1 * Changed FactorGraph::clamp and DAIAlg::clamp interfaces (the variable to be

2 clamped is now indicated by its index, not as a Var) and marked the old

3 interface as obsolete

4 * [Patrick Pletscher] Fixed performance issue in FactorGraph::clamp

5 * [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state

6 (only for BP)

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

9 git ae0fc30e10be6683cbfc209dcee56f34234a6cb8

10 --------------------------------------------

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

12 * Improvements of TFactor<T>:

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

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

15 * Added BipartiteGraph::eraseEdge

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

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

18 * [Charlie Vaske] Added Expectation Maximization code.

19 * Added MatLab QuickStart to README.

20 * MEX file dai now also returns variable and factor beliefs.

21 * Cleanups and extra documentation of the code contributed by Frederik Eaton

22 * Removed erroneous 'inline' directives in gibbs.cpp

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

24 * [Frederik Eaton] Updated doxygen.conf to version 1.5.9

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

26 * [Frederik Eaton] Added FactorGraph::clampVar and FactorGraph::clampFactor

27 * [Frederik Eaton] Changed BP to be able to record order in which messages are sent (for use by BBP)

28 * [Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor

29 * [Frederik Eaton]: Extended InfAlg interface with beliefV() and beliefF() methods;

30 * [Frederik Eaton]: Improved PropertySet class:

31 - Added default constructor

32 - Allow construction from string

33 - Added method allKeys() to produce list of keys

34 - In getStringAs(), check for typeid(ValueType) before typeid(std::string)

35 (this fixes a strange bug for empty string property)

36 * [Frederik Eaton]: Added some utility macros (DAI_PV, DAI_DMSG, DAI_ACCMUT, DAI_IFVERB)

37 and functions (concat(),rnd()) to include/dai/util.h

38 * [Frederik Eaton] Added backwards compatibility layer for edge interface to

39 BipartiteGraph and FactorGraph (which will be obsoleted soon)

40 * [Frederik Eaton] Added BP_dual, BBP and CBP algorithms

41 * [Frederik Eaton] Added Gibbs::state() accessors/mutators

42 * [Frederik Eaton] Fixed Gibbs::getVarDist(size_t) to return uniform

43 distribution if no state is allowed

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

45 alias substitutions

46 * Interface changes:

47 TProb<T>::minVal() -> TProb<T>::min()

48 TFactor<T>::minVal() -> TFactor<T>::min()

49 TProb<T>::maxVal() -> TProb<T>::max()

50 TFactor<T>::maxVal() -> TFactor<T>::max()

51 TProb<T>::totalSum() -> TProb<T>sum()

52 TFactor<T>::totalSum() -> TFactor<T>::sum()

53 * [Frederik Eaton] Added methods setUniform (), sumAbs(), argmax() to TProb<T>

54 * [Frederik Eaton] Added TAGS, lib targets to Makefile

55 * [Frederik Eaton] Add useful aliases to aliases.conf

56 * [Frederik Eaton] Removed unnecessary copy constructors and assignment

57 operators

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

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

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

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

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

63 variables with the same labels

64 * [Giuseppe Passino] Added prefix ++ operator to State (State::operator++())

65 * [Giuseppe Passino] Added iterators to FactorGraph (FactorGraph::begin,

66 FactorGraph::end)

67 * [Giuseppe Passino] Added iterators to TFactor (TFactor::begin, TFactor::end)

68 * [Giuseppe Passino] Added iterators to TProb (TProb::begin, TProb::end)

69 * [Giuseppe Passino] Added BP::findMaximum(), which can be used after running

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

71 * Improved Makefile (libDAI now also builds out-of-the-box on MacOSX,

72 thanks to Dan Preston; merged Makefile.win and Makefile.shared into Makefile)

73 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where

74 states with zero probability mass were clamped, leading to NaNs or assertion

75 errors (thanks to Dan Preston for reporting this)

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

77 * Exception objects now remember their error code

78 * Added examples/example_sprinkler.cpp

79 * [Peter Gober] Made libDAI build out-of-the-box on Cygwin.

