[News (including bugs)] [Stable version] [Development version] [Python version] [Version used for Liao et al, AAAI-19 paper] [Benchmarks] [Publications on the theory behind GOBNILP] [Publications using GOBNILP]
GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear Programming) is a C program which learns Bayesian networks from complete discrete data or from local scores. GOBNILP uses the SCIP framework for Constraint Integer Programming. Detailed information on installing, running, licence etc can be found in the:
which is also contained in the GOBNILP distribution.
GOBNILP has been developed by James Cussens and Mark Bartlett. It was supported by MRC grant A graphical model approach to pedigree construction using constrained optimisation (G1002312) until Feb 2015. Goblin 'P' logo courtesy of Robby Higgins.
Download GOBNILP (stable release).
The current stable version of GOBNILP does not work with recent versions of SCIP, use SCIP 3.2.1 instead.
The source code for the development version of GOBNILP is available at this bitbucket git repo. This version works with SCIP 6.0.1. Doxygen documentation for a recent development version (not always the latest) is available here. You can generate documentation for the latest development version by running 'make docs' once you have downloaded/cloned the development version. The development version is highly unstable and contains many undocumented features.
pygobnilp, a Python version of GOBNILP, is available. The stable Python version (currently pygobnilp 1.0) is described in the
pygobnilp can be installed using pip: pip install pygobnilp. pygobnilp relies on many Python packages and also the Gurobi MIP solver. Installing Gurobi and Anaconda Python together is a convenient way of getting most (not all) of what pygobnilp needs to function. pygobnilp is slower than the C development (or stable) version, but is useful for experimentation.
Available here .
GOBNILP has been developed using a set of local score files used originally in the paper Bayesian network learning with cutting planes. Most of these local score input files are in this gzipped tar file. The local score input files alarm, mirna, phen and wdbc were kindly sent to me by Tommi Jaakkola, the others I generated myself. More recently a local score input file (developed by Mark Bartlett) for learning pedigrees has been used as part of the Pedigree Reconstruction using Integer Linear Programming project. The current release can learn directly form data (as well as from local scores files). Some of the the original datasets and the local scores generated from them are available from this directory. However, these original datasets are in a format incompatible with the current GOBNILP release. (This directory also contain some local score files where the data from which they were generated is not available.)
The 'Mildew' local score files in the gzipped tar file contain errors. The correct local scores for 'Mildew' instances can be found in this this directory. For all other instances the same (correct) local scores can be found in either place. Thanks to Peter van Beek for spotting this problem.
The following table provides a summary of benchmarking results for GOBNILP 1.6 using default parameter setttings. (The current release is 1.6.1 but on the input used for these benchmarks 1.6 and 1.6.1 are identical.) All times are in seconds. The GOBNILP output for each of these runs is available in this single file. Both the summary and the full output were generated using SCIP's "make test" utility. (Benchmark results for older GOBNILP versions are available here.)
Benchmarks run on a single core of the following machine: Linux pc435h 3.13.0-49-generic #83-Ubuntu SMP Fri Apr 10 20:11:33 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux. Processor was: Intel(R) Core(TM) i5 CPU 650 @ 3.20GHz
GOBNILP can run into memory problems and immediately abort on sufficiently big problems. The 'Link' learning problems mentioned later are like this and are not included in the following table. Note that GOBNILP did not solve the Diabetes_10000_1_2 or the Pigs_10000_1_2 problem which are in the table. It did however make some progress towards a solution before aborting. Consult the full output for details.
