Hi Sean
Ok.. I was confused whether I was meant to find it in the sources.
But while you're reading this, is there a brief way to describe the
difference between the older:package
org.apache.ctakes.assertion.medfacts.cleartk;
and
org.apache.ctakes.assertion.medfacts.cleartk.windowed
Peter
On Tue, Jan 4, 2022 at 7:47 AM Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Peter,
>
> I created a second engine that just used text matching or regular
> expressions given the discovered events. It also uses covering section
> types, formatted text and other things, but the text match might be the
> most impactful item.
>
> You are an accomplished developer so the email scratch below is for the
> benefit of others who search archives.
>
> class LazyHistoryFinder extends JCasAnnotator_ImplBase {
> String[] HISTORY = { "history of", "h/o", "h / o" };
>
> boolean isHistory( EventMention event ) {
> text = e.getCoveredText().toLowerCase();
> return Arrays.stream( HISTORY ).anyMatch( text::startsWith );
> }
>
> void process( JCas jcas ) throws Analysis*Ex {
> JCasUtil.select( jcas, EventMention.class )
> .stream()
> .filter( this::isHistory )
> .foreach( e -> e.setHistoryOf(
> CONST.NE_HISTORY_OF_PRESENT ) );
> }
> }
>
> It requires a stroll through the monstrous cas array and it certainly
> isn't sexy, but it gets the job done.
>
> Sean
>
>
> ________________________________________
> From: Peter Abramowitsch <pabramowit...@gmail.com>
> Sent: Monday, January 3, 2022 10:23 PM
> To: dev@ctakes.apache.org
> Subject: Re: Performance of the cleartk history module [EXTERNAL]
>
> * External Email - Caution *
>
>
> Thanks Sean
>
> By "following engine", you mean a second instance of the history engine
> that uses only the event spans, or you modified the current one to traverse
> the event-span within the context window? I see you made some source
> changes in that area and will check tomorrow.
>
> Peter
>
> On Mon, Jan 3, 2022 at 2:26 PM Finan, Sean <
> sean.fi...@childrens.harvard.edu>
> wrote:
>
> > Hi Peter,
> >
> > I have noticed this and just added a following engine that recognized
> text
> > within event spans. It is a lazy solution, but it fit my needs and
> > available time.
> >
> > Sean
> > ________________________________________
> > From: Peter Abramowitsch <pabramowit...@gmail.com>
> > Sent: Monday, January 3, 2022 5:03 PM
> > To: dev@ctakes.apache.org
> > Subject: Performance of the cleartk history module [EXTERNAL]
> >
> > * External Email - Caution *
> >
> >
> > Hi All
> >
> > I've noticed that the HistoryCleartkAnalysisEngine misses many common
> forms
> > of subject history including the obvious "h/o" prefix. Looking into
> the
> > distribution, there's a model.jar and what appears to be a weights file
> > containing trigger words:
> > resources/org/apache/ctakes/assertion/models/history.txt where h, o, /
> > are all given their own weights. But I'm not sure that they're actually
> > used in this way: see below. However, there's also a tiny file:
> > /org/apache/ctakes/assertion/semantic_classes/history.txt
> > which does contain a few entries including "h/o" which I assume is used
> for
> > training but is never referred to anywhere.
> >
> > Here's the behavior I'm seeing:
> > example input condition term found history feature marked range text
> > history of pregnancies "history of" included in the cu_term and prefterm
> > yes
> > no history of pregnancies
> > history of adenopathy "history of" not included in the cu_term or
> prefterm
> > yes yes adenopathy
> > H/O postpartum psychosis "h/o" not included in the prefterm or cu_term
> yes
> > yes postpartum psychosis
> > H/O: postpartum psychosis "h/o" not included in the prefterm or cu_term
> yes
> > no postpartum psychosis
> > H/O pregnancies "h/o" included in the cu_term yes no h/o pregnancies
> >
> > You can see that it is quite perverse - there is a pattern suggesting
> that
> > if the concept definition occupies the history words, then they cannot be
> > seen by the history annotation engine.
> >
> > Has anyone else noticed this - and have they done anything about it?
> >
> > Peter
> >
>
