Merge branch 'pletscher'
[libdai.git] / ChangeLog
1 * Added init parameter to HAK/GBP to allow for random initialization
2 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
3 dai::Exception and is even active if NDEBUG is defined
4 * Added a constructor TProb<T>::TProb<T>( const std::vector<S> &v )
5 * Introduced CCNODEBUGFLAGS in Makefile
6 * Updated copyright headers
7 * Added max-product functionality to JTree
8 * [Charlie Vaske] EM bugfix (was using abs() instead of fabs() in
9 determining EM termination, which caused a loss of precision).
10 * [Charlie Vaske] New constructor in Permute for canonical variable ordering
11 * [Charlie Vaske] New constructor in Factor that reorders variables to canonical ordering
12 * [Charlie Vaske] New accessor in Properties for getting all keys
13 * [Charlie Vaske] New function for getting inferred parameters
14 * Cleaned up error handling by introducing the DAI_THROWE macro
15 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
16 * Changed FactorGraph::clamp and DAIAlg::clamp interfaces (the variable to be
17 clamped is now indicated by its index, not as a Var) and marked the old
18 interface as obsolete
19 * [Patrick Pletscher] Fixed performance issue in FactorGraph::clamp
20 * [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
21 (only for BP)
22 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
23
24 git ae0fc30e10be6683cbfc209dcee56f34234a6cb8
25 --------------------------------------------
26 * Added work-around for bug in Boost Graph Library
27 * Improvements of TFactor<T>:
28 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
29 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
30 * Added BipartiteGraph::eraseEdge
31 * Removed all the virtual default constructors *::create(), as they are not used.
32 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
33 * [Charlie Vaske] Added Expectation Maximization code.
34 * Added MatLab QuickStart to README.
35 * MEX file dai now also returns variable and factor beliefs.
36 * Cleanups and extra documentation of the code contributed by Frederik Eaton
37 * Removed erroneous 'inline' directives in gibbs.cpp
38 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
39 * [Frederik Eaton] Updated doxygen.conf to version 1.5.9
40 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
41 * [Frederik Eaton] Added FactorGraph::clampVar and FactorGraph::clampFactor
42 * [Frederik Eaton] Changed BP to be able to record order in which messages are sent (for use by BBP)
43 * [Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor
44 * [Frederik Eaton]: Extended InfAlg interface with beliefV() and beliefF() methods;
45 * [Frederik Eaton]: Improved PropertySet class:
46 - Added default constructor
47 - Allow construction from string
48 - Added method allKeys() to produce list of keys
49 - In getStringAs(), check for typeid(ValueType) before typeid(std::string)
50 (this fixes a strange bug for empty string property)
51 * [Frederik Eaton]: Added some utility macros (DAI_PV, DAI_DMSG, DAI_ACCMUT, DAI_IFVERB)
52 and functions (concat(),rnd()) to include/dai/util.h
53 * [Frederik Eaton] Added backwards compatibility layer for edge interface to
54 BipartiteGraph and FactorGraph (which will be obsoleted soon)
55 * [Frederik Eaton] Added BP_dual, BBP and CBP algorithms
56 * [Frederik Eaton] Added Gibbs::state() accessors/mutators
57 * [Frederik Eaton] Fixed Gibbs::getVarDist(size_t) to return uniform
58 distribution if no state is allowed
59 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
60 alias substitutions
61 * Interface changes:
62 TProb<T>::minVal() -> TProb<T>::min()
63 TFactor<T>::minVal() -> TFactor<T>::min()
64 TProb<T>::maxVal() -> TProb<T>::max()
65 TFactor<T>::maxVal() -> TFactor<T>::max()
66 TProb<T>::totalSum() -> TProb<T>sum()
67 TFactor<T>::totalSum() -> TFactor<T>::sum()
68 * [Frederik Eaton] Added methods setUniform (), sumAbs(), argmax() to TProb<T>
69 * [Frederik Eaton] Added TAGS, lib targets to Makefile
70 * [Frederik Eaton] Add useful aliases to aliases.conf
71 * [Frederik Eaton] Removed unnecessary copy constructors and assignment
