*** For cross-validation, you can evaluate de-identified notes data from i2b2 challenge** * https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-scrubber-deid/data/models/
*Methods for model generation of FeatureSet described here: * *Improved de-identification of physician notes through integrative modeling of both public and private medical text* http://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-13-112 Major objective of that study was to help provide external examples to cross train / retrain other methods. hope this helps, --Andy On Thu, Mar 10, 2016 at 1:27 PM, Savova, Guergana < guergana.sav...@childrens.harvard.edu> wrote: > You can re-build the models that feed into MIST. I personally would not > use the default model that MIST comes with as it is not trained on clinical > data. In our previous work we found that hand-annotating about 200 docs for > PHI (representative of the sample you are going to run the models on) > results in building a pretty good model - in the 90's for p, r and f1. > However, even with that high performance, the institution that owns the > data might be still reluctant to share as it might pose a violation of > HIPAA through some potential PHI leaks. In cTAKES our approach has been to > de-couple the de-identifcation from the NLP/information extraction. If a > user has the need for de-identified data, they could choose their method -- > manual or otherwise -- and then process through cTAKES. Our focus is the > NLP/IE space, while de-identification is a blend of that plus policy.... > > --Guergana > > -----Original Message----- > From: Azad Dehghan [mailto:azad.dehg...@gmail.com] > Sent: Thursday, March 10, 2016 4:19 PM > To: dev@ctakes.apache.org > Subject: RE: Combining Knowledge- and Data-driven Methods for > De-identification of Clinical Narratives > > Thanks Guergana. > > > Yes, the current release of cTAKES has a module for the temporal > expressions which includes dates. The normalizer for the temporal > expressions is Steven Bethard's timenorm code. > > > > Great. > > > However, if you do de-identification of dates/temporal expressions, > > you > run the risk of creating incorrect timelines as many of the relative > temporal expressions (e.g. spring of this year, x-mas time, etc.) are > unlikely to be correctly shifted by any de-identification tool. > > > Indeed, a reason I have not included the dates component. > > > One de-identification tool is MIST -- > https://urldefense.proofpoint.com/v2/url?u=http-3A__mist-2Ddeid.sourceforge.net_&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=FlURWGr18rKbgM76o8Hxoo1rbC2D2h-kk611lbKnPik&s=5awdXn2I-hRE0-161tqFDGgmYgQQviQg360uHI4fs2s&e= > . > > > I don't remember them doing well in the community held evaluation in 2014. > Hence, cDeid :) > > > > Guergana Savova, PhD, FACMI > > Associate Professor > > PI Natural Language Processing Lab > > Boston Children's Hospital and Harvard Medical School > > 300 Longwood Avenue > > Mailstop: BCH3092 > > Enders 144.1 > > Boston, MA 02115 > > Tel: (617) 919-2972 > > Fax: (617) 730-0817 > > Harvard Scholar: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.harvard.ed > > u_guergana-5Fk-5Fsavova_biocv&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J > > ZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGm > > RCJNAr-rCmP&m=FlURWGr18rKbgM76o8Hxoo1rbC2D2h-kk611lbKnPik&s=3taiTxFp55 > > iQUnc6A6Yemg-XzFQrRjo5QZRQeKHQ29c&e= > > > > -----Original Message----- > > From: Azad Dehghan [mailto:azad.dehg...@gmail.com] > > Sent: Thursday, March 10, 2016 3:42 PM > > To: dev@ctakes.apache.org > > Subject: Re: Combining Knowledge- and Data-driven Methods for > De-identification of Clinical Narratives > > > > > This means both training data folders? I have access to the data but > > > not > > to the challenge description. > > > > Yes. Is there any specific information that you are missing? > > > > > > > > >> 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. > > > > > > > > > I'll take a look. > > > > > > I do not know how much time I can invest this month. Let's see how > > > many > > phases I can translate. > > > > > > I added the rules for age. Are there jape rules for creating date > > annotations? > > > > > > > No. I believe cTAKES has existing component(s) to capture dates? > > > > > After all rules are translated, they need some major refactoring. > > > Jape > > and Ruta are quite different in some aspects. > > > > > Ok. > > > > > > > > > > > > > > > > > > > >> 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.klu...@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.klu...@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.klu...@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.dehg...@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.klu...@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.klu...@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://urldefense.proofpoint.com/v2/url?u=https-3 > > >>>>>>>>>>>>>>>>>> A_ > > >>>>>>>>>>>>>>>>>> _www.i2b2.org_NLP_DataSets_Main.php&d=BQIFaQ&c=qS4g > > >>>>>>>>>>>>>>>>>> oW > > >>>>>>>>>>>>>>>>>> BT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNn > > >>>>>>>>>>>>>>>>>> J9 > > >>>>>>>>>>>>>>>>>> mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP > > >>>>>>>>>>>>>>>>>> &m > > >>>>>>>>>>>>>>>>>> =1Qpd4A2PgVD13w31PkkvmJf6I0PTCatCzgBgsnetPOg&s=aAEe > > >>>>>>>>>>>>>>>>>> OR yMtz7NCv-6EEgiABVY_Rf6zLnJghQh2DA_CKQ&e= > > > >>>>>>>>>>>>>>>>>> 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 > > >>>>>>>>>>>>>>>>>> > > >>> > > > >
