1 git b6efbfd9e4e76de65c44e4060a9b56f99543b70a (head of branch eaton before merge)

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

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

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

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

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

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

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

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

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

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

12 * [Frederik Eaton]: Improved PropertySet class:

13 - Added default constructor

14 - Allow construction from string

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

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

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

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

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

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

21 BipartiteGraph and FactorGraph (which will be obsoleted soon)

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

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

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

25 distribution if no state is allowed

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

27 alias substitutions

28 * Interface changes:

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

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

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

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

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

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

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

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

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

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

39 operators

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

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

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

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

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

45 variables with the same labels

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

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

48 FactorGraph::end)

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

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

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

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

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

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

55 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where

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

57 errors (thanks to Dan Preston for reporting this)

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

59 * Exception objects now remember their error code

60 * Added examples/example_springler.cpp

63 git 065eae35cbfcc36f1a945ae3053c80c23f366306

64 --------------------------------------------

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

66 * [Frederik Eaton] Added Gibbs sampler to algorithms

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

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

69 Merged TODO and FILEFORMAT into doxygen documentation

70 * examples/

71 - Moved example.cpp to examples/

72 - Added examples/example_bipgraph.cpp

73 - Added examples/example_varset.cpp

74 * Interface changes:

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

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

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

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

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

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

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

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

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

84 * Miscellaneous small changes and cleanups:

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

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

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

88 - Cleanup of matlab interface code

89 - Small improvement of utils/fginfo

90 - Small cleanup of BP code

91 - Switched Makefile.win to GNU Make syntax

94 libDAI-0.2.2 (2008-09-30)

95 -------------------------

97 New features:

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

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

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

101 * Added ExactInf class for brute force exact inference.

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

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

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

105 of a double is too small.

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

107 * Improved documentation.

109 Improved architecture:

110 * Added Exceptions framework.

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

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

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

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

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

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

117 made easy by using boost::foreach.

118 * Added conditional compilation of inference methods.

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

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

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

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

123 specialization with T = Var.

124 * Improved ClusterGraph implementation, yielding significant speedups

125 for the JunctionTree algorithm on large factorgraphs.

127 Code cleanup:

128 * Moved everything into namespace "dai".

129 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.

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

131 * Removed utils/remove_short_loops and matlab/remove_short_loops.

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

133 * Improved index.h:

134 - Renamed Index -> IndexFor

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

136 25% speedup of testregression

137 - Replaced multind by Permute

138 - Added MultiFor

139 - Added State

140 * New funcstionality of factor.h.

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

142 inference algorithm, because the Properties framework was not as

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

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

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

146 entangled) code.

147 * Removed x2x.

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

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

151 Miscellaneous improvements:

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

153 GCC under cygwin.

154 * Contributions by Peter Gober:

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

156 * Misc contributions by Giuseppe Passino:

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

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

159 - changed #ifndefs to GNU style;

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

161 - dai::TProb:

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

163 o implementation of some methods via STL algorithms;

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

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

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

167 * Misc contributions by Christian Wojek:

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

169 and variables;

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

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

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

173 normtype is now Prob::NORMPROB by default.

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

176 Interface changes:

177 * VarSet::

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

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

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

181 - removed bool operator||

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

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

184 * FactorGraph::

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

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

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

188 - vars() -> vars

189 - factors() -> factors

190 - removed MakeFactorCavity(size_t)

191 - removed ExactMarginal(const VarSet &)

192 - removed ExactlogZ()

193 - removed updatedFactor(size_t)

194 - removed _normtype and NormType()

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

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

197 - undoProb(size_t) -> restoreFactor(size_t)

198 - saveProb(size_t) -> backupFactor(size_t)

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

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

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

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

203 - removed hasNegatives()

204 * RegionGraph::

205 - nr_ORs() -> nrORs()

206 - nr_IRs() -> nrIRs()

207 - ORs() -> ORs

208 - IRs() -> IRs

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

210 * Renamed Index -> IndexFor

211 * Diffs:

212 - max() -> maxDiff()

213 - max_size() -> maxSize()

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

215 * Factor::

216 - max() -> maxVal()

217 - part_sum() -> partSum()

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

219 * VarSet::operator&&

220 * Properties -> PropertySet

223 libDAI-0.2.1 (2008-05-26)

224 -------------------------

226 Bugfix release.

227 * added missing cstdio header in util.h

228 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*

229 * added description of the factor graph fileformat

230 * improved Makefile

233 libDAI-0.2.0 (2006-11-30)

234 -------------------------

236 First public release.

239 0.1.5 (2006-11-30)

240 ------------------

242 Regressions

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

245 - EXACT method does not work anymore.