72 operators
73 * [Frederik Eaton] Change cout to cerr in warnings and error messages
74 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
75 set instead of the linear search (which can yield enormous speedups - a
76 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
77 * Added debug assertions to Var which check for inconsistent dimensions of
78 variables with the same labels
79 * [Giuseppe Passino] Added prefix ++ operator to State (State::operator++())
80 * [Giuseppe Passino] Added iterators to FactorGraph (FactorGraph::begin,
81 FactorGraph::end)
82 * [Giuseppe Passino] Added iterators to TFactor (TFactor::begin, TFactor::end)
83 * [Giuseppe Passino] Added iterators to TProb (TProb::begin, TProb::end)
84 * [Giuseppe Passino] Added BP::findMaximum(), which can be used after running
85 max-product BP to construct a global state with maximum probability
86 * Improved Makefile (libDAI now also builds out-of-the-box on MacOSX,
87 thanks to Dan Preston; merged Makefile.win and Makefile.shared into Makefile)
88 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where
89 states with zero probability mass were clamped, leading to NaNs or assertion
90 errors (thanks to Dan Preston for reporting this)
91 * toc() now returns POSIX system time with maximum accuracy of microseconds
92 * Exception objects now remember their error code
93 * Added examples/example_sprinkler.cpp
94 * [Peter Gober] Made libDAI build out-of-the-box on Cygwin.
95 * [Frederik Eaton] Added Gibbs sampler to algorithms
96 * Improved documentation of include/dai/{bipgraph.h, prob.h, smallset.h,
97 var.h, varset.h, factor.h, enum.h} and of examples/example.cpp
98 Merged TODO and FILEFORMAT into doxygen documentation
99 * examples/
100 - Moved example.cpp to examples/
101 - Added examples/example_bipgraph.cpp
102 - Added examples/example_varset.cpp
103 * Interface changes:
104 - Replaced TProb<T>::log0() by TProb<T>::log(true)
105 - Replaced TProb<T>::takeLog0() by TProb<T>::takeLog(true)
106 - Replaced TFactor<T>::log0() by TFactor<T>::log(true)
107 - Removed TProb<T>::hasNonPositives()
108 - Renamed smallSet<T> to SmallSet<T>
109 - Removed TFactor<T>::divided_by, use operator/ instead
110 - Removed TFactor<T>::divide, use operator/= instead
111 - Removed TFactor<T>::partSum(const VarSet&), use marginal(const VarSet&,true) instead
112 - Improved constructors of TProb and TFactor to use iterators instead of pointers
113 * Miscellaneous small changes and cleanups:
114 - Changed regression test so that it also works under Windows
115 - Changed output stream operator<< for Var and VarSet
116 - Added TProb::draw() function, which draws a random index
117 - Cleanup of matlab interface code
118 - Small improvement of utils/fginfo
119 - Small cleanup of BP code
120 - Switched Makefile.win to GNU Make syntax
121
122
123 libDAI-0.2.2 (2008-09-30)
124 -------------------------
125
126 New features:
127 * Approximate inference methods now report the number of iterations needed.
128 * Added damping to various algorithms to improve convergence properties.
129 * Added more features to utils/createfg for creating factor graphs.
130 * Added ExactInf class for brute force exact inference.
131 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
132 whether calculations are done in the log-domain or in the linear domain;
133 doing calculations in the log-domain may help if the numerical range
134 of a double is too small.
135 * [Claudio Lima] Added Max-Product functionality to BP.
136 * Improved documentation.
137
138 Improved architecture:
139 * Added Exceptions framework.
140 * Pervasive change of BipartiteGraph implementation (based on an idea by
141 Giuseppe Passino). BipartiteGraph no longer stores the node properties
142 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
143 nor an edge list. Instead, it stores the graph structure as lists of
144 neighboring nodes. This yields a significant memory/speed improvement for
145 large factor graphs, and is more elegant as well. Iterating over neighbors is
146 made easy by using boost::foreach.
147 * Added conditional compilation of inference methods.
