Merge branch 'master' of git.tuebingen.mpg.de:libdai
[libdai.git] / ChangeLog
1 libDAI-0.2.7 (2010-08-19)
2 -------------------------
3
4 * Replaced all Name members by name() virtual functions and removed global variable DAINames
5 (this fixes a bug in matlab/dai.cpp reported by Thomas Mensink)
6 * Removed interfaces deprecated in 0.2.6.
7 * Fixed a bug in JTree::findMaximum() (reported by zhengyun84 and Dhruv Batra):
8 if one or more variables had a MAP belief with more than one maximum, an
9 incorrect MAP state could result.
10
11
12 libDAI-0.2.6 (2010-08-05)
13 -------------------------
14
15 New features:
16 * Added decimation algorithm DecMAP for MAP inference (decmap.h/cpp).
17 * Added source code for one of the winning solvers of the
18 UAI 2010 Approximate Inference Challenge (examples/uai2010-aie-solver.cpp).
19 * Added support for reading files in the UAI Approximate Inference Challenge
20 format, supporting both the 2006/2008 evidence file format and the 2010
21 evidence file format (io.h/cpp).
22
23 Miscellaneous improvements:
24 * 'maxtime' property added to various algorithms (BP, Gibbs, HAK, TreeEP)
25 for setting an upper limit on execution time.
26 * 'maxmem' property added to JTree for setting an upper limit on memory usage.
27 * SmallSet:
28 - Added SmallSet::erase( const T& t ).
29 * VarSet:
30 - nrStates() now returns a long double instead of a size_t.
31 * Permute:
32 - Added ranges() accessor.
33 - Added inverse() method.
34 - Added optional reverse argument to Permute( const std::vector<Var>& ) constructor.
35 * Factor:
36 - Added createFactorDelta( const VarSet& vs, size_t state ).
37 * ClusterGraph:
38 - Added ClusterGraph(const FactorGraph& fg, bool onlyMaximal) constructor.
39 - Added findCluster( const VarSet& cl ).
40 - Added elimVar( size_t i ).
41 - Added 'maxStates' argument to VarElim( EliminationChoice f, size_t maxStates=0 ).
42 * FactorGraph:
43 - Added isMaximal(size_t).
44 - Added maximalFactor(size_t).
45 - Added FactorGraph::logScore( const std::vector<size_t>& statevec ).
46 * Gibbs:
47 - Added 'restart' property.
48 - Added Gibbs::findMaximum() for MAP inference.
49 * HAK:
50 - Optimized region graph construction for HAK/GBP with clusters=BETHE.
51 * examples/examples_imagesegmentation.cpp:
52 - [Peter Rockett] Improved Makefiles for image segmentation example.
53 - Added build flag to specify the CImg version.
54 * util.h/cpp:
55 - Added fromString<>( const std::string& x ).
56
57 Interface changes (the old interface is marked obsolete and will be removed in the next release):
58 * Added InfAlg::setMaxIter(size_t) for setting the maximum number of iterations.
59 * Deprecated Graph::Neighbor, BipartiteGraph::Neighbor and DAG::Neighbor
60 and replaced them by a globally defined Neighbor structure
61 * Deprecated Graph::Neighbors, BipartiteGraph::Neighbors and DAG::Neighbors
62 and replaced them by a globally defined Neighbors type
63 * Deprecated Graph::Edge, BipartiteGraph::Edge and DAG::Edge
64 and replaced them by a globally defined Edge type
65 * Renamed 'iters' property of Gibbs algorithm into 'maxiter'.
66 * ClusterGraph::findVar( const Var& n ) no longer throws an exception if the
67 variable is not found.
68 * Deprecated 'void tokenizeString( const string&, vector<string>&, const string& )'
69 and replaced it with an improved version
70 'vector<string> tokenizeString( const string&, bool, const string& )'
71 * Removed interfaces deprecated in 0.2.5.
72
73 Bug fixes:
74 * Fixed a problem with isnan() on FreeBSD; it is now in the dai namespace.
75 * Workaround for older g++ compilers (e.g. version 4.0.0 on Darwin 9.8.0)
76 which have problems when comparing const_reverse_iterator with
77 reverse_iterator.
78 * [Matt Dunham] Fixed a bug in Factors2mx in src/matlab/matlab.cpp
79 (segfault if factors depending on 0 variables were passed to MatLab)
80
81
82 libDAI-0.2.5 (2010-05-09)
83 -------------------------
84
85 New features:
86 * Added unit tests for var, smallset, varset, graph, dag, bipgraph,
87 weightedgraph, enum, util, exceptions, properties, index, prob,
88 factor, factorgraph, clustergraph, regiongraph, daialg, alldai
89 * [Ofer Meshi] Added a script for converting from FastInf to libDAI format
90 * Added utils/uai2fg, a utility to convert the UAI inference competition file
91 formats to the libDAI factor graph file format
92 * Added dag.h/cpp, an implementation of Directed Acyclic Graphs
93 * Added examples/example_imagesegmentation
94
95 Miscellaneous improvements:
96 * TRWBP:
97 - Added initialization of TRWBP weights by sampling spanning trees
98 * MF:
99 - Added an "init" option that allows to initialize randomly
100 - Added an "updates" option that allows to choose between standard
101 mean field and "hard-spin" mean field
102 * MR:
103 - rewrote response propagation implementation with help of BBP
104 - now uses GraphAL to represent the Markov graph
105 - miscellaneous smaller cleanups
106 * TreeEP:
107 - Now also supports disconnected factor graphs
108 * JTree:
109 - Now also supports disconnected factor graphs
110 * ExactInf:
111 - Added findMaximum()
112 * RegionGraph:
113 - Added error checking code
114 - Changed the way a RegionGraph is streamed to an std::ostream.
