1 git HEAD

2 --------

4 * Improved BipartiteGraph code:

5 - Fixed bug in BipartiteGraph::eraseNode1()

6 - Fixed bug in BipartiteGraph::eraseNode2()

7 - Fixed bug in BipartiteGraph::isTree()

8 - Added BipartiteGraph::hasEdge()

9 - Added BipartiteGraph::findNb1()

10 - Added BipartiteGraph::findNb2()

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

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

13 * Improved GraphAL code:

14 - Fixed bug in GraphAL::nrEdges()

15 - Fixed bug in GraphAL::addEdge()

16 - Fixed bug in GraphAL::isTree()

17 - Fixed bug in GraphAL::eraseNode()

18 - Fixed bug in GraphAL::printDot()

19 - Fixed bug in createGraphGrid3D()

20 - Fixed bug in createGraphRegular()

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

22 * Improved SmallSet code:

23 - The sizeHint argument of the iterator constructor

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

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

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

27 constructor.

28 * Removed RandomDRegularGraph()

29 * Compressed Makefile

30 * Added unit tests for Var, SmallSet, VarSet, Graph, BipartiteGraph

31 * Added unit testing framework

32 * Added initialization of TRWBP weights by sampling spanning trees

33 * Cleaned up MR code:

34 - rewrote response propagation implementation with help of BBP

35 - now uses GraphAL to represent the Markov graph

36 - miscellaneous smaller cleanups

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

38 assignment from happening

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

40 * Removed deprecated functionality

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

44 libDAI-0.2.4 (2010-02-11)

45 -------------------------

47 New features:

48 * Implemented Tree-Reweighted BP

49 * [Frederik Eaton] Implemented Fractional Belief Propagation

51 Miscellaneous improvements:

52 * Improved documentation

53 * [Frederik Eaton] Added constructors for BBPCostFunction

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

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

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

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

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

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

60 marginals calculated by the algorithm.

61 * Strengthened convergence criteria of various algorithms

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

63 similar to (but simpler than) BipartiteGraph

64 * Added some functionality to create various standard factors

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

66 * Added examples example_sprinkler_gibbs and example_sprinkler_em

67 * Implemented various heuristics for choosing a variable elimination sequence

68 in JTree

69 * Added BETHE method for GBP/HAK cluster choice

70 * Made alias support official part of the library

72 Build system:

73 * Moved platform independent build options into Makefile.ALL

74 * Windows platform now needs Boost 1.37 or higher

76 Code cleanup:

77 * Cleaned up utils/createfg and tests/testdai

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

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

81 * Removed obsolete/deprecated stuff

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

83 * Renamed some functions of BipartiteGraph:

84 add1() -> addNode1()

85 erase1() -> eraseNode1()

86 nr1() -> nrNodes1()

87 add2() -> addNode2()

88 erase2() -> eraseNode2()

89 nr2() -> nrNodes2()

90 * Renamed some functions in ClusterGraph:

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

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

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

94 * Changed interface of one RegionGraph constructor

95 * Renamed "Clamped BP" into "Conditioned BP"

97 Bug fixes:

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

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

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

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

102 and using log-domain updates

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

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

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

108 libDAI-0.2.3 (2009-11-16)

109 -------------------------

111 New features:

112 * Complete doxygen documentation (although more detailed documentation still

113 has to be written)

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

115 Expectation Maximization

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

117 octave interfaces

118 * Added Max-Product functionality to JTree

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

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

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

123 Code cleanup:

124 * Updated copyright headers

125 * Cleaned up error handling by introducing the DAI_THROWE macro

126 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern

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

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

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

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

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

133 Miscellaneous improvements:

134 * BipartiteGraph:

135 - Added eraseEdge( size_t n1, size_t n2 )

136 - [Frederik Eaton] Improved documentation of Neighbor

137 * TProb<T>:

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

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

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

141 - [Frederik Eaton] Added setUniform()

142 - [Frederik Eaton] Added sumAbs()

143 - [Frederik Eaton] Added argmax()

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

145 * TFactor<T>:

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

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

148 which reorders variables to canonical ordering before storing the table

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

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

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

152 * State:

153 - [Giuseppe Passino] Added prefix ++ operator

154 * Permute:

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

156 * FactorGraph:

157 - [Frederik Eaton] Added clampVar()

158 - [Frederik Eaton] Added clampFactor()

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

160 * PropertySet:

161 - Added keys(), for getting all keys

162 - [Frederik Eaton] Added default constructor

163 - [Frederik Eaton] Added constructor from string

164 * InfAlg:

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

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

167 * ExactInf:

168 - Added calcMarginal(const VarSet &)

