Replaced doubles by Reals, fixed two bugs
[libdai.git] / ChangeLog
1 * Replaced constructor
2 TFactor<T>::TFactor( const VarSet& vars, TIterator begin )
3 by two constructors
4 TFactor<T>::TFactor( const VarSet& vars, const T* p )
5 TFactor<T>::TFactor( const VarSet& vars, const std::vector<S> &x )
6 * Fixed bugs (min and max were reversed) in
7 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
8 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
9 * Renamed RegionGraph::Check_Counting_Numbers into
10 RegionGraph::checkCountingNumbers
11 (and provided an alias for backwards compatibility)
12 * Renamed RegionGraph::Calc_Counting_Numbers into
13 RegionGraph::calcCountingNumbers
14 (and provided an alias for backwards compatibility)
15 * Renamed Permute::convert_linear_index into Permute::convertLinearIndex
16 (and provided an alias for backwards compatibility)
17 * Added examples/example_permute.cpp
18 * Added TProb<T>::divided_by(const TProb<T>&) const
19 * Fixed bug in BipartiteGraph::eraseEdge()
20 * Added python and octave ports for examples/example_sprinkler.cpp
21 * [Patrick Pletscher] Added SWIG wrapper code for python and octave
22 * Added init parameter to HAK/GBP to allow for random initialization
23 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
24 dai::Exception and is even active if NDEBUG is defined
25 * Added a constructor TProb<T>::TProb<T>( const std::vector<S> &v )
26 * Introduced CCNODEBUGFLAGS in Makefile
27 * Updated copyright headers
28 * Added max-product functionality to JTree
29 * [Charlie Vaske] EM bugfix (was using abs() instead of fabs() in
30 determining EM termination, which caused a loss of precision).
31 * [Charlie Vaske] New constructor in Permute for canonical variable ordering
32 * [Charlie Vaske] New constructor in Factor that reorders variables to canonical ordering
33 * [Charlie Vaske] New accessor in Properties for getting all keys
34 * [Charlie Vaske] New function for getting inferred parameters
35 * Cleaned up error handling by introducing the DAI_THROWE macro
36 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
37 * Changed FactorGraph::clamp and DAIAlg::clamp interfaces (the variable to be
38 clamped is now indicated by its index, not as a Var) and marked the old
39 interface as obsolete
40 * [Patrick Pletscher] Fixed performance issue in FactorGraph::clamp
41 * [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
42 (only for BP)
43 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
44
45 git ae0fc30e10be6683cbfc209dcee56f34234a6cb8
46 --------------------------------------------
47 * Added work-around for bug in Boost Graph Library
48 * Improvements of TFactor<T>:
49 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
50 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
51 * Added BipartiteGraph::eraseEdge
52 * Removed all the virtual default constructors *::create(), as they are not used.
53 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
54 * [Charlie Vaske] Added Expectation Maximization code.
55 * Added MatLab QuickStart to README.
56 * MEX file dai now also returns variable and factor beliefs.
57 * Cleanups and extra documentation of the code contributed by Frederik Eaton
58 * Removed erroneous 'inline' directives in gibbs.cpp
59 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
60 * [Frederik Eaton] Updated doxygen.conf to version 1.5.9
61 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
62 * [Frederik Eaton] Added FactorGraph::clampVar and FactorGraph::clampFactor
63 * [Frederik Eaton] Changed BP to be able to record order in which messages are sent (for use by BBP)
64 * [Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor
65 * [Frederik Eaton]: Extended InfAlg interface with beliefV() and beliefF() methods;
66 * [Frederik Eaton]: Improved PropertySet class:
67 - Added default constructor
68 - Allow construction from string
69 - Added method allKeys() to produce list of keys
70 - In getStringAs(), check for typeid(ValueType) before typeid(std::string)
71 (this fixes a strange bug for empty string property)
72 * [Frederik Eaton]: Added some utility macros (DAI_PV, DAI_DMSG, DAI_ACCMUT, DAI_IFVERB)
73 and functions (concat(),rnd()) to include/dai/util.h
