Graphs of Consistent Concepts

Data mining in a medical domain(Pawel Matykiewicz, Wlodzislaw

Duch, John Pestian)

The story(1)• Hospital workflow:

– Chest X-Ray order (Electronical Medical Record)– Chest X-Ray (High Quality JPEG)– Dictation ( “CLINICAL HISTORY: 9-month-29-day-old male with a history of cough.

Rule out pneumonia.PROCEDURE COMMENTS: None.COMPARISON: XX/XX/XX.FINDINGS: There is mild hyperinflation of the lungs with increased peribronchial

markings most consistent with viral versus reactive airway disease. Hazy increased density is seen in the right middle lobe, left lower lobe which could represent subsegmental atelectasis. Hazy increased density is also noted at the lingula with partial effacement of the left heart contour which could represent atelectasis versus early pneumonia. No pleural effusion is noted. The cardiothymic silhouette is within normal limits. Soft tissues and bony structures are unchanged.

IMPRESSION: Findings most consistent with viral versus reactive airway disease. Patchy atelectasis is associated. Lingular early infiltrate cannot be excluded.” )

– Billing ( ICD9CM 590.8 = INFECTIONS OF KIDNEY: OTHER PYELONEPHRITIS OR PYONEPHROSIS, NOT SPECIFIED AS ACUTE OR CHRONIC )

Creating a novel tool(2)

Semantic memory

Recognition memory

Episodic memory

Full text annotation

UMLS (3)• UMLS = Unified Medical Language System• UMLS contains:

– 1,195,781 unique English concepts (CUI)– 2,873,310 unique English phrases (SUI) – 3,283,983 unique English, normalized words

(WUI)– 88 different ontologies (e.g. ICD9CM = 15871

CUIS)– 36,627,948 relations– 11,495,405 co-occurrence relations

Example(4)• Concept description:

– ENG|zygopleurage zygospora|C1473040|L5302079|S6018172|

– C1533582|ENG|P|L5432111|PF|S6215413|Y|A7881881|2532798015|412807000||SNOMEDCT|PT|412807000|Serum inhibin measurement|4|N||

• Relation description:– C0000039|A6841046|CODE|RO|C0364349|A0683492|CODE|has_component|R39728053||LNC|LNC||Y|N||

WUI WUI

WUI

SUI

SUI SUI

SUI

CUI

CUI CUI

CUI

CUI

Sense Disambiguation(5)• Word Sense Disambiguation:

– “cold” (word):• "I am taking aspirin for my cold" • "Let's go inside, I'm cold“

• Phrase Sense Disambiguation:– “cold” (WUI):

• cold temperature (CUI)• Common Cold (CUI)• Cold Therapy (CUI)• Chronic Obstructive Airway Disease (CUI)• Cold Sensation (CUI)• Cold brand of chlorpheniramine-phenylpropanolamine

(CUI)

Concept Mapping(6)• Tough way:

• Easy way:

Graphs of consistent concepts(7)

X versus Y Z => ( C(YZ) => C(XZ) )

X is associated => ( C(X) => P(X) = 1 )

JJ(X) => ( NN(Y) => C(XY) )

Graphs of consistent concepts(8)

Graphs of consistent concepts(9)

Summary(10)• Data set:

– 30 training documents ( 6 ICD9CM codes, 137 CUIs )– 30 testing documents ( 6 ICD9CM codes, 301 CUIs )

– 30 training documents ( 6 ICD9CM codes, 301 CUIs )– 30 testing documents ( 6 ICD9CM codes, 137 CUIs )

• To do:– Construction finding– Concept discovery– State discovery

before learning

after learning

training 66% 99%

testing 53% 66%

before learning

after learning

testing 53% 80%

training 66% 85%