NLP

Qing Zeng, PhD
Poll Question

• There are over 1 billion clinical notes i

VINCI rep y ository: how would you like 

them? Which types of notes?
Poll Question

• What Text Processing tools have you u

Metamap, MEDLEE, ARC)?
Overview

• V3NLP is a system that intends to facil

end‐user use of text process functions

• It provides a framework that supports

heterogeneous NLP modules

• It is designed to meet the big text pro

needs
Components

• User Interface• Backend Framework• Repository of processing modules
Sample Text

Diagnoses 

Rule out polymyalgia rheumatica versus early inflammatory

arthritis versus diffuse osteoarthritis. She will continue on 

as needed. I have urged her to start Aleve, 1 tablet twice a 

with usual precautions. I have sent today for sedimentatio

Lab CRP, rheumatoid factor, ANA, and CBC. She is quite relucta

have a blood drawn, but I have told her it is very important 

guide her treatment. I will be in touch with her when resu

available, and we briefly discussed the possibility of starting

d ll ff f ll h

Orders

steroids. I will arrange office follow up in 1 month.

Treatment Options
Sample Processing Pipe

Un‐labeled

Med Records Reader

Word Slot: V l S t Section Term 

Med. Records

cTAKES

cTAKES

Value Sentence 

Symptom

W it

NegEx Concept

C

Naïve Bayes

Model

HiTEX MetaMap

W More Framew

riter

Shapes 

Med. Records w/

Labeled Symptom

Annotations

Line 
Interface

• Using existing processing pipelines

• Customize existing processing processing pipeline

pipeline

• Create new existing processing pipelin• Review NLP results
Backend Framework

FLAP SL
Repositories

Derma Bones

• Git Repositories • Git Repositories • Maven Projects

• Collaboration Quality

ki b d

• Git Repositories• Maven Projects

• Production Qua

• Working but not tested oduct o Qua 

• Tested• Documentation• Solar, Huston ho
VINCI/CHIR NLP Tea

• Diana Carter

• Ryan Cornia

• Guy Divita• Scott DuVall• Tom Ginter• Shirl Nielson• Doug Redd• Ben Sunder
V3NLP Poll Question

• How likely are you to use a tool like V

processing clinical notes

– Extremely likely– Probably– Maybe– Not very likely

• What additional features would you 

see?
4/30/2012 12:00pm New Natural Language Processing 

tools available on VINCI 

VA Informatics and Computing 

Infrastructure 

Cornia, Ryan and Qing 

Treitler Zeng 

Please find below the written responses to the unanswered questions from the VINCI Cyberseminar

on 04/30/12; follow up questions should be directed to the VINCI staff.

Question: Is there a way to view all of the available modules that perform the same task (e.g., all of the

pos taggers that are available) so that a more sophisticated user can select a particular module?

‐Yes, you can view and select the available modules (e.g. we have two POS modules).

Question: Great work, I look forward to learning more. For cohort identification does the MRN need to

be within the document for one to retrace to the patient, or will there be a field in the production

version?

‐The notes do have MRN associated with them, though V3NLP does not support retrieval directly. We

have developed a query tool for structured and free text called Voogo, which we hope to release

soon.

Question: How viable is NLP for large‐scale data extraction for national research. For example, is it

possible to extract every EF listed from every echo for research use?

‐It is feasible to use NLP to process all VINCI data, especially for less demanding tasks like extracting EF

values.  We have tested the speed of the several pipelines and estimated the most computationally

intensive tasks would take several weeks for the 1.8 billion notes.  However, we are currently

experiencing a network connection problem.  

Question: When will the pathology report module become available?

‐We hope to bring those modules to VINCI in the next 6 to 12 months.

Comment from VINCI staff:  This is from VINCI. V3NLP will be working on radiology text. The report text

in radiology is similar to that in TIU notes.

Question: Is the output of VNLP stored in flat files or database?

‐Currently the result is stored in flat files through the interface. In batch processing, both options have

been implemented.

Question: Are there processes to word crunch files to determine what terms lie in unfamiliar files? Ways

to figure out what is in the file on which to base your search? For instance, if you want to search "heart

disease" you need to see how to code the concept. Can we see the terms existing in the TIU to figure out

what search terms to use?
4/30/2012 12:00pm New Natural Language Processing 

tools available on VINCI 

VA Informatics and Computing 

Infrastructure 

Cornia, Ryan and Qing 

Treitler Zeng 

‐ We have developed a query tool called Voogo that would support such exploration, which we hope

to release soon.

Comment:  We are extremely likely to use something like V3NLP, but would probably need more

orientation 1‐to‐1.

Question: Does this system work with dental records?

‐ The tool is expected to work on all note types, but is likely to require some customization and

refinement to achieve high extraction accuracy.

Question: Can V3NLP be used for a completely different type of data, obviously with different terms and

concepts? I am looking for a tool to use to analyze free‐text responses to the all‐employee survey. The

high number of responses speaks to having software to assist in identifying concepts in the comments.

‐ The tool is expected to work on all note types, but is likely to require some customization and

refinement to achieve high extraction accuracy.

Question: Neophyte though interested in this area; I need some NLP background to be able to see how i

would use this.  Plus, there are restrictions to the VINCI data; would like to use it on other VA data,

either local or CDW, would that be possible somehow?

‐ We are making the V3NLP open source and we are happy to distribute it within the VA.  

Question: Can one use v3NLP's extraction to obtain ejection fractions > 50%, that is to say, use formulas,

rather than specific values.

‐ Yes, this can be easily done using regular expressions.

Question: Are notes classified by note type: e.g. can you differentiate between Pathology notes vs.

admission notes?

‐ Each note has a type. While there are pipelines specializing on different note types, the processing

modules we have are not type‐specific.

Question: How do I bring notes the problem related notes??

‐If the question is about uploading the notes, VINCI staff could help. If the quest is about searching for

notes related to a particular problem, we hope to release a query tool soon.