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1321 Commits

Author SHA1 Message Date
Tiago Gomes
f3bd8ad414 Use the word option instead of key. Key reminds me of hashes 2013-01-10 22:59:12 +00:00
Tiago Gomes
f7fcfec8ce PFL manual: some rewording 2013-01-10 22:42:23 +00:00
Tiago Gomes
d3e2abd677 Don't use the name horus in documentation. 
It is just an internal code name.
 2013-01-10 22:39:46 +00:00
Tiago Gomes
fdeca2852a Use only one interface for options. 
set_pfl_flag/2 now can be called for setting options for solvers written in Prolog and for solvers in Horus.
 2013-01-10 22:10:22 +00:00
Tiago Gomes
e5e224d89b Fix typo 2013-01-10 21:51:45 +00:00
Tiago Gomes
bd84949f09 Trivial 2013-01-10 17:23:09 +00:00
Tiago Gomes
1bb1138b3a Fix EM typos 2013-01-10 13:45:24 +00:00
Vitor Santos Costa
b7ef6576a6 add keys within learning 2013-01-09 18:34:19 +00:00
Vitor Santos Costa
6cee85bd60 fix cases where you get repeated keys or a(X,X) keys in PFL. 2013-01-09 18:22:01 +00:00
Vitor Santos Costa
46fbc539bf handle repeated query vars with evidence 2013-01-09 17:49:07 +00:00
Vitor Santos Costa
ff953eb20a Merge branch 'master' of https://github.com/tacgomes/yap6.3 2013-01-09 16:48:16 +00:00
tacgomes
2feac46e54 PFL manual: several improvements 2013-01-09 16:45:01 +00:00
tacgomes
7f452d2397 Refactor the benchmarks 2013-01-09 15:25:14 +00:00
tagomes@fc.up.pt
7fabfcf4c9 Trivial 2013-01-09 11:43:40 +00:00
Tiago Gomes
24271157ce Clean unecessary latex documents 2013-01-08 22:55:27 +00:00
Tiago Gomes
59ae52623c PFL manual: several improvements 2013-01-08 22:51:44 +00:00
Tiago Gomes
6755e50525 PFL manual: small improvements 2013-01-08 22:00:31 +00:00
Tiago Gomes
ea054468bc Improve hcli usage string 2013-01-08 21:17:56 +00:00
Tiago Gomes
dc536fabc2 Beautify setHorusFlag 2013-01-08 21:13:58 +00:00
Tiago Gomes
2738d83302 Remove some alias for hve 2013-01-08 20:48:46 +00:00
Tiago Gomes
dfd7360291 Allow the use of solver as an alias of ground_solver 2013-01-08 20:47:12 +00:00
Tiago Gomes
dbd35a20a2 PFL manual: improve introduction section 2013-01-08 19:40:20 +00:00
Tiago Gomes
9c8fd804df PFL manual: add a further information section 2013-01-08 19:39:39 +00:00
Tiago Gomes
f94032d06c PFL manual: add an installation section 2013-01-08 19:39:03 +00:00
Tiago Gomes
1b9c4e96e7 Prefix with bp_ some bp flags 2013-01-08 17:06:40 +00:00
Tiago Gomes
da0514a779 Add support for more infernce keys. 
Add support for export_libdai, export_uai, export_gv and print_fg.
Document these keys.
