stochastic-arrow 0.3.0

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Arrow

“... even if the previous millisecond is closer to us than the birth of the universe, it is equally out of reach.” ― Jean-Christophe Valtat, Luminous Chaos

Concept

This library implements a generalized version of the Gillespie Algorithm, a stochastic approach to numerically solving discrete systems. Each iteration, the algorithm will calculate the propensities for each reaction given a rate and the counts of the reactants present in the current state of the system, then selects one reaction to occur and the interval of time between the previous reaction and the current reaction. Iterating this produces a trajectory (or history) of the state vector over the course of the simulation.

Installation

Add the following to your requirements.txt, or pip install stochastic-arrow:

stochastic-arrow

Usage

The arrow library presents a single class as an interface, StochasticSystem, which operates on a set of reactions (encoded as a numpy matrix of stoichiometrix coefficients) and associated reaction rates:

from arrow import StochasticSystem
import numpy as np

# Each row is a reaction and each column is a molecular species (or other
# entity). The first reaction here means that the first and second elements
# combine to create the third, while the fourth is unaffected.
stoichiometric_matrix = np.array([
    [1, 1, -1, 0],
    [-2, 0, 0, 1],
    [-1, -1, 1, 0]], np.int64)

# Once we have a matrix of reactions, we can
# construct the system.
system = StochasticSystem(stoichiometric_matrix)

Now that the system has been instantiated, we can invoke it with any initial state vector and set of reaction rates and then run it for a given time interval:

# This gives the initial state of the system (counts of each molecular species,
# for instance).
state = np.array([1000, 1000, 0, 0])

# We also specify how long we want the simulation to run. Here we set it to one
# second.
duration = 1

# Each reaction has an associated rate for how probable that reaction is.
rates = np.array([3.0, 1.0, 1.0])

Once we have an initial state and rates, we can run the simulation for the given duration. evolve returns a dictionary with five keys:

• steps - the number of steps the simulation took
• time - at what time point each event took place
• events - the events that occurred
• occurrences - the number of times each event occurred (derived directly from events)
• outcome - the final state of the system

result = system.evolve(state, duration, rates)

If you are interested in the history of states for plotting or otherwise, these can be derived from the list of events and the stoichiometric matrix, along with the inital state. reenact_events will do this for you:

from arrow import reenact_events

history = reenact_events(stoichiometry, result['events'], state)

Testing

arrow uses pytest. To test it:

> make clean compile
> pytest

NOTE: make compile without an explicit clean might not fully build the extension.

There are more command line features in test_arrow:

> python -m arrow.test.test_arrow --complexation

> python -m arrow.test.test_arrow --plot

> python -m arrow.test.test_arrow --obsidian

> python -m arrow.test.test_arrow --memory

> python -m arrow.test.test_arrow --time

Changelog

Version 0.3.0

• Introduced backwards-incompatible API change for supplying rates at evolve() time rather than __init__() for StochasticSystem.