code-duality

Code for the paper Duality between predictability and recontructability in complex systems

Requirements and dependencies

• numpy>=1.20.3
• scipy>=1.7.1
• psutil>=5.8.0
• tqdm>=4.56.0
• networkx>=2.8
• netrd
• seaborn
• graphinf>=0.2.4
• basegraph==1.0.0

Installation

First, clone this repository.

git clone https://github.com/DynamicaLab/code-duality

Second, use pip to install the module.

pip install ./code-duality

Usage

The package is basically wrapper around graphinf which does the heavy lifting for all bayesian computations. The main objects of the package are factories, for instanciating the graph and data models, configs and metrics. The configs should be subclasses of Config, and can also be instanciated using json files. Here is an example of config instanciation:

from code_duality import Config

# A basic config
config = Config(x=1, y="Hello world")

# A nested config, that has a config as an attribute
nested = Config(c=config, name="nested_config")

# This is a sequenced config, that can be iterated over.
# `seq1` and `seq2` are sequenced parameters
sequenced = Config(seq1=[1,2,3], seq2=["a", "b"] n=nested)

# We take the cartesian product between all sequenced parameters
assert len(sequenced) == 6
for s in sequenced.to_sequence():
    # `s` is a non-sequenced config where the parameter `seq1` and `seq2`
    # are iterated over [1,2,3] and ["a", "b"], respectively.
    print(s) 

The Metrics class is a utility class for performing computations in parallel. All subclasses of Metrics come with a compute method that performs the computation for a sequenced config. The compute must be provided with n_workers and n_async_jobs, corresponding to the number of available processors and the number of config computations that are allowed to perform in parallel. The subclass ExpectationMetrics does sampling in parallel and outputs an Monte Carlo expectation. The results are saved in the attribute data in the form of a pandas.DataFrame.

import pandas as pd, os
from code_duality import Config
from code_duality.metrics import BayesianInformationMetrics, CheckPoint


config = Config.load("path/to/the/config.json")

metrics = BayesianInformationMetrics()
metrics.compute(
    config, 
    n_workers=4, 
    n_async_jobs=1, 
    callbacks=[
        # This checkpoint saves the metrics dataframe in a folder at each iteration
        CheckPoint.to_setup(
            patience=1,
            savepath="path/to/data/folder"
        ) 
    ])
print(metrics.data) # Prints the metrics dataframe
df = pd.read_pickle(
    # The metrics saves its measure in a file named after its short name class attribute.
    os.path.join("path/to/data/folder"), metrics.shortname + ".pkl"
) 
print(df) # Prints the same metircs dataframe as above

Results reproduceability

The results of the paper can all be reproduced using the main.py script. The configs for each figure is located here. To run the script, use the command-line interface:

python main.py
    --config path/to/the/config.json
    --n-workers 4
    --n-async-joibs 1
    --ouput-path path/to/data/folder
    --save-patience 1