Author: dligach
Date: Tue Apr 2 20:18:13 2013
New Revision: 1463733
URL: http://svn.apache.org/r1463733
Log:
new package for xmi file analysis
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes
Author: dligach
Date: Tue Apr 2 20:20:18 2013
New Revision: 1463737
URL: http://svn.apache.org/r1463737
Log:
print events and their contexts to a file fur further analysis
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Tue Apr 2 20:33:22 2013
New Revision: 1463745
URL: http://svn.apache.org/r1463745
Log:
remove hard coded path to my home directory
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java
Modified
Author: dligach
Date: Fri Apr 5 18:06:07 2013
New Revision: 1465078
URL: http://svn.apache.org/r1465078
Log:
Updates to account for the new directory structure in SVN
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified
Author: dligach
Date: Mon Apr 8 16:06:54 2013
New Revision: 1465671
URL: http://svn.apache.org/r1465671
Log:
added fine grain stats (e.g. counts of as-ss entity pairs)
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data
Author: dligach
Date: Mon Apr 8 18:09:57 2013
New Revision: 1465698
URL: http://svn.apache.org/r1465698
Log:
now calculating the stats for degree_of
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java
Author: dligach
Date: Mon Apr 8 19:34:33 2013
New Revision: 1465737
URL: http://svn.apache.org/r1465737
Log:
calculating number of candidate entity pairs for location_of and degree_of
separately.
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes
Author: dligach
Date: Tue Apr 9 14:05:34 2013
New Revision: 1466038
URL: http://svn.apache.org/r1466038
Log:
added calcs for average distance between arguments
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data
Author: dligach
Date: Wed Apr 10 18:23:35 2013
New Revision: 1466608
URL: http://svn.apache.org/r1466608
Log:
switched from using WordToken to BaseToken
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java
Modified
Author: dligach
Date: Tue Apr 23 19:13:34 2013
New Revision: 1471101
URL: http://svn.apache.org/r1471101
Log:
Baseline that marks "CONTAINS" relation between a time expression and the
nearest event mention
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/t
Author: dligach
Date: Tue Apr 23 19:39:06 2013
New Revision: 147
URL: http://svn.apache.org/r147
Log:
Fixed a bug (changed the order of time and event as arguments of CONTAINS)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines
Author: dligach
Date: Tue Apr 23 19:48:29 2013
New Revision: 1471117
URL: http://svn.apache.org/r1471117
Log:
removed uneeded print statements
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/BaselineEventTimeRelationAnnotator.java
Modified
Author: dligach
Date: Tue Apr 23 20:04:08 2013
New Revision: 1471126
URL: http://svn.apache.org/r1471126
Log:
cleanup
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/BaselineEventTimeRelationAnnotator.java
Modified:
ctakes/trunk/ctakes-temporal
Author: dligach
Date: Mon Apr 29 15:45:44 2013
New Revision: 1477161
URL: http://svn.apache.org/r1477161
Log:
use configuration parameters instead of hard-coded values
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Tue Apr 30 14:31:54 2013
New Revision: 1477662
URL: http://svn.apache.org/r1477662
Log:
code to print gold standard relations and their contexts
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Tue Apr 30 20:15:53 2013
New Revision: 1477808
URL: http://svn.apache.org/r1477808
Log:
added feature based on event's doc time rel
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java
Mod
Author: dligach
Date: Wed May 1 15:59:13 2013
New Revision: 1478064
URL: http://svn.apache.org/r1478064
Log:
added UMLS typeID feature extractor
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java
Modified:
ctakes/trunk
Author: dligach
Date: Mon May 6 18:36:57 2013
New Revision: 1479669
URL: http://svn.apache.org/r1479669
Log:
rought draft of the code to expand NP headwords -> NP
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor
Author: dligach
Date: Mon May 6 18:44:31 2013
New Revision: 1479670
URL: http://svn.apache.org/r1479670
Log:
minor improvements + cleanup
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java
Modified
Author: dligach
Date: Mon May 6 19:01:24 2013
New Revision: 1479679
URL: http://svn.apache.org/r1479679