80 * [Frederik Eaton] Added Gibbs sampler to algorithms

81 * Improved documentation of include/dai/{bipgraph.h, prob.h, smallset.h,

82 var.h, varset.h, factor.h, enum.h} and of examples/example.cpp

83 Merged TODO and FILEFORMAT into doxygen documentation

84 * examples/

85 - Moved example.cpp to examples/

86 - Added examples/example_bipgraph.cpp

87 - Added examples/example_varset.cpp

88 * Interface changes:

89 - Replaced TProb<T>::log0() by TProb<T>::log(true)

90 - Replaced TProb<T>::takeLog0() by TProb<T>::takeLog(true)

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

92 - Removed TProb<T>::hasNonPositives()

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

94 - Removed TFactor<T>::divided_by, use operator/ instead

95 - Removed TFactor<T>::divide, use operator/= instead

96 - Removed TFactor<T>::partSum(const VarSet&), use marginal(const VarSet&,true) instead

97 - Improved constructors of TProb and TFactor to use iterators instead of pointers

98 * Miscellaneous small changes and cleanups:

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

100 - Changed output stream operator<< for Var and VarSet

101 - Added TProb::draw() function, which draws a random index

102 - Cleanup of matlab interface code

103 - Small improvement of utils/fginfo

104 - Small cleanup of BP code

105 - Switched Makefile.win to GNU Make syntax

108 libDAI-0.2.2 (2008-09-30)

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

111 New features:

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

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

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

115 * Added ExactInf class for brute force exact inference.

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

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

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

119 of a double is too small.

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

121 * Improved documentation.

123 Improved architecture:

124 * Added Exceptions framework.

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

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

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

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

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

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

131 made easy by using boost::foreach.

132 * Added conditional compilation of inference methods.

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

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

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

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

137 specialization with T = Var.

138 * Improved ClusterGraph implementation, yielding significant speedups

139 for the JunctionTree algorithm on large factorgraphs.

141 Code cleanup:

142 * Moved everything into namespace "dai".

143 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

145 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

147 * Improved index.h:

148 - Renamed Index -> IndexFor

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

150 25% speedup of testregression

151 - Replaced multind by Permute

152 - Added MultiFor

153 - Added State

154 * New funcstionality of factor.h.

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

156 inference algorithm, because the Properties framework was not as

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

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

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

160 entangled) code.

161 * Removed x2x.

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

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

165 Miscellaneous improvements:

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

167 GCC under cygwin.

168 * Contributions by Peter Gober:

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

170 * Misc contributions by Giuseppe Passino:

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

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

173 - changed #ifndefs to GNU style;

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

175 - dai::TProb:

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

177 o implementation of some methods via STL algorithms;

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

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

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

181 * Misc contributions by Christian Wojek:

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

183 and variables;

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

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

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

187 normtype is now Prob::NORMPROB by default.

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

190 Interface changes:

191 * VarSet::

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

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

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

195 - removed bool operator||

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

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

198 * FactorGraph::

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

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

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

202 - vars() -> vars

203 - factors() -> factors

204 - removed MakeFactorCavity(size_t)

205 - removed ExactMarginal(const VarSet &)

206 - removed ExactlogZ()

207 - removed updatedFactor(size_t)

208 - removed _normtype and NormType()

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

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

211 - undoProb(size_t) -> restoreFactor(size_t)

212 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

217 - removed hasNegatives()

218 * RegionGraph::

219 - nr_ORs() -> nrORs()

220 - nr_IRs() -> nrIRs()

221 - ORs() -> ORs

222 - IRs() -> IRs

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

224 * Renamed Index -> IndexFor

225 * Diffs:

226 - max() -> maxDiff()

227 - max_size() -> maxSize()

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

229 * Factor::

230 - max() -> maxVal()

231 - part_sum() -> partSum()

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

233 * VarSet::operator&&

234 * Properties -> PropertySet

237 libDAI-0.2.1 (2008-05-26)

238 -------------------------

240 Bugfix release.

241 * added missing cstdio header in util.h

242 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

243 * added description of the factor graph fileformat

244 * improved Makefile

247 libDAI-0.2.0 (2006-11-30)

248 -------------------------

250 First public release.

253 0.1.5 (2006-11-30)

254 ------------------

256 Regressions

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

259 - EXACT method does not work anymore.