115 * ClusterGraph:
116 - Added nrVars() method
117 - Added var( size_t ) method
118 - Added cluster( size_t ) method
119 * FactorGraph:
120 - clamped() now contains a delta factor for the clamped variable
121 - Added MarkovGraph()
122 * TFactor:
123 - Added takeAbs()
124 - Added takeExp()
125 - Added takeLog( bool )
126 - Added operator-() const
127 - Added sumAbs() const
128 - Added operator==( const TFactor<T> &y )
129 - Added get(size_t), set(size_t,T)
130 * TProb:
131 - Added operator==( const TProb<T> &q )
132 - accumulate() now also applies op2 to init
133 - operator/= (T x) now yields 0 when dividing by 0
134 - Added resize(size_t)
135 - Added get(size_t) and set(size_t,T)
136 - Changed format of TProb<T> when streamed to an ostream
137 * multifor:
138 - Added reset()
139 * PropertySet:
140 - Added size()
141 - Added clear()
142 - Added erase()
143 * util.h/cpp:
144 - Added std::string toString( const T& x )
145 * weightedgraph.h/cpp:
146 - Added option to MaxSpanningTree and MinSpanningTree for
147 choosing between Prim's algorithm and Kruskal's algorithm
148 - Better error checking in RootedTree constructor
149 - Added GraphEL::GraphEL( const GraphAL& G ) constructor
150 * BipartiteGraph:
151 - Added hasEdge()
152 - Added findNb1()
153 - Added findNb2()
154 - Added nb1Set()
155 - Added nb2Set()
156 - Added operator==( const BipartiteGraph& )
157 - Added BipartiteGraph( size_t nr1, size_t nr2 ) constructor
158 - Added operator<<( std::ostream&, const BipartiteGraph& )
159 * GraphAL:
160 - Added hasEdge(size_t,size_t)
161 - Added nbSet(size_t)
162 - Added operator==( const GraphAL& )
163 - Added operator<<( std::ostream&, const GraphAL& )
164 * SmallSet:
165 - Added insert( const T& t ) method
166 * Improved regression test
167 * Made all "verbose" properties optional
168 * utils/createfg now has a new factor type ('ISINGUNIFORM') and the old
169 'ISING' factor type has been renamed to 'ISINGGAUSS'
170 * tests/testdai option "marginals" now has five possible values: NONE
171 outputs no marginals, VAR only variable marginals, FAC only factor
172 marginals, VARFAC both types of marginals, and ALL outputs all
173 marginals calculated by the algorithm.
174 * Compressed Makefile
175
176 Interface changes (the old interface is marked obsolete and will be removed in the next release):
177 * Removed RandomDRegularGraph(), please use createGraphRegular() instead
178 * TreeEP:
179 - Changed construct( const RootedTree& ) into
180 construct( const FactorGraph&, const RootedTree& )
181 * JTree:
182 - Changed construct( const std::vector<VarSet>&, bool ) into
183 construct( const FactorGraph&, const std::vector<VarSet>&, bool )
184 - Changed GenerateJT( const std::vector<VarSet> & )
185 into GenerateJT( const FactorGraph &, const std::vector<VarSet> & )
186 * RegionGraph:
187 - Made (previously public) members G, ORs, IRs and fac2OR protected and
188 added DAG() accessor which returns a reference to the region graph DAG
189 structure (currently implemented as a BipartiteGraph).
190 - Renamed calcCountingNumbers() into calcCVMCountingNumbers() and made it
191 protected, because exposing it to the world serves no purpose.
192 - Removed partial constructor RegionGraph( const FactorGraph& fg )
193 - Made RecomputeORs(), RecomputeORs( const VarSet& ) and RecomputeOR( size_t )
194 protected and renamed them by changing the "Recompute" into "recompute",
195 because exposing them to the world serves no purpose.
196 * ClusterGraph:
197 - Made (previously public) members G, vars and clusters private and added
198 bipGraph(), vars() and clusters() methods which offer read-only access
199 to these members.
200 - Deprecated toVector()
201 - Renamed size() into nrClusters()
202 * FactorGraph:
203 - Renamed Cliques() into maximalFactorDomains() and made it faster
204 - findVars( const VarSet& ) now returns a SmallSet<size_t>
205 and its argument now has a const-qualifier (which fixes a small bug).
206 - Made (previously public) member G private and added the
207 bipGraph() method, which offers read-only access to it.
208 - Deprecated the iterator interface:
209 o FactorGraph::iterator typedef
210 o FactorGraph::const_iterator typedef
211 o FactorGraph::begin() members
212 o FactorGraph::end() members
213 - Deprecated factor(size_t) which offered write access to a factor
214 because using this functionality in the descendant RegionGraph is dangerous,
215 as the outer regions are not automatically recomputed.
216 * TFactor:
217 - Renamed states() into nrStates()
218 - Added get(size_t) and set(size_t,T) operators;
219 get() is equivalent to "operator[](size_t) const" and set() should
220 be used instead of the non-const operator[], which has been deprecated
221 * TProb:
222 - Deprecated TProb( TIterator begin, TIterator end, size_t sizeHint=0 )
223 constructor: the sizeHint argument no longer defaults to 0
224 - Deprecated accumulate( T init, binOp op1, unOp op2 );
225 instead, accumulateSum( T init, unOp op ) and
226 accumulateMax( T init, unOp op, bool minimize ) should be used.
227 - Deprecated TProb::NormType and TProb::DistType;
228 ProbNormType and ProbDistType should be used instead.
229 - Fixed bug by renaming operator<=() to operator<()
230 - Added get(size_t) and set(size_t,T) operators;
231 get() is equivalent to "operator[](size_t) const" and set() should
232 be used instead of the non-const operator[], which has been deprecated
233 * PropertySet:
234 - Renamed Set() -> set()
235 - Renamed Get() -> get()
236 - Renamed GetAs<T>() -> getAs<T>()
237 - Renamed ConvertTo<T>() -> convertTo<T>()
238 * util.h/cpp:
239 - Removed max( const std::vector<Real> &v )
240 * weightedgraph.h/cpp:
241 - Renamed MaxSpanningTreePrims into MaxSpanningTree
242 - Renamed MinSpanningTreePrims into MinSpanningTree
243 - The vertices in DEdge and UEdge are now named "first" and "second"
244 for compatibility with a std::pair<size_t,size_t>
245 * BipartiteGraph:
246 - delta1() and delta2() now return a SmallSet<size_t> instead of a vector<size_t>
247 * SmallSet:
248 - The sizeHint argument of the iterator constructor
249 SmallSet::SmallSet( TIterator begin, TIterator end, size_t sizeHint=0 )
250 no longer has a default value in order to avoid confusion with the
251 SmallSet::SmallSet( const T &t1, const T &t2 )
252 constructor.
