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

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42
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2answers
9k views

How can I use Mathematica's graph functions to cheat at Boggle?

This question is inspired by a Stack Overflow question that I decided to solve using Mathematica. In addition to Mathematica, I thought I'd use some of the new version's graph-related functionality, ...
58
votes
3answers
1k views

Automatically generating a dependency graph of an arbitrary Mathematica function?

Has anyone written a function to pull the function dependencies of a function? That is, it would be nice to have a function that returns a list of function dependencies as a set of rules, terminating ...
21
votes
3answers
1k views

Generating graphs interactively (GUI)

I want to create graphs interactively using a GUI. I thought of using a ClickPane[] environment. The code I have (in part borrowed from the Documentation) works ...
13
votes
1answer
626 views

How can I conveniently call igraph through RLink?

Mathematica has lots of functions for working with graphs, but this functionality is not yet as mature as the igraph library. It is useful to have access to igraph from Mathematica, both for ...
14
votes
4answers
460 views

Can TreeForm be displayed “sideways”?

One recurrent problem I'm having with displays generated with TreeForm is that the expressions to be so displayed often at least one level with many (> 20) nodes ...
13
votes
4answers
373 views

How can I remove B -> A from a list if A -> B is in the list?

I have a list of transformations like this: list = {"A" -> "B", "B" -> "A", "C" -> "D"} As this is used to plot an undirected graph with ...
22
votes
2answers
3k views

How to play with Facebook data inside Mathematica?

I saw this post from Wolfram here and I would like to know how to import facebook data into Mathematica.
20
votes
2answers
2k views

Cycles of length N in a graph

If I have an undirected graph represented with an adjacency matrix, how can I find all the subgraphs which are a cycle of length N? I don't really know the math nor the programming language well, so ...
8
votes
1answer
742 views

How to speed up Minimum Spanning Tree algorithm?

How to speed up MST algorithm? I work with graphs and I have adopted Prim's algorithm for my needs, from here. The graphs which I use are very dense (number of vertexes: $V=500$ and every vertex is ...
15
votes
2answers
3k views

Solving the Travelling Salesman Problem

I've been trying to find some kind of mathematical computer software to solve the Travelling Salesman Problem. The Excel Solver is able to do it, but I've noticed there is a built-in function in ...
13
votes
1answer
362 views

Transform an expression into a graph that can be plotted with TreeGraph (not TreeForm)

I would like to plot an expression (like TreeForm does), but using the new TreeGraph functionality. ...
11
votes
2answers
1k views

Simple algorithm to find cycles in edge list

I have the edge list of an undirected graph which consists of disjoint "cycles" only. Example: {{1, 2}, {2, 3}, {3, 4}, {4, 1}, {5, 6}, {6, 7}, {7, 5}} Each ...
7
votes
2answers
634 views
21
votes
2answers
2k views

How to plot planar graphs as such?

A planar graph is a graph that can be drawn in the plane such that no two edges cross. For example, the graph ...
7
votes
3answers
222 views

Preserving labels when using graph functions

I am finding that some functions that accept a graph and return a transformed graph lose all the vertex and edge labels of the graph being transformed. For example, when I define a graph like this: ...
4
votes
3answers
612 views

How to find all graph isomorphisms in FindGraphIsomorphism

I found the second definition of the function FindGraphIsomorphism not working. Here's the definition Mathematica 8 gives: ...
29
votes
5answers
6k views

Custom arrow shaft

Inspired by Sjoerd C. de Vries' nice answer to this question, and the desire to pimp a Graph I did with Mathematica recently I would like to know if there are ways to customize the arrow's shaft ...
28
votes
1answer
937 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 ...
11
votes
4answers
9k views

Finding all simple paths between two vertices in a graph

There are built-in methods to find a shortest path between two vertices in a graph, and the question on finding all shortest paths between two vertices has gathered quite a bit of attention. A path ...
25
votes
3answers
3k views

Finding all shortest paths between two vertices

The built-in FindShortestPath and GraphDistance functions find the shortest path between two particular vertices in a graph. I ...
18
votes
2answers
757 views

Graph layout on a grid

Is it possible for Mathematica to layout a graph so that the connections lie on a grid? Furthermore, for graphs with multiple edges per vertex, is it possible to specify the location on the vertex ...
17
votes
3answers
2k views

How to get graph layout that reflects edge weights?

My heart soared to discover that Mathematica 8 offers support for specifying a weighted adjacency matrix in WeightedAdjacencyGraph. But it seems that, regardless of the weights between edges, the ...
14
votes
3answers
3k views

How to generate random directed acyclic graphs?

How to programmatically build random directed acyclic graphs (DAG)? I know about the AcyclicGraphQ predicate and the ...
18
votes
5answers
915 views

How can I replace bi-directional DirectedEdge pairs in a Graph with a single UndirectedEdge?

