september1999 october 2000 artificialintelligencecenter representing dna structure and using...

September1999October 2000October 2000

ArtificialArtificialIntelligenceIntelligence

CenterCenter

Representing DNA Structure andUsing Metaphors & Analogies

Srinivas Narayanan

Vinay K. Chaudhri



CenterCenter Hypothesis

Knowledge is grounded in small number of building blocks that are extended by composition and analogy



CenterCenter 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



CenterCenter 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



CenterCenter 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



CenterCenter Outine



CenterCenter DNA Structure

A DNA molecule consists of two long polynucleotide 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-phosphate-sugar-phosphate.



CenterCenter 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.



CenterCenter 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)



CenterCenter 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



CenterCenter 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).



CenterCenter 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))))))




Need a generic representation component modeling chains

Need to state spatial direction



CenterCenter 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.



CenterCenter 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))) ……..




Need representation components for Hold Together. Need representation of Bonds.



CenterCenter 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.



CenterCenter 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?



CenterCenter

Variations of Hold(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



CenterCenter

Technical Issues

Need a general structure that captures more complicated force interactions and processes.



CenterCenter

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)))))



CenterCenter

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))))



CenterCenter 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



CenterCenter 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



CenterCenter 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



CenterCenter

INITIAL SCREEN

Base Case Domain Target Case Domain

Original Individuals New Individuals

Original Statements New Statements

Correspondences Candidate Inferences

OLD CASE NEW CASE

New

Delete

Accept



CenterCenter

BASE LOADED





DNA Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond

DNA HAS PART DNA-Chain

Phosphodigester Linkage

[7]

[9]

[19]

[21]

#

DNA-Chain

DNA HAS SHAPE Double Helix

DNA-Chain HAS PART Nucleotide

Nucleotide HAS PART Deoxyribpse



CenterCenter

TARGET WITH INDIVIDUALS





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain




#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA

#N Original Individual #N New Individual



CenterCenter

ADDING TARGET ISA STATEMENTS





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain




#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA


[33] RNA ISA Chemical Compound

RNA-Chain ISA Chain[34]



CenterCenter

SUGGESTING CORRESPONDENCES





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain




#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA

#N Original Individual #N New Individual[1] DNA [66] RNA

[33] RNA ISA Chemical Compound

RNA-Chain ISA Chain[34]



CenterCenter

RESULTS OF INITIAL MATCHING





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain




#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA


[78]

[82]

RNA HAS PART RNA-Chain

RNA -Chain HAS PART Nucleotide

[1] DNA [66] RNA[2] AT-Bond [67] AU-Bond[3] CG-Bond [69] CG-Bond[4] DNA-Chain [70] RNA-Chain

Nucleotide HAS PART Deoxyribose[57]

RNA HAS SHAPE Double Helix[48]



CenterCenter

DELETING CORRESPONDENCES





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain


DNA-Chain HAS PART D-Nucleotide


#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA


[78]

[82]


RNA-Chain HAS PART Nucleotide

[1] DNA [66] RNA[2] AT-Bond [67] AU-Bond[3] CG-Bond [69] CG-Bond[4] DNA-Chain [70] RNA-Chain

Nucleotide HAS PART Deoxyribose[57]

RNA HAS SHAPE Double Helix[48]



CenterCenter

ADDING TARGET KNOWLEDGE





DNA Cell Cell

OLD CASE NEW CASE

New

Delete

Accept

[1]

[2]

[4]

[3]

[5]

#

DNA

AT- Bond

CG-Bond



[7]

[9]

[19]

[21]

#

DNA-Chain


DNA-Chain HAS PART D-Nucleotide


#

#

[66]

[67]

[69]

[70]

[74]

RNA

CG- Bond

AU- Bond

RNA-Chain


RNA


[78]

[82]


RNA-Chain HAS PART Nucleotide

[1] DNA [66] RNA[3] CG-Bond [69] CG-Bond[4] DNA-Chain [70] RNA-Chain

RNA-Chain HAS SHAPE Chain[99]

[101]R-Nucleotide HAS PART Ribose



CenterCenter

Conclusion

Representing the structure of DNA draws building blocks from space, force dynamicsand event structure metaphors.

RNA structure can be specified using a within-domain analogy with DNA.

We have a design and are working on animplementation of the relevant concepts.

september1999 october 2000 artificialintelligencecenter representing dna structure and using...

Documents