Log:
for now, keep only token and pos features (others are experimental at this
point)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Tue May 14 18:22:17 2013
New Revision: 1482511
URL: http://svn.apache.org/r1482511
Log:
pipeline that uses a trained event extraction model to extract events from
notes in a directory
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal
Author: dligach
Date: Tue May 14 18:54:55 2013
New Revision: 1482521
URL: http://svn.apache.org/r1482521
Log:
Added a class to print event annotations in xmi files
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventPrintingPipeline.java
Author: dligach
Date: Tue May 14 19:40:47 2013
New Revision: 1482537
URL: http://svn.apache.org/r1482537
Log:
Added a pipeline that creates automatic event and time annotations
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines
Author: dligach
Date: Tue May 14 20:19:15 2013
New Revision: 1482556
URL: http://svn.apache.org/r1482556
Log:
default model location in prev. version was incorrect
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java
Author: dligach
Date: Wed May 22 14:02:21 2013
New Revision: 1485214
URL: http://svn.apache.org/r1485214
Log:
removed a hardcoded path; removed explicit type system mentions
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines
Author: dligach
Date: Wed May 22 14:15:31 2013
New Revision: 1485217
URL: http://svn.apache.org/r1485217
Log:
fixed typos in option captions
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java
Author: dligach
Date: Wed May 22 14:59:38 2013
New Revision: 1485236
URL: http://svn.apache.org/r1485236
Log:
fixed a couple of typos in option caption
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java
Author: dligach
Date: Wed May 29 15:20:58 2013
New Revision: 1487513
URL: http://svn.apache.org/r1487513
Log:
Baseline requested by reviewer 2 (second set of revisions)
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines
Author: dligach
Date: Wed May 29 15:42:29 2013
New Revision: 1487519
URL: http://svn.apache.org/r1487519
Log:
The new baseline requiested by reviewer 2 became baseline2. Old baseline3
became baseline4.
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes
Author: dligach
Date: Wed May 29 18:07:57 2013
New Revision: 1487583
URL: http://svn.apache.org/r1487583
Log:
Baseline for degree_of requested by reviewer 2 (second round of reviews)
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines
Author: dligach
Date: Fri May 31 14:11:11 2013
New Revision: 1488241
URL: http://svn.apache.org/r1488241
Log:
simplified this pipeline
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java
Modified
Author: dligach
Date: Fri May 31 14:13:06 2013
New Revision: 1488242
URL: http://svn.apache.org/r1488242
Log:
renamed to better reflect what this pipeline does
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines
Author: dligach
Date: Fri May 31 14:18:41 2013
New Revision: 1488245
URL: http://svn.apache.org/r1488245
Log:
filtering out obvious classifier errors
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationViewer.java
Author: dligach
Date: Fri May 31 14:22:51 2013
New Revision: 1488246
URL: http://svn.apache.org/r1488246
Log:
added another filter (arg1 must be an anatomical site)
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines
Author: dligach
Date: Tue Jun 4 18:31:21 2013
New Revision: 1489548
URL: http://svn.apache.org/r1489548
Log:
display the relations whose arg1 is defined in a separate file
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines
Author: dligach
Date: Tue Jun 4 18:53:35 2013
New Revision: 1489560
URL: http://svn.apache.org/r1489560
Log:
using constants instead of hard-coded values
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines
Author: dligach
Date: Tue Jun 4 19:18:29 2013
New Revision: 1489571
URL: http://svn.apache.org/r1489571
Log:
moved the consumer inside the pipeline class
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java
Author: dligach
Date: Tue Jun 4 19:27:18 2013
New Revision: 1489573
URL: http://svn.apache.org/r1489573
Log:
moved the consumer inside the pipeline class definition
Removed:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Wed Jun 5 19:25:14 2013
New Revision: 1490011
URL: http://svn.apache.org/r1490011
Log:
fix: now only training set annotation are displayed (instead of train+test+dev
