Hierarchical random graphs

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Hierarchical random graphs

Fitting and sampling hierarchical random graph models.

Keywords
graphs
Usage
hrg.fit (graph, hrg = NULL, start = FALSE, steps = 0)
hrg.consensus (graph, hrg = NULL, start = FALSE, num.samples = 10000)

hrg.create (graph, prob) hrg.dendrogram (hrg)

hrg.game (hrg)

hrg.predict (graph, hrg = NULL, start = FALSE, num.samples = 10000, num.bins = 25)

## S3 method for class 'igraphHRG': print(x, type=c("auto", "tree", "plain"), level = 3, ...) ## S3 method for class 'igraphHRGConsensus': print(x, \dots)

Arguments
graph
The graph to fit the model to. Edge directions are ignored in directed graphs.
hrg
A hierarchical random graph model, in the form of an igraphHRG object. hrg.fit allows this to be NULL, in which case a random starting point is used for the fitting. hrg.consensus and h
start
Logical, whether to start the fitting/sampling from the supplied igraphHRG object, or from a random starting point.
steps
The number of MCMC steps to make. If this is zero, then the MCMC procedure is performed until convergence.
num.samples
Number of samples to use for consensus generation or missing edge prediction.
prob
A vector of probabilities, one for each vertex, in the order of vertex ids.
num.bins
Number of bins for the edge probabilities. Give a higher number for a more accurate prediction.
x
igraphHRG or igraphHRGConsensus object to print.
type
How to print the dendrogram, see details below.
level
The number of top levels to print from the dendrogram.
...
Additional arguments, not used currently.
Details

A hierarchical random graph is an ensemble of undirected graphs with $n$ vertices. It is defined via a binary tree with $n$ leaf and $n-1$ internal vertices, where the internal vertices are labeled with probabilities. The probability that two vertices are connected in the random graph is given by the probability label at their closest common ancestor.

Please see references below for more about hierarchical random graphs. igraph contains functions for fitting HRG models to a given network (hrg.fit, for generating networks from a given HRG ensemble (hrg.game), converting an igraph graph to a HRG and back (hrg.create, hrg.dendrogram), for calculating a consensus tree from a set of sampled HRGs (hrg.consensus) and for predicting missing edges in a network based on its HRG models (hrg.predict). The igraph HRG implementation is heavily based on the code published by Aaron Clauset, at his website, http://tuvalu.santafe.edu/~aaronc/hierarchy/.

hrg.fit fits a HRG to a given graph. It takes the specified steps number of MCMC steps to perform the fitting, or a convergence criteria if the specified number of steps is zero. hrg.fit can start from a given HRG, if this is given in the hrg argument and the start argument is TRUE.

hrg.consensus creates a consensus tree from several fitted hierarchical random graph models, using phylogeny methods. If the hrg argument is given and start is set to TRUE, then it starts sampling from the given HRG. Otherwise it optimizes the HRG log-likelihood first, and then samples starting from the optimum.

hrg.create creates a HRG from an igraph graph. The igraph graph must be a directed binary tree, with $n-1$ internal and $n$ leaf vertices. The prob argument contains the HRG probability labels for each vertex; these are ignored for leaf vertices.

hrg.dendrogram creates the corresponsing igraph tree of a hierarchical random graph model.

hrg.game samples a graph from a given hierarchical random graph model.

hrg.predict uses a hierarchical random graph model to predict missing edges from a network. This is done by sampling hierarchical models around the optimum model, proportionally to their likelihood. The MCMC sampling is stated from hrg, if it is given and the start argument is set to TRUE. Otherwise a HRG is fitted to the graph first.

Value

  • hrg.fit returns an igraphHRG object. This is a list with the following members:
  • leftVector that contains the left children of the internal tree vertices. The first vertex is always the root vertex, so the first element of the vector is the left child of the root vertex. Internal vertices are denoted with negative numbers, starting from -1 and going down, i.e. the root vertex is -1. Leaf vertices are denoted by non-negative number, starting from zero and up.
  • rightVector that contains the right children of the vertices, with the same encoding as the left vector.
  • probThe connection probabilities attached to the internal vertices, the first number belongs to the root vertex (i.e. internal vertex -1), the second to internal vertex -2, etc.
  • edgesThe number of edges in the subtree below the given internal vertex.
  • verticesThe number of vertices in the subtree below the given internal vertex, including itself.
  • hrg.consensus returns a list of two objects. The first is an igraphHRGConsensus object, the second is an igraphHRG object. The igraphHRGConsensus object has the following members:
  • parentsFor each vertex, the id of its parent vertex is stored, or zero, if the vertex is the root vertex in the tree. The first n vertex ids (from 0) refer to the original vertices of the graph, the other ids refer to vertex groups.
  • weightsNumeric vector, counts the number of times a given tree split occured in the generated network samples, for each internal vertices. The order is the same as in the parents vector.
  • hrg.create returns an igraphHRG object.

