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

10 formats to the libDAI factor graph file format

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

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

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

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

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

16 marginals calculated by the algorithm.

17 * Improved mf.h/cpp:

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

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

20 mean field and "hard-spin" mean field

21 * Improved exactinf.h/cpp:

22 - Added ExactInf::findMaximum()

23 * Improved treeep.h/cpp:

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

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

26 - Now also supports disconnected factor graphs

27 * Improved jtree.h/cpp:

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

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

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

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

32 - Now also supports disconnected factor graphs

33 - Fixed a bug in JTree::findMaximum() and simplified the code

34 * Improved regiongraph.h/cpp:

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

36 RegionGraph::IRs and RegionGraph::fac2OR protected.

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

38 - Added some error checking code

39 - Renamed RegionGraph::calcCountingNumbers() into

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

41 exposing it to the world serves no purpose.

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

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

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

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

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

47 purpose.

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

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

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

51 NOT_IMPLEMENTED exception.

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

53 * Improved clustergraph.h/cpp:

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

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

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

57 read-only access to these members.

58 - Deprecated ClusterGraph::toVector()

59 - Added ClusterGraph::nrVars() method

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

61 - Added ClusterGraph::var( size_t ) method

62 - Added ClusterGraph::cluster( size_t ) method

63 * Improved factorgraph.h/cpp:

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

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

66 - Added FactorGraph::MarkovGraph()

67 - Fixed bug in FactorGraph::clone()

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

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

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

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

72 - Deprecated the iterator interface:

73 o FactorGraph::iterator typedef

74 o FactorGraph::const_iterator typedef

75 o FactorGraph::begin() members

76 o FactorGraph::end() members

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

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

79 as the outer regions are not automatically recomputed.

80 * Improved factor.h/cpp:

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

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

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

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

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

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

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

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

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

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

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

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

93 * Improved prob.h/cpp:

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

95 constructor: the sizeHint argument no longer defaults to 0

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

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

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

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

100 ProbNormType and ProbDistType should be used instead.

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

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

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

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

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

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

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

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

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

110 * Improved index.h/cpp:

111 - Added multifor::reset()

112 * Improved properties.h/cpp:

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

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

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

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

117 - Added PropertySet::size()

118 - Added PropertySet::clear()

119 - Added PropertySet::erase()

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

121 * Improved util.h/cpp:

122 - Fixed a bug in rnd_seed()

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

124 * Improved weightedgraph.h/cpp:

125 - Renamed MaxSpanningTreePrims into MaxSpanningTree

126 - Renamed MinSpanningTreePrims into MinSpanningTree

127 - Added option to MaxSpanningTree and MinSpanningTree for

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

129 - Better error checking in RootedTree constructor

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

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

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

133 * Improved bipgraph.h/cpp:

134 - Fixed bug in BipartiteGraph::eraseNode1()

135 - Fixed bug in BipartiteGraph::eraseNode2()

136 - Fixed bug in BipartiteGraph::isTree()

137 - Added BipartiteGraph::hasEdge()

138 - Added BipartiteGraph::findNb1()

139 - Added BipartiteGraph::findNb2()

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

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

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

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

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

145 * Improved graph.h/cpp:

146 - Fixed bug in GraphAL::nrEdges()

147 - Fixed bug in GraphAL::addEdge()

148 - Fixed bug in GraphAL::isTree()

149 - Fixed bug in GraphAL::eraseNode()

150 - Fixed bug in GraphAL::printDot()

151 - Fixed bug in createGraphGrid3D()

152 - Fixed bug in createGraphRegular()

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

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

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

156 * Improved smallset.h/cpp:

157 - The sizeHint argument of the iterator constructor

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

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

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

161 constructor.

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

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

164 * Compressed Makefile

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

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

167 factor, factorgraph, clustergraph, regiongraph, daialg, alldai

168 * Added unit testing framework

169 * Added initialization of TRWBP weights by sampling spanning trees

170 * Cleaned up MR code:

171 - rewrote response propagation implementation with help of BBP

172 - now uses GraphAL to represent the Markov graph

173 - miscellaneous smaller cleanups

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

175 assignment from happening

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

177 * Removed deprecated functionality

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

181 libDAI-0.2.4 (2010-02-11)

182 -------------------------

184 New features:

185 * Implemented Tree-Reweighted BP

186 * [Frederik Eaton] Implemented Fractional Belief Propagation

188 Miscellaneous improvements:

189 * Improved documentation

190 * [Frederik Eaton] Added constructors for BBPCostFunction

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

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

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

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

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

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

197 marginals calculated by the algorithm.

