Introduced DAI_DEBASSERT macro to abbreviate a common pattern
[libdai.git] / ChangeLog
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
8
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
106
107
108 libDAI-0.2.2 (2008-09-30)
109 -------------------------
110
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.
122
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.
140
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" :)).
164
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).
189
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
235
236
237 libDAI-0.2.1 (2008-05-26)
238 -------------------------
239
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
245
246
247 libDAI-0.2.0 (2006-11-30)
248 -------------------------
249
250 First public release.
251
252
253 0.1.5 (2006-11-30)
254 ------------------
255
256 Regressions
257
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.
262
263 General framework
264
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.
297
298 Bugfixes
299
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).
312
313 New functionality
314
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
352
353 Improvements of existing code
354
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
402
403 Testing framework
404
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
423
424 Miscellaneous
425
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
432
433
434 revision 252
435 ------------
436
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).
453
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.
480
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
494
495
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).
516
517
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.*
529
530
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.
539
540
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.
553
554
555 0.1.0 (2006-02-28)
556 --------------------
557 First version worthy a version number.