building knowledge bases compositionally bruce porter, peter clark ken barker, art souther, john...
TRANSCRIPT
Building Knowledge Bases Compositionally
Bruce Porter, Peter Clark
Ken Barker, Art Souther, John Thompson
James Fan, Dan Tecuci, Peter Yeh
Marwan Elrakabawy, Sarah Tierney
Our Approach to RKF• Our goal: SME’s build knowledge bases by simply
instantiating and assembling pre-built components.• Our approach: We build a Component Library
containing representations of domain-specific concepts as well as common: actions, such as Get and Enter states, such as Be-Attached-To entities, such as Barrier and Catalyst property values, such as three microns and rapidAnd we develop computational methods for: combining them and using them to answer questions.
Generic Actions• About 200 actions, in about 20 clusters, based on
linguistic studies and other KB projects• Are these sufficient?
– Yes, based on an analysis of 6 chapters of the Alberts text and the encoding of much of chapter 7
– To test their coverage outside microbiology, we’ll be building dozens of KB’s this semester
– Our Component Evaluation will provide hard data
• Why keep it small?– So the Library will be easy to learn and use– So we can provide rich semantics for each action
Generic States
• A state, such as Be-Attached-To, represents a “temporarily stable” set of properties. It serves to link:– An action that creates the state (i.e. Attach)– An action that ends the state (i.e. Detach)– Those actions that are affected by the state (e.g.
Move)
Generic Entities
• small number of role concepts, defined by their participation in actions or states. Examples: container, sequence, nutrient, portal, portal covering
Generic Relations
• small number (78) of very general relations– Roles, such as agent, object, instrument, location– Properties, such as size, shape, frequency,
direction
• Why keep it small?– So the Library will be easy to learn and use– So we can provide rich semantics for each
relation
An Example:Bacterial RNA Transcription
• main participantsbacterial dna, rna polymerase, rna transcript
• scenario– polymerase makes contact with dna– polymerase moves along dna– polymerase recognizes promoter– polymerase transcribes gene, moving along DNA until it reaches terminator
– transcript detaches from polymerase– polymerase breaks contact with dna
Participants from Pump Priming
• bacterial dna, rna polymerase, rna transcript– in the domain-specific hierarchy
• example– Bacterial-DNA has
location: a Place regions: a Gene (abuts the Promoter region) (abuts the Terminator region) a Promoter a Terminator
etc.
Events in the Process from the “Component Library”
• example: Make-Contact– aka touch, adjoin, meet, contact
Make-Contactdestination
Entity
Entity
Place
object
object
Be-Touching
Move
Move
objectPlace
Place
source
source
destination
destination
object
locationlocation
Bacterial RNA Transcription
Bacterial-DNA RNA-Polymerase
Place
location
Bacterial-RNA-Transcription-Scenario
RNA-Transcript
GenePromoter Terminator
regions
causerobject result
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching
location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
object
destination
regions
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching
location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object
source
destination
path
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object
source
destination
path
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object causer
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object causer result
subevent
Move
object
dest
source
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object causer result
subevent
Move
object
dest
source
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object
location
object
object
Be-Attached-To
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
object
location
object
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
location
object
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
object
Be-Touching location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
location
object
Bacterial RNA Transcription
Make-Contact
Bacterial-DNA RNA-Polymerase
Place
location
location
Move Recognize Transcribe Detach Break-Contact
RNA-Transcript
GenePromoter Terminator
regions
location
object
Summary
• SME assembles a declarative representation from both generic and domain-specific components– SME specifies only the components and the links in the
assembly; most of the complexity within components is kept “under the hood”
• KANAL can “exercise” the declarative representation, verifying completeness and consistency
• KM’s simulator can execute the declarative representation to answer questions