| 6294dbe | SMHendryx | 05 July 2017, 22:44:24 UTC | Updated output of Scala SortByScore application to output csv containing: feature_family_subset,(f1, precision, recall, (sparseness_mean, sparseness_SE), (numFeatures_mean, numFeatures_SE)) | 05 July 2017, 22:44:24 UTC |
| fffb38a | SMHendryx | 29 June 2017, 20:24:04 UTC | Implemented ScoreExtractor class with overloaded getScores function defintions | 29 June 2017, 20:24:04 UTC |
| bf7e8dc | SMHendryx | 28 June 2017, 20:12:35 UTC | Merge branch 'LinearContextEngine' into SortByF1 | 28 June 2017, 20:12:35 UTC |
| 554dfdd | SMHendryx | 28 June 2017, 20:12:02 UTC | starting work on sort by F1 but save all scores | 28 June 2017, 20:12:02 UTC |
| ea330ab | Enrique Noriega | 28 June 2017, 20:01:41 UTC | Added denseness information to the cross validation results class | 28 June 2017, 20:01:41 UTC |
| 33f0cbc | Enrique Noriega | 28 June 2017, 18:20:29 UTC | Small refactor for file names | 28 June 2017, 18:20:29 UTC |
| 7c7faea | SMHendryx | 22 June 2017, 00:08:21 UTC | Implemented score sorter | 22 June 2017, 00:08:21 UTC |
| 6c7a19d | SMHendryx | 21 June 2017, 23:21:04 UTC | Implemented ScoreExtractor.scala | 21 June 2017, 23:21:04 UTC |
| 7cf789b | Enrique Noriega | 20 June 2017, 19:36:54 UTC | Added a time delay to the CV script to fire up the processes more smoothly | 20 June 2017, 19:36:54 UTC |
| 89d53fb | Enrique Noriega | 20 June 2017, 19:19:35 UTC | CV paralelization bash script for feature selection | 20 June 2017, 19:19:35 UTC |
| 63bca98 | Enrique Noriega | 20 June 2017, 19:18:56 UTC | Creates the Cv output directory if it doesn't exist | 20 June 2017, 19:18:56 UTC |
| 68cbc3f | Enrique Noriega | 20 June 2017, 18:38:30 UTC | Small refactor to the CV file code | 20 June 2017, 18:38:30 UTC |
| a17b798 | SMHendryx | 18 June 2017, 18:33:12 UTC | added functionality to write serialized cross validation output to directory specified as third argument. | 18 June 2017, 18:33:12 UTC |
| 84f06a4 | SMHendryx | 13 June 2017, 22:40:03 UTC | fixed comment typo | 13 June 2017, 22:40:03 UTC |
| e6b0eaa | Enrique Noriega | 13 June 2017, 18:33:16 UTC | Added code to serialize the cross validation results for feature selection | 13 June 2017, 18:33:16 UTC |
| 3232687 | Enrique Noriega | 13 June 2017, 17:42:47 UTC | Refactores the application.conf definition of the entry for feature selection of the context classifier | 13 June 2017, 17:42:47 UTC |
| a071c9b | SMHendryx | 12 June 2017, 22:40:13 UTC | Added functionality to extract feature families from config file as opposed to hardcoded, inline. Also changed the 'Depedency()' [sic] class in FeatureFamily Trait to 'Dependency()', changing elsewhere where needed in code base. | 12 June 2017, 22:40:13 UTC |
| 50ffa5e | SMHendryx | 12 June 2017, 22:39:06 UTC | add functionality to extract feature families from config file as opposed to hardcoded, inline. Also changed the 'Depedency()' [sic] class in FeatureFamily Trait to 'Dependency()', changing elsewhere where needed. | 12 June 2017, 22:39:06 UTC |
