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