148 * VarSet is now implemented using a std::vector<Var> instead of a
149 std::set<Var>, which yields a significant speed improvement. Furthermore,
150 the implementation has been generalized, resulting in the small_set<T> class
151 which can be used to represent sets of small cardinality; VarSet is the
152 specialization with T = Var.
153 * Improved ClusterGraph implementation, yielding significant speedups
154 for the JunctionTree algorithm on large factorgraphs.
155
156 Code cleanup:
157 * Moved everything into namespace "dai".
158 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
159 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
160 * Removed utils/remove_short_loops and matlab/remove_short_loops.
161 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
162 * Improved index.h:
163 - Renamed Index -> IndexFor
164 - Added some .reserve()'s to IndexFor methods which yields a
165 25% speedup of testregression
166 - Replaced multind by Permute
167 - Added MultiFor
168 - Added State
169 * New funcstionality of factor.h.
170 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
171 inference algorithm, because the Properties framework was not as
172 convenient as I hoped, and not every inference algorithm needs a maxdiff
173 variable. Also, replaced some FactorGraph functionality in InfAlg by a
174 function that returns the FactorGraph. The result is cleaner (less
175 entangled) code.
176 * Removed x2x.
177 * Replaced Complex with real numbers (negative potentials are just too rare
178 to warrant the additional "complexity" :)).
179
180 Miscellaneous improvements:
181 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
182 GCC under cygwin.
183 * Contributions by Peter Gober:
184 - Renamed variable _N in mr.* for compatibility with g++ under cygwin.
185 * Misc contributions by Giuseppe Passino:
186 - removed "using namespace std;" from header files - bad practice;
187 - moved header files in include/dai and sources in src;
188 - changed #ifndefs to GNU style;
189 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
190 - dai::TProb:
191 o removed copy constructor and assignment operators (redundant);
192 o implementation of some methods via STL algorithms;
193 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
194 o explicit constructor (prevents implicit conversion from size_t to TProb);
195 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
196 * Misc contributions by Christian Wojek:
197 - New FactorGraph constructor that constructs from given ranges of factors
198 and variables;
199 - Optimization of FactorGraph constructors using tr1::unordered_map.
200 * FactorGraph constructors no longer check for short loops (huge speed
201 increase for large factor graphs), nor for negative entries. Also, the
202 normtype is now Prob::NORMPROB by default.
203 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
204
205 Interface changes:
206 * VarSet::
207 - VarSet::stateSpace() -> nrStates(const VarSet &)
208 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
209 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
210 - removed bool operator||
211 - operator&&(const VarSet&) -> intersects(const VarSet&)
212 - operator&&(const Var&) -> contains(const Var&)
213 * FactorGraph::
214 - delta(const Var &) -> delta(size_t)
215 - Delta(const Var &) -> Delta(size_t)
216 - makeCavity(const Var &) -> makeCavity(size_t)
217 - vars() -> vars
218 - factors() -> factors
219 - removed MakeFactorCavity(size_t)
220 - removed ExactMarginal(const VarSet &)
221 - removed ExactlogZ()
222 - removed updatedFactor(size_t)
223 - removed _normtype and NormType()
224 - removed hasShortLoops(...) and removeShortLoops(...)
225 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
226 - undoProb(size_t) -> restoreFactor(size_t)
227 - saveProb(size_t) -> backupFactor(size_t)
228 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
229 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
230 - ReadFromFile(const char*) returns void (throws on error)
231 - WriteToFile(const char*) returns void (throws on error)
232 - removed hasNegatives()
233 * RegionGraph::
234 - nr_ORs() -> nrORs()
235 - nr_IRs() -> nrIRs()
236 - ORs() -> ORs
237 - IRs() -> IRs
238 * *::Regenerate() -> *::construct()
239 * Renamed Index -> IndexFor
240 * Diffs:
241 - max() -> maxDiff()
242 - max_size() -> maxSize()
243 * Prob::max() -> Prob::maxVal()
244 * Factor::
245 - max() -> maxVal()
246 - part_sum() -> partSum()
247 * toc() in util.h now returns seconds as a double
248 * VarSet::operator&&
249 * Properties -> PropertySet
250
251
252 libDAI-0.2.1 (2008-05-26)
253 -------------------------
254
255 Bugfix release.
256 * added missing cstdio header in util.h
257 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
258 * added description of the factor graph fileformat
259 * improved Makefile
260
261
262 libDAI-0.2.0 (2006-11-30)
263 -------------------------
264
265 First public release.
266
267
268 0.1.5 (2006-11-30)
269 ------------------
270
271 Regressions
272
273 - tests/testlcbp and tests/testlcbp are broken.
