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

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7
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0answers
41 views

What system functions use VertexWeights?

EdgeWeights -> are used by a lot of functions, but I can't find any exposed usage for VertexWeights ->. I'm not asking ...
7
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0answers
74 views

Graph: PropertyValue changes and Dynamic

I almost never work with Graph in Mathematica but lately I helped someone with it. For this, I tried to make an animation using ...
6
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0answers
98 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 ...
5
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0answers
122 views

How to generate a random flow graph?

A flow graph is a rooted directed graph that the root reaches all other vertices. I need to generate a random flow graph in Mathematica. My idea is to use ...
5
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0answers
178 views

How to draw block diagrams as Graph objects?

In the documentation ClosedLoopResponsesWithAPIDController, There is a very nice block diagram. I want to create my own block diagrams similar to this. I clicked on the diagram and pressed ...
5
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0answers
180 views

Citation of the algorithms used in FindGraphCommunities

For my research work I need to put a comparison of different community detection algorithms. Instead of implementing all those algorithms once again, I would like to use the methods already provided ...
5
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0answers
230 views

How to draw hypercube graphs

I'd like to draw hypercube projections like those on the Wikipedia page: I tried with HypercubeGraph[6] but the graph does not look right; it is not ...
4
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0answers
125 views

Efficient Generation of Subgraphs (or, unfriend a friend a day)

NB: If you're not interested in the back-story, you could simply jump forward to the code which I'm seeking to optimize. Also, I believe this code would only work for MMA 8.0 and above. My friends ...
4
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0answers
323 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 ...
4
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0answers
479 views

Finding a Graph Shortest Path with Custom Graph Distance Function

What is the best way to find a shortest path by using a custom distance function? I'm trying to play a little bit with the concept of using distributions instead of a deterministic weight value for ...
3
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0answers
41 views

Undocumented options for “BalloonEmbedding” in GraphLayout

From an error message, I see some options of the BalloonEmbedding method for GraphLayout: ...
3
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0answers
58 views

FindGraphCommunities method options?

FindGraphCommunitites has a couple of method options: "Modularity", "Hierarchical", ...
3
votes
0answers
149 views

Undirected Network and its Monte Carlo Simulation

So I have this array of points, in the form {x, {y,z}}, where x is the node number assigned when I used the locator pane to make a network, and y and z are its unitary coordinates. The graph is made ...
3
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0answers
52 views

Does anyone know the options for “HierarchicalEdgeBundling” in Mathematica?

I'm looking to reproduce the types of graph layout that are possible in D3 (http://bl.ocks.org/mbostock/7607999) in Mathematica. Since Mathematica doesn't explicitly support force directed edge ...
3
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0answers
193 views

Understanding performance: graph connected components

I need to analyze directed graphs with 10M edges, 1M vertices, and 300K strongly connected components, so that the largest one contains 400K vertices. I read some explanations of Leonid Shifrin here, ...
3
votes
0answers
121 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
321 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 ...
3
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0answers
281 views

How to compute the Lovász number for the given graph in Mathematica?

Here is a graph whose adjacency matrix is ...
2
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0answers
28 views

Custom graph distribution

I am working with random graphs a lot. It's quite easy to describe random graph using, adjacency matrix or just a list of edges. However I am thinking that I might benefit from describing random ...
2
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0answers
98 views
+50

How can I scrape the social network for a subset of users in Twitter?

Clearly one cannot scrawl the entire network... but I'd like to extract a statistically representative sample from the network. More specifically, I'd like to access the graph induced by scraping the ...
2
votes
0answers
37 views

Replicate CommunityGraphPlot as a Graph

Is it possible to format a Graph object in a similar way to CommunityGraphPlot, but retain it as a Graph? I've been playing with FindGraphCommunities but I'm obviously missing some of the ...
2
votes
0answers
46 views

Bugs in VertexContract function?

I think there may be two bugs in the VertexContract function: 1) The updated graph does not include reasonable edgeweights 2) The function does not actually reduce the number of vertices in the ...
2
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0answers
61 views

Choosing a List as VertexWeight for a TreeGraph

I would like to map every vertex of my TreeGraph to an List. ...
2
votes
0answers
64 views

Belief Network, Bayesian network

There is already a question about simulating Bayesian networks with Mathematica (Mathematica Package for Bayesian Networks). However, are there any packages or approaches which help in computing the ...
2
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0answers
59 views

Finding quasi-cliques

Is it possible to find quasi-cliques in a graph in Mathematica 10? I don't think it has been implemented, so are there any solutions to do this? Or do I have to export the graph data somehow and do ...
2
votes
0answers
56 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 ...
2
votes
0answers
190 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 ...
2
votes
0answers
295 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 ...
2
votes
0answers
182 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 ...
2
votes
0answers
111 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) ...
2
votes
0answers
218 views

