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Understanding the Aging Process with Artificial Intelligence
Mark Farrell
Bioinformatics Researcher
Center for Research and Education on AgingLawrence Berkeley National Laboratory
University of California, Berkeley
September 4th, 2014
Outline
1 About Me
2 Understanding the Aging Process
3 Knowledge Extraction
4 What Next?
About Me Understanding the Aging Process Knowledge Extraction What Next?
Who I amMark Farrell
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
What I’m StudyingComputer Science
Year 2
Program Bachelor of Computer Science
Faculty Mathematics
Institution University of Waterloo
Location Waterloo, Ontario, Canada
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
Where I’m fromAtlantic Canada
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How I Became a Researcher at CREAProf. Garan Emailed the University of Waterloo Computer Science Club
Mark Farrell Understanding the Aging Process with Artificial Intelligence
Outline
1 About Me
2 Understanding the Aging Process
3 Knowledge Extraction
4 What Next?
About Me Understanding the Aging Process Knowledge Extraction What Next?
What does CREA want to do?CREA Wants to Understand Aging and Increase Human Lifespan
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
Why is it Difficult to Understand Aging?High Number of Publications; Growing Rate of Discovery
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
Why is it Difficult to Understand Aging?High Number of Publications; Growing Rate of Discovery
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How can CREA Understand Aging?Build a Knowledge Base that Describes and Reasons about Aging
AcquireBiomedicalArticles
ExtractKnowledge
MachineHuman
GraphicalUser
Interface
Is aboutAging?
UpdateAgingTheory
Discardyesno
Mark Farrell Understanding the Aging Process with Artificial Intelligence
Outline
1 About Me
2 Understanding the Aging Process
3 Knowledge Extraction
4 What Next?
About Me Understanding the Aging Process Knowledge Extraction What Next?
What is Knowledge Extraction?Knowledge Extraction is the Act of Reading and Understanding Text
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
What is Knowledge Extraction?An Example of Knowledge Extraction
Input
... The pyridinoline and desmosine were examined as candidate sensitizerchromophores contained in collagen and elastin, respectively. ...
Output
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?An Overview of Knowledge Extraction
Tokenization Input a text document and read it, one sentence at a time.
Parsing For each sentence, generate a constituent tree that describes its phrasestructure.
Compilation Extract facts by pattern matching on each constituent tree.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?An Example of How Knowledge is Extracted From Text
Input Token - a Sentence
The man walks the dog.
Output Fact - an Understanding of the Sentence
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Tokenization: Begin by Reading a Sentence
The man walks the dog.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Parsing: Generate a Constituent Tree for the Sentence
ROOT
S
@S
NP
DT
The
NN
man
VP
VBZ
walks
NP
DT
the
NN
dog
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?A Brief Lesson on Parsing Sentences
Assign each Word a Part-of-Speech TagTag Meaning ExampleDT Determiner theIN Preposition ofJJ Adjective blueRB Adverb quicklyCC Coordinating Conjunction andNN Singular Noun monkey
NNS Plural Noun monkeysVB Base Verb fall
VBZ Singular Present Verb fallsVBD Past Tense Verb fellVBN Past Participle Verb fallenVBG Gerund Verb falling
... ... ...
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?A Brief Lesson on Parsing Sentences
Group Words into Phrases
Tag Meaning Example
NP Noun Phrase the womanVP Verb Phrase calls the manPP Prepositional Phrase from the store
ADVP Adverb Phrase quickly and quietlyADJP Adjective Phrase blue and redCONJP Conjunctive Phrase as well as
... ... ...
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?A Brief Lesson on Parsing Sentences
Group Phrases into Clauses - Containing Facts
Tag Meaning Example
S Declarative Clause the dog walksSBAR Conjunction + Clause that the dog walks... ... ...
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Find Clauses in the Constituent TreeROOT
S
@S
NP
DT
The
NN
man
VP
VBZ
walks
NP
DT
the
NN
dog
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Find Predicates - Actions that Relate Literal Nouns to Form FactsROOT
S
@S
NP
DT
The
NN
man
VP
VBZ
walks
NP
DT
the
NN
dog
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Rewrite the Constituent Tree - Include the PredicateROOT
S
@S
NP
DT
The
NN
man
〈predicate:walk〉
NP
DT
the
NN
dog
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Find Literal Nouns
ROOT
S
@S
NP
DT
The
NN
man
〈predicate:walk〉
NP
DT
the
NN
dog
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Rewrite the Constituent Tree - Include Literal Nouns
ROOT
S
@S
〈argument:man〉 〈predicate:walk〉
〈argument:dog〉
.
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Rewrite the Constituent Tree - Apply Arguments to the Predicate to Form a Fact
ROOT
〈predicate:walk〉
〈argument:man〉 〈argument:dog〉
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
How is Knowledge Extracted from Text?Compilation: Understand the Meaning of the Sentence
Output Fact
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
Why is Knowledge Extraction Useful for Understanding the Aging Process?Let’s Examine a Visualization of Knowledge Extracted from PubMed Abstracts to Find Out
Mark Farrell Understanding the Aging Process with Artificial Intelligence
Outline
1 About Me
2 Understanding the Aging Process
3 Knowledge Extraction
4 What Next?
About Me Understanding the Aging Process Knowledge Extraction What Next?
What Next?
Task Assignees
Research Direction Steve GaranKnowledge Extraction Mark FarrellText Article Retrieval Grace Park, Jeremy Wan
Knowledge Visualization Mark FarrellGraphical User Interface Mark FarrellBiomedical Spam Filtering —Automated Reasoning —
Mark Farrell Understanding the Aging Process with Artificial Intelligence
About Me Understanding the Aging Process Knowledge Extraction What Next?
Get InvolvedContact Me for More Information
Email m4farrel@csclub.uwaterloo.ca
Website markfarrell.ca
Mark Farrell Understanding the Aging Process with Artificial Intelligence
Questions?