Extended InfAlg interface with setProperties(), getProperties() and printProperties()
[libdai.git] / ChangeLog
1 * Extended InfAlg interface with setProperties(), getProperties() and printProperties()
2 * Declared class Diffs as obsolete
3 * Declared calcPairBeliefsNew() as obsolete (its functionality is now part
4 of calcPairBeliefs())
5 * Declared calcMarginal2ndO() as obsolete
6 * Removed DAI_ACCMUT macro because it didn't yield satisfactory doxygen documentation
7 * Replaced constructor
8 TFactor<T>::TFactor( const VarSet& vars, TIterator begin )
9 by two constructors
10 TFactor<T>::TFactor( const VarSet& vars, const T* p )
11 TFactor<T>::TFactor( const VarSet& vars, const std::vector<S> &x )
12 * Fixed bugs (min and max were reversed) in
13 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
14 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
15 * Renamed RegionGraph::Check_Counting_Numbers into
16 RegionGraph::checkCountingNumbers
17 (and provided an alias for backwards compatibility)
18 * Renamed RegionGraph::Calc_Counting_Numbers into
19 RegionGraph::calcCountingNumbers
20 (and provided an alias for backwards compatibility)
21 * Renamed Permute::convert_linear_index into Permute::convertLinearIndex
22 (and provided an alias for backwards compatibility)
23 * Added examples/example_permute.cpp
24 * Added TProb<T>::divided_by(const TProb<T>&) const
25 * Fixed bug in BipartiteGraph::eraseEdge()
26 * Added python and octave ports for examples/example_sprinkler.cpp
27 * [Patrick Pletscher] Added SWIG wrapper code for python and octave
28 * Added init parameter to HAK/GBP to allow for random initialization
29 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
30 dai::Exception and is even active if NDEBUG is defined
31 * Added a constructor TProb<T>::TProb<T>( const std::vector<S> &v )
32 * Introduced CCNODEBUGFLAGS in Makefile
33 * Updated copyright headers
34 * Added max-product functionality to JTree
35 * [Charlie Vaske] EM bugfix (was using abs() instead of fabs() in
36 determining EM termination, which caused a loss of precision).
37 * [Charlie Vaske] New constructor in Permute for canonical variable ordering
38 * [Charlie Vaske] New constructor in Factor that reorders variables to canonical ordering
39 * [Charlie Vaske] New accessor in Properties for getting all keys
40 * [Charlie Vaske] New function for getting inferred parameters
41 * Cleaned up error handling by introducing the DAI_THROWE macro
42 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
43 * Changed FactorGraph::clamp and DAIAlg::clamp interfaces (the variable to be
44 clamped is now indicated by its index, not as a Var) and marked the old
45 interface as obsolete
46 * [Patrick Pletscher] Fixed performance issue in FactorGraph::clamp
47 * [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
48 (only for BP)
49 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
50
51 git ae0fc30e10be6683cbfc209dcee56f34234a6cb8
52 --------------------------------------------
53 * Added work-around for bug in Boost Graph Library
54 * Improvements of TFactor<T>:
55 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
56 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
57 * Added BipartiteGraph::eraseEdge
58 * Removed all the virtual default constructors *::create(), as they are not used.
59 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
60 * [Charlie Vaske] Added Expectation Maximization code.
61 * Added MatLab QuickStart to README.
62 * MEX file dai now also returns variable and factor beliefs.
