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From "Abramowitsch, Peter" <pabramowit...@hearst.com>
Subject Re: Unable to understand the importance of attributes in IdentifiedAnnotations [EXTERNAL]
Date Fri, 05 Jan 2018 12:49:16 GMT
Sorry for the very wordy contribution here ....   Following on Tim's
answer,  I've found the historyOf mechanism to be very weak in its ability
to detect more than just a few possible permutations, and one frequent
issue is span where history Of modifies a series of concepts.

----------------------------------------

Here's an example from real notes

"The patient is a 57-year-old woman with a past medical history of OSA ,
asthma , CAD status post CABG..."

Using my CAS post processor on the output I get this.


================PROBLEMS====================
  [,,History of ,SNOMEDCT_US:78275009/C0520679] Sleep Apnea, Obstructive
OSA  
past medical history of OSA , asthma , CAD status po

  [,,,SNOMEDCT_US:195967001/C0004096] Asthma asthma
edical history of OSA , asthma , CAD status post CABG.>

  [,,,SNOMEDCT_US:414024009/C1956346] Coronary Artery Disease CAD
story of OSA , asthma , CAD status post CABG.>--

=================MEDICATIONS==================
==============SIGNS=====================
=================PROCEDURES==================
  [,,History of ,SNOMEDCT_US:90205004/C0010055] Coronary Artery Bypass
Surgery CABG  
sthma , CAD status post CABG.>--


I print the history of, confidence, and polarity flags in the [,,, ]
section before the SNOMED code of each identified annotation.   Notice
that it found history of OSA but not Asthma or CAD. It did find History of
again for the procedure CABG because of the word POST.


Here's another example

"Cardiac transplant 15 years ago as stated above with chronic
immunosuppressives , history of gout , hypertension , renal insufficiency."


================PROBLEMS====================
  [,,History of ,SNOMEDCT_US:90560007/C0018099] Gout gout  2018-01-01
15:00:00 +0100~
ppressives , history of gout , hypertension , renal i

  [,,,SNOMEDCT_US:28119000/C0020544] Renal hypertension hypertension ,
renal  2018-01-01 15:00:00 +0100~
ves , history of gout , hypertension , renal insufficiency.>--

  [,,,SNOMEDCT_US:236423003/C1565489] Renal Insufficiency renal
insufficiency  2018-01-01 15:00:00 +0100~
f gout , hypertension , renal insufficiency.>--

=================MEDICATIONS==================
  [,,,SNOMEDCT_US:372823004/C0021081] Immunosuppressive Agents
immunosuppressives  2018-01-01 15:00:00 +0100~
ated above with chronic immunosuppressives , history of gout , hype

==============SIGNS=====================
  [,,,SNOMEDCT_US:161451004/C0455492] H/O: gout history of gout
2018-01-01 15:00:00 +0100~
ic immunosuppressives , history of gout , hypertension , renal i

=================PROCEDURES==================
  [,,,SNOMEDCT_US:32413006/C0018823] Heart Transplantation Cardiac
transplant 15 2018-01-01 15:00:00 +0100~
--<Cardiac transplant 15 years ago as stated a



Again, it picked up the History Of in the first clause where "history of"
preceded its predicate, but not subsequent ones, or after a time
expression indicating the past.

I have a mind to work on this one day, but I think I'll be doing it in my
CAS post processor rather than the annotator itself as the problem really
involves a whole new solution that looks at the semantics of the whole
sentence and not just "history of (x)"  For that we'd start looking at the
conldep nodes, time annotations, and more.

Peter





On 1/5/18, 12:58 PM, "Miller, Timothy"
<Timothy.Miller@childrens.harvard.edu> wrote:

