Improved documentation of include/dai/index.h
[libdai.git] / ChangeLog
1 * Renamed Permute::convert_linear_index into Permute::convertLinearIndex
2 (and provided an alias for backwards compatibility)
3 * Added examples/example_permute.cpp
4 * Added TProb<T>::divided_by(const TProb<T>&) const
5 * Fixed bug in BipartiteGraph::eraseEdge()
6 * Added python and octave ports for examples/example_sprinkler.cpp
7 * [Patrick Pletscher] Added SWIG wrapper code for python and octave
8 * Added init parameter to HAK/GBP to allow for random initialization
9 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
10 dai::Exception and is even active if NDEBUG is defined
11 * Added a constructor TProb<T>::TProb<T>( const std::vector<S> &v )
12 * Introduced CCNODEBUGFLAGS in Makefile
13 * Updated copyright headers
14 * Added max-product functionality to JTree
15 * [Charlie Vaske] EM bugfix (was using abs() instead of fabs() in
16 determining EM termination, which caused a loss of precision).
17 * [Charlie Vaske] New constructor in Permute for canonical variable ordering
18 * [Charlie Vaske] New constructor in Factor that reorders variables to canonical ordering
19 * [Charlie Vaske] New accessor in Properties for getting all keys
20 * [Charlie Vaske] New function for getting inferred parameters
21 * Cleaned up error handling by introducing the DAI_THROWE macro
22 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
23 * Changed FactorGraph::clamp and DAIAlg::clamp interfaces (the variable to be
24 clamped is now indicated by its index, not as a Var) and marked the old
25 interface as obsolete
26 * [Patrick Pletscher] Fixed performance issue in FactorGraph::clamp
27 * [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
28 (only for BP)
29 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
30
31 git ae0fc30e10be6683cbfc209dcee56f34234a6cb8
32 --------------------------------------------
33 * Added work-around for bug in Boost Graph Library
34 * Improvements of TFactor<T>:
35 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
36 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
37 * Added BipartiteGraph::eraseEdge
38 * Removed all the virtual default constructors *::create(), as they are not used.
39 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
40 * [Charlie Vaske] Added Expectation Maximization code.
41 * Added MatLab QuickStart to README.
42 * MEX file dai now also returns variable and factor beliefs.
43 * Cleanups and extra documentation of the code contributed by Frederik Eaton
44 * Removed erroneous 'inline' directives in gibbs.cpp
45 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
46 * [Frederik Eaton] Updated doxygen.conf to version 1.5.9
47 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
48 * [Frederik Eaton] Added FactorGraph::clampVar and FactorGraph::clampFactor
49 * [Frederik Eaton] Changed BP to be able to record order in which messages are sent (for use by BBP)
50 * [Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor
51 * [Frederik Eaton]: Extended InfAlg interface with beliefV() and beliefF() methods;
52 * [Frederik Eaton]: Improved PropertySet class:
53 - Added default constructor
54 - Allow construction from string
55 - Added method allKeys() to produce list of keys
56 - In getStringAs(), check for typeid(ValueType) before typeid(std::string)
57 (this fixes a strange bug for empty string property)
58 * [Frederik Eaton]: Added some utility macros (DAI_PV, DAI_DMSG, DAI_ACCMUT, DAI_IFVERB)
59 and functions (concat(),rnd()) to include/dai/util.h
60 * [Frederik Eaton] Added backwards compatibility layer for edge interface to
61 BipartiteGraph and FactorGraph (which will be obsoleted soon)
62 * [Frederik Eaton] Added BP_dual, BBP and CBP algorithms
63 * [Frederik Eaton] Added Gibbs::state() accessors/mutators
64 * [Frederik Eaton] Fixed Gibbs::getVarDist(size_t) to return uniform
65 distribution if no state is allowed
66 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
67 alias substitutions
68 * Interface changes:
69 TProb<T>::minVal() -> TProb<T>::min()
70 TFactor<T>::minVal() -> TFactor<T>::min()
71 TProb<T>::maxVal() -> TProb<T>::max()
72 TFactor<T>::maxVal() -> TFactor<T>::max()
73 TProb<T>::totalSum() -> TProb<T>sum()
74 TFactor<T>::totalSum() -> TFactor<T>::sum()
