From 169c93d29e353c0f22fe67009702124b32be6daf Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Sat, 5 Dec 2020 12:46:53 +0100
Subject: [PATCH] Improved performance of simulate methods: elimination of the
unecessary call of isabsorbing() during the simulation.
Now the package is a bit more efficient than DiffEqJump.jl with the
Catalyst.jl interface which is encouraging, see bench/pkg/catalyst.jl.
---
bench/pkg/catalyst.jl | 32 +++++++
core/biochemical_network.jl | 183 ++++++++++++++++++++++++++++++++++++
core/model.jl | 33 ++++---
models/ER.jl | 4 +
models/SIR.jl | 4 +
5 files changed, 242 insertions(+), 14 deletions(-)
create mode 100644 bench/pkg/catalyst.jl
create mode 100644 core/biochemical_network.jl
diff --git a/bench/pkg/catalyst.jl b/bench/pkg/catalyst.jl
new file mode 100644
index 0000000..1f81b00
--- /dev/null
+++ b/bench/pkg/catalyst.jl
@@ -0,0 +1,32 @@
+
+using BenchmarkTools
+using MarkovProcesses
+using Catalyst
+using DiffEqJump
+
+load_model("ER")
+set_param!(ER, "k1", 0.2)
+set_param!(ER, "k2", 40.0)
+ER.buffer_size = 100
+ER.estim_min_states = 8000
+
+b_pkg = @benchmark simulate(ER)
+
+rs = @reaction_network begin
+ c1, S + E --> SE
+ c2, SE --> S + E
+ c3, SE --> P + E
+end c1 c2 c3
+p = (0.2,40.0,1.0) # [c1,c2,c3]
+tspan = (0., 100.)
+u0 = [100., 100., 0., 0.] # [S,E,SE,P]
+
+# solve JumpProblem
+dprob = DiscreteProblem(rs, u0, tspan, p)
+jprob = JumpProblem(rs, dprob, Direct())
+jsol = solve(jprob, SSAStepper())
+
+b_catalyst = @benchmark solve(jprob, SSAStepper())
+
+#plot(jsol,lw=2,title="Gillespie: Michaelis-Menten Enzyme Kinetics")
+
diff --git a/core/biochemical_network.jl b/core/biochemical_network.jl
new file mode 100644
index 0000000..c2592c4
--- /dev/null
+++ b/core/biochemical_network.jl
@@ -0,0 +1,183 @@
+
+using MacroTools
+
+function get_multiplicand_and_species(expr::Expr)
+ @assert expr.args[1] == :*
+ multiplicand = reduce(*, expr.args[2:(end-1)])
+ str_species = String(expr.args[end])
+ return (multiplicand, str_species)
+end
+get_multiplicand_and_species(sym::Symbol) = (1, String(sym))
+
+function get_str_propensity(propensity::Expr, dict_species::Dict, dict_params::Dict)
+ str_propensity = ""
+ for op in propensity.args[2:end]
+ str_op = String(op)
+ if haskey(dict_species, str_op)
+ str_propensity *= "xn[$(dict_species[str_op])] * "
+ elseif haskey(dict_params, str_op)
+ str_propensity *= "p[$(dict_params[str_op])] * "
+ else
+ str_propensity *= "$(str_op) * "
+ end
+ end
+ return str_propensity[1:(end-2)]
+end
+function get_str_propensity(propensity::Symbol, dict_species::Dict, dict_params::Dict)
+ str_propensity = String(propensity)
+ if haskey(dict_species, str_propensity)
+ str_propensity = "xn[$(dict_species[str_propensity])]"
+ elseif haskey(dict_params, str_propensity)
+ str_propensity = "p[$(dict_params[str_propensity])]"
+ else
+ str_propensity = "$(str_propensity)"
+ end
+ return str_propensity
+end
+
+macro biochemical_network(expr_name,expr_network)
+ transitions = String[]
+ dict_species = Dict{String,Int}()
+ dict_params = Dict{String,Int}()
+ dim_state = 0
+ dim_params = 0
+ list_expr_reactions = Any[]
+ # First we detect all of the species
+ for expr_reaction in expr_network.args
+ local isreaction = @capture(expr_reaction, TR_: (reactants_ => products_, propensity_))
+ if isreaction
+ push!(list_expr_reactions, expr_reaction)
+ push!(transitions, String(TR))
+ # Parsing reactants, products
+ for reaction_part in [reactants, products]
+ # If there's several species interacting / produced