| 79528b2 | SMHendryx | 12 June 2017, 19:10:34 UTC | adding functionality to extract feature families from config file as opposed to hardcoded, inline. | 12 June 2017, 19:10:34 UTC |
| fd66ec9 | SMHendryx | 09 June 2017, 21:50:08 UTC | Corrected confusion matrix print out | 09 June 2017, 21:50:08 UTC |
| 019834f | SMHendryx | 09 June 2017, 19:54:14 UTC | First commit of branch to extract features by family. Passed test in that it produces same precision results as LinearContextEngine branch when using all features. Currently extracts the features from hardcoded set of feature families. | 09 June 2017, 19:54:14 UTC |
| 3705d18 | SMHendryx | 09 June 2017, 17:35:42 UTC | development branch of extracting features by family. Has not passed tests. | 09 June 2017, 17:35:42 UTC |
| ef71984 | SMHendryx | 07 June 2017, 22:44:01 UTC | Added comments to explain what code is doing. Implemented case matching to select features of specified feature family. Added POS() to FeatureFamily.scala. | 07 June 2017, 22:44:01 UTC |
| 90cef3f | Enrique Noriega | 05 June 2017, 23:04:46 UTC | Progress in making PairFeatures handle optional parameters | 05 June 2017, 23:04:46 UTC |
| 65fe5d7 | Enrique Noriega | 30 May 2017, 19:00:22 UTC | Feature families | 30 May 2017, 19:00:22 UTC |
| eaa1599 | Enrique Noriega | 26 March 2017, 17:37:22 UTC | Progress: Multiple improvements for feature computing and data set balancing | 26 March 2017, 17:37:22 UTC |
| 2df9626 | Enrique Noriega | 22 March 2017, 18:51:29 UTC | Progress | 22 March 2017, 18:51:29 UTC |
| 479b3e8 | Enrique Noriega | 10 March 2017, 00:10:21 UTC | Progress on phi features | 10 March 2017, 00:10:21 UTC |
| 6a2f8cc | Enrique Noriega | 06 March 2017, 23:55:26 UTC | Progress | 06 March 2017, 23:55:26 UTC |
| bace65c | Enrique Noriega | 26 February 2017, 19:32:33 UTC | Changes | 26 February 2017, 19:32:33 UTC |
| d54fb0d | Enrique Noriega | 23 February 2017, 02:28:18 UTC | Changes to Dataset Annotator | 23 February 2017, 02:28:18 UTC |
| a65b198 | Enrique Noriega | 17 February 2017, 01:36:26 UTC | Adapted the code to parse Zechy's output into the linear context engine | 17 February 2017, 01:36:26 UTC |
| 31564d3 | Enrique Noriega | 16 February 2017, 22:23:15 UTC | Merge branch 'master' into LinearContextEngine | 16 February 2017, 22:23:15 UTC |
| 87beb58 | Tom Hicks | 16 February 2017, 19:56:37 UTC | Use consistent SBT version across projects. | 16 February 2017, 19:56:37 UTC |
| d0b824f | Tom Hicks | 14 February 2017, 22:21:55 UTC | Merge pull request #486 from clulab/lumup Up-version ai.lum.common to match Processors. | 14 February 2017, 22:21:55 UTC |
| 4ce3005 | Tom Hicks | 14 February 2017, 21:54:27 UTC | Up-version ai.lum.common to match Processors. | 14 February 2017, 21:54:27 UTC |
| 4533d75 | Enrique Noriega | 14 February 2017, 21:48:44 UTC | Merge branch 'master' into LinearContextEngine # Conflicts: # main/src/main/resources/application.conf # src/main/scala/org/clulab/reach/ReachCLI.scala | 14 February 2017, 21:48:44 UTC |
| c2f559e | Tom Hicks | 14 February 2017, 21:13:54 UTC | Merge pull request #485 from clulab/menj Retrying pull request | 14 February 2017, 21:13:54 UTC |
