Download HPKB Final Briefing - Artificial Intelligence Center

Artificial
Intelligence
Center
Representing DNA Structure and
Using Metaphors & Analogies
Srinivas Narayanan
Vinay K. Chaudhri
September1999
October 2000
Artificial
Intelligence
Center
Hypothesis
 Knowledge is grounded in small number of building
blocks that are extended by composition and analogy
September1999
October 2000
Artificial
Intelligence
Center
Our Work
 Investigate metaphors as an organizational principle
in the knowledge base

Orthogonal to taxonomic organization
 Represent about 20-30 metaphors grounded in
processes and forces
 Use structural invariants as a basis for analogical
inference propagation and validation
September1999
October 2000
Artificial
Intelligence
Center
Contribution to E2E Goals
 A more natural organization for the KB
 Provide some of the building blocks for the core
knowledge
 Be able to use structure mapping in the E2E system
September1999
October 2000
Artificial
Intelligence
Center
Outline
 Representing DNA Structure
 Pump priming
 A first cut representation
 Metaphors used in DNA representation
 Chemical bond and connector
—Holding together
 Sample Questions
 Constructing RNA representation from DNA
 Using Analogy GUI from NWU
September1999
October 2000
Artificial
Intelligence
Center
Outine
September1999
October 2000
Artificial
Intelligence
Center
DNA Structure
 A DNA molecule consists of two long polynucleotide
October 2000
chains composed of four types of nucleotide
subunits.
 The two chains are held together by hydrogen bonds
between the base portions of the nucleotides. As we
saw in Chapter 2, nucleotides are composed of a
five-carbon sugar to which are attached one or more
phosphate group.
 The nucleotides are covalently linked together in a
chain through the sugars and phosphates, which thus
form a backbone of alternating sugar-phosphateSeptember1999
sugar-phosphate.
Artificial
Intelligence
Center
Pump Priming
 Domain-specific concepts that should already be in
the KB







Nucleotide
Chemical Bond
Five Carbon Sugar
Phosphate Group
Covalent Bond
Ribose and Deoxyribose
Chemical Elements: Nitrogen, Hydrogen, etc.
September1999
October 2000
Artificial
Intelligence
Center
Representing Nucleotide
(every Nucleotide has
(parts ((a RingCompound with
((name ((Base)))
(parts ((a Nitrogen with
(linkedTo
((the FiveCarbonSugar parts of Self))))))))
(a FiveCarbonSugar with
(instance-of ((constraint ((:set Ribose Deoxyribose)
includes TheValue)))))
(a PhosphateGroup with
(linkedTo ((the FiveCarbonSugar parts of Self))))
(at-least 1 PhosphateGroup)
(exactly 1 Base)
(exactly 1 FiveCarbonSugar))))
(MELD Translation is available)
October 2000
September1999
Artificial
Intelligence
Center
Technical Issues
 SMEs must be able to specialize by adding additional
constraints

Simply connecting the components does not seem to be
enough
 Possible Solutions
 GKB-style constraint editing
 Use dialogs to elicit constraints
September1999
October 2000
Artificial
Intelligence
Center
Representing DNA Chains
 A DNA chain consists of Nucleotide element each of
which has one of Adenine, Gyanine, Thymine, or
Cytosine as a base
 Ends of the DNA chain have polarity (a 5’ and a 3’
end).
September1999
October 2000
Artificial
Intelligence
Center
Representing DNA Chain
(every DNA-Chain has
((prettyName (("DNA Chain" "DNA Strand")))
(name ((DNA-Chain DNA-Strand)))
(chainEnd ((the1 chainElement of Self with
((name ((threeprimeEnd)))
(parts ((a DeoxyRibose with
(exactly 0 connectedTo))))))
(the last chainElement of Self with
((name ((fiveprimeEnd)))
(parts ((a PhosphateGroup with
(exactly 0 connectedTo))))))))
(chainElement ((must-be-a a Nucleotide with
((constraint ((instance-of (:set Adenine Gyanine Cytosine Thymine)))))
(orientation ((VectorFromToFn FiveMinuteEnd ThreeMinuteEnd))))))
September1999
October 2000
Artificial
Intelligence
Center
Technical Issues
 Need a generic representation component modeling
chains
 Need to state spatial direction
September1999
October 2000
Artificial
Intelligence
Center
Representing DNA Molecule
 A DNA molecule has the shape of a double helix.