+ if typeof(reaction_part) <: Expr && reaction_part.args[1] == :+
+ for operand in reaction_part.args[2:end]
+ mult, str_species = get_multiplicand_and_species(operand)
+ if !haskey(dict_species, str_species)
+ dim_state += 1
+ dict_species[str_species] = dim_state
+ end
+ end
+ else
+ mult, str_species = get_multiplicand_and_species(reaction_part)
+ if !haskey(dict_species, str_species)
+ dim_state += 1
+ dict_species[str_species] = dim_state
+ end
+ end
+ end
+ end
+ if !isreaction && !(typeof(expr_reaction) <: LineNumberNode)
+ error("Error in an expression describing a reaction")
+ end
+ end
+ list_species = [species for species in keys(dict_species)]
+ # Then we detect parameters in propensity expressions
+ # Parameters are the symbols that are not species (at this point we know all of the involved species)
+ for expr_reaction in list_expr_reactions
+ local isreaction = @capture(expr_reaction, TR_: (reactants_ => products_, propensity_))
+ if typeof(propensity) <: Expr
+ @assert propensity.args[1] == :* "Only product of species/params/constants are allowed in propensity"
+ for operand in propensity.args[2:end]
+ if typeof(operand) <: Symbol
+ str_op = String(operand)
+ # If it's not a species, it's a parameter
+ if !(str_op in list_species) && !haskey(dict_params, str_op)
+ dim_params += 1
+ dict_params[str_op] = dim_params
+ end
+ end
+ end
+ elseif typeof(propensity) <: Symbol
+ str_op = String(propensity)
+ if !(str_op in list_species) && !haskey(dict_params, str_op)
+ dim_params += 1
+ dict_params[str_op] = dim_params
+ end
+ end
+ if !isreaction && !(typeof(expr_reaction) <: LineNumberNode)
+ error("Error in an expression describing a reaction")
+ end
+ end
+ # Let's write some lines that creates the function f! (step of a simulation) for this biochemical network
+ nbr_rand = rand(1:1000)
+ nbr_reactions = length(list_expr_reactions)
+ basename_func = "$(replace(expr_name, ' '=>'_'))_$(nbr_rand)"
+ expr_model_f! = "function $(basename_func)_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Union{Nothing,String}}, xn::Vector{Int}, tn::Float64, p::Vector{Float64})\n\t"
+ # Computation of nu and propensity functions in f!
+ str_l_a = "l_a = ("
+ str_test_isabsorbing = "("
+ l_nu = [zeros(Int, dim_state) for i = 1:nbr_reactions]
+ for (i, expr_reaction) in enumerate(list_expr_reactions)
+ local isreaction = @capture(expr_reaction, TR_: (reactants_ => products_, propensity_))
+ # Writing of propensities function
+ str_propensity = get_str_propensity(propensity, dict_species, dict_params)
+ expr_model_f! *= "a$(i) = " * str_propensity * "\n\t"
+ # Anticipating the write of the function isabsorbing
+ str_test_isabsorbing *= str_propensity * "+"
+ # Update the nu of the i-th reaction
+ nu = l_nu[i]
+ if typeof(reactants) <: Expr && reactants.args[1] == :+
+ for operand in reactants.args[2:end]
+ mult, str_species = get_multiplicand_and_species(operand)
+ nu[dict_species[str_species]] -= mult
+ end
+ else
+ mult, str_species = get_multiplicand_and_species(reactants)
+ nu[dict_species[str_species]] -= mult
+ end
+ if typeof(products) <: Expr && products.args[1] == :+
+ for operand in products.args[2:end]
+ mult, str_species = get_multiplicand_and_species(operand)
+ nu[dict_species[str_species]] += mult
+ end
+ else
+ mult, str_species = get_multiplicand_and_species(products)
+ nu[dict_species[str_species]] += mult
+ end
+ expr_model_f! *= "nu_$i = $(Tuple(nu))\n\t"
+ # Anticipating the line l_a = (..)
