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Drawing the Graph of a complex chemical reaction network
I'm interested in how Mathematica or IGraph/M package can help with the visualization of complex chemical reaction mechanisms applied in fields like combustion, biochemistry, water radiolysis, or...
View ArticleConvert a graph to Lad format using a concise method
The LAD format is a kind of graph formats; see https://perso.liris.cnrs.fr/christine.solnon/SIP.htmlThe specific format requirements are as follows:Each graph is described in a text file. If the graph...
View ArticleSimulating network evolution based on common neighbors
I am new to studying networks in Mathematica and I would like to model the following network evolution process:Start with a random graph $g_0$ with $n$ nodes, $n$ even.At each time $t$, ach node $i$ is...
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How to construct a layered 3D graph of three community structures?
Consider:ClearAll["Global`*"];select[matrix_, lB_, uB_] := matrix*Map[Boole[lB <= # < uB] &, matrix, {-1}];SeedRandom[131];mm = RandomReal[1, {15, 15}]*...
View ArticleSierpinski carpet with GraphData
Is this graph in the list among the so-called "standard" structures used in GraphData? However, I have not found yet anything like "Carpet" or "Sponge" in the list of the objects that can be built....
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Graph with fixed vertex layout but curved edges
I have constructed a graph (network) whose vertices I want to be arranged in a square grid, I have already done this by means of the "GridEmbedding" GraphLayout, however this layout makes every edge a...
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How to get the optimal arrangement minimizing depth and maximizing level...
Given a graph like as follows:graph=Graph[{"Model14", "Model2", "Model5", "Model1", "Model8", "Model11", "Model9", "Model3", "Model10", "Model6", "Model13", "Model7", "Model4", "Model12"}, {"Model14"...
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How do I find all the nets of a polyhedron?
The following will show me a single example net of a polyhedronPolyhedronData["Dodecahedron", "Net"]AndPolyhedronData["Dodecahedron", "NetCount"]tells me that there are 43,380 ways to unfold a...
View ArticleEfficient Implementation of resistance distance for graphs?
Is there an implementation of the resistance distance matrix (or just resistance matrix) for graphs available in Mathematica?
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Why are WeightedAdjacencyMatrix and WeightedAdjacencyGraph inconsistent?
I have a weighted adjacent matrix of a graph:weightedMatrix]={{0, 0, 0, 1, -1, 1}, {0, 0, 0, 1, 1, -1}, {0, 0, 0, 0, 0, 1}, {1, 1, 0, 0, 1, 1}, {-1, 1, 0, 1, 0, 0}, {1, -1, 1, 1, 0, 0}};But when I try...
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How to generate random directed acyclic graphs?
How to programmatically build random directed acyclic graphs (DAG)? I know about the AcyclicGraphQ predicate and the TopologicalSorting function, though Mathematica does not offer any algorithm to...
View ArticleVisibility Graph of Polygon
Could anyone provide a function that takes a polygon as input and outputs its visibility graph ? Visibility GraphIf not, is there a function that checks whether a line segment lies inside a polygon?
View ArticleOrdering the Boundary Points of a Polygon
I feel like this should be simple, but I keep running into walls.Say someone gives you the coordinates of the vertices of a pentagon and the center point of the hexagon. Is there any way to get an...
View ArticleA cryptic message when converting a Graph to Graphics
In Mathematica 13.3 (Windows 11) I doGraph[{1, 2}, 1 \[UndirectedEdge] 2]then right-click on the result and choose "Convert To Graphics" from the menu that appears. Conversion is done seemingly...
View ArticleHow to speed up data stream (with graph6 format) reading?
I attempt to filter connected graphs with 8 vertices, 14 edges, and matching number three using the 'geng' tool and IGraphM.First way:<< IGraphM`;AbsoluteTiming[ Length[Select[IGImport["!geng 8...
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How to obtain positions of graphs satisfying certain conditions?
I first generate some random graphs, and then the following code can filter graphs with maximum degree 8.glist= Table[RandomGraph[{10, 25}], {i, 1, 10}];Select[glist, Max@VertexDegree[#] == 8 &]But...
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Odd behaviors of FindKPlex
Bug introduced in 9.0 and persisting through 14.0FindKPlex is new in 9.0.I have an example about it.g = Graph[{1 -> 4, 1 -> 7, 1 -> 9, 1 -> 16, 2 -> 5, 2 -> 6, 2 -> 8, 2 -> 18,...
View ArticleNetGraph won't accept EmbeddingLayers of different n
Why doesn't this work:NetGraph[{PartLayer[{1}], PartLayer[{2}],EmbeddingLayer[50, "Input" -> NetEncoder[{"Class", {"male", "female"}}]],EmbeddingLayer[50, "Input" -> NetEncoder[{"Class",...
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How can a directed network model be linked to Dataset[ ] for further...
REVISED Question:My only request is to know how to monitor the evolution of {agentStates, steps} in simulateSlow[...] function. In particular, how can I insert Monitor[Nest[...], StepMonitor :>...
View ArticleCan 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 at, which results in many...
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