor graphs using graphviz.

628 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

636 - Added Martijn's x2x

638 Improvements of existing code

640 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

644 outer regions from the factors.

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

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

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

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

649 timing and convergence criteria.

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

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

652 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

660 marginal functions to approximate cavity marginals.

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

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

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

664 arguments, randomize(), RemoveFirstOrderInteractions) and similar

665 operations to Prob

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

667 (tests/test is done).

668 - Renamed some FactorGraph methods:

669 nr_vars -> nrVars

670 nr_factors -> nrFactors

671 varind -> findVar

672 factorind -> findFactor

673 makeFacCavity -> makeFactorCavity

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

675 - Implemented RandomDRegularGraph

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

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

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

679 disconnected factor graphs).

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

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

682 - Removed calcCavityDist and calcCavityDist2ndO

683 - No longer depends on GSL.

684 - Increased portability by combining platform dependant utility functions

685 in util.{h,cpp}.

686 - Wrote *.m files providing help

688 Testing framework

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

691 functionality from the command line.

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

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

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

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

696 errors, relative logZ error and MaxDiff().

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

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

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

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

701 allow for easy visualization of the results using PyX.

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

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

704 regression testing).

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

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

707 results stored in tests/testfast.out

709 Miscellaneous

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

712 - Experimental MATLAB code added for StarEP approximation on cavity

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

714 - Renamed JunctionTree to JTree.

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

716 - Improved README

719 revision 252

720 ------------

722 Functionality

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

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

725 RegionGraph.

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

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

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

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

730 and when not.

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

732 it does not automatically merge factors anymore.

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

734 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

739 Implementation / code

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

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

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

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

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

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

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

747 multiple inheritance and polymorphism.

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

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

750 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

764 instead of initial pancakes.

766 Minor changes

767 - Started writing DoxyGen documentation

768 - Renamed lcptab2fg.m matlab/ai_writefg.m

769 - Moved all matlab stuff to matlab/

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

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

772 - Improved testing suite.

773 - Removed logreal support.

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

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

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

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

778 - Added FactorGraph::WriteToDotFile

781 0.1.4 (2006-04-13)

782 ------------------

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

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

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

786 handle (partially) negative factors.

787 - Added test suite.

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

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

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

791 Now uses precalculated indices for optimization.

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

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

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

795 _parallel_ updates).

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

797 original single variable beliefs, for all AI methods.

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

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

800 (see ai.h).

803 0.1.3 (2006-03-22)

804 --------------------

805 - All AI methods now return maxdiff

806 - ai.cpp:

807 o Now returns maxdiffinner and maxdiffouter

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

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

810 - bp.cpp:

811 o New CavityDist2ndO which estimates 2nd order cavity interactions

812 - Makefile:

813 o Bugfix: removed dependencies on algwim.*

816 0.1.2 (2006-02-28)

817 --------------------

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

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

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

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

822 the output arguments Q, Q0 of ai).

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

826 0.1.1 (2006-02-28)

827 --------------------

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

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

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

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

832 of BipGraph checks for the existence of short loops.

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

834 description in the help).

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

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

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

840 0.1.0 (2006-02-28)

841 --------------------

842 First version worthy of a version number.