75 * [Frederik Eaton] Added methods setUniform (), sumAbs(), argmax() to TProb<T>
76 * [Frederik Eaton] Added TAGS, lib targets to Makefile
77 * [Frederik Eaton] Add useful aliases to aliases.conf
78 * [Frederik Eaton] Removed unnecessary copy constructors and assignment
79 operators
80 * [Frederik Eaton] Change cout to cerr in warnings and error messages
81 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
82 set instead of the linear search (which can yield enormous speedups - a
83 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
84 * Added debug assertions to Var which check for inconsistent dimensions of
85 variables with the same labels
86 * [Giuseppe Passino] Added prefix ++ operator to State (State::operator++())
87 * [Giuseppe Passino] Added iterators to FactorGraph (FactorGraph::begin,
88 FactorGraph::end)
89 * [Giuseppe Passino] Added iterators to TFactor (TFactor::begin, TFactor::end)
90 * [Giuseppe Passino] Added iterators to TProb (TProb::begin, TProb::end)
91 * [Giuseppe Passino] Added BP::findMaximum(), which can be used after running
92 max-product BP to construct a global state with maximum probability
93 * Improved Makefile (libDAI now also builds out-of-the-box on MacOSX,
94 thanks to Dan Preston; merged Makefile.win and Makefile.shared into Makefile)
95 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where
96 states with zero probability mass were clamped, leading to NaNs or assertion
97 errors (thanks to Dan Preston for reporting this)
98 * toc() now returns POSIX system time with maximum accuracy of microseconds
99 * Exception objects now remember their error code
100 * Added examples/example_sprinkler.cpp
101 * [Peter Gober] Made libDAI build out-of-the-box on Cygwin.
102 * [Frederik Eaton] Added Gibbs sampler to algorithms
103 * Improved documentation of include/dai/{bipgraph.h, prob.h, smallset.h,
104 var.h, varset.h, factor.h, enum.h} and of examples/example.cpp
105 Merged TODO and FILEFORMAT into doxygen documentation
106 * examples/
107 - Moved example.cpp to examples/
108 - Added examples/example_bipgraph.cpp
109 - Added examples/example_varset.cpp
110 * Interface changes:
111 - Replaced TProb<T>::log0() by TProb<T>::log(true)
112 - Replaced TProb<T>::takeLog0() by TProb<T>::takeLog(true)
113 - Replaced TFactor<T>::log0() by TFactor<T>::log(true)
114 - Removed TProb<T>::hasNonPositives()
115 - Renamed smallSet<T> to SmallSet<T>
116 - Removed TFactor<T>::divided_by, use operator/ instead
117 - Removed TFactor<T>::divide, use operator/= instead
118 - Removed TFactor<T>::partSum(const VarSet&), use marginal(const VarSet&,true) instead
119 - Improved constructors of TProb and TFactor to use iterators instead of pointers
120 * Miscellaneous small changes and cleanups:
121 - Changed regression test so that it also works under Windows
122 - Changed output stream operator<< for Var and VarSet
123 - Added TProb::draw() function, which draws a random index
124 - Cleanup of matlab interface code
125 - Small improvement of utils/fginfo
126 - Small cleanup of BP code
127 - Switched Makefile.win to GNU Make syntax
128
129
130 libDAI-0.2.2 (2008-09-30)
131 -------------------------
132
133 New features:
134 * Approximate inference methods now report the number of iterations needed.
135 * Added damping to various algorithms to improve convergence properties.
136 * Added more features to utils/createfg for creating factor graphs.
137 * Added ExactInf class for brute force exact inference.
138 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
139 whether calculations are done in the log-domain or in the linear domain;
140 doing calculations in the log-domain may help if the numerical range
141 of a double is too small.
142 * [Claudio Lima] Added Max-Product functionality to BP.
143 * Improved documentation.
144
145 Improved architecture:
146 * Added Exceptions framework.
147 * Pervasive change of BipartiteGraph implementation (based on an idea by
148 Giuseppe Passino). BipartiteGraph no longer stores the node properties
149 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
150 nor an edge list. Instead, it stores the graph structure as lists of
151 neighboring nodes. This yields a significant memory/speed improvement for
152 large factor graphs, and is more elegant as well. Iterating over neighbors is
153 made easy by using boost::foreach.