74 * [Frederik Eaton] Added backwards compatibility layer for edge interface to
75 BipartiteGraph and FactorGraph (which will be obsoleted soon)
76 * [Frederik Eaton] Added BP_dual, BBP and CBP algorithms
77 * [Frederik Eaton] Added Gibbs::state() accessors/mutators
78 * [Frederik Eaton] Fixed Gibbs::getVarDist(size_t) to return uniform
79 distribution if no state is allowed
80 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
81 alias substitutions
82 * Interface changes:
83 TProb<T>::minVal() -> TProb<T>::min()
84 TFactor<T>::minVal() -> TFactor<T>::min()
85 TProb<T>::maxVal() -> TProb<T>::max()
86 TFactor<T>::maxVal() -> TFactor<T>::max()
87 TProb<T>::totalSum() -> TProb<T>sum()
88 TFactor<T>::totalSum() -> TFactor<T>::sum()
89 * [Frederik Eaton] Added methods setUniform (), sumAbs(), argmax() to TProb<T>
90 * [Frederik Eaton] Added TAGS, lib targets to Makefile
91 * [Frederik Eaton] Add useful aliases to aliases.conf
92 * [Frederik Eaton] Removed unnecessary copy constructors and assignment
93 operators
94 * [Frederik Eaton] Change cout to cerr in warnings and error messages
95 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
96 set instead of the linear search (which can yield enormous speedups - a
97 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
98 * Added debug assertions to Var which check for inconsistent dimensions of
99 variables with the same labels
100 * [Giuseppe Passino] Added prefix ++ operator to State (State::operator++())
101 * [Giuseppe Passino] Added iterators to FactorGraph (FactorGraph::begin,
102 FactorGraph::end)
103 * [Giuseppe Passino] Added iterators to TFactor (TFactor::begin, TFactor::end)
104 * [Giuseppe Passino] Added iterators to TProb (TProb::begin, TProb::end)
105 * [Giuseppe Passino] Added BP::findMaximum(), which can be used after running
106 max-product BP to construct a global state with maximum probability
107 * Improved Makefile (libDAI now also builds out-of-the-box on MacOSX,
108 thanks to Dan Preston; merged Makefile.win and Makefile.shared into Makefile)
109 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where
110 states with zero probability mass were clamped, leading to NaNs or assertion
111 errors (thanks to Dan Preston for reporting this)
112 * toc() now returns POSIX system time with maximum accuracy of microseconds
113 * Exception objects now remember their error code
114 * Added examples/example_sprinkler.cpp
115 * [Peter Gober] Made libDAI build out-of-the-box on Cygwin.
116 * [Frederik Eaton] Added Gibbs sampler to algorithms
117 * Improved documentation of include/dai/{bipgraph.h, prob.h, smallset.h,
118 var.h, varset.h, factor.h, enum.h} and of examples/example.cpp
119 Merged TODO and FILEFORMAT into doxygen documentation
120 * examples/
121 - Moved example.cpp to examples/
122 - Added examples/example_bipgraph.cpp
123 - Added examples/example_varset.cpp
124 * Interface changes:
125 - Replaced TProb<T>::log0() by TProb<T>::log(true)
126 - Replaced TProb<T>::takeLog0() by TProb<T>::takeLog(true)
127 - Replaced TFactor<T>::log0() by TFactor<T>::log(true)
128 - Removed TProb<T>::hasNonPositives()
129 - Renamed smallSet<T> to SmallSet<T>
130 - Removed TFactor<T>::divided_by, use operator/ instead
131 - Removed TFactor<T>::divide, use operator/= instead
132 - Removed TFactor<T>::partSum(const VarSet&), use marginal(const VarSet&,true) instead
133 - Improved constructors of TProb and TFactor to use iterators instead of pointers
134 * Miscellaneous small changes and cleanups:
135 - Changed regression test so that it also works under Windows
136 - Changed output stream operator<< for Var and VarSet
137 - Added TProb::draw() function, which draws a random index
138 - Cleanup of matlab interface code
139 - Small improvement of utils/fginfo
140 - Small cleanup of BP code
141 - Switched Makefile.win to GNU Make syntax
142
143
144 libDAI-0.2.2 (2008-09-30)
145 -------------------------
146
147 New features:
148 * Approximate inference methods now report the number of iterations needed.
149 * Added damping to various algorithms to improve convergence properties.
150 * Added more features to utils/createfg for creating factor graphs.
151 * Added ExactInf class for brute force exact inference.
