mining literature and medical records
TRANSCRIPT
![Page 1: Mining literature and medical records](https://reader038.vdocuments.net/reader038/viewer/2022103114/554e8a29b4c90573338b49b5/html5/thumbnails/1.jpg)
Lars Juhl Jensen
Mining literature and medical records
>10 km
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exponential growth
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~45 seconds per paper
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outline
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information retrieval
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named entity recognition
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augmented browsing
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information extraction
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text corpora
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web resources
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electronic health records
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medical text mining
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questions
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information retrieval
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find the relevant papers
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ad hoc retrieval
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user-specified query
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“yeast AND cell cycle”
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PubMed
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indexing
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fast lookup
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stemming
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word endings
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dynamic query expansion
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MeSH terms
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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no tool will find that
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named entity recognition
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identify the concepts
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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 lexicon
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small molecules
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proteins
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cellular components
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tissues
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organisms
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environments
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diseases
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phenotypes
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behaviors
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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orthographic variation
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prefixes and postfixes
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CDC28 vs. Cdc28p
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Myc vs. c-Myc
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singular and plural forms
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noun and adjective forms
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flexible matching
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upper- and lower-case
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spaces and hyphens
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disambiguation
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homonyms
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“black list”
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unfortunate names
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SDS
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a
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scalable implementation
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>10 km<10 hours
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augmented browsing
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show relevant information
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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Reflect
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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browser add-on
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Firefox
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Google Chrome
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Safari
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Internet Explorer
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PDF viewer
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Utopia Documents
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web services
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still too much to read
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information extraction
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formalize the facts
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the starting point
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named entity recognition
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two approaches
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co-mentioning
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within documents
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within paragraphs
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within sentences
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weighted counts
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co-mentioning score
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absolute co-mentionings
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relative overrepresentation
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NLPNatural Language Processing
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grammatical analysis
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part-of-speech tagging
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noun, verb, etc.
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multiword detection
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semantic tagging
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binding, regulation, etc.
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sentence parsing
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Gene and protein names
Cue words for entity recognition
Verbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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extract stated facts
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handle negations
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high precision
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poor recall
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highly domain specific
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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text corpora
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a body of text
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most use abstracts
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few use full-text articles
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no access
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~22 mio. abstracts
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~1.8 mio. free articles
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~1.4 mio. Elsevier articles
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~7.5 mio. patents
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web resources
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information on proteins
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iHOP
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STRING
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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text mining channel
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what is known
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not in databases
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human proteins
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co-mentioning dominates
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NLP provides actions
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homology transfer
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STITCH
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small molecules
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COMPARTMENTS
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subcellular localization
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DISEASES
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human diseases
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search for a protein
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search for a disease
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STRING payload
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evidence viewers
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electronic health records
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what happens at a hospital
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Jensen et al., Nature Reviews Genetics, 2012
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two types of data
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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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clinical narrative
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getting access
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patient consent
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opt-out
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opt-in
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ethical approval
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medical question
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no explorative studies
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data security
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not anonymized
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not transferable
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hospital IT systems
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not standardized
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clinical narrative
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not normal language
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trouble for NLP
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in native language
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not English
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few tools
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no dictionaries
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by busy doctors and nurses
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typos
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medical text mining
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what is possible?
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a psychiatric corpus
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clinical narrative
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in Danish
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dictionaries
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diseases
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drugs
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adverse drug reactions
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disease comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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multiple testing
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comorbidity matrix
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Roque et al., PLoS Computational Biology, 2011
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patient clustering
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Jensen et al., Nature Reviews Genetics, 2012
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clustering algorithm
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Roque et al., PLoS Computational Biology, 2011
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patient stratification
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temporal correlation
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drug treatment
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adverse drug events
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Eriksson et al., in preparation, 2012
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pharmacovigilance
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thank you!
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questions?