154 * Added conditional compilation of inference methods.
155 * VarSet is now implemented using a std::vector<Var> instead of a
156 std::set<Var>, which yields a significant speed improvement. Furthermore,
157 the implementation has been generalized, resulting in the small_set<T> class
158 which can be used to represent sets of small cardinality; VarSet is the
159 specialization with T = Var.
160 * Improved ClusterGraph implementation, yielding significant speedups
161 for the JunctionTree algorithm on large factorgraphs.
162
163 Code cleanup:
164 * Moved everything into namespace "dai".
165 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
166 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
167 * Removed utils/remove_short_loops and matlab/remove_short_loops.
168 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
169 * Improved index.h:
170 - Renamed Index -> IndexFor
171 - Added some .reserve()'s to IndexFor methods which yields a
172 25% speedup of testregression
173 - Replaced multind by Permute
174 - Added MultiFor
175 - Added State
176 * New funcstionality of factor.h.
177 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
178 inference algorithm, because the Properties framework was not as
179 convenient as I hoped, and not every inference algorithm needs a maxdiff
180 variable. Also, replaced some FactorGraph functionality in InfAlg by a
181 function that returns the FactorGraph. The result is cleaner (less
182 entangled) code.
183 * Removed x2x.
184 * Replaced Complex with real numbers (negative potentials are just too rare
185 to warrant the additional "complexity" :)).
186
187 Miscellaneous improvements:
188 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
189 GCC under cygwin.
190 * Contributions by Peter Gober:
191 - Renamed variable _N in mr.* for compatibility with g++ under cygwin.
192 * Misc contributions by Giuseppe Passino:
193 - removed "using namespace std;" from header files - bad practice;
194 - moved header files in include/dai and sources in src;
195 - changed #ifndefs to GNU style;
196 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
197 - dai::TProb:
198 o removed copy constructor and assignment operators (redundant);
199 o implementation of some methods via STL algorithms;
200 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
201 o explicit constructor (prevents implicit conversion from size_t to TProb);
202 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
203 * Misc contributions by Christian Wojek:
204 - New FactorGraph constructor that constructs from given ranges of factors
205 and variables;
206 - Optimization of FactorGraph constructors using tr1::unordered_map.
207 * FactorGraph constructors no longer check for short loops (huge speed
208 increase for large factor graphs), nor for negative entries. Also, the
209 normtype is now Prob::NORMPROB by default.
210 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
211
212 Interface changes:
213 * VarSet::
214 - VarSet::stateSpace() -> nrStates(const VarSet &)
215 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
216 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
217 - removed bool operator||
218 - operator&&(const VarSet&) -> intersects(const VarSet&)
219 - operator&&(const Var&) -> contains(const Var&)
220 * FactorGraph::
221 - delta(const Var &) -> delta(size_t)
222 - Delta(const Var &) -> Delta(size_t)
223 - makeCavity(const Var &) -> makeCavity(size_t)
224 - vars() -> vars
225 - factors() -> factors
226 - removed MakeFactorCavity(size_t)
227 - removed ExactMarginal(const VarSet &)
228 - removed ExactlogZ()
229 - removed updatedFactor(size_t)
230 - removed _normtype and NormType()
231 - removed hasShortLoops(...) and removeShortLoops(...)
232 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
233 - undoProb(size_t) -> restoreFactor(size_t)
234 - saveProb(size_t) -> backupFactor(size_t)
235 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
236 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
237 - ReadFromFile(const char*) returns void (throws on error)
238 - WriteToFile(const char*) returns void (throws on error)
239 - removed hasNegatives()
240 * RegionGraph::
241 - nr_ORs() -> nrORs()
242 - nr_IRs() -> nrIRs()
243 - ORs() -> ORs
244 - IRs() -> IRs
245 * *::Regenerate() -> *::construct()
246 * Renamed Index -> IndexFor
247 * Diffs:
248 - max() -> maxDiff()
249 - max_size() -> maxSize()
250 * Prob::max() -> Prob::maxVal()
251 * Factor::
252 - max() -> maxVal()
253 - part_sum() -> partSum()
254 * toc() in util.h now returns seconds as a double
255 * VarSet::operator&&
256 * Properties -> PropertySet
257
258
259 libDAI-0.2.1 (2008-05-26)