 A DNA molecule consists of a pair of DNA chains.
 The Chains are anti-parallel.
 The Chains are held together by chemical bonds
between the complementary bases along each chain.
The complementary bases are A-T and C-G. The
bonds are AT-bond and CG bond.
September1999
October 2000
Artificial
Intelligence
Center
Representing DNA Molecule
(every DNA-Molecule has
((shape ((DoubleHelix)))
(parts ((:seq ((a DNA-Chain with
((chainElement
((a Nucleotide with
((parts ((a Base with
((location ((the interior of Self)))
(heldBy ((a ChemicalBond with
((held ((Self)
(a chainElement of
(the2 DNA-Chain part of Self))))
constraint
((instance-of
(:set AT-Bond GC-Bond))))))))
(exactly 1 heldby)))
……..
September1999
October 2000
Artificial
Intelligence
Center
Technical Issues
 Need representation components for Hold Together.
 Need representation of Bonds.
September1999
October 2000
Artificial
Intelligence
Center
Representing Holds
 Holding objects in place involves the application of a
holding force which maintains the relative position
and orientation of the objects.
 Holding Together is a hold whose holding force is
directed inward (relative to the objects). The
tendency of the objects is to move apart.
 Holding Apart is a hold whose holding force is
directed outward (relative to the objects). The
tendency of the objects is to move toward each other.
September1999
October 2000
Artificial
Intelligence
Center
Representing Hold
(every Hold has
((holdingForce ((a Force with
((experiencer ((the patient of Self)))))))
(patient ((a PartiallyTangible)))
(maintainsInPosition ((the experiencer of Self)))
(pcs-list
((:triple (forall (the held of Self)) location ?loc)
(:triple (forall (the held of Self)) orientation ?orientation)
(:triple (the magnitude of holdingForce) > 0)))))
Issue: How is maintainsInPosition represented?
September1999
October 2000
Variations of Hold
Artificial
Intelligence
Center
(every HoldTogether has
((patient ((:seq
(a PartiallyTangible with
(potentialDirectionOfMotion
((VectorFromToFn (the2 patient of Self) (the1 patient of Self)))))
(a PartiallyTangible with
(potentialDirectionOfMotion
((VectorFromToFn (the1 patient of Self) (the2 patient of Self)))))))
(holdingForce ((a Force with
(composedOf
((a Force with
((direction ((VectorFromToFn
(the1 patient of Self) (the2 patient of Self))))
(experiencer (the1 patient of Self))))
(a Force with
((direction ((VectorFromToFn
(the2 patient of Self) (the1 patient Of Self))))
……….
OTHER VARIATIONS: HOLD APART, HOLD AT A DISTANCE, HOLD IN
September1999
October 2000
Technical Issues
Artificial
Intelligence
Center
Need a general structure that captures more
complicated force interactions and processes.
September1999
October 2000
Artificial
Intelligence
Center
Chemical Bonds as Connectors
Instance of the General Metaphor Mapping
Forces => Force-bearing Objects
Chemical Bonds are broken, created, fragile,
weak, destroyed, etc.
(every Connector has
(primaryFunction ((HoldTogether)))
(ChemicalBond has
((construedAs ((Connector)))))
September1999
October 2000
Artificial
Intelligence
Center
Representing Metaphors
in the Knowledge Base
(every DomainMap has
((source ((a Thing)))
(target ((a Thing)))))
(*ConnectorBondMap with
(source ((a Connector)))
(target ((a ChemicalBond with
((primaryFunction ((the primaryFunction of Self))))
September1999
October 2000
Artificial
Intelligence
Center
Sample Questions
 The nucleotide sequence of one DNA strand of a
DNA double helix is 5’-GGATTTTCCCAAGG-3’.
What is the sequence of the other strand?