198 * Strengthened convergence criteria of various algorithms

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

200 similar to (but simpler than) BipartiteGraph

201 * Added some functionality to create various standard factors

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

203 * Added examples example_sprinkler_gibbs and example_sprinkler_em

204 * Implemented various heuristics for choosing a variable elimination sequence

205 in JTree

206 * Added BETHE method for GBP/HAK cluster choice

207 * Made alias support official part of the library

209 Build system:

210 * Moved platform independent build options into Makefile.ALL

211 * Windows platform now needs Boost 1.37 or higher

213 Code cleanup:

214 * Cleaned up utils/createfg and tests/testdai

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

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

218 * Removed obsolete/deprecated stuff

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

220 * Renamed some functions of BipartiteGraph:

221 add1() -> addNode1()

222 erase1() -> eraseNode1()

223 nr1() -> nrNodes1()

224 add2() -> addNode2()

225 erase2() -> eraseNode2()

226 nr2() -> nrNodes2()

227 * Renamed some functions in ClusterGraph:

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

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

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

231 * Changed interface of one RegionGraph constructor

232 * Renamed "Clamped BP" into "Conditioned BP"

234 Bug fixes:

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

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

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

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

239 and using log-domain updates

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

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

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

245 libDAI-0.2.3 (2009-11-16)

246 -------------------------

248 New features:

249 * Complete doxygen documentation (although more detailed documentation still

250 has to be written)

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

252 Expectation Maximization

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

254 octave interfaces

255 * Added Max-Product functionality to JTree

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

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

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

260 Code cleanup:

261 * Updated copyright headers

262 * Cleaned up error handling by introducing the DAI_THROWE macro

263 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern

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

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

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

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

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

270 Miscellaneous improvements:

271 * BipartiteGraph:

272 - Added eraseEdge( size_t n1, size_t n2 )

273 - [Frederik Eaton] Improved documentation of Neighbor

274 * TProb<T>:

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

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

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

278 - [Frederik Eaton] Added setUniform()

279 - [Frederik Eaton] Added sumAbs()

280 - [Frederik Eaton] Added argmax()

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

282 * TFactor<T>:

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

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

285 which reorders variables to canonical ordering before storing the table

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

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

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

289 * State:

290 - [Giuseppe Passino] Added prefix ++ operator

291 * Permute:

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

293 * FactorGraph:

294 - [Frederik Eaton] Added clampVar()

295 - [Frederik Eaton] Added clampFactor()

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

297 * PropertySet:

298 - Added keys(), for getting all keys

299 - [Frederik Eaton] Added default constructor

300 - [Frederik Eaton] Added constructor from string

301 * InfAlg:

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

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

304 * ExactInf:

305 - Added calcMarginal(const VarSet &)

306 * HAK:

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

308 * BP:

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

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

311 * JTree:

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

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

314 * MatLab interface:

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

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

317 (only for BP and JTree)

318 * README is now created automatically from doxygen documentation

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

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

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

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

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

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

325 alias substitutions

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

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

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

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

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

331 variables with the same labels

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

333 * Exception objects now remember their error code

334 * Examples:

335 - Moved example.cpp to examples/

336 - Added examples/example_bipgraph.cpp

337 - Added examples/example_varset.cpp

338 - Added examples/example_sprinkler.cpp

339 - Added examples/example_permute.cpp

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

342 Build system:

343 * Improved Makefile:

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

345 - Macros DAI_VERSION and DAI_DATE have been introduced,

346 in order to store this information in a central place

347 - Introduced CCNODEBUGFLAGS in Makefile

348 - Switched Makefile.win to GNU Make syntax

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

350 * Compatibility:

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

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

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

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

356 * Var:

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

358 * VarSet:

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

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

361 * Permute:

