10,000 foot view of what I am working on
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10,000 foot view of what I am working on
Wendy W. Chapman, PhD
University of Pittsburgh
Dept of Biomedical Informatics
Biomedical Language Understanding
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BackgroundB
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U of UtahU of Utah WisconsinWisconsin U of UtahU of Utah U of PittsburghU of Pittsburgh
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Biomedical Language Understanding
www.dbmi.pitt.edu/blulabHenk Harkema, Danielle Mowery, Mike Conway,Lee Christensen, Qi Li, Wendy Chapman
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Topaz
• Named entity recognition– Maps UMLS concepts to higher-level concepts
• Contextual property assignment (ConText)– Existence (affirmed, negated)– Experiencer (patient, other)– Historicity (current, historical)– Realis (actual, non-specific/hypothetical)– Certainty (uncertain, certain)– Reason for exam (yes, no)– Quality of exam (diagnostic, limited)
Harkema, B Chapman, Hwa
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ConText: Determine Values for Contextual Properties
Patient denies cough but complains of headache.No change in the patient’s chest pain.
trigger term
terminationtermpseudo-trigger
term
scope
Clinical condition: CoughNegation: Negated
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ConText: Historical
Past history of pneumonia presentingtoday with cough and fever.
trigger term terminationterm
scope
Clinical condition: PneumoniaTemporality: Historical
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Onyx
Onyx
At (translucency, numberEight) &
surfaceOf (numberEight, mesial) &
stateOf (translucency, possible)
Semantic Models
Semantic Models
Syntactic AnalyzerSyntactic Analyzer
Context-free Grammar
Context-free Grammar
TrainingCorpusTrainingCorpus
Semantic AnalyzerSemantic Analyzer
Eight mesial might have a slight translucency
Haug, Schleyer
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Knowledge-rich Frame-based Mapping
ProbabilisticFrames
SemanticNetwork
- Frame slots map to semantic network- Relationships between slots are probabilistic
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Annotation Interfacewith active learning and help from Onyx
TemplatesTemplates
Semantic ModelSemantic Model
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Speech NLP Chart
Onyx
Dental ExamsNumber one Is missing. Two is fine. Caries on Tooth 3.
Titus Schleyer, Lee Christensen, Peter Haug, Jeannie Irwin, Henk Harkema
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Ontology Development-Information Extraction (ODIE)
Ontology
Text
Ontology EnrichmentUse IE to find new concepts and relationships to add
Information ExtractionUse ontology to improve IE from text
Rebecca Crowley, Mayo Clinic, Stanford NCBO
SurgicalPathologySurgical
PathologyChest
RadiographyChest
Radiography
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View Overlap of Ontologies
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Suggest Concepts
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Results Review/Error Analysis
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Schema for Clinical Condition Properties
Properties of Condition Concept
Existence Yes, NoExperiencer Patient, OtherChange Unmarked, Unchanging, Changing, Increasing, Decreasing,
Improving, Worsening, RecurrenceIntermittent Unmarked, Yes, NoCertainty Unmarked, High, Moderate, LowMental State Yes, NoGeneralized/Conditional Yes, NoCurrent Visit Relation Before, Meets_Overlaps, After
Wiebe, Jordan, Mowery, Harkema
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Schema for Temporal Relations
Time Words Points, DurationsOrdering Words Precedes, During, FollowsAspectual Words Initiation, Continuation, Culmination
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Application Ontology for Syndromic Surveillance
Consensus of developers/users across countryConway, Buckeridge
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Temporality Schema
Topaz
NLP Repository
AnaphoricReference
Onyx
BLU Lab NLP Sampler
OntologyEnrichment
ResultsReview/Error
Analysis
OntologyFor
SyndromicSurveillance
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Anaphoric Reference in Clinical ReportsCrowey, Savova, Zeng
• Adapted MUC schema for clinical reports• Three experts annotated 180 reports
Five types—Mayo, UPMC
• identity• part/whole• set/subset
• Characterize anaphoric reference in reports• Train/test resolution algorithms