274 - EXACT method does not work anymore.
275 - The Properties framework gives a speed penalty because of the lookup
276 costs involved; inner loops should be optimized.
277
278 General framework
279
280 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
281 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
282 functions to forward functionality from either FactorGraph or RegionGraph
283 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
284 and in RegionGraph and no explicit interface is needed in descendants.
285 - New abstract base class InfAlg added, representing an inference algorithm,
286 from which DAIAlg<T> inherits. This solves the incompatibility problems of
287 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
288 DAIAlg<RegionGraph>). More work is required to reduce code duplication
289 (make FactorGraph part of InfAlg).
290 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
291 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
292 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
293 one to save a few factors, modify them (e.g. clamp them), and then restore them
294 to their old values. Undo should also init the corresponding messages / beliefs.
295 This can be used if a given factor graph repeatedly needs to be clamped in
296 different ways and an approximation method is run for each clamping; using the
297 saveProbs/undoProbs can give a significant speed increase.
298 - Switched to a general Properties framework that handles the parameters of
299 all inference methods in a uniform manner. The Properties class is a map of
300 several properties in boost::any objects, indexed by their names (strings).
301 It can read from a stream and write to a stream. It is recursive, in the sense
302 that a Properties object can hold a variable of type Properties as well.
303 - Added a generic way of constructing inference algorithms from a factor graph,
304 name and properties object. Added the newInfAlg function which constructs
305 the requested object. This is used by LCBP, the Matlab interface and the
306 command line (test) interface.
307 - Added a generic enum framework for enum parameters. Although implemented as a
308 hack, it is quite useful in that it drastically simplifies and reduces the
309 amount of code for handling enum parameters.
310 - Provided generic functions for calculating marginals in different ways that
311 work for all approximate inference methods.
312
313 Bugfixes
314
315 - Fixed GBP free energy.
316 - Fixed bug in junctiontree (it didn't init the _vars variable).
317 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
318 the logical NOT of what they should return).
319 - Fixed bug in RegionGraph::RecomputeOR(s).
320 - Fixed bug in utils/create_dreg_fg:
321 graph structure was not random for given parameters (forgot to call srand()).
322 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
323 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
324 that consists of one outer region only.
325 - Fixed INIT bug in LCBP2::UpdatePancake().
326 - Fixed MaxDiffs flow (except for MR).
327
328 New functionality
329
330 - HAK supports several default cluster choices:
331 minimal (only factors)
332 delta (Markov blankets)
333 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
334 Only the maximal clusters are used as outer clusters.
335 - Implemented TreeEP. It generalizes the heuristic method described in the
336 Minka & Qi paper for obtaining a tree with the most relevant interactions to
337 higher order interactions. Almost all optimizations described in the Minka & Qi
338 paper are used, except that evidence is passed over the whole tree instead of
339 relevant subsets (the latter is almost implemented but buggy). Also added
340 alternative (worst-case) algorithm that uses a maximum spanning tree on the
341 weighted graph where the weight between neighbours i and j is given by
342 N(psi,i,j), where psi is the product of all the factors involving both i and j
343 (which is an upper bound on the effective interaction between i and j).
344 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
345 to be able to handle connectivities larger than 3 (in principle, up to 32).
346 It supports different initialization methods (the original RESPPROP,
347 the CLAMPING method and EXACT which uses JTree) and different update methods
348 (FULL and LINEAR).
349 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
350 networks and uses some approximate inference method on them for calculating
351 marginals.
352 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
353 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
354 interactions and LCBPL is LCBPI improved for higher-order interactions.