------------------+------+--- Original --+-- Presolved --+----------------+----------------+------+---------+--------+-------+----------+---------+-------- Name | Type | Conss | Vars | Conss | Vars | Dual Bound | Primal Bound | Gap% | Iters | Nodes | Time | To First | To Best | ------------------+------+-------+-------+-------+-------+----------------+----------------+------+---------+--------+-------+----------+---------+-------- Diabetes_100_1_2 CIP 4809 7386 5089 7329 -47697.4126 -47697.4126 0.0 1251 1 50.4 14.2 50.4 ok Diabetes_1000_1_2 CIP 15555 31406 17553 31368 -268847.008 -268847.008 0.0 5193 3 367.9 23.9 366.9 ok Diabetes_10000_1_2 -- 0 0 0 0 -1e+20 1e+20 -- 0 0 0.0 0.0 0.0 abort Mildew_100_1_3 CIP 854 3988 991 3974 -6380.72748 -6380.72748 0.0 107 1 2.2 1.3 2.2 ok Mildew_1000_1_3 CIP 156 245 143 232 -52258.8572 -52258.8572 0.0 135 3 0.7 0.0 0.7 ok Mildew_10000_1_3 CIP 461 744 478 737 -454894.404 -454894.404 0.0 310 1 1.1 0.1 1.1 ok Pigs_100_1_2 CIP 2907 4368 2837 4288 -41017.047 -41017.047 0.0 1156 1 22.8 17.5 22.8 ok Pigs_1000_1_2 CIP 13848 24383 14434 24383 -340449.646 -340449.646 0.0 6276 1 65.5 24.8 65.5 ok Pigs_10000_1_2 -- 0 0 0 0 -1e+20 1e+20 -- 0 0 0.0 0.0 0.0 abort Water_100_1_3 CIP 308 679 341 676 -1500.96839 -1500.96839 0.0 1668 3 3.9 0.5 3.8 ok Water_1000_1_3 CIP 504 889 563 889 -13262.3418 -13262.3418 0.0 3532 3 3.2 0.1 3.2 ok Water_10000_1_3 CIP 687 1391 772 1391 -128705.65 -128705.65 0.0 12733 89 7.7 0.2 5.2 ok alarm_100_1_3 CIP 742 1330 782 1329 -1349.22742 -1349.22742 0.0 668 1 1.5 0.2 1.5 ok alarm_1000_1_3 CIP 1010 2523 1157 2522 -11240.3471 -11240.3471 0.0 1913 1 2.6 0.3 2.6 ok alarm_10000_1_3 CIP 1486 7356 2123 7355 -105226.512 -105226.512 0.0 31906 91 63.0 1.0 35.4 ok asia_100_1_99 CIP 47 65 47 64 -245.644264 -245.644264 0.0 23 3 0.0 0.0 0.0 ok asia_1000_1_99 CIP 115 175 126 175 -2317.41151 -2317.41151 0.0 70 1 0.1 0.0 0.1 ok asia_10000_1_99 CIP 123 237 149 237 -22466.3965 -22466.3965 0.0 495 3 1.3 0.0 0.9 ok carpo_100_1_3 CIP 3011 6830 3285 6819 -1829.30685 -1829.30685 0.0 173497 442 278.0 2.0 225.6 ok carpo_1000_1_3 CIP 1899 4946 2166 4939 -17718.948 -17718.948 0.0 24307 19 46.2 1.1 45.2 ok carpo_10000_1_3 CIP 2844 18086 4700 18085 -174130.564 -174130.564 0.0 94221 131 308.7 4.5 272.0 ok hailfinder_100_1_3 CIP 237 357 223 322 -6019.46993 -6019.46993 0.0 207 1 0.4 0.0 0.4 ok hailfinder_1000_1_ CIP 632 1136 679 1133 -52473.2456 -52473.2456 0.0 1382 3 3.2 0.2 3.2 ok hailfinder_10000_1 CIP 1542 4693 1860 4693 -497631.796 -497631.796 0.0 20297 46 35.4 0.6 24.5 ok insurance_100_1_3 CIP 288 448 285 441 -1686.22588 -1686.22588 0.0 131 1 0.3 0.1 0.3 ok insurance_1000_1_3 CIP 592 1126 625 1125 -13887.3501 -13887.3501 0.0 708 1 1.1 0.2 1.1 ok insurance_10000_1_ CIP 1117 4316 1442 4315 -132968.577 -132968.577 0.0 5334 2 9.1 0.9 9.1 ok kredit_1000_1_3 CIP 67 104 62 98 -16695.6695 -16695.6695 0.0 28 3 0.1 0.0 0.1 ok kredit_1000_1_99 CIP 67 104 62 98 -16695.6695 -16695.6695 0.0 28 3 0.1 0.0 0.1 ok alarm CIP 1441 6484 1738 6483 -9944.3113 -9944.3113 0.0 3644 1 6.4 0.9 6.4 ok mirna CIP 845 1789 900 1789 -2653.7505 -2653.7505 0.0 978 1 1.9 0.2 1.9 ok phen CIP 648 2678 731 2677 -6070.7502 -6070.7502 0.0 1855 1 4.0 0.4 4.0 ok wdbc CIP 1946 7079 2462 7078 -6804.2458 -6804.2458 0.0 6024 1 16.3 0.9 16.3 ok pedigree1 CIP 1267 1954 1267 1954 -1466.59852 -1466.59852 0.0 599 1 4.0 0.6 4.0 ok ------------------+------+-------+-------+-------+-------+----------------+----------------+------+---------+--------+-------+----------+---------+-------- ------------------------------[Nodes]---------------[Time]--------------[ToFirst]-----------[ToLast]----- Cnt Pass Time Fail total(k) geom. total geom. total geom. total geom. --------------------------------------------------------------------------------------------------------- 34 32 0 2 0 3.0 1309.1 5.6 96.9 1.5 1176.3 5.3 shifted geom. [ 100/ 10.0] 15.2 11.6 1.9 10.8 --------------------------------------------------------------------------------------------------------- @02 timelimit: 0 @01 SCIP(3.1.1)cpx(12.6.0.0):default [GitHash: bade511]
Peter van Beek has kindly made available the problem instances used in this paper. Here are the results of running GOBNILP 1.6.1 on these instances. (Same machine used as for above.)