253
254 Bug fixes:
255 * [Stefano Pellegrini] Fixed bug in JTree::findMaximum()
256 * [Stefano Pellegrini] Fixed bug in BP[logdomain=1,inference=MAXPROD]
257 * Fixed some bugs in the MatLab interface build system
258 * Fixed a bug in utils/fginfo.cpp
259 * Fixed a bug in JTree::findMaximum() and simplified the code
260 * Fixed bug in BBPCostFunction::operator=() which prevented the desired
261 assignment from happening
262 * RegionGraph::WriteToFile( const char* ), RegionGraph::ReadFromFile( const char * )
263 and RegionGraph::printDot( std::ostream& ) incorrectly called their respective
264 FactorGraph ancestor methods; this has been corrected by letting them throw a
265 NOT_IMPLEMENTED exception.
266 * Fixed bug in FactorGraph::clone()
267 * Fixed bug in min( const TFactor<T> &, const TFactor<T> & )
268 * Fixed bug in max( const TFactor<T> &, const TFactor<T> & )
269 * Fixed bug by renaming TProb<T>::operator<=() to TProb<T>::operator<()
270 * Fixed bug in PropertySet::setAsString<T>()
271 * Fixed a bug in rnd_seed()
272 * BipartiteGraph:
273 - Fixed bug in eraseNode1()
274 - Fixed bug in eraseNode2()
275 - Fixed bug in isTree()
276 * GraphAL:
277 - Fixed bug in nrEdges()
278 - Fixed bug in addEdge()
279 - Fixed bug in isTree()
280 - Fixed bug in eraseNode()
281 - Fixed bug in printDot()
282 * Fixed bug in createGraphGrid3D()
283 * Fixed bug in createGraphRegular()
284
285
286 libDAI-0.2.4 (2010-02-11)
287 -------------------------
288
289 New features:
290 * Implemented Tree-Reweighted BP
291 * [Frederik Eaton] Implemented Fractional Belief Propagation
292
293 Miscellaneous improvements:
294 * Improved documentation
295 * [Frederik Eaton] Added constructors for BBPCostFunction
296 * [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
297 * [Frederik Eaton] Added unary minus to TProb<>
298 * [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
299 * [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
300 * tests/testdai option "marginals" now has three possible values: NONE
301 outputs no marginals, VAR only variable marginals, and ALL outputs all
302 marginals calculated by the algorithm.
303 * Strengthened convergence criteria of various algorithms
304 * Added GraphAL, an adjacency list implementation for graphs,
305 similar to (but simpler than) BipartiteGraph
306 * Added some functionality to create various standard factors
307 (the functions whose names start with "createFactor")
308 * Added examples example_sprinkler_gibbs and example_sprinkler_em
309 * Implemented various heuristics for choosing a variable elimination sequence
310 in JTree
311 * Added BETHE method for GBP/HAK cluster choice
312 * Made alias support official part of the library
313
314 Build system:
315 * Moved platform independent build options into Makefile.ALL
316 * Windows platform now needs Boost 1.37 or higher
317
318 Code cleanup:
319 * Cleaned up utils/createfg and tests/testdai
320 * Cleanup of some duplicate code in BP, FBP, TRWBP
321
322 Interface changes (the old interface is marked obsolete and will be removed in the next release):
323 * Removed obsolete/deprecated stuff
324 * Renamed Graph into GraphEL (for Graph, implemented as Edge List)
325 * Renamed some functions of BipartiteGraph:
326 add1() -> addNode1()
327 erase1() -> eraseNode1()
328 nr1() -> nrNodes1()
329 add2() -> addNode2()
330 erase2() -> eraseNode2()
331 nr2() -> nrNodes2()
332 * Renamed some functions in ClusterGraph:
333 ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill()
334 ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) )
335 ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
336 * Changed interface of one RegionGraph constructor
337 * Renamed "Clamped BP" into "Conditioned BP"
338
339 Bug fixes:
340 * Fixed regression in scripts/regenerate-properties (now all errors are
341 gathered before throwing the exception, as used to be the case)
342 * Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
343 * [Alexander Schwing] Fixed error in BP that occured with damping
344 and using log-domain updates
345 * Fixed bug in HAK for trivial region graphs (with only one outer region
346 and no inner regions), reported by Alejandro Lage.