Follows from the structure of DNA and the definition of AT
and CG bonds
Need to figure out if KM inference engine will do this
inference
September1999
October 2000
Artificial
Intelligence
Center
Sample Questions
 Which of the following DNAs would melt first?




5’-GCGGGGCCAGCCT-3’
3’-CGCCCCGGTCGGA-5’
5’-AAATTTTAAAAGAAA-3’
3’-TTTAAAATTTTCTTT-5’
 Involves use of problem solving knowledge
 Need to represent qualitative relations
September1999
October 2000
Artificial
Intelligence
Center
Outline
 Representing DNA Structure
 Pump priming
 A first cut representation
 Metaphors used in DNA representation
 Chemical bond and connector
—Holding together
 Sample Questions
 Constructing RNA representation from DNA
 Using Analogy GUI from NWU
September1999
October 2000
INITIAL SCREEN
Artificial
Intelligence
Center
OLD CASE
Base Case
Domain
Original Individuals
Original Statements
Correspondences
NEW CASE
Target Case
Domain
New Individuals
New Statements
Candidate Inferences
New
Delete
Accept
October 2000
September1999
BASE LOADED
Artificial
Intelligence
Center
NEW CASE
OLD CASE
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
Domain
New Individuals
[1] DNA
[2] AT- Bond
[3] CG-Bond
[4] DNA-Chain
[5] Phosphodigester Linkage
#
Original Statements
New Statements
[7] DNA HAS SHAPE Double Helix
[9] DNA HAS PART DNA-Chain
[19] DNA-Chain HAS PART Nucleotide
[21] Nucleotide HAS PART Deoxyribpse
Correspondences
Candidate Inferences
New
Delete
Accept
October 2000
September1999
TARGET WITH INDIVIDUALS
Artificial
Intelligence
Center
NEW CASE
OLD CASE
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
New Individuals
[1] DNA
#
[66]
RNA
[2] AT- Bond
[67]
AU- Bond
[3] CG-Bond
[69]
CG- Bond
[4] DNA-Chain
[70]
RNA-Chain
[5] Phosphodigester Linkage
[74]
Phosphodigester Linkage
#
Original Statements
#
Cell
New Statements
[7] DNA HAS SHAPE Double Helix
[9] DNA HAS PART DNA-Chain
[19] DNA-Chain HAS PART Nucleotide
[21] Nucleotide HAS PART Deoxyribpse
Correspondences
New
Candidate Inferences
#N Original Individual
#N New Individual
Delete
Accept
October 2000
September1999
ADDING TARGET ISA STATEMENTS
Artificial
Intelligence
Center
NEW CASE
OLD CASE
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
New Individuals
[1] DNA
#
[66]
RNA
[2] AT- Bond
[67]
AU- Bond
[3] CG-Bond
[69]
CG- Bond
[4] DNA-Chain
[70]
RNA-Chain
[5] Phosphodigester Linkage
[74]
Phosphodigester Linkage
#
Original Statements
#
Cell
New Statements
[7] DNA HAS SHAPE Double Helix
[33] RNA ISA Chemical Compound
[9] DNA HAS PART DNA-Chain
[34] RNA-Chain ISA Chain
[19] DNA-Chain HAS PART Nucleotide
[21] Nucleotide HAS PART Deoxyribpse
Correspondences
New
Candidate Inferences
#N Original Individual
#N New Individual
Delete
Accept
October 2000
September1999
SUGGESTING CORRESPONDENCES
Artificial
Intelligence
Center
NEW CASE
OLD CASE
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
New Individuals
[1]
DNA
#
[66]
[2]
AT- Bond
[67]
AU- Bond
[3]
CG-Bond
[69]
CG- Bond
[4]
DNA-Chain
[70]
RNA-Chain
[5]
Phosphodigester Linkage
[74]
Phosphodigester Linkage
#
Original Statements
#
Cell
RNA
New Statements
[7] DNA HAS SHAPE Double Helix
