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

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0
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1answer
74 views

FindCycle not working as expected for multigraph

Say I have a simple multigraph like so: edges = {DirectedEdge[a, b], DirectedEdge[b, c], DirectedEdge[c, a]}; g = Graph[Join[edges, edges]] ...
2
votes
0answers
59 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
votes
1answer
76 views

Finding if a graph contains an even cycle

I am looking for a simple boolean-like function which could check if a graph contains an even cycle. I'm aware there is ExtractCycles but I'm looking for a true/false output than a list of cycles.
6
votes
1answer
377 views

Is it possible to draw a curved edge between two vertexes of a graph? [duplicate]

The following code generates a graph. ...
4
votes
1answer
218 views

Intelligent vertex placement in large tree graphs

This question about graph layout is fairly general, but can be illustrated in the case of the Collatz Conjecture. Collatz created the following function over integers greater than 1: If the integer ...
3
votes
1answer
107 views

How to change the vertex shape

(Using V9 on Ubuntu) Consider the following code, to create a graph. ...
2
votes
1answer
167 views

(Tree) Graph Layout

I am trying to draw a graph in a tree-like form. I can't use TreeGraph because what I am drawing is not properly a tree (has loops) so TreeGraph won't draw it. Here is the code: ...
0
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2answers
115 views

Normalize centrality measures

How I can normalise centrality measures? Can I use Normalize function? I give example of unnormalized measures ...
2
votes
1answer
102 views

Overlapping EdgeLabels

I have to make a directed graph for a maximum flow algorithm assignment. Although I have managed to make the graph for the better part, it still needs some work. The problem is that Mathematica ...
3
votes
2answers
141 views

Slow rendering in GraphPlot3D

Is there a way to speed up this rendering? I have to make this call many times in order to make an animation of some dynamics on the graph g. Thus dynamics are carried in the list var. Each entry in ...
1
vote
1answer
120 views

Coloring vertices according to a function using GraphPlot3D

This question is similar but not identical to a related question called: coloring-vertices-using-graphplot . I need to color the vertices of a graph according to a function, f that is defined on the ...
2
votes
4answers
170 views

Invisible graph edges

I have a fairly sparse adjacency matrix for which I can draw the graph. Right now, two nodes $i$ and $j$ are connected, or not ($w_{ij} \in \{0,1\}$). However, I have come up with a way to define new ...
1
vote
1answer
57 views

Having trouble using different options with GraphPlot [closed]

I am extremely new to Mathematica and I am trying to plot some graphs. GraphPlot[{1->2, 2->3, 3->1}] works just fine. But as soon as I try to use ...
3
votes
1answer
187 views

Interpreting a formula from Graph Theory - where do x and y come from?

I'm trying to understand the generating function for OEIS A062734, which is in Mathematica. Essentially, despite knowing no Mathematica at all, I think I can parse most of it, but where do $x$ and $y$ ...
2
votes
1answer
47 views

VertexConnectivity and FindVertexCut disagree [duplicate]

I'm trying to use Mathematica to compute the minimal vertex cut for graphs. From what I understood, VertexConnectivity of a graph should correspond to the number of vertices in the minimal vertex cut. ...
2
votes
1answer
312 views

Vertex Names as Labels in GraphPlots

I'm trying to use GraphPlot to draw a Graph which is constructed from an adjacency matrix and am having trouble with the labels in the plot. I am doing (data is a silly example) the following: ...
3
votes
0answers
90 views

FindGraphCommunities method options?

FindGraphCommunitites has a couple of method options: "Modularity", "Hierarchical", ...
1
vote
2answers
123 views

Split graph into independent maximal cliques?

Does Mathematica have a method to partition the vertices of a graph into maximal independent subsets, such that each subset generates a complete subgraph? Edit: The partition should be maximal in the ...
2
votes
0answers
96 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
1answer
89 views

Twisting a graph layout (by fixing the $x$ coordinate of all its vertices)

I would like to draw a given graph $G$ in a specific way and I would like to know whether Mathematica can do it in a (semi-)automated way. My goal is to draw the graph $G$ in 2D, fixing all the $x$ ...
0
votes
1answer
82 views

How to use Hold on a variable defined as a graph

I'm working on doing operations on different graphs and getting their probability node degree distributions using a simple algorithm. If I have many defined graphs, for example: ...
4
votes
1answer
143 views

Minimal Colouring of Graph Vertices

Is there a way to colour graph vertices minimally in new Mathematica? I tried loading MinimalVertexColoring with the old Combinatorica package but it doesn't work ...
7
votes
3answers
318 views

Drawing a graph with vertex avoiding edges? (Handling vertices that must be colinear?)