152 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
153 whether calculations are done in the log-domain or in the linear domain;
154 doing calculations in the log-domain may help if the numerical range
155 of a double is too small.
156 * [Claudio Lima] Added Max-Product functionality to BP.
157 * Improved documentation.
158
159 Improved architecture:
160 * Added Exceptions framework.
161 * Pervasive change of BipartiteGraph implementation (based on an idea by
162 Giuseppe Passino). BipartiteGraph no longer stores the node properties
163 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
164 nor an edge list. Instead, it stores the graph structure as lists of
165 neighboring nodes. This yields a significant memory/speed improvement for
166 large factor graphs, and is more elegant as well. Iterating over neighbors is
167 made easy by using boost::foreach.
168 * Added conditional compilation of inference methods.
169 * VarSet is now implemented using a std::vector<Var> instead of a
170 std::set<Var>, which yields a significant speed improvement. Furthermore,
171 the implementation has been generalized, resulting in the small_set<T> class
172 which can be used to represent sets of small cardinality; VarSet is the
173 specialization with T = Var.
174 * Improved ClusterGraph implementation, yielding significant speedups
175 for the JunctionTree algorithm on large factorgraphs.
176
177 Code cleanup:
178 * Moved everything into namespace "dai".
179 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
180 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
181 * Removed utils/remove_short_loops and matlab/remove_short_loops.
182 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
183 * Improved index.h:
184 - Renamed Index -> IndexFor
185 - Added some .reserve()'s to IndexFor methods which yields a
186 25% speedup of testregression
187 - Replaced multind by Permute
188 - Added MultiFor
189 - Added State
190 * New funcstionality of factor.h.
191 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
192 inference algorithm, because the Properties framework was not as
193 convenient as I hoped, and not every inference algorithm needs a maxdiff
194 variable. Also, replaced some FactorGraph functionality in InfAlg by a
195 function that returns the FactorGraph. The result is cleaner (less
196 entangled) code.
197 * Removed x2x.
198 * Replaced Complex with real numbers (negative potentials are just too rare
199 to warrant the additional "complexity" :)).
200
201 Miscellaneous improvements:
202 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
203 GCC under cygwin.
204 * Contributions by Peter Gober:
205 - Renamed variable _N in mr.* for compatibility with g++ under cygwin.
206 * Misc contributions by Giuseppe Passino:
207 - removed "using namespace std;" from header files - bad practice;
208 - moved header files in include/dai and sources in src;
209 - changed #ifndefs to GNU style;
210 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
211 - dai::TProb:
212 o removed copy constructor and assignment operators (redundant);
213 o implementation of some methods via STL algorithms;
214 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
215 o explicit constructor (prevents implicit conversion from size_t to TProb);
216 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
217 * Misc contributions by Christian Wojek:
218 - New FactorGraph constructor that constructs from given ranges of factors
219 and variables;
220 - Optimization of FactorGraph constructors using tr1::unordered_map.
221 * FactorGraph constructors no longer check for short loops (huge speed
222 increase for large factor graphs), nor for negative entries. Also, the
223 normtype is now Prob::NORMPROB by default.
224 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
225
226 Interface changes:
227 * VarSet::
228 - VarSet::stateSpace() -> nrStates(const VarSet &)
229 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
230 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
231 - removed bool operator||
232 - operator&&(const VarSet&) -> intersects(const VarSet&)
233 - operator&&(const Var&) -> contains(const Var&)
234 * FactorGraph::
235 - delta(const Var &) -> delta(size_t)
236 - Delta(const Var &) -> Delta(size_t)
237 - makeCavity(const Var &) -> makeCavity(size_t)
238 - vars() -> vars
239 - factors() -> factors
240 - removed MakeFactorCavity(size_t)
241 - removed ExactMarginal(const VarSet &)
242 - removed ExactlogZ()
243 - removed updatedFactor(size_t)
244 - removed _normtype and NormType()
245 - removed hasShortLoops(...) and removeShortLoops(...)