355 - Wrote one single program utils/createfg for creating various types of
356 random factor graphs.
357 - Wrote utility to visualize factor graphs using graphviz.
358 (it uses the BOOST Program Options library)
359 - Added fginfo utility that displays some info about a .fg file.
360 - Implemented Factor::strength function that calculates the potential strength
361 N(psi,i,j) between variables i and j as described in cs.IT:0504030
362 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
363 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
364 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
365 - Implemented a MATLAB interface ai_potstrength for Factor::strength
366 - Added Martijn's x2x
367
368 Improvements of existing code
369
370 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
371 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
372 associates outer region indices to factor indices (no powers yet, this
373 is deemed superfluous) and provides functions to recompute (some of) the
374 outer regions from the factors.
375 - InfAlg descendants run() methods now stop immediately and return NAN in case
376 they detect NANs. Only BP does not do NAN checking for performance reasons.
377 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
378 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
379 timing and convergence criteria.
380 - Implemented logZ() for JTree. It does the calculation during message-passing.
381 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
382 hopefully this will give more accurate approximations.
383 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
384 for a faster way of calculating marginals, which does not require a call to init()
385 nor cloning the whole object for each clamping. This leads to a significant speedup.
386 - LCBP (and LCBP2) now have complete flexibility in the specification of the
387 inner method, i.e. the method used to generate the initial cavity approximations.
388 One can pass two strings, a name and a properties string, and LCBP simply invokes
389 newInfAlg to construct the corresponding inference algorithm and uses the generic
390 marginal functions to approximate cavity marginals.
391 - Replaced the global "method" variable by local properties and removed ai.h
392 - Added some methods to Factor (operators *, *=, /, /= with doubles as
393 second argument, operators -, +=, -= with other Factors as second
394 arguments, randomize(), RemoveFirstOrderInteractions) and similar
395 operations to Prob
396 - Moving towards boost::program_options for handling command line arguments
397 (tests/test is done).
398 - Renamed some FactorGraph methods:
399 nr_vars -> nrVars
400 nr_factors -> nrFactors
401 varind -> findVar
402 factorind -> findFactor
403 makeFacCavity -> makeFactorCavity
404 - LCBP_SEQMAXRES has been removed because it did strange things.
405 - Implemented RandomDRegularGraph
406 - Implemented JTree::calcMarginal for marginals that are not confined
407 within one cluster (using cut-set conditioning).
408 - Added isConnected() method to FactorGraph (some methods do not work with
409 disconnected factor graphs).
410 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
411 - Removed single node interaction "correction" code from clamping methods
412 - Removed calcCavityDist and calcCavityDist2ndO
413 - No longer depends on GSL.
414 - Increased portability by combining platform dependant utility functions
415 in util.{h,cpp}.
416 - Wrote *.m files providing help
417
418 Testing framework
419
420 - Made a new and significantly improved testing framework that provides most
421 functionality from the command line.
422 - The basis is provided by tests/test, which uses the newInfAlg functionality
423 and enables the user to easily compare from the command line different
424 inference methods on a given factorgraph. All parameters can be specified.
425 Output consists of CPU time, average and maximum single variable marginal
426 errors, relative logZ error and MaxDiff().
427 - tests/aliases.conf contains aliases for standard combinations of methods
428 and their options (which can be used in tests/test).
429 - tests/large contains several bash/python scripts that create random factor
430 graphs, compare several approximate inference algorithms (using tests/test) and
431 allow for easy visualization of the results using PyX.
432 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
433 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
434 regression testing).
435 - Added a regression test to the Makefile which is included in the standard
436 target. It compares all inference methods on tests/testfast.fg with the
437 results stored in tests/testfast.out
438
439 Miscellaneous
440
441 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
442 - Experimental MATLAB code added for StarEP approximation on cavity
443 - Renamed project to libDAI and changed directory name accordingly.
444 - Renamed JunctionTree to JTree.
445 - Fixed licensing (now it's officially GPL).
446 - Improved README
447
448
449 revision 252
450 ------------
451
452 Functionality
453 - Added RegionGraph, GBP, CVM and HAK (double-loop).
