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Lars Juhl Jensen jensenlab.org Introduction to text mining

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Page 1: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Lars Juhl Jensen jensenlab.org

Introduction to text mining!

Page 2: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

>10 km

Page 3: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

patent literature

Page 4: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

grant proposals

Page 5: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

too much to read

Page 6: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

computer

Page 7: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

as smart as a dog

Page 8: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

teach it specific tricks

Page 9: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity
Page 10: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity
Page 11: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

named entity recognition!

Page 12: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

dictionary

Page 13: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

genes / proteins

Page 14: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

diseases / phenotypes

Page 15: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

drugs / metabolites

Page 16: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

synonyms

Page 17: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

alpha-synuclein

Page 18: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

SNCA

Page 19: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

PARK1

Page 20: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

not comprehensive

Page 21: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

orthographic variation

Page 22: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

spaces and hyphens

Page 23: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

alpha-synuclein

Page 24: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

alpha synuclein

Page 25: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

prefixes and suffixes

Page 26: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

SNCA

Page 27: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

hSNCA

Page 28: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

alternative forms

Page 29: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Parkinson’s disease

Page 30: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Parkinson’s disorder

Page 31: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Parkinson’s syndrome

Page 32: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

acronyms

Page 33: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

PD

Page 34: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

curated blacklist

Page 35: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

SDS

Page 36: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

software

Page 37: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

C++ tagger

Page 38: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

>1000 abstracts / second

Page 39: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

70–80% recall

Page 40: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

80–90% precision

Page 41: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

open source bitbucket.org/larsjuhljensen/tagger/

Page 42: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Docker hub.docker.com/r/larsjuhljensen/tagger/

Page 43: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

web service tagger.jensenlab.org

Page 44: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

EXTRACT extract.jensenlab.org

Page 45: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity
Page 46: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

information retrieval!

Page 47: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

three approaches

Page 48: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

ad hoc retrieval

Page 49: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

PubMed

Page 50: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

text indexing

Page 51: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

document similarity

Page 52: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

recommendation engines

Page 53: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

term vectors

Page 54: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

weighting scheme

Page 55: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

vector similarity

Page 56: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

NER-based retrieval

Page 57: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

synonyms

Page 58: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

alpha-synuclein

Page 59: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

SNCA

Page 60: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

ontologies

Page 61: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Parkinson’s disease

Page 62: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

neurodegenerative disease

Page 63: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

concept indexing

Page 64: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

improved recall

Page 65: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

too much to read

Page 66: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

information extraction!

Page 67: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

two approaches

Page 68: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

natural language processing

Page 69: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

syntactic parsing

Page 70: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

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]

Saric et al., Proceedings of ACL, 2004

Page 71: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

manually crafted rules

Page 72: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

a lot of work

Page 73: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

machine learning

Page 74: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

manually annotated corpus

Page 75: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

even more work

Page 76: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

co-mentioning

Page 77: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

counting

Page 78: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

within document

Page 79: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

within paragraph

Page 80: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

within sentence

Page 81: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

weighted count

Page 82: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity
Page 83: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

normalization

Page 84: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity
Page 85: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

z-scores

Page 86: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

database resources

Page 87: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

STRING

Page 88: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

string-db.org

Page 89: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

STITCH

Page 90: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

stitch-db.org

Page 91: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

COMPARTMENTS

Page 92: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Binder et al., Database, 2014 compartments.jensenlab.org

Page 93: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

TISSUES

Page 94: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Palasca et al., Database, 2018 tissues.jensenlab.org

Page 95: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

DISEASES

Page 96: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

knowledge discovery!

Page 97: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

indirect associations

Page 98: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Raynaud’s disease

Page 99: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

blood viscosity

Page 100: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

fish oil

Page 101: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

open discovery

Page 102: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

one-node search

Page 103: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

A → B → C

Page 104: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

generate novel hypotheses

Page 105: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

too many hypotheses

Page 106: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

closed discovery

Page 107: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

two-node search

Page 108: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

A → B ← C

Page 109: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

find plausible explanations

Page 110: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

experimental observation

Page 111: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

trend discovery

Page 112: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

unknown patterns

Page 113: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

known individual facts

Page 114: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

enrichment analysis

Page 115: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

temporal patterns

Page 116: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

conclusions!

Page 117: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

broadly applicable

Page 118: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

keep it simple

Page 119: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

free tools

Page 120: Introduction to text miningIntroduction to text mining! >10 km patent literature grant proposals too much to read computer as smart as a dog teach it specific tricks named entity

Efficient DSP ASE Programming in C: Tips and Tricks...Efficient DSP ASE Programming in C: Tips and Tricks, Revision 01.22 5 1 Overview The MIPS® DSP ASE (Application Specific Extension)

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