+ str_l_a *= "a$(i), "
+ end
+ str_test_isabsorbing = str_test_isabsorbing[1:(end-2)] * ")"
+ str_l_a = str_l_a[1:(end-2)] * ")\n\t"
+ expr_model_f! *= str_l_a
+ expr_model_f! *= "asum = sum(l_a)\n\t"
+ expr_model_f! *= "if asum == 0.0\n\t\t"
+ expr_model_f! *= "copyto!(xnplus1, xn)\n\t\t"
+ expr_model_f! *= "return nothing\n\t"
+ expr_model_f! *= "end\n\t"
+ # Computation of array of transitions
+ expr_model_f! *= "l_nu = (" * reduce(*, ["nu_$i, " for i = 1:nbr_reactions])[1:(end-2)] * ")\n\t"
+ expr_model_f! *= "l_str_R = $(Tuple(transitions))\n\t"
+ # Simulation of the reaction
+ expr_model_f! *= "u1 = rand()\n\t"
+ expr_model_f! *= "u2 = rand()\n\t"
+ expr_model_f! *= "tau = - log(u1) / asum\n\t"
+ expr_model_f! *= "b_inf = 0.0\n\t"
+ expr_model_f! *= "b_sup = a1\n\t"
+ expr_model_f! *= "reaction = 0\n\n\t"
+ expr_model_f! *= "for i = 1:$(nbr_reactions)\n\t\t"
+ expr_model_f! *= "if b_inf < asum*u2 < b_sup\n\t\t\t"
+ expr_model_f! *= "reaction = i\n\t\t\t"
+ expr_model_f! *= "break\n\t\t"
+ expr_model_f! *= "end\n\t\t"
+ expr_model_f! *= "b_inf += l_a[i]\n\t\t"
+ expr_model_f! *= "b_sup += l_a[i+1]\n\t"
+ expr_model_f! *= "end\n\t"
+ expr_model_f! *= "nu = l_nu[reaction]\n\t"
+ expr_model_f! *= "for i = 1:$(dim_state)\n\t\t"
+ expr_model_f! *= "xnplus1[i] = xn[i]+nu[i]\n\t"
+ expr_model_f! *= "end\n\t"
+ expr_model_f! *= "l_t[1] = tn + tau\n\t"
+ expr_model_f! *= "l_tr[1] = l_str_R[reaction]\n"
+ expr_model_f! *= "end\n"
+
+ expr_model_isabsorbing = "isabsorbing_$(basename_func)(p::Vector{Float64},xn::Vector{Int}) = $(str_test_isabsorbing) === 0.0"
+ model_f! = eval(Meta.parse(expr_model_f!))
+ model_isabsorbing = eval(Meta.parse(expr_model_isabsorbing))
+ return :(ContinuousTimeModel($dim_state, $dim_params, $dict_species, $dict_params, $transitions,
+ $(zeros(dim_params)), $(zeros(Int, dim_state)), 0.0, $model_f!, $model_isabsorbing; g = $list_species))
+end
+
diff --git a/core/model.jl b/core/model.jl
index 894a7a3..26136ba 100644
--- a/core/model.jl
+++ b/core/model.jl
@@ -67,16 +67,13 @@ function simulate(m::ContinuousTimeModel; p::Union{Nothing,AbstractVector{Float6
for i = 2:m.estim_min_states
m.f!(vec_x, l_t, l_tr, xn, tn, p_sim)
tn = l_t[1]
- if tn > m.time_bound
+ if tn > m.time_bound ||Â vec_x == xn
+ isabsorbing = (vec_x == xn)
break
end
n += 1
copyto!(xn, vec_x)
_update_values!(full_values, times, transitions, xn, tn, l_tr[1], i)
- isabsorbing = m.isabsorbing(p_sim,xn)
- if isabsorbing
- break
- end
end
# If simulation ended before the estimation of states
if n < m.estim_min_states
@@ -97,17 +94,18 @@ function simulate(m::ContinuousTimeModel; p::Union{Nothing,AbstractVector{Float6
i += 1
m.f!(vec_x, l_t, l_tr, xn, tn, p_sim)
