medical data and text mining: linking diseases, drugs, and adverse reactions
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Medical data and text mining: Linking diseases, drugs, and adverse reactionsTRANSCRIPT
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Medical data and text mining
Linking diseases, drugs, and adverse reactions
Lars Juhl Jensen
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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unstructured data
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central registries
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individual hospitals
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opt-out
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opt-in
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Danish registries
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civil registration system
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CPR number
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established in 1968
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Jensen et al., Nature Reviews Genetics, 2012
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national discharge registry
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14 years
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6.2 million patients
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45 million admissions
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68 million records
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119 million diagnosis
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ICD-10
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Jensen et al., Nature Reviews Genetics, 2012
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not research
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reimbursement
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diagnosis trajectories
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naïve approach
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comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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confounding factors
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“known knowns”
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gender
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age
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type of hospital encounter
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Jensen et al., Nature Communications, 2014
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“known unknowns”
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smoking
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diet
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“unknown unknowns”
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reporting biases
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matched controls
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temporal correlations
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multiple testing
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trajectories
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Jensen et al., Nature Communications, 2014
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trajectory networks
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Jensen et al., Nature Communications, 2014
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key diagnoses
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Jensen et al., Nature Communications, 2014
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direct medical implications
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electronic health records
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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unstructured data
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free text
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Danish
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busy doctors
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typos
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psychiatric patients
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text mining
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computer
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as smart as a dog
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teach it specific tricks
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comprehensive dictionary
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diseases
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drugs
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adverse drug reactions
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expansion rules
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Clozapine
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Clozapineclozapi
n
clossapin
klozapine
chlosapin
chlosapine
chlozapin
chlozapine
klossapin
closapine
klozapinklosapi
n
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flexible matching
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compound nouns
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post-coordination rules
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failure of kidney
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kidney failure
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“black list”
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three-letter acronyms
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pharmacovigilance
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clinical trials
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spontaneous reports
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underreporting
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data mining
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structured data
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medication
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semi-structured data
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drug indications
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known ADRs
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unstructured data
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adverse drug reactions
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temporal correlations
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hand-crafted rules
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Eriksson et al., Drug Safety, 2014
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Eriksson et al., Drug Safety, 2014
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Eriksson et al., Drug Safety, 2014
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Eriksson et al., Drug Safety, 2014
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recall known ADRs
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estimate ADR frequencies
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Eriksson et al., Drug Safety, 2014
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discover new ADRs
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Drug substance ADE p-value
Chlordiazepoxide Nystagmus 4.0e-8
Simvastatin Personality changes
8.4e-8
Dipyridamole Visual impairment
4.4e-4
Citalopram Psychosis 8.8e-4
Bendroflumethiazide
Apoplexy 8.5e-3
Eriksson et al., Drug Safety, 2014
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AcknowledgmentsDisease trajectoriesAnders Bøck JensenTudor OpreaPope MoseleySøren Brunak
Adverse drug reactionsRobert ErikssonThomas WergeSøren Brunak
EHR text mining
Peter Bjødstrup Jensen
Robert ErikssonHenriette SchmockFrancisco S. Roque
Anders JuulMarlene Dalgaard
Massimo AndreattaSune FrankildEva Roitmann
Thomas HansenKaren Søeby
Søren BredkjærThomas Werge
Søren Brunak