 2013-01-08 17:01:03 +00:00
Tiago Gomes
4220069d90 PFL manual: use the Unix end-of-line marker 2013-01-08 15:34:56 +00:00
Tiago Gomes
75b652b0c9 PFL manual: improve title page and reword a sentence 2013-01-08 15:33:55 +00:00
Tiago Gomes
6375d05a93 PFL manual: add section for horus cli 2013-01-08 15:31:52 +00:00
Tiago Gomes
182429252e Update the usage string for hcli 2013-01-08 14:47:21 +00:00
Tiago Gomes
c92b7c3e7e Install hcli to the bin directory 2013-01-08 00:33:01 +00:00
Tiago Gomes
f598881cc5 Explain better the potential value order 2013-01-07 22:21:52 +00:00
Tiago Gomes
9bb43360a2 Rearrange the probabilities to do a clean diff against the exported model 2013-01-07 22:18:50 +00:00
Tiago Gomes
ba32ebc5f5 Add support for bayesian networks defined in an UAI file format 2013-01-07 22:17:05 +00:00
Tiago Gomes
82a4cc508b Change burglary-alarm.uai to be bayes instead of markov 2013-01-07 22:01:49 +00:00
Tiago Gomes
bafd7320a5 Rework a bit the examples 2013-01-07 14:59:51 +00:00
Tiago Gomes
91dbd60ad4 Allow calling set_horus_flag/2 without loading clpbn_horus 2013-01-07 14:05:56 +00:00
Tiago Gomes
96f4e7ea1b Fix typo 2013-01-07 14:04:44 +00:00
David Vaz
cdc15e8cd8 merge with yap-6.3 2013-01-06 20:09:48 +00:00
Tiago Gomes
ec2d9e0967 Trivial 2013-01-05 12:04:43 +00:00
Tiago Gomes
f0768e76f2 Improve Makefile 2013-01-05 01:02:19 +00:00
Tiago Gomes
f55ccdef33 Add a manual for PFL written in Latex 2013-01-05 00:49:39 +00:00
Tiago Gomes
c5a390460d Chanse use_logarithms default to true. 
Reasoning:
- In small networks, the use of logarithms is not noticed in terms of performance.
- In large networks, the chance to have a division by 0 is too high when not using logarithms.
 2013-01-04 19:48:31 +00:00
Tiago Gomes
f2682374fb Forgot to update the Makefile in the previous commit 2013-01-04 15:42:03 +00:00
Tiago Gomes
3347f0e676 Rename two examples 2013-01-03 23:44:30 +00:00
Tiago Gomes
d4d11cd4b4 Fix sprinkler probability order 2013-01-03 18:48:15 +00:00
Tiago Gomes
ea5dbe2bca Trivial 2013-01-03 18:26:12 +00:00
Tiago Gomes
d293c5e5a9 Trivial 2012-12-28 15:40:32 +00:00
Tiago Gomes
3363019c93 Remove unnecessary methods 2012-12-28 01:35:59 +00:00
Tiago Gomes
7d9af75c35 Improve solver flags 2012-12-27 23:21:32 +00:00
Tiago Gomes
d36b63ece3 Trivial 2012-12-27 22:29:20 +00:00
Tiago Gomes
c96496720b Trivial 2012-12-27 22:28:19 +00:00
Tiago Gomes
485c3e34b2 Use more DISALLOW_COPY_AND_ASSIGN 2012-12-27 22:25:45 +00:00
Tiago Gomes
7b7f663ac6 Don't use public members for solver flags 2012-12-27 15:44:40 +00:00
Tiago Gomes
b996436b24 Reorganize 2012-12-27 15:05:40 +00:00
Tiago Gomes
de0a118ae5 Move belief propagation stuff out from Horus.h 2012-12-27 15:00:30 +00:00
Tiago Gomes
cbea630fbf Cosmetic fixes 2012-12-27 12:54:58 +00:00
David Vaz
e6c2fa30ee Added uthash to store indexed predicates info 2012-12-27 12:11:14 +00:00
Tiago Gomes
8bdcb65907 Improve variable elimination 2012-12-26 22:55:48 +00:00
Tiago Gomes
188f359496 Fix a warning about a unitialized var 2012-12-26 21:48:05 +00:00
Tiago Gomes
d8c5725b2e This shouldn't be on the repository 2012-12-21 15:20:28 +00:00
Tiago Gomes
4b901d26d7 Improve error messages 2012-12-20 23:34:53 +00:00
Tiago Gomes
01d8f8e178 More whitespace cleanups 2012-12-20 23:19:10 +00:00
Vítor Santos Costa
3565a01f1e upstream 2012-12-20 21:41:06 +00:00
Tiago Gomes
421d6f72ee Place the constructor on the right place 2012-12-20 21:32:40 +00:00
Vitor Santos Costa
4098b9b964 fix compilation MT in win32 2012-12-20 21:15:01 +00:00
Tiago Gomes
57339760b9 Merge LiftedKc and LiftedCircuit in one file 2012-12-20 21:11:51 +00:00
Tiago Gomes
b44ed7db39 Improve the error messages 2012-12-20 18:07:50 +00:00
Tiago Gomes
685f46dc27 Fix 2012-12-20 17:41:52 +00:00
Tiago Gomes
053fa31bb2 Exit is better than abort. 
