Change Log

• Release 0.20.2 (Fri Oct 18 11:25:54 2024)
  • BNDC: Bug fixed that tried to calculate traceS for discrete variables.
  • Input values inspection improved for discrete values.
• Release 0.20.1 (Fri Oct 4 21:52:37 2024)
  • BNRC & BNDC: Bug fixed in outputting invalid B-spline parameters.
  • BNRC & BNDC: Bug fixed in calculating ECv with lv=0 and missing values.
• Release 0.20.0 (Wed Jul 3 17:08:34 2024)
  • BNRC & BNDC: The calculation of degree of freedom of B-spline curves (trace of S) has been implemented. The new edge property "bspline.trS" will be added after the score calculation of the network.
• Release 0.19.1 (Mon May 20 14:18:58 2024)
  • No functionally updated.
  • BNRC score implementation updated for faster calculation.
  • Ampere Arm processor support and gcc + OpenBLAS support added.
  • From this release, for HGC SHIROKANE supercomputer, gcc + OpenBLAS is regarded as the primary compilation environment.
• Release 0.19.0 (Sun Sep 17 23:13:41 2023)
  • CGHC, Greedy (HC): Bug fixed in MPI bootstrap parallelization in storing results in files including "--single-file" support.
  • ING: Multiple networks in a single ING file supported.
• Release 0.18.1 (Wed Sep 6 21:41:02 2023)
  • Fixed a bug in exchanging a constraint graph between MPI processces.
  • GenDataFilter : (EXPERIMENTAL) "rand_type" argument added and supported uniform distribution for random values.
  • Improved log messages.
• Release 0.18.0 (Wed Jul 5 18:33:43 2023)
  • NNSR : Supports the "output" argument to output all the subnetworks into files.
  • PaList: Added arguments for reading the subnetwork files output by the NNSR algorithm.
  • EdgeContribFilter : Improved the memory error detection.
• Release 0.17.0 (Tue May 9 16:41:14 2023)
  • Multi-thread support implemented. Set "USE_OMP=1" option when compiling the binary and set the "OMP_NUM_THREADS" variable for the number of threads to use when you execute the calculation.
  • Error output improved. Important error messages are now output to the standard error regardless of setting -L (logging mode) option.
• Release 0.16.1 (Fri Mar 10 13:44:05 2023)
  • Fixed a bug in the NNSR algorithm that occurs with more than 2560 processes.
• Release 0.16.0 (Mon Sep 12 22:43:19 2022)
  • Multiple file standard input/output function is implemented. Use "--stdin", "--stdout" or "--stdio" to enable this function.
  • PRFilter : Fixed a bug that generates an empty .PL file when the primary ID is not available.
  • Fixed a bug that is able to read size 0 file as input data.
  • (EXPERIMENTAL) Windows support.
• Release 0.15.0 (Tue Jun 7 18:16:57 2022)
  • Fixed a bug that causes segmentation fault when you read a constrain graph that contains no edge properties.
  • SGN3 : Improved an error message when the file is broken.
  • Parsing key=value expressions in arguments now allows spaces after "=". This is very useful if your shell does not complete file names after "=".
  • Terms "skeleton" was replaced with "constrain". This is applied for all the option names related to structure contraining options. Note that the old option names are still available.
• Release 0.14.0 (Fri Jan 28 10:50:00 2022)
  • FileCheckFilter : implemented.
  • ScoreFilter : A bug fixed in printing variable types in a log file.
  • BNDC : A bug fixed in storing parameters of discrete-continuous mixed model.
  • BNDC : Detailed documents for node and edge properties added.
• Release 0.13.0 (Wed Aug 18 16:38:13 2021)
  • Fixed memory leakage problems in filter application processes with MPI execution.
  • EdgeContribFilter : "edgeprop=off", "method=ECv2", and "nan=" option are implemented.
• Release 0.12.0 (Fri Aug 6 22:00:00 2021)
  • PRCFilter : Name chaned to use the correct word and PR-AUC calculation implemented. Default values of the parameters are also changed (bg and ed).
  • ScoreFilter : A bug fixed that causes a segmentation fault when categorical values are included in the input data.
• Release 0.11.4 (Mon Jul 19 15:37:20 2021)
  • NNSR : Able to recognize BNRC hyperparameter settings via -S option.
• Release 0.11.3 (Thu Jul 15 18:09:35 2021)
  • GDF : "csv" option added for allowing to read comma separated text file, in addtion to tab separated files.
