To save you a little trouble, in ctakes-temporal we rely a lot on an outside library called ClearTK that has some evaluation APIs built in that work well with UIMA frameworks and typical NLP tasks. We use the following classes: http://cleartk.github.io/cleartk/apidocs/2.0.0/org/cleartk/eval/AnnotationStatistics.html http://cleartk.github.io/cleartk/apidocs/2.0.0/org/cleartk/eval/Evaluation_ImplBase.html
The simplest place to start looking in ctakes-temporal is probably the EventAnnotator and its evaluation, since they are simple one word spans. Then the TimeAnnotator is slightly more complicated with multi-word spans. Then if you are interested in evaluating relations I would suggest switching over to ctakes-relation-extractor which is more stable than the ctakes-temporal relation code, which is an area of highly active (i.e., funded) research and so the code has not been cleaned up as much. Tim ________________________________________ From: Leander Melms <me...@students.uni-marburg.de> Sent: Friday, March 17, 2017 3:05 PM To: dev@ctakes.apache.org Subject: Re: Evaluate cTAKES perfomance Thanks! I'll have a look at it and will try to give something back to the community! Leander > On 17 Mar 2017, at 19:42, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Ah - you meant best way to test. Sorry, I misread your inquiry as a best way > to write output. > > Yes, that is a great introduction document for ctakes and early tests. There > are a few small test classes in ctakes that read anafora files, run ctakes > and run agreement numbers. You can find some in the ctakes-temporal module. > I didn't write them, and I think that they are built-to-fit purpose-driven > classes, but you could try to adapt them to a general purpose case. That > would be a great thing to have in ctakes! > > Sean > > -----Original Message----- > From: Leander Melms [mailto:me...@students.uni-marburg.de] > Sent: Friday, March 17, 2017 1:46 PM > To: dev@ctakes.apache.org > Subject: Re: Evaluate cTAKES perfomance > > Hi Sean, > > thank you (again) for your help and feedback! I'll give it a try! Seems like > the authors of the publication "Mayo clinical Text analysis and Knowledge > Extraction System" > (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2995668_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=PZ0f8s12PJA8W5B4hMlw-0F83VAM9m6E1ypWVaT2hcM&s=Isgii7k_fUy_qLsyqEdh15wKLAnFT6_KeE7zN1dE73Q&e= > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2995668_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=PZ0f8s12PJA8W5B4hMlw-0F83VAM9m6E1ypWVaT2hcM&s=Isgii7k_fUy_qLsyqEdh15wKLAnFT6_KeE7zN1dE73Q&e= > >) did this as well. > > Thank you > Leander > > > >> On 17 Mar 2017, at 18:33, Finan, Sean <sean.fi...@childrens.harvard.edu> >> wrote: >> >> Hi Leander, >> >> There is no single correct way to do this, but a couple of similar >> classes exist. Well, one sat in my sandbox for two years until about 5 >> seconds ago as I only just checked it in. Anyway, take a look at two >> classes in ctakes-core org.apache.ctakes.core They are TextSpanWriter and >> CuiCountFileWriter. >> >> TextSpanWriter writes annotation name | span | covered text in a file, one >> per document. >> >> CuiCountFileWriter writes a list of discovered cuis and their counts. >> >> It sounds like you are interested in a combination of both - basically >> TextSpanWriter with the added output of CUIs. >> >> You can also have a look at EntityCollector of >> org.apache.ctakes.core.pipeline. It has an annotation engine that keeps a >> running list of "entities" for the whole run, doc ids, spans, text and cuis. >> >> Sean >> >> >> -----Original Message----- >> From: Leander Melms [mailto:me...@students.uni-marburg.de] >> Sent: Friday, March 17, 2017 1:09 PM >> To: dev@ctakes.apache.org >> Subject: Re: Evaluate cTAKES perfomance >> >> Sorry for writing again. I just have a quick question: My idea is to parse >> the cTAKES output to a text file with a structure like this >> DocName|Spans|CUI|CoveredText|ConceptType and do the same with the cold >> standart (from anafora). >> >> Is this a correct way to do this? >> >> I'm new to the subject and happy about the tiniest information on the topic. >> >> Thanks >> Leander >> >> I >>> On 17 Mar 2017, at 12:05, Leander Melms <me...@students.uni-marburg.de> >>> wrote: >>> >>> Hi, >>> >>> I've integrated a custom dictionary, retrained some of the OpenNLP models >>> and would like to evaluate the changes on a gold standard. I'd like to >>> calculate the precision, the recall and the f1-score to compare the results. >>> >>> My question is: Does cTAKES ship with some evaluation / test scripts? What >>> is the best strategry to do this? Has anyone dealt with this topic before? >>> >>> I'm happy to share the results afterwards if there is interest for it. >>> >>> Thanks >>> Leander >>> >> >> > >