Also use a macro instead of integer to indicate failure.
 2012-12-20 17:37:59 +00:00
David Vaz
4efa594f0a UDI: more work 2012-12-20 17:13:30 +00:00
Tiago Gomes
2ca31ca14a Don't abort if opening a file to export to graphviz fails 2012-12-20 17:11:11 +00:00
Tiago Gomes
af8497af6e Sort the logical vars of the constraint tree when exporting to graphviz 2012-12-20 16:20:38 +00:00
David Vaz
a655c0bb51 Rtree working as a plugin in UDI 2012-12-20 10:21:55 +00:00
Tiago Gomes
046af409ba Change the default solver to be hve 2012-12-19 18:25:47 +00:00
Tiago Gomes
c407594146 Whitespace clean 2012-12-19 18:22:47 +00:00
Tiago Gomes
60ff9daafd Remove old example 2012-12-19 18:13:47 +00:00
Tiago Gomes
48254ba7d7 Lkc: fix some memory leaks 2012-12-19 17:45:53 +00:00
Tiago Gomes
2d1f5edc91 There is no more to do 2012-12-18 23:52:56 +00:00
Tiago Gomes
691188d5c9 Handle better formulas like f(X,X) 2012-12-18 23:51:51 +00:00
Tiago Gomes
0a661b0462 More cleanups 2012-12-18 22:47:43 +00:00
David Vaz
43e459b8f8 Changes Rtree so almost working 2012-12-18 18:26:59 +00:00
Tiago Gomes
4b0acbf8c1 Cleanups 2012-12-18 12:11:45 +00:00
Tiago Gomes
c7a4adcefb Fix finalizing horus ground solvers on EM 2012-12-17 23:59:52 +00:00
Tiago Gomes
5fa5dda579 Remove BP from clpbn interface to EM 2012-12-17 23:29:21 +00:00
Tiago Gomes
e1c862ebbe Refactor the way we set the inference solver 2012-12-17 23:14:54 +00:00
Tiago Gomes
f1499f99f3 Introduce set_em_solver and use it 2012-12-17 21:19:47 +00:00
Tiago Gomes
40a72a0a63 Improve error handling for choosing EM solver 2012-12-17 21:03:13 +00:00
David Vaz
8511e87e32 packages udi as module 2012-12-17 20:29:59 +00:00
David Vaz
bd25c61fbf New work on UDI 2012-12-17 20:23:03 +00:00
Tiago Gomes
9861f4aadb Is the EM solver that we want 2012-12-17 18:50:36 +00:00
Tiago Gomes
3eb6b76ddd Whitespace clean 2012-12-17 18:39:42 +00:00
Tiago Gomes
2f2f88e571 Several whitespace fixes 2012-12-17 17:57:00 +00:00
Tiago Gomes
409a230826 Use the same convetion for module import and export 2012-12-17 14:50:12 +00:00
Tiago Gomes
2738c0fb56 Use tabs instead of spaces for consistency 2012-12-17 12:13:08 +00:00
Tiago Gomes
d03ea1509e Trivial 2012-12-17 11:56:15 +00:00
Tiago Gomes
e35cf51476 Reorders and some reindentation 2012-12-17 11:53:57 +00:00
Tiago Gomes
9ff9be2f49 Don't pass around the Solver for EM 2012-12-15 16:11:03 +00:00
Tiago Gomes
81ac6f1913 Don't pass around the Solver in run_horus_ground_solver 2012-12-15 15:56:05 +00:00
Tiago Gomes
ea931f2f93 Comment 2012-12-15 00:41:00 +00:00
Tiago Gomes
55292ab745 Clean ups and don't forget cbp 2012-12-15 00:29:03 +00:00
Tiago Gomes
1174486576 VE??? 2012-12-15 00:16:06 +00:00
Tiago Gomes
2996a0b8b3 Comment does not apply 2012-12-15 00:14:45 +00:00
Tiago Gomes
e5479ff17c CLPBNs first, PFLs next 2012-12-15 00:13:53 +00:00
Tiago Gomes
6c95c50eb4 Merge branch 'master' of ssh://yap.git.sourceforge.net/gitroot/yap/yap-6.3 2012-12-14 14:05:22 +00:00
Vitor Santos Costa
84b0529060 improve prism compatibility (fix asia). 2012-12-14 08:26:56 +00:00
