Mendes Multistate Model

Taken from Gupta and Mendes, An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems, Computation, 6 (9), 2018.

using Catalyst, JumpProcesses, JumpProblemLibrary, Plots, Statistics
fmt = :png

:png

Our model is

jprob = JumpProblemLibrary.prob_jump_multistate
rn  = jprob.network
reactions(rn)

18-element Vector{Catalyst.Reaction}:
 kon, S1 + S2 --> S4
 kAon, S1 + S3 --> S5
 kon, S2 + S5 --> S6
 koff, S4 --> S1 + S2
 kAon, S3 + S4 --> S6
 kAoff, S5 --> S1 + S3
 koff, S6 --> S2 + S5
 kAoff, S6 --> S3 + S4
 kAp, S6 --> S7
 koff, S7 --> S2 + S8
 kAoff, S7 --> S4 + S9
 kAdp, S7 --> S6
 kon, S2 + S8 --> S7
 kAon, S1 + S9 --> S8
 kAon, S4 + S9 --> S7
 kAoff, S8 --> S1 + S9
 kAdp, S8 --> S5
 kAdp, S9 --> S3

Plot solutions by each method

methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve(), RDirect())
shortlabels = [string(leg)[15:end-2] for leg in methods]
tf      = 10.0 * jprob.tstop
prob    = DiscreteProblem(rn, jprob.u0, (0.0, tf), jprob.rates)
varlegs = ["A_P" "A_bound_P" "A_unbound_P" "RLA_P"]
@variables t S7(t) S8(t) S9(t)
varsyms = [
    [S7,S8,S9],
    [S9],
    [S7,S8],
    [S7]
]
varidxs = []
for vars in varsyms
    push!(varidxs, [findfirst(isequal(sym),unknowns(rn)) for sym in vars])
end

p = []
for (i,method) in enumerate(methods)
    jump_prob = JumpProblem(rn, prob, method, save_positions=(false, false))
    sol = solve(jump_prob, SSAStepper(), saveat=tf/1000.)
    solv = zeros(1001, 4)
    for (i,varidx) in enumerate(varidxs)
        solv[:,i] = sum(sol[varidx,:], dims=1)
    end
    if i < length(methods)
        push!(p, plot(sol.t, solv, title=shortlabels[i], legend=false, format=fmt))
    else
        push!(p, plot(sol.t, solv, title=shortlabels[i], legend=false, format=fmt))
    end
end
push!(p, plot((1:4)', framestyle = :none, legend=:inside, labels=varlegs))
plot(p..., layout=(6,2), format=fmt)

Benchmarking performance of the methods

function run_benchmark!(t, jump_prob, stepper)
    sol = solve(jump_prob, stepper)
    @inbounds for i in 1:length(t)
        t[i] = @elapsed (sol = solve(jump_prob, stepper))
    end
end

run_benchmark! (generic function with 1 method)

nsims = 100
benchmarks = Vector{Vector{Float64}}()
for method in methods
    jump_prob = JumpProblem(rn, prob, method, save_positions=(false, false))
    stepper = SSAStepper()
    time = Vector{Float64}(undef, nsims)
    run_benchmark!(time, jump_prob, stepper)
    push!(benchmarks, time)
end

medtimes = Vector{Float64}(undef,length(methods))
stdtimes = Vector{Float64}(undef,length(methods))
avgtimes = Vector{Float64}(undef,length(methods))
for i in 1:length(methods)
    medtimes[i] = median(benchmarks[i])
    avgtimes[i] = mean(benchmarks[i])
    stdtimes[i] = std(benchmarks[i])
end
using DataFrames

df = DataFrame(names=shortlabels, medtimes=medtimes, relmedtimes=(medtimes/medtimes[1]),
               avgtimes=avgtimes, std=stdtimes, cv=stdtimes./avgtimes)

sa = [text(string(round(mt,digits=3),"s"),:center,12) for mt in df.medtimes]
bar(df.names,df.relmedtimes,legend=:false, fmt=fmt)
scatter!(df.names, .05 .+ df.relmedtimes, markeralpha=0, series_annotations=sa, fmt=fmt)
ylabel!("median relative to Direct")
title!("Multistate Model")

Appendix

These benchmarks are a part of the SciMLBenchmarks.jl repository, found at: https://github.com/SciML/SciMLBenchmarks.jl. For more information on high-performance scientific machine learning, check out the SciML Open Source Software Organization https://sciml.ai.