169 * HAK:

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

171 * BP:

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

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

174 * JTree:

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

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

177 * MatLab interface:

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

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

180 (only for BP and JTree)

181 * README is now created automatically from doxygen documentation

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

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

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

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

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

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

188 alias substitutions

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

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

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

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

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

194 variables with the same labels

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

196 * Exception objects now remember their error code

197 * Examples:

198 - Moved example.cpp to examples/

199 - Added examples/example_bipgraph.cpp

200 - Added examples/example_varset.cpp

201 - Added examples/example_sprinkler.cpp

202 - Added examples/example_permute.cpp

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

205 Build system:

206 * Improved Makefile:

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

208 - Macros DAI_VERSION and DAI_DATE have been introduced,

209 in order to store this information in a central place

210 - Introduced CCNODEBUGFLAGS in Makefile

211 - Switched Makefile.win to GNU Make syntax

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

213 * Compatibility:

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

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

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

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

219 * Var:

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

221 * VarSet:

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

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

224 * Permute:

225 - Renamed convert_linear_index into convertLinearIndex

226 * TProb<>:

227 - Replaced log0() by log(true)

228 - Replaced takeLog0() by takeLog(true)

229 - Removed hasNonPositives()

230 - Renamed minVal() to min()

231 - Renamed maxVal() to max()

232 - Renamed totalSum() to sum()

233 * TFactor<>:

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

235 - Removed divided_by, use operator/ instead

236 - Removed divide, use operator/= instead

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

238 - Renamed minVal() to min()

239 - Renamed maxVal() to max()

240 - Renamed totalSum() to sum()

241 * FactorGraph:

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

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

244 * RegionGraph:

245 - Renamed Check_Counting_Numbers into checkCountingNumbers

246 - Renamed Calc_Counting_Numbers into calcCountingNumbers

247 * Miscellaneous:

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

249 - Replaced UEdgeVec by Graph

250 - Replaced DEdgeVec by new RootedTree class

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

252 - Merged calcPairBeliefsNew() into calcPairBeliefs()

253 - Removed calcMarginal2ndO()

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

255 - Removed class Diffs

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

257 BipartiteGraph and FactorGraph (which will be obsoleted soon)

259 Bug fixes:

260 * Fixed reversal of min and max in

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

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

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

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

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

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

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

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

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

270 for reporting this)

273 libDAI-0.2.2 (2008-09-30)

274 -------------------------

276 New features:

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

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

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

280 * Added ExactInf class for brute force exact inference.

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

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

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

284 of a double is too small.

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

286 * Improved documentation.

288 Improved architecture:

289 * Added Exceptions framework.

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

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

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

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

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

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

296 made easy by using boost::foreach.

297 * Added conditional compilation of inference methods.

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

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

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

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

302 specialization with T = Var.

303 * Improved ClusterGraph implementation, yielding significant speedups

304 for the JunctionTree algorithm on large factorgraphs.

306 Code cleanup:

307 * Moved everything into namespace "dai".

308 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

310 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

312 * Improved index.h:

313 - Renamed Index -> IndexFor

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

315 25% speedup of testregression

316 - Replaced multind by Permute

317 - Added MultiFor

318 - Added State

319 * New funcstionality of factor.h.

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

321 inference algorithm, because the Properties framework was not as

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

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

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

325 entangled) code.

326 * Removed x2x.

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

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

330 Miscellaneous improvements:

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

332 GCC under cygwin.

333 * Contributions by Peter Gober:

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

335 * Misc contributions by Giuseppe Passino:

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

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

338 - changed #ifndefs to GNU style;

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

340 - dai::TProb:

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

342 o implementation of some methods via STL algorithms;

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

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

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

346 * Misc contributions by Christian Wojek:

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

348 and variables;

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

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

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

352 normtype is now Prob::NORMPROB by default.

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

355 Interface changes:

356 * VarSet::

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

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

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

360 - removed bool operator||

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

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

363 * FactorGraph::

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

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

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

367 - vars() -> vars

368 - factors() -> factors

369 - removed MakeFactorCavity(size_t)

370 - removed ExactMarginal(const VarSet &)

371 - removed ExactlogZ()

372 - removed updatedFactor(size_t)

373 - removed _normtype and NormType()

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

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

376 - undoProb(size_t) -> restoreFactor(size_t)

377 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

382 - removed hasNegatives()

383 * RegionGraph::

384 - nr_ORs() -> nrORs()

385 - nr_IRs() -> nrIRs()

386 - ORs() -> ORs

387 - IRs() -> IRs

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

389 * Renamed Index -> IndexFor

390 * Diffs:

391 - max() -> maxDiff()

392 - max_size() -> maxSize()

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

394 * Factor::

395 - max() -> maxVal()

396 - part_sum() -> partSum()

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

398 * VarSet::operator&&

399 * Properties -> PropertySet

402 libDAI-0.2.1 (2008-05-26)

403 -------------------------

405 Bugfix release.

406 * added missing cstdio header in util.h

407 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

408 * added description of the factor graph fileformat

409 * improved Makefile

412 libDAI-0.2.0 (2006-11-30)

413 -------------------------

415 First public release.

418 0.1.5 (2006-11-30)

419 ------------------

421 Regressions

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

424 - EXACT method does not work anymore.