Tiago Gomes
971b8b7487 Merge branch 'master' of ssh://yap.git.sourceforge.net/gitroot/yap/yap-6.3 2012-12-13 23:48:16 +00:00
Tiago Gomes
eea7ce2885 Fix file names 2012-12-13 19:02:04 +00:00
Tiago Gomes
0594d43539 Cosmetic fixes 2012-12-13 17:51:43 +00:00
Tiago Gomes
05e53eaf37 Merge sch32 and school32_data and rename to school_32 2012-12-13 17:08:54 +00:00
Tiago Gomes
6b8301d9c4 CLP(BN) is dead. Long live the PFL 2012-12-13 17:04:14 +00:00
Tiago Gomes
d78baa48a1 Don't special case the tables in city.pfl 
Its hard to make them work in lifted networks
:
 2012-12-13 16:50:39 +00:00
Vitor Santos Costa
c4448d066a allow backtracking over possible values of constraints.a 2012-12-13 15:53:01 +00:00
Tiago Gomes
8b996c5dc9 Lkc: show that we exported the circuit to graphviz when debugging 2012-12-13 14:21:16 +00:00
Tiago Gomes
48413deae7 Ops: deleted this by accident in the previous commit 2012-12-13 14:08:16 +00:00
Tiago Gomes
dd8a92aaf3 Merge with upstream code 2012-12-13 12:55:55 +00:00
Tiago Gomes
11e688ffd7 Lkc: use utility function 2012-12-12 21:19:22 +00:00
Tiago Gomes
f2173d001e Lkc: fix bug when adding weights 2012-12-12 21:16:36 +00:00
Tiago Gomes
c7588c9361 Trivial 2012-12-12 17:03:11 +00:00
Tiago Gomes
4683d30d8e Trivial 2012-12-12 17:01:30 +00:00
Tiago Gomes
39bf95fe2b trivial 2012-12-12 16:28:18 +00:00
Tiago Gomes
8eb657aec2 Change extension of school parschema to pfl 2012-12-12 16:00:21 +00:00
Tiago Gomes
0f46c97481 Trivial 2012-12-12 15:47:09 +00:00
Tiago Gomes
e66ff6777c Be consistent: constraint is always on top 2012-12-12 15:41:41 +00:00
Tiago Gomes
66cd58655b Place the debug_school predicate into a different file 2012-12-12 15:36:38 +00:00
Tiago Gomes
01dfc5e2be Change extension of school_params 
school_params does not define any pfl network, so it shouldn't have pfl as the extension
 2012-12-12 15:26:49 +00:00
Tiago Gomes
108e310a0f Rework the learning examples 2012-12-12 15:16:30 +00:00
Tiago Gomes
f128b6de7a school_32 should use clp(bn) 2012-12-12 00:27:32 +00:00
Tiago Gomes
27a235f65b Remove text explaning pfl. 
The text is badly written and explanaing pfl shouldn't be in *.pfl files, but rather in paper or README file
 2012-12-11 23:36:10 +00:00
Tiago Gomes
4310e42562 rework examples 2012-12-11 23:06:09 +00:00
Tiago Gomes
ccba2d4177 update Makefile to reflect the change of extension to .pfl 2012-12-11 21:02:26 +00:00
Tiago Gomes
1641d1fa30 Remove files that souldn't be in the repository 2012-12-11 16:22:38 +00:00
Tiago Gomes
47bc8f22fc Examples: sprinker was converted from clpbn to pfl 2012-12-11 16:20:55 +00:00
Tiago Gomes
d8a7b7aad6 Examples: change extension to pfl 2012-12-11 16:19:59 +00:00
Tiago Gomes
a59c152962 Lkc: Fix smoothing in atom counting nodes 2012-12-11 16:02:48 +00:00
Tiago Gomes
bb68afe91d Fix an error caused by a temporary being out of scope 2012-12-11 15:52:20 +00:00
Tiago Gomes
1d732594e2 smooth circuit 
Smooth the circuit independent of the verbosity level, but don't smooth it when the compilation has fail.
