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From Azad Dehghan <azad.dehg...@gmail.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Thu, 10 Mar 2016 19:29:15 GMT
Thanks Peter,

The rules were modeled using the training data.

It would be good to incorporate/refactor (basically, GATE API needs to be
replaced with UIMA API to generate annotation) the two-pass recognition
method for cTAKES - which has a wider application on longitudinal data.
This method is used on-top of a number NERs.

Please let me know where I can help. I will be available again in April.

Cheers,
Azad

On 10 March 2016 at 13:13, Peter Klügl <peter.kluegl@averbis.com> wrote:

> Hi,
>
> sorry, I was quite busy last month.
>
> I added a new patch, which needs to be applied.
>
> No new rules, but it's possible now to evaluate everything against the
> labelled data of the challenge.
>
> @Azad:
> Which documents exactly did you use to develop the rules?
> training-PHI-Gold-Set1, training-PHI-Gold-Set2 or testing-PHI-Gold-fixed?
>
> Best,
>
> Peter
>
> Am 03.02.2016 um 09:05 schrieb Peter Klügl:
> > Hi,
> >
> > the last patch fixed almost all problems.
> >
> > I added another one that adds the csv file for the unit test and extends
> > svn-ignore.
> >
> > Best,
> >
> > Peter
> >
> > Am 02.02.2016 um 09:16 schrieb Peter Klügl:
> >> Hi,
> >>
> >> I added another patch. I missed to manually add one test file to version
> >> control, and there are still duplicate lines.
> >> I hope this patch fixes the remaining problems.
> >>
> >> Best,
> >>
> >> Peter
> >>
> >>
> >> Am 29.01.2016 um 10:34 schrieb Peter Klügl:
> >>> Hi,
> >>>
> >>> the problems were caused by the svn client in my Eclipse. Sorry for the
> >>> trouble, I should have looked more closely at the ciomplete patch.
> >>>
> >>> I attached a new patch created with commandline tools wich looks
> correct
> >>> now.
> >>>
> >>> Pei, can you apply the new patch?
> >>>
> >>> Best,
> >>>
> >>> Peter
> >>>
> >>> Am 28.01.2016 um 15:57 schrieb Peter Klügl:
> >>>> Thanks Pei.
> >>>>
> >>>> I fear there was again a problem with the patch. All new files are
> >>>> missing (and also the svn-ignore settings).
> >>>>
> >>>> Can you take a look?
> >>>>
> >>>> Best,
> >>>>
> >>>> Peter
> >>>>
> >>>> Am 28.01.2016 um 14:43 schrieb Pei Chen:
> >>>>> patch applied.
> >>>>> Thanks,
> >>>>> Pei
> >>>>>
> >>>>> On Thu, Jan 28, 2016 at 4:14 AM, Peter Klügl <
> peter.kluegl@averbis.com> wrote:
> >>>>>> Hi Pei,
> >>>>>>
> >>>>>> can you commit the recent patch for us?
> >>>>>>
> >>>>>> CTAKES-384-20160120.patch
> >>>>>>
> >>>>>> Best,
> >>>>>>
> >>>>>> Peter
> >>>>>>
> >>>>>> Am 20.01.2016 um 19:35 schrieb Pei Chen:
> >>>>>>> Hi,
> >>>>>>> Sorry I was swamped recently.
> >>>>>>> But yeah, we can even create an extended type system to
store
> these items temporarily and add them into the main/core type system
> afterwards.
> >>>>>>> There was an existing item to upgrade UIMA, but agreed-
it will
> require much more testing.  If it works, we can upgrade it in our sandbox
> area or create a branch if necessary.
> >>>>>>>
> >>>>>>> —Pei
> >>>>>>>
> >>>>>>>> On Jan 18, 2016, at 9:06 AM, Peter Klügl <
> peter.kluegl@averbis.com> wrote:
> >>>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> a new patch is attached.
> >>>>>>>>
> >>>>>>>> @Pei:
> >>>>>>>> are there suitable annotation types in the cTAKES type
system?
> Some
> >>>>>>>> project in cTAKES uses something like OntologyMatch...
I map it to
> >>>>>>>> IdentifiedAnnotation right now, but there are many empty