How to predict some constant number of values with NeuralNetworks

Example: << NeuralNetworks` data = {Sin[#]} & /@ Range[0, 4 Pi, 0.5]; learn = data[[1 ;; 15]]; Now, lets fit our neural network: ...
1
vote
0answers
28 views

ConnectedComponents problem of syntactic structure

In Mathematica 10, ConnectedComponent computes the list of vertices belonging to strongly connected components. In the following simple example with a graph with no edges, the result is as follows: ...
1
vote
0answers
25 views

DataRange not working in GraphPlot

I am trying to create a a GUI that uses the GraphPlot function to automatically generate graph vertices. I am using the VertexCoordinateRules option to designate that I want some of the vertices to be ...
1
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0answers
57 views

Better layout for large a directed graph?

This shows a directed graph for an iterated n-bit pseudo-random function parameterized by s. ...
1
vote
0answers
37 views

Better control of vertex positions in GraphPlot?

I am trying to graphically visualize a sort of a transformation network. My program generates a list of vertices and edges and I want to turn that into a visually clear graph fulfilling a few ...
1
vote
0answers
73 views

Draw mesh edge / map a graph to a mesh

I am doing a "force density" method to generate a mesh under certain load. The original mesh is like this: Then, I generate a IncidenceMatrix from the graph for further matrix transformation and ...
1
vote
0answers
33 views

Successive addition or deletion of vertices (or edges) in graph

I am trying to perform a kind of dynamic graph simulation where vertices and edges of graph are added and deleted according to the current state of the graph at each time step. I know that there are ...
1
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0answers
48 views

What do the default shapes/colors in DiscreteMarkovProcess Graph mean?

In making markov chains, I know how to do that, but I am curious as to what the different colors, and shapes of the vertexes in the graph output mean. as example; ...
1
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0answers
20 views

FindIndependentEdgeSet behaves differently in v9 and v10

The following code gets different output in v9 and v10. ...
1
vote
0answers
41 views

Purpose of VertexWeight

I am trying to partition a graph into partitions of equal weight (on the vertex). I looked at the documentation, and found VertexWeight, which seems to attach a weight to a vertex. In the details, ...
1
vote
0answers
52 views

Multi-named Nodes (or Overlapping Nodes) in TreePlot, or Merging Trees

If there is a series of rules from which a TreePlot is made: {D->C, C->B, B->A} And a new node is added that is technically the same as an existing ...
1
vote
0answers
36 views

Export format for graphs loses type information?

I have a situation where I am adding properties to vertices in my graph. In my case, I am adding a moduleId, which is an integer, and a kind, which is a string. I attach a weight to the edge as well. ...
1
vote
0answers
78 views

Is there a minor bug in Neal Alexander's TopologicalSortAll[]?

There is an amazing answer to this question: All possible topological orderings of a graph By Neal Alexander. However, as user "dark blue" (I am not this user) notes: ...
1
vote
0answers
47 views

Finding optimal inclusion cutoff to define subgraph of a “large” weighted graph

I have a weighted graph G with ~2.5K vertices and ~250K edges. (The edge weights are all in (0, 1), and the weight of each vertex is derived as the maximum of the ...
1
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0answers
68 views

Spread multiple edges by a specified scaled distance (Mathematica 10)

Is there way to spread multiple edges by a specified scaled distance for Graph function in Mathematica 10, something similar to MultiedgeStyle in GraphPlot for example, I would like to write: ...
1
vote
0answers
88 views

Using NMinimize to solve the Multi Commodity Flow problem

I have the following optimization problem and I was hoping to solve it with NMinimize. Unfortunately, I don't get the desired result. I would like to get an optimal vector for $d_{e}$. This is how ...
1
vote
0answers
125 views

Replace part in a matrix that matches specific pattern

I have the following problem. Given a matrix L which looks as follows, Matrix L is a link, route matrix. Further, I got the following vector (d), which indicates the demand per vertex combination. ...
1
vote
0answers
53 views

Graph plotting: specify layers for layered drawing

Mathematica can do layered graph drawing with LayeredGraphPlot or GraphLayout -> "LayeredEmbedding". Is it possible to ...
1
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0answers
226 views

Triangular lattice with periodic boundary conditions

I am trying to generate an equilateral triangular lattice with fixed vertices and periodic boundary conditions. I am supposed to assign an index (starting from 0) to each vertex in my lattice and then ...
1
vote
0answers
59 views

GraphPlot not working properly

The code ...