Improve your skills with one of the hot innovations in the industry: Natural Language Processing. Apache cTAKES bridges the gap between humans and machines by transforming clinical thinking from provider notes into semi-structured data that can be processed by machines. This talk will also comprise of a demo analyzing and visualizing healthcare records using Apache cTAKES , running using Docker. From A-Z in 5 minutes. This talk was presented during Apache Roadshow [1] [1] - https://apachecon.com/usroadshowdc19/schedule.html

1. Apache cTAKES
NLP in Healthcare
Alex Zbarcea (FannieMae / cTAKES committer)

2. 2
Episode of Care
medications
imaging
pathology
inpatient
services and procedures
outpatient
services and procedures
medications
imaging
pathology
inpatient
services and procedures
outpatient
services and procedures
research
EMR
notes

3. Natural Language Processing (NLP)
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“A way for computers to analyze, understand and derive
meaning from human language” - algorithmia [1]
[1] - https://blog.algorithmia.com/introduction-natural-language-processing-nlp/
● Feasibility
Big Data / Machine Learning / Apache Projects
● Challenges
Ontology / Specialization / Anonymization

4. ● Approaches:
Extraction
Generation
● Algorithms:
Rule-based
Machine Learning
● Linguistic annotations:
Penn TreeBank [1]
GENIA [2]
How it works
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corpus
[1] - https://www.clips.uantwerpen.be/pages/mbsp-tags
[2] - https://orbit.nlm.nih.gov/browse-repository/dataset/human-annotated/83-genia-corpus

5. 5
Apache cTAKES: Overview
plain text
CDA
Named Entity
* drug
* disease/disorder
* sign/symptom
* anatomical site
* procedures
Pipeline based - combining techniques:
● Rule-based
● Machine Learning (ML)
Java, Modular
Measurable performance (standard)

6. Boundary detection
Tokenization
Normalization (Lemma)
Part-of-speech
Shallow parsing
Entity recognition
cTAKES System
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NLM
Apache OpenNLP
SPECIALIST NLP Tools
Apache Lucene
UMLS, SNOMED-CT, RxNORM
ICD10/9, Mayo Clinic, Custom

7. Tasks in NLP
(cTAKES example)
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8. cTAKES: Pipelines
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(e.g. examples/pipeline/ProcessDir.piper )
// This file contains commands and parameters to run the ctakes-examples "Hello World"
pipeline
readFiles org/apache/ctakes/examples/notes
// Load a simple token processing pipeline from another pipeline file
load DefaultTokenizerPipeline.piper
// Add non-core annotators
add ContextDependentTokenizerAnnotator
// Collect discovered Entity information for post-run access
collectEntities
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files

9. ● Documentation (confluence [3])
● ctakes-examples
● main Classes
[alex ~/ctakes {trunk %} ]$ grep -nRI --include="*.java" "main(String[] args)" | wc -l
171
cTAKES: Exploring Examples
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[1] - https://builds.apache.org/analysis
[2] - https://builds.apache.org/view/C/view/Apache%20cTAKES/
[3] - https://cwiki.apache.org//confluence/display/CTAKES
● smokingstatus
● coreference
● NexEx
● pipelines
● training
● temporal
● relationextractor
● etc
● Run on real data (i.a. LibreHealth / OpenEMR)

10. Apache cTAKES Demo
10 [1] - https://github.com/azbarcea/ctakes-examples

11. Apache Software Foundation
● Community
○ Linguist experts
Users
Developers
● Mature Software Lifecycle
○ Support
Issues
SCM - Collaboration
Jenkins
Sonar
Distribution
● Popularize
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12. Get involved
(You don’t need to be a software developer)
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● Help new users and provide feedback
● Give feedback on required features
● Write or Update documentation
● Test the code and report bugs
● Fix bugs
● Write and update the software
● Create artwork
● Extend docs references
● Recommend the project to others
● Gamification
● Volunteer valuable skills
● Learn about communities - the Apache Way
● Requirements Engineering
● Learn about NLP and Healthcare
● What a strong product is about
● Test Automation and Software Engineering
● Develop code with high quality
● Build strong Software Development skills
● Explore your creativity
● Marketing
● Use your time wisely
● Help research community
git: https://github.com/apache/ctakes
wiki: https://cwiki.apache.org//confluence/display/CTAKES
e-mail: https://ctakes.apache.org/mailing-lists.html

13. Thanks!
Any questions?
You can find me at:
● https://linkedin.com/in/azbarcea
● alexz@apache.org
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