I'd like to draw something like the following graph: ...
4
votes
1answer
139 views

FindShortestPath with VertexWeight

I have a weighted graph on which I want to perform some FindShortestPath calculations. However, the problem is that my weights are defined for vertices with ...
0
votes
2answers
198 views

Using different colors in TreeForm?

I've used TreeForm, and I appreciate that the syntax is fairly short, especially in comparison with TreeGraph. Is it possible ...
7
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0answers
48 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 ...
6
votes
2answers
157 views

Test existence of a path from one side of a graph to another

I'm trying to determine how I can test if a path exists from one side of a graph to another as efficiently as possible. If I have the Lines given by: ...
28
votes
1answer
582 views

Visual representation of a Ranking over time (image provided)

[Disclaimer: I initially posted this question on stackOverflow 2 months ago and think it might be better suited for this forum (link to original question)] The graph below shows a ranking of ...
4
votes
1answer
86 views

Edge Labels with distance between vertices

I am trying to make traveling salesman type graph using the locations of NFL stadiums as the vertices. I need to get the EdgeLabels to appear was the distance between the vertices. I was able to ...
6
votes
2answers
151 views

Visualizing subgraphs while specifying the locations of vertexes

I would like to visualize separate connected components of a graph defined by data points lying in the two-dimensional plane by surrounding each connected component subgraph by a bounding curve. I ...
4
votes
1answer
152 views

System of differential equations on a directed graph

I want to use Mathematica to model blood flow through a capillary network. The approach we are using is going to be to create a directed graph, and have a system of differential equations at each ...
1
vote
2answers
129 views

How do you apply an algorithm individually to an array with many graphs

I have and array with many graphs to which I want to apply an algorithm (below) to each graph in an array that contains all my graphs. ...
2
votes
1answer
172 views

Community detection on weighted graphs?

The documentation says that FindGraphCommunities works with weighted graphs. I've been playing around with a complete graph with weighted edges, and FindGraphCommunities always returns a single ...
2
votes
0answers
70 views

Choosing a List as VertexWeight for a TreeGraph

I would like to map every vertex of my TreeGraph to an List. ...
3
votes
1answer
164 views

Visually Separating Cliques in Graphs

I have a graph with 189 vertices, more than 10,000 edges and 20 cliques. As one can imagine, this graph is a mess when trying to display it. I'd really like to display the graph, separated into ...
0
votes
0answers
62 views

Transform NMinimze into LinearProgramming formulation

I have the following maximization problem that I currently try to solve with Minimize/NMinimize. Unfortunately, this kind of solution method takes really long for large systems of equations and ...
1
vote
1answer
151 views

Computing Domination Numbers of Graphs

Is there a way to get Mathematica to compute the domination number (size of the smallest dominating set) of a graph? There doesn't seem to be a direct command for this, so I'm not sure if there would ...
1
vote
1answer
240 views

Changing the size of arrows in a directed graph?

How can I change the size of arrows in a directed graph? By default, the arrows are too big and clutter the graph.
2
votes
0answers
101 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 ...
1
vote
0answers
44 views

“Partial” graph layout (with a fixed core)?

Is there a way to apply a graph lay out algorithm to a Graph object in such a way that a subset of its vertices and a subset of its edges are fixed beforehand, and ...
1
vote
0answers
69 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 ...
5
votes
0answers
151 views

Finding quasi-cliques

What is the best way to identify quasi-cliques in a graph in Mathematica? 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 ...
2
votes
1answer
71 views

How to invoke default VertexShapeFunction and EdgeShapeFunction from custom ones?

For this question, g is a Graph object (of order ~2K) such that the VertexWeight and ...
1
vote
3answers
107 views

How to control which nodes get placed at each radius with GraphLayout → “RadialEmbedding”?

I have a directed graph each of whose nodes belongs to exactly one of three groups: "sources", "sinks", and "both". As these names suggest, nodes in the "sources" group have only outgoing edges; ...
1
vote
1answer
170 views

Can degenerating Nicomachus' triangle down to $0$ area by using `Graph` be done?

I noticed a pattern in Nicomachus' Triangle that might be used to reduce the triangle to the number line. If the Edge size could be set to the absolute difference ...
2
votes
2answers
163 views

Speeding up the generation of all k-edge-coloring of a graph

A $k$-edge-coloring of a graph $G=(V,E)$ is a function from $E$ to $\{1,\ldots,k\}$, so in other words every edge of $G$ receives one of the $k$ colors available. (In particular, note that we are not ...
12
votes
2answers
237 views

Graph smoothing keeping vertices fixed?

Context Given a Graph like this one: ...
1
vote
0answers
76 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
127 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
148 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. ...