Genetic Programming

SS: The "next step" of Genetic Algorithms is Genetic Programming. Instead to evolve the input of a program you directy evolve the program itself! This is a little genetic programming framework for Tcl, based on a stack based virtual machine where every program is valid. I had no time to hack more on this, so it's probably better to just post it as a starting point for others interested in this subject.

Currently there is an "experiment" already configured that search the best function to square a number. It will reach "dup *" after some iteration. Please if you have specific questions about the code write them at the bottom of this page.

Example output:

 BEST: 'peek' with fitness 41
 BEST: 'peek' with fitness 41
 BEST: 'peek' with fitness 41
 BEST: 'peek' with fitness 41
 BEST: 'peek' with fitness 41
 BEST: '{const 9}' with fitness 37
 BEST: '{const 9}' with fitness 37
 BEST: '{const 9}' with fitness 37
 BEST: '{const 9}' with fitness 37
 BEST: 'mod dup *' with fitness 3
 BEST: 'mod dup *' with fitness 3
 BEST: 'mod dup *' with fitness 3
 BEST: 'dup *' with fitness 2

This is the code:

 # Genetic programming in Tcl, using a stack based approach.
 # Copyright (C) 2004 Salvatore Sanfilippo <[email protected]>
 # This code is released under the BSD license.
 
 ################################################################################
 # Virtual Machine
 ################################################################################
 
 # Define a simple stack virtual machine.
 # It's as simple as possible, and there is no program that will
 # cause an error. Every program composed of valid words is valid.
 
 # The following is a list populated by the [instr] procedure.
 set ::instructions {}
 
 # Define a new instruction for the VM
 proc instr {name arglist body} {
     lappend ::instructions $name
     proc $name $arglist $body
 }
 
 # Prepare the VM state for the execution of a new program
 proc init stackval {
     set ::stack $stackval ;# The VM stack
     set ::ip -1 ;# The VM istruction pointer
 }
 
 # Push and pop from the VM stack.
 proc push element {
     lappend ::stack $element
 }
 
 proc pop {} {
     set element [lindex $::stack end]
     set ::stack [lrange [lindex [list $::stack [unset ::stack]] 0] 0 end-1]
     return $element
 }
 
 # Check if the stack length is at least 'n', otherwise
 # force the caller procedure to return.
 proc needlen n {
     if {[llength $::stack] < $n} {
         return -code return
     }
 }
 
 # VM instructions
 instr + {} {
     needlen 2
     push [expr {[pop]+[pop]}]
 }
 
 instr - {} {
     needlen 2
     push [expr {[pop]-[pop]}]
 }
 
 instr * {} {
     needlen 2
     push [expr {[pop]*[pop]}]
 }
 
 proc divmod op {
     needlen 2
     set a [pop]
     set b [pop]
     if {!$b} {
         push $b
         push $a
         return
     }
     push [expr "$a $op $b"]
 }
 
 instr / {} {divmod /}
 instr mod {} {divmod %}
 
 instr dup {} {
     needlen 1
     set a [pop]
     push $a
     push $a
 }
 
 instr dup2 {} {
     needlen 2
     set a [pop]
     set b [pop]
     push $b
     push $a
     push $b
     push $a
 }
 
 instr swap {} {
     needlen 2
     set a [pop]
     set b [pop]
     push $a
     push $b
 }
 
 instr drop {} {
     needlen 1
     pop
 }
 
 instr rot {} {
     needlen 3
     set c [pop]
     set b [pop]
     set a [pop]
     push $c
     push $a
     push $b
 }
 
 instr peek {} {
     needlen 2
     push [lindex $::stack end-1]
 }
 
 instr > {} {
     needlen 2
     push [expr {[pop]>[pop]}]
 }
 
 instr < {} {
     needlen 2
     push [expr {[pop]<[pop]}]
 }
 
 instr == {} {
     needlen 2
     push [expr {[pop]==[pop]}]
 }
 
 instr jz {{n {-10 10}}} {
     needlen 1
     if {[pop] == 0} {
         incr ::ip $n
         if {$::ip < -1} {
             set ::ip -1
         }
     }
 }
 
 instr jnz {{n {-10 10}}} {
     needlen 1
     if {[pop] != 0} {
         incr ::ip $n
         if {$::ip < -1} {
             set ::ip -1
         }
     }
 }
 
 # Nop istruction is important to kill some istruction by mutation.
 instr nop {} {
 }
 
 # Return if zero
 instr retz {} {
     needlen 1
     if {[pop] == 0} {
         set ::ip 100000
     }
 }
 
 # Return if nonzero
 instr retnz {} {
     needlen 1
     if {[pop] != 0} {
         set ::ip 100000
     }
 }
 
 # Reiterate the program if zero
 instr againifz {} {
     needlen 1
     if {[pop] == 0} {
         set ::ip -1
     }
 }
 