63 * Cleanups and extra documentation of the code contributed by Frederik Eaton
64 * Removed erroneous 'inline' directives in gibbs.cpp
65 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
66 * [Frederik Eaton] Updated doxygen.conf to version 1.5.9
67 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
68 * [Frederik Eaton] Added FactorGraph::clampVar and FactorGraph::clampFactor
69 * [Frederik Eaton] Changed BP to be able to record order in which messages are sent (for use by BBP)
70 * [Frederik Eaton] Improved documentation of BipartiteGraph::Neighbor
71 * [Frederik Eaton]: Extended InfAlg interface with beliefV() and beliefF() methods;
72 * [Frederik Eaton]: Improved PropertySet class:
73 - Added default constructor
74 - Allow construction from string
75 - Added method allKeys() to produce list of keys
76 - In getStringAs(), check for typeid(ValueType) before typeid(std::string)
77 (this fixes a strange bug for empty string property)
78 * [Frederik Eaton]: Added some utility macros (DAI_PV, DAI_DMSG, DAI_ACCMUT, DAI_IFVERB)
79 and functions (concat(),rnd()) to include/dai/util.h
80 * [Frederik Eaton] Added backwards compatibility layer for edge interface to
81 BipartiteGraph and FactorGraph (which will be obsoleted soon)
82 * [Frederik Eaton] Added BP_dual, BBP and CBP algorithms
83 * [Frederik Eaton] Added Gibbs::state() accessors/mutators
84 * [Frederik Eaton] Fixed Gibbs::getVarDist(size_t) to return uniform
85 distribution if no state is allowed
86 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
87 alias substitutions
88 * Interface changes:
89 TProb<T>::minVal() -> TProb<T>::min()
90 TFactor<T>::minVal() -> TFactor<T>::min()
91 TProb<T>::maxVal() -> TProb<T>::max()
92 TFactor<T>::maxVal() -> TFactor<T>::max()
93 TProb<T>::totalSum() -> TProb<T>sum()
94 TFactor<T>::totalSum() -> TFactor<T>::sum()
95 * [Frederik Eaton] Added methods setUniform (), sumAbs(), argmax() to TProb<T>
96 * [Frederik Eaton] Added TAGS, lib targets to Makefile
97 * [Frederik Eaton] Add useful aliases to aliases.conf
98 * [Frederik Eaton] Removed unnecessary copy constructors and assignment
99 operators
100 * [Frederik Eaton] Change cout to cerr in warnings and error messages
101 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
102 set instead of the linear search (which can yield enormous speedups - a
103 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
104 * Added debug assertions to Var which check for inconsistent dimensions of
105 variables with the same labels
106 * [Giuseppe Passino] Added prefix ++ operator to State (State::operator++())
107 * [Giuseppe Passino] Added iterators to FactorGraph (FactorGraph::begin,
108 FactorGraph::end)
109 * [Giuseppe Passino] Added iterators to TFactor (TFactor::begin, TFactor::end)
110 * [Giuseppe Passino] Added iterators to TProb (TProb::begin, TProb::end)
111 * [Giuseppe Passino] Added BP::findMaximum(), which can be used after running
112 max-product BP to construct a global state with maximum probability
113 * Improved Makefile (libDAI now also builds out-of-the-box on MacOSX,
114 thanks to Dan Preston; merged Makefile.win and Makefile.shared into Makefile)
115 * Fixed bug in calcMarginal, calcPairBeliefs, calcPairBeliefsNew where
116 states with zero probability mass were clamped, leading to NaNs or assertion
117 errors (thanks to Dan Preston for reporting this)
118 * toc() now returns POSIX system time with maximum accuracy of microseconds
119 * Exception objects now remember their error code
120 * Added examples/example_sprinkler.cpp
121 * [Peter Gober] Made libDAI build out-of-the-box on Cygwin.
122 * [Frederik Eaton] Added Gibbs sampler to algorithms
123 * Improved documentation of include/dai/{bipgraph.h, prob.h, smallset.h,
124 var.h, varset.h, factor.h, enum.h} and of examples/example.cpp
125 Merged TODO and FILEFORMAT into doxygen documentation
126 * examples/
127 - Moved example.cpp to examples/
128 - Added examples/example_bipgraph.cpp
129 - Added examples/example_varset.cpp
130 * Interface changes:
131 - Replaced TProb<T>::log0() by TProb<T>::log(true)
132 - Replaced TProb<T>::takeLog0() by TProb<T>::takeLog(true)
133 - Replaced TFactor<T>::log0() by TFactor<T>::log(true)
134 - Removed TProb<T>::hasNonPositives()
135 - Renamed smallSet<T> to SmallSet<T>
136 - Removed TFactor<T>::divided_by, use operator/ instead
137 - Removed TFactor<T>::divide, use operator/= instead
138 - Removed TFactor<T>::partSum(const VarSet&), use marginal(const VarSet&,true) instead
139 - Improved constructors of TProb and TFactor to use iterators instead of pointers
140 * Miscellaneous small changes and cleanups:
141 - Changed regression test so that it also works under Windows
142 - Changed output stream operator<< for Var and VarSet
143 - Added TProb::draw() function, which draws a random index
144 - Cleanup of matlab interface code
145 - Small improvement of utils/fginfo
146 - Small cleanup of BP code
147 - Switched Makefile.win to GNU Make syntax
148
149
150 libDAI-0.2.2 (2008-09-30)
151 -------------------------
152
153 New features:
154 * Approximate inference methods now report the number of iterations needed.