| 34c99cb | Tom Hicks | 14 February 2017, 20:44:04 UTC | Update Travis to use scala 2.11.8. | 14 February 2017, 20:44:04 UTC |
| 6f21299 | Tom Hicks | 13 February 2017, 18:32:55 UTC | Update very outdated CHANGES file. | 13 February 2017, 18:32:55 UTC |
| 5ca5403 | Tom Hicks | 13 February 2017, 18:32:05 UTC | Rename output to serial-json format. | 13 February 2017, 18:32:05 UTC |
| 12a3665 | Tom Hicks | 10 February 2017, 04:56:02 UTC | Add outputter for Mentions-JSON format and allow its use in ReachCLI and specification in application.conf. | 10 February 2017, 04:56:02 UTC |
| 2cb81bf | Mihai Surdeanu | 07 February 2017, 21:54:20 UTC | Merge pull request #481 from clulab/iss477 Fix: previous file handling changes did not create empty restart file. | 07 February 2017, 21:54:20 UTC |
| 83747f4 | Tom Hicks | 07 February 2017, 21:24:05 UTC | Fix: previous file handling changes did not create empty restart file. | 07 February 2017, 21:24:05 UTC |
| 38d2c43 | Mihai Surdeanu | 28 January 2017, 01:11:08 UTC | Merge pull request #479 from clulab/slow find shortest path between heads only | 28 January 2017, 01:11:08 UTC |
| 76d3216 | Mihai Surdeanu | 28 January 2017, 00:42:56 UTC | Fixed trigger in the Negative_${ ruleType }_in_response_to rule, which was affecting countSemanticNegatives. | 28 January 2017, 00:42:56 UTC |
| c6978b9 | Marco Antonio Valenzuela Escárcega | 26 January 2017, 23:43:21 UTC | find shortest path between heads only | 26 January 2017, 23:43:21 UTC |
| 1083706 | Tom Hicks | 24 January 2017, 19:53:16 UTC | Merge pull request #473 from clulab/phase3usecase Phase3usecase | 24 January 2017, 19:53:16 UTC |
| 6692bea | Mihai Surdeanu | 14 January 2017, 23:54:54 UTC | Merge pull request #476 from clulab/multi-out Produce multiple output formats per input file | 14 January 2017, 23:54:54 UTC |
| 8d7f2fb | Gus Hahn-Powell | 14 January 2017, 21:49:34 UTC | bug fixes | 14 January 2017, 21:49:34 UTC |
| 956db06 | Gus Hahn-Powell | 14 January 2017, 21:05:39 UTC | Resolves #475 | 14 January 2017, 21:05:39 UTC |
| eca5be9 | Mihai Surdeanu | 12 January 2017, 22:56:14 UTC | Better queries for use case 3 | 12 January 2017, 22:56:14 UTC |
| b7f88bc | Mihai Surdeanu | 12 January 2017, 22:08:28 UTC | Reverted to default use case | 12 January 2017, 22:08:28 UTC |
| 1493c85 | Mihai Surdeanu | 12 January 2017, 22:04:51 UTC | Added use cases for Phase III eval. | 12 January 2017, 22:04:51 UTC |
| e51a3ab | Mihai Surdeanu | 11 January 2017, 15:32:23 UTC | Merge pull request #472 from clulab/restart Adds restart capability, enhanced logging to ReachCLI | 11 January 2017, 15:32:23 UTC |
| c2d16e7 | Tom Hicks | 11 January 2017, 06:50:54 UTC | Add more processing statistics to ReachCLI logging via new class. | 11 January 2017, 06:50:54 UTC |
| 97dda89 | Tom Hicks | 10 January 2017, 21:28:25 UTC | Update for past breaking logging changes: obsoleting of log file. | 10 January 2017, 21:28:25 UTC |
| b1219ae | Tom Hicks | 10 January 2017, 21:27:28 UTC | Remove obsoleted log file parameter from ReachCLI. | 10 January 2017, 21:27:28 UTC |
