Combinatory Chemistry

This is the code for simulating the system described in "Emergence of Self-Reproducing Metabolisms as Recursive Algorithms in an Artificial Chemistry" by Germán Kruszewski and Tomas Mikolov.

Requirements

Running this code requires clojure and the leiningen project manager.

Usage

lein run will start a simulation reporting some statistics on the standard output.

A better way is running it to log information to the disk, as follows:

lein run --log LOG_DIRECTORY --scrolling-log.

This will log information to metrics.edn andreactions.log files in the given log directory. The second argument is to avoid showing information on the standard output, which makes the simulation slower.

Some important arguments are --size which controls the total number of combinators in the system, --time to control the simulation length and --threads for multi-processing support.

Other options are listed with lein run -H.

Examples

The following command runs the simulation for 1000 time units, initializing the system with 10k uniformly distributed S, K and I combinators:

lein run --scrolling-log --size=10000 --time=1000 --log "my-experiment"

Reaction rate constants are defined with --condensation-rate, --reduction-rate (for K and I combinators), and --S-reduction-rate (for the S combinator). The default values correspond to those reported in the paper.

The volume of the container is controlled with --volume and set to be equal to --size by default.

Log files

metrics.edn log some statistics, like number of expressions, diversity, etc. at every unit interval of time.

reactions.log contain every single reaction that was registered in the system. This can be leveraged, for instance, to plot reactant consumption rates.

Plots

Dependencies

Plotting is based on the oz package. See the documentation for troubleshooting and installation requirements.

Usage

The recommended way to plot is using the REPL (either from your editor or directly in the command line). All plots can be produced with the plot-selected! helper function.

For instance, to plot the consumption of a set of selected reactants weighted by the information metric, you can use:

=> (use 'cc.plot)
=> (plot-selected! "<log-directory-path (without a filename)>" 
                  "<output-path>"
                  [:reactants-consumption]
                  {
                  :only-keys '[S K I (S S) (K I) (K K) (S K) (S I) (S I I) (S (S I) I)]}]
                  :smoothing 20
                  :apply-weighting true ;set to to false to use raw counts
                  :dest-filename "selected-reactants-by-consumption.svg"})

If you set the output path to be nil, then the plot is displayed in a web server available at localhost:10666.

See extra/plots.clj for code snippets to reproduce the figures in the paper.