260 -------------------------
261
262 Bugfix release.
263 * added missing cstdio header in util.h
264 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
265 * added description of the factor graph fileformat
266 * improved Makefile
267
268
269 libDAI-0.2.0 (2006-11-30)
270 -------------------------
271
272 First public release.
273
274
275 0.1.5 (2006-11-30)
276 ------------------
277
278 Regressions
279
280 - tests/testlcbp and tests/testlcbp are broken.
281 - EXACT method does not work anymore.
282 - The Properties framework gives a speed penalty because of the lookup
283 costs involved; inner loops should be optimized.
284
285 General framework
286
287 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
288 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
289 functions to forward functionality from either FactorGraph or RegionGraph
290 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
291 and in RegionGraph and no explicit interface is needed in descendants.
292 - New abstract base class InfAlg added, representing an inference algorithm,
293 from which DAIAlg<T> inherits. This solves the incompatibility problems of
294 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
295 DAIAlg<RegionGraph>). More work is required to reduce code duplication
296 (make FactorGraph part of InfAlg).
297 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
298 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
299 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
300 one to save a few factors, modify them (e.g. clamp them), and then restore them
301 to their old values. Undo should also init the corresponding messages / beliefs.
302 This can be used if a given factor graph repeatedly needs to be clamped in
303 different ways and an approximation method is run for each clamping; using the
304 saveProbs/undoProbs can give a significant speed increase.
305 - Switched to a general Properties framework that handles the parameters of
306 all inference methods in a uniform manner. The Properties class is a map of
307 several properties in boost::any objects, indexed by their names (strings).
308 It can read from a stream and write to a stream. It is recursive, in the sense
309 that a Properties object can hold a variable of type Properties as well.
310 - Added a generic way of constructing inference algorithms from a factor graph,
311 name and properties object. Added the newInfAlg function which constructs
312 the requested object. This is used by LCBP, the Matlab interface and the
313 command line (test) interface.
314 - Added a generic enum framework for enum parameters. Although implemented as a
315 hack, it is quite useful in that it drastically simplifies and reduces the
316 amount of code for handling enum parameters.
317 - Provided generic functions for calculating marginals in different ways that
318 work for all approximate inference methods.
319
320 Bugfixes
321
322 - Fixed GBP free energy.
323 - Fixed bug in junctiontree (it didn't init the _vars variable).
324 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
325 the logical NOT of what they should return).
326 - Fixed bug in RegionGraph::RecomputeOR(s).
327 - Fixed bug in utils/create_dreg_fg:
328 graph structure was not random for given parameters (forgot to call srand()).
329 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
330 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
331 that consists of one outer region only.
332 - Fixed INIT bug in LCBP2::UpdatePancake().
333 - Fixed MaxDiffs flow (except for MR).
334
335 New functionality
336
337 - HAK supports several default cluster choices:
338 minimal (only factors)
339 delta (Markov blankets)
340 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
341 Only the maximal clusters are used as outer clusters.
342 - Implemented TreeEP. It generalizes the heuristic method described in the
343 Minka & Qi paper for obtaining a tree with the most relevant interactions to
344 higher order interactions. Almost all optimizations described in the Minka & Qi
345 paper are used, except that evidence is passed over the whole tree instead of
346 relevant subsets (the latter is almost implemented but buggy). Also added
347 alternative (worst-case) algorithm that uses a maximum spanning tree on the
348 weighted graph where the weight between neighbours i and j is given by
349 N(psi,i,j), where psi is the product of all the factors involving both i and j
350 (which is an upper bound on the effective interaction between i and j).
351 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
352 to be able to handle connectivities larger than 3 (in principle, up to 32).
353 It supports different initialization methods (the original RESPPROP,
354 the CLAMPING method and EXACT which uses JTree) and different update methods
355 (FULL and LINEAR).
356 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
357 networks and uses some approximate inference method on them for calculating
358 marginals.