246 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
247 - undoProb(size_t) -> restoreFactor(size_t)
248 - saveProb(size_t) -> backupFactor(size_t)
249 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
250 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
251 - ReadFromFile(const char*) returns void (throws on error)
252 - WriteToFile(const char*) returns void (throws on error)
253 - removed hasNegatives()
254 * RegionGraph::
255 - nr_ORs() -> nrORs()
256 - nr_IRs() -> nrIRs()
257 - ORs() -> ORs
258 - IRs() -> IRs
259 * *::Regenerate() -> *::construct()
260 * Renamed Index -> IndexFor
261 * Diffs:
262 - max() -> maxDiff()
263 - max_size() -> maxSize()
264 * Prob::max() -> Prob::maxVal()
265 * Factor::
266 - max() -> maxVal()
267 - part_sum() -> partSum()
268 * toc() in util.h now returns seconds as a double
269 * VarSet::operator&&
270 * Properties -> PropertySet
271
272
273 libDAI-0.2.1 (2008-05-26)
274 -------------------------
275
276 Bugfix release.
277 * added missing cstdio header in util.h
278 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
279 * added description of the factor graph fileformat
280 * improved Makefile
281
282
283 libDAI-0.2.0 (2006-11-30)
284 -------------------------
285
286 First public release.
287
288
289 0.1.5 (2006-11-30)
290 ------------------
291
292 Regressions
293
294 - tests/testlcbp and tests/testlcbp are broken.
295 - EXACT method does not work anymore.
296 - The Properties framework gives a speed penalty because of the lookup
297 costs involved; inner loops should be optimized.
298
299 General framework
300
301 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
302 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
303 functions to forward functionality from either FactorGraph or RegionGraph
304 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
305 and in RegionGraph and no explicit interface is needed in descendants.
306 - New abstract base class InfAlg added, representing an inference algorithm,
307 from which DAIAlg<T> inherits. This solves the incompatibility problems of
308 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
309 DAIAlg<RegionGraph>). More work is required to reduce code duplication
310 (make FactorGraph part of InfAlg).
311 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
312 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
313 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
314 one to save a few factors, modify them (e.g. clamp them), and then restore them
315 to their old values. Undo should also init the corresponding messages / beliefs.
316 This can be used if a given factor graph repeatedly needs to be clamped in
317 different ways and an approximation method is run for each clamping; using the
318 saveProbs/undoProbs can give a significant speed increase.
319 - Switched to a general Properties framework that handles the parameters of
320 all inference methods in a uniform manner. The Properties class is a map of
321 several properties in boost::any objects, indexed by their names (strings).
322 It can read from a stream and write to a stream. It is recursive, in the sense
323 that a Properties object can hold a variable of type Properties as well.
324 - Added a generic way of constructing inference algorithms from a factor graph,
325 name and properties object. Added the newInfAlg function which constructs
326 the requested object. This is used by LCBP, the Matlab interface and the
327 command line (test) interface.
328 - Added a generic enum framework for enum parameters. Although implemented as a
329 hack, it is quite useful in that it drastically simplifies and reduces the
330 amount of code for handling enum parameters.
331 - Provided generic functions for calculating marginals in different ways that
332 work for all approximate inference methods.
333
334 Bugfixes
335
336 - Fixed GBP free energy.
337 - Fixed bug in junctiontree (it didn't init the _vars variable).
338 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
339 the logical NOT of what they should return).
340 - Fixed bug in RegionGraph::RecomputeOR(s).
341 - Fixed bug in utils/create_dreg_fg:
342 graph structure was not random for given parameters (forgot to call srand()).
343 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
344 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
345 that consists of one outer region only.
346 - Fixed INIT bug in LCBP2::UpdatePancake().
347 - Fixed MaxDiffs flow (except for MR).
348
349 New functionality
350
351 - HAK supports several default cluster choices:
352 minimal (only factors)
353 delta (Markov blankets)
354 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
355 Only the maximal clusters are used as outer clusters.
356 - Implemented TreeEP. It generalizes the heuristic method described in the
357 Minka & Qi paper for obtaining a tree with the most relevant interactions to
358 higher order interactions. Almost all optimizations described in the Minka & Qi
359 paper are used, except that evidence is passed over the whole tree instead of
360 relevant subsets (the latter is almost implemented but buggy). Also added
361 alternative (worst-case) algorithm that uses a maximum spanning tree on the
362 weighted graph where the weight between neighbours i and j is given by
363 N(psi,i,j), where psi is the product of all the factors involving both i and j
364 (which is an upper bound on the effective interaction between i and j).
365 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
366 to be able to handle connectivities larger than 3 (in principle, up to 32).
