Heterogeneous lags for networks with delay #104

lindnemi · 2021-10-25T16:18:17Z

Delays are now implemented by passing the history function to the components. This allows to define several different lags at every network component and to directly control these lags via the parameter tuple p = (vertexp, edgep). Hence, there is no need for the 3-tuple syntax anymore and it is removed from the codebase. This refactor is important, since previously only homogeneous lags were possible.

For fast solving with heterogeneous parameters we rely on efficient interpolations via h(p,t, idxs=idxs). However, due to a bug in the Julia compiler, some type instability occurs and the performance suffers when using the idxs=idxs interface (SciML/DelayDiffEq.jl#218).

For a diffusion on a small complete graph with 10 vertices and with homogeneous lags i observed 10x slower solving than in the previous versions which used a mutating history function h(buffer, p,t), see test/delay_test.jl.

I am hesitant to merge this PR before the bug has been resolved.

lindnemi · 2021-11-22T10:36:13Z

The history function is now wrapped, such that it always has access to the global parameters and the global index ranges of the corresponding vertices. As a consequence a call to h has now a shorter syntax. A typical component looks like:

function delay_coupling(e, θ_s, θ_d, h_θ_s, h_θ_d, p, t)
    hist = h_θ_s(t - p[1]; idxs=1)
    e[1] = p[2] * sin(hist - θ_d[1])
    return nothing
end

This should provide reasonable support for heterogeneous delays. However due to the interpolation bug mentioned above even medium-sized heterogeneous systems take very long to solve.

hexaeder · 2022-06-22T09:53:10Z

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
 fail-fast: false
 matrix:
 version:
- - '1.6'
+ - '1.8'


Suggested change

- '1.8'

- '1.6'

- '1.8'

we shouldn't skip testing LTS?

hexaeder · 2022-06-22T09:57:17Z

examples/Project.toml

@@ -18,4 +19,4 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

 [compat]
-NetworkDynamics = "0.5"
+NetworkDynamics = "≥ 0.5"


Are the examples really compatible with all breaking versions since 0.5 and also in the future? Maybe we should remove the compat all together in this file as this might be misleading...

hexaeder · 2022-06-22T10:45:25Z

src/ComponentFunctions.jl

@@ -285,7 +285,7 @@ Here `dv`, `v`, `p` and `t` are the usual ODE arguments, while

 - `dim` is the number of independent variables in the edge equations and
 - `sym` is an array of symbols for these variables.
- - `coupling` is a Symbol describing if the EdgeFunction is intended for a directed graph (`:directed`) or for an undirected graph (`{:undirected, :fiducial}`). `:directed` is intended for directed graphs. `:undirected` is the default option and is only compatible with SimpleGraph. in this case f! should specify the coupling from a source vertex to a destination vertex. `:fiducial` lets the user specify both the coupling from src to dst, as well as the coupling from dst to src and is intended for advanced users.
+ - `coupling` is a Symbol describing if the EdgeFunction is intended for a directed graph (`:directed`) or for an undirected graph (`{:undirected, :fiducial}`). `:directed` is intended for directed graphs. `:undirected` is the default option and is only compatible with SimpleGraph. in this case f should specify the coupling from a source vertex to a destination vertex. `:fiducial` lets the user specify both the coupling from src to dst, as well as the coupling from dst to src and is intended for advanced users.


Only tangentially related to this PR, but this docstring should really mention how fiducial work. I.e. you specify the dimensionality N, you get passed a 2N state vector where the first N elements will be presented to the dst and the second N elements will be presented to src

hexaeder · 2022-06-22T10:50:19Z

src/ComponentFunctions.jl

+ dim % 2 == 0 ? nothing : error("Fiducial edges are required to have even dim.
+  The first dim args are used for src -> dst,
+  the second for dst -> src coupling.")


The old version with && is more idomatic than using the ternary operator i'd say. Also, multi line strings are possible in Julia, but only from 1.7 onwards if I remeber correctly. Therefore, the " and , solution is better because it does not include all of the whitespace in the literal string

src/NetworkDiffEq.jl

hexaeder · 2022-06-22T10:54:36Z

src/NetworkDiffEq.jl

@@ -111,15 +120,14 @@ end
 # struct for both cases

 #@Base.kwdef struct NetworkDE{G, GDB, elV, elE, TUV, TUE, Th<:AbstractArray{elV}}
-Base.@kwdef struct NetworkDE{G,GDB,elV,elE,TUV,TUE,Th<:Union{AbstractArray,Nothing}}
+@Base.kwdef struct NetworkDE{G, GDB, elV, elE, TUV, TUE}


most styleguides ommit those spaces afaik

src/Utilities.jl

Co-authored-by: Hans Würfel <git@wuerfel.io>

lindnemi

i agree with all your suggestions. some of them had already been adressed in main but accidentally leaked from this 8 month old branch. thanks for the review!

lindnemi added 12 commits October 18, 2021 10:46

refactor submodules

691e542

remove unused code

9d85d93

set up a simple test

b8a0b02

remove internal exports

c3c82dd

first attempts

115f163

adding type information everywhere

7b95aa2

minor

06236f4

Static Edge promotion is not used anymore

872cf3d

remove history from NetworkDE

c0ac04c

tuple syntax not necessary anymore

a8abe62

fixing the tests

f03df36

simplify tests (minor)

0bdb6d4

lindnemi added the do-not-pull label Oct 25, 2021

lindnemi added 2 commits November 18, 2021 12:21

new example with delay

2ef5325

wrap h, change function signature

33e60b9

lindnemi added 5 commits November 22, 2021 11:38

Merge branch 'main' into hetero_delay

57eadcf

Merge branch 'main' into hetero_delay

7889fe5

adjustments to new conventions

a2cb157

bump version

25effce

test on 1.8

ad40cd4

lindnemi removed the do-not-pull label Jun 22, 2022

hexaeder reviewed Jun 22, 2022

View reviewed changes

lindnemi added 7 commits June 22, 2022 14:15

update docs with DDE

f9681b1

update dde test

e53caa4

Literate compatible example

9f1caf8

rename

5c5a582

remove compat

aff297e

fix arguments

eeadf9b

Update tests.yml

1f80006

lindnemi and others added 5 commits June 22, 2022 14:23

Update src/NetworkDiffEq.jl

c5993ef

Co-authored-by: Hans Würfel <git@wuerfel.io>

Update NetworkDiffEq.jl

ba0ff11

Improve docstrings

18efdc4

fix test

f77f25e

Apply suggestions from code review

8691c06

Co-authored-by: Hans Würfel <git@wuerfel.io>

lindnemi commented Jun 22, 2022

View reviewed changes

hopefully lower docs build time

066d8fa

lindnemi merged commit 9978f01 into main Jun 22, 2022

lindnemi deleted the hetero_delay branch June 22, 2022 16:14

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Heterogeneous lags for networks with delay #104

Heterogeneous lags for networks with delay #104

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Heterogeneous lags for networks with delay #104

Heterogeneous lags for networks with delay #104

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