 # non-zero version
 instr againifnz {} {
     needlen 1
     if {[pop] != 0} {
         set ::ip -1
     }
 }
 
 # Not
 instr not {} {
     needlen 1
     push [expr {![pop]}]
 }
 
 instr const {{n {-10 10}}} {
     push $n
 }
 
 # Run the program
 proc run {prg stack {maxinstr 100}} {
     init $stack
     set instrcount 0 ; # Counter used to limit the total program run time.
     while 1 {
         incr ::ip
         set instr [lindex $prg $::ip]
         if {$instr eq {}} break
         if {[llength $instr] == 1} {
             $instr
         } else {
             [lindex $instr 0] [lindex $instr 1]
         }
         incr instrcount
         if {$instrcount > $maxinstr} break
     }
     return $::stack
 }
 
 ################################################################################
 # The evolution engine
 ################################################################################
 
 # Generate a random integer in the min-max (both included) interval.
 proc rand {min max} {
     expr {$min+int(rand()*(($max-$min)+1))}
 }
 
 # Returns a random element from the list
 proc lrand list {
     lindex $list [expr {int(rand()*[llength $list])}]
 }
 
 # Returns a random instruction
 proc randinstr {} {
     set instr [lrand $::instructions]
     set arglist [info args $instr]
     if {$arglist eq {}} {
         return $instr
     } else {
         info default $instr [lindex $arglist 0] l
         foreach {min max} $l break
         return [list $instr [rand $min $max]]
     }
 }
 
 # Create a random program of length 'n'
 proc randprog n {
     while {[incr n -1] >= 0} {
         lappend prg [randinstr]
     }
     return $prg
 }
 
 # Create an initial population of programs
 # of the specified number of individuals with length in
 # the specified range.
 proc randpopulation {n minlen maxlen} {
     while {[incr n -1] >= 0} {
         lappend result [randprog [rand $minlen $maxlen]]
     }
     return $result
 }
 
 # Two points crossover. This is used to create two offsprings
 # from two programs. An example about how it works:
 #
 # Given two programs: {A B C D E F} and {1 2 3 4 5 6 7 8 9}
 # We identify two random points in both the programs:
 #
 # {A B C D E F}
 #    ^   ^
 #
 # {1 2 3 4 5 6 7 8 9}
 #  ^         ^
 #
 # The two offsprings are created using the external part of
 # the first and the internal part of the second, and vice versa,
 # So the first offspring will be:
 #
 # {A 1 2 3 4 5 6 E F}
 #
 # And the second
 #
 # {B C D 7 8 9}
 #
 # The input programs are 'a' and 'b', the two crossovers are
 # returnes as a two elements list.
 proc crossover {a b} {
     # Get the four crossover points
     set a0 [rand 0 [expr {[llength $a]-1}]]
     set a1 [rand 0 [expr {[llength $a]-1}]]
     set b0 [rand 0 [expr {[llength $b]-1}]]
     set b1 [rand 0 [expr {[llength $b]-1}]]
     # Swap the two points if needed to be sure a0>=a1 and b0>=b1
     if {$a0 > $a1} {set t $a0; set a0 $a1; set a1 $t}
     if {$b0 > $b1} {set t $b0; set b0 $b1; set b1 $t}
     # Get the left/center/right part of every program
     set aleft [lrange $a 0 [expr {$a0-1}]]
     set acenter [lrange $a $a0 $a1]
     set aright [lrange $a [expr {$a1+1}] end]
     set bleft [lrange $b 0 [expr {$b0-1}]]
     set bcenter [lrange $b $b0 $b1]
     set bright [lrange $b [expr {$b1+1}] end]
     # Now create the crossovers by mean of list contatenation
     set x0 [concat $aleft $bcenter $aright]
     set x1 [concat $bleft $acenter $bright]
     list $x0 $x1
 }
 
 # Given a program returns a mutated one where every istruction
 # of the original program will be substituted (or a new one
 # inserted just after it) with the specified probability '$p'.
 proc mutate {program prob} {
     for {set i 0} {$i < [llength $program]} {incr i} {
         if {[expr {rand()}] <= $prob} {
             lset program $i [randinstr]
         }
         if {[expr {rand()}] <= $prob} {
             set program [linsert $program $i [randinstr]]
         }
     }
     return $program
 }
 