[33] RNA ISA Chemical Compound
[9] DNA HAS PART DNA-Chain
[34] RNA-Chain ISA Chain
[19] DNA-Chain HAS PART Nucleotide
[21] Nucleotide HAS PART Deoxyribpse
Correspondences
New
Delete
Accept
October 2000
Candidate Inferences
#N Original Individual
[1] DNA
#N New Individual
[66] RNA
September1999
RESULTS OF INITIAL MATCHING
Artificial
Intelligence
Center
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
[1]
DNA
[2]
AT- Bond
[67]
AU- Bond
[3]
CG-Bond
[69]
CG- Bond
[4]
DNA-Chain
[70]
RNA-Chain
[5]
Phosphodigester Linkage
[74]
Phosphodigester Linkage
Original Statements
#
Cell
New Individuals
#
[66]
#
RNA
New Statements
[7] DNA HAS SHAPE Double Helix
[78] RNA HAS PART RNA-Chain
[9] DNA HAS PART DNA-Chain
[82] RNA -Chain HAS PART Nucleotide
[19] DNA-Chain HAS PART Nucleotide
[57] Nucleotide HAS PART Deoxyribose
[21] Nucleotide HAS PART Deoxyribpse
[48] RNA HAS SHAPE Double Helix
Correspondences
New
Delete
Accept
October 2000
NEW CASE
OLD CASE
Candidate Inferences
#N Original Individual
[1] DNA
[2] AT-Bond
[3] CG-Bond
[4] DNA-Chain
#N New Individual
[66] RNA
[67] AU-Bond
[69] CG-Bond
[70] RNA-Chain
September1999
DELETING CORRESPONDENCES
Artificial
Intelligence
Center
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
[1]
DNA
[2]
AT- Bond
[67]
AU- Bond
[3]
CG-Bond
[69]
CG- Bond
[4]
DNA-Chain
[70]
RNA-Chain
[5]
Phosphodigester Linkage
[74]
Phosphodigester Linkage
Original Statements
#
Cell
New Individuals
#
[66]
#
RNA
New Statements
[7] DNA HAS SHAPE Double Helix
[78] RNA HAS PART RNA-Chain
[9] DNA HAS PART DNA-Chain
[82] RNA-Chain HAS PART Nucleotide
[19] DNA-Chain HAS PART D-Nucleotide
[57] Nucleotide HAS PART Deoxyribose
[21] Nucleotide HAS PART Deoxyribpse
[48] RNA HAS SHAPE Double Helix
Correspondences
New
Delete
Accept
October 2000
NEW CASE
OLD CASE
Candidate Inferences
#N Original Individual
[1] DNA
[2] AT-Bond
[3] CG-Bond
[4] DNA-Chain
#N New Individual
[66] RNA
[67] AU-Bond
[69] CG-Bond
[70] RNA-Chain
September1999
ADDING TARGET KNOWLEDGE
Artificial
Intelligence
Center
DNA
Base Case
Domain
#
Original Individuals
Cell
Target Case
RNA
Domain
[1]
DNA
[2]
AT- Bond
[67]
AU- Bond
[3]
CG-Bond
[69]
CG- Bond
[4]
DNA-Chain
[70]
RNA-Chain
[5]
Phosphodigester Linkage
[74]
Phosphodigester Linkage
Original Statements
#
Cell
New Individuals
#
[66]
#
RNA
New Statements
[7] DNA HAS SHAPE Double Helix
[78] RNA HAS PART RNA-Chain
[9] DNA HAS PART DNA-Chain
[82] RNA-Chain HAS PART Nucleotide
[19] DNA-Chain HAS PART D-Nucleotide
[99] RNA-Chain HAS SHAPE Chain
[21] Nucleotide HAS PART Deoxyribpse
[101]R-Nucleotide HAS PART Ribose
Correspondences
New
Delete
Accept
October 2000
NEW CASE
OLD CASE
Candidate Inferences
#N Original Individual
[1] DNA
[3] CG-Bond
[4] DNA-Chain
#N New Individual
[66] RNA
[69] CG-Bond
[70] RNA-Chain
September1999
Conclusion
Artificial
Intelligence
Center
Representing the structure of DNA draws
building blocks from space, force dynamics
and event structure metaphors.
RNA structure can be specified using a
within-domain analogy with DNA.
We have a design and are working on an
implementation of the relevant concepts.
September1999
October 2000