wfunkenbusch-markov-chain-monte-carlo

Markov-Chain-Monte-Carlo

Performs a Markov Chain Monte-Carlo simulation on a set of nodes to determine the best graphs for a particular weight function.

The relative probability of accepting a graph, $j$, from a graph $i$ is given by

$$f({X_i},{X_j}) = e^{-(\Theta(X_j) - \Theta(X_i))/T}$$

where

$$\Theta(X_i) = r \sum_e w_e + \sum_k^M \sum_{e \in p_{0k}} w_e$$

where $e$ is an edge, $w_e$ is the weight of an edge (the distance between the two nodes it connects), $k$ is a node, $M$ is the total number of nodes, and $p_{0k}$ is the shortest path length between the source node (index 0) and node $k$. r is a constant which determines the importance of total edge weight versus shortest path length. A larger r value gives more importance to total graph edge weight. T represents the ease of accepting the proposal distribution. A larger T makes it easier to accept the proposal distribution.

Implementation:

• Run using Javascript, node.js (v8 or above)
• Needs the following modules installed: jsnetworkx, lodash-clonedeep, command-line-args, mocha (for testing), assert (for testing), istanbul (for coverage), and coveralls mocha-lcov-reporter (for coverage)

1. npm install wfunkenbusch-markov-chain-monte-carlo
2. Create a .js file which calls the main function and sets inputs
3. node file name.js

Alternatively,

1. git clone https://github.com/wfunkenbusch/Markov-Chain-Monte-Carlo
2. Enter repository
3. node ./lib/index.js/ --nodes nodes --T T --r r --N N

Ex. .js file

const mcmc = require('wfunkenbusch-markov-chain-monte-carlo') var options = {}; options.nodes = '0, 0, 1, 1, 1, -1, -1, 1'; options.T = 1; options.r = 1; options.N = 100; mcmc.main(options);

Arguments:

• nodes

  • type: string
  • Node coordinates given as comma separated values in a string. The format is 'x1, y1, x2, y2, x3, y3, ..., xM, yM', where xi is the x coordinate of node i, and yi is the y coordinate of node i.

• T

  • type: float
  • Scaling factor for the ease of acceptance of a new proposal distribution. A larger T makes it easier to accept a proposal distribution. Must be positive.

• r

  • type: float
  • Scaling factor for the relative importance of total edge weight versus shortest path length. A larger r gives more importance to total edge weight.

• N

  • type: integer
  • Total number of times to run the Markov Chain Monte-Carlo simulation. As the number of nodes increase, this value should also increase. The value should be large enough that the effect of the initial distribution is small.

Outputs:

All outputs are printed to the console.

• Current iteration number, for keeping track of code progress. To suppress, comment out console.log(i + 1) in main(). To reduce the number of outputs, console.log(i + 1) may be replaced with:

if ((i + 1) % n === 0) { console.log(i + 1) }

where n is the fraction of outputs to print.

• The top 1% of adjacency matrices, followed by the number of times they appeared. Prioritizes graphs which appeared earlier. To change the percentage of top graphs printed, replace the line

var nBestGraphs = Math.floor(Fun.AList.length / 100 + 1);

with

var nBestGraphs = Math.floor(Fun.AList.length * (fraction to print) + 1);

• The expected number of edges connected to the source node.
• The expected number of edges in the graph.
• The expected value of the maximum shortest path from the source node to all other nodes.

Note: the total number of adjacency matrices is N + 1.