Questions about handling graphs in Mathematica, graph theory, graph visualization, GraphPlot, the built-in Graph type and the Combinatorica` package.

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2
votes
1answer
59 views

Reversibly abstracting a list of strings as a graph object where vertices represent strings and edge connect pairs of strings based on various tests

Imagine I provide you a list of arbitrary strings, say: Map[StringJoin, Tuples[{"0", "1", "2"}, 4]]. I'd like to abstract these strings as a graph object in ...
3
votes
2answers
175 views

How to make a recursive code from this iterative code? (drawing tree graph)

I have a question about drawing tree graph. I use my iterative code to build a tree graph. Here it is. ...
1
vote
0answers
55 views

Get correlation matrix when using FindGraphCommunities

Does somebody know how to get the correlation matrix when using FindGraphCommunities (Social Network analysis) using the "Spectra" option? Can somebody tell me as ...
1
vote
1answer
82 views

Social Network Analysis - Get the List of InBoundEdges for Directed Graph

I wish to get the list of inwards edges for a node. IncidenceList provides both inwards and outwards list. I can of course filter with ...
5
votes
3answers
697 views

Fast code to generate large random graph with fixed degree sequence

I'm trying to create a function so to generate large random graph with a fixed degree sequence $\{v_1,v_2,\dots,v_N\}$, where $N$ is the number of vertices in the graph. The Mathematica function that ...
3
votes
1answer
185 views

Social Network Analysis - Get the End Points of an Edge

I want to get the end points of an Edge of a Graph. For example see the following source, ...
4
votes
1answer
219 views

Katz Centrality [closed]

I want to calculate the Katz Centrality of large graphs. The Mathematica command to do that is KatzCentrality[g, $\alpha$] and it is also fast. However I realized that there is a mismatch between ...
1
vote
1answer
268 views

Display a labeled multigraph

Despite the integration of graphs and networks, multigraphs are not supported in Mathematica 8+. In Mathematica 9+, GraphPlot misbehaves for multigraphs having ...
6
votes
1answer
227 views

Generating a (random) 2-dimensional cellular network

I want to generate a network of random cells like the following picture: The general idea is to generate some random points (x,y) as coordinate of a vertex and then randomly choose some of these ...
6
votes
2answers
280 views

Flow/graph-based programming in Mathematica?

Is it possible in Mathematica to write a program inside a graph? For example if you have a bunch of different If[] statements that you need to embed within one ...
1
vote
1answer
79 views

Extracting a single weakly connected component from a network of many weakly connected components?

Hello Mathematica friends! I've got a network with thousands of edges and vertices, but not all in one connected component. I'm trying to extract specific connected components from the network, and ...
1
vote
0answers
122 views

How to make Layer Directed Graphs (LDG) in mathematica?

I am wondering if I can make a graph like that somehow: I am new to mathematica, I tried to play with Creating a graph with variable size of vertices and variable thickness of edges . I figured if I ...
2
votes
0answers
292 views

Why my Mathematica 9.0.1 wont work with some samples of Mathematica in Graph Theory?

I updated my Mathematica recently to 9.0.1 cause the previous version was giving me freaky result especially in FindMinimumCostFlow and ...
8
votes
1answer
573 views

How can I display a multigraph with different colored edges?

I'm new to Mathematica(version 9) and I'm trying to display a multigraph with different colored edges. Here's my code so far: ...
2
votes
1answer
121 views

Using EdgeList on a once empty Graph crashes the kernel

Note: this is fixed in version 9. Calling EdgeList on a non-empty graph which was previously empty causes the math kernel to crash. For example, ...
15
votes
1answer
897 views

How to export and import Graphs with additional data?

I'm trying to export and then later import graphs with additional data added such as VertexLabels and EdgeLabels. When I export ...
1
vote
1answer
249 views

How to import and visualize a network stored as an edge list in CSV file? [closed]

I'm extremely new to Mathematica, and I'm trying to import an edgelist representing a network, but I think I'm missing something major. Here is my process so far just to import and visualize the ...
6
votes
1answer
985 views

Analysis of Facebook group

I am the admin of a Facebook group for our year at university and wanted to graph the members of the group like you can with your own friends so we can find the isolated people and get rid of them (as ...
6
votes
3answers
225 views

Enumerate the 1-factors (perfect matchings) of $K_n$

Introduction I would like to enumerate the 1-factors, or (near-)perfect matchings, of the complete graph Kn. The adjacency list representation for Kn is basically { (x, y) | 1 ≤ x < y ≤ n }. For ...
3
votes
1answer
599 views

Combinatorica vs Built-in functions: Use of MinimumSpanningTree

What kind of argument is expected by MinimumSpanningTree (from the package Combinatorica`)? Is it possible that I am providing ...
2
votes
1answer
353 views

GraphPath: *all* shortest paths for 2 vertices, edge lengths negative

Mathematica uses Bellman-Ford to find a shortest path between two vertices when the edge lengths are negative: ...
4
votes
1answer
2k views

How can I draw the transition diagram of a Markov chain?

