GAFramework is a framework for writing genetic algorithms in Julia. It supports parallelism by calculating crossovers and fitness using Julia's multi-threading capabilities.

Since GAFramework stores the entire state of your genetic algorithm in an object, it allows you to save the entire state to file. It allows you to continue running your GA after you load your state from file or after you stop at a generation. It allows you to change parameters such as crossover/mutation parameters after you stop at a generation and then continue from where you stopped.

GAFramework is replicable with respect to pseudo-randomness. So, if you specify a random number generator, GAFramework will fully replicate your GA run as long as the number of threads used is the same for both runs.

GAFramework also contains a genetic algorithm implementation that
"minimizes" any function `f : R^n -> R`

over a box in a Coordinate
space.

`Pkg.add("GAFramework")`

or `Pkg.clone("https://github.com/vvjn/GAFramework.jl")`

This requires the JLD package.

To create a GA for a specific problem, we need to create concrete
sub-types of the abstract types `GAModel`

and `GACreature`

, and then
create relevant functions for the sub-types.

To demonstrate this, we create a GA for optimizing a function over a box in a
Coordinate space, i.e., a function `f : R^n -> R`

.

First, we import the `GAFramework`

module and import relevant
functions.

```
using GAFramework
import GAFramework: fitness, genauxga, crossover, mutate, selection,
randcreature,printfitness, savecreature
```

Next, we create a sub-type of `GAModel`

, which contains the function
`f`

, the corners of the box (`xmin`

and `xmax`

), and the span of
the box (`xspan`

). It also contains the `clamp`

field: if ```
clamp
= true
```

then we will clamp mutated or crossovered points back into the
box, so that our solutions will be inside the box;
otherwise, our solutions will not be constrained.

```
immutable CoordinateModel{F,T} <: GAModel
f::F
xmin::T
xmax::T
xspan::T # xmax-xmin
clamp::Bool
end
function CoordinateModel(f::F,xmin,xmax,clamp::Bool=true) where {F}
xspan = xmax .- xmin
CoordinateModel{F,typeof(xspan)}(f,xmin,xmax,xspan,clamp)
end
```

Then, we create a sub-type of `GACreature`

, which contains the
"chromosomes" of the creature (`value`

field) and the objective value of the
function (`objvalue`

field). We calculate the objective value when creating a
`CoordinateCreature{T}`

object.

```
immutable CoordinateCreature{T} <: GACreature
value :: T
objvalue :: Float64
end
CoordinateCreature(value::T, model::CoordinateModel{F,T}) where {F,T} =
CoordinateCreature{T}(value, model.f(value))
```

Since we are minimizing the objective value, we set `fitness`

to be
negative of the objective value. Depending on the selection function
used, `fitness(::GACreature)`

might need to be non-negative, be a
probability value, etc. But in general, you would want this function to be
at the very least monotonic with respect to `objvalue`

. A further
note: the bulk of the calculation should be relegated to when the
`CoordinateCreature{T}`

object is created; the `fitness`

function
below, since it will be repeatedly called during selection and
sorting, should be a very fast and simple function such as identity or negation.

```
fitness(x::CoordinateCreature) = -x.objvalue
```

The following creates a randomly generated `CoordinateCreature`

object. It creates a random point drawn with uniform probability
from the box. Note: `aux`

is used to store auxiliary scratch space in
case we want to minimize memory allocations. `aux`

can be created by
overloading the `genauxga(model::CoordinateModel)`

function, which is
used to produce memory-safe (with respect to multi-threading) auxiliary scratch
space. In this example, we do not need any scratch space.

```
randcreature(m::CoordinateModel{F,T}, aux, rng) where {F,T} =
CoordinateCreature(m.xmin .+ m.xspan .* rand(rng,length(m.xspan)), m)
```

The following defines the crossover operator. We define a crossover as
the average of two points (not the greatest crossover operator). Note:
we re-use memory from the `z`

object when creating
the new `CoordinateCreature`

.

```
function crossover(z::CoordinateCreature{T}, x::CoordinateCreature{T},
y::CoordinateCreature{T}, m::CoordinateModel{F,T},
params, curgen, aux, rng) where {F,T}
z.value[:] = 0.5 .* (x.value .+ y.value)
CoordinateCreature(z.value, m)
end
```

The following defines the mutation operator. We draw a vector from a circular normal distribution, scale it by the box, and shift the original point with the drawn vector (again, not the greatest mutation operator). Clamping is optionally done to restrict points to be inside the box.

```
function mutate(x::CoordinateCreature{T}, m::CoordinateModel{F,T},
params, curgen, aux, rng) where {F,T}
if rand(rng) < params[:rate]
x.value .+= 0.01 .* m.xspan .* randn(rng,length(x.value))
if m.clamp
x.value .= clamp.(x.value, m.xmin, m.xmax)
end
CoordinateCreature(x.value, m)
else
x
end
end
```

We use tournament selection as our selection operator.

```
selection(pop::Vector{<:CoordinateCreature}, n::Integer, rng) =
selection(TournamentSelection(2), pop, n, rng)
```

This defines how to print details of our creature in a compressed form.

