Semantic Medline:Semantic Medline:Multi-Document SummarizationMulti-Document Summarization

and Visualizationand Visualization

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

Halil Kilicoglu,Halil Kilicoglu, M.S. M.S.

Lister Hill National Center for Lister Hill National Center for Biomedical CommunicationsBiomedical Communications

Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 2

Information management applicationInformation management application

Manipulate information in addition to documentsManipulate information in addition to documents Manage the results of PubMed searchesManage the results of PubMed searches

Help users decide what to readHelp users decide what to read

Connect knowledge from various sourcesConnect knowledge from various sources Integrate application interfaces Integrate application interfaces

Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 3

Managing retrieval resultsManaging retrieval results

Information retrieval

summarization

Semantic Medline

breast cancer

Network of relations

retrieval

500 citations

Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 4

Managing retrieval resultsManaging retrieval results

breast cancer

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Seamless integration of technologiesSeamless integration of technologies

Information retrievalInformation retrieval PubMed - MEDLINEPubMed - MEDLINE

Natural language processing: Natural language processing: SemRepSemRep Represent content of text with semantic predicationsRepresent content of text with semantic predications

Abstraction summarizationAbstraction summarization Informative: Overview of most salient informationInformative: Overview of most salient information

VisualizationVisualization Indicative: Links to source text and additional informationIndicative: Links to source text and additional information

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StructuredBiomedical

DataUMLS

SemanticPredications

SemRep

InformativeGraph

Visualize

SalientSemanticPredications

Summarize

Semantic Medline Semantic Medline OverviewOverview

Text

MEDLINEClinicalTrials.gov

PubMedQuery

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StructuredBiomedical

DataUMLS

SemanticPredications

SemRep

InformativeGraph

Visualize

SalientSemanticPredications

Summarize

Document selectionDocument selection

Text

MEDLINEClinicalTrials.gov

PubMedQuery ““breast cancer”breast cancer”““breast cancer”breast cancer”

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StructuredBiomedical

DataUMLS

SemanticPredications

SemRep

InformativeGraph

Visualize

SalientSemanticPredications

Summarize

MEDLINE citationsMEDLINE citations

MEDLINEClinicalTrials.gov

PubMedQuery

Text

… … aromatase inhibitor provides aromatase inhibitor provides mortality benefit in early breast mortality benefit in early breast carcinomacarcinoma ……

……determined the spectrum and determined the spectrum and frequency of ATM missense frequency of ATM missense variants in 443 breast cancer variants in 443 breast cancer patientspatients ……

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StructuredBiomedical

Data

InformativeGraph

Visualize

SalientSemanticPredications

Summarize

Semantic intepretationSemantic intepretation

MEDLINEClinicalTrials.gov

PubMedQuery

UMLS

SemanticPredications

SemRep

Text

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Semantic interpretationSemantic interpretation

... ... aromatase inhibitor provides mortality benefit in early breast carcinoma … …

Aromatase Inhibitors Breast Carcinomatreats

… … determined the spectrum and frequency of ATM missense variants in 443 breast cancer patients … …

ATM gene Breast Carcinomaassociated_with

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StructuredBiomedical

DataUMLS

SemRep

InformativeGraph

Visualize

SalientSemanticPredications

Summarize

Semantic predicationsSemantic predications

Text

MEDLINEClinicalTrials.gov

PubMedQuery

SemanticPredications

Aromatase Inhibitors Breast Carcinomatreats

ATM gene Breast Carcinomaassociated_with

Tamoxifen Breast Carcinomatreats

Tamoxifen Patientstreats

Breast Carcinoma Individualprocess_of

… … …

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StructuredBiomedical

DataUMLS

SemRep

InformativeGraph

Visualize

SummarizationSummarization

Text

MEDLINEClinicalTrials.gov

PubMedQuery

SalientSemanticPredications

Summarize

SemanticPredications

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Abstraction summarizationAbstraction summarization

AllPredications

Reduction SalientPredications

Specify a topicSpecify a topic Retain predications on the topicRetain predications on the topic Eliminate uninformative predicationsEliminate uninformative predications Retain most frequent predicationsRetain most frequent predications

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StructuredBiomedical

DataUMLS

SemRep

InformativeGraph

VisualizeSummarize

Salient semantic predicationsSalient semantic predications

Text

MEDLINEClinicalTrials.gov

PubMedQuery

SemanticPredications

SalientSemanticPredications

Aromatase Inhibitors Breast Carcinomatreats

ATM gene Breast Carcinomaassociated_with

Tamoxifen Breast Carcinomatreats

Tamoxifen Patientstreats

Breast Carcinoma Individualprocess_of

… … …

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StructuredBiomedical

DataUMLS

SemRep Summarize

VisualizationVisualization

Text

MEDLINEClinicalTrials.gov

PubMedQuery

SemanticPredications

InformativeGraph

Visualize

SalientSemanticPredications

Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 16

SemRep Summarize

Informative graphInformative graph

MEDLINEClinicalTrials.gov

PubMedQuery

SemanticPredications

Visualize

SalientSemanticPredications

StructuredBiomedical

DataUMLS

Text InformativeGraph

treats

associated_with

treats

Aromatase InhibitorsTamoxifen

ATM gene

Breast Carcinoma

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Semantic Medline Semantic Medline LiveLive

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Home pageHome page

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Search MEDLINESearch MEDLINE

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Summarization optionsSummarization options

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Summarization resultsSummarization results

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More detailMore detail

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Substance interactionsSubstance interactions

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AcknowledgmentsAcknowledgments

Caroline AhlersCaroline Ahlers Marcelo FiszmanMarcelo Fiszman Philip GoetzPhilip Goetz Halil KilicogluHalil Kilicoglu Anna RippleAnna Ripple Graciela RosemblatGraciela Rosemblat