I apologize for my heaviness as I am a Mathematica novice. Is there a kind soul who can tell me how to draw diagrams like those shown on page 158, 160 and 161 of this document.Chaine de Markov I ...
1
vote
1answer
99 views

Connecting a vertex to middle of an edge with GraphPlot?

using GraphPlot I'd like to make directed arrow connecting a vertex (node) to the middle of an edge but couldn't find a way. Is this even possible using GraphPlot or other graphics-related commands in ...
2
votes
1answer
169 views

Saving a graph of a great number of nodes

I'm developing a code where I get graphs with over 10K nodes. These graphs have a particular relationship between clustering and degree that I need to save for future analysis. The problem is when I ...
5
votes
2answers
150 views

Improving performance in the generation of random (directed acyclic) graphs

I need to generate large (directed, acyclic, transitive) graphs. My code in Mathematica gets very slow for large numbers of vertices. I've tried a number of approaches and I can't find any significant ...
3
votes
0answers
114 views

Using Graph to cull correlated lists

I have a set of lists that represent molecular descriptors. I need to identify which descriptors are highly correlated and eliminate the correlated pairs. I can represent the connectivity by ...
3
votes
0answers
308 views

A* algorithm for finding shortest path in a graph

FindShortestPath finds the shortest path between two vertices in an edge-weighted graph, allowing a choice between the Dijkstra and Bellman-Ford algorithms. In my (limited) understanding, both of ...
0
votes
1answer
184 views

Why is my PageRank result in Mathematica converging this way?

I am using this technique to find the PR of these 3 pages. It converges to something it shouldn't be. I tried the same iteration in Java and 2 pages come up with 1.333 and the other one as 0.666. ...
19
votes
2answers
398 views

Packed Graph or GraphPlot output with non-square layout?

Graph or GraphPlot produce square layouts for disconnected graphs: Graph[Table[i -> Mod[i^3, 100], {i, 1, 100}]] I´d like to get a rectangular layout with ...
2
votes
2answers
87 views

Checking connectedness of a graph

I am trying to use the Combinatorica package in a Mathematica version 8 in the following code: ...
7
votes
1answer
304 views

Visualize a tree structure using TreeGraph

I have a code that generates a tree of graphics objects. The structure can be visualized like this, with each Rule constituting a parent child relationship: ...
5
votes
1answer
524 views

How to display each step of an A star algorithm?

I wrote a pathfinding program: A*, which is an extension of Dijkstra. I want to see the result of each step at a time. Which function should I use? The main program is the notebook Astar, which is ...
5
votes
1answer
142 views

How to impose control over vertex-to-vertex Graph edges?

I’m working on a Markov Chain and hope there is a way to impose control over how Mathematica places edges to connect vertices in a Graph. My Markov Chain currently consists of 4 vertices with 2 of the ...
8
votes
3answers
290 views

Pairwise distances of points and classification using GraphDistanceMatrix

The challenge Given $n$ points in $\mathbf{R}^3$ and a cutoff distance, $d$, I would like to determine all pairs of points that are separated by less than the given cutoff distance, $d$, and all ...
2
votes
1answer
100 views

Signed Graph from positive and negative correlations

I want to create a signed graph where the edges of my graph are either green (for a positive correlation) or red (for a negative correlation). I only managed to create a graph from a tresholded ...
2
votes
1answer
143 views

GridGraph layout with added edges

I noticed that the nice symmetric layout of a grid graph gets distorted when additional edges are added to the graph. Is there way to prevent that from happening and to keep the rectangular, grid-like ...
2
votes
2answers
525 views

Generating social network graph from a CSV file

I am new to Mathematica and wanted to generate undirected graph for data sets that show the relationships of organizations with each other. The data is in a square matrix. The cells of the matrix ...
1
vote
1answer
115 views

Reflecting the Polya-Aeppli distribution

How would I go about reflecting the Polya-Aeppli distribution in Mathematica about a y-axis (switching left and right) while keeping the command. The distribution will not allow negative parameters ...
3
votes
2answers
174 views

Assigning weights to edges of a hypercube based on the Gray code labels for vertices being connected

Say I want to construct an $n$-dimensional hypercube graph $G$ using the command: G = HypercubeGraph[n]. I'd like to assign edge weights to the $2^{(n-1)}n$ edges ...
2
votes
1answer
395 views

Create a graph from KML file

I'm wondering how I can take a .KML (Keyhole Markup Language) file and convert/express it as a graph for use in Mathematica. Even just in general, is it possible to convert a KML file to a graph? I'm ...
2
votes
2answers
236 views

Fast randomization of a graph, while keeping the graph connected

I'm looking for a very efficient method for randomizing graph of a given size (N nodes, L links), but keeping them connected. Assume you have the adjacency matrix A of a given connected graph. You ...
7
votes
1answer
369 views

Adding/deleting weighted edges to a weighted graph

How can I add and delete weighted edges in a weighted graph? Using Graph in Mathematica I want to add a weighted edge to a weighted graph. The problem is ...
1
vote
0answers
228 views

How to extract connected bipartite graph from incidence matrix

I'm trying to extract a connected bipartite graph Bconn from the a given incidence matrix B- I have a matrix representing a bipartite graph - the incidence matrix B (weighted or not is unimportant). ...
0
votes
1answer
189 views

Subset of edges with a different color

I want to color a subset of the edges of my graph with a different color. My graph currently has a large number of edges, so the following is just a toy example ...
20
votes
1answer
483 views

How to visualize large graphs with directed edge bundling

I'm wondering if anyone has implemented edge bundled graph plotting? http://www.win.tue.nl/~dholten/papers/forcebundles_eurovis.pdf
2
votes
1answer
105 views

What is the best way to save a large graph object, allowing it to be reloaded quickly in a new kernel?

I generated a very large graph, too large to simply display and manipulate with copy/paste operations. How can I somehow save the graph to a file to allow it to be rapidly reloaded after I quit out ...
7
votes
1answer
397 views

How to visualize the structure of this dynamic programming code

I am studying Mr. Wizard's answer to this question which tries to identify elementary circles in a graph. That answer uses dynamic programming technique to simplify the code. The underlying guideline ...
1
vote
3answers
155 views

Deleting Vertices in GridGraph

Take a simple GridGraph: g = GridGraph[{3, 3}, VertexLabels -> "Name", ImageSize -> 150, ImagePadding -> 10] I am ...