| ba981d3 | Tom Hicks | 10 January 2017, 04:50:21 UTC | Add processing restart capability, debugging of configuration to ReachCLI. Add/use root path in application.conf file. | 10 January 2017, 04:50:21 UTC |
| 5af7782 | Mihai Surdeanu | 07 January 2017, 08:12:08 UTC | Merge pull request #471 from clulab/issue459 Issue459: Complex formation is direct | 07 January 2017, 08:12:08 UTC |
| 25853f8 | Dane Bell | 06 January 2017, 22:50:44 UTC | Merge branch 'master' into issue459 | 06 January 2017, 22:50:44 UTC |
| 187a660 | Dane Bell | 06 January 2017, 22:50:11 UTC | Complex formation is always direct | 06 January 2017, 22:50:11 UTC |
| e42974c | Gus Hahn-Powell | 24 December 2016, 04:48:07 UTC | Merge pull request #470 from clulab/demeter Hide embedded implementation of KB resolution from users. | 24 December 2016, 04:48:07 UTC |
| 77edc79 | Tom Hicks | 24 December 2016, 02:55:43 UTC | Hide embedded implementation of KB resolution from users. | 24 December 2016, 02:55:43 UTC |
| 1b623a4 | Mihai Surdeanu | 21 December 2016, 01:16:56 UTC | Merge pull request #469 from clulab/issue454 Issue 454: Knockdown, silencing, etc. | 21 December 2016, 01:16:56 UTC |
| 2c10015 | Dane Bell | 20 December 2016, 22:55:17 UTC | Cleanup debug printlns | 20 December 2016, 22:55:17 UTC |
| 4b60c11 | Dane Bell | 20 December 2016, 21:30:33 UTC | Add negative-polarity expressions for complex events | 20 December 2016, 21:30:33 UTC |
| 2cc731c | Dane Bell | 20 December 2016, 20:08:01 UTC | Merge branch 'master' into issue454 | 20 December 2016, 20:08:01 UTC |
| 07bb1a6 | Gus Hahn-Powell | 14 December 2016, 05:01:43 UTC | Merge pull request #466 from clulab/cmuformat Cmuformat | 14 December 2016, 05:01:43 UTC |
| 9f50603 | Gus Hahn-Powell | 14 December 2016, 03:48:20 UTC | Merge branch 'master' into cmuformat | 14 December 2016, 03:48:20 UTC |
| 5b2a637 | Gus Hahn-Powell | 14 December 2016, 03:48:07 UTC | Merge pull request #462 from clulab/newline remove newlines from logger calls | 14 December 2016, 03:48:07 UTC |
| 4ce1a54 | Gus Hahn-Powell | 14 December 2016, 03:43:49 UTC | refactor of column-based export formats | 14 December 2016, 03:43:49 UTC |
| 76f4b53 | Mihai Surdeanu | 14 December 2016, 00:25:48 UTC | Added nested controllers to the CMU format. | 14 December 2016, 00:25:48 UTC |
| 0db1161 | Mihai Surdeanu | 13 December 2016, 03:56:57 UTC | Added skeleton for the identification of nested controllers. | 13 December 2016, 03:56:57 UTC |
| 736191c | Mihai Surdeanu | 13 December 2016, 03:29:05 UTC | Better handling of complexes | 13 December 2016, 03:29:05 UTC |
| 20d0434 | Mihai Surdeanu | 13 December 2016, 02:45:58 UTC | better filtering of events in cmuFilter | 13 December 2016, 02:45:58 UTC |
| e6ae54b | Mihai Surdeanu | 12 December 2016, 23:02:41 UTC | added normalization of locations | 12 December 2016, 23:02:41 UTC |
| 2ddfe0b | Mihai Surdeanu | 12 December 2016, 22:36:34 UTC | We now output element info and locations. | 12 December 2016, 22:36:34 UTC |
| 349dae8 | Mihai Surdeanu | 12 December 2016, 02:04:39 UTC | Converted name spaces to element types for CMU format | 12 December 2016, 02:04:39 UTC |
