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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 Tue, 15 Mar 2016 08:49:54 GMT
Hi,

this is essentially just a decision of design. For a single longitudinal
record, there is no problem at all. We can solve this even with some
simple ruta rules, or with some cutom analysis engine. If we want to
process a set of record of the same patient jointly, then we cannot
apply a single pipeline. I propose to postpone the decison and implement
it only for single documents for now.

Best,

Peter


Am 11.03.2016 um 20:03 schrieb Azad Dehghan:
>>
>> 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?
>>
> The two pass method will have a broader applicability for NER on
> longitudinal records...
>
>
>> btw, the CRF models are not part of the contribution, right?
>>
>>
> The CRF  (UK,US) models will be released but this will be together with a
> more mature software planned for August 2016.
>
> 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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