To locally run this benchmark, do the following commands:

using SciMLBenchmarks
SciMLBenchmarks.weave_file("benchmarks/Jumps","Mendes_multistate_example.jmd")

Computer Information:

Julia Version 1.10.7
Commit 4976d05258e (2024-11-26 15:57 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 128 × AMD EPYC 7502 32-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver2)
Threads: 1 default, 0 interactive, 1 GC (on 128 virtual cores)
Environment:
  JULIA_CPU_THREADS = 128
  JULIA_DEPOT_PATH = /cache/julia-buildkite-plugin/depots/5b300254-1738-4989-ae0a-f4d2d937f953

Package Information:

Status `/cache/build/exclusive-amdci3-0/julialang/scimlbenchmarks-dot-jl/benchmarks/Jumps/Project.toml`
  [6e4b80f9] BenchmarkTools v1.6.0
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  [37e2e46d] LinearAlgebra
  [9a3f8284] Random
  [10745b16] Statistics v1.10.0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`

And the full manifest:

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  [efce3f68] WoodburyMatrices v1.0.0
  [ddb6d928] YAML v0.4.12
  [c2297ded] ZMQ v1.4.0
⌅ [68821587] Arpack_jll v3.5.1+1
  [6e34b625] Bzip2_jll v1.0.8+4
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [2702e6a9] EpollShim_jll v0.0.20230411+1
  [2e619515] Expat_jll v2.6.4+3
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [f5851436] FFTW_jll v3.3.10+3
  [a3f928ae] Fontconfig_jll v2.15.0+0
  [d7e528f0] FreeType2_jll v2.13.3+1
  [559328eb] FriBidi_jll v1.0.16+0
  [0656b61e] GLFW_jll v3.4.0+2
  [d2c73de3] GR_jll v0.73.12+0
  [78b55507] Gettext_jll v0.21.0+0
  [f8c6e375] Git_jll v2.47.1+0
  [7746bdde] Glib_jll v2.82.4+0
  [3b182d85] Graphite2_jll v1.3.14+1
  [2e76f6c2] HarfBuzz_jll v8.5.0+0
⌅ [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.1.1+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.1+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [aae0fff6] LSODA_jll v0.1.2+0
  [dd4b983a] LZO_jll v2.10.3+0
⌅ [e9f186c6] Libffi_jll v3.2.2+2
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.7.0+0
  [7add5ba3] Libgpg_error_jll v1.51.1+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [4b2f31a3] Libmount_jll v2.40.3+0
  [89763e89] Libtiff_jll v4.7.1+0
  [38a345b3] Libuuid_jll v2.40.3+0
⌅ [856f044c] MKL_jll v2024.2.0+0
  [e7412a2a] Ogg_jll v1.3.5+1
  [458c3c95] OpenSSL_jll v3.0.15+3
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.55.5+0
⌅ [30392449] Pixman_jll v0.43.4+0
⌅ [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.2+0
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+2
  [2381bf8a] Wayland_protocols_jll v1.36.0+0
  [02c8fc9c] XML2_jll v2.13.5+0
  [aed1982a] XSLT_jll v1.1.42+0
  [ffd25f8a] XZ_jll v5.6.4+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+3
  [0c0b7dd1] Xorg_libXau_jll v1.0.12+0
  [935fb764] Xorg_libXcursor_jll v1.2.3+0
  [a3789734] Xorg_libXdmcp_jll v1.1.5+0
  [1082639a] Xorg_libXext_jll v1.3.6+3
  [d091e8ba] Xorg_libXfixes_jll v6.0.0+0
  [a51aa0fd] Xorg_libXi_jll v1.8.2+0
  [d1454406] Xorg_libXinerama_jll v1.1.5+0
  [ec84b674] Xorg_libXrandr_jll v1.5.4+0
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+1
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.2+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+3
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+1
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.6+1
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.1+0
  [8f1865be] ZeroMQ_jll v4.3.5+3
  [3161d3a3] Zstd_jll v1.5.7+0
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.56.3+0
  [1a1c6b14] gperf_jll v3.1.1+1
  [a4ae2306] libaom_jll v3.11.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.45+1
  [a9144af2] libsodium_jll v1.0.20+3
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+2
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [9abbd945] Profile
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`