pypge

Python implementation of the PGE algorithm (voted Best Paper Gecco 2013)

If you publish using this library, please cite the above paper.

PGE stands for Prioritized Grammar Enumeration and is the method for solving the Symbolic Regression problem.

This package is under heavy development until this comment is removed

Installation

Clone the repository.

Pip is no longer the recommended method.

Dependencies

Docker.

Running PyPGE

You will want to run an evaluation server, runtime is much better this way.

docker run -d -p 8080:8080 --name evalr verdverm/pypge-eval

Then you can run the experimenter container:

docker run --rm -it --name pypge \
    -v `pwd`:/pycode \
    -p 8888:8888 \
    verdverm/pypge-experiments \
    /bin/bash

You will find a run.sh bash script. Running from within the docker is the best place to run pypge at the moment. There is a lot of parameteriztion matching that happens behind the scenes. Much of the configuration change and file moving can happen outside of the docker because we mount the repository into the docker. All scripts should be run from inside, however, out put will also persist outside of the container.

run -x <config_folder> -s <problem_type> -p <problem_set>

The <config_folder> should contain one or more yaml configuration files.

The <problem_type> must be explicit or diffeq. Your yaml config filenames must contain one of these strings.

The <problem_set> is a file in the prob_sets directory and is a simple bash list.

You can also use the -P option to see what experiments will be performed without actually running anything.

Running Directly

For those interested, follow the flow:

experiments/megarun.sh
experiments/run.sh
experiments/scripts/helpers.sh
experiments/main.py

Create a New Experiment

Right now, namimg is a bit intertwined with the configuration and where PyPGE run script looks for different files and directories.

You will need to create a directory in the experiments folder. It's name should match the <config_folder> arg. Inside of this folder, you will have your config files for PyPGE.

You will need to place your data in the data/benchmarks/{diffeq,explicit}/<problem_name>.csv

You will also need to create a <problem_set> in the experiments/prob_sets

Config files

These are the recommended default settings. You should change the workers and remote cores to match the machine you are using. Be careful when changing other parameters. Both logical and runtime performance are very sensative.

Sample config file:

name: "explicit_final"

workers: 4
queue_size: 4096
remote_eval: true
remote_cores: 4
remote_host: "ws://172.17.0.1:8080/echo"

max_iter: 12

pop_count: 3
peek_count: 12
peek_npts: 0

min_size: 1
max_size: 64
min_depth: 1
max_depth: 6

max_power: 6
zero_epsilon: 0.000001

excluded_cols: []

usable_funcs: []
 - "sin"
 - "cos"

algebra_methods: []

multi_expander_params:
  - name: "level_1"
    pop_count: 3
    usable_funcs: 
     - "sin" 
     - "cos"
    grow_params:
      func_level: "linear"
      init_level: "med"
      grow_level: "med"
      subs_level: "med"
      shrinker: false
      add_xtop: true
      grow_filter: false
      limiting_depth: 4

err_method: "rmse"

fitness_func_params:
 - "normalize" 
 - "-(1)jpsz" 
 - "-score" 
 - "+bic"
 - "-(1)psz" 

print_timing: true
log_details: true

Things to know

When pretty printing, sympy performs simplification, which can remove terms if the floating point print precision is not sufficient (looks like zero)

Todo

The biggest todo on my list is moving the main loop back to Golang. Python will then only be used for the SymPy functionality.

The reason for this is that Python is slow as shit and there will be a massive performance boost by switching back to Golang.

Sometimes implementation matters.

Contributing

Branching practices follow the methodology outlined at: http://nvie.com/posts/a-successful-git-branching-model/

verdverm / pypge

readme