155 * Added damping to various algorithms to improve convergence properties.
156 * Added more features to utils/createfg for creating factor graphs.
157 * Added ExactInf class for brute force exact inference.
158 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
159 whether calculations are done in the log-domain or in the linear domain;
160 doing calculations in the log-domain may help if the numerical range
161 of a double is too small.
162 * [Claudio Lima] Added Max-Product functionality to BP.
163 * Improved documentation.
164
165 Improved architecture:
166 * Added Exceptions framework.
167 * Pervasive change of BipartiteGraph implementation (based on an idea by
168 Giuseppe Passino). BipartiteGraph no longer stores the node properties
169 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
170 nor an edge list. Instead, it stores the graph structure as lists of
171 neighboring nodes. This yields a significant memory/speed improvement for
172 large factor graphs, and is more elegant as well. Iterating over neighbors is
173 made easy by using boost::foreach.
174 * Added conditional compilation of inference methods.
175 * VarSet is now implemented using a std::vector<Var> instead of a
176 std::set<Var>, which yields a significant speed improvement. Furthermore,
177 the implementation has been generalized, resulting in the small_set<T> class
178 which can be used to represent sets of small cardinality; VarSet is the
179 specialization with T = Var.
180 * Improved ClusterGraph implementation, yielding significant speedups
181 for the JunctionTree algorithm on large factorgraphs.
182
183 Code cleanup:
184 * Moved everything into namespace "dai".
185 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
186 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
187 * Removed utils/remove_short_loops and matlab/remove_short_loops.
188 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
189 * Improved index.h:
190 - Renamed Index -> IndexFor
191 - Added some .reserve()'s to IndexFor methods which yields a
192 25% speedup of testregression
193 - Replaced multind by Permute
194 - Added MultiFor
195 - Added State
196 * New funcstionality of factor.h.
197 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
198 inference algorithm, because the Properties framework was not as
199 convenient as I hoped, and not every inference algorithm needs a maxdiff
200 variable. Also, replaced some FactorGraph functionality in InfAlg by a
201 function that returns the FactorGraph. The result is cleaner (less
202 entangled) code.
203 * Removed x2x.
204 * Replaced Complex with real numbers (negative potentials are just too rare
205 to warrant the additional "complexity" :)).
206
207 Miscellaneous improvements:
208 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
209 GCC under cygwin.
210 * Contributions by Peter Gober:
211 - Renamed variable _N in mr.* for compatibility with g++ under cygwin.
212 * Misc contributions by Giuseppe Passino:
213 - removed "using namespace std;" from header files - bad practice;
214 - moved header files in include/dai and sources in src;
215 - changed #ifndefs to GNU style;
216 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
217 - dai::TProb:
218 o removed copy constructor and assignment operators (redundant);
219 o implementation of some methods via STL algorithms;
220 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
221 o explicit constructor (prevents implicit conversion from size_t to TProb);
222 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
223 * Misc contributions by Christian Wojek:
224 - New FactorGraph constructor that constructs from given ranges of factors
225 and variables;
226 - Optimization of FactorGraph constructors using tr1::unordered_map.
227 * FactorGraph constructors no longer check for short loops (huge speed
228 increase for large factor graphs), nor for negative entries. Also, the
229 normtype is now Prob::NORMPROB by default.
230 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
231
232 Interface changes:
233 * VarSet::
234 - VarSet::stateSpace() -> nrStates(const VarSet &)
235 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
236 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
237 - removed bool operator||
238 - operator&&(const VarSet&) -> intersects(const VarSet&)
239 - operator&&(const Var&) -> contains(const Var&)
240 * FactorGraph::
241 - delta(const Var &) -> delta(size_t)
242 - Delta(const Var &) -> Delta(size_t)
243 - makeCavity(const Var &) -> makeCavity(size_t)
244 - vars() -> vars
245 - factors() -> factors
246 - removed MakeFactorCavity(size_t)
247 - removed ExactMarginal(const VarSet &)
248 - removed ExactlogZ()
249 - removed updatedFactor(size_t)
250 - removed _normtype and NormType()
251 - removed hasShortLoops(...) and removeShortLoops(...)
