added in forest fire graph generator and needed helper functions by charlescolley · Pull Request #71 · JuliaGraphs/MatrixNetworks.jl

charlescolley · 2023-02-14T00:19:23Z

No description provided.

codecov · 2023-02-14T00:23:44Z

Codecov Report

Merging #71 (417f88c) into master (7203a2a) will increase coverage by 0.30%.
The diff coverage is 99.03%.

@@            Coverage Diff             @@
##           master      #71      +/-   ##
==========================================
+ Coverage   92.38%   92.68%   +0.30%     
==========================================
  Files          21       22       +1     
  Lines        2126     2228     +102     
==========================================
+ Hits         1964     2065     +101     
- Misses        162      163       +1

Impacted Files	Coverage Δ
src/generators.jl	`95.36% <98.71%> (+0.86%)`	⬆️
src/network_formatting.jl	`100.00% <100.00%> (ø)`

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dgleich

Can you look at the comments?

dgleich · 2023-02-14T02:13:00Z

src/generators.jl

+                           seed::Union{Nothing,UInt}=nothing,
+                           random_node=x->rand(1:x)) where S
+
+    if !(seed === nothing)


Can you replace this with specifying the RNG where Random.GlobalRNG is the default? Then they can give StableRNG(seed) if they want reliable seeds...

GIven that we let the user pass in the random_node function as well, how should I adapt it to work with an rng variable?

Seems like random_node=(x,rng)->rand(rng,1:x)) would force the user to think about a seed if they want to adjust the parent's probability of being selected.

The convention is for rand functions in Julia to take in an optional random number generator to avoid using the global one. Users should have to think about how to make their random results reproducible if they want them :), but it should be easy enough ... The random node stuff is just a placeholder right now, let's not worry about it.

dgleich · 2023-02-14T02:14:23Z

src/generators.jl

+
+    end 
+
+    A =  list_of_list_to_sparse_matrix(neighbors)


Can you use the parametric types to handle this?

e.g. _convert_to_output(input, sparse) which will convert sparse to input type?

dgleich · 2023-02-14T02:17:19Z

src/generators.jl

+end 
+
+
+function _burn!(neighbors::Vector{Vector{S}},new_v::Int,v0::Int,burn_p::Float64,


IF this is easy --- can we make this a top level function? e.g. there are other instances where you want to do forest fire sampling... Since the process is the same, it'd be nice to be able to reuse the function.

What's the best interface for this to be a top function? burn(A,v0::Int,p::Float64) for just a single step and return final neighbor list of the random walk? Or something like burn(A,steps::Int, rand_v::Int->Int) which runs the process for a number of steps and selects random nodes by calling rand_v().

burn(A,v0,p) and burn!(A,v0,p,temparrays...) are the best top level interface

dgleich · 2023-02-14T02:18:12Z

src/network_formatting.jl

+matrix_to_list_of_list(A::MatrixNetwork) = matrix_to_list_of_list(eltype(A.ci),A)
+
+
+function matrix_to_list_of_list(::Type{S}, A::MatrixNetwork) where S 


Can you write these in terms of getting the rowptr/colval/etc.

These is the matrix_to_list_of_lists

dgleich · 2023-02-14T02:18:50Z

src/network_formatting.jl

@@ -0,0 +1,43 @@
+matrix_to_list_of_list(A::SparseMatrixCSC) = matrix_to_list_of_list(eltype(A.rowval),A)
+
+function matrix_to_list_of_list(::Type{S}, A::SparseMatrixCSC) where S 


There is a subtle bug here, this is correct for undirected graphs, but not for directed graphs since that will transpose in-edges to out-edges.

Not sure what the best solution for this is. When I wrote them it was intended for undirected graphs because the
forest_fire_graph is expecting an undirected input, and generates new edges with the intention of symmetrizing them.

I can either

Rename list_of_list_to_matrixto reference they’re for undirected neighbor lists

Write a _get_inedges for MatrixNetworks to be more careful, but we’d also need to rename the list_of_list_to_matrix function to better express what the output is, because it won’t be an undirected neighbor list.

Convert MatrixNetwork to a SparseCSCMatrix before calling the code, but this seems like a bad solution as the package is about the MatrixNetwork.

The standard solution in MatrixNetworks is just to take a transpose... if they want to avoid that, then they use a MatrixNetwork type instead.

ah, I was thinking about the wrong function! Ok that works

dgleich

Still a few small changes on burn...

dgleich · 2023-02-20T02:54:30Z

src/generators.jl


-function _burn!(neighbors::Vector{Vector{S}},new_v::Int,v0::Int,burn_p::Float64,
-                      toburn,burnt,burning,alive) where S 
+"""


Sorry if there was any misunderstanding, burn should not add the edges to the graph. It should simply return the the set of burned vertices. e.g. if you wanted to run a forest fire sample of an existing graph, you want to run "burn" from multiple vertices. This is a sampled graph that should have similar properties to the original. But you definitely don't want to add anything.

Taken care of! Any suggestions on tests that can be added to this routine? Currently just ensuring seeded calls return the same for MatrixNetwork and SparseMatrixCSC inputs.

dgleich · 2023-02-20T02:55:24Z

src/generators.jl

-   (i >= 1 && i <= size(A,1)) || throw(ArgumentError("i must be in {1,...,size(A,1)}"))
-   return A.ci[A.rp[i]:A.rp[i+1]-1],A.vals[A.rp[i]:A.rp[i+1]-1]
+    @boundscheck (i >= 1 && i <= size(A,1)) || throw(ArgumentError("i must be in {1,...,$(size(A,1))}"))
+    return A.ci[A.rp[i]:A.rp[i+1]-1],A.vals[A.rp[i]:A.rp[i+1]-1]


Do you need to return an array? can you return a generator or a view?

They're now returning views, and matrix_to_list_of_list uses collect to allocate the arrays needed.

src/generators.jl

…erators now, and small documentation changes.

added in forest fire graph generator and needed helper functions

3b6738e

dgleich reviewed Feb 14, 2023

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addressed comments in PR

e7e816c

dgleich reviewed Feb 20, 2023

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dgleich reviewed Feb 20, 2023

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updated interface to burn to return an Array, get_in/outedges use gen…

417f88c

…erators now, and small documentation changes.

		end


		function _burn!(neighbors::Vector{Vector{S}},new_v::Int,v0::Int,burn_p::Float64,

		matrix_to_list_of_list(A::MatrixNetwork) = matrix_to_list_of_list(eltype(A.ci),A)


		function matrix_to_list_of_list(::Type{S}, A::MatrixNetwork) where S

		@@ -0,0 +1,43 @@
		matrix_to_list_of_list(A::SparseMatrixCSC) = matrix_to_list_of_list(eltype(A.rowval),A)

		function matrix_to_list_of_list(::Type{S}, A::SparseMatrixCSC) where S

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charlescolley commented Feb 14, 2023

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