359 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
360 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
361 interactions and LCBPL is LCBPI improved for higher-order interactions.
362 - Wrote one single program utils/createfg for creating various types of
363 random factor graphs.
364 - Wrote utility to visualize factor graphs using graphviz.
365 (it uses the BOOST Program Options library)
366 - Added fginfo utility that displays some info about a .fg file.
367 - Implemented Factor::strength function that calculates the potential strength
368 N(psi,i,j) between variables i and j as described in cs.IT:0504030
369 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
370 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
371 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
372 - Implemented a MATLAB interface ai_potstrength for Factor::strength
373 - Added Martijn's x2x
374
375 Improvements of existing code
376
377 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
378 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
379 associates outer region indices to factor indices (no powers yet, this
380 is deemed superfluous) and provides functions to recompute (some of) the
381 outer regions from the factors.
382 - InfAlg descendants run() methods now stop immediately and return NAN in case
383 they detect NANs. Only BP does not do NAN checking for performance reasons.
384 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
385 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
386 timing and convergence criteria.
387 - Implemented logZ() for JTree. It does the calculation during message-passing.
388 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
389 hopefully this will give more accurate approximations.
390 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
391 for a faster way of calculating marginals, which does not require a call to init()
392 nor cloning the whole object for each clamping. This leads to a significant speedup.
393 - LCBP (and LCBP2) now have complete flexibility in the specification of the
394 inner method, i.e. the method used to generate the initial cavity approximations.
395 One can pass two strings, a name and a properties string, and LCBP simply invokes
396 newInfAlg to construct the corresponding inference algorithm and uses the generic
397 marginal functions to approximate cavity marginals.
398 - Replaced the global "method" variable by local properties and removed ai.h
399 - Added some methods to Factor (operators *, *=, /, /= with doubles as
400 second argument, operators -, +=, -= with other Factors as second
401 arguments, randomize(), RemoveFirstOrderInteractions) and similar
402 operations to Prob
403 - Moving towards boost::program_options for handling command line arguments
404 (tests/test is done).
405 - Renamed some FactorGraph methods:
406 nr_vars -> nrVars
407 nr_factors -> nrFactors
408 varind -> findVar
409 factorind -> findFactor
410 makeFacCavity -> makeFactorCavity
411 - LCBP_SEQMAXRES has been removed because it did strange things.
412 - Implemented RandomDRegularGraph
413 - Implemented JTree::calcMarginal for marginals that are not confined
414 within one cluster (using cut-set conditioning).
415 - Added isConnected() method to FactorGraph (some methods do not work with
416 disconnected factor graphs).
417 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
418 - Removed single node interaction "correction" code from clamping methods
419 - Removed calcCavityDist and calcCavityDist2ndO
420 - No longer depends on GSL.
421 - Increased portability by combining platform dependant utility functions
422 in util.{h,cpp}.
423 - Wrote *.m files providing help
424
425 Testing framework
426
427 - Made a new and significantly improved testing framework that provides most
428 functionality from the command line.
429 - The basis is provided by tests/test, which uses the newInfAlg functionality
430 and enables the user to easily compare from the command line different
431 inference methods on a given factorgraph. All parameters can be specified.
432 Output consists of CPU time, average and maximum single variable marginal
433 errors, relative logZ error and MaxDiff().
434 - tests/aliases.conf contains aliases for standard combinations of methods
435 and their options (which can be used in tests/test).
436 - tests/large contains several bash/python scripts that create random factor
437 graphs, compare several approximate inference algorithms (using tests/test) and
438 allow for easy visualization of the results using PyX.
439 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
440 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
441 regression testing).
442 - Added a regression test to the Makefile which is included in the standard
443 target. It compares all inference methods on tests/testfast.fg with the
444 results stored in tests/testfast.out
445
446 Miscellaneous
447
448 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
449 - Experimental MATLAB code added for StarEP approximation on cavity
450 - Renamed project to libDAI and changed directory name accordingly.
451 - Renamed JunctionTree to JTree.
452 - Fixed licensing (now it's officially GPL).
453 - Improved README
454
455
456 revision 252
457 ------------
458
459 Functionality
460 - Added RegionGraph, GBP, CVM and HAK (double-loop).