------------------+------+--- Original --+-- Presolved --+----------------+----------------+------+---------+--------+-------+----------+---------+-------- Name | Type | Conss | Vars | Conss | Vars | Dual Bound | Primal Bound | Gap% | Iters | Nodes | Time | To First | To Best | ------------------+------+-------+-------+-------+-------+----------------+----------------+------+---------+--------+-------+----------+---------+-------- abalone_BIC CIP 152 279 182 278 -16171.1923 -16171.1923 0.0 224 1 0.2 0.0 0.2 solved not verified adult_BIC CIP 290 719 360 718 -330559.759 -330559.759 0.0 402 1 0.5 0.1 0.5 solved not verified alarm1000_BIC CIP 807 1484 880 1482 -11783.0463 -11783.0463 0.0 1017 1 2.2 0.2 2.2 solved not verified alarm100_BIC CIP 195 342 188 335 -1594.60952 -1594.60952 0.0 189 1 0.5 0.0 0.5 solved not verified alarm_BIC CIP 483 950 524 942 -14390.7825 -14390.7825 0.0 485 3 0.5 0.1 0.5 solved not verified aus_BIC CIP 80 126 78 122 -5011.10158 -5011.10158 0.0 61 3 0.1 0.0 0.1 solved not verified autos_BIC CIP 1182 3091 1536 3090 -1577.15977 -1577.15977 0.0 6416 15 13.3 0.4 13.2 solved not verified balance_BIC CIP 12 18 8 13 -4521.01778 -4521.01778 0.0 0 1 0.0 0.0 0.0 solved not verified bands_BIC CIP 740 1333 808 1325 -5117.94929 -5117.94929 0.0 1663 1 5.2 0.3 4.7 solved not verified barley1000_BIC CIP 164 349 145 327 -67699.7393 -67699.7393 0.0 104 1 0.4 0.0 0.4 solved not verified bc_BIC CIP 31 47 22 34 -2785.97529 -2785.97529 0.0 17 3 0.0 0.0 0.0 solved not verified bc-wisc_BIC CIP 197 350 223 349 -3334.10035 -3334.10035 0.0 314 1 0.3 0.0 0.1 solved not verified carpo1000_BIC CIP 990 2052 1108 2046 -17976.7646 -17976.7646 0.0 3158 5 6.5 0.3 6.5 solved not verified carpo100_BIC CIP 353 639 339 622 -2000.21325 -2000.21325 0.0 366 1 0.7 0.1 0.7 solved not verified carpo500_BIC CIP 723 1272 753 1259 -9195.48572 -9195.48572 0.0 1376 3 2.8 0.2 2.8 solved not verified credit_BIC CIP 65 111 62 106 -6392.47961 -6392.47961 0.0 69 3 0.2 0.0 0.0 solved not verified diabetes_BIC CIP 31 53 27 49 -3692.79661 -3692.79661 0.0 34 7 0.1 0.0 0.1 solved not verified ecoli_BIC CIP 52 80 51 77 -1778.74275 -1778.74275 0.0 27 1 0.1 0.0 0.0 solved not verified flag_BIC CIP 650 1132 703 1132 -2748.10513 -2748.10513 0.0 698 1 1.9 0.2 1.9 solved not verified glass_BIC CIP 44 66 39 61 -1365.8638 -1365.8638 0.0 32 3 0.1 0.0 0.1 solved not verified hailfinder100_BIC CIP 130 228 101 194 -6414.53453 -6414.53453 0.0 104 1 0.6 0.0 0.6 solved not verified hailfinder500_BIC CIP 363 647 362 640 -27777.5516 -27777.5516 0.0 286 1 0.6 0.1 0.6 solved not verified heart-cl_BIC CIP 50 96 44 90 -3430.48929 -3430.48929 0.0 31 1 0.1 0.0 0.0 solved not verified heart-hu_BIC CIP 81 138 78 135 -2384.00702 -2384.00702 0.0 61 3 0.1 0.0 0.1 solved not verified heart-st_BIC CIP 59 105 55 101 -2860.86628 -2860.86628 0.0 82 3 0.2 0.0 0.1 solved not verified hepatitis_BIC CIP 234 413 238 412 -1647.96991 -1647.96991 0.0 340 1 0.9 0.0 0.9 solved not verified horse_BIC CIP 427 742 454 740 -4524.66273 -4524.66273 0.0 331 1 0.9 0.1 0.9 solved not verified insurance1000_BIC CIP 447 779 463 776 -14350.4705 -14350.4705 0.0 466 1 0.8 0.1 0.8 solved not verified insurance100_BIC CIP 124 253 119 247 -1782.71458 -1782.71458 0.0 144 1 0.3 0.0 0.3 solved not verified iris_BIC CIP 31 43 31 43 -465.43503 -465.43503 0.0 15 1 0.0 0.0 0.0 solved not verified letter_BIC CIP 691 4847 1430 4847 -209774.055 -209774.055 0.0 5288 26 6.4 0.8 5.5 solved not verified liver_BIC CIP 14 20 10 15 -1321.96265 -1321.96265 0.0 6 1 0.0 0.0 0.0 solved not verified lung-cancer_BIC CIP 195 418 178 396 -1379.28597 -1379.28597 0.0 290 1 1.0 0.0 1.0 solved not verified lympho_BIC CIP 118 218 116 216 -1972.63595 -1972.63595 0.0 100 1 0.3 0.0 0.3 solved not verified mildew1000_BIC CIP 97 177 81 160 -57238.0239 -57238.0239 0.0 72 3 0.4 0.0 0.4 solved not verified mildew100_BIC CIP 45 57 10 15 -6655.3931 -6655.3931 0.0 6 1 0.0 0.0 0.0 solved not verified mushroom_BIC CIP 1165 13711 3501 13710 -89683.4535 -89683.4535 0.0 2131157 4229 2654.8 3.5 1454.2 solved not verified pg-block_BIC CIP 74 120 75 119 -12711.762 -12711.762 0.0 51 3 0.1 0.0 0.0 solved not verified post-op_BIC -- 11 10 2 0 -645.00339 -645.00339 0.0 0 1 0.0 0.0 0.0 solved not verified promoters_BIC CIP 71 89 14 31 -8552.14186 -8552.14186 0.0 0 1 0.0 0.0 0.0 solved not verified segment_BIC CIP 425 1306 603 1305 -15171.6049 -15171.6049 0.0 2251 1 6.0 0.2 5.8 solved not verified shuttle_BIC CIP 126 335 171 334 -98774.3553 -98774.3553 0.0 1324 7 3.5 0.0 3.5 solved not verified soybean_BIC CIP 1684 6930 2540 6927 -3122.06298 -3122.06298 0.0 30368 43 66.5 1.3 49.5 solved not verified spectf_BIC CIP 676 1033 692 1028 -8135.31187 -8135.31187 0.0 674 1 2.3 0.2 2.3 solved not verified sponge_BIC CIP 466 951 470 942 -2072.61151 -2072.61151 0.0 660 1 2.1 0.1 2.1 solved not verified steel_BIC -- 0 0 0 0 -1e+20 1e+20 -- 0 0 0.0 0.0 0.0 abort thyroid_BIC CIP 19 32 16 29 -602.06851 -602.06851 0.0 11 1 0.0 0.0 0.0 solved not verified tic-tac_BIC CIP 162 192 164 186 -9396.37586 -9396.37586 0.0 403 1 1.0 0.0 1.0 solved not verified tumour_BIC CIP 227 351 231 349 -3194.25203 -3194.25203 0.0 167 1 0.3 0.0 0.3 solved not verified vehicle_BIC CIP 508 1065 602 1065 -7965.40348 -7965.40348 0.0 1118 1 2.8 0.2 2.8 solved not verified voting_BIC CIP 597 2196 866 2195 -3205.78531 -3205.78531 0.0 2220 1 2.6 0.3 2.6 solved not verified water1000_BIC CIP 159 249 159 242 -13290.1069 -13290.1069 0.0 115 1 0.3 0.0 0.3 solved not verified water100_BIC CIP 88 138 76 124 -1465.27372 -1465.27372 0.0 48 3 0.2 0.0 0.2 solved not verified wdbc_BIC CIP 2259 15951 3538 15951 -6602.11732 -6602.11732 0.0 27710 20 158.3 3.2 155.6 solved not verified wine_BIC CIP 118 227 120 227 -1891.69481 -1891.69481 0.0 68 3 0.1 0.0 0.1 solved not verified yeast_BIC CIP 28 44 24 40 -8039.97506 -8039.97506 0.0 17 1 0.0 0.0 0.0 solved not verified zoo_BIC CIP 405 795 459 795 -773.48608 -773.48608 0.0 342 1 0.9 0.1 0.9 solved not verified abalone_BDe CIP 156 412 207 412 -15946.5748 -15946.5748 0.0 443 1 0.5 0.1 0.5 solved not verified adult_BDe CIP 356 977 443 977 -329373.73 -329373.73 0.0 1146 19 0.8 0.2 0.7 solved not verified aus_BDe CIP 132 204 132 201 -4997.83478 -4997.83478 0.0 110 3 0.2 0.0 0.2 solved not verified autos_BDe CIP 1437 26080 5189 26080 -1418.12127 -1418.12127 0.0 584969 951 1614.8 10.3 1251.3 solved not verified balance_BDe CIP 12 18 8 13 -4549.05536 -4549.05536 0.0 0 1 0.0 0.0 0.0 solved not verified bc_BDe CIP 31 47 22 34 -2781.62239 -2781.62239 0.0 14 3 0.0 0.0 0.0 solved not verified bc-wisc_BDe CIP 193 350 211 349 -3315.51218 -3315.51218 0.0 320 1 0.3 0.0 0.3 solved not verified credit_BDe CIP 129 198 128 194 -6185.72434 -6185.72434 0.0 149 9 0.2 0.0 0.2 solved not verified diabetes_BDe CIP 42 65 40 63 -3678.57293 -3678.57293 0.0 39 5 0.1 0.0 0.1 solved not verified ecoli_BDe CIP 74 115 77 115 -1715.92338 -1715.92338 0.0 51 3 0.1 0.0 0.0 solved not verified flag_BDe CIP 817 1811 927 1810 -2693.08869 -2693.08869 0.0 2419 2 7.2 0.3 7.1 solved not verified glass_BDe CIP 118 176 125 175 -1288.92632 -1288.92632 0.0 59 1 0.1 0.0 0.1 solved not verified heart-cl_BDe CIP 50 96 44 90 -3450.06475 -3450.06475 0.0 42 7 0.1 0.0 0.0 solved not verified heart-hu_BDe CIP 97 169 96 166 -2376.52921 -2376.52921 0.0 111 3 0.2 0.0 0.1 solved not verified heart-st_BDe CIP 63 119 59 115 -2867.53657 -2867.53657 0.0 65 3 0.1 0.0 0.0 solved not verified hepatitis_BDe CIP 377 724 381 720 -1615.68231 -1615.68231 0.0 334 1 1.2 0.1 1.2 solved not verified horse_BDe CIP 437 749 458 746 -4531.56021 -4531.56021 0.0 437 1 1.2 0.1 1.2 solved not verified insurance1000_BDe CIP 595 1147 628 1145 -13872.3332 -13872.3332 0.0 867 1 1.6 0.2 1.6 solved not verified insurance100_BDe CIP 315 487 317 484 -1669.43462 -1669.43462 0.0 167 1 0.3 0.1 0.3 solved not verified iris_BDe CIP 33 45 33 45 -452.21429 -452.21429 0.0 15 1 0.0 0.0 0.0 solved not verified letter_BDe CIP 695 19247 2881 19247 -200768.883 -200768.883 0.0 61485 56 201.8 9.5 149.7 solved not verified liver_BDe CIP 16 26 13 22 -1309.67331 -1309.67331 0.0 9 1 0.0 0.0 0.0 solved not verified lympho_BDe CIP 339 543 332 