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

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1answer
304 views

Adjacency Matrix for an Undirected Graph

Here is an undirected graph ...
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0answers
97 views

shortest paths in probabilistically weighted edges? [duplicate]

I understand Mathematica can find shortest paths. However, is it also able to find the most probable paths? I mean this is a case where edges are given probabilistic wights (from 0 to 1) and the most ...
1
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1answer
137 views

How can I stop DiscreteMarkovProcess[] from relabeling vertices?

I'm attempting to calculate the mean first passage time between two vertices, $v_1$ and $v_2$, provided some undirected graph $G$. However, I noticed that running the following script: ...
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0answers
83 views

What algorithm is Mathematica using for FirstPassageTimeDistribution[]?

What algorithm is Mathematica 9 using for FirstPassageTimeDistribution[]? Is it attempting to use PseudoInverse[] on the ...
0
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2answers
127 views

How can I efficiently and uniformly sample the set of vertices a fixed edge-wise distance away from a chosen vertex?

I have a large graph $G$, which may be either directed or undirected. How would I use DepthFirstScan[] or BreadthFirstScan[] to ...
2
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2answers
443 views

Draw network graph and get the coordinates of each node

I would like to draw an undirected graph by specifying the nodes and the edges among them. This is currently done by, for example: ...
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1answer
134 views

How can I extract coordinates of the nodes of my graph?

I have this output for my graph. ...
2
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3answers
389 views

Drawing a complete graph of an ego network

I have an ego network (a network of a person (ego) and his friends). It is drawn with the ego at the center surrounded by the friends. It might be possible that all the friends are connected to each ...
2
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0answers
195 views

Fast calculation of commute distances on large graphs (i.e. fast computation of the pseudo-inverse of a large Laplacian / Kirchhoff matrix)

I have a large, locally connected and undirected graph $G$ with $\approx 10^4$ vertices and $\approx 10^5$ to $\approx 10^6$ edges. Moreover I can bound the maximum vertex degree as $Q_{max}$. I ...
9
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1answer
331 views

Caching of Graph Graphics

In this answer, Simon Woods concludes that when you display an expression with head graph more than once, something is getting stored somewhere. I looked into it too and found out this only happens if ...
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3answers
292 views

Converting Mesh in Density Plots to a Graph

Consider the following line of code: ...
4
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0answers
338 views

Counting paths of a certain length between a source and sink vertex

I have a graph $G$, which may be directed or not, and I was wondering if there was an efficient way of using, say, BreadthFirstScan[] and FindShortestPath[] to count the number of paths between some ...
1
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1answer
217 views

How do I create a graph with randomly directed edges starting from a undirected graph?

I have an undirected graph $G$. How would I randomly assign directions to some fraction $p$ of the edges? How might I do this efficiently / quickly provided I have a large graph structure? For ...
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2answers
334 views

How to specify VertexCoordinates as geographic coordinates of cities?

I have been very busy these days with giving the VertexCoordinates of the cities the geographic coordinates from ...
3
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1answer
166 views

How to get a list of 3-connected graphs?

I'd like to use GraphData to get a list of graphs with vertex connectivity at least 3. I know GraphData["Nonplanar", 6] gives ...
2
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1answer
122 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 ...
5
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1answer
165 views

Why do vertex labels disappear when I edit with drawing tools?

I'm trying to change the text and arrow style in GraphPlot using the drawing tool, but the the vertex labels disappear when I do that: ...
3
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1answer
176 views

double arrow in GraphPlot

Is it possible to combine two edges into one with a double arrow? For example: ...
7
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2answers
115 views

How can I recover a graph from a graphical output in a notebook after resetting the kernel?

I have an old Mathematica notebook with an output for a graph structure $G$ I would like to recover. However, the routine for building up the graph is stochastic, so I can't simply rerun the code. ...
7
votes
1answer
252 views

Making FindShortestPath a little bit sloppy [duplicate]

I have a dense graph, and I'd like to find multiple "almost shortest" paths from a source vertex, $v_s$, to a sink vertex, $v_s$, on an undirected graph $G$. How can I repeatedly run ...
5
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2answers
283 views

Is there something akin to “SubgraphIsomorphismQ” in Mathematica 9?

Provided two unlabeled graphs, $G$ and $H$, I would like to test where $H$ is a subgraph of $G$. In other words, I'd like to test whether we can prune some fixed number of vertices or edges from $G$ ...
11
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1answer
420 views

Dynamic visualization of Graph[] on a webpage

How can we embed a dynamic version of a Graph object on a web page, similar to the one showcased on the networkx home page? This sort of dynamic visualization can ...
5
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2answers
241 views

Graph does not evaluate some options when not displayed

How can I force Graph to evaluate all its options without actually displaying the graph itself? Evaluating the following code ignores the ...
1
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1answer
246 views

Weighted Kirchhoff Matrix?

I have a weighted graph and I want its graph Laplacian matrix (what Mathematica calls the Kirchhoff matrix in the unweighted case). Is there an easy way to get this? For example, the command: ...
2
votes
1answer
128 views

Is it possible for me to explicitly specify a point list for SpatialGraphDistribution?

The function RandomGraph[SpatialGraphDistribution[n, r]] generates a random geometric graph over $[0,1]^2$ where vertices are connected if they are within a ...
2
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1answer
149 views

Determining whether two k-chromatic graphs are equivalent (not simply isomorphic) using IsomorphicGraphQ?

