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Simulate the continuous-time threshold model on static networks.

Project description

Simulate the continuous-time threshold model on static networks using Gillespie’s SSA. The networks can be directed and weighted.

Install

git clone https://github.com/benmaier/thresholdmodel.git
pip install ./thresholdmodel

Example

Simulate on an ER random graph.

import numpy as np
import networkx as nx
import matplotlib.pyplot as plt

from thresholdmodel import ThreshModel

N = 1000
k = 10

thresholds = 0.1
initially_activated = np.arange(100)

G = nx.fast_gnp_random_graph(N, k/(N-1.0))

Thresh = ThreshModel(G,initially_activated,thresholds)
t, a = Thresh.simulate()

plt.plot(t,a)
plt.show()

trajectory

API

Simulate

Given a networkx-Graph object G (can be a networkx.DiGraph, too), and values for initially_activated and thresholds, simulate like this

Thresh = ThreshModel(G,initially_activated,thresholds)
t, a = Thresh.simulate()

t is a numpy.ndarray containing the times at which node activations happened. a is a numpy.ndarray containing the relative cascade size at the corresponding time in t. Note that the whole process is modeled as a Poisson process such that the time t will be given in units of the node activation rate gamma = 1.0. If you want to simulate for another node activation rate, simply rescale time as t /= gamma.

When the simulation is started with the save_activated_nodes=True flag, a list of activated nodes per time leap is saved in ThreshModel.activated_nodes.

t, a = Thresh.simulate(save_activated_nodes=True)
print(Thresh.activated_nodes)

You can repeat a simulation with the same initial conditions by simply calling Thresh.simulate() again, all the necessary things will be reset automatically.

Set initially activated nodes

Set nodes 3, 5, and 8 to be activated initially.

initially_activated = [3, 5, 8] # this could also be a numpy array

Choose 20% of all nodes randomly to be activated initially. When the simulation is restarted, the same nodes will be chosen as initial conditions.

initially_activated = 0.2

Choose 35 randomly selected nodes to be activated initially. When the simulation is restarted, the same nodes will be chosen as initial conditions.

initially_activated = 35

Set thresholds

Activation thresholds can be set for all nodes

thresholds = np.random.rand(G.number_of_nodes())

Note that thresholds need to lie in the domain [0,1].

You can also set a universal threshold

thresholds = 0.1

Here, 10% of a node’s neighbor’s need to be activated in order for the node to become active, too.

Directed networks

A node will become active if the sufficient number of nodes pointing towards the node are active. This means that the in-degree will be the important measure to determine wether a node will become active.

Weighted networks

If you want to simulate on a weighted network, provide the weight keyword

Thresh = ThreshModel(G,initially_activated,thresholds,weight='weight')

Similar to the networkx-documentation: ``weight`` (string, optional (default=``None``)) - The attribute name to obtain the edge weights. E.g.: G.edges[0,1]['weight'].

A focal node will become active when the cumulative edge weights of all activated nodes pointing towards the focal node will reach > threshold*in_degree.

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