367 It supports different initialization methods (the original RESPPROP,
368 the CLAMPING method and EXACT which uses JTree) and different update methods
369 (FULL and LINEAR).
370 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
371 networks and uses some approximate inference method on them for calculating
372 marginals.
373 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
374 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
375 interactions and LCBPL is LCBPI improved for higher-order interactions.
376 - Wrote one single program utils/createfg for creating various types of
377 random factor graphs.
378 - Wrote utility to visualize factor graphs using graphviz.
379 (it uses the BOOST Program Options library)
380 - Added fginfo utility that displays some info about a .fg file.
381 - Implemented Factor::strength function that calculates the potential strength
382 N(psi,i,j) between variables i and j as described in cs.IT:0504030
383 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
384 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
385 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
386 - Implemented a MATLAB interface ai_potstrength for Factor::strength
387 - Added Martijn's x2x
388
389 Improvements of existing code
390
391 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
392 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
393 associates outer region indices to factor indices (no powers yet, this
394 is deemed superfluous) and provides functions to recompute (some of) the
395 outer regions from the factors.
396 - InfAlg descendants run() methods now stop immediately and return NAN in case
397 they detect NANs. Only BP does not do NAN checking for performance reasons.
398 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
399 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
400 timing and convergence criteria.
401 - Implemented logZ() for JTree. It does the calculation during message-passing.
402 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
403 hopefully this will give more accurate approximations.
404 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
405 for a faster way of calculating marginals, which does not require a call to init()
406 nor cloning the whole object for each clamping. This leads to a significant speedup.
407 - LCBP (and LCBP2) now have complete flexibility in the specification of the
408 inner method, i.e. the method used to generate the initial cavity approximations.
409 One can pass two strings, a name and a properties string, and LCBP simply invokes
410 newInfAlg to construct the corresponding inference algorithm and uses the generic
411 marginal functions to approximate cavity marginals.
412 - Replaced the global "method" variable by local properties and removed ai.h
413 - Added some methods to Factor (operators *, *=, /, /= with doubles as
414 second argument, operators -, +=, -= with other Factors as second
415 arguments, randomize(), RemoveFirstOrderInteractions) and similar
416 operations to Prob
417 - Moving towards boost::program_options for handling command line arguments
418 (tests/test is done).
419 - Renamed some FactorGraph methods:
420 nr_vars -> nrVars
421 nr_factors -> nrFactors
422 varind -> findVar
423 factorind -> findFactor
424 makeFacCavity -> makeFactorCavity
425 - LCBP_SEQMAXRES has been removed because it did strange things.
426 - Implemented RandomDRegularGraph
427 - Implemented JTree::calcMarginal for marginals that are not confined
428 within one cluster (using cut-set conditioning).
429 - Added isConnected() method to FactorGraph (some methods do not work with
430 disconnected factor graphs).
431 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
432 - Removed single node interaction "correction" code from clamping methods
433 - Removed calcCavityDist and calcCavityDist2ndO
434 - No longer depends on GSL.
435 - Increased portability by combining platform dependant utility functions
436 in util.{h,cpp}.
437 - Wrote *.m files providing help
438
439 Testing framework
440
441 - Made a new and significantly improved testing framework that provides most
442 functionality from the command line.
443 - The basis is provided by tests/test, which uses the newInfAlg functionality
444 and enables the user to easily compare from the command line different
445 inference methods on a given factorgraph. All parameters can be specified.
446 Output consists of CPU time, average and maximum single variable marginal
447 errors, relative logZ error and MaxDiff().
448 - tests/aliases.conf contains aliases for standard combinations of methods
449 and their options (which can be used in tests/test).
450 - tests/large contains several bash/python scripts that create random factor
451 graphs, compare several approximate inference algorithms (using tests/test) and
452 allow for easy visualization of the results using PyX.
453 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
454 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
455 regression testing).
456 - Added a regression test to the Makefile which is included in the standard
457 target. It compares all inference methods on tests/testfast.fg with the
458 results stored in tests/testfast.out
459
460 Miscellaneous
461
462 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
463 - Experimental MATLAB code added for StarEP approximation on cavity
464 - Renamed project to libDAI and changed directory name accordingly.
465 - Renamed JunctionTree to JTree.