In a previous question of mine, I asked whether Mathematica's built-in routines could determine an isomorphism for two $k$-chromatic graphs, Determining whether two $k$-chromatic graphs are isomorphic ...
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2answers
302 views

Determining whether two $k$-chromatic graphs are isomorphic (respecting vertex coloration)

Consider the case where I have two $k$-chromatic graphs $G_1$ and $G_2$, i.e. two graphs where individual vertices can be colored with one of a set of $k$ total colors, and I would like to determine ...
5
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3answers
774 views

How to create a planar graph from a set of random points

Question Given a set of points in the plane, how can you create a planar graph in the standard graph representation of Mathematica (version 9 or higher), from these points? Background A planar ...
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1answer
114 views

How does SocialMediaData determine vertex size

How does SocialMediaData determine the size of graph vertices, e.g. on what does the vertex size depend in, say, a Facebook friend network graph?
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2answers
190 views

HighlightGraph with style

In this picture you see a graph. The shortest path between vertex 5 and vertex 3 is highlighted in red. Instead I want blue highlighted edges of thickness 10. ...
6
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1answer
134 views

Tooltip not working in web deployed cdf

I deployed a CDF file in a web page. I used both Mouseover and Tooltip functions. They both work in the raw CDF file. The ...
1
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2answers
799 views

How do I divide the columns of a matrix by the sum of its elements?

I am trying to create a transition matrix for a network. In order to do this, I need to sum down the column (the out degree), and then divide the column by the out degree in order to normalize it. ...
5
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2answers
250 views

Is there something wrong with VertexConnectivity

Note: this is fixed in version 10. As I noticed in the documentation VertexConnectivity is defined as the following The vertex connectivity of a graph $g$ is ...
4
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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 ...
3
votes
1answer
713 views

Adjacency List representation of a graph

I am looking to draw a graph knowing a simple adjacency representation of the graph like: A = {{1, 3}, {2, 3}, {3, 4, 5}, {4, 5}, {5}} Where ...
7
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3answers
2k views

Travelling salesman with start and end points for 30 points

I am doing a route optimisation for delivery vehicles and failing dismally. Please see problem statement below. My current solution uses FindShortestTour, but this does not have defined start and end ...
1
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0answers
104 views

Extracting Facebook Managed accounts (pages) in Mathematica? [duplicate]

I want to use Mathematica to explore various relationships on my Facebook pages. I've been able to successfully extract information on my personal Facebook page using the build in Social Media ...
0
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1answer
80 views

combining NeighborhoodGraph and RandomGraph

I have Combinatorica` and GraphUtilities` loaded in version 9 of Mathematica. If I then set: ...
3
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2answers
138 views

CommunityGraphPlot doesn't size

When I need to plot a 'large' graph with CommunityGraphPlot the output is always sized at the Mathematica default value. The Graph object itself can be resized with ImageSize option. However that ...
6
votes
3answers
400 views

Export Graph to PDF

I know that I exported Graphs to PDFs before but it doesn't seem to work any more. I tried K5 = GraphData[{"Complete", 5}] Export["K5.PDF", K5] And I get a PDF ...
3
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2answers
219 views

The same value of VertexSize for vertices in different graphs causes different vertices size

I generated some graphs. The smallest vertices in the 1st graph should be the same size as the smallest vertices in the second graph. The smallest vertices have the same size (...
3
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1answer
199 views

How to get VertexDelete to work?

I'm using Mathematica 9 and want to delete a single vertex and all associated edges on a graph but can't seem to get the function VertexDelete function to work. My code is below. I declare a graph ...
11
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2answers
553 views

Dynamic graphics are less responsive inside a Manipulate

I have some code which displays a GraphPlot and allows the user to click on any vertex in the graph to display some information about that vertex in a popup window. ...
1
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2answers
236 views

Number of edges to each polygon of a graph constructed from an image

I have an image which looks like from How to convert an image to a graph and get the positions of the edges? which by using MorphologicalGraph becomes a graph ...
2
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0answers
114 views

Strange double evaluation using MorphologicalGraph

(MMA 9.0.0 on Mac OS/X 10.8) Please consider the following snippet (this is as SMALL as I could make it -- my attempts at making a smaller repro-case eliminated the effect that I am investigating) ...
3
votes
1answer
718 views

How to label the Vertex and, or Edge labels with their weight

I noticed that the Mathematica 9.0 documentation only mentions the usage of "Name" to label the vertexlabel or edgelabel in the Graph. Is there an option to use the Weights automatically just as ...
31
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1answer
1k views

Finding the likeliest path in a Markov process

With Mathematica 9, we have the addition of various processes, among which the discrete Markov process. Given a transition probability matrix m, such a process is ...
2
votes
2answers
175 views

Most efficient way to output a cycle starting from an unordered list of graph vertices

I have some graph $G$ and a list of vertices $(v_1, ..., v_N) \in V$. Using graph structures in Mathematica version 9.0, what is the most efficient way to determine whether or not $(v_1, ..., v_N)$ ...
6
votes
1answer
298 views

What algorithm is Mathematica 9 using for “SpectralEmbedding” of graphs?

When I specify that a graph should be realized using the "SpectralEmbedding" procedure, what paper / algorithm for spectral embedding is this based on? I was unable to find any documentation for ...
8
votes
1answer
304 views

How can I sequentially apply different graph embeddings?

Imagine I have some graph G, and I perform a graph embedding using a command like: ...