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From Jeffrey Miller <jeff...@gmail.com>
Subject Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL]
Date Sat, 09 Mar 2019 17:54:05 GMT
Sean,

I may just be missing something obvious, but having signed up for the
confluence wiki I don't see any Edit button on the cTAKES pages even though
it does look like everyone has permission to edit.

On Fri, Feb 22, 2019 at 11:01 AM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Jeff,
>
> >Do you accept documentation
> contributions?
>
> Of course!! We are completely open source, documentation included.  I
> think that you should be able to edit the wiki after signing up on
> confluence:
> https://cwiki.apache.org/confluence/signup.action
>
> Cheers,
> Sean
>
> ________________________________________
> From: Jeffrey Miller <jeffmax@gmail.com>
> Sent: Friday, February 22, 2019 10:57 AM
> To: dev@ctakes.apache.org
> Subject: Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL]
>
> Thank you Sean, that clears it up for me. Do you accept documentation
> contributions? I might be able to document a few of the things I have
> learned along the way setting up ctakes.
>
> On Tue, Feb 19, 2019 at 12:14 PM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi Jeff,
> >
> > The short answer: No, LVG is not in the pipeline created by the
> > DefaultFastPipeline.piper
> >
> > Longer answer:
> > In older versions of dictionary lookup the Lexical Variant Generator
> > module (LVG) was recommended to capture lexical variants of terms.
> > However, the dictionary resource already contains variants so the LVG
> > module should not make much of a difference. When the fast lookup was new
> > several years ago I ran a test with and without LVG on two datasets and
> the
> > difference was along the lines of +1-2% recall, -1% precision.
> >
> > I think that ClinicalPipelineFactory.getFastPipeline() was a copy-paste
> of
> > the previous .getClinicalPipeline() but with the dictionary module
> > replaced.  So, LVG is still in that method -created pipeline.
> >
> > When I (more recently) wrote that piper file that you reference I left
> out
> > LVG as the added burden didn't seem to warrant its presence.  When I say
> > burden I don't just mean speed decrease and memory footprint.  There have
> > been a lot of configuration problems with LVG on various systems which
> led
> > to difficulty using ctakes.
> >
> > The diagram that you reference places LVG after the dictionary lookup,
> and
> > after the part of speech tagger, while the page on lvg
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BLVG&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Odd-RqfBFrKxLVWy-Nf_-gmZ-UKh9phdcGO0ifqffis&s=ly656xPq-DlDPCj5eTsrlErYHA6FU7gC8h_nofoZRTo&e=
> lists
> > those as the two modules that may benefit from its presence.  That
> diagram
> > is very old and should definitely be updated.  Both the diagram and the
> > page on lvg include information that precedes (does not account for) the
> > existence of the fast dictionary lookup.
> >
> > Sean
> >
> >
> > ________________________________________
> > From: Jeffrey Miller <jeffmax@gmail.com>
> > Sent: Tuesday, February 19, 2019 10:53 AM
> > To: dev@ctakes.apache.org
> > Subject: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL]
> >
> > Hi,
> >
> > I was wondering if the LVG Annotator is included
> DefaultFastPipeline.piper
> > <
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dclinical-2Dpipeline-2Dres_src_main_resources_org_apache_ctakes_clinical_pipeline_DefaultFastPipeline.piper&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=3Sgs1Jc-C37kcy1efCEhU_3RV4aFipAt1lbTO0Wu_Ns&e=
> > >.
> > I have tried to trace through all the includes, but I cannot find it.
> > However, when I look at the code for the
> > ClinicalPipelineFactory.getFastPipeline() it seems to be included.
> > <
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_blob_513bb49ebb98c4ac63f690c7b88a82aff18947b8_ctakes-2Dclinical-2Dpipeline_src_main_java_org_apache_ctakes_clinicalpipeline_ClinicalPipelineFactory.java-23L98&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=kmZDExXBOyXg84kix__UvgD3LniSHa8MgL8K5fK3XC4&e=
> > >
> > From
> > documentation in this flow diagram
> > <
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_download_attachments_68718172_ctakes-2D3.1-2Ddependencies.png-3Fversion-3D1-26modificationDate-3D1488992146000-26api-3Dv2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=4yYVqkyLiodAWATji1EjSwoMh-YpU7qTz2J8tZvRT6I&e=
> > >
> > from
> > the components documentation page
> > <
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2BComponent-2BUse-2BGuide&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=m-9MenhmNTr2vdVAhCvKgBt48OUiQB8R2TkR7fEYtsY&e=
> > >,
> > it seems to be a recommended component for the dictionary annotator.
> >
> > Thanks for your help,
> > Jeff
> >
>

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