How to Execute an Exploration Task

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Overview πŸ”—

In this tutorial, you will learn how to prepare and run an experiment, in order to explore a simple model. The toy model is Ants.nlogo, since we already know how to import and run it from the previous tutorial.

The simplest numerical experiments that can be done with such a stochastic model are:
  • run the model several times with the same parameter values to understand the statistics of its behavior,
  • run the model with different parameter values to have a glimpse of their influence on the model's behavior.
We will cover both in this tutorial.

Replicating the Ants model πŸ”—

A stochastic model ran several times with the same parameter set will give different outputs. It is the case of the Ants model we used in the previous tutorial. In order to repeat easily a model execution and concatenate the results, OpenMOLE provides the Replication task.

Workflow πŸ”—

As the model has a random seed parameter named mySeed, it can be passed to the Replication task as an argument. The task will then attribute seeds itself to each model run (necessary for exact reproducibility).
Warning: The default value for mySeed must be removed from the model task, otherwise it will overwrite the seeds generated by the Replication task.

// Input values
val mySeed = Val[Int]
val diffusionRate = Val[Int]
val evaporationRate = Val[Int]
val population = Val[Int]

// Output values
val countFood = Val[Double]
val finalTicksFood1 = Val[Double]
val finalTicksFood2 = Val[Double]
val finalTicksFood3 = Val[Double]

// NetLogo commands list
val launch = List(
    "setup",
    "go ;;You should set your stopping criteria here instead"
)

// NetLogo task
val antsTask = NetLogo6Task(
    workDirectory / "ants.nlogo", // netlogo file
    launch,                       // launching commands
    seed = mySeed                 // set the random seed
) set (
    inputs += diffusionRate mapped "diffusion-rate",
    inputs += evaporationRate mapped "evaporation-rate",
    inputs += population mapped "population",

    outputs += countFood mapped "count-food",
    outputs += finalTicksFood1 mapped "final-ticks-food1",
    outputs += finalTicksFood2 mapped "final-ticks-food2",
    outputs += finalTicksFood3 mapped "final-ticks-food3",

    // Default values. Can be removed if OpenMOLEΒ Vals are set by values coming from the workflow
    diffusionRate := 21,
    evaporationRate := 9,
    population := 125
)

// Define the replication task
val replications = Replication(
    evaluation = antsTask, // the model to run
    seed = mySeed,         // the seed variable
    sample = 100           // the number of model executions
)

// Workflow
// Note: here we use a hook which gathers all the outputs of the replication and writes them into a csv file
replications hook (workDirectory / "replications_results.csv")

You can run this workflow by clicking on the Run button in the GUI.

Results πŸ”—

Once the execution is over, refresh your workspace by clicking on the second-to-last icon on the left of the GUI (circle with two arrows). A new file will appear named replications_results.csv, this is the file that our workflow created, containing the replication results! You can click on it.


You won't have the same numbers as above, since the random seed won't be the same. However, you should have the same column names and 100 lines of results: one for each model execution.

Exploring the parameter space πŸ”—

The results from the previous experiment gave us information about the statistical distributions of outputs, their covariance structure, etc.), we know more about the role of stochasticity in this setting of the model. However, we do not know anything about the influence of the input parameters diffusionRate, evaporationRate, and population on these outputs. This is exactly the aim of sensitivity analysis and exploration methods which are integrated into OpenMOLE.

Workflow πŸ”—

Let's illustrate a simple experiment of a grid search of the parameter space. Each input parameter will take a finite number of values within a defined interval.
Rate parameters diffusionRate and evaporationRate are between 0 and 100, and let's say we consider ant populations of sizes comprised between 50 and 150. With a step of 50 for each interval, the complete grid has a size of 27 (3x3x3) parameter sets to explore.

We use the DirectSampling method, which takes as arguments the sampling itself (i.e. the grid we just defined with the parameter values), and the model to evaluate. Instead of running one instance of the model for each parameter set of our grid, which would not make much sense because of the model's stochasticity we discussed above, we will replicate each one 100 times with the Replication task. This way, statistics can then be computed for each parameter set.
The script is the following:

// Input values
val mySeed = Val[Int]
val diffusionRate = Val[Int]
val evaporationRate = Val[Int]
val population = Val[Int]

// Output values
val countFood = Val[Double]
val finalTicksFood1 = Val[Double]
val finalTicksFood2 = Val[Double]
val finalTicksFood3 = Val[Double]

// NetLogo commands list
val launch = List(
    "setup",
    "go ;;You should set your stopping criteria here instead"
)

// NetLogo task
val antsTask = NetLogo6Task(
    workDirectory / "ants.nlogo", // netlogo file
    launch,                       // launching commands
    seed = mySeed                 // set the random seed
) set (
    inputs += diffusionRate mapped "diffusion-rate",
    inputs += evaporationRate mapped "evaporation-rate",
    inputs += population mapped "population",

    outputs += countFood mapped "count-food",
    outputs += finalTicksFood1 mapped "final-ticks-food1",
    outputs += finalTicksFood2 mapped "final-ticks-food2",
    outputs += finalTicksFood3 mapped "final-ticks-food3"
)

// Define the replication task
val replications = Replication(
    evaluation = antsTask, // the model to run
    seed = mySeed,         // the seed variable
    sample = 100           // the number of model executions
)

// Define the grid sampling task
val exploration = DirectSampling(
    evaluation = replications, // here we evaluate the Replication task for each value of the sampling
    sampling =
        (diffusionRate in (0 to 100 by 50)) x
        (evaporationRate in (0 to 100 by 50)) x
        (population in (50 to 150 by 50))
)

// Workflow
exploration hook (workDirectory / "grid_results.csv")

Results πŸ”—

In the same way we did before, after refreshing your workspace you will find a new file named grid_results.csv, containing the results of our grid sampling. You can then use the results to better understand how your model behaves.

To go further πŸ”—

In the next tutorial, an other example of direct sampling with a NetLogo model will give a deeper insight on how to understand and analyze the results of such an experiment.