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

261 costs involved; inner loops should be optimized.

263 General framework

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

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

267 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

274 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

282 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

291 command line (test) interface.

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

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

294 amount of code for handling enum parameters.

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

296 work for all approximate inference methods.

298 Bugfixes

300 - Fixed GBP free energy.

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

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

303 the logical NOT of what they should return).

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

305 - Fixed bug in utils/create_dreg_fg:

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

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

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

309 that consists of one outer region only.

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

311 - Fixed MaxDiffs flow (except for MR).

313 New functionality

315 - HAK supports several default cluster choices:

316 minimal (only factors)

317 delta (Markov blankets)

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

319 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

331 It supports different initialization methods (the original RESPPROP,

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

333 (FULL and LINEAR).

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

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

336 marginals.

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

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

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

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

341 random factor graphs.

342 - Wrote utility to visualize factor graphs using graphviz.

343 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

351 - Added Martijn's x2x

353 Improvements of existing code

355 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

359 outer regions from the factors.

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

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

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

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

364 timing and convergence criteria.

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

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

367 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

375 marginal functions to approximate cavity marginals.

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

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

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

379 arguments, randomize(), RemoveFirstOrderInteractions) and similar

380 operations to Prob

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

382 (tests/test is done).

383 - Renamed some FactorGraph methods:

384 nr_vars -> nrVars

385 nr_factors -> nrFactors

386 varind -> findVar

387 factorind -> findFactor

388 makeFacCavity -> makeFactorCavity

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

390 - Implemented RandomDRegularGraph

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

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

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

394 disconnected factor graphs).

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

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

397 - Removed calcCavityDist and calcCavityDist2ndO

398 - No longer depends on GSL.

399 - Increased portability by combining platform dependant utility functions

400 in util.{h,cpp}.

401 - Wrote *.m files providing help

403 Testing framework

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

406 functionality from the command line.

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

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

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

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

411 errors, relative logZ error and MaxDiff().

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

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

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

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

416 allow for easy visualization of the results using PyX.

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

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

419 regression testing).

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

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

422 results stored in tests/testfast.out

424 Miscellaneous

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

427 - Experimental MATLAB code added for StarEP approximation on cavity

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

429 - Renamed JunctionTree to JTree.

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

431 - Improved README

434 revision 252

435 ------------

437 Functionality

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

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

440 RegionGraph.

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

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

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

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

445 and when not.

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

447 it does not automatically merge factors anymore.

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

449 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

454 Implementation / code

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

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

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

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

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

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

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

462 multiple inheritance and polymorphism.

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

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

465 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

479 instead of initial pancakes.

481 Minor changes

482 - Started writing DoxyGen documentation

483 - Renamed lcptab2fg.m matlab/ai_writefg.m

484 - Moved all matlab stuff to matlab/

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

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

487 - Improved testing suite.

488 - Removed logreal support.

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

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

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

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

493 - Added FactorGraph::WriteToDotFile

496 0.1.4 (2006-04-13)

497 ------------------

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

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

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

501 handle (partially) negative factors.

502 - Added test suite.

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

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

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

506 Now uses precalculated indices for optimization.

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

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

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

510 _parallel_ updates).

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

512 original single variable beliefs, for all AI methods.

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

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

515 (see ai.h).

518 0.1.3 (2006-03-22)

519 --------------------

520 - All AI methods now return maxdiff

521 - ai.cpp:

522 o Now returns maxdiffinner and maxdiffouter

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

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

525 - bp.cpp:

526 o New CavityDist2ndO which estimates 2nd order cavity interactions

527 - Makefile:

528 o Bugfix: removed dependencies on algwim.*

531 0.1.2 (2006-02-28)

532 --------------------

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

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

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

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

537 the output arguments Q, Q0 of ai).

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

541 0.1.1 (2006-02-28)

542 --------------------

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

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

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

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

547 of BipGraph checks for the existence of short loops.

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

549 description in the help).

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

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

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

555 0.1.0 (2006-02-28)

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

557 First version worthy a version number.