SimpleHypergraphs.jl - loading hypergraph from text file

Question

I'm using the SimpleHypergraphs.jl library and trying to construct a hypergraph from a text file such as a csv.

For example, I'd like to load a hypergraph from a csv file like this:

0.0, 7.0, 0.0, 0.0
1.3, 2.8, 4.5, 0.0
0.0, 1.3, 3.1, 4.2
1.2, 0.0, 5.6, 5.0

using SimpleHypergraphs
using CSV

df = CSV.read("edge_weights.csv", DataFrame)
m = Matrix{Float64}(df)
h = Hypergraph(m)

I receive the following error: "ERROR: MethodError: no method matching Hypergraph(::Matrix{Float64})"

I'm new to Julia and I would really appreciate an example of how I could accomplish this. Thanks!

score 2 · Accepted Answer · answered May 03 '21 at 21:56

The matrix that is passed as a Hypergraph constructor should have elements of type Union{Nothing, T} where T is some numeric type (e.g. Matrix{Union{Float64,Nothing}} rather than just be a Matrix{Float64}.

In SimpleHypegraphs.jl, we use nothing (rather than 0) to represent that a vertex does not belong to a hyperedge since in many hypergraph algorithms/applications it is possible for a vertex to belong to a hyper-edge with a zero weight.

Hence you could read your file with the following code (for reproducibility I put the file content into a text variable):

using DataFrames, CSV, SimpleHypergraphs

txt = """0.0, 7.0, 0.0, 0.0
1.3, 2.8, 4.5, 0.0
0.0, 1.3, 3.1, 4.2
1.2, 0.0, 5.6, 5.0"""

df = CSV.read(IOBuffer(txt), DataFrame;header=0)

mat = Matrix{Union{Float64,Nothing}}(df)

This matrix can now easily be used as a Hypergraph constructor.

julia> h1 = Hypergraph(mat)
4×4 Hypergraph{Float64, Nothing, Nothing, Dict{Int64, Float64}}:
 0.0  7.0  0.0  0.0
 1.3  2.8  4.5  0.0
 0.0  1.3  3.1  4.2
 1.2  0.0  5.6  5.0

However, this might be not exactly what you need because zeros (0.0) represent a situation where vertices belong to hyperedges with zero weights:

draw(h1, HyperNetX)

Hence, you might actually want to convert zeros to nothings to represent situation where the vertices do not belong to hyperedges:

h2 = Hypergraph(replace(mat, 0 => nothing))

Now you get what you wanted:

draw(h2, HyperNetX)

SimpleHypergraphs.jl - loading hypergraph from text file

1 Answers1