| 2e18358 | Mihai Surdeanu | 09 December 2016, 22:09:46 UTC | More stuff for CMU format | 09 December 2016, 22:09:46 UTC |
| 4f4cc52 | Mihai Surdeanu | 08 December 2016, 22:42:03 UTC | Merge branch 'master' into cmuformat | 08 December 2016, 22:42:03 UTC |
| c17b028 | Mihai Surdeanu | 07 December 2016, 23:38:56 UTC | Merge pull request #464 from clulab/restrictAntecedents Antecedent selection more restricted by grounding | 07 December 2016, 23:38:56 UTC |
| 5dddd4d | Dane Bell | 07 December 2016, 21:58:11 UTC | Antecedent selection more restricted by grounding | 07 December 2016, 21:58:11 UTC |
| 897110a | Marco Antonio Valenzuela Escárcega | 02 December 2016, 17:01:24 UTC | remove newlines from logger calls | 02 December 2016, 17:01:24 UTC |
| 5e3e267 | Dane Bell | 30 November 2016, 20:18:15 UTC | Check nn and prep_of for negative polarity | 30 November 2016, 20:18:15 UTC |
| df3f84e | Mihai Surdeanu | 29 November 2016, 02:55:26 UTC | Merge pull request #458 from clulab/harvardKB Harvard KBs | 29 November 2016, 02:55:26 UTC |
| d7cd890 | Tom Hicks | 29 November 2016, 01:18:07 UTC | Update to use Bioresources 1.1.19 containing Bioentities project KBs. | 29 November 2016, 01:18:07 UTC |
| 66281b2 | Mihai Surdeanu | 28 November 2016, 22:57:02 UTC | Updated changes | 28 November 2016, 22:57:02 UTC |
| a65664d | Mihai Surdeanu | 28 November 2016, 22:55:42 UTC | Merge branch 'master' into cmuformat | 28 November 2016, 22:55:42 UTC |
| f11ee8d | Mihai Surdeanu | 28 November 2016, 22:54:59 UTC | The src/dest arguments are now correctly saved. | 28 November 2016, 22:54:59 UTC |
| 8183887 | Tom Hicks | 28 November 2016, 21:10:03 UTC | Update regulation events test for BE KBs. | 28 November 2016, 21:10:03 UTC |
| 954f64f | Mihai Surdeanu | 28 November 2016, 20:00:10 UTC | Merge branch 'cmuformat' of https://github.com/clulab/reach into cmuformat | 28 November 2016, 20:00:10 UTC |
| 306e095 | Mihai Surdeanu | 28 November 2016, 19:58:42 UTC | Added src/dest to arizona format. Not working for now. | 28 November 2016, 19:58:42 UTC |
| 1f40854 | Tom Hicks | 28 November 2016, 19:23:56 UTC | Update JSON test for BE KBs. | 28 November 2016, 19:23:56 UTC |
| 6eaa502 | Tom Hicks | 28 November 2016, 00:40:36 UTC | Add test of some sample families now grounded by the BE KB. | 28 November 2016, 00:40:36 UTC |
| 7c0300c | Tom Hicks | 26 November 2016, 22:54:56 UTC | Add NER override group tests for BE entries. | 26 November 2016, 22:54:56 UTC |
| d57fe26 | Tom Hicks | 26 November 2016, 03:34:04 UTC | Add override test for entries kept despite clash with BE KBs. | 26 November 2016, 03:34:04 UTC |
| 939d968 | Tom Hicks | 26 November 2016, 02:52:20 UTC | Refactor overrides test to use method. | 26 November 2016, 02:53:18 UTC |
| d77b6a5 | Mihai Surdeanu | 25 November 2016, 05:14:53 UTC | Working on the CMU format. | 25 November 2016, 05:14:53 UTC |
| f368abd | Mihai Surdeanu | 24 November 2016, 02:12:03 UTC | Merge pull request #456 from clulab/dsv-parser-safety Safer splitting of csv rows | 24 November 2016, 02:12:03 UTC |