252 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
253 - undoProb(size_t) -> restoreFactor(size_t)
254 - saveProb(size_t) -> backupFactor(size_t)
255 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
256 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
257 - ReadFromFile(const char*) returns void (throws on error)
258 - WriteToFile(const char*) returns void (throws on error)
259 - removed hasNegatives()
260 * RegionGraph::
261 - nr_ORs() -> nrORs()
262 - nr_IRs() -> nrIRs()
263 - ORs() -> ORs
264 - IRs() -> IRs
265 * *::Regenerate() -> *::construct()
266 * Renamed Index -> IndexFor
267 * Diffs:
268 - max() -> maxDiff()
269 - max_size() -> maxSize()
270 * Prob::max() -> Prob::maxVal()
271 * Factor::
272 - max() -> maxVal()
273 - part_sum() -> partSum()
274 * toc() in util.h now returns seconds as a double
275 * VarSet::operator&&
276 * Properties -> PropertySet
277
278
279 libDAI-0.2.1 (2008-05-26)
280 -------------------------
281
282 Bugfix release.
283 * added missing cstdio header in util.h
284 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
285 * added description of the factor graph fileformat
286 * improved Makefile
287
288
289 libDAI-0.2.0 (2006-11-30)
290 -------------------------
291
292 First public release.
293
294
295 0.1.5 (2006-11-30)
296 ------------------
297
298 Regressions
299
300 - tests/testlcbp and tests/testlcbp are broken.
301 - EXACT method does not work anymore.
302 - The Properties framework gives a speed penalty because of the lookup
303 costs involved; inner loops should be optimized.
304
305 General framework
306
307 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
308 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
309 functions to forward functionality from either FactorGraph or RegionGraph
310 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
311 and in RegionGraph and no explicit interface is needed in descendants.
312 - New abstract base class InfAlg added, representing an inference algorithm,
313 from which DAIAlg<T> inherits. This solves the incompatibility problems of
314 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
315 DAIAlg<RegionGraph>). More work is required to reduce code duplication
316 (make FactorGraph part of InfAlg).
317 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
318 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
319 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
320 one to save a few factors, modify them (e.g. clamp them), and then restore them
321 to their old values. Undo should also init the corresponding messages / beliefs.
322 This can be used if a given factor graph repeatedly needs to be clamped in
323 different ways and an approximation method is run for each clamping; using the
324 saveProbs/undoProbs can give a significant speed increase.
325 - Switched to a general Properties framework that handles the parameters of
326 all inference methods in a uniform manner. The Properties class is a map of
327 several properties in boost::any objects, indexed by their names (strings).
328 It can read from a stream and write to a stream. It is recursive, in the sense
329 that a Properties object can hold a variable of type Properties as well.
330 - Added a generic way of constructing inference algorithms from a factor graph,
331 name and properties object. Added the newInfAlg function which constructs
332 the requested object. This is used by LCBP, the Matlab interface and the
333 command line (test) interface.
334 - Added a generic enum framework for enum parameters. Although implemented as a
335 hack, it is quite useful in that it drastically simplifies and reduces the
336 amount of code for handling enum parameters.
337 - Provided generic functions for calculating marginals in different ways that
338 work for all approximate inference methods.
339
340 Bugfixes
341
342 - Fixed GBP free energy.
343 - Fixed bug in junctiontree (it didn't init the _vars variable).
344 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
345 the logical NOT of what they should return).
346 - Fixed bug in RegionGraph::RecomputeOR(s).
347 - Fixed bug in utils/create_dreg_fg:
348 graph structure was not random for given parameters (forgot to call srand()).
349 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
350 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
351 that consists of one outer region only.
352 - Fixed INIT bug in LCBP2::UpdatePancake().
353 - Fixed MaxDiffs flow (except for MR).
354
355 New functionality
356
357 - HAK supports several default cluster choices:
358 minimal (only factors)
359 delta (Markov blankets)
360 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
361 Only the maximal clusters are used as outer clusters.
362 - Implemented TreeEP. It generalizes the heuristic method described in the
363 Minka & Qi paper for obtaining a tree with the most relevant interactions to
364 higher order interactions. Almost all optimizations described in the Minka & Qi
365 paper are used, except that evidence is passed over the whole tree instead of
366 relevant subsets (the latter is almost implemented but buggy). Also added
367 alternative (worst-case) algorithm that uses a maximum spanning tree on the
368 weighted graph where the weight between neighbours i and j is given by
369 N(psi,i,j), where psi is the product of all the factors involving both i and j
370 (which is an upper bound on the effective interaction between i and j).