as before)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data
Author: dligach
Date: Thu Jun 6 15:52:28 2013
New Revision: 1490330
URL: http://svn.apache.org/r1490330
Log:
expanded the size of the context that's used to display a relation
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/ana
Author: dligach
Date: Fri Jun 7 14:28:44 2013
New Revision: 1490662
URL: http://svn.apache.org/r1490662
Log:
added dependency path features
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java
ctakes/trunk/ctakes-temporal
Author: dligach
Date: Fri Jun 7 15:51:29 2013
New Revision: 1490695
URL: http://svn.apache.org/r1490695
Log:
modified the dependency path feature to exclude the words on both ends of the
path
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Mon Jun 10 15:22:08 2013
New Revision: 1491495
URL: http://svn.apache.org/r1491495
Log:
relation extraction as described in jamia submission
Added:
ctakes/branches/jamia-submission-relation-extractor/
- copied from r1491494, ctakes/trunk/
Author: dligach
Date: Tue Jun 11 20:16:19 2013
New Revision: 1491939
URL: http://svn.apache.org/r1491939
Log:
removed unneeded checks for "Argument" and "Related_to"
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relatio
Author: dligach
Date: Mon Jul 22 17:37:17 2013
New Revision: 1505739
URL: http://svn.apache.org/r1505739
Log:
added a version of NP expander that simply returns the text of the enclosing NP
Modified:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae
Author: dligach
Date: Tue Aug 6 18:37:43 2013
New Revision: 1511067
URL: http://svn.apache.org/r1511067
Log:
Script for printing gold standard events of a given UMLS semantic type
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Tue Aug 20 18:53:36 2013
New Revision: 1515921
URL: http://svn.apache.org/r1515921
Log:
fixed a few documentation typos/erros
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
Modified:
ctakes
Author: dligach
Date: Tue Aug 20 19:13:32 2013
New Revision: 1515932
URL: http://svn.apache.org/r1515932
Log:
switch to using system event mentions formerly known as entity mentions
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Wed Aug 21 15:48:08 2013
New Revision: 1516193
URL: http://svn.apache.org/r1516193
Log:
first attempt at running time annotator in "stand-alone" mode
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPip
Author: dligach
Date: Thu Aug 22 14:56:57 2013
New Revision: 1516475
URL: http://svn.apache.org/r1516475
Log:
switch to backward time annotator
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
Modified:
ctakes/trunk
Author: dligach
Date: Thu Aug 22 16:12:30 2013
New Revision: 1516499
URL: http://svn.apache.org/r1516499
Log:
first shot at finding durations of sign/symptoms
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
(with props
Author: dligach
Date: Thu Aug 22 19:55:13 2013
New Revision: 1516568
URL: http://svn.apache.org/r1516568
Log:
use nearest time to an event
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified:
ctakes/trunk/ctakes
Author: dligach
Date: Tue Aug 27 14:39:06 2013
New Revision: 1517832
URL: http://svn.apache.org/r1517832
Log:
using jcas directly instead of system view
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified:
ctakes
Author: dligach
Date: Tue Aug 27 16:49:45 2013
New Revision: 1517879
URL: http://svn.apache.org/r1517879
Log:
add calc for frequencies over various time granularities
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Author: dligach
Date: Tue Sep 3 18:34:41 2013
New Revision: 1519789
URL: http://svn.apache.org/r1519789
Log:
updated the path to the chunker model
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
Modified:
ctakes/trunk
Author: dligach
Date: Wed Sep 4 18:05:12 2013
New Revision: 1520087
URL: http://svn.apache.org/r1520087
Log:
printing durations as vectors (for matlab)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified:
ctakes
Author: dligach
Date: Tue Sep 17 18:59:54 2013
New Revision: 1524179
URL: http://svn.apache.org/r1524179
Log:
more readable implementation of the same logic
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified
Author: dligach
Date: Tue Sep 17 20:17:41 2013
New Revision: 1524207
URL: http://svn.apache.org/r1524207
Log:
now capturing abbreviations like hr, min, etc.