347 * Fixed long-standing bug in TreeEP (now, within-loop propagation optimization works)
348
349
350 libDAI-0.2.3 (2009-11-16)
351 -------------------------
352
353 New features:
354 * Complete doxygen documentation (although more detailed documentation still
355 has to be written)
356 * [Charles Vaske] Added parameter learning for conditional probabilities by
357 Expectation Maximization
358 * [Patrick Pletscher] Added SWIG wrapper code for experimental python and
359 octave interfaces
360 * Added Max-Product functionality to JTree
361 * [Frederik Eaton] Added Back-Belief-Propagation
362 * [Frederik Eaton] Added approximate inference method "Clamped Belief Propagation"
363 * [Frederik Eaton] Added approximate inference method "Gibbs sampling"
364
365 Code cleanup:
366 * Updated copyright headers
367 * Cleaned up error handling by introducing the DAI_THROWE macro
368 * Introduced DAI_DEBASSERT macro to abbreviate a common pattern
369 * Replaced the standard assert() macro by DAI_ASSERT, which throws a
370 dai::Exception and is even active if NDEBUG is defined
371 * Removed all the virtual default constructors *::create(), as they are not used
372 * [Frederik Eaton] Removed unnecessary copy constructors and assignment operators
373 * [Frederik Eaton] Change cout to cerr in warnings and error messages
374
375 Miscellaneous improvements:
376 * BipartiteGraph:
377 - Added eraseEdge( size_t n1, size_t n2 )
378 - [Frederik Eaton] Improved documentation of Neighbor
379 * TProb<T>:
380 - Added divided_by(const TProb<T>&) const
381 - Added constructor TProb<T>( const std::vector<S> &v )
382 - Added size_t draw(), which draws a random index
383 - [Frederik Eaton] Added setUniform()
384 - [Frederik Eaton] Added sumAbs()
385 - [Frederik Eaton] Added argmax()
386 - [Giuseppe Passino] Added begin(), end()
387 * TFactor<T>:
388 - [Giuseppe Passino] Added begin(), end()
389 - [Charles Vaske] Added TFactor( const std::vector<Var> &vars, const std::vector<T> &p ),
390 which reorders variables to canonical ordering before storing the table
391 - Added constructor TFactor<T>( const VarSet &vars, const std::vector<S> &v )
392 - Extended functionality of TFactor<T>::operators +,-,+=,-= to handle different VarSets
393 - Added TFactor<T>::maxMarginal (similar to marginal but with max instead of sum)
394 * State:
395 - [Giuseppe Passino] Added prefix ++ operator
396 * Permute:
397 - [Charles Vaske] Added constructor in Permute for canonical variable ordering
398 * FactorGraph:
399 - [Frederik Eaton] Added clampVar()
400 - [Frederik Eaton] Added clampFactor()
401 - [Giuseppe Passino] Added begin(), end()
402 * PropertySet:
403 - Added keys(), for getting all keys
404 - [Frederik Eaton] Added default constructor
405 - [Frederik Eaton] Added constructor from string
406 * InfAlg:
407 - Added setProperties(), getProperties() and printProperties()
408 - [Frederik Eaton] Added beliefV(), beliefF()
409 * ExactInf:
410 - Added calcMarginal(const VarSet &)
411 * HAK:
412 - Added "init" parameter to allow for random initialization
413 * BP:
414 - [Giuseppe Passino] Added findMaximum(), which can be used after running
415 max-product BP to construct a global state with maximum probability
416 * JTree:
417 - Added findMaximum(), which can be used after running
418 max-product JTree to construct a global state with maximum probability
419 * MatLab interface:
420 - MEX file dai now also returns variable and factor beliefs
421 - [Sebastian Nowozin] MEX file dai now also optionally returns the MAP state
422 (only for BP and JTree)
423 * README is now created automatically from doxygen documentation
424 * [Frederik Eaton] Added script for automatically generating properties code (used by CBP and BBP)
425 * [Frederik Eaton] Added newInfAlgFromString to alldai.h/cpp
426 * [Frederik Eaton] Added some utility macros (DAI_PV, DAI_DMSG, DAI_IFVERB)
427 and functions (concat(),rnd()) to util.h
428 * Changed output stream operator<< for Var and VarSet
429 * [Frederik Eaton] Improved parsing code in tests/testdai to allow recursive
430 alias substitutions
431 * [Frederik Eaton] Added useful aliases to aliases.conf
432 * [Giuseppe Passino] Optimised maximum-residual BP by using a reversed ordered
433 set instead of the linear search (which can yield enormous speedups - a
434 factor 500 has been measured on a binary Ising grid with 128x128 variables!)
435 * Added debug assertions to Var which check for inconsistent dimensions of
436 variables with the same labels
437 * toc() now returns POSIX system time with maximum accuracy of microseconds
438 * Exception objects now remember their error code
439 * Examples:
440 - Moved example.cpp to examples/
441 - Added examples/example_bipgraph.cpp
442 - Added examples/example_varset.cpp
443 - Added examples/example_sprinkler.cpp
444 - Added examples/example_permute.cpp
445 - Added python and octave ports for examples/example_sprinkler.cpp
446
447 Build system:
448 * Improved Makefile:
449 - Merged Makefile.win and Makefile.shared into Makefile
450 - Macros DAI_VERSION and DAI_DATE have been introduced,
451 in order to store this information in a central place
452 - Introduced CCNODEBUGFLAGS in Makefile
453 - Switched Makefile.win to GNU Make syntax
454 - [Frederik Eaton] Added TAGS, lib targets to Makefile
455 * Compatibility:
456 - [Peter Gober] libDAI can now be built on Cygwin
457 - [Dan Preston] libDAI can now be built on Mac OS X
458 - Changed regression test so that it also works under Windows
459
460 Interface changes (the old interface is marked obsolete and will be removed in the next release):
461 * Var:
462 - Variable labels are now nonnegative (of type size_t)
463 * VarSet:
464 - Replaced calcState() by non-member calcLinearState()
465 - Replaced calcStates() by non-member calcState()
466 * Permute:
467 - Renamed convert_linear_index into convertLinearIndex
468 * TProb<>:
469 - Replaced log0() by log(true)
470 - Replaced takeLog0() by takeLog(true)
471 - Removed hasNonPositives()
472 - Renamed minVal() to min()
473 - Renamed maxVal() to max()
474 - Renamed totalSum() to sum()
475 * TFactor<>:
476 - Replaced log0() by TFactor<T>::log(true)
477 - Removed divided_by, use operator/ instead
478 - Removed divide, use operator/= instead
479 - Removed partSum(const VarSet&), use marginal(const VarSet&,false) instead
480 - Renamed minVal() to min()
481 - Renamed maxVal() to max()
482 - Renamed totalSum() to sum()
483 * FactorGraph:
484 - Changed clamp and clamp interfaces (the variable to be
485 clamped is now indicated by its index, not as a Var)
486 * RegionGraph:
487 - Renamed Check_Counting_Numbers into checkCountingNumbers
488 - Renamed Calc_Counting_Numbers into calcCountingNumbers
489 * Miscellaneous:
490 - Renamed Treewidth(const FactorGraph &) into boundTreewidth(const FactorGraph &)
491 - Replaced UEdgeVec by Graph
492 - Replaced DEdgeVec by new RootedTree class
493 - Moved functionality of GrowRootedTree() into constructor of RootedTree
494 - Merged calcPairBeliefsNew() into calcPairBeliefs()
495 - Removed calcMarginal2ndO()
496 - Renamed smallSet<T> to SmallSet<T>
497 - Removed class Diffs
498 - [Frederik Eaton] Added backwards compatibility layer for edge interface to
499 BipartiteGraph and FactorGraph (which will be obsoleted soon)
500
501 Bug fixes:
502 * Fixed reversal of min and max in
503 TFactor<T> min( const TFactor<T> &, const TFactor<T> & )
504 TFactor<T> max( const TFactor<T> &, const TFactor<T> & )
505 * [Sebastian Nowozin] Fixed memory leak in MEX file dai
506 * [Frederik Eaton] In PropertySet::getStringAs(), check for typeid(ValueType)
507 before typeid(std::string) (this fixes a strange bug for empty string property)
508 * Added work-around for bug in Boost Graph Library
509 * Fixed bug in MaxSpanningTree (it wrongly assumed that the tree was not empty).