>Uncertainty is when the text indicates some hedging about the concept:
>"possible asthma" should have asthma as an IdentifiedAnnotation with the
>uncertainty flag set to 1.
>This is done by machine learning and it is not easy so it is not perfect.
>
>HistoryOf is for concepts that are explicitly in patient history, often
>in a history section.
>"history of lymphoma as a child"
>lymphoma should have its history flag set to 1.
>This is done by machine learning and it is not easy so it is not perfect.
>
>Confidence is a field that I don't believe gets set by any current
>annotators, but in theory it is for methods that might use statistical
>methods that output a score to set the score there.
>The cTAKES dictionary lookup either hits or doesn't, so it doesn't set
>that score.
>
>DiscoveryTechnique is a way to flag which entities were annotated by
>which annotator, since it's possible to have, e.g., multiple clinical
>concept taggers. We use it occasionally internally
>to separate gold standard entities from system-discovered entities (in a
>machine learning evaluation) but I don't know if any standard pipeline
>components set it.
>
>Tim
>
>________________________________________
>From: Kumari,Puja <Puja.Kumari3@cerner.com>
>Sent: Friday, January 5, 2018 12:03 AM
>To: dev@ctakes.apache.org
>Subject: Re: Unable to understand the importance of attributes in
>IdentifiedAnnotations [EXTERNAL]
>
>Hi,
>
>
>
>Thanks for the replies but I am still not able to understand the
>significance of the attributes such as Uncertainty, HistoryOf,
>Confidence, DiscoveryTechniques.
>
>Can anyone give some examples or any information which will help me to
>understand these concepts in more depth?
>
>
>
>Thanks.
>
>Puja Kumari
>
>
>
>On 1/4/18, 5:30 PM, "Gandhi Rajan Natarajan"
><Gandhi.Natarajan@arisglobal.com> wrote:
>
>
>
>    Try out this link -
>"https://urldefense.proofpoint.com/v2/url?u=https-3A__na01.safelinks.prote
>ction.outlook.com_-3Furl-3Dhttps-253A-252F-252Fcwiki.apache.org-252Fconflu
>ence-252Fdisplay-252FCTAKES-252FcTAKES-252B4.0-252B-2D-252BAssertion-26dat
>a-3D02-257C01-257CPuja.Kumari3-2540cerner.com-257C989437995db145fcbaa808d5
>536ac609-257Cfbc493a80d244454a815f4ca58e8c09d-257C0-257C0-257C636506640417
>310103-26sdata-3D8WN2HIq9RiCiZJiTtp0i6Sk7ZVDMgNGoUbJRW1Hevp4-253D-26reserv
>ed-3D0&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg
>9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=muQ5_Uh4Q-5Uui87e
>9eAWy2afrJRgcg4FrOmy2VyFP8&s=0NlpH8OCzjaVbZq3yTy4pQcWgTYtUKJOD5orbrpKGro&e
>="
>
>
>
>    Regards,
>
>    Gandhi
>
>
>
>
>
>    -----Original Message-----
>
>    From: Kumari,Puja [mailto:Puja.Kumari3@cerner.com]
>
>    Sent: Thursday, January 04, 2018 3:11 PM
>
>    To: dev@ctakes.apache.org
>
>    Subject: Re: Unable to understand the importance of attributes in
>IdentifiedAnnotations
>
>
>
>    Hi,
>
>
>
>    Thanks for your reply Krishnareddy but the link given says ³page not
>found². Any other suggestions/links that you can share would be
>appreciable.
>
>
>
>    Thanks
>
>    Puja Kumari
>
>
>
>    On 1/4/18, 2:51 PM, "Krishnareddy" <krishnareddyn@kpmd.biz> wrote:
>
>
>
>        Hi,
>
>
>
>          You can find related information about these attributes in
>following link
>
>
>
>        
>_*https://urldefense.proofpoint.com/v2/url?u=https-3A__na01.safelinks.prot
>ection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fcwiki.apache.org-252Fconfl
>uence-252Fdisplay-252FCTAKES-252FcTAKES-252B4.0-252B-2D-252BAssertion-2A-5
>F-26data-3D02-257C01-257CPuja.Kumari3-2540cerner.com-257C738752ad0ee24b8ba
>e6208d553547f25-257Cfbc493a80d244454a815f4ca58e8c09d-257C0-257C0-257C63650
>6544740520408-26sdata-3DTjBeskHtrWn8ycT16NaoDopB8bTX0SJTNfWMOG8-252B5fo-25
>3D-26reserved-3D0&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
>=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=muQ5_U
>h4Q-5Uui87e9eAWy2afrJRgcg4FrOmy2VyFP8&s=NmbWV7FVYRENHOhWtMCOu2UoOaw-esE6uy
>r0W8KKtpA&e=
>
>
>
>
>
>        Thank You
>
>
>
>        Krishna Reddy
>
>
>
>
>
>        On Thursday 04 January 2018 12:31 PM, Kumari,Puja wrote:
>
>        > Hi,
>
>        > I am working on IdentifiedAnnotations in apache cTAKES and I am
>not able to  interpret the meaning of the following attributes under
>IdentifiedAnnotations:
>
>        > 1.Uncertainty
>
>        > 2.History
>
>        > 3.Confidence
>
>        > 4.Discovery Techniques
>
>        >
>
>        > What is the importance of these attributes?
>
>        > How can we make use of these to make our work efficient?
>
>        > Any suggestion / link to understand more would be helpful.
>
>        >
>
>        >
>
>        > Thanks.
>
>        > Puja Kumari
>
>        > puja.kumari3@cerner.com<mailto:puja.kumari3@cerner.com>
>
>        >
>
>        >
>
>        >
>
>        >
>
>        >
>
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