371 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
372 to be able to handle connectivities larger than 3 (in principle, up to 32).
373 It supports different initialization methods (the original RESPPROP,
374 the CLAMPING method and EXACT which uses JTree) and different update methods
375 (FULL and LINEAR).
376 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
377 networks and uses some approximate inference method on them for calculating
378 marginals.
379 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
380 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
381 interactions and LCBPL is LCBPI improved for higher-order interactions.
382 - Wrote one single program utils/createfg for creating various types of
383 random factor graphs.
384 - Wrote utility to visualize factor graphs using graphviz.
385 (it uses the BOOST Program Options library)
386 - Added fginfo utility that displays some info about a .fg file.
387 - Implemented Factor::strength function that calculates the potential strength
388 N(psi,i,j) between variables i and j as described in cs.IT:0504030
389 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
390 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
391 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
392 - Implemented a MATLAB interface ai_potstrength for Factor::strength
393 - Added Martijn's x2x
394
395 Improvements of existing code
396
397 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
398 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
399 associates outer region indices to factor indices (no powers yet, this
400 is deemed superfluous) and provides functions to recompute (some of) the
401 outer regions from the factors.
402 - InfAlg descendants run() methods now stop immediately and return NAN in case
403 they detect NANs. Only BP does not do NAN checking for performance reasons.
404 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
405 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
406 timing and convergence criteria.
407 - Implemented logZ() for JTree. It does the calculation during message-passing.
408 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
409 hopefully this will give more accurate approximations.
410 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
411 for a faster way of calculating marginals, which does not require a call to init()
412 nor cloning the whole object for each clamping. This leads to a significant speedup.
413 - LCBP (and LCBP2) now have complete flexibility in the specification of the
414 inner method, i.e. the method used to generate the initial cavity approximations.
415 One can pass two strings, a name and a properties string, and LCBP simply invokes
416 newInfAlg to construct the corresponding inference algorithm and uses the generic
417 marginal functions to approximate cavity marginals.
418 - Replaced the global "method" variable by local properties and removed ai.h
419 - Added some methods to Factor (operators *, *=, /, /= with doubles as
420 second argument, operators -, +=, -= with other Factors as second
421 arguments, randomize(), RemoveFirstOrderInteractions) and similar
422 operations to Prob
423 - Moving towards boost::program_options for handling command line arguments
424 (tests/test is done).
425 - Renamed some FactorGraph methods:
426 nr_vars -> nrVars
427 nr_factors -> nrFactors
428 varind -> findVar
429 factorind -> findFactor
430 makeFacCavity -> makeFactorCavity
431 - LCBP_SEQMAXRES has been removed because it did strange things.
432 - Implemented RandomDRegularGraph
433 - Implemented JTree::calcMarginal for marginals that are not confined
434 within one cluster (using cut-set conditioning).
435 - Added isConnected() method to FactorGraph (some methods do not work with
436 disconnected factor graphs).
437 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
438 - Removed single node interaction "correction" code from clamping methods
439 - Removed calcCavityDist and calcCavityDist2ndO
440 - No longer depends on GSL.
441 - Increased portability by combining platform dependant utility functions
442 in util.{h,cpp}.
443 - Wrote *.m files providing help
444
445 Testing framework
446
447 - Made a new and significantly improved testing framework that provides most
448 functionality from the command line.
449 - The basis is provided by tests/test, which uses the newInfAlg functionality
450 and enables the user to easily compare from the command line different
451 inference methods on a given factorgraph. All parameters can be specified.
452 Output consists of CPU time, average and maximum single variable marginal
453 errors, relative logZ error and MaxDiff().
454 - tests/aliases.conf contains aliases for standard combinations of methods
455 and their options (which can be used in tests/test).
456 - tests/large contains several bash/python scripts that create random factor
457 graphs, compare several approximate inference algorithms (using tests/test) and
458 allow for easy visualization of the results using PyX.
459 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
460 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
461 regression testing).
462 - Added a regression test to the Makefile which is included in the standard
463 target. It compares all inference methods on tests/testfast.fg with the
464 results stored in tests/testfast.out
465
466 Miscellaneous
467
468 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
469 - Experimental MATLAB code added for StarEP approximation on cavity
470 - Renamed project to libDAI and changed directory name accordingly.