tn = l_t[1]
- if tn > m.time_bound
+ if tn > m.time_bound
+ i -= 1
+ break
+ end
+ if vec_x == xn
+ isabsorbing = true
i -= 1
break
end
copyto!(xn, vec_x)
_update_values!(full_values, times, transitions,
xn, tn, l_tr[1], m.estim_min_states+size_tmp+i)
- isabsorbing = m.isabsorbing(p_sim,xn)
- if isabsorbing
- break
- end
end
# If simulation ended before the end of buffer
if i < m.buffer_size
@@ -172,7 +170,8 @@ function simulate(product::SynchronizedModel; p::Union{Nothing,AbstractVector{Fl
for i = 2:m.estim_min_states
m.f!(vec_x, l_t, l_tr, xn, tn, p_sim)
tn = l_t[1]
- if tn > m.time_bound
+ if tn > m.time_bound ||Â vec_x == xn
+ isabsorbing = (vec_x == xn)
break
end
n += 1
@@ -181,7 +180,6 @@ function simulate(product::SynchronizedModel; p::Union{Nothing,AbstractVector{Fl
next_state!(Snplus1, A, xn, tn, tr_n, Sn; verbose = verbose)
_update_values!(full_values, times, transitions, xn, tn, tr_n, i)
copyto!(Sn, Snplus1)
- isabsorbing = m.isabsorbing(p_sim,xn)
isacceptedLHA = isaccepted(Snplus1)
if isabsorbing ||Â isacceptedLHA
break
@@ -214,13 +212,17 @@ function simulate(product::SynchronizedModel; p::Union{Nothing,AbstractVector{Fl
i -= 1
break
end
+ if vec_x == xn
+ isabsorbing = true
+ i -= 1
+ break
+ end
copyto!(xn, vec_x)
tr_n = l_tr[1]
next_state!(Snplus1, A, xn, tn, tr_n, Sn; verbose = verbose)
_update_values!(full_values, times, transitions,
xn, tn, tr_n, m.estim_min_states+size_tmp+i)
copyto!(Sn, Snplus1)
- isabsorbing = m.isabsorbing(p_sim,xn)
isacceptedLHA = isaccepted(Snplus1)
if isabsorbing || isacceptedLHA
break
@@ -288,11 +290,14 @@ function volatile_simulate(product::SynchronizedModel;
i -= 1
break
end
+ if vec_x == xn
+ isabsorbing = true
+ break
+ end
copyto!(xn, vec_x)
tr_n = l_tr[1]
next_state!(Snplus1, A, xn, tn, tr_n, Sn; verbose = verbose)
copyto!(Sn, Snplus1)
- isabsorbing = m.isabsorbing(p_sim,xn)
isacceptedLHA = isaccepted(Snplus1)
n += 1
end
diff --git a/models/ER.jl b/models/ER.jl
index f8a6fe7..11e703b 100644
--- a/models/ER.jl
+++ b/models/ER.jl
@@ -16,6 +16,10 @@ function ER_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Union{No
a3 = p[3] * xn[3]
l_a = (a1, a2, a3)
asum = sum(l_a)
+ if asum == 0.0
+ copyto!(xnplus1, xn)
+ return nothing
+ end
nu_1 = (-1, -1, 1, 0)
nu_2 = (1, 1, -1, 0)
nu_3 = (1, 0, -1, 1)
diff --git a/models/SIR.jl b/models/SIR.jl
index 82ea26f..93fbbb9 100644
--- a/models/SIR.jl
+++ b/models/SIR.jl
@@ -15,6 +15,10 @@ function SIR_f!(xnplus1::Vector{Int}, l_t::Vector{Float64}, l_tr::Vector{Union{N
a2 = p[2] * xn[2]
l_a = (a1, a2)
asum = sum(l_a)
+ if asum == 0.0
+ copyto!(xnplus1, xn)
+ return nothing
+ end
# column-major order
nu_1 = (-1, 1, 0)
nu_2 = (0, -1, 1)
--
GitLab