    hrg.dendrogram returns an igraph graph.

    hrg.game returns an igraph graph.

concept

Hierarchical random graphs

Printing HRGs to the screen

igraphHRG objects can be printed to the screen in two forms: as a tree or as a list, depending on the type argument of the print function. By default the auto type is used, which selects tree for small graphs and simple (=list) for bigger ones. The tree format looks like this: Hierarchical random graph, at level 3: g1 p= 0 '- g15 p=0.33 1 '- g13 p=0.88 6 3 9 4 2 10 7 5 8 '- g8 p= 0.5 '- g16 p= 0.2 20 14 17 19 11 15 16 13 '- g5 p= 0 12 18 This is a graph with 20 vertices, and the top three levels of the fitted hierarchical random graph are printed. The root node of the HRG is always vertex group #1 (g1 in the the printout). Vertex pairs in the left subtree of g1 connect to vertices in the right subtree with probability zero, according to the fitted model. g1 has two subgroups, g15 and g8. g15 has a subgroup of a single vertex (vertex 1), and another larger subgroup that contains vertices 6, 3, etc. on lower levels, etc.

The plain printing is simpler and faster to produce, but less visual: Hierarchical random graph: g1 p=0.0 -> g12 g10 g2 p=1.0 -> 7 10 g3 p=1.0 -> g18 14 g4 p=1.0 -> g17 15 g5 p=0.4 -> g15 17 g6 p=0.0 -> 1 4 g7 p=1.0 -> 11 16 g8 p=0.1 -> g9 3 g9 p=0.3 -> g11 g16 g10 p=0.2 -> g4 g5 g11 p=1.0 -> g6 5 g12 p=0.8 -> g8 8 g13 p=0.0 -> g14 9 g14 p=1.0 -> 2 6 g15 p=0.2 -> g19 18 g16 p=1.0 -> g13 g2 g17 p=0.5 -> g7 13 g18 p=1.0 -> 12 19 g19 p=0.7 -> g3 20 It lists the two subgroups of each internal node, in as many columns as the screen width allows.

Consensus dendrograms (igraphHRGConsensus objects) are printed simply by listing the children of each internal node of the dendrogram: HRG consensus tree: g1 -> 11 12 13 14 15 16 17 18 19 20 g2 -> 1 2 3 4 5 6 7 8 9 10 g3 -> g1 g2 The root of the dendrogram is g3 (because it has no incoming edges), and it has two subgroups, g1 and g2.

References

A. Clauset, C. Moore, and M.E.J. Newman. Hierarchical structure and the prediction of missing links in networks. Nature 453, 98--101 (2008);

A. Clauset, C. Moore, and M.E.J. Newman. Structural Inference of Hierarchies in Networks. In E. M. Airoldi et al. (Eds.): ICML 2006 Ws, Lecture Notes in Computer Science 4503, 1--13. Springer-Verlag, Berlin Heidelberg (2007).

Aliases
  • HRG
  • hrg.consensus
  • hrg.game
  • hrg.create
  • hrg.predict
  • hrg.dendrogram
  • hrg.fit
  • print.igraphHRG
  • print.igraphHRGConsensus
Examples
## We are not running these examples any more, because they
## take a long time (~15 seconds) to run and this is against the CRAN
## repository policy. Copy and paste them by hand to your R prompt if
## you want to run them.

## A graph with two dense groups
g <- erdos.renyi.game(10, p=1/2) + erdos.renyi.game(10, p=1/2)
hrg <- hrg.fit(g)
hrg

## The consensus tree for it
hrg.consensus(g, hrg=hrg, start=TRUE)

## Prediction of missing edges
g2 <- graph.full(4) + (graph.full(4) - path(1,2))
hrg.predict(g2)
Documentation reproduced from package igraph, version 0.6.5-2, License: GPL (>= 2)

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