4/2/2013

Identifying Abdominal Aortic Aneurysm Cases and Controls using Natural Language Processing of Radiology Reports
Sunghwan Sohn, Zi Ye, Hongfang Liu, Christopher G. Chute, Iftikhar J. Kullo Mayo Clinic

Abdominal Aortic Aneurysm (AAA)

AAA is present in about 10% of men

older than 65 years

the most severe complication is

rupture high mortality rate of 90% (14th leading cause of death in the U.S.A)

AAA is typically diagnosed by

physical examination, ultrasound, or CT scan

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AAA identification

Medical experts can manually review

radiology reports to identify AAA

impractical for large-scale clinical study

An automated way of information

extraction from clinical text

NLP tool

This study describes a natural

language processing (NLP) tool

1) To identify patients with AAA 2) To extract AAA size with date

NLP tool basis - MedTagger

Developed by Mayo NLP

team

Includes basic NLP

components

UIMA framework A fast clinical concept

indexing pipeline

Efficient to process a
large clinical data

MedTagger AAA components

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Methods

Step 1: select potential AAA reports

using keywords

Step 2: classify reports into AAAcase vs. non-case using rules

Step 3: determine the AAA patient

cohort based on a report-level classification

Step 1: Selection of potential AAA reports

Not all radiology reports contain AAA

information

Select reports based on CPT (current

protocol terminology) codes and code descriptions

Missed many AAA-related reports

A better alternative is to use

keywords

aorta and abdominal relevant terms

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aorta and abdominal terms

Expanded
through both UMLS concepts and the most frequent terms used in Mayo clinical notes

aorta terms aorta aortae aortas aortic

abdominal terms abdominal abd abdomen abdomens abdomina abdominals abdominopelvic region abdominopelvic regions abdominopelvis ccs_abdominal intrabdominal

Step 2: AAA report classification case vs. non-case

AAA case
contains abdominal aorta or
abdominal aorta aneurysm related terms and aneurysm size >= 3 cm

Non case
1) status post (e.g., s/p AAA repair,
aortic endograft, etc.) 2) only AAA terms w/o size 3) normal AAA indication 4) no AAA information

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AAA related keywords (normalized through LVG)

AA
infrarenal aorta abdominal aorta aorta abdominal infrarenal location

AAA
a.a.a. abdominal aortic aneurysm aneurysm abdominal aorta aneurysm abdominal aneurysm abdominal aortic aorta abdominal aneurysm aortic aneurysm abdominal infrarenal abdominal aorta infrarenal aortic aneurysm

S/P
post a.a.a. repair s/p a.a.a. repair endograft endovascular aneurysm sac bifurcate endograft endoleak

Normal
normal caliber abdominal aorta normal distal aorta abdominal aorta normal caliber aorta normal caliber

AAA size description

Described in numerous ways

4.4cm, measuring 4.45.3 cm,
4.45.36.1 cm, maximum AP diameter of 3.7cm and a transverse diameter of 3.7cm, etc.

Can have more than one size

mentions in a report due to previous history

Aim to extract the largest size of AP

or transverse (excluding length) only on the exam date

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AAA size extraction

Regular expression Selects the max value from AP and
transverse and then normalizes the value to cm

Exclude the size

Not from the exam date are excluded: the size that comes with previous indication
words (e.g., previously/earlier previous measurement(s) was/were prior exam compared to/with increased from) Associated with other than abdominal aneurysm

Step 3: AAA Patient cohort identification

Generally, patients have more than

one report (examination)

If any report of a given patient is an

AAA case, classify as a AAA patient

Generate aneurysm size variations

with examination date
PatientID|2.5cm:**/**/1999|3.2cm:**/**/2008|3.5cm:**/**/2009|3 .5cm:**/**/2009|3.6cm:**/**/2010|3.8cm:**/**/2011

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AAA annotations visualized through UIMA CVD

Results
Classification: AAA vs. Non-AAA Training set: 400 reports Test set: 250 reports
Report-level classification Patient-level classification

Evaluation precision recall F-score size accuracy

value 0.939 0.984 0.961 0.984

Evaluation value precision 0.926 recall F-score 1 0.962

61 TPs, 4 FPs, and 1 FNs

25 TPs, 2 FPs, and 0 FNs

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False Positive cases

incorrect negation
abdominal aorta negative for
aneurysm

incorrect size determination

under 3cm

incorrect association with other than

abdominal aorta

a fusiform 5.5cm aneurysm of the

distal thoracic and upper abdominal aorta extending

Summary
Our system classified most AAA-case
reports with a high F-score A NLP system showed a good capability to identify an AAA patient cohort with size enables large-scale clinical study

Our approach may be adjusted to other

types of arterial aneurysms studies the presence of pathologies from radiology reports, which have sizebased criteria