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

247 costs involved; inner loops should be optimized.

249 General framework

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

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

253 functions to forward functionality from either FactorGraph or RegionGraph

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

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

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

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

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

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

260 (make FactorGraph part of InfAlg).

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

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

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

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

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

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

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

268 saveProbs/undoProbs can give a significant speed increase.

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

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

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

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

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

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

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

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

277 command line (test) interface.

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

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

280 amount of code for handling enum parameters.

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

282 work for all approximate inference methods.

284 Bugfixes

286 - Fixed GBP free energy.

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

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

289 the logical NOT of what they should return).

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

291 - Fixed bug in utils/create_dreg_fg:

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

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

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

295 that consists of one outer region only.

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

297 - Fixed MaxDiffs flow (except for MR).

299 New functionality

301 - HAK supports several default cluster choices:

302 minimal (only factors)

303 delta (Markov blankets)

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

305 Only the maximal clusters are used as outer clusters.

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

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

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

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

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

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

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

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

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

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

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

317 It supports different initialization methods (the original RESPPROP,

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

319 (FULL and LINEAR).

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

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

322 marginals.

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

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

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

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

327 random factor graphs.

328 - Wrote utility to visualize factor graphs using graphviz.

329 (it uses the BOOST Program Options library)

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

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

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

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

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

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

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

337 - Added Martijn's x2x

339 Improvements of existing code

341 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph

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

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

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

345 outer regions from the factors.

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

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

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

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

350 timing and convergence criteria.

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

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

353 hopefully this will give more accurate approximations.

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

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

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

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

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

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

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

361 marginal functions to approximate cavity marginals.

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

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

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

365 arguments, randomize(), RemoveFirstOrderInteractions) and similar

366 operations to Prob

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

368 (tests/test is done).

369 - Renamed some FactorGraph methods:

370 nr_vars -> nrVars

371 nr_factors -> nrFactors

372 varind -> findVar

373 factorind -> findFactor

374 makeFacCavity -> makeFactorCavity

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

376 - Implemented RandomDRegularGraph

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

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

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

380 disconnected factor graphs).

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

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

383 - Removed calcCavityDist and calcCavityDist2ndO

384 - No longer depends on GSL.

385 - Increased portability by combining platform dependant utility functions

386 in util.{h,cpp}.

387 - Wrote *.m files providing help

389 Testing framework

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

392 functionality from the command line.

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

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

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

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

397 errors, relative logZ error and MaxDiff().

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

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

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

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

402 allow for easy visualization of the results using PyX.

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

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

405 regression testing).

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

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

408 results stored in tests/testfast.out

410 Miscellaneous

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

413 - Experimental MATLAB code added for StarEP approximation on cavity

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

415 - Renamed JunctionTree to JTree.

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

417 - Improved README

420 revision 252

421 ------------

423 Functionality

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

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

426 RegionGraph.

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

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

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

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

431 and when not.

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

433 it does not automatically merge factors anymore.

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

435 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp

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

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

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

440 Implementation / code

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

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

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

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

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

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

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

448 multiple inheritance and polymorphism.

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

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

451 that can be used by FactorGraph-based DAIAlgs.

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

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

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

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

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

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

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

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

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

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

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

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

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

465 instead of initial pancakes.

467 Minor changes

468 - Started writing DoxyGen documentation

469 - Renamed lcptab2fg.m matlab/ai_writefg.m

470 - Moved all matlab stuff to matlab/

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

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

473 - Improved testing suite.

474 - Removed logreal support.

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

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

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

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

479 - Added FactorGraph::WriteToDotFile

482 0.1.4 (2006-04-13)

483 ------------------

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

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

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

487 handle (partially) negative factors.

488 - Added test suite.

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

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

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

492 Now uses precalculated indices for optimization.

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

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

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

496 _parallel_ updates).

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

498 original single variable beliefs, for all AI methods.

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

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

501 (see ai.h).

504 0.1.3 (2006-03-22)

505 --------------------

506 - All AI methods now return maxdiff

507 - ai.cpp:

508 o Now returns maxdiffinner and maxdiffouter

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

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

511 - bp.cpp:

512 o New CavityDist2ndO which estimates 2nd order cavity interactions

513 - Makefile:

514 o Bugfix: removed dependencies on algwim.*

517 0.1.2 (2006-02-28)

518 --------------------

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

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

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

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

523 the output arguments Q, Q0 of ai).

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

527 0.1.1 (2006-02-28)

528 --------------------

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

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

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

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

533 of BipGraph checks for the existence of short loops.

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

535 description in the help).

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

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

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

541 0.1.0 (2006-02-28)

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

543 First version worthy a version number.