454 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
455 RegionGraph.
456 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
457 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
458 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
459 it over all subsuming outer regions. See README for when negative factors are known to work
460 and when not.
461 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
462 it does not automatically merge factors anymore.
463 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
464 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
465 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
466 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
467 such that it does not store the complete pancakes, but represents them as little factor graphs).
468
469 Implementation / code
470 - Made a seperate type WeightedGraph, which until now only implements Prim's
471 maximal spanning tree algorithm and is only used by the junction tree code. It might
472 be good to make it a class somewhere in the future and extend it's interface.
473 - Made a seperate class ClusterGraph, which is only used by the junction tree
474 code. It's main purpose is a graph-theoretical variable elimination algorithm.
475 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
476 - Massive code cleanup, moving towards "generic" programming style, using
477 multiple inheritance and polymorphism.
478 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
479 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
480 that can be used by FactorGraph-based DAIAlgs.
481 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
482 and VarSet) and provides functionality for it (which is used by TFactor<T>).
483 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
484 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
485 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
486 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
487 o using Prob's instead of Factor's;
488 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
489 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
490 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
491 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
492 that takes the cavitydists and multiplies them with the relevant factors. This
493 resulted in an API change in AI which now accepts and returns initial cavitydists
494 instead of initial pancakes.
495
496 Minor changes
497 - Started writing DoxyGen documentation
498 - Renamed lcptab2fg.m matlab/ai_writefg.m
499 - Moved all matlab stuff to matlab/
500 - More detailed reporting (also reports clocks used).
501 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
502 - Improved testing suite.
503 - Removed logreal support.
504 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
505 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
506 full and periodic 2D Ising networks according to some command line parameters.
507 - Now logZ really returns logZ instead of -logZ.
508 - Added FactorGraph::WriteToDotFile
509
510
511 0.1.4 (2006-04-13)
512 ------------------
513 - Added file IO routines to read and write factorgraphs.
514 - Added L-infinity normalization for use with (partially) negative factors.
515 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
516 handle (partially) negative factors.
517 - Added test suite.
518 - All probabilities are now represented using double instead of LogReal<double>.
519 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
520 - Combined several variants of BP into doBP. Several update schemes possible.
521 Now uses precalculated indices for optimization.
522 - Renamed Node -> Var and Potential -> Factor.
523 - Extensive code cleanup. More use of OO techniques. Changed API.
524 - MaxIter now means maximum number of passes (corresponding to number of
525 _parallel_ updates).
526 - MaxDiff now means the maximum L-infinity distance between the updated and
527 original single variable beliefs, for all AI methods.
528 - Implemented RBP which converges faster than BP for difficult problems.
529 - Now uses method parameter which is a bitmask combining outmethod and inmethod
530 (see ai.h).
531
532
533 0.1.3 (2006-03-22)
534 --------------------
535 - All AI methods now return maxdiff
536 - ai.cpp:
537 o Now returns maxdiffinner and maxdiffouter
538 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
539 o New InitCav outermethod (only create initial cavity distributions)
540 - bp.cpp:
541 o New CavityDist2ndO which estimates 2nd order cavity interactions
542 - Makefile:
543 o Bugfix: removed dependencies on algwim.*
544
545
546 0.1.2 (2006-02-28)
547 --------------------
548 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
549 - Added the possibility to provide initial cavity distributions as an input
550 argument to ai (not much error checking is done, so be careful).
551 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
552 the output arguments Q, Q0 of ai).
553 - Removed algwim.* since it does not work.
554
555
556 0.1.1 (2006-02-28)
557 --------------------
558 - The constructors of (Log)FactorGraph and LogFactorGraph from a
559 vector<(Log)Potential> now merge potentials to prevent short loops (of length
560 4) in the factor graph. These are used in ai to construct the factor graphs
561 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
562 of BipGraph checks for the existence of short loops.
563 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
564 description in the help).
565 - ai does not hook cout anymore (which caused weird segfaults).
566 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
567 - Removed network.* since it is not useful.
568
569
570 0.1.0 (2006-02-28)
571 --------------------
572 First version worthy a version number.