531 -1908.35311 -1908.35311 0.0 298 1 1.3 0.1 1.3 solved not verified mildew1000_BDe CIP 162 255 149 241 -51939.6265 -51939.6265 0.0 106 1 0.5 0.0 0.5 solved not verified mildew100_BDe CIP 55 88 21 43 -6423.33723 -6423.33723 0.0 13 1 0.0 0.0 0.0 solved not verified mushroom_BDe -- 0 0 0 0 -1e+20 1e+20 -- 0 0 0.0 0.0 0.0 abort pg-block_BDe CIP 184 388 207 388 -12455.5969 -12455.5969 0.0 272 3 0.5 0.2 0.5 solved not verified post-op_BDe -- 11 10 2 0 -647.3529 -647.3529 0.0 0 1 0.0 0.0 0.0 solved not verified segment_BDe CIP 687 6892 1275 6891 -14281.7847 -14281.7847 0.0 43710 63 66.0 2.3 52.6 solved not verified shuttle_BDe CIP 190 920 307 919 -97635.7197 -97635.7197 0.0 7992 43 4.5 0.3 3.5 solved not verified steel_BDe -- 0 0 0 0 -1e+20 1e+20 -- 0 0 0.0 0.0 0.0 abort thyroid_BDe CIP 44 69 44 69 -577.52089 -577.52089 0.0 45 1 0.1 0.0 0.1 solved not verified tic-tac_BDe CIP 98 121 90 115 -9423.06831 -9423.06831 0.0 46 1 0.1 0.0 0.1 solved not verified tumour_BDe CIP 270 431 281 430 -3191.18567 -3191.18567 0.0 328 1 0.8 0.0 0.8 solved not verified vehicle_BDe CIP 716 3542 1126 3542 -7545.55964 -7545.55964 0.0 5727 1 15.1 0.6 14.6 solved not verified voting_BDe CIP 590 2284 863 2283 -3192.66656 -3192.66656 0.0 2324 1 2.6 0.4 2.6 solved not verified wdbc_BDe CIP 2224 14793 3351 14793 -6596.70042 -6596.70042 0.0 53778 46 250.4 2.9 238.2 solved not verified wine_BDe CIP 159 308 164 308 -1866.40612 -1866.40612 0.0 166 1 0.3 0.0 0.3 solved not verified yeast_BDe CIP 38 67 34 63 -7938.59791 -7938.59791 0.0 24 1 0.0 0.0 0.0 solved not verified zoo_BDe CIP 540 3168 797 3167 -642.25866 -642.25866 0.0 12399 40 22.4 1.1 21.8 solved not verified ------------------+------+-------+-------+-------+-------+----------------+----------------+------+---------+--------+-------+----------+---------+-------- ------------------------------[Nodes]---------------[Time]--------------[ToFirst]-----------[ToLast]----- Cnt Pass Time Fail total(k) geom. total geom. total geom. total geom. --------------------------------------------------------------------------------------------------------- 97 94 0 3 5 2.3 5145.9 2.0 41.6 1.1 3478.9 2.0 shifted geom. [ 100/ 10.0] 11.7 4.2 0.4 3.9 --------------------------------------------------------------------------------------------------------- @02 timelimit: 0 @01 SCIP(3.1.1)cpx(12.6.0.0):default [GitHash: bade511]
The results in the above tables are for learning from precomputed local scores. These local scores were computed from synthetic data generated from various BNs. The following table gives information on those BNs in the first table, the synthetic data and the local scores. Importantly it gives the time taken to compute these local scores.
