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