```
printfitness(curgen::Integer, x::CoordinateCreature) =
println("curgen: $curgen value: $(x.value) obj. value: $(x.objvalue)")
```

This defines how to save our creature to file. `GAFramework`

will save
the best creature to file using this function.

```
savecreature(file_name_prefix::AbstractString, curgen::Integer,
creature::CoordinateCreature, model::CoordinateModel) =
save("$(file_name_prefix)_creature_$(curgen).jld", "creature", creature)
```

That takes care of how to implement our problem using
`GAFramework`

. Now, we define our problem by creating a
`CoordinateModel`

.

For fun, we want to minimize the function `x sin(1/x)`

over the
`[-1,1]`

interval.

```
model = CoordinateModel(x -> x[1]==0 ? 0.0 : x[1] * sin(1/x[1]), [-1.0], [1.0])
```

Or, we want to minimize the function `<x, sin(1/x)>`

in 2D
Euclidean space over the `[-1,1]^2`

rectangle.

```
model = CoordinateModel(x -> any(x.==0) ? 0.0 : dot(x, sin.(1./x)),
[-1.,-1.], [1.,1.])
```

Or, we want to minimize the function `|x - (0.25,0.25,0.5,0.5,0.5)|_1`

in
5-dimensional Euclidean space over the `[-1,1]^5`

box.

```
x0 = [0.25,0.25,0.5,0.5,0.5]
model = CoordinateModel(x -> norm(x-x0,1),
[-1.,-1.,-1.,-1.,-1], # minimum corner
[1.,1.,1.,1.,1]) # maximum corner in box
```

Here, we create the GA state, with population size 1000, maximum
number of generations 100, fraction of elite creatures 0.01, and
mutation rate 0.1, printing the objective value every 10
iterations. The `GAState`

function generates the population and
`state`

contains all data required to start/restart a GA. Each
generation, the GA will create children (using `crossover`

) from
selected (using `selection`

) parents, replace the non-elites in the
current generation with the children (with respect to `fitness`

), and
then mutate everyone in the population (using `mutate`

).

```
state = GAState(model, ngen=100, npop=1000, elite_fraction=0.01,
mutation_params=Dict(:rate=>0.1),
print_fitness_iter=10)
```

This runs the GA and we are done.

```
ga(state)
```

`state.pop[1]`

gives you the creature with the best fitness.

A version of `CoordinateModel`

and `CoordinateCreature`

are included `GAFramework`

. It can be used by executing the statement `using GAFramework.CoordinateGA`

.

After we finish a GA run using `ga(state)`

, if we decide that we
want to continue optimizing for a few more generations, we can do the
following. Here, we change maximum number of generations to 200, and
then restart the GA, continuing on from where the GA stopped earlier.

```
state.ngen = 200
ga(state)
```

Although `GAFramework`

uses pseudo-random numbers for many operations, we
can replicate a GA run using the `baserng`

option and by using only the random number
generators provided by the functions to generate random numbers. Setting `baserng`

to be an
object that is a sub-type of `AbstractRNG`

will percolate it throughout the GA, allowing us to replicate a run. By default, `baserng`

is
set to `Base.GLOBAL_RNG`

.

```
state1 = GAState(model, ngen=100, npop=1000, elite_fraction=0.01,
mutation_params=Dict(:rate=>0.1),
print_fitness_iter=10, baserng=MersenneTwister(12))
best1 = ga(state1)
state2 = GAState(model, ngen=100, npop=1000, elite_fraction=0.01,
mutation_params=Dict(:rate=>0.1),
print_fitness_iter=10, baserng=MersenneTwister(12))
best2 = ga(state2)
println(all([getfield(state1,x) == getfield(state2,x) for x in fieldnames(GAState)]))
# true
println(best1 == best2)
# true
```

We can save the creature to file every 10 iterations using the following.

```
state = GAState(m, ngen=100, npop=1000, elite_fraction=0.01,
mutation_params=Dict(:rate=>0.1), print_fitness_iter=10,
save_creature_iter=10, file_name_prefix="minexp_6000")
```

After we finish a GA run using `ga(state)`

, and we decide that we
want to save the best creature to file afterwards, we can do the following.

```
savecreature("minexp_6000", state.ngen, state.pop[1], model)
```

This save the full GA state to file every 100 iterations using the
following. Note: unfortunately, this doesn't work with
`CoordinateModel{F,T}`

since it contains the function `f::F`

as a field. It should
work for other types that do not contain functions.

```
state = GAState(m, ngen=100, npop=1000, elite_fraction=0.01,
mutation_params=Dict(:rate=>0.1), print_fitness_iter=10,
save_state_iter=100, file_name_prefix="minexp_6000")
```

If something happens during the middle of running `ga(state)`

, we can
reload the state from file from the 100th generation as follows, and
then restart the GA from the saved generation.

```
state = loadgastate("minexp_6000_state_100.jld")
ga(state)
```

We can also directly save the state using the following.

```
savegastate("minexp_6000", state.ngen, state)
```

10/12/2017

10 months ago

17 commits