510 * Fixed bug in calcMarginal and calcPairBeliefs where states with zero probability
511 mass were clamped, leading to NaNs or assertion errors (thanks to Dan Preston
512 for reporting this)
513
514
515 libDAI-0.2.2 (2008-09-30)
516 -------------------------
517
518 New features:
519 * Approximate inference methods now report the number of iterations needed.
520 * Added damping to various algorithms to improve convergence properties.
521 * Added more features to utils/createfg for creating factor graphs.
522 * Added ExactInf class for brute force exact inference.
523 * [Giuseppe Pasino] Added "logdomain" property to BP, a boolean that controls
524 whether calculations are done in the log-domain or in the linear domain;
525 doing calculations in the log-domain may help if the numerical range
526 of a double is too small.
527 * [Claudio Lima] Added Max-Product functionality to BP.
528 * Improved documentation.
529
530 Improved architecture:
531 * Added Exceptions framework.
532 * Pervasive change of BipartiteGraph implementation (based on an idea by
533 Giuseppe Passino). BipartiteGraph no longer stores the node properties
534 (former _V1 and _V2), nor does it store a dense adjacency matrix anymore,
535 nor an edge list. Instead, it stores the graph structure as lists of
536 neighboring nodes. This yields a significant memory/speed improvement for
537 large factor graphs, and is more elegant as well. Iterating over neighbors is
538 made easy by using boost::foreach.
539 * Added conditional compilation of inference methods.
540 * VarSet is now implemented using a std::vector<Var> instead of a
541 std::set<Var>, which yields a significant speed improvement. Furthermore,
542 the implementation has been generalized, resulting in the small_set<T> class
543 which can be used to represent sets of small cardinality; VarSet is the
544 specialization with T = Var.
545 * Improved ClusterGraph implementation, yielding significant speedups
546 for the JunctionTree algorithm on large factorgraphs.
547
548 Code cleanup:
549 * Moved everything into namespace "dai".
550 * Renamed DEBUG to DAI_DEBUG to avoid conflicts.
551 * Replaced ENUM2,ENUM3,ENUM4,ENUM5,ENUM6 by single DAI_ENUM macro.
552 * Removed utils/remove_short_loops and matlab/remove_short_loops.
553 * Replaced sub_nb class in mr.h by boost::dynamic_bitset.
554 * Improved index.h:
555 - Renamed Index -> IndexFor
556 - Added some .reserve()'s to IndexFor methods which yields a
557 25% speedup of testregression
558 - Replaced multind by Permute
559 - Added MultiFor
560 - Added State
561 * New funcstionality of factor.h.
562 * Moved Properties and MaxDiff frameworks from InfAlg to each individual
563 inference algorithm, because the Properties framework was not as
564 convenient as I hoped, and not every inference algorithm needs a maxdiff
565 variable. Also, replaced some FactorGraph functionality in InfAlg by a
566 function that returns the FactorGraph. The result is cleaner (less
567 entangled) code.
568 * Removed x2x.
569 * Replaced Complex with real numbers (negative potentials are just too rare
570 to warrant the additional "complexity" :)).
571
572 Miscellaneous improvements:
573 * Now compiles also with MS Visual C++ (thanks to Jiuxiang Hu) and with
574 GCC under Cygwin.
575 * Contributions by Peter Gober:
576 - Renamed variable _N in mr.* for compatibility with g++ under Cygwin.
577 * Misc contributions by Giuseppe Passino:
578 - removed "using namespace std;" from header files - bad practice;
579 - moved header files in include/dai and sources in src;
580 - changed #ifndefs to GNU style;
581 - added extra warning checks (-W -Wextra) and fixed resulting warnings;
582 - dai::TProb:
583 o removed copy constructor and assignment operators (redundant);
584 o implementation of some methods via STL algorithms;
585 o added methods takeExp, takeLog, takeLog0 for transformation in-place;
586 o explicit constructor (prevents implicit conversion from size_t to TProb);
587 o added operator+,+=,-,-=, with argument T (for calculations in log-scale);
588 * Misc contributions by Christian Wojek:
589 - New FactorGraph constructor that constructs from given ranges of factors
590 and variables;
591 - Optimization of FactorGraph constructors using tr1::unordered_map.
592 * FactorGraph constructors no longer check for short loops (huge speed
593 increase for large factor graphs), nor for negative entries. Also, the
594 normtype is now Prob::NORMPROB by default.
595 * Improved MaxSpanningTreePrims algorithm (uses boost::graph).
596
597 Interface changes:
598 * VarSet::
599 - VarSet::stateSpace() -> nrStates(const VarSet &)
600 - VarSet( const std::set<Var> ) -> VarSet( begin, end, sizeHint=0 )
601 - VarSet( const std::vector<Var> ) -> VarSet( begin, end, sizeHint=0 )
602 - removed bool operator||
603 - operator&&(const VarSet&) -> intersects(const VarSet&)
604 - operator&&(const Var&) -> contains(const Var&)
605 * FactorGraph::
606 - delta(const Var &) -> delta(size_t)
607 - Delta(const Var &) -> Delta(size_t)
608 - makeCavity(const Var &) -> makeCavity(size_t)
609 - vars() -> vars
610 - factors() -> factors
611 - removed MakeFactorCavity(size_t)
612 - removed ExactMarginal(const VarSet &)
613 - removed ExactlogZ()
614 - removed updatedFactor(size_t)
615 - removed _normtype and NormType()
616 - removed hasShortLoops(...) and removeShortLoops(...)