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified
Author: dligach
Date: Tue Sep 17 20:40:06 2013
New Revision: 1524216
URL: http://svn.apache.org/r1524216
Log:
added a method to print annotation context
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified:
ctakes
Author: dligach
Date: Wed Sep 18 15:04:42 2013
New Revision: 1524439
URL: http://svn.apache.org/r1524439
Log:
removed some duration patterns that are too general
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified
Author: dligach
Date: Wed Sep 18 20:04:27 2013
New Revision: 1524552
URL: http://svn.apache.org/r1524552
Log:
added two rules to filter out non-duration patterns
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified
Author: dligach
Date: Thu Sep 26 15:08:08 2013
New Revision: 1526550
URL: http://svn.apache.org/r1526550
Log:
simplified the way in which nearest time mention is found
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Author: dligach
Date: Thu Sep 26 16:12:03 2013
New Revision: 1526592
URL: http://svn.apache.org/r1526592
Log:
added a method to output the duration distribution in a machine/human readable
format
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis
Author: dligach
Date: Fri Sep 27 21:14:39 2013
New Revision: 1527081
URL: http://svn.apache.org/r1527081
Log:
attempting to use event durations as features
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventDurationFeatureExtractor.java
(with
Author: dligach
Date: Fri Sep 27 21:33:55 2013
New Revision: 1527090
URL: http://svn.apache.org/r1527090
Log:
no_duration feature if no data is available
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventDurationFeatureExtractor.java
Modified
Author: dligach
Date: Fri Oct 4 15:05:39 2013
New Revision: 1529175
URL: http://svn.apache.org/r1529175
Log:
removed hard-coded path and added a constructor for Callback
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Fri Nov 29 21:22:52 2013
New Revision: 1546652
URL: http://svn.apache.org/r1546652
Log:
removed unused import
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
Modified:
ctakes/trunk/ctakes
Author: dligach
Date: Thu Dec 5 15:30:48 2013
New Revision: 1548166
URL: http://svn.apache.org/r1548166
Log:
updated the path to several resources (chunker, LookupDesc_Db.xml, OrangeBook)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval
Author: dligach
Date: Fri Dec 6 15:29:15 2013
New Revision: 1548562
URL: http://svn.apache.org/r1548562
Log:
using expected event duration as a feature instead of the full distribution
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Fri Dec 6 17:28:03 2013
New Revision: 1548604
URL: http://svn.apache.org/r1548604
Log:
added scaling by number of seconds in a year
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventDurationFeatureExtractor.java
Modified
Author: dligach
Date: Mon Dec 9 17:56:23 2013
New Revision: 1549631
URL: http://svn.apache.org/r1549631
Log:
added a duration feature extractor to be used with docTimeRel
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Mon Dec 9 19:27:23 2013
New Revision: 1549657
URL: http://svn.apache.org/r1549657
Log:
feature extractor to use the entire distribution as features
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Wed Dec 11 20:02:51 2013
New Revision: 1550243
URL: http://svn.apache.org/r1550243
Log:
refactoring + new duration features for event-time relations
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Thu Dec 12 21:43:36 2013
New Revision: 1550543
URL: http://svn.apache.org/r1550543
Log:
added duration distribution features
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DurationEventEventFeatureExtractor.java
Modified
Author: dligach
Date: Thu Dec 19 16:45:05 2013
New Revision: 1552350
URL: http://svn.apache.org/r1552350
Log:
features that capture the time unit (e.g. "weeks") of temporal expressions
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/
Author: dligach
Date: Fri Dec 20 16:46:40 2013
New Revision: 1552731
URL: http://svn.apache.org/r1552731
Log:
using duration in seconds rather than the name of the time unit
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature
Author: dligach
Date: Fri Dec 20 16:48:48 2013
New Revision: 1552732
URL: http://svn.apache.org/r1552732
Log:
moved duration features to separate package
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/
ctakes/trunk/ctakes-temporal/src
Author: dligach
Date: Fri Dec 20 19:53:45 2013
New Revision: 1552796
URL: http://svn.apache.org/r1552796
Log:
AE to remove event-time relations for which we have no time or event duration
data.
