Continuous-time HMMs

Before diving into this vignette, we recommend reading the vignette Introduction to LaMa.

The regular HMM formulation needs a key assumption to be applicable, namely the data need to be observed at regular, equidistant time-points such that the transition probabilties can be interpreted meaningfully w.r.t. a specific time unit. If this is not the case, the model used should acocunt for this by building on a mathematical formulation in continuous time. The obvious choice here is to retain most of the HMM model formulation, but replace the unobserved discrete-time Markov chain with a continuous-time Markov chain. However, here it is important to note that the so-called snapshot property needs to be fulfilled, i.e. the observed process at time t can only depend on the state at that time instant and not on the interval since the previous observation. For more details see Glennie et al. (2023).

A continuous-time Markov chain is characterised by a so-called (infinitesimal) generator matrix $$ Q = \begin{pmatrix} q_{11} & q_{12} & \cdots & q_{1N} \\ q_{21} & q_{22} & \cdots & q_{2N} \\ \vdots & \vdots & \ddots & \vdots \\ q_{N1} & q_{N2} & \cdots & q_{NN} \\ \end{pmatrix}, $$ where the diagonal entries are qii = −∑j ≠ iqij, qij ≥ 0 for i ≠ j. This matrix can be interpreted as the derivative of the transition probability matrix and completely describes the dynamics of the state process. The time-spent in a state i is exponentially distributed with rate −qii and conditional on leaving the state, the probability to transition to a state j ≠ i is ωij = qij/ − qii. For a more detailed introduction see Dobrow (2016) (pp. 265 f.). For observation times t1 and t2, we can then obtain the transition probability matrix between these points via the identity Γ(t1, t2) = exp (Q(t2 − t1)), where exp () is the matrix expoential. This follows from the so-called Kolmogorov forward equations, but for more details see Dobrow (2016).

Example 1: two states

Setting parameters for simulation

# loading the package
library(LaMa)
#> Loading required package: RTMB

We start by setting parameters to simulate data. In this example, state 1 has a smaller rate and the state dwell time in state one follows and Exp(0.5) distribution, i.e. it exhibits longer dwell times than state 2 with rate 1.

# generator matrix Q:
Q = matrix(c(-0.5, 0.5, 1, -1), 
           nrow = 2, byrow = TRUE)

# parameters for the state-dependent (normal) distributions
mu = c(5, 20)
sigma = c(2, 5)

Simulating data

We simulate the continuous-time Markov chain by drawing the exponentially distributed state dwell-times. Within a stay, we can assume whatever structure we like for the observation times, as these are not explicitly modeled. Here we choose to generate them by a Poisson process with rate λ = 1, but this choice is arbitrary. For more details on Poisson point processes, see the MM(M)PP vignette.

set.seed(123)

k = 200 # number of state switches
trans_times = s = rep(NA, k) # time points where the chain transitions
s[1] = sample(1:2, 1) # initial distribuion c(0.5, 0.5)
# exponentially distributed waiting times
trans_times[1] = rexp(1, -Q[s[1],s[1]])
n_arrivals = rpois(1, trans_times[1])
obs_times = sort(runif(n_arrivals, 0, trans_times[1]))
x = rnorm(n_arrivals, mu[s[1]], sigma[s[1]])
for(t in 2:k){
  s[t] = c(1,2)[-s[t-1]] # for 2-states, always a state swith when transitioning
  # exponentially distributed waiting times
  trans_times[t] = trans_times[t-1] + rexp(1, -Q[s[t], s[t]])
  n_arrivals = rpois(1, trans_times[t]-trans_times[t-1])
  obs_times = c(obs_times, 
                sort(runif(n_arrivals, trans_times[t-1], trans_times[t])))
  x = c(x, rnorm(n_arrivals, mu[s[t]], sigma[s[t]]))
}

Let’s visualise the simulated continuous-time HMM:

color = c("orange", "deepskyblue")

n = length(obs_times)
plot(obs_times[1:50], x[1:50], pch = 16, bty = "n", xlab = "observation times", 
     ylab = "x", ylim = c(-5,25))
segments(x0 = c(0,trans_times[1:48]), x1 = trans_times[1:49], 
         y0 = rep(-5,50), y1 = rep(-5,50), col = color[s[1:49]], lwd = 4)
legend("topright", lwd = 2, col = color, 
       legend = c("state 1", "state 2"), box.lwd = 0)