461 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
462 RegionGraph.
463 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
464 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
465 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
466 it over all subsuming outer regions. See README for when negative factors are known to work
467 and when not.
468 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
469 it does not automatically merge factors anymore.
470 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
471 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
472 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
473 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
474 such that it does not store the complete pancakes, but represents them as little factor graphs).
475
476 Implementation / code
477 - Made a seperate type WeightedGraph, which until now only implements Prim's
478 maximal spanning tree algorithm and is only used by the junction tree code. It might
479 be good to make it a class somewhere in the future and extend it's interface.
480 - Made a seperate class ClusterGraph, which is only used by the junction tree
481 code. It's main purpose is a graph-theoretical variable elimination algorithm.
482 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
483 - Massive code cleanup, moving towards "generic" programming style, using
484 multiple inheritance and polymorphism.
485 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
486 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
487 that can be used by FactorGraph-based DAIAlgs.
488 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
489 and VarSet) and provides functionality for it (which is used by TFactor<T>).
490 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
491 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
492 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
493 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
494 o using Prob's instead of Factor's;
495 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
496 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
497 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
498 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
499 that takes the cavitydists and multiplies them with the relevant factors. This
500 resulted in an API change in AI which now accepts and returns initial cavitydists
501 instead of initial pancakes.
502
503 Minor changes
504 - Started writing DoxyGen documentation
505 - Renamed lcptab2fg.m matlab/ai_writefg.m
506 - Moved all matlab stuff to matlab/
507 - More detailed reporting (also reports clocks used).
508 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
509 - Improved testing suite.
510 - Removed logreal support.
511 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
512 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
513 full and periodic 2D Ising networks according to some command line parameters.
514 - Now logZ really returns logZ instead of -logZ.
515 - Added FactorGraph::WriteToDotFile
516
517
518 0.1.4 (2006-04-13)
519 ------------------
520 - Added file IO routines to read and write factorgraphs.
521 - Added L-infinity normalization for use with (partially) negative factors.
522 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
523 handle (partially) negative factors.
524 - Added test suite.
525 - All probabilities are now represented using double instead of LogReal<double>.
526 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
527 - Combined several variants of BP into doBP. Several update schemes possible.
528 Now uses precalculated indices for optimization.
529 - Renamed Node -> Var and Potential -> Factor.
530 - Extensive code cleanup. More use of OO techniques. Changed API.
531 - MaxIter now means maximum number of passes (corresponding to number of
532 _parallel_ updates).
533 - MaxDiff now means the maximum L-infinity distance between the updated and
534 original single variable beliefs, for all AI methods.
535 - Implemented RBP which converges faster than BP for difficult problems.
536 - Now uses method parameter which is a bitmask combining outmethod and inmethod
537 (see ai.h).
538
539
540 0.1.3 (2006-03-22)
541 --------------------
542 - All AI methods now return maxdiff
543 - ai.cpp:
544 o Now returns maxdiffinner and maxdiffouter
545 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
546 o New InitCav outermethod (only create initial cavity distributions)
547 - bp.cpp:
548 o New CavityDist2ndO which estimates 2nd order cavity interactions
549 - Makefile:
550 o Bugfix: removed dependencies on algwim.*
551
552
553 0.1.2 (2006-02-28)
554 --------------------
555 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
556 - Added the possibility to provide initial cavity distributions as an input
557 argument to ai (not much error checking is done, so be careful).
558 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
559 the output arguments Q, Q0 of ai).
560 - Removed algwim.* since it does not work.
561
562
563 0.1.1 (2006-02-28)
564 --------------------
565 - The constructors of (Log)FactorGraph and LogFactorGraph from a
566 vector<(Log)Potential> now merge potentials to prevent short loops (of length
567 4) in the factor graph. These are used in ai to construct the factor graphs
568 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
569 of BipGraph checks for the existence of short loops.
570 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
571 description in the help).
572 - ai does not hook cout anymore (which caused weird segfaults).
573 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
574 - Removed network.* since it is not useful.
575
576
577 0.1.0 (2006-02-28)
578 --------------------
579 First version worthy a version number.