> features...
> >>>>>>>>
> >>>>>>>> @Azad:
> >>>>>>>> I changed the rules a bit, especially the capitalization
like I
> use it
> >>>>>>>> in ruta normally. The wordlist are compiled to a trie
by the maven
> >>>>>>>> plugin. I also added the two regexes for url and email.
I
> extended the
> >>>>>>>> regex for the url. I also changed the evaluation order
of some
> rules
> >>>>>>>> (with @). Feel free to add simple examples to examples.csv
for
> the unit
> >>>>>>>> tests.
> >>>>>>>>
> >>>>>>>> Let me know if you need more information about the changes.
> >>>>>>>>
> >>>>>>>> Do you wanna have help with the other rule sets? Or
should we
> split them up?
> >>>>>>>>
> >>>>>>>> Best,
> >>>>>>>>
> >>>>>>>> Peter
> >>>>>>>>
> >>>>>>>> Am 18.01.2016 um 11:04 schrieb Peter Klügl:
> >>>>>>>>> Hi,
> >>>>>>>>>
> >>>>>>>>> great. I will integrate them in the project and
in the next
> patch.
> >>>>>>>>>
> >>>>>>>>> Best,
> >>>>>>>>>
> >>>>>>>>> Peter
> >>>>>>>>>
> >>>>>>>>> Am 18.01.2016 um 00:58 schrieb Azad Dehghan:
> >>>>>>>>>> Three NERs translated and uploaded.
> >>>>>>>>>>
> >>>>>>>>>> PS. I will validate all NERs once we have them
all completed.
> >>>>>>>>>>
> >>>>>>>>>> Cheers,
> >>>>>>>>>> Azad
> >>>>>>>>>>
> >>>>>>>>>> On 24 November 2015 at 10:37, Azad Dehghan <
> azad.dehghan@gmail.com> wrote:
> >>>>>>>>>>
> >>>>>>>>>>> This is on my todo list for Dec. as well.
If there are any
> more volunteers
> >>>>>>>>>>> for translating JAPE to RUTA, please get
in touch.
> >>>>>>>>>>>
> >>>>>>>>>>> Cheers,
> >>>>>>>>>>> Azad
> >>>>>>>>>>>
> >>>>>>>>>>> On 24 Nov 2015 09:55, "Peter Klügl" <peter.kluegl@averbis.com>
> wrote:
> >>>>>>>>>>>> Hi,
> >>>>>>>>>>>>
> >>>>>>>>>>>> I just wanted to mention that I haven't
forgot about it.
> Unfortunately,
> >>>>>>>>>>>> there is just no spare time right now.
I hope I will be able
> to provide
> >>>>>>>>>>>> the patches in December.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Best,
> >>>>>>>>>>>>
> >>>>>>>>>>>> Peter
> >>>>>>>>>>>>
> >>>>>>>>>>>> Am 06.11.2015 um 16:40 schrieb Pei Chen:
> >>>>>>>>>>>>> Hi Peter,
> >>>>>>>>>>>>> I think the ctakes-examples is probably
a good starting
> point at least
> >>>>>>>>>>>>> in terms of maven modules, etc.
 I think it would be good if
> we use
> >>>>>>>>>>>>> uimaFIT style as primary approach
to wiring components
> together and
> >>>>>>>>>>>>> generate desc's as secondary...
> >>>>>>>>>>>>> I think the actual components that
would be required is
> probably best
> >>>>>>>>>>>>> left up to what is actually required
for best performing
> c-deid.  The
> >>>>>>>>>>>>> output would be interesting, I'm
not sure if we should treat
> this as
> >>>>>>>>>>>>> an independent preprocessing component
or part of a pipeline
> (in which
> >>>>>>>>>>>>> case, we may need to propose a change
to the type system or
> perhaps an
> >>>>>>>>>>>>> alternative JCas view.  You can
probably open up that
> discussion to
> >>>>>>>>>>>>> the dev group as you see fit.)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> My 2 cents...
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Fri, Nov 6, 2015 at 3:38 AM,
Peter Klügl <
> peter.kluegl@averbis.com>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>>>> Hi,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Is there a cTAKES project that
may serve as an example on
> how the
> >>>>>>>>>>> cTAKES
> >>>>>>>>>>>>>> community develops or how a
project should look like?
> >>>>>>>>>>>>>> I learned that different people