'BN' is the name of the BN from which the data was originally generated. 'p' is the number of variables in the original dataset (and thus in the optimal BN). 'n' is the number of datapoints in the data. 'palim' is the limit on the size of parent sets in any learned BN. '|PaSets|' is the number of candidate parent sets generated by GOBNILP's local scoring algorithm - this is the size of the input to the main GOBNILP learning algorithm. '1.4.1' is time in seconds to compute all the local scores using GOBNILP 1.4.1. '1.6' is the time taken using GOBNILP 1.6 (using default ADtree parameter settings). '1.6.1' is the time taken using GOBNILP 1.6.1 (using default ADtree parameter settings). The machines used for '1.4.1' and '1.6'/'1.6.1' were similar but not identical.
Parameter settings for the current release (1.6.1) are conservative to help avoid running out of memory on small machines. Faster computation is often possible with non-default values. For example, setting gobnilp/scoring/rmin to a non-default value of 100 allows GOBNILP 1.6.1 to compute local scores for Pigs_1000 and Link_1000 in 144s and 679s, respectively. However, such non-default values can sometimes slow down local score computation; with gobnilp/scoring/rmin set to 100 GOBNILP 1.6.1 takes 336s to compute local scores for kredit with no parent set limit, as opposed to 207s with its default value.
BN | p | n | palim | |PaSets| | 1.4.1 | 1.6 | 1.6.1 |
---|---|---|---|---|---|---|---|
Diabetes | 413 | 100 | 2 | 4441 | 1135 | 191 | 170 |
Diabetes | 413 | 1000 | 2 | 21493 | 2754 | 550 | 437 |
Diabetes | 413 | 10000 | 2 | 262129 | 5497 | 2007 | 1479 |
Link | 724 | 100 | 2 | 7431402 | 411 | 496 | 358 |
Link | 724 | 1000 | 2 | 2379361 | 1150 | 892 | 1424 |
Link | 724 | 10000 | 2 | 2421283 | 9005 | 6373 | 4502 |
Mildew | 35 | 100 | 3 | 3520 | 17 | 8 | 10 |
Mildew | 35 | 1000 | 3 | 161 | 64 | 25 | 12 |
Mildew | 35 | 10000 | 3 | 463 | 167 | 79 | 19 |
Pigs | 441 | 100 | 2 | 2692 | 151 | 99 | 63 |
Pigs | 441 | 1000 | 2 | 15847 | 203 | 189 | 213 |
Pigs | 441 | 10000 | 2 | 304219 | 2082 | 1270 | 832 |
Water | 32 | 100 | 3 | 482 | 1 | 1 | 1 |
Water | 32 | 1000 | 3 | 573 | 1 | 1 | 1 |
Water | 32 | 10000 | 3 | 961 | 7 | 2 | 1 |
alarm | 37 | 100 | 3 | 907 | 1 | 1 | 1 |
alarm | 37 | 1000 | 3 | 1928 | 3 | 2 | 1 |
alarm | 37 | 10000 | 3 | 6473 | 16 | 6 | 2 |
asia | 8 | 100 | ∞ | 41 | 1 | 1 | 1 |
asia | 8 | 1000 | ∞ | 112 | 1 | 1 | 1 |
asia | 8 | 10000 | ∞ | 169 | 1 | 1 | 1 |
carpo | 60 | 100 | 3 | 5068 | 5 | 8 | 2 |
carpo | 60 | 1000 | 3 | 3827 | 14 | 12 | 7 |
carpo | 60 | 10000 | 3 | 16391 | 99 | 24 | 6 |
hailfinder | 56 | 100 | 3 | 244 | 20 | 17 | 3 |
hailfinder | 56 | 1000 | 3 | 761 | 39 | 49 | 10 |
hailfinder | 56 | 10000 | 3 | 3768 | 124 | 214 | 26 |
insurance | 27 | 100 | 3 | 279 | 1 | 1 | 1 |
insurance | 27 | 1000 | 3 | 774 | 1 | 1 | 1 |
insurance | 27 | 10000 | 3 | 3652 | 5 | 2 | 1 |
kredit | 18 | 1000 | 3 | 70 | 1 | 1 | 1 |
kredit | 18 | 1000 | ∞ | 70 | 248 | 2370 | 207 |
alarm | 37 | 5630 | |||||
mirna | 22 | 1279 | |||||
phen | 25 | 2296 | |||||
wdbc | 31 | 5921 | |||||
pedigree1 | 100 | 1195 |
Last modified: Thu Jan 26 18:06:13 GMT 2017