The Cayley graphs produced by Mathematica 8.0's CayleyGraph function represent actions that are their own inverses in an unconventional way: rather than using a ...
12
votes
4answers
1k views

Finding elementary cycles of (directed) graphs

I need to enumerate all the simple cycles (i.e. elementary cycles where no vertex is repeated other than the starting) of a graph which has both directed and undirected edges, where we can treat the ...
8
votes
2answers
231 views

Cases[data,Colon[key,_]] vs. Cases[data,key:_] toward XPath, XQuery

Exploring methods to index and search tree-structured key:value pairs via named-entity index (key paths) as opposed to Position-based indexing. Using Rule as ...
5
votes
3answers
315 views

Centrality measures for single nodes

I am producing a graph, generated by a list of adjacent nodes. (The list looks like {1 ->583, 1->2977, 2->14, 4->1293, 5->221, ...}. Each node of my ...
2
votes
2answers
295 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 ...
1
vote
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 ...
14
votes
3answers
494 views

Determining all possible traversals of a tree

I have a list: B={423, {{53, {39, 65, 423}}, {66, {67, 81, 423}}, {424, {25, 40, 423}}}}; This list can be visualized as a tree using ...
21
votes
1answer
572 views

Strategies for solving problems involving searches

As an example of a search-oriented problem, consider finding all constrained $n$-colorings of a graph. An "$n$-coloring" associates one of $n \ge 1$ colors to each vertex in such a way that no edge ...
13
votes
5answers
456 views

Graph from binary matrix (not adjacency) respecting the original matrix positions

I have a binary matrix. My objective is to connect every close (without "jump") elements with value equal to 1, but I must keep the point positions, just like it's shown at the image. Can somebody ...
21
votes
3answers
825 views

Finding a “not-shortest” path between two vertices

In designing a routine for making a simple three dimensional (5x5x5) labyrinth, I realized that my solutions (a solution is a labyrinth includes a single path from {1, 1, 1} to {5, 5, 5} in a 5 x5x5 ...
13
votes
2answers
1k views

Creating a graph with variable size of vertices and variable thickness of edges

I'm trying to create a graph to represent transitions between different states of a system. I would like to represent the time the systems spent in a state with the size of the vertex and the ...
10
votes
3answers
736 views

How to plot layered graphs?

Given a directed acyclic graph, there is always a possibility to plot the graph as layers, where nodes always send edges into one direction (usually down), to successive layers, and never backwards. ...
7
votes
1answer
762 views

Drawing a graph with specified edge lengths

I was wondering if it was possible to ask Mathematica to draw a graph provided some set of vertices: $(v_1, ..., v_N) \in V$ connected by $M$ edges $(e_1, ..., e_M) \in E$, where the length of each ...
4
votes
3answers
713 views

Minimum spanning Tree from a weighted adjacency graph

Note: Cross-posted at http://community.wolfram.com/groups/-/m/t/137658?p_p_auth=8QnKtT9I I have a really big graph, 40x40. Here is my code ...
4
votes
2answers
833 views

Finding face vertices from the face adjacency graph

I have a question about face adjacency graphs. Suppose that I have an adjacency matrix ...
12
votes
2answers
307 views

Listing subgraphs of G isomorphic to SubG

If I have an undirected graph G, how could I write a function in Mathematica to obtain a list of subgraphs of G that are isomorphic to some other undirected graph SubG? I'd like to learn how to ...
10
votes
2answers
273 views

Using Gather to rearrange my data

I have a list of elements: {{1, 2}, {1, 5}, {2, 6}, {3, 7}, {4, 8}, {5, 6}, {5, 9}, {9, 13}, {10,11}, {11, 12}, {11, 15}, {15, 16}} I have to divide it into ...
7
votes
2answers
793 views

Is it possible to export a graph as graphic to Excel?

It is straightforward to export lists to Excel with Export. Can I export a graphic image, too? This does not work: ...
6
votes
1answer
812 views

Mathematica Package for Bayesian Networks

Are there any packages that allow the simulation of Bayesian Networks with Mathematica? I found what seemed to be a promising package (Dynamics) on a Brown University URL, ...
5
votes
3answers
157 views

Converting expressions to “edges” for use in TreePlot, Graph

This question is similar to this: Nested list to graph. How to "flatten" an arbitrary expression, eg expr = a[b[c, d[e][f], g], h] to a list of key-value pairs ...
5
votes
3answers
227 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
5
votes
2answers
217 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 ...
3
votes
2answers
283 views

Combinatorica: Girth[] and FindCycle[] disagreement

Warning: run the following code in a fresh Mma session, as some symbols could be shadowed (depending on your Mma version) While trying to answer this question, I fell into the following: ...
1
vote
1answer
495 views

Adding an image background to a graph that uses vertexposition

Hello Mathematica stackexchange community! I need your help on a research project. I'm looking to create a graph g with vertices in specifies places and then use an image I have as the background of ...
1
vote
1answer
138 views

How can I change the Graph required data such as EdgeWeight,VertexWeight,EdgeCapacity,VertexCapacity in the Graph?

I asked this question in different form and because I couldn't receive the proper answer so I have to change my question.I know that was my fault sorry.I need to change the Matrix Data of nodes and ...
10
votes
4answers
565 views

Ordering vertices in GraphPlot

I'm new here, so forgive me if this question is not well-posed/duplicates an earlier question - although I've searched for similar questions without success. I'm trying to present a plot of ...
7
votes
0answers
268 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 ...