  • NNSR : (EXPERIMENTAL) Able to use with the bootstrap method ("-B 1").
• Release 0.11.2 (Wed Jun 2 14:58:50 2021)
  • CompFilter : "output" option added.
• Release 0.11.1 (Tue Mar 30 20:49:43 2021)
  • Time expanded dynamic and static hybrid Bayesian network estimation has been implemented. Use "-H" option to use this.
  • Fixed a bug that both -y and -Y can be specified.
• Release 0.11.0 (Wed Mar 24 22:15:45 2021)
  • Time expanded or T-time step dynamic Bayesian network estimation has been implmenented. Use "-Y" option to use this.
  • Fixed a bug where the filtered network cannot be saved with "-o" option.
  • NNSR : Bug fixed that stops the algorithm with "-S linear" option.
  • Fixed a bug in saving data in GDF format if both secondaryid and time sample attributes exist.
  • GenDataFilter : "normalize" option added.
• Release 0.10.0 (Thu Jan 7 14:20:52 2021)
  • MPI parallelization of filter applications implemented. Only limited filters currently support MPI parallelization.
  • ScoreFilter : MPI parallelization supported.
  • EdgeContribFilter : MPI parallelization supported and documentation updated.
  • ROCFilter : "output" option added.
  • ReadFilter : MPI parallelization supported. The root rank (process) reads the file and the network are distributed among processes.
  • WriteFilter : MPI parallelization supported. "mpi" option added.
• Release 0.9.3 (Wed Jun 3 16:23:54 2020)
  • GDF : Bug Fixed that displays log messages for debugging.
• Release 0.9.2 (Wed May 27 20:43:57 2020)
  • GDF : Changed to ignore empty cells in row attribute names (lines with %)
  • GDF : Meta key "$GDF" is treated as the column = variable marker.
• Release 0.9.1 (Mon May 25 11:09:39 2020)
  • Effective for only MPI enabled version.
  • NNSR : Bug fixed that "reset" was on by default.
• Release 0.9.0 (Thu May 21 10:55:50 2020)
  • NNSR algorithm implemented. This is enabled with the MPI enabled executable.
  • Greedy (HC): MPI parallelization supported with the MPI enabled executable.
  • TXT : binding character changed for the "name" option.
  • EdgeContribFilter : Parent_Child style name column can be added with "name" option in the output file.
  • GDF : Bug fixed that causes SEGV when l=2 is specified.
• Release 0.8.6 (Fri May 1 13:49:46 2020)
  • All the memory allocation failure is now being tracked.
• Release 0.8.5 (Wed Apr 29 12:09:37 2020)
  • CGHC, SDHybrid : Added "bs_check" option to disable secondary ID length consistency check.
• Release 0.8.4 (Fri Apr 24 16:05:56 2020)
  • EdgeContribFilter : New "RC2" method implmented for improving the vidualization of individual networks.
  • New bootstrap mode "--B-mode list" implemented, that resamples sets of samples at once listed in a file. Use "--B-file" to specify the list file.
• Release 0.8.3 (Thu Feb 27 20:38:04 2020)
  • BNDC, BNRC : max_loops and stop arguments added.
  • BNDC : Fixed a bug in handling missing values when calculating sample likelihood and deviances.
• Release 0.8.2 (Fri Jan 31 17:06:26 2020)
  • BNDC : Bug fixed in handling missing values that causes 0 ECvs.
• Release 0.8.1 (Wed Dec 25 19:10:39 2019)
  • ScoreFilter : Fixed a bug in selecting nodes.
• Release 0.8.0 (Tue Dec 24 15:02:35 2019)
  • BNDC : "ecv_clip" argument added that replaces the clipped values.
  • GenDataFilter : "use_net_func" argument added.
  • ScoreFilter : Supports the input data file not used to estimate the input network.
  • ScoreFilter : "save" option added.
• Release 0.7.1 (Fri Nov 22 19:08:12 2019)
  • GDF : "assume_real" option added.
  • GDF : "split_xy" option added.
  • PRFilter : Implemented calculation of Z scores and sample devience.
  • ScoreFilter : "node_score" option added.
  • BSFilter : Fixed a bug in the calculation of median values.
  • SearchFilter : "outdist" option added.
  • Improved the error check for the dynamic model.
  • Supported the pid bootstrap mode for the static model (--bs-mode).
  • Normal greedy HC algorithm reimplemented (-a hc).