617 - WriteToDotFile(const char *filename) -> printDot( std::ostream& os )
618 - undoProb(size_t) -> restoreFactor(size_t)
619 - saveProb(size_t) -> backupFactor(size_t)
620 - undoProbs(const VarSet &) -> restoreFactors(const VarSet &)
621 - saveProbs(const VarSet &) -> backupFactors(const VarSet &)
622 - ReadFromFile(const char*) returns void (throws on error)
623 - WriteToFile(const char*) returns void (throws on error)
624 - removed hasNegatives()
625 * RegionGraph::
626 - nr_ORs() -> nrORs()
627 - nr_IRs() -> nrIRs()
628 - ORs() -> ORs
629 - IRs() -> IRs
630 * *::Regenerate() -> *::construct()
631 * Renamed Index -> IndexFor
632 * Diffs:
633 - max() -> maxDiff()
634 - max_size() -> maxSize()
635 * Prob::max() -> Prob::maxVal()
636 * Factor::
637 - max() -> maxVal()
638 - part_sum() -> partSum()
639 * toc() in util.h now returns seconds as a double
640 * VarSet::operator&&
641 * Properties -> PropertySet
642
643
644 libDAI-0.2.1 (2008-05-26)
645 -------------------------
646
647 Bugfix release.
648 * added missing cstdio header in util.h
649 * fixed Properties in MR_CLAMPING_* and MR_EXACT_*
650 * added description of the factor graph fileformat
651 * improved Makefile
652
653
654 libDAI-0.2.0 (2006-11-30)
655 -------------------------
656
657 First public release.
658
659
660 0.1.5 (2006-11-30)
661 ------------------
662
663 Regressions
664
665 - tests/testlcbp and tests/testlcbp are broken.
666 - EXACT method does not work anymore.
667 - The Properties framework gives a speed penalty because of the lookup
668 costs involved; inner loops should be optimized.
669
670 General framework
671
672 - DAIAlg is now a template class; typedefs for DAIAlg<FactorGraph> and for
673 DAIAlg<RegionGraph> are provided. In this way, we do not have to write "wrapper"
674 functions to forward functionality from either FactorGraph or RegionGraph
675 to DAIAlg. Functionality like clamping can be implemented in FactorGraph
676 and in RegionGraph and no explicit interface is needed in descendants.
677 - New abstract base class InfAlg added, representing an inference algorithm,
678 from which DAIAlg<T> inherits. This solves the incompatibility problems of
679 DAIAlg<T> for different T (e.g. DAIAlg<FactorGraph> was incompatible with
680 DAIAlg<RegionGraph>). More work is required to reduce code duplication
681 (make FactorGraph part of InfAlg).
682 - Added generic interface (nrVars(), Vars(), nrFactors(), factor(size_t),
683 beliefs(), belief(VarSet &), ...) to InfAlg and descendants.
684 - Added a saveProbs/undoProbs interface to InfAlg and descendants that enables
685 one to save a few factors, modify them (e.g. clamp them), and then restore them
686 to their old values. Undo should also init the corresponding messages / beliefs.
687 This can be used if a given factor graph repeatedly needs to be clamped in
688 different ways and an approximation method is run for each clamping; using the
689 saveProbs/undoProbs can give a significant speed increase.
690 - Switched to a general Properties framework that handles the parameters of
691 all inference methods in a uniform manner. The Properties class is a map of
692 several properties in boost::any objects, indexed by their names (strings).
693 It can read from a stream and write to a stream. It is recursive, in the sense
694 that a Properties object can hold a variable of type Properties as well.
695 - Added a generic way of constructing inference algorithms from a factor graph,
696 name and properties object. Added the newInfAlg function which constructs
697 the requested object. This is used by LCBP, the Matlab interface and the
698 command line (test) interface.
699 - Added a generic enum framework for enum parameters. Although implemented as a
700 hack, it is quite useful in that it drastically simplifies and reduces the
701 amount of code for handling enum parameters.
702 - Provided generic functions for calculating marginals in different ways that
703 work for all approximate inference methods.
704
705 Bugfixes
706
707 - Fixed GBP free energy.
708 - Fixed bug in junctiontree (it didn't init the _vars variable).
709 - Corrected two bugs in operator&& and operator|| in VarSet (they returned
710 the logical NOT of what they should return).
711 - Fixed bug in RegionGraph::RecomputeOR(s).
712 - Fixed bug in utils/create_dreg_fg:
713 graph structure was not random for given parameters (forgot to call srand()).
714 - TreeEP bug workaround: use the complete junction tree instead of a subtree.
715 - Fixed bug in JTree::HUGIN() and JTree:ShaferShenoy() in case of junction tree
716 that consists of one outer region only.
717 - Fixed INIT bug in LCBP2::UpdatePancake().
718 - Fixed MaxDiffs flow (except for MR).
719
720 New functionality
721
722 - HAK supports several default cluster choices:
723 minimal (only factors)
724 delta (Markov blankets)
725 loop (all loops consisting of loops consisting of <loopdepth> or less variables)
726 Only the maximal clusters are used as outer clusters.
727 - Implemented TreeEP. It generalizes the heuristic method described in the
728 Minka & Qi paper for obtaining a tree with the most relevant interactions to
729 higher order interactions. Almost all optimizations described in the Minka & Qi
730 paper are used, except that evidence is passed over the whole tree instead of
731 relevant subsets (the latter is almost implemented but buggy). Also added
732 alternative (worst-case) algorithm that uses a maximum spanning tree on the
733 weighted graph where the weight between neighbours i and j is given by
734 N(psi,i,j), where psi is the product of all the factors involving both i and j
735 (which is an upper bound on the effective interaction between i and j).
736 - Implemented MR (MontanariRizzo) based on Bastian's code, but extended it
737 to be able to handle connectivities larger than 3 (in principle, up to 32).
738 It supports different initialization methods (the original RESPPROP,
739 the CLAMPING method and EXACT which uses JTree) and different update methods
740 (FULL and LINEAR).