471 - Renamed JunctionTree to JTree.
472 - Fixed licensing (now it's officially GPL).
473 - Improved README
474
475
476 revision 252
477 ------------
478
479 Functionality
480 - Added RegionGraph, GBP, CVM and HAK (double-loop).
481 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
482 RegionGraph.
483 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
484 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
485 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
486 it over all subsuming outer regions. See README for when negative factors are known to work
487 and when not.
488 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
489 it does not automatically merge factors anymore.
490 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
491 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
492 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
493 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
494 such that it does not store the complete pancakes, but represents them as little factor graphs).
495
496 Implementation / code
497 - Made a seperate type WeightedGraph, which until now only implements Prim's
498 maximal spanning tree algorithm and is only used by the junction tree code. It might
499 be good to make it a class somewhere in the future and extend it's interface.
500 - Made a seperate class ClusterGraph, which is only used by the junction tree
501 code. It's main purpose is a graph-theoretical variable elimination algorithm.
502 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
503 - Massive code cleanup, moving towards "generic" programming style, using
504 multiple inheritance and polymorphism.
505 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
506 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
507 that can be used by FactorGraph-based DAIAlgs.
508 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
509 and VarSet) and provides functionality for it (which is used by TFactor<T>).
510 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
511 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
512 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
513 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
514 o using Prob's instead of Factor's;
515 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
516 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
517 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
518 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
519 that takes the cavitydists and multiplies them with the relevant factors. This
520 resulted in an API change in AI which now accepts and returns initial cavitydists
521 instead of initial pancakes.
522
523 Minor changes
524 - Started writing DoxyGen documentation
525 - Renamed lcptab2fg.m matlab/ai_writefg.m
526 - Moved all matlab stuff to matlab/
527 - More detailed reporting (also reports clocks used).
528 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
529 - Improved testing suite.
530 - Removed logreal support.
531 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
532 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
533 full and periodic 2D Ising networks according to some command line parameters.
534 - Now logZ really returns logZ instead of -logZ.
535 - Added FactorGraph::WriteToDotFile
536
537
538 0.1.4 (2006-04-13)
539 ------------------
540 - Added file IO routines to read and write factorgraphs.
541 - Added L-infinity normalization for use with (partially) negative factors.
542 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
543 handle (partially) negative factors.
544 - Added test suite.
545 - All probabilities are now represented using double instead of LogReal<double>.
546 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
547 - Combined several variants of BP into doBP. Several update schemes possible.
548 Now uses precalculated indices for optimization.
549 - Renamed Node -> Var and Potential -> Factor.
550 - Extensive code cleanup. More use of OO techniques. Changed API.
551 - MaxIter now means maximum number of passes (corresponding to number of
552 _parallel_ updates).
553 - MaxDiff now means the maximum L-infinity distance between the updated and
554 original single variable beliefs, for all AI methods.
555 - Implemented RBP which converges faster than BP for difficult problems.
556 - Now uses method parameter which is a bitmask combining outmethod and inmethod
557 (see ai.h).
558
559
560 0.1.3 (2006-03-22)
561 --------------------
562 - All AI methods now return maxdiff
563 - ai.cpp:
564 o Now returns maxdiffinner and maxdiffouter
565 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
566 o New InitCav outermethod (only create initial cavity distributions)
567 - bp.cpp:
568 o New CavityDist2ndO which estimates 2nd order cavity interactions
569 - Makefile:
570 o Bugfix: removed dependencies on algwim.*
571
572
573 0.1.2 (2006-02-28)
574 --------------------
575 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
576 - Added the possibility to provide initial cavity distributions as an input
577 argument to ai (not much error checking is done, so be careful).
578 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
579 the output arguments Q, Q0 of ai).
580 - Removed algwim.* since it does not work.
581
582
583 0.1.1 (2006-02-28)
584 --------------------
585 - The constructors of (Log)FactorGraph and LogFactorGraph from a
586 vector<(Log)Potential> now merge potentials to prevent short loops (of length
587 4) in the factor graph. These are used in ai to construct the factor graphs
588 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
589 of BipGraph checks for the existence of short loops.
590 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
591 description in the help).
592 - ai does not hook cout anymore (which caused weird segfaults).
593 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
594 - Removed network.* since it is not useful.
595
596
597 0.1.0 (2006-02-28)
598 --------------------
599 First version worthy a version number.