-----------------------------------------------------------------------------
- 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 MH4
- 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:                                             4
- '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 MH4.static.report.2016.09.07.08.10.03.txt
- Number of best networks tracked:                                          1
- Max. time:                                                            5.0 m
- 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:                                     1473250203798
-----------------------------------------------------------------------------
- Number of threads:                                                        1
-----------------------------------------------------------------------------
- 'Must be present' edges, as loaded:                                        
-----------------------------------------------------------------------------
7
0 3 1 2 3  	  
1 0  	  
2 0  	  
3 3 4 5 6  	  
4 2 5 6  	  
5 1 6  	  
6 0  	  
-----------------------------------------------------------------------------

Memory info before starting the search: Banjo is using 5 mb of memory
Prep. time used: 49.0 ms
Beginning to search: expect a status report every 10.0 m



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


Network score: -2565.4766, first found at iteration 1
7
0 3 1 2 3
1 0
2 0
3 3 4 5 6
4 2 5 6
5 1 6
6 0


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

Statistics collected in searcher 'SearcherSimAnneal':
  Number of networks examined: 252696000
  Total time used: 5.0 m
  High score: -2565.4766, first found at iteration 1
  Number of re-anneals: 2045

Statistics collected in proposer 'ProposerRandomLocalMove':
  Additions -- proposed:    187623296
  Deletions -- proposed:    32535577
  Reversals -- proposed:    32537126

Statistics collected in cycle checker 'CycleCheckerCheckThenApply':
  Additions -- considered:  187623296,  acyclic:  115818708
  Deletions -- no cyclicity test necessary
  Reversals -- considered:  32537126,  acyclic:  28827598

Statistics collected in evaluator 'EvaluatorBDe':
  Scores computed:          11323201
  Scores (cache)            placed         fetched        
      with 0 parents:       3              45852980       
      with 1 parents:       13             85574154       
      with 2 parents:       6362995        15111696       
      with 3 parents:       791928         19925182       
      with 4 parents:       3920750        28110012       
      with 5 parents:       247512         112279         

Statistics collected in decider 'DeciderMetropolis':
  Additions -- considered:  115818708,  better score:  0,  other accepted:  32535579
  Deletions -- considered:  32535577,  better score:  32535577,  other accepted:  0
  Reversals -- considered:  28827598,  better score:  15529434,  other accepted:  6378660
  Average permissivity:     0.301

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


Network score: -2565.4766, found by thread 1
7
0 3 1 2 3
1 0
2 0
3 3 4 5 6
4 2 5 6
5 1 6
6 0

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

Influence score for   (3,0) ->   (0,0)   .0000
Influence score for   (2,0) ->   (0,0)   .2177
Influence score for   (1,0) ->   (0,0)   .0000
Influence score for   (6,0) ->   (3,0)   .0533
Influence score for   (5,0) ->   (3,0)   -.0665
Influence score for   (4,0) ->   (3,0)   .0000
Influence score for   (6,0) ->   (4,0)   .0000
Influence score for   (5,0) ->   (4,0)   .0000
Influence score for   (6,0) ->   (5,0)   -.1930

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

digraph abstract { 

label = "Banjo Version 2.2.0\nHigh scoring network, score: -2565.4766\nProject: Literature Genes MH4\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"];

    1->0;
    2->0;
    3->0;
    4->3;
    5->3;
    6->3;
    5->4;
    6->4;
    6->5;
}