 # The core of the GP engine.
 # Creates a random population of the specified size, and starts
 # the evolution process rating every program using the 'fitness function'
 # specified. At every itearation 1/3 of the population having the
 # best fitness is used to create another 1/3 of the population
 # by offsprings, and another 1/3 by simple mutation of the original
 # programs. The evolution is then reiterated.
 #
 # The fitness function should return an integer representing the
 # amount of error in the computation done by the program.
 # It takes as input an individual. Usually the fitness function
 # will use the "run" procedure to execute the script with a
 # significant input stack and will rate the program observing the
 # output.
 #
 # At every iteration, the individual with best fitness is printed
 # on the screen.
 #
 # Parameters specification:
 #
 # individuals: The number of individuals in the whole population.
 #              This number is approximated to a multiple of 3.
 # len:         Max length of individuals of the initial population.
 # fitnessfunc: The fitness function (a Tcl procedure name).
 # mutprob:     Mutation probability used for the 'mutate' procedure.
 proc evolve {individuals len fitnessfunc mutprob} {
     set population [randpopulation $individuals 1 $len]
     while 1 {
         # Run every program, and populate a list with it and its fitness.
         set res {}
         foreach prg $population {
             set fitness [$fitnessfunc $prg]
             lappend res [list $fitness $prg]
         }
         # Sort the individuals by fitness (low fitness == better)
         set sorted [lsort -integer -index 0 $res]
         # Get the lead population
         set l [expr {[llength $sorted]/3}]
         set leaders [lrange $sorted 0 [expr {$l-1}]]
         # Generate another 1/3 of population by offsprings of random leaders.
         set offsprings {}
         while 1 {
             set x [rand 0 [expr {[llength $leaders]-1}]]
             set parent0 [lindex $leaders $x 1]
             set x [rand 0 [expr {[llength $leaders]-1}]]
             set parent1 [lindex $leaders $x 1]
             foreach {offspring0 offspring1} [crossover $parent0 $parent1] break
             lappend offsprings $offspring0
             if {[llength $offsprings] == $l} break
             lappend offsprings $offspring1
             if {[llength $offsprings] == $l} break
         }
         set mutated {}
         # Generate the last 1/3 of population mutating the leaders.
         foreach leader $leaders {
             lappend mutated [mutate [lindex $leader 1] $mutprob]
         }
         # Glue the three populations (leaders, offsprings, mutated) to
         # create the population for the next iteration.
         set new {}
         foreach leader $leaders {
             lappend new [lindex $leader 1]
         }
         set population [concat $new $offsprings $mutated]
         # Print the best individual in this iteration:
         puts "BEST: '[lindex $leaders 0 1]' with fitness [lindex $leaders 0 0]"
         # Print the population
         #puts $population
         if 0 {
             foreach p $population {
                 puts $p
             }
         }
     }
 }
 
 ################################################################################
 # Usage example. Evolve a program that computes the square of a number
 # The best program is "DUP *".
 ################################################################################
 
 # Calculate the fitness.
 # Best fitness is 2 (no errors with all the inputs, program len == 2).
 proc squareFitness prg {
     set fitness 0
     foreach i {1 2 3 4 5} o {1 4 9 16 25} {
         set stack [run $prg $i]
         set result [lindex $stack end]
         if {$result eq {}} {
             incr fitness 50
         } else {
             set delta [expr {abs($o-$result)}]
             if {$delta > 1000} {
                 # anti overflow
                 set delta 1000
             }
             incr fitness $delta
         }
     }
     return [expr {$fitness+[llength $prg]}]
 }
 
 # Uncomment the following to run this example
 evolve 90 5 squareFitness 0.1

See also Brute force meets Goedel


Harm Olthof: This is not what is generally considered with the phrase Genetic Programming (GP) In GP you have a tree: each node is a function or a terminal (constant) The parameters of the function are the branches of the subtrees, which is a function or a terminal. You start with the root and work your way through the branches, resulting in one nested call to the main function in the root. Take a population of trees and in the evolutionary cycle exchange subbranches between the trees. Trees with higher fitness have higher change to exchange their subbranches with other trees. see [2 ]. This is not exacty the same as Genetic Algorithms: see eg. Una-May O'Reilly thesis. ([1 ])


Note that the tree is just an implementation detail. To use the tree or the stack is the same, and actually there is quite a lot of literature about stack-based GP. See for example [3 ]. Both with the tree or the stack-based approach programs are mixed together, and resulting programs are always valid. With the stack-based approach GP is more directly related to GA because the program looks a lot like random "data".


AM (6 april 2005) Some musings:

  • How to randomly select floating-point numbers - the problem is that very small and very large values may be necessary - you need to come up with a decent distribution...
  • Converting a stack-based program into a nice little mathematical formula may not be trivial
  • A nice little exercise: let the script come up with a solution for squaring a number without *
  • I wonder what happens if the cost (fitness is not very intuitive a word here) does not depend on the size ...