• Release 0.6.0 (Wed Sep 11 11:19:52 2019)
  • TXT : "name" argument added for writing in TXT format.
  • SDHybrid : --fixed argument supported.
• Release 0.5.0 (Fri Aug 23 13:03:37 2019)
  • EdgeContribFilter : Supported Arbitrary data for EC calculations.
  • ING : Fixed a bug that treats all the real values as float when reading files.
  • ScoreFilter : ingore option added.
  • Precise specification of modeling range supported by --read-range.
• Release 0.4.0 (Wed Jun 12 16:46:14 2019)
  • BNDC, BNRC : Refactored internal implementation.
  • BNDC, BNRC : Fixed a bug that releases input data when finalizing the score.
  • Fixed a bug that causes segmentation fault when specifying -y without specifying an input data file.
  • CGHC : Fixed a bug that fails to calculate node and edge properties when a fixed graph is specified.
• Release 0.3.8 (Thu Mar 28 10:21:45 2019)
  • GDF : Fixed a bug that failed to read and write the GDF file with "primaryid" for sample attributes.
  • BNDC : Fixed a bug that failed to interpret the old BNRC model parameters.
  • Threshold of warning changed for high rate missing value variables from 0.4 to 0.3.
  • ING : Memory leak fixed.
• Release 0.3.7 (Tue Mar 19 11:15:19 2019)
  • BNDC, BNRC : Fixed a bug in calculating scores with missing values.
• Release 0.3.6 (Mon Mar 18 20:34:23 2019)
  • BNDC, BNRC : Fixed a bug in calculating scores with missing values.
  • ScoreFilter : j (target) argument added to calculate only the specified target.
  • BNDC : Modified to warn invalid scores when 1-to-1 score calculation.
• Release 0.3.5 (Tue Mar 12 11:40:14 2019)
  • BNDC : Modified not to stop when a low variance is detected.
• Release 0.3.4 (Mon Mar 11 09:26:46 2019)
  • SGN3 : Fixed a bug in parsing properties.
  • ScoreTestFilter : Newly implemented.
• Release 0.3.3 (Fri Mar 8 15:23:22 2019)
  • ING : Fixed a bug that failed to parse the initial character.
• Release 0.3.2 (Fri Mar 8 13:14:02 2019)
  • GDF : TSV output mode supported.
  • ING : NaN and infinity values supported.
  • ING : Improved internal module (ytJSON) error messages.
• Release 0.3.1 (Fri Feb 22 13:32:30 2019)
  • Fixed a bug in reading a SGN3 file with discrete model parameters.
• Release 0.3.0 (Fri Feb 22 12:04:19 2019)
  • The name of JSON based file format JSN was changed to ING. This format is treated as the primary format of INGOR.
  • EdgeContribFilter : Continuous discrete mixed model supported.
• Release 0.2.3 (Wed Feb 20 14:36:50 2019)
  • EdgeContribFilter : Fixed a bug in ECv method, that resulted in 1 or 0 for all the values.
• Release 0.2.2 (Tue Feb 19 15:37:07 2019)
  • EdgeContribFilter : Fixed a bug in mode=each.
• Release 0.2.1 (Mon Feb 18 21:07:26 2019)
  • CGHC : Fixed a bug that ignores memory specification for the score function.
  • ScoreFilter : Fixed a bug that failed to convert data for dynamic model.
  • ScoreFilter : SDhybrid model supported.
  • ScoreFilter : Fixed a bug that does not tell the maximum number of parents to the score function, causing too much memory allocation.
  • --total-mem specification is now passed to every filters.
    • ScoreFilter, PRFilter, EdgeContribFilter supported to receive this information from the main program.
• Release 0.2.0 (Fri Feb 15 15:20:35 2019)
  • LayoutFilter : Newly implemented.
• Release 0.1.40 (Thu Feb 14 15:35:26 2019)
  • BNDC : Fixed a bug that fails to calculate scores when the memory level is 0.
  • EdgeContribFilter : Fixed a bug that forgot to specify the number of max parents to the score function.
• Release 0.1.39 (Wed Feb 13 16:21:12 2019)
  • BNDC : "outer" argument added.
• Release 0.1.38 (Tue Feb 12 15:24:49 2019)
  • BNRC : Fixed a bug in BNRC score calculation that caused segmentation fault.
• Release 0.1.37 (Fri Feb 8 17:42:22 2019)
  • EdgeContribFilter : Name changed from RelContribFilter.
  • EdgeContribFilter : Some new metrics implemented.