466 - Fixed licensing (now it's officially GPL).
467 - Improved README
468
469
470 revision 252
471 ------------
472
473 Functionality
474 - Added RegionGraph, GBP, CVM and HAK (double-loop).
475 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
476 RegionGraph.
477 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
478 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
479 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
480 it over all subsuming outer regions. See README for when negative factors are known to work
481 and when not.
482 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
483 it does not automatically merge factors anymore.
484 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
485 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
486 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
487 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
488 such that it does not store the complete pancakes, but represents them as little factor graphs).
489
490 Implementation / code
491 - Made a seperate type WeightedGraph, which until now only implements Prim's
492 maximal spanning tree algorithm and is only used by the junction tree code. It might
493 be good to make it a class somewhere in the future and extend it's interface.
494 - Made a seperate class ClusterGraph, which is only used by the junction tree
495 code. It's main purpose is a graph-theoretical variable elimination algorithm.
496 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
497 - Massive code cleanup, moving towards "generic" programming style, using
498 multiple inheritance and polymorphism.
499 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
500 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
501 that can be used by FactorGraph-based DAIAlgs.
502 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
503 and VarSet) and provides functionality for it (which is used by TFactor<T>).
504 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
505 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
506 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
507 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
508 o using Prob's instead of Factor's;
509 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
510 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
511 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
512 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
513 that takes the cavitydists and multiplies them with the relevant factors. This
514 resulted in an API change in AI which now accepts and returns initial cavitydists
515 instead of initial pancakes.
516
517 Minor changes
518 - Started writing DoxyGen documentation
519 - Renamed lcptab2fg.m matlab/ai_writefg.m
520 - Moved all matlab stuff to matlab/
521 - More detailed reporting (also reports clocks used).
522 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
523 - Improved testing suite.
524 - Removed logreal support.
525 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
526 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
527 full and periodic 2D Ising networks according to some command line parameters.
528 - Now logZ really returns logZ instead of -logZ.
529 - Added FactorGraph::WriteToDotFile
530
531
532 0.1.4 (2006-04-13)
533 ------------------
534 - Added file IO routines to read and write factorgraphs.
535 - Added L-infinity normalization for use with (partially) negative factors.
536 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
537 handle (partially) negative factors.
538 - Added test suite.
539 - All probabilities are now represented using double instead of LogReal<double>.
540 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
541 - Combined several variants of BP into doBP. Several update schemes possible.
542 Now uses precalculated indices for optimization.
543 - Renamed Node -> Var and Potential -> Factor.
544 - Extensive code cleanup. More use of OO techniques. Changed API.
545 - MaxIter now means maximum number of passes (corresponding to number of
546 _parallel_ updates).
547 - MaxDiff now means the maximum L-infinity distance between the updated and
548 original single variable beliefs, for all AI methods.
549 - Implemented RBP which converges faster than BP for difficult problems.
550 - Now uses method parameter which is a bitmask combining outmethod and inmethod
551 (see ai.h).
552
553
554 0.1.3 (2006-03-22)
555 --------------------
556 - All AI methods now return maxdiff
557 - ai.cpp:
558 o Now returns maxdiffinner and maxdiffouter
559 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
560 o New InitCav outermethod (only create initial cavity distributions)
561 - bp.cpp:
562 o New CavityDist2ndO which estimates 2nd order cavity interactions
563 - Makefile:
564 o Bugfix: removed dependencies on algwim.*
565
566
567 0.1.2 (2006-02-28)
568 --------------------
569 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
570 - Added the possibility to provide initial cavity distributions as an input
571 argument to ai (not much error checking is done, so be careful).
572 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
573 the output arguments Q, Q0 of ai).
574 - Removed algwim.* since it does not work.
575
576
577 0.1.1 (2006-02-28)
578 --------------------
579 - The constructors of (Log)FactorGraph and LogFactorGraph from a
580 vector<(Log)Potential> now merge potentials to prevent short loops (of length
581 4) in the factor graph. These are used in ai to construct the factor graphs
582 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
583 of BipGraph checks for the existence of short loops.
584 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
585 description in the help).
586 - ai does not hook cout anymore (which caused weird segfaults).
587 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
588 - Removed network.* since it is not useful.
589
590
591 0.1.0 (2006-02-28)
592 --------------------
593 First version worthy a version number.