Turing and ODEs

Using Julia and Turing to fit compartmental models.

Bayes
Turing
Julia
Epidemiology
Author
Affiliation
Published

August 13, 2022

Exploring Julia and ODEs

This post is exploring the use of Julia, Turing, and ODEs and largely expands on the work from Simon Frost’s awesome epirecipes.

Getting Started with Julia

Julia as a statistical programming language/environment has some really neat properties.

Speed, generally speed.

Turing also has some neat elements when it comes to probabilistic computing/programming. The key feature that interests me is the ability to switch between sampling approaches (e.g., Gibbs, Hamiltonian Monte Carlo, no u-turn sampling, sequential) while keeping the same syntax and model structure. While I absolutely love Stan and have spent many hours learning and the syntax (and it is actively developed, highly optimized, etc), I sometimes wish I could explore other sampling approaches due to strange posteriors (especially when it comes to times when SMC might be better).

The Approach

This is a pretty vanilla post, in which we will first create some fake data from a known distribution and then fit said data. As always, we will bring in the required packages.

using DifferentialEquations
using DiffEqSensitivity
using Random
using Distributions
using Turing
using DataFrames
using StatsPlots

Now we can generate a simple three compartment model, with S (susceptibles), I, (infected), and R (recovered).

Additionally:

  • On average 10 contacts are made per day
  • The contact rate is 0.05 (probability of passing infection to any given contact)
  • Those who are infected recover on average every 5 days
  • Immunity lasts for a 180 days on average before people become susceptible again
  • Population size of 6,000 individuals
  • Standard mass-action approach

Something that looks like the following:

using Luxor
using MathTeXEngine
Drawing(200, 200, "sirs.png")
origin()
setline(10)
Luxor.arrow(Point(-40,0),Point(0,0))
Luxor.arrow(Point(-0,0),Point(40,0))
fontsize(15)
Luxor.text(L"S",Point(-40,20), halign = :center)

Luxor.text(L"I",Point(0,20), halign = :center)
Luxor.text(L"R",Point(40,20), halign = :center)
fontsize(12)
Luxor.text(L"β*c",Point(-20,10), halign = :center)
Luxor.text(L"γ",Point(20,10), halign = :center)
Luxor.text(L"δ",Point(0,-15), halign = :center)

loopx = 30
loopy = 40
adjx = 6
adjy = -2
Luxor.arrow(
    Point(40,0) + Point(-adjx,adjy),
    Point(40,0) + Point(-loopx,-loopy),
    Point(-40,0)+ Point(loopx,-loopy),
    Point(-40,0)+Point(adjx,adjy)
)
finish()

SIRS Compartmental Model

function sir_ode!(du,u,p,t)
    (S,I,R,C) = u
    (β,c,γ, δ) = p
    N = S+I+R
    infection = β*c*I*S/N
    recovery = γ*I
    wane = δ * R
    @inbounds begin
        du[1] = -infection + wane
        du[2] = infection - recovery
        du[3] = recovery - wane
        du[4] = infection 
    end
    nothing
end;


tmax = 365.0
tspan = (0.0,tmax)
obstimes = 1.0:1.0:tmax
u0 = [5990.0,10.0,0.0,0.0] # S,I.R,C
p = [0.05,10.0,0.20, 1.0/180]; # β, c, γ, δ


prob_ode = ODEProblem(sir_ode!,u0,tspan,p);


sol_ode = solve(prob_ode,
            Tsit5(),
            saveat = 1.0);

We can then visualize our expected cases:

C = Array(sol_ode)[4,:] # Cumulative cases
X = C[2:end] - C[1:(end-1)];


Random.seed!(1234)
Y = rand.(Poisson.(X));


bar(obstimes,Y,legend=false)
plot!(obstimes,X,legend=false)

Note the second wave of cases occuring as immunity begins to wane.

Solve Using Turing

Now we build our model in Turing, using our prior defined ODE. Note that I included a check on the ODE output to try and catch values less than one, otherwise the sampler would reject the solution (because Poisson distributions cannot have a rate parameters less than 0).

@model bayes_sir(y) = begin
  # Calculate number of timepoints
  l = length(y)
  i₀  ~ Uniform(0.0,.2)
  β ~ Uniform(0, .1)
  immunity ~ Uniform(90,365)

  I = i₀*6000.0
  u0=[6000.0-I,I,0.0,0.0]
  p=[β,10.0,0.2, 1.0/immunity]
  tspan = (0.0,float(l))
  prob = ODEProblem(sir_ode!,
          u0,
          tspan,
          p)
  sol = solve(prob,
              Tsit5(),
              saveat = 1.0)
  sol_C = Array(sol)[4,:] # Cumulative cases
  sol_X = sol_C[2:end] - sol_C[1:(end-1)]
  l = length(y)
  for i in 1:l
    y[i] ~ Poisson(ifelse(sol_X[i] <0 , 1e-6, sol_X[i] ))
  end
end;

mod = bayes_sir(Y[1:200]);

ode_nuts = sample(mod, NUTS(0.65),10000);
describe(ode_nuts)
2-element Vector{ChainDataFrame}:
 Summary Statistics (3 x 8)
 Quantiles (3 x 6)

Now let’s see if we were able to recover our parameters:

plot(ode_nuts)
posterior = DataFrame(ode_nuts);
beta_hat = mean(posterior[!,:β])
immunity_hat = mean(posterior[!, :immunity])
println("Estimate for  β: ", beta_hat)
println("Estimate for immunity duration: ", immunity_hat)
println("Estimate for initial proportion infected: ", mean(posterior[!, :i₀]))
Estimate for  β: 0.04984659207646735
Estimate for immunity duration: 178.34561091700505
Estimate for initial proportion infected: 0.0016216537054861632

Not too bad! Now we can simulate the dynamics going forward:

function predict(y,chain)
    # Length of data
    l = length(y)
    # Length of chain
    m = length(chain)
    # Choose random
    idx = sample(1:m)
    i₀ = chain[:i₀][idx]
    β = chain[:β][idx]
    immunity = chain[:immunity][idx]
    I = i₀*6000.0
    u0=[6000.0-I,I,0.0,0.0]
    p=[β,10.0,0.2, 1.0/immunity]
    tspan = (0.0,float(l))
    prob = ODEProblem(sir_ode!,
            u0,
            tspan,
            p)
    sol = solve(prob,
                Tsit5(),
                saveat = 1.0)
    out = Array(sol)
    sol_X = [0.0; out[4,2:end] - out[4,1:(end-1)]]
    hcat(sol_ode.t,out',sol_X)
end;


Xp = []
for i in 1:365
    pred = predict(Y,ode_nuts)
    push!(Xp,pred[2:end,6])
end


scatter(obstimes,Y,legend=false, ylims = [0,600])
plot!(obstimes,Xp,legend=false, color = "grey50", alpha = .2)

Conclusions

This shows a very intuitive approach towards compartmental modeling in a Bayesian framework using Julia.

Reuse

Citation

BibTeX citation:
@online{dewitt2022,
  author = {Michael DeWitt},
  editor = {},
  title = {Turing and {ODEs}},
  date = {2022-08-13},
  url = {https://michaeldewittjr.com/programming/2022-08-13-turing-and-odes},
  langid = {en}
}
For attribution, please cite this work as:
Michael DeWitt. 2022. “Turing and ODEs.” August 13, 2022. https://michaeldewittjr.com/programming/2022-08-13-turing-and-odes.