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

426 costs involved; inner loops should be optimized.

428 General framework

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

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

432 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

439 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

447 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

456 command line (test) interface.

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

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

459 amount of code for handling enum parameters.

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

461 work for all approximate inference methods.

463 Bugfixes

465 - Fixed GBP free energy.

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

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

468 the logical NOT of what they should return).

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

470 - Fixed bug in utils/create_dreg_fg:

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

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

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

474 that consists of one outer region only.

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

476 - Fixed MaxDiffs flow (except for MR).

478 New functionality

480 - HAK supports several default cluster choices:

481 minimal (only factors)

482 delta (Markov blankets)

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

484 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

496 It supports different initialization methods (the original RESPPROP,

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

498 (FULL and LINEAR).

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

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

501 marginals.

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

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

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

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

506 random factor graphs.

507 - Wrote utility to visualize factor graphs using graphviz.

508 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

516 - Added Martijn's x2x

518 Improvements of existing code

520 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

524 outer regions from the factors.

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

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

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

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

529 timing and convergence criteria.

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

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

532 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

540 marginal functions to approximate cavity marginals.

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

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

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

544 arguments, randomize(), RemoveFirstOrderInteractions) and similar

545 operations to Prob

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

547 (tests/test is done).

548 - Renamed some FactorGraph methods:

549 nr_vars -> nrVars

550 nr_factors -> nrFactors

551 varind -> findVar

552 factorind -> findFactor

553 makeFacCavity -> makeFactorCavity

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

555 - Implemented RandomDRegularGraph

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

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

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

559 disconnected factor graphs).

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

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

562 - Removed calcCavityDist and calcCavityDist2ndO

563 - No longer depends on GSL.

564 - Increased portability by combining platform dependant utility functions

565 in util.{h,cpp}.

566 - Wrote *.m files providing help

568 Testing framework

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

571 functionality from the command line.

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

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

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

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

576 errors, relative logZ error and MaxDiff().

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

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

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

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

581 allow for easy visualization of the results using PyX.

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

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

584 regression testing).

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

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

587 results stored in tests/testfast.out

589 Miscellaneous

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

592 - Experimental MATLAB code added for StarEP approximation on cavity

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

594 - Renamed JunctionTree to JTree.

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

596 - Improved README

599 revision 252

600 ------------

602 Functionality

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

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

605 RegionGraph.

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

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

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

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

610 and when not.

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

612 it does not automatically merge factors anymore.

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

614 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

619 Implementation / code

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

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

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

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

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

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

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

627 multiple inheritance and polymorphism.

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

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

630 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

644 instead of initial pancakes.

646 Minor changes

647 - Started writing DoxyGen documentation

648 - Renamed lcptab2fg.m matlab/ai_writefg.m

649 - Moved all matlab stuff to matlab/

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

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

652 - Improved testing suite.

653 - Removed logreal support.

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

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

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

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

658 - Added FactorGraph::WriteToDotFile

661 0.1.4 (2006-04-13)

662 ------------------

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

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

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

666 handle (partially) negative factors.

667 - Added test suite.

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

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

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

671 Now uses precalculated indices for optimization.

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

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

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

675 _parallel_ updates).

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

677 original single variable beliefs, for all AI methods.

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

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

680 (see ai.h).

683 0.1.3 (2006-03-22)

684 --------------------

685 - All AI methods now return maxdiff

686 - ai.cpp:

687 o Now returns maxdiffinner and maxdiffouter

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

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

690 - bp.cpp:

691 o New CavityDist2ndO which estimates 2nd order cavity interactions

692 - Makefile:

693 o Bugfix: removed dependencies on algwim.*

696 0.1.2 (2006-02-28)

697 --------------------

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

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

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

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

702 the output arguments Q, Q0 of ai).

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

706 0.1.1 (2006-02-28)

707 --------------------

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

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

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

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

712 of BipGraph checks for the existence of short loops.

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

714 description in the help).

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

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

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

720 0.1.0 (2006-02-28)

721 --------------------

722 First version worthy a version number.