-----------------------------------------------------------------------------
- Banjo                        Bayesian Network Inference with Java Objects -
- Release 2.2.0                                                 15 Apr 2008 -
- Licensed from Duke University                                             -
- Copyright (c) 2005-08 by Alexander J. Hartemink                           -
- All rights reserved                                                       -
-----------------------------------------------------------------------------
- Project:                                                   Literature Genes
- User:                                                              lsand039
- Dataset:                                   7-vars-377-temporal-observations
- Notes:                                    static bayesian network inference
-----------------------------------------------------------------------------
- Settings file:                                                             
-----------------------------------------------------------------------------
- Input directory:                                 data/release2.0/runB/input
- Observations file:                                               lgenes.txt
- Observation count:                                                      377
- Number of variables:                                                      7
- Variables are in rows:                                                  yes
- Variable names:                                                      inFile
- Discretization policy:                                                   i7
- Exceptions to the discretization policy:                               none
-----------------------------------------------------------------------------
- Initial structure file:                                                    
- 'Must be present' edges file:                                              
- 'Must not be present' edges file:                                          
- Min. Markov lag:                                                          0
- Max. Markov lag:                                                          0
- Max. parent count:                                                        5
- Equivalent sample size for Dirichlet parameter prior:                   1.0
-----------------------------------------------------------------------------
- Searcher:                                                 SearcherSimAnneal
- Proposer:                                           ProposerRandomLocalMove
- Evaluator:                                        defaulted to EvaluatorBDe
- Decider:                                     defaulted to DeciderMetropolis
-----------------------------------------------------------------------------
- Pre-compute logGamma:                                                    no
- Cache:                                                           fastLevel1
- Cycle checking method:                                   Depth-first Search
-----------------------------------------------------------------------------
- Initial temperature:                                                  10000
- Cooling factor:                                                         0.7
- Reannealing temperature:                                                800
- Max. accepted networks before cooling:                                 2500
- Max. proposed networks before cooling:                                10000
- Min. accepted networks before reannealing:                              500
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- Output directory:                               data/release2.0/runB/output
- Report file:         Literature Genes.static.report.2016.09.02.19.18.19.txt
- Number of best networks tracked:                                          1
- Max. time:                                                            1.0 h
- Max. restarts:                                                       100000
- Min. networks before checking:                                         1000
- Screen reporting interval:                                           10.0 m
- File reporting interval:                                             2.05 h
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- Compute influence scores:                                               yes
- Compute consensus graph:                                                yes
- Create consensus graph as HTML:                                         yes
- Create 'dot' output:                                                    yes
- Location of 'dot':  /usr/bin/dot /usr/bin/X11/dot /usr/share/man/man1/dot.1.gz
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- XML output directory:                           data/release2.0/runB/output
- XML Report file:                                                           
- XML settings to export:                                                    
- XML parser:                             org.apache.xerces.parsers.SAXParser
- Banjo XML format version:                                               1.0
-----------------------------------------------------------------------------
- Seed for starting search:                                     1472858299743
-----------------------------------------------------------------------------
- Number of threads:                                                        1
-----------------------------------------------------------------------------

Memory info before starting the search: Banjo is using 1 mb of memory

-----------------------------------------------------------------------------
- Pre-processing                                        Discretization report
-----------------------------------------------------------------------------
 Variable | Discr. | Min. Val. | Max. Val. |  Orig. |  Used  |               
          |        |           |           | points | points |               
-----------------------------------------------------------------------------
      0   |    i7  |      0.0  |      1.0  |     2  |     2  |
      1   |    i7  |     20.0  |    101.0  |    57  |     7  |
      2   |    i7  |      0.0  |      1.0  |     2  |     2  |
      3   |    i7  |      0.0  |      2.0  |     3  |     3  |
      4   |    i7  |      0.0  |      2.0  |     3  |     3  |
      5   |    i7  |      0.0  |      2.0  |     3  |     3  |
      6   |    i7  |      0.0  |      2.0  |     3  |     3  |
-----------------------------------------------------------------------------

Prep. time used: 115.0 ms
Beginning to search: expect a status report every 10.0 m

Status:  Networks   268525000
         Time       10.0 m (16.6% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   533875000
         Time       20.0 m (33.3% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   792988000
         Time       30.0 m (50.0% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   1052519000
         Time       40.0 m (66.6% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   1309612000
         Time       50.0 m (83.3% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   1570165000
         Time       1.0 h (100.0% of max. 1.0 h)
         Re-anneals  0 (0.0% of max. 100000)
         Banjo is using 5 mb of memory



-----------------------------------------------------------------------------
- Final report                                           Best network overall
-----------------------------------------------------------------------------


Network score: -2359.1884, first found at iteration 1557
7
0 0
1 1 0
2 1 0
3 0
4 1 0
5 1 0
6 0


-----------------------------------------------------------------------------
- Search Statistics                                                          
-----------------------------------------------------------------------------

Statistics collected in searcher 'SearcherSimAnneal':
  Number of networks examined: 1570165000
  Total time used: 1.0 h
  High score: -2359.1884, first found at iteration 1557
  Number of re-anneals: 0

Statistics collected in proposer 'ProposerRandomLocalMove':
  Additions -- proposed:    523393209
  Deletions -- proposed:    523413675
  Reversals -- proposed:    523358115

Statistics collected in cycle checker 'CycleCheckerCheckThenApply':
  Additions -- considered:  523393209,  acyclic:  435238495
  Deletions -- no cyclicity test necessary
  Reversals -- considered:  523358115,  acyclic:  523357371

Statistics collected in evaluator 'EvaluatorBDe':
  Scores computed:          286074096
  Scores (cache)            placed         fetched        
      with 0 parents:       7              1046760818     
      with 1 parents:       42             402212412      
      with 2 parents:       286072154      270319308      
      with 3 parents:       1720           318            
      with 4 parents:       161            15             
      with 5 parents:       12             1              

Statistics collected in decider 'DeciderMetropolis':
  Additions -- considered:  435238495,  better score:  4871,  other accepted:  17575
  Deletions -- considered:  523413675,  better score:  17580,  other accepted:  4862
  Reversals -- considered:  523357371,  better score:  209358283,  other accepted:  9914
  Average permissivity:     0.0

Memory info after completing the search: Banjo is using 5 mb of memory


Network score: -2359.1884, found by thread 1
7
0 0
1 1 0
2 1 0
3 0
4 1 0
5 1 0
6 0

-----------------------------------------------------------------------------
- Post-processing                                            Influence scores
-----------------------------------------------------------------------------

Influence score for   (0,0) ->   (1,0)   .2636
Influence score for   (0,0) ->   (2,0)   .3277
Influence score for   (0,0) ->   (4,0)   .0000
Influence score for   (0,0) ->   (5,0)   .0000

-----------------------------------------------------------------------------
- Post-processing                                  DOT graphics format output
-----------------------------------------------------------------------------

digraph abstract { 

label = "Banjo Version 2.2.0\nHigh scoring network, score: -2359.1884\nProject: Literature Genes\nUser: lsand039\nDataset: 7-vars-377-temporal-observations"; 
labeljust="l"; 

    0 [label="Alzheimer"];
    1 [label="age"];
    2 [label="sex"];
    3 [label="PSEN2"];
    4 [label="PSEN1"];
    5 [label="APP"];
    6 [label="APOE"];

    0->1;
    0->2;
    0->4;
    0->5;
}

