Knowledge-Based Semantic Interpretationfor Summarizing Biomedical Text

Thomas C. Rindflesch, Ph.D.Marcelo Fiszman, M.D., Ph.D.

Halil Kilicoglu, M.S.

National Library of Medicine

Artificial General Intelligence Research Institute Workshop

Overview

Symbol grounding Meaning consists of the manipulation of an internal

system of relationships among concepts (Rapaport 1995)

Illustrate the viability of this approach Semantic interpretation for biomedical research literature

Suggest that the system adumbrates intelligence Provides the basis for reasoning about medical topics

Unified Medical Language System (UMLS)

Developed at the National Library of Medicine Compilation of more than 100 terminologies in the

biomedical domain Two domain knowledge components

Metathesaurus: concepts Semantic Network: relationships

Constitutes the “meaning” of medicine Incomplete Inconsistent Useful

Metathesaurus

More than 1,000,000 concepts in biomedicine Disorders Organisms Anatomy, physiologic functions Drugs, procedures

Synonyms Hierarchical structure Each concept assigned semantic types (or

categories)

Metathesaurus Concept

Drug Therapy, Combination; Combination Chemotherapy;Polychemotherapy

Therapeutic or Preventive Procedure

•Analytical, Diagnostic and Therapeutic Techniques and Equipment

•Therapeutics•Drug Therapy

Metathesaurus Concept

Mycoplasma pneumonia; Eatons agent pneumonia;Endemic pneumonia; et al.

Disease or Syndrome

•Respiratory Tract Diseases • Lung Diseases

•Pneumonia•Pneumonia, Bacterial

Semantic Network

134 semantic types Disease or Syndrome Therapeutic or Preventive Procedure Pharmacologic Substance Body Part, Organ, or Organ Component

In two hierarchies: Entity, Event

54 Relationships between semantic types

Bacterium - CAUSES - Pathologic Function

Pathologic Function - PROCESS_OF - Organism

affects

functionally_related_to

brings_about

physicallyspatially

temporallyconceptually

associated_withSemantic Network Predicates

occurs_in

TREATS

affects

functionally_related_to

brings_about

physicallyspatially

temporallyconceptually

associated_withSemantic Network Predicates

CO-OCCURS_WITH

PREVENTS

OCCURS_IN

CAUSES

LOCATION_OF

affects

functionally_related_to

brings_about

physicallyspatially

temporallyconceptually

associated_withSemantic Network Predication

occurs_in

Occupational Activity

Health Care Activity

Therapeutic or Preventive Procedure

Disease or Syndrome

Biologic Function

Pathologic Function

treats

Semantic Interpretation: SemRep

Exploit the UMLS for processing medical text Interpret (some of) the meaning asserted in

language Map words in language to concepts

Metathesaurus

Use syntactic structure to identify relationships between concepts Semantic Network

SemRep Output

Mycoplasma pneumonia is an infection of the lung caused by Mycoplasma pneumoniae.

Mycoplasma Pneumonia ISA Infection Lung LOCATION_OF InfectionLung LOCATION_OF Mycoplasma PneumoniaMycoplasma pneumoniae CAUSES Infection Mycoplasma pneumoniae CAUSES Mycoplasma Pneumonia

Related Research in Biomedicine

BioMedLEE, GENIES Semantic grammar

AQUA Definite clause grammar

MPLUS Chart parser

MEDSYNDIKATE Dependency grammar

[Friedman, et al.]

[Haug, et al.]

[Johnson, Campbell]

[Hahn, et al.]

Lexical semantics Contribution of words to interpretation

Meaning-text theory Network of semantic predications Syntax rules are interpretive devices

Ontological semantics Applied interpretation Ontology is the main metalanguage of meaning

Semantics Framework

[Mel’cuk]

[Nirenburg & Raskin]

[Cruse; Pustejovsky]

SPECIALISTLexicon

MetaMap ParserMetathesaurus

SemRep: System Overview

SemanticNetwork

ConstructRelation

MedicalText

MedPostTagger

LexicalLook-up

ResolveAmbiguity

SemanticPredication

Input

The aim of this study was the characterization of the specific effects of alprazolam versus imipramine in the treatment of panic disorder with agoraphobia and the delineation of dose-response and possible plasma level-response relationships.

SPECIALISTLexicon

Parser

Syntactic Processing

TextMedPostTagger

LexicalLook-up

ResolveAmbiguity

Syntactic Processing

The aim of this study was the characterization of the specific effects

NP[of alprazolam] [versus] NP[imipramine]

NP[in the treatment]Nominalization

NP[of panic disorder] NP[with Agoraphobia] and the delineation of dose-response and possible plasma level-response relationships.

MetaMap: Metathesaurus Concepts

SPECIALISTLexicon

MetaMap ParserMetathesaurus

TextMedPostTagger

LexicalLook-up

ResolveAmbiguity

MetaMap: Metathesaurus Concepts

The aim of this study was the characterization of the specific effects

NP[of Alprazolam] [versus] NP[Imipramine]

NP[in treatment]Nominalization

NP[of Panic Disorder] NP[with Agoraphobia] and the delineation of dose-response and possible plasma level-response relationships.

Semantic Types

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

Pharmacologic Substance

Disease or Syndrome

Construct Predication

MetaMap ParserMetathesaurus

SemanticNetwork

ConstructRelation

MedicalText

MedPostTagger

LexicalLook-up

ResolveAmbiguity

SemanticPredication

SPECIALISTLexicon

Semantic Interpretation

Indicator rules Establish a link between

Words in text Predicates in the Semantic Network

Argument identification rules Syntactic constraints

Interpretation of semantic predications UMLS Semantic Network

Indicator Rules

inpreposition TREATSHemofiltration in digoxin overdose

inpreposition HAS_LOCATION

Severe infections in both feet

Establish a correspondence between a syntactic item and a Semantic Network predicate

ItemStructure Semantic Network

treatment TREATS

Drugs for the treatment of schizophrenia

nominalization

Semantic Types

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

Pharmacologic SubstanceDisease or Syndrome

Apply Indicator Rule

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

TREATS

Argument Constraints

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

TREATS

Semantic Network Predication

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

medd-TREATS-dsyn

phsu-TREATS-dsyn

topp-TREATS-dsyn

topp-TREATS-inpo

Match Semantic Types

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[phsu] NP[in treatment]Nominalization

NP[of dsyn] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

medd-TREATS-dsyn

phsu-TREATS-dsyn

topp-TREATS-dsyn

topp-TREATS-inpo

Substitute Concepts

The aim of this study was the characterization of the specific effects

NP[of phsu] [versus] NP[Alprazolam] NP[in treatment]Nominalization

NP[of Panic Disorder] NP[with dsyn] and the delineation of dose-response and possible plasma level response relationships.

Alprazolam-TREATS-Panic Disorder

Manipulate Predications

Abstraction summarization on a given topic Treatment of disease

Apply to predications from multiple documents Devise summarization rules

Relevance: “Stick to the point” Predications adhere to a schema for treatment of disease

Novelty: “Don’t tell me what I already know” Eliminate arguments high in the UMLS hierarchy

Salience: “Give me the main points” Eliminate low frequency predications

[Hahn]

Summary Results

Search Medline Limit to previous year: 294 citations

Summarize retrieved documents Provide an informative overview

Further reasoning on the summarized predications is feasible