362 - Renamed convert_linear_index into convertLinearIndex

363 * TProb<>:

364 - Replaced log0() by log(true)

365 - Replaced takeLog0() by takeLog(true)

366 - Removed hasNonPositives()

367 - Renamed minVal() to min()

368 - Renamed maxVal() to max()

369 - Renamed totalSum() to sum()

370 * TFactor<>:

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

372 - Removed divided_by, use operator/ instead

373 - Removed divide, use operator/= instead

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

375 - Renamed minVal() to min()

376 - Renamed maxVal() to max()

377 - Renamed totalSum() to sum()

378 * FactorGraph:

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

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

381 * RegionGraph:

382 - Renamed Check_Counting_Numbers into checkCountingNumbers

383 - Renamed Calc_Counting_Numbers into calcCountingNumbers

384 * Miscellaneous:

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

386 - Replaced UEdgeVec by Graph

387 - Replaced DEdgeVec by new RootedTree class

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

389 - Merged calcPairBeliefsNew() into calcPairBeliefs()

390 - Removed calcMarginal2ndO()

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

392 - Removed class Diffs

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

394 BipartiteGraph and FactorGraph (which will be obsoleted soon)

396 Bug fixes:

397 * Fixed reversal of min and max in

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

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

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

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

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

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

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

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

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

407 for reporting this)

410 libDAI-0.2.2 (2008-09-30)

411 -------------------------

413 New features:

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

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

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

417 * Added ExactInf class for brute force exact inference.

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

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

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

421 of a double is too small.

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

423 * Improved documentation.

425 Improved architecture:

426 * Added Exceptions framework.

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

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

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

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

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

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

433 made easy by using boost::foreach.

434 * Added conditional compilation of inference methods.

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

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

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

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

439 specialization with T = Var.

440 * Improved ClusterGraph implementation, yielding significant speedups

441 for the JunctionTree algorithm on large factorgraphs.

443 Code cleanup:

444 * Moved everything into namespace "dai".

445 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

447 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

449 * Improved index.h:

450 - Renamed Index -> IndexFor

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

452 25% speedup of testregression

453 - Replaced multind by Permute

454 - Added MultiFor

455 - Added State

456 * New funcstionality of factor.h.

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

458 inference algorithm, because the Properties framework was not as

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

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

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

462 entangled) code.

463 * Removed x2x.

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

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

467 Miscellaneous improvements:

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

469 GCC under cygwin.

470 * Contributions by Peter Gober:

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

472 * Misc contributions by Giuseppe Passino:

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

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

475 - changed #ifndefs to GNU style;

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

477 - dai::TProb:

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

479 o implementation of some methods via STL algorithms;

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

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

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

483 * Misc contributions by Christian Wojek:

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

485 and variables;

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

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

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

489 normtype is now Prob::NORMPROB by default.

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

492 Interface changes:

493 * VarSet::

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

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

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

497 - removed bool operator||

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

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

500 * FactorGraph::

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

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

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

504 - vars() -> vars

505 - factors() -> factors

506 - removed MakeFactorCavity(size_t)

507 - removed ExactMarginal(const VarSet &)

508 - removed ExactlogZ()

509 - removed updatedFactor(size_t)

510 - removed _normtype and NormType()

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

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

513 - undoProb(size_t) -> restoreFactor(size_t)

514 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

519 - removed hasNegatives()

520 * RegionGraph::

521 - nr_ORs() -> nrORs()

522 - nr_IRs() -> nrIRs()

523 - ORs() -> ORs

524 - IRs() -> IRs

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

526 * Renamed Index -> IndexFor

527 * Diffs:

528 - max() -> maxDiff()

529 - max_size() -> maxSize()

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

531 * Factor::

532 - max() -> maxVal()

533 - part_sum() -> partSum()

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

535 * VarSet::operator&&

536 * Properties -> PropertySet

539 libDAI-0.2.1 (2008-05-26)

540 -------------------------

542 Bugfix release.

543 * added missing cstdio header in util.h

544 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

545 * added description of the factor graph fileformat

546 * improved Makefile

549 libDAI-0.2.0 (2006-11-30)

550 -------------------------

552 First public release.

555 0.1.5 (2006-11-30)

556 ------------------

558 Regressions

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

561 - EXACT method does not work anymore.

