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
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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 ...
2
votes
1answer
59 views

Check Specific Connections within Graph

Say you have the skeleton of a graph: nodeset= PolyhedronData["Icosahedron", "SkeletonRules"] and you've an arbitrary list of some fraction of those nodes, say ...
3
votes
2answers
177 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
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0answers
56 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 ...
3
votes
1answer
187 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, ...
6
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2answers
389 views

Don't understand why Mathematica is complaining about my Graph expression; how can I fix it?

The Tube in Arrow problem is fixed in version 10. Note that in version 10 Graph3D must be ...
0
votes
1answer
94 views

Network graph with lights not working

So I have ...
4
votes
1answer
221 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 ...
5
votes
3answers
724 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 ...
2
votes
1answer
315 views

Display a labeled multigraph

Introduced in version 9, fixed in version 10. Thanks Szabolcs for providing this screenshot showing that the bug is fixed. Despite the integration of graphs and networks, multigraphs are ...
8
votes
2answers
307 views

Finding All Chordless Simple Cycles In A Graph

I am doing a research on networks which consists of polygons with different number of sides. I am trying to find all simple cycles in a network which are chordless. As an example, consider the ...
1
vote
1answer
80 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
1answer
260 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 ...
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 ...
6
votes
3answers
228 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 ...
7
votes
3answers
310 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
4
votes
1answer
71 views

How can I change VertexWeights in a Graph?

Fixed in version 10. I evaluate ...
6
votes
1answer
1k 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 ...
2
votes
1answer
170 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
155 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
119 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
312 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 ...
6
votes
2answers
285 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 ...
3
votes
1answer
198 views

Writing results directly to file

I am trying to find all simple paths in a large directed graph (542 vertex, density ~ 5%) between two nodes. For this purpose, I use the algorithm from this thread. Unfortunately, my computer is ...
6
votes
1answer
233 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 ...
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
309 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: ...
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 ...
5
votes
1answer
146 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 ...
2
votes
1answer
102 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 ...
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. ...
8
votes
3answers
291 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
144 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
539 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 ...
0
votes
2answers
263 views

Generating a random tree of given cardinality, depth, and labeling

For demo, exploration and teaching purposes, I would like to be able (and asking you for help) to generate these special instances of trees: For given: N - number of nodes in the tree D - depth of ...
3
votes
2answers
175 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
410 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
240 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 ...
1
vote
0answers
231 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). ...
1
vote
1answer
116 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 ...
7
votes
1answer
399 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
159 views

Deleting Vertices in GridGraph

Take a simple GridGraph: g = GridGraph[{3, 3}, VertexLabels -> "Name", ImageSize -> 150, ImagePadding -> 10] I am ...
3
votes
1answer
283 views

Nicely illustrating the evolution and end-state of a discrete-time Markov chain

I'm simulating a discrete time Markov process on a finite state space corresponding to a linear interval $(x_1, x_2, ..., x_N) \in X$, where each time step $t_i$ involves updating the state of some ...
5
votes
1answer
541 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 ...
1
vote
1answer
166 views

GraphPlot3D: How to plot undirected graph with a list of edges?

I have a list of edges defined based on vertices like this: ...
4
votes
2answers
191 views

Visualize difference between members of the list

I want to visualize the difference between members of a set: set = {20, 36, 70, 96, 152, 301} This way I get the diffs: ...
0
votes
1answer
81 views

Subgraph, HighlightGraph not acting as expected

I'm trying to create a simple graph from a matrix and then highlight a particular subgraph. My code (simplified from a bigger task) is as follows. I keep getting the "Subgraph::graph: A graph object ...
1
vote
1answer
193 views

How to construct a graph from a list of edges

I have a list of pairs of numbers, representing connections between objects in the real world. Each number is the identifier of an object, there are gaps in the range from the smallest number to the ...
3
votes
2answers
366 views

random geometric graph generation problem

I'm new to Mathematica. I'm trying to generate a random geometric graph in which to have a secure link between any two arbitrary nodes they should share a common key in their key rings (have assigned ...