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Mon Dec 30 22:42:55 2013
New Revision: 1554330
URL: http://svn.apache.org/r1554330
Log:
simplified to isolate an error
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/PreserveCertainEventTimeRelationsInGold.java
- copied, changed
Author: dligach
Date: Thu Jan 2 20:20:16 2014
New Revision: 1554897
URL: http://svn.apache.org/r1554897
Log:
fixed a bug; now checking for type of arg1/2
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/PreserveCertainEventTimeRelationsInGold.java
Author: dligach
Date: Thu Jan 2 20:23:22 2014
New Revision: 1554901
URL: http://svn.apache.org/r1554901
Log:
deleted old version
Removed:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/PreserveCertainEventTimeRelations.java
Author: dligach
Date: Fri Jan 3 20:56:37 2014
New Revision: 1555253
URL: http://svn.apache.org/r1555253
Log:
now using difference in seconds between durations of time and event
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration
Author: dligach
Date: Mon Jan 6 16:03:27 2014
New Revision: 1555878
URL: http://svn.apache.org/r1555878
Log:
assume gold only has relations that have duration data
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration
Author: dligach
Date: Mon Jan 6 17:05:55 2014
New Revision: 1555921
URL: http://svn.apache.org/r1555921
Log:
added logic to remove events and times that have no duration data
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Tue Jan 7 19:05:41 2014
New Revision: 1556320
URL: http://svn.apache.org/r1556320
Log:
refactoring
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java
Modified:
ctakes/trunk
Author: dligach
Date: Tue Jan 7 19:09:40 2014
New Revision: 1556321
URL: http://svn.apache.org/r1556321
Log:
refactoring/removed unused imports
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java
Author: dligach
Date: Tue Jan 7 20:35:19 2014
New Revision: 1556347
URL: http://svn.apache.org/r1556347
Log:
AE to remove all events from gold view except those that have duration data
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Wed Jan 22 18:15:13 2014
New Revision: 1560453
URL: http://svn.apache.org/r1560453
Log:
initial commit to ctakes sandbox
Added:
ctakes/sandbox/ctakes-wsd/
Author: dligach
Date: Wed Jan 22 18:15:34 2014
New Revision: 1560454
URL: http://svn.apache.org/r1560454
Log: (empty)
Added:
ctakes/sandbox/ctakes-wsd/.classpath (with props)
ctakes/sandbox/ctakes-wsd/.project (with props)
ctakes/sandbox/ctakes-wsd/.settings/
ctakes/sandbox
Author: dligach
Date: Thu Jan 23 21:32:27 2014
New Revision: 1560816
URL: http://svn.apache.org/r1560816
Log:
got the preprocessing pipeline to load gold annotations from SHARP data using
SHARP knowtator reader
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/wsd
Author: dligach
Date: Fri Jan 24 18:39:08 2014
New Revision: 1561107
URL: http://svn.apache.org/r1561107
Log:
added code to retrieve UMLS info (like CUIs)
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/wsd/pipelines/Analyze.java
Modified:
ctakes/sandbox/ctakes-wsd/src
Author: dligach
Date: Fri Jan 24 19:22:24 2014
New Revision: 1561125
URL: http://svn.apache.org/r1561125
Log:
Generate concept / CUI counts
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/wsd/pipelines/Analyze.java
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org
Author: dligach
Date: Mon Jan 27 22:16:48 2014
New Revision: 1561884
URL: http://svn.apache.org/r1561884
Log:
a script useful for checking which temporal expressions in gold data can be
normalized by steve bethard's normalizer
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/a
Author: dligach
Date: Mon Jan 27 22:31:17 2014
New Revision: 1561890
URL: http://svn.apache.org/r1561890
Log:
forgot to lowercase the timex(s) last time
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java
Author: dligach
Date: Tue Jan 28 18:04:34 2014
New Revision: 1562132
URL: http://svn.apache.org/r1562132
Log:
outputting stats about polysemy wrt semantic type
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/wsd/pipelines/Analyze.java
Modified:
ctakes/sandbox/ctakes
Author: dligach
Date: Wed Jan 29 21:21:11 2014
New Revision: 1562598
URL: http://svn.apache.org/r1562598
Log:
added cui printer for cui-polysemy analysis
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/wsd/pipelines/Analyze.java
Modified:
ctakes/sandbox/ctakes-wsd/src
Author: dligach
Date: Tue Feb 25 16:13:22 2014
New Revision: 1571722
URL: http://svn.apache.org/r1571722
Log:
refactored so that it can be now used for sign/symptoms as well as
disease/disorders (and other event mentions)
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes
Author: dligach
Date: Thu Mar 13 15:23:37 2014
New Revision: 1577196
URL: http://svn.apache.org/r1577196
Log:
Moved various utility methods used by duration-related classes to one place
(feature.duration.Utils)
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Thu Mar 13 15:39:14 2014
New Revision: 1577204
URL: http://svn.apache.org/r1577204
Log:
Moved pointer to duration distribution file to one place (Utils.java)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
Author: dligach
Date: Thu Mar 13 19:04:24 2014
New Revision: 1577288
URL: http://svn.apache.org/r1577288
Log:
Code related to evaluating the effect of adding duration features for
event-event relations
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae
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