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

563 costs involved; inner loops should be optimized.

565 General framework

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

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

569 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

576 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

584 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

593 command line (test) interface.

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

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

596 amount of code for handling enum parameters.

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

598 work for all approximate inference methods.

600 Bugfixes

602 - Fixed GBP free energy.

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

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

605 the logical NOT of what they should return).

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

607 - Fixed bug in utils/create_dreg_fg:

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

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

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

611 that consists of one outer region only.

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

613 - Fixed MaxDiffs flow (except for MR).

615 New functionality

617 - HAK supports several default cluster choices:

618 minimal (only factors)

619 delta (Markov blankets)

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

621 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

633 It supports different initialization methods (the original RESPPROP,

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

635 (FULL and LINEAR).

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

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

638 marginals.

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

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

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

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

643 random factor graphs.

644 - Wrote utility to visualize factor graphs using graphviz.

645 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

653 - Added Martijn's x2x

655 Improvements of existing code

657 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

661 outer regions from the factors.

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

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

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

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

666 timing and convergence criteria.

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

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

669 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

677 marginal functions to approximate cavity marginals.

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

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

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

681 arguments, randomize(), RemoveFirstOrderInteractions) and similar

682 operations to Prob

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

684 (tests/test is done).

685 - Renamed some FactorGraph methods:

686 nr_vars -> nrVars

687 nr_factors -> nrFactors

688 varind -> findVar

689 factorind -> findFactor

690 makeFacCavity -> makeFactorCavity

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

692 - Implemented RandomDRegularGraph

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

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

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

696 disconnected factor graphs).

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

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

699 - Removed calcCavityDist and calcCavityDist2ndO

700 - No longer depends on GSL.

701 - Increased portability by combining platform dependant utility functions

702 in util.{h,cpp}.

703 - Wrote *.m files providing help

705 Testing framework

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

708 functionality from the command line.

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

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

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

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

713 errors, relative logZ error and MaxDiff().

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

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

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

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

718 allow for easy visualization of the results using PyX.

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

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

721 regression testing).

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

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

724 results stored in tests/testfast.out

726 Miscellaneous

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

729 - Experimental MATLAB code added for StarEP approximation on cavity

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

731 - Renamed JunctionTree to JTree.

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

733 - Improved README

736 revision 252

737 ------------

739 Functionality

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

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

742 RegionGraph.

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

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

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

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

747 and when not.

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

749 it does not automatically merge factors anymore.

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

751 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

756 Implementation / code

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

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

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

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

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

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

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

764 multiple inheritance and polymorphism.

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

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

767 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

781 instead of initial pancakes.

783 Minor changes

784 - Started writing DoxyGen documentation

785 - Renamed lcptab2fg.m matlab/ai_writefg.m

786 - Moved all matlab stuff to matlab/

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

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

789 - Improved testing suite.

790 - Removed logreal support.

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

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

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

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

795 - Added FactorGraph::WriteToDotFile

798 0.1.4 (2006-04-13)

799 ------------------

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

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

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

803 handle (partially) negative factors.

804 - Added test suite.

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

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

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

808 Now uses precalculated indices for optimization.

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

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

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

812 _parallel_ updates).

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

814 original single variable beliefs, for all AI methods.

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

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

817 (see ai.h).

820 0.1.3 (2006-03-22)

821 --------------------

822 - All AI methods now return maxdiff

823 - ai.cpp:

824 o Now returns maxdiffinner and maxdiffouter

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

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

827 - bp.cpp:

828 o New CavityDist2ndO which estimates 2nd order cavity interactions

829 - Makefile:

830 o Bugfix: removed dependencies on algwim.*

833 0.1.2 (2006-02-28)

834 --------------------

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

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

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

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

839 the output arguments Q, Q0 of ai).

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

843 0.1.1 (2006-02-28)

844 --------------------

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

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

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

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

849 of BipGraph checks for the existence of short loops.

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

851 description in the help).

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

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

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

857 0.1.0 (2006-02-28)

858 --------------------

859 First version worthy of a version number.