741 - Implemented LCBP2, an analogon of LCBP which represents pancakes as little
742 networks and uses some approximate inference method on them for calculating
743 marginals.
744 - Now there are several LCBP variants (LCBP, LCBPI, LCBPJ, LCBPK, LCBPL);
745 LCBPJ works only for pairwise, LCBPK is LCBP improved for higher order
746 interactions and LCBPL is LCBPI improved for higher-order interactions.
747 - Wrote one single program utils/createfg for creating various types of
748 random factor graphs.
749 - Wrote utility to visualize factor graphs using graphviz.
750 (it uses the BOOST Program Options library)
751 - Added fginfo utility that displays some info about a .fg file.
752 - Implemented Factor::strength function that calculates the potential strength
753 N(psi,i,j) between variables i and j as described in cs.IT:0504030
754 - Wrote a general MatLab interface matlab/dai (similar to tests/test);
755 this unified the matlab functions dai, dai_bp, dai_mf, dai_jt, dai_tep, dai_cvm.
756 - Added MATLAB routine that returns contraction matrix A for BP convergence analysis.
757 - Implemented a MATLAB interface ai_potstrength for Factor::strength
758 - Added Martijn's x2x
759
760 Improvements of existing code
761
762 - Reimplemented RegionGraph and descendants: a RegionGraph ISA FactorGraph
763 and also a BipartiteGraph<FRegion,Region>. It now also keeps a map that
764 associates outer region indices to factor indices (no powers yet, this
765 is deemed superfluous) and provides functions to recompute (some of) the
766 outer regions from the factors.
767 - InfAlg descendants run() methods now stop immediately and return NAN in case
768 they detect NANs. Only BP does not do NAN checking for performance reasons.
769 - LCBP now works with factors containing zeroes (by defining x/0 = 0).
770 - HAK, GBP and DoubleLoop now conform to the standards for verbose reporting,
771 timing and convergence criteria.
772 - Implemented logZ() for JTree. It does the calculation during message-passing.
773 - Marginal2ndO now optionally divides by the single node beliefs (to the power n-2);
774 hopefully this will give more accurate approximations.
775 - Marginal and Marginal2ndO (optionally) use the new saveProbs/undoProbs functionality
776 for a faster way of calculating marginals, which does not require a call to init()
777 nor cloning the whole object for each clamping. This leads to a significant speedup.
778 - LCBP (and LCBP2) now have complete flexibility in the specification of the
779 inner method, i.e. the method used to generate the initial cavity approximations.
780 One can pass two strings, a name and a properties string, and LCBP simply invokes
781 newInfAlg to construct the corresponding inference algorithm and uses the generic
782 marginal functions to approximate cavity marginals.
783 - Replaced the global "method" variable by local properties and removed ai.h
784 - Added some methods to Factor (operators *, *=, /, /= with doubles as
785 second argument, operators -, +=, -= with other Factors as second
786 arguments, randomize(), RemoveFirstOrderInteractions) and similar
787 operations to Prob
788 - Moving towards boost::program_options for handling command line arguments
789 (tests/test is done).
790 - Renamed some FactorGraph methods:
791 nr_vars -> nrVars
792 nr_factors -> nrFactors
793 varind -> findVar
794 factorind -> findFactor
795 makeFacCavity -> makeFactorCavity
796 - LCBP_SEQMAXRES has been removed because it did strange things.
797 - Implemented RandomDRegularGraph
798 - Implemented JTree::calcMarginal for marginals that are not confined
799 within one cluster (using cut-set conditioning).
800 - Added isConnected() method to FactorGraph (some methods do not work with
801 disconnected factor graphs).
802 - Pair beliefs are now calculated in a symmetrical way by calcPairBeliefs
803 - Removed single node interaction "correction" code from clamping methods
804 - Removed calcCavityDist and calcCavityDist2ndO
805 - No longer depends on GSL.
806 - Increased portability by combining platform dependant utility functions
807 in util.{h,cpp}.
808 - Wrote *.m files providing help
809
810 Testing framework
811
812 - Made a new and significantly improved testing framework that provides most
813 functionality from the command line.
814 - The basis is provided by tests/test, which uses the newInfAlg functionality
815 and enables the user to easily compare from the command line different
816 inference methods on a given factorgraph. All parameters can be specified.
817 Output consists of CPU time, average and maximum single variable marginal
818 errors, relative logZ error and MaxDiff().
819 - tests/aliases.conf contains aliases for standard combinations of methods
820 and their options (which can be used in tests/test).
821 - tests/large contains several bash/python scripts that create random factor
822 graphs, compare several approximate inference algorithms (using tests/test) and
823 allow for easy visualization of the results using PyX.
824 - Added several .fg files for test purposes to /tests (e.g. two ALARM versions
825 alarm.fg and alarm_bnt.fg; testfast.fg, a 4x4 periodic Ising grid for
826 regression testing).
827 - Added a regression test to the Makefile which is included in the standard
828 target. It compares all inference methods on tests/testfast.fg with the
829 results stored in tests/testfast.out
830
831 Miscellaneous
832
833 - Expanded all tabs to spaces (":set tabstop 4\n:set expandtab\n:retab" in vim)
834 - Experimental MATLAB code added for StarEP approximation on cavity
835 - Renamed project to libDAI and changed directory name accordingly.
836 - Renamed JunctionTree to JTree.
837 - Fixed licensing (now it's officially GPL).
838 - Improved README
839
840
841 revision 252
842 ------------
843
844 Functionality
845 - Added RegionGraph, GBP, CVM and HAK (double-loop).
846 - Added JunctionTree (with two update algorithms, HUGIN and Shafer-Shenoy), which is a
847 RegionGraph.
848 - NormType is now chosen automatically (in case of negative factors, Prob::NORMLINF is used,
849 otherwise the default Prob::NORMPROB is used). Also, in case of negative factors, the
850 RegionGraph constructors assign each Factor to a unique outer region instead of dividing
851 it over all subsuming outer regions. See README for when negative factors are known to work
852 and when not.