 2012-12-10 19:39:09 +00:00
Tiago Gomes
8371e395dd fix typo 2012-12-10 19:37:41 +00:00
Tiago Gomes
a25f4584c8 support printing LitLvTypes objects 2012-12-10 18:48:54 +00:00
Tiago Gomes
9c8827c309 always copy clauses for backup 2012-12-09 22:57:39 +00:00
Tiago Gomes
90736156ae some clean ups 2012-12-09 22:13:58 +00:00
Tiago Gomes
e46d2177b7 rework a bit the test infrastructure for lkc 2012-12-09 22:04:33 +00:00
Tiago Gomes
907144db32 don't use a stack for atom counting operator 2012-12-09 19:46:14 +00:00
Tiago Gomes
57a31c2c36 fix showing the weights on edge labels when there is a SetOrNode ancestor 2012-12-09 17:33:36 +00:00
Tiago Gomes
59f653aabd move implementation of copyClauses to another file 2012-12-08 19:32:19 +00:00
Tiago Gomes
4edbcf86b8 Use pointers to refer to clauses for better performance 2012-12-08 19:17:19 +00:00
Vítor Santos Costa
354dbbf802 follow pldoc 2012-12-08 10:52:39 +00:00
Tiago Gomes
73b3594c97 lifted kc: when not debuging don't keep track of the origin clauses 2012-12-07 11:47:50 +00:00
Vitor Santos Costa
b98b09e7de improve utf-8 2012-12-07 08:10:21 +00:00
Vitor Santos Costa
a813a13412 mysqldb interface vs Prolog 2012-12-04 14:49:29 +00:00
Vitor Santos Costa
36ae500118 fixes 2012-12-03 12:39:25 +00:00
Vítor Santos Costa
d9d954abe1 fix handling of methods and classes with named objects: just use PyObject_Call() 2012-12-02 13:19:10 +00:00
Vitor Santos Costa
3c0e16030c imprive python interface 2012-12-01 14:28:25 +00:00
Tiago Gomes
ee1b7dcd21 abort when compilation failed 2012-11-27 16:54:02 +00:00
Vitor Santos Costa
683032432c more examples 2012-11-27 13:50:18 +00:00
Vítor Santos Costa
e529e79582 more progress 2012-11-27 12:10:41 +00:00
Vitor Santos Costa
f1874ecec0 inprove python interface. 2012-11-27 00:16:34 +00:00
Tiago Gomes
610e55a4a2 Improve debbuging for lifted knowledge compilation 2012-11-26 14:46:45 +00:00
Tiago Gomes
1f1d194326 remove unnecessary std set 2012-11-26 14:46:00 +00:00
Tiago Gomes
a2429a1eec Merge branch 'master' of github.com:tacgomes/yap6.3 2012-11-26 11:48:24 +00:00
Vítor Santos Costa
57ac65c83b new swi version. 2012-11-25 23:48:41 +00:00
Vítor Santos Costa
e470dfcdc7 more python stuff. 2012-11-25 23:37:28 +00:00
Vitor Santos Costa
d5b97ac15e quoting. 2012-11-24 12:23:00 +00:00
Tiago Gomes
e09c25bd59 remove grounding stub form lifted knowledge compilation. its hard to implement 2012-11-22 16:34:24 +00:00
Tiago Gomes
4afe6c8161 refactor horus_ground and horus_lifted 2012-11-22 16:33:22 +00:00
Tiago Gomes
992d06656d refactor horus_ground.yap 2012-11-22 15:54:30 +00:00
Vitor Santos Costa
027632456a Merge branch 'master' of https://github.com/tacgomes/yap6.3 2012-11-22 12:29:37 +00:00
Vitor Santos Costa
bb4d75f428 avoid messing up lifted solvers 2012-11-22 12:27:33 +00:00
Tiago Gomes
85db763d9c small improvement in HorusYap 2012-11-16 22:38:14 +00:00
