Understanding the Aging Process with Artificial Intelligence
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Mark Farrell is a bioinformatics researcher at the Center for Research and Education on Aging who is using artificial intelligence to help understand the aging process. His work involves extracting knowledge from biomedical articles on aging to build a knowledge base that can describe and reason about the aging process. This involves techniques such as tokenization, parsing, and compilation to analyze text, extract facts, and represent the knowledge in a structured way. The extracted knowledge will help researchers understand the large and growing body of publications on aging.
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Understanding the Aging Process with Artificial Intelligence
- 1. Understanding the Aging Process with Arti
- 2. cial Intelligence Mark Farrell Bioinformatics Researcher Center for Research and Education on Aging Lawrence Berkeley National Laboratory University of California, Berkeley September 4th, 2014
- 3. Outline 1 About Me 2 Understanding the Aging Process 3 Knowledge Extraction 4 What Next?
- 4. About Me Understanding the Aging Process Knowledge Extraction What Next? Who I am Mark Farrell Mark Farrell Understanding the Aging Process with Arti
- 6. About Me Understanding the Aging Process Knowledge Extraction What Next? What I'm Studying Computer 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 Arti
- 8. About Me Understanding the Aging Process Knowledge Extraction What Next? Where I'm from Atlantic Canada Mark Farrell Understanding the Aging Process with Arti
- 10. About Me Understanding the Aging Process Knowledge Extraction What Next? How I Became a Researcher at CREA Prof. Garan Emailed the University of Waterloo Computer Science Club Mark Farrell Understanding the Aging Process with Arti
- 12. Outline 1 About Me 2 Understanding the Aging Process 3 Knowledge Extraction 4 What Next?
- 13. 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 Arti
- 15. About Me Understanding the Aging Process Knowledge Extraction What Next? Why is it Dicult to Understand Aging? High Number of Publications; Growing Rate of Discovery Mark Farrell Understanding the Aging Process with Arti
- 17. About Me Understanding the Aging Process Knowledge Extraction What Next? Why is it Dicult to Understand Aging? High Number of Publications; Growing Rate of Discovery Mark Farrell Understanding the Aging Process with Arti
- 19. 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 Acquire Biomedical Articles Human Machine Extract Knowledge Graphical User Interface Is about Aging? Update Aging Theory no yes Discard Mark Farrell Understanding the Aging Process with Arti
- 21. Outline 1 About Me 2 Understanding the Aging Process 3 Knowledge Extraction 4 What Next?
- 22. 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 Arti
- 24. 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 sensitizer chromophores contained in collagen and elastin, respectively. ... Output Mark Farrell Understanding the Aging Process with Arti
- 26. 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 phrase structure. Compilation Extract facts by pattern matching on each constituent tree. Mark Farrell Understanding the Aging Process with Arti
- 28. 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 Arti
- 30. 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 Arti
- 32. 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 Arti
- 34. 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 Tag Tag Meaning Example DT Determiner the IN Preposition of JJ Adjective blue RB Adverb quickly CC Coordinating Conjunction and NN Singular Noun monkey NNS Plural Noun monkeys VB Base Verb fall VBZ Singular Present Verb falls VBD Past Tense Verb fell VBN Past Participle Verb fallen VBG Gerund Verb falling ... ... ... Mark Farrell Understanding the Aging Process with Arti
- 36. 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 woman VP Verb Phrase calls the man PP Prepositional Phrase from the store ADVP Adverb Phrase quickly and quietly ADJP Adjective Phrase blue and red CONJP Conjunctive Phrase as well as ... ... ... Mark Farrell Understanding the Aging Process with Arti
- 38. 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 walks SBAR Conjunction + Clause that the dog walks ... ... ... Mark Farrell Understanding the Aging Process with Arti
- 40. 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 Tree ROOT S @S NP DT The NN man VP VBZ walks NP DT the NN dog . Mark Farrell Understanding the Aging Process with Arti
- 42. 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 Facts ROOT S @S NP DT The NN man VP VBZ walks NP DT the NN dog . Mark Farrell Understanding the Aging Process with Arti
- 44. 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 Predicate ROOT S @S NP DT The NN man hpredicate:walki NP DT the NN dog . Mark Farrell Understanding the Aging Process with Arti
- 46. 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 hpredicate:walki NP DT the NN dog . Mark Farrell Understanding the Aging Process with Arti
- 48. 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 hargument:mani hpredicate:walki hargument:dogi . Mark Farrell Understanding the Aging Process with Arti
- 50. 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 hpredicate:walki hargument:mani hargument:dogi Mark Farrell Understanding the Aging Process with Arti
- 52. 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 Arti
- 54. 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 Arti
- 56. Outline 1 About Me 2 Understanding the Aging Process 3 Knowledge Extraction 4 What Next?
- 57. About Me Understanding the Aging Process Knowledge Extraction What Next? What Next? Task Assignees Research Direction Steve Garan Knowledge Extraction Mark Farrell Text Article Retrieval Grace Park, Jeremy Wan Knowledge Visualization Mark Farrell Graphical User Interface Mark Farrell Biomedical Spam Filtering | Automated Reasoning | Mark Farrell Understanding the Aging Process with Arti
- 59. About Me Understanding the Aging Process Knowledge Extraction What Next? Get Involved Contact Me for More Information Email [email protected] Website markfarrell.ca Mark Farrell Understanding the Aging Process with Arti
- 61. Questions?