Towards an automated biological programming tool
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Towards an automated biological programming tool

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University of Ottawa IT Fair Poster Competition, Graduate student scholarship winner, Franck Binard

University of Ottawa IT Fair Poster Competition, Graduate student scholarship winner, Franck Binard

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    Towards an automated biological programming tool Towards an automated biological programming tool Presentation Transcript

    • A GENE MAY HAVE A NON-LOCALIZED EFFECT ON THE A IT IS A CLOSED GENE ENCODES A UNIT OF COMPUTATION. WHOLE GENOTYPE. SOME GENES ARE FUNCTIONS THAT GOALTYPE IS THE TYPE OF THE SOLUTION PROGRAM. FOR EXAMPLE, IF EACH TYPE. THE GENE’S TYPE PROGRAMMING MODULE. GENES HAS A TAKE OTHER GENES OF A SPECIFIC TYPE AS ARGUMENTS. THE PROGRAM THAT NEEDS TO BE EVOLVED RETURNS AN INTEGER AND SOME GENES ARE FUNCTIONS THAT TAKE TYPES AS TAKES TWO ARGUMENTS, AN INTEGER AND A STRING, GOALTYPE WILL SPECIFIES HOW AND WHEN IT CAN BE COMBINED WITH ANOTHER GENE DIRECTION→DIRECTION→ ARGUMENTS. SOME GENES ARE VALUES. “INT -> STRING -> INT” BE (DIRECTION→OBJECT→ACTION)→ACTION TO PRODUCE A MORE COMPLEX STRUCTURE.. X→(OBJECT→X)→X Correct value on test cases | TT X . X→X→X LAB TT X DIRECTION UAB DIRECTION→(DIRECTION→OBJECT→ACTION)→ACTION TT X . X→X→X X→X→X LAB X X →(OBJECT→X)→X UAB x (DIRECTION→OBJECT→ACTION)→ACTION Test cases | LAB X→X UAB X→X→X LAB LAB x LAB X X y X (OBJECT→X)→X X DIRECTION LAB X→X ACTION y Y LAB X x x LAB X Term | z DIRECTION→OBJECT→ACTION Term | X X y y x FA FA X X OBJECT→X OBJECT OBJECT→ACTION) (OBJECT→ACTION)→ACTION y OBJECT→X ACTION DIRECTION→OBJECT→ACTION pheromone THE PRE-EVALUATION EVALUATION FA FA EVALUATION OF THE GENOTYPES ACTION→(OBJECT→ACTION)→ACTION PARSING DIRECTION OBJECT z PROBLEM INDEPENDENT PROBLEM DEPENDENT PROVIDES A WAY TO MEASURE THE FITNESS TA wait x TT X . X→(OBJECT→X)→X pheromone OF THE GENES IN THE GENE POOL. THE BEST DIRECTION ACTION ACTION FA DIRECTION→(TT X . X→(OBJECT→X)→X) GENES TEND TO BE CARRIED BY FITTER DIRECTION OBJECT DIRECTION FA DIRECTION detect x ORGANISMS ACROSS SPECIES. GENES ARE west y move Term values on test cases | food north SELECTED BASED IN PROPORTION TO THE Genotype fitness score | east Genotype | DIRECTION PERFORMANCE OF THE ORGANISMS THAT CARRY (TT X . X→(OBJECT→X)→X)→OBJECT→(TTY.Y→Y→Y) DIRECTION→(TT X . X→(OBJECT→X)→X) DIRECTION → ACTION move (TT X . X→(OBJECT→X)→X)→DIRECTION→DIRECTION→ACTION THEM. detect LAB DIRECTION→DIRECTION→ACTION RAW FITNESS SCORING POPULATION contains LAB DIRECTION→ACTION x DIRECTION → ACTION TT X . X→(OBJECT→X)→X LAB Y TT X . X→(OBJECT→X)→X ACTION DIRECTION z DIRECTION FA ACTION DIRECTION→(TT X . X→(OBJECT→X)→X) FA ACTION FA DIRECTION ACTION→ACTION DIRECTION move ACTION→ACTION→ACTION z FA FA detect GENOTYPES north DIRECTION → ACTION ARE SCORED IN PROPORTION DIRECTION TTY.Y→Y→Y ACTION DIRECTION → ACTION TA 1 TO THEIR ABILITY TO SOLVE A PARTICULAR FA ACTION OBJECT→(TTY.Y→Y→Y) FA DIRECTION PROBLEM move y west food move MaxComp (TT X . X→(OBJECT→X)→X)→OBJECT→(TTY.Y→Y→Y) FA DIRECTION → ACTION OBJECT 0 0.95 1.59 3.18 contains (DIRECTION→TT X . X→X→X)→ x DIRECTION→(DIRECTION→ACTION)→ACTION (OBJECT→DIRECTION)→DIRECTION TT X . X→(OBJECT→X)→X ONCE ALL THE ORGANISMS IN THE SYSTEM HAVE LAB DIRECTION→(TT X . X→X→X) 2 DIRECTION→(DIRECTION→ACTION)→ACTION LAB x FA (DIRECTION→ACTION)→ACTION BEEN ASSIGNED A FITNESS VALUE, GENES CAN DIRECTION→(OBJECT→DIRECTION)→DIRECTION Y LAB DIRECTION DIRECTION BE GRADED AS WELL. A GENE’S FITNESS IS THE ACTION ALL GENOTYPES ARE KILLED z DIRECTION → ACTION FA TA TT X . X→(OBJECT→X)→X ACTION east AND A SELECTION ACTION→ACTION AVERAGE OF THE FITNESSES OF THE ORGANISMS FA DIRECTION OPERATION IS ACTIVATED FA z ACTION→ACTION→ACTION y DIRECTION IN WHICH IT FINDS ITSELF. DIRECTION→(TT X . X→(OBJECT→X)→X) DIRECTION → ACTION ON BOTH THE GENE POOL FA TA TTY.Y→Y→Y wait DIRECTION AND THE SPECIES IN THE ACTION FA detect ACTION north DIRECTION→(TT X . X→X→X) ECOSYSTEM x NEW y GENES ARE CONSTRUCTED BUILT DIRECTION AS MUTATIONS OF EXISTING GENES 4 SelComp 0 0.6 1 2.01 THE LANGUAGE THAT IS USED TO ENCODE THE GENES IS CALLED THE NEXT STEP IS TO ASSIGN A SYSTEM F FITNESS VALUE TO THE SPECIES 3 LAB UAB THE ECOSYSTEM EACH IS A SET OF GENOTYPES. GENOTYPE BELONGS TO A SPECIES. EACH GENOTYPE IN THE ECOSYSTEM CAN BE READ AS A COMPLETE PROGRAM THAT x GOALTYPE. EVALUATES TO A VALUE OF TYPE TA FA GENES THE x ARE STORED IN A GENE POOL. GENE POOL wait CONTAINS ONE COPY OF EACH GENE. WITHIN THE GENE POOL, GENES ARE CATEGORIZED BY TYPES. EACH GENE IN ITS CATEGORY IS GIVEN A UNIQUE TTX.X → (ACTION → X)→ X ACTION ID WHICH WILL BE USED AS POINTER BY THE CARRIER Gene Gene ORGANISMS. ID ID ORGANISMS THE ARE ARRANGEMENTS OF SPECIFIC GENES. ARRANGEMENT IS SPECIFIED BY THE PROOF ASSOCIATED WITH THE Gene Gene ID ID SPECIES TO WHICH THE ORGANISM BELONGS, SO EACH ORGANISM IN A GIVEN SPECIES IS BUILT BASED ON THE SAME PATTERN. WITHIN A OBJECT Gene SPECIES HOWEVER, EACH ORGANISM IS UNIQUE BECAUSE IT IS ID COMPOSED OF A UNIQUE SET OF GENES. Gene Gene ID ID Gene ID DIRECTION DIRECTION → ACTION Gene ID Gene ID Gene ID ACTION TTX.X→ X→ X Gene ID Gene ID Gene ID Gene ID Gene ACTION ID Gene ID ACTION DIRECTION→ACTION DIRECTION Gene ID (DIRECTION→DIRECTION→ACTION)→DIRECTION→ACTION DIRECTION→DIRECTION→ACTION DIRECTION→DIRECTION DIRECTION (OBJECT→ACTION)→ACTION OBJECT→ACTION MaxComp DIRECTION→DIRECTION→DIRECTION DIRECTION 0 0.95 1.59 3.18 ACTION→(OBJECT→ACTION)→ACTION ACTION TT X.X→X→X DIRECTION This is the total AN complexity of The ABSTRACTION-BASED gene pool TTX.X→(OBJECT→X)→X ACTION A SPECIES IS AN ARRANGEMENT OF TYPES. THE CURRY-HOWARD ISOMORPHISM ESTABLISHES A CORRESPONDENCE ACTION GENETIC PROGRAMMING SO A SPECIES IS REALLY A SECOND-ORDER LOGIC GOALTYPE IS ACTION BETWEEN THE TYPE SYSTEM AND SECOND-ORDER LOGIC. DIRECTION→ACTION DIRECTION CONSTRUCTIVE PROOF SYSTEM