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From Peter Klügl <peter.klu...@averbis.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Fri, 11 Mar 2016 13:19:28 GMT
Hi,

I had a quick look on PassTwo. This is not directly translatable into
UIMA if the functionlity is based on analysis engines. Normally,
analysis engines process one document at a time in a pipeline. My first
quick guess is the we either need two pipelines (result is a program not
a component) or we need a different definition of a CAS (joining all
documents of a patient). Overall, it depends on the targeted use case of
the project. Should it be usable in a cTAKES/uimaFIT pipeline?

btw, the CRF models are not part of the contribution, right?

Best,

Peter

Am 10.03.2016 um 20:29 schrieb Azad Dehghan:
> 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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