• Release 0.1.36 (Thu Feb 7 15:45:29 2019)
  • BNDC : Fixed a bug in handling missing values of discrete variables.
  • BNRC : Traditional BNRC score function implemented.
• Release 0.1.35 (Tue Feb 5 14:51:05 2019)
  • CGHC : Fixed a bug not considering skeleton when calculating continuous-discrete pair candidates.
• Release 0.1.34 (Mon Feb 4 19:08:35 2019)
  • SearchFilter : Newly implemented.
• Release 0.1.33 (Fri Feb 1 16:28:00 2019)
  • RelContribFilter : Newly implemented.
• Release 0.1.32 (Wed Jan 30 16:16:39 2019)
  • BNDC : Arguments for tuning hyperparameter search range added.
• Release 0.1.31 (Mon Jan 28 15:47:13 2019)
  • TXT : Fixed a bug that mishandles children's properties when reading.
• Release 0.1.30 (Wed Jan 23 18:29:14 2019)
  • DagFilter : Newly Added.
• Release 0.1.29 (Wed Jan 23 15:58:20 2019)
  • CGHC : Fixed a bug mishandling edges when trying to add them.
• Release 0.1.28 (Tue Jan 22 16:41:11 2019)
  • TXT : Fixed a bug when reading a TXT file with empty cells at the end of lines.
• Release 0.1.27 (Mon Jan 21 12:02:45 2019)
  • TXT : Changed default setting for handling node indices when reading.
  • TXT : Modified to check if the node IDs are complete if use_index is specified.
• Release 0.1.26 (Fri Jan 18 14:28:09 2019)
  • ScoreFilter : Node number inconsistency check implemented.
  • MCToolFilter : (Experimental implementation)
• Release 0.1.25 (Wed Jan 16 17:31:49 2019)
  • TXT : Fixed a bug causing wrong node index when reading TXT format files.
  • BNDC : Fixed a bug casing segmentation fault when dynamic mode.
• Release 0.1.24 (Thu Dec 27 11:07:15 2018)
  • ScoreFilter : Implemented aberrant score check.
  • MCMCFilter : MCMC implemented. For test and evaluation only.
• Release 0.1.23 (Wed Dec 19 14:52:52 2018)
  • GDF : Value validity check implemented.
  • BNDC : Fixed a bug in handling missing values in discrete variables.
• Release 0.1.22 (Fri Dec 14 14:37:42 2018)
  • GDF : Empty cells are detected in the data section. It causes an error when detected.
  • GDF : empty argument added to ignore empty cells in the data setion when reading files. See API document for details.
  • NodeList : sort, and header arguments are added for writing in NodeList format. See API document for details.
  • CGHC, BNDC : An aberrant gain value is converted to NaN.
  • BNDC : Missing value ratio is output in the log message.
  • ScoreFilter : args argument is chaned to score_args.
• Release 0.1.21 (Mon Dec 3 20:54:37 2018)
  • CGHC, BNDC : Improved aberrant score detection and handling.
  • BSFilter : Fixed a bug in handling edge properties written in the different order.
• Release 0.1.20 (Fri Nov 30 15:07:51 2018)
  • CGHC, BNDC : Improved aberrant score detection.
  • CGHC, BNDC : Fixed a bug in handling discrete values with contious values when bootstrapping.
  • BSFilter : Fixed a bug in handling bootstrapped network with different numbers of edge properties.
• Release 0.1.19 (Tue Nov 27 20:43:28 2018)
  • CGHC : Bug fixed in detecting aberrant scores, that caused narrow search space for the greedy algorithm, existing in r0.1.12 through r0.1.18.
  • CGHC : Improved aberrant score detection.
  • GDF : EDF writing support when reading a GDF file (write_edf option).
  • BNDC : Warning added when outputting primary ID specific log-likelihoods.
• Release 0.1.18 (Fri Nov 16 15:11:57 2018)
  • PRFilter : Modified to ignore nan and inf values when summing up primary ID specific log-liklihood calculation.
• Release 0.1.17 (Wed Nov 14 18:12:12 2018)
  • PRFilter : Primary ID specific log-likelihood calculation supported.
• Release 0.1.16 (Mon Nov 12 12:18:11 2018)
  • CGHC : Bug fixed in resetting the random number seed implemented in Rel 0.1.9.
  • inger : Multiple --skel-args acceptable.
• Release 0.1.15 (Thu Nov 8 13:34:16 2018)
  • ingor : --skel and --skel-type can be specified multiple times.
