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

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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
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3answers
187 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 ...
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3answers
225 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
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1answer
53 views
4
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1answer
412 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 ...
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1answer
149 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 ...
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2answers
125 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 ...
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93 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
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0answers
199 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 ...
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2answers
200 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 ...
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1answer
169 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
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1answer
192 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 ...
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1answer
60 views
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80 views

Checking connectedness of a graph

I am trying to use the Combinatorica package in a Mathematica version 8 in the following code: ...
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1answer
222 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: ...
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1answer
94 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 ...
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1answer
105 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
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1answer
79 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 ...
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1answer
156 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. ...
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3answers
247 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
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1answer
117 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
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2answers
340 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 ...
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2answers
188 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 ...
2
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2answers
139 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
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1answer
239 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 ...
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2answers
197 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 ...
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0answers
168 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). ...
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1answer
105 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
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1answer
322 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 ...
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3answers
129 views

Deleting Vertices in GridGraph

Take a simple GridGraph: g = GridGraph[{3, 3}, VertexLabels -> "Name", ImageSize -> 150, ImagePadding -> 10] I am ...
2
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1answer
230 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
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1answer
380 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 ...
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1answer
121 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
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2answers
176 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: ...
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1answer
64 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 ...
0
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1answer
136 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 ...
2
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2answers
293 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 ...
3
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2answers
203 views

Manually adjust graph vertex location by dragging?

Sometimes I have a graph and I want to make tweaks to the vertex locations. Is there any way to manually adjust graph vertex location by dragging? If I double click to edit, I can move around the ...
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1answer
181 views

Vertex labels versus vertex names in VertexRenderingFunction

The VertexRenderingFunction seems to only use names, not labels. For example: ...
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1answer
104 views

GraphPlot with black edges no rendering function

Is there any way to make the edges of a GraphPlot black without tediously writing out a long "EdgeRenderingFunction"? I guess you could ask the same kind of question about vertex labeling. For ...
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2answers
163 views

How to apply GraphLayout to parts of a graph?

I'm trying to sketch polymers. Here is how I do it for the monomer: ...
3
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1answer
90 views

Is there really a bug in the following code, taken from the reference documentation for PetersenGraph?

PetersenGraph[5, 2, EdgeLabels -> {8 \[UndirectedEdge] 9 -> "hello"}] appears to evaluate perfectly, as expected, but in my version 9.0.1.0, the option ...
2
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1answer
158 views

Finding a Moore neighborhood connected path of bright pixels along the contour of a text character

I have a simple image, for example a blowup of a Times New Roman character like 'R' saved as a PNG. I then perform the following operations to extract a minimum representation of the contour lines ...
4
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1answer
145 views

Dijkstra without Combinatorica

There is some overlap between Combinatorica and the Graph related framework but there are also various elements missing. As far as I can see there is no 'Dijkstra' method or algorithm in Mathematica ...
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1answer
184 views

Mean path length of randomly generated graphs

I am looking to find the the average path length of 1000 random graphs with the following degree distribution, a few of the vertex degrees are included below ...
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0answers
60 views

GraphHighlightStyle with multiple datasets

I am trying to highlight several subgraphs of a graph using the following command: ...
5
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1answer
195 views

Shortest polygonal path

I'd like to find the shortest distance between some points (every point must be visited), such as between these 3 points: ...
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1answer
110 views

Connected components of a graph

I am trying to find the number of connected components of numerous named graphs within Combinatorica. The obvious answer seems to be: ...
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0answers
128 views

Tools for finding minimal or almost-minimal graph vertex colorations in Mathematica v9?

I'm looking to compute minimum vertex colorations (s.t. no two vertices of the same color share an edge: http://en.wikipedia.org/wiki/Graph_coloring) for graphs in Mathematica v9 with potentially up ...
3
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3answers
284 views

Generating a graph where vertices correspond to points in an integer lattice and edges connect points less than a threshold distance apart

I'd like to automatically generate a graph where vertices correspond to (and have the coordinates of) points in an $A \times B$ integer lattice, and a graph is generated by connected vertices within a ...