853 - FactorGraph::FactorGraph(const vector<Factor>) only gives a warning in case of short loops,
854 it does not automatically merge factors anymore.
855 - Removed BP_SEQMAXRESNOCLEAR (all cavity initialization methods now are implicitly NOCLEAR)
856 - Added MATLAB interface functions ai_readfg, ai_removeshortloops and ai_bp
857 - Added LCBP-III type that should be equivalent to LCBP-II, but can handle zeroes
858 in potentials. Note that it is significantly slower than LCBP-II (and has to be reimplemented
859 such that it does not store the complete pancakes, but represents them as little factor graphs).
860
861 Implementation / code
862 - Made a seperate type WeightedGraph, which until now only implements Prim's
863 maximal spanning tree algorithm and is only used by the junction tree code. It might
864 be good to make it a class somewhere in the future and extend it's interface.
865 - Made a seperate class ClusterGraph, which is only used by the junction tree
866 code. It's main purpose is a graph-theoretical variable elimination algorithm.
867 - Implemented the heuristic "minimum-new-edges-in-clique-graph" for variable elimination.
868 - Massive code cleanup, moving towards "generic" programming style, using
869 multiple inheritance and polymorphism.
870 o BP, LCBP, MF, HAK and JunctionTree now inherit from a common DAIAlg class
871 o Made generic functions Marginal, Marginal2ndO, calcCavityDist, calcCavityDist2ndO, clamp
872 that can be used by FactorGraph-based DAIAlgs.
873 o Created TProb<T> class, which stores a probability vector (without the accompanying indexing
874 and VarSet) and provides functionality for it (which is used by TFactor<T>).
875 o Rewrote the VarSet class. It now caches its statespace(). It now privately inherits from set<Var>.
876 I had to overload the insert methods of set<Var> so that they calculate the new statespace.
877 o Rewrote the TFactor class. The TFactor class now HAS a TProb and HAS a VarSet.
878 - Rewrote BP to use the new TProb<T> interface. Performance of BP improved up to a factor 6 by:
879 o using Prob's instead of Factor's;
880 o splitting the multiplication of the messages into two parts (thanks to Vicenc!);
881 o optimizing the calculation of the beliefs (only the message calculations were optimized till now).
882 o replacing FactorGraph::_nb1 and _nb2 (which were set<size_t>) by vector<size_t>
883 - LCBP now seperately stores cavitydists and pancakes. Added InitPancakes() method
884 that takes the cavitydists and multiplies them with the relevant factors. This
885 resulted in an API change in AI which now accepts and returns initial cavitydists
886 instead of initial pancakes.
887
888 Minor changes
889 - Started writing DoxyGen documentation
890 - Renamed lcptab2fg.m matlab/ai_writefg.m
891 - Moved all matlab stuff to matlab/
892 - More detailed reporting (also reports clocks used).
893 - Marginal and Marginal2ndO now use *differences* in logZ to avoid NaNs.
894 - Improved testing suite.
895 - Removed logreal support.
896 - FactorGraph now also supports input streams and ignores comment lines in .fg files.
897 - Added tests/create_full_fg.cpp and tests/create_ising_fg.cpp which create
898 full and periodic 2D Ising networks according to some command line parameters.
899 - Now logZ really returns logZ instead of -logZ.
900 - Added FactorGraph::WriteToDotFile
901
902
903 0.1.4 (2006-04-13)
904 ------------------
905 - Added file IO routines to read and write factorgraphs.
906 - Added L-infinity normalization for use with (partially) negative factors.
907 - Renamed BetheF, MFF to logZ, which now use complex numbers to be able to
908 handle (partially) negative factors.
909 - Added test suite.
910 - All probabilities are now represented using double instead of LogReal<double>.
911 - Combined Alg and Alg3 into LCBP. Several update schemes possible.
912 - Combined several variants of BP into doBP. Several update schemes possible.
913 Now uses precalculated indices for optimization.
914 - Renamed Node -> Var and Potential -> Factor.
915 - Extensive code cleanup. More use of OO techniques. Changed API.
916 - MaxIter now means maximum number of passes (corresponding to number of
917 _parallel_ updates).
918 - MaxDiff now means the maximum L-infinity distance between the updated and
919 original single variable beliefs, for all AI methods.
920 - Implemented RBP which converges faster than BP for difficult problems.
921 - Now uses method parameter which is a bitmask combining outmethod and inmethod
922 (see ai.h).
923
924
925 0.1.3 (2006-03-22)
926 --------------------
927 - All AI methods now return maxdiff
928 - ai.cpp:
929 o Now returns maxdiffinner and maxdiffouter
930 o New BP2ndO innermethod (estimate only 2nd order cavity interactions)
931 o New InitCav outermethod (only create initial cavity distributions)
932 - bp.cpp:
933 o New CavityDist2ndO which estimates 2nd order cavity interactions
934 - Makefile:
935 o Bugfix: removed dependencies on algwim.*
936
937
938 0.1.2 (2006-02-28)
939 --------------------
940 - Cleaned up alg.cpp (removed Alg2 and its corresponding data structures).
941 - Added the possibility to provide initial cavity distributions as an input
942 argument to ai (not much error checking is done, so be careful).
943 - Potentials2mx now correctly sets the dimensions of the P field (i.e. for
944 the output arguments Q, Q0 of ai).
945 - Removed algwim.* since it does not work.
946
947
948 0.1.1 (2006-02-28)
949 --------------------
950 - The constructors of (Log)FactorGraph and LogFactorGraph from a
951 vector<(Log)Potential> now merge potentials to prevent short loops (of length
952 4) in the factor graph. These are used in ai to construct the factor graphs
953 from the psi argument. If compiled with DEBUG defined, the method calc_nb()
954 of BipGraph checks for the existence of short loops.
955 - Changed calling syntax of ai (now the actual syntax *does* correspond to its
956 description in the help).
957 - ai does not hook cout anymore (which caused weird segfaults).
958 - Fixed a bug in an assert statement in the matlab interface code in ai.cpp.
959 - Removed network.* since it is not useful.
960
961
962 0.1.0 (2006-02-28)
963 --------------------
964 First version worthy of a version number.