set up UIMA project in a
> quite
> >>>>>>>>>>> different
> >>>>>>>>>>>>>> manner and I do not what to
get inspired by "some sort of
> out-dated"
> >>>>>>>>>>>>>> approach in the cTAKES repo.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Are there restriction or preferences
about the preprocessing
> >>>>>>>>>>> components
> >>>>>>>>>>>>>> that should be used and the
kind of "output" of the project.
> >>>>>>>>>>>>>> Components: On which components
may the componetns rely:
> tokenizer,
> >>>>>>>>>>> ...
> >>>>>>>>>>>>>> parser, ... dict lookup?
> >>>>>>>>>>>>>> "output": Should the project
provide a pipeline or a single
> AE?
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> More comments below.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Am 03.11.2015 um 16:54 schrieb
Azad Dehghan:
> >>>>>>>>>>>>>>>> Who else plans to provide
patches for it? Just to avoid
> duplicate
> >>>>>>>>>>> work
> >>>>>>>>>>>>>>>> and to coordnate the
efforts ...
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> I would like to help with
the translating JAPE to RUTA.
> >>>>>>>>>>>>>> You can already go ahead with
the UIMA Ruta Workbench if
> you want, or
> >>>>>>>>>>>>>> wait until I set up the project
with ruta integration.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> If any questions arise, just
ask :-)
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> Is there a development
dataset which was utilized for the
> initial
> >>>>>>>>>>>>>>>> development, and if
yes, is it possible to contribute it
> too?
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> The data set is unfortunately
not publicly available; i2b2
> >>>>>>>>>>>>>>> <https://www.i2b2.org/NLP/DataSets/Main.php>
typically
> releases the
> >>>>>>>>>>> data
> >>>>>>>>>>>>>>> sets 12 months after a given
challenge; this is done on an
> >>>>>>>>>>> individual basis
> >>>>>>>>>>>>>>> and involve a Data Use Agreement.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> However, I will be able
to conduct and coordinate the
> validation.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Ok, I'll investigate if we have
already access to the
> dataset here.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> My first step would
be:
> >>>>>>>>>>>>>>>> - set up a maven project
> >>>>>>>>>>>>>>>> - set up a development
pipeline in a test (with cTAKES
> components
> >>>>>>>>>>>>>>>> replacing the previous
ANNIE preprocessing)
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> But one item that we
need to review is the 3rd party libs
> jars that
> >>>>>>>>>>>>>>>> were included to ensure
compatibility.  I’ll be sure to
> take a look
> >>>>>>>>>>> at
> >>>>>>>>>>>>>>>> that over the next few
weeks.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> —Pei
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> @Pei - once ANNIE components
are replaced there is should
> not be a
> >>>>>>>>>>> need to
> >>>>>>>>>>>>>>> worry about the 3rd party
libs.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Also, just a thought: we
may want to create an independent
> component
> >>>>>>>>>>> for
> >>>>>>>>>>>>>>> the Two Pass recognition
(TwoPass.java) as this method
> have shown
> >>>>>>>>>>> useful
> >>>>>>>>>>>>>>> for general NER on longitudinal
data and surely useful
> independent
> >>>>>>>>>>> of the
> >>>>>>>>>>>>>>> deid component.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Cheers,
> >>>>>>>>>>>>>>> Azad
> >>>>>>>>>>>>>>>
>
>

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