  • ingor : --skel-write, --skel-write-type, and --skel-write-args added.
• Release 0.1.14 (Wed Nov 7 20:29:28 2018)
  • BNDC : Bug fixed for missing value handling when a discrete variable exists.
• Release 0.1.13 (Tue Nov 6 14:54:04 2018)
  • CGHC : minor update for suppress warning.
• Release 0.1.12 (Tue Nov 6 14:23:40 2018)
  • CGHC : NaN/Inf score handling improved.
• Release 0.1.11 (Fri Nov 2 13:58:04 2018)
  • CGHC : Fixed a fixed permutation for debugging.
• Release 0.1.10 (Thu Nov 1 15:40:35 2018)
  • ingor : -L 2 added that forces to output logs in a file.
• Release 0.1.9 (Thu Nov 1 14:11:10 2018)
  • ingor : Added the --bs-seed-adjust option.
  • CGHC : Added the reset option.
  • CGHC : Improved infinity value handling so that the algorithm does not stop the estimation even if it gets infinity values from the score function.
• Release 0.1.8 (Tue Oct 30 13:38:31 2018)
  • EdgePropFilter : Added.
• Release 0.1.7 (Fri Oct 26 18:25:54 2018)
  • SubnetFilter : Supports edge property extraction.
  • NodeList : Supports sorted output by the number of children.
• Release 0.1.6 (Mon Oct 22 21:39:46 2018)
  • ingor.r : Fixed a bug in the R script that fails to handle edges with NA children.
  • ingor.r : iz option added for bspline.logliklihood() to avoid -Inf and/or NaN.
  • Implemented zero replacement for -Inf local score nodes.
• Release 0.1.5 (Wed Oct 10 10:52:58 2018)
  • Fixed a bug in TXT format with the full option.
• Release 0.1.4 (Thu Oct 4 17:20:21 2018)
  • Fixed a bug in partial residual calculation with missing values.
  • --output-data and PRFilter supports log likelihood calculation.
• Release 0.1.3 (Thu Oct 4 10:43:42 2018)
  • GDF : New meta keys $PrimaryIDType and $SecondaryIDType supported.
  • CompFilter : Bug fixed failing auto file type detection for tp, fn, and fp networks.
• Release 0.1.2 (Tue Oct 2 19:41:55 2018)
  • Fixed a bug in partial residual calculation.
  • Fixed a bug in score calculation if discrete variables are parents of continuous variables.
  • Changed the default value to 2 for the --md option.
• Release 0.1.1 (Tue Oct 2 11:38:40 2018)
  • PRFilter : Fixed a bug not using range values in the "bspline" edge property.
  • PRFilter : "fit" option added.
  • GenDataFilter : Supports dynamic data output in EDF mode.
• Release 0.1.0 (Mon Oct 1 10:28:57 2018)
  • SDHybrid : Static-dynamic hybrid model implemented.
  • Fixed a bug that crashes if the format type is not set for the fixed network.
  • Fixed a bug in partial residual calculation.
  • Fixed a bug in reading a simplest TXT format file.
• Release 0.0.8 (Fri Sep 21 17:42:33 2018)
  • BSFilter : da_mode argument added.
  • Combinatorial Greedy Hill-Climbing Algorithm : skip argument added.
• Release 0.0.7 (Fri Sep 21 11:11:40 2018)
  • PRFilter implemented.
  • ingor.r improved.
• Release 0.0.6 (Thu Sep 20 10:36:50 2018)
  • BNDC : Temporarily disabled output of some node properties.
• Release 0.0.5 (Tue Sep 18 18:31:20 2018).
  • Fixed a bug in the CGHC (Greedy HC) algorithm for dynamic model.
• Release 0.0.4 (Tue Sep 18 13:09:46 2018).
  • Fixed a bug in EDF mode that mishandle the primary and secondary IDs when reading the input file.
  • CompFilter : Writing the comparison results in files supported.
  • ScoreFilter : Node and edge property calculation implemented.
  • TXT : Fixed a bug in reading the TXT format file.
• Release 0.0.3 (Fri Sep 14 13:30:58 2018).
  • Fixed a bug in handling missing values.
  • ingor.r supports missing values.
• Release 0.0.2 (Fri Sep 7 18:58:03 2018).
  • Fixed bugs in calculating the BNDC score under Linux + netlib BLAS/LAPACK.
• Release 0.0.1 (Fri Sep 7 12:05:36 2018).
  • First release of INGOR.