Tiago Gomes
51eef45b2d refactor HorusYap 2012-11-16 17:10:04 +00:00
Tiago Gomes
59fd21bf33 use only 1 lifted solver instance 2012-11-16 16:50:19 +00:00
Tiago Gomes
c2791748d2 Merge branch 'master' of ssh://yap.git.sourceforge.net/gitroot/yap/yap-6.3 2012-11-16 00:57:41 +00:00
Vitor Santos Costa
114a6732f0 add_factor should succeed if Constraints are satisfied 2012-11-15 17:28:57 +00:00
Tiago Gomes
51fd48cd46 Ouchgit statusgit status! forgot to add these to index 2012-11-14 23:17:39 +00:00
Tiago Gomes
4522850cd6 one step close to use one solver instatiation to solve several queries 2012-11-14 23:13:46 +00:00
Tiago Gomes
b673dfd462 fix type in an example 2012-11-14 23:12:03 +00:00
Tiago Gomes
64a27847cc Introduce a lifted solver class 2012-11-14 21:55:51 +00:00
Tiago Gomes
6e7d0d1d0a remove old TODOs 2012-11-14 21:17:04 +00:00
Tiago Gomes
cad22da9f5 fixes & cleanups 2012-11-14 21:05:55 +00:00
Tiago Gomes
d9e48e6290 log domain calculations fixes for lifted knowledge compilation 2012-11-14 18:40:03 +00:00
Vitor Santos Costa
416b407faa fixes i r..eal 2012-11-14 16:00:35 +00:00
Tiago Gomes
9202e286f8 IncExc: check if log vars are count normalized 2012-11-14 14:43:56 +00:00
Tiago Gomes
f5c85ffcc9 shatter agains the query in lifted knowledge compilation 2012-11-12 15:20:42 +00:00
Tiago Gomes
4776817603 move more code around 2012-11-10 00:18:20 +00:00
Tiago Gomes
07bcc89a76 factor out some lifted operations in a new class 2012-11-09 23:52:35 +00:00
Tiago Gomes
8ab622e0aa more work to support inference with lifted knowledge compilation 2012-11-09 18:42:21 +00:00
Tiago Gomes
c53220aa61 Merge branch 'master' of ssh://yap.git.sourceforge.net/gitroot/yap/yap-6.3 2012-11-09 16:29:24 +00:00
Tiago Gomes
6a200760ca initial code to support calling a lifted knowledge compilation solver 2012-11-08 21:54:47 +00:00
Tiago Gomes
0ed89d3eeb add flag to lifted knowledge compilation and s/fove/lve 2012-11-08 15:05:48 +00:00
Tiago Gomes
a8c4f4fc52 fix one more TODO 2012-11-08 14:02:18 +00:00
Tiago Gomes
f7db522c6c InxExc: improve the code 2012-11-07 23:45:43 +00:00
Tiago Gomes
6db4d37684 Independence: consider also counted log vars 2012-11-07 21:21:42 +00:00
Tiago Gomes
d2ae171bb5 Improve Clause constructor 2012-11-07 18:43:13 +00:00
Tiago Gomes
278f8f77f5 Improve independence 2012-11-07 18:42:11 +00:00
Tiago Gomes
07c6509a79 cleanups, refactorings & renamings 2012-11-07 15:28:33 +00:00
Tiago Gomes
83c1e58674 clean ups 2012-11-07 12:37:22 +00:00
Tiago Gomes
b599b45bc6 AC: only allow one counting node per branch 2012-11-06 23:56:52 +00:00
Tiago Gomes
829f2248ee use utility method 2012-11-06 23:39:18 +00:00
Tiago Gomes
06a59ad659 IPG: verify that the root log vars appear in the same positions 2012-11-06 23:35:14 +00:00
Tiago Gomes
1e38743462 fix ipgCandidates 2012-11-06 16:24:59 +00:00