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

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88 views

How do I show the transition probabilities in a graph of a Markov process?

How do I get Graph to display the transition probabilities for a Markov process as labels on the graph's edges? The information is clearly present in the graph, but ...
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1answer
56 views

What does the VertexMoving method for FindGraphCommunities do?

I've been applying the VertexMoving method to some graph data, and it's producing very useful results. However, I've got no clue as to what this method actually is, and the documentation is ...
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1answer
127 views

Get histogram of number of vertices per component of graph H

I have a huge graph with ~8k vertices and ~1k components. I want a histogram showing the number of vertices for each component. How do I do this? EDIT: I'm trying ubpdqn's approach, but not gettting ...
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2answers
104 views

How to find number of connected components of graph G?

Is there a command that can count the number of components of a graph, in the same way that VertexCount[G] counts vertices?
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1answer
56 views

Importing adjacency matrix from file of 0/1 arrays

Is it possible to import adjacency matrix for graph representation, from simple text file with NxN (rows x columns) of 0s/1s: 0 1 0 0 1 0 1 1 0 1 0 0 0 1 0 0
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2answers
105 views

TreePlot, VertexRenderingFunction and stretched vertices issue

Recently I found the following TreePlot issue. For simplicity, I took an example from Mathematica Tree Drawing Tutorial and set ...
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1answer
82 views

References on functions FindGraphPartition and FindGraphCommunties

Does somebody have some interesting references on the FindGraphPartition and FindGraphCommunties[.., Method -> "Spectral"] ...
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1answer
98 views

How do I upload a graph as an adjacency list and find the betweenness centrality?

I have an undirected simple graph in a .txt file formatted as an adjacency list like this: 100 200 200 300 300 400 500 600 700 800 900 ... Every number is a node ...
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2answers
91 views

How to sort the adjecency matrix of bipartite graph so to have two off-diagonal blocks

In a bipartite graphs there are two class of nodes, say A and B. Each node of class A may interact only with nodes of the class B, and viceversa. The corresponding adjecency matrix is thus composed by ...
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1answer
54 views

How do I visualize the result of EdgeColoring[g]?

Combinatorica has a heuristic edge-coloring function EdgeColoring. When I execute it on a graph, the result is a list of integers. My guess is that an integer $i$ ...
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0answers
48 views

Why does Network`GraphPlot`wrapper appear in my GraphPlot?

I'm making a GraphPlot of data similar to this: ...
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3answers
203 views

Different colors for nodes in tree plot

I have some list of numbers which I am plotting using TreePlot. This is the code: ...
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0answers
79 views

HighlightGraph and Hyperlink

In the documentation of Mathematica it is mentioned that you can use Hyperlink and Tooltip as wrapper in a similar manner as ...
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1answer
67 views

How do I use Subgraph to sample the $n$ vertices of a graph with the greatest connectivity?

Let $G$ be an arbitrary graph with some number of vertices $||V||$ and some number of edges $||E||$. We can use Subgraph to generate, well, a subgraph of ...
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1answer
70 views

How to efficiently distinguish the rewired edges in WattsStrogatzGraphDistribution?

The WattsStrogatzGraphDistribution function is a way to construct random graphs based on Watts and Strogatz small world model. The ...
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1answer
108 views

Plotting Network with LayeredGraphPlot with specific order

I have a network and want to plot it. I use LayeredGraphPlot, and the network is described as: ...
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0answers
52 views

Can BreadthFirstScan be modified?

I would like to obtain a "slick" implementation of A*-search algorithm on Graph objects, using the built-in BreadthFirstScan (if that is possible at all). I noticed that BreadthFirstScan is static in ...
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2answers
188 views

Horizontal Tree Layout? [duplicate]

I need to display arbitrary Expressions in TreeForm, but the standard vertical layout produces too many horizontally overlapping boxes. Am I doomed to rewriting ...
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1answer
52 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 ...
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1answer
34 views

Check Specific Connections within Graph

Say you have the skeleton of a graph: fullSkele = PolyhedronData["GreatRhombicosidodecahedron", "SkeletonRules"] and you've an arbitrary list of some fraction of ...
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2answers
104 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. ...
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0answers
43 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 ...
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1answer
71 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 ...
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1answer
141 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, ...
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2answers
281 views
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1answer
83 views
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1answer
114 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 ...
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3answers
311 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 ...
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1answer
127 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 ...
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0answers
87 views

Finding rings in a network

I am doing a research on networks which consist of polygons with different number of sides. Is there a way to find rings by BreadthFirstScan function. For ...
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1answer
56 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 ...
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1answer
83 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 ...
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0answers
105 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 ...
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3answers
184 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
215 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
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1answer
52 views
4
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1answer
311 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
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1answer
140 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
124 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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0answers
90 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 ...
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0answers
190 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
187 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
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1answer
164 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
185 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
57 views
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2answers
78 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
208 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
92 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 ...
4
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1answer
94 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 ...
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1answer
75 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 ...