-----------------------------------------------------------------------------
- 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:                                                   Correlated 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:                                               cgenes.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
-----------------------------------------------------------------------------
- Output directory:                               data/release2.0/runB/output
- Report file:         Correlated Genes.static.report.2016.09.02.19.15.03.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
-----------------------------------------------------------------------------
- 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
-----------------------------------------------------------------------------
- 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:                                     1472858102995
-----------------------------------------------------------------------------
- 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  |      0.0  |      2.0  |     3  |     3  |
      2   |    i7  |      0.0  |      2.0  |     3  |     3  |
      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: 90.0 ms
Beginning to search: expect a status report every 10.0 m

Status:  Networks   397411000
         Time       10.0 m (16.6% of max. 1.0 h)
         Re-anneals 776 (0.7% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   784620000
         Time       20.0 m (33.3% of max. 1.0 h)
         Re-anneals 1481 (1.4% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   1185032000
         Time       30.0 m (50.0% of max. 1.0 h)
         Re-anneals 2269 (2.2% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   1597202000
         Time       40.0 m (66.6% of max. 1.0 h)
         Re-anneals 3082 (3.0% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   2004832000
         Time       50.0 m (83.3% of max. 1.0 h)
         Re-anneals 3872 (3.8% of max. 100000)
         Banjo is using 5 mb of memory

Status:  Networks   2398528000
         Time       1.0 h (100.0% of max. 1.0 h)
         Re-anneals 4641 (4.6% of max. 100000)
         Banjo is using 5 mb of memory



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


Network score: -1291.3698, first found at iteration 120887
7
0 1 1
1 0
2 2 0 3
3 2 0 4
4 1 1
5 2 3 6
6 2 2 3


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

Statistics collected in searcher 'SearcherSimAnneal':
  Number of networks examined: 2398528000
  Total time used: 1.0 h
  High score: -1291.3698, first found at iteration 120887
  Number of re-anneals: 4641

Statistics collected in proposer 'ProposerRandomLocalMove':
  Additions -- proposed:    800671863
  Deletions -- proposed:    798915821
  Reversals -- proposed:    798940315

Statistics collected in cycle checker 'CycleCheckerCheckThenApply':
  Additions -- considered:  800671863,  acyclic:  344813004
  Deletions -- no cyclicity test necessary
  Reversals -- considered:  798940315,  acyclic:  470485901

Statistics collected in evaluator 'EvaluatorBDe':
  Scores computed:          434692543
  Scores (cache)            placed         fetched        
      with 0 parents:       7              245187025      
      with 1 parents:       42             1004145741     
      with 2 parents:       166343598      128865725      
      with 3 parents:       244260846      242860651      
      with 4 parents:       23718299       28899776       
      with 5 parents:       369751         49222          

Statistics collected in decider 'DeciderMetropolis':
  Additions -- considered:  344813004,  better score:  48834098,  other accepted:  16884186
  Deletions -- considered:  798915821,  better score:  16893783,  other accepted:  48824491
  Reversals -- considered:  470485901,  better score:  141932265,  other accepted:  56713118
  Average permissivity:     0.087

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


Network score: -1291.3698, found by thread 1
7
0 1 1
1 0
2 2 0 3
3 2 0 4
4 1 1
5 2 3 6
6 2 2 3

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

Influence score for   (1,0) ->   (0,0)   -.8664
Influence score for   (3,0) ->   (2,0)   .0000
Influence score for   (0,0) ->   (2,0)   .2718
Influence score for   (4,0) ->   (3,0)   .0000
Influence score for   (0,0) ->   (3,0)   .1805
Influence score for   (1,0) ->   (4,0)   .0000
Influence score for   (6,0) ->   (5,0)   .0000
Influence score for   (3,0) ->   (5,0)   .4048
Influence score for   (3,0) ->   (6,0)   .0000
Influence score for   (2,0) ->   (6,0)   .1642

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

digraph abstract { 

label = "Banjo Version 2.2.0\nHigh scoring network, score: -1291.3698\nProject: Correlated Genes\nUser: lsand039\nDataset: 7-vars-377-temporal-observations"; 
labeljust="l"; 

    0 [label="Alzheimer"];
    1 [label="GNG4"];
    2 [label="THBS1"];
    3 [label="SIX6"];
    4 [label="GRIK1"];
    5 [label="WWC1"];
    6 [label="KIR2DS3"];

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