Writing the negative log-likelihood function

The likelhood of a continuous-time HMM for observations xt1, …, xtT at irregular time points t1, …, tT has the exact same structure as the regular HMM likelihood: L(θ) = δ(1)Γ(t1, t2)P(xt2)Γ(t2, t3)P(xt3)…Γ(tT − 1, tT)P(xtT)1t, where δ(1), P and 1t are as usual and Γ(tk, tk + 1) is computed as explained above. Thus we can fit such models using the standard implementation of the general forward algorithm forward_g() with time-varying transition probability matrices. We can use the generator() function to compute the infinitesimal generator matrix from an unconstrained parameter vector and tpm_cont() to compute all matrix exponentials.

nll = function(par, timediff, x, N){
  mu = par[1:N]
  sigma = exp(par[N+1:N])
  Q = generator(par[2*N+1:(N*(N-1))]) # generator matrix
  Pi = stationary_cont(Q) # stationary dist of CT Markov chain
  Qube = tpm_cont(Q, timediff) # this computes exp(Q*timediff)
  allprobs = matrix(1, nrow = length(x), ncol = N)
  ind = which(!is.na(x))
  for(j in 1:N){
    allprobs[ind,j] = dnorm(x[ind], mu[j], sigma[j])
  }
  -forward_g(Pi, Qube, allprobs)
}

Fitting a continuous-time HMM to the data

par = c(mu = c(5, 15), # state-dependent means
        logsigma = c(log(3), log(5)), # state-dependent sds
        qs = c(log(1), log(0.5))) # off-diagonals of Q

timediff = diff(obs_times)

system.time(
  mod <- nlm(nll, par, timediff = timediff, x = x, N = 2)
)
#>    user  system elapsed 
#>   0.293   0.192   0.249

Results

N = 2
# mu
round(mod$estimate[1:N],2)
#> [1]  5.06 20.24
# sigma
round(exp(mod$estimate[N+1:N]))
#> [1] 2 5
Q = generator(mod$estimate[2*N+1:(N*(N-1))])
round(Q,3)
#>        [,1]   [,2]
#> [1,] -0.479  0.479
#> [2,]  0.905 -0.905

Example 2: three states

Setting parameters for simulation

# generator matrix Q:
Q = matrix(c(-0.5,0.2,0.3,
             1,-2, 1,
             0.4, 0.6, -1), nrow = 3, byrow = TRUE)

# parameters for the state-dependent (normal) distributions
mu = c(5, 15, 30)
sigma = c(2, 3, 5)

Simulating data

The simulation is very similar but we now also have to draw which state to transition to, as explained in the beginning.

set.seed(123)

k = 200 # number of state switches
trans_times = s = rep(NA, k) # time points where the chain transitions
s[1] = sample(1:3, 1) # uniform initial distribuion
# exponentially distributed waiting times
trans_times[1] = rexp(1, -Q[s[1],s[1]])
n_arrivals = rpois(1, trans_times[1])
obs_times = sort(runif(n_arrivals, 0, trans_times[1]))
x = rnorm(n_arrivals, mu[s[1]], sigma[s[1]])
for(t in 2:k){
  # off-diagonal elements of the s[t-1] row of Q divided by the diagonal element
  # give the probabilites of the next state
  s[t] = sample(c(1:3)[-s[t-1]], 1, prob = Q[s[t-1],-s[t-1]]/-Q[s[t-1],s[t-1]])
  # exponentially distributed waiting times
  trans_times[t] = trans_times[t-1] + rexp(1, -Q[s[t], s[t]])
  n_arrivals = rpois(1, trans_times[t]-trans_times[t-1])
  obs_times = c(obs_times, 
                sort(runif(n_arrivals, trans_times[t-1], trans_times[t])))
  x = c(x, rnorm(n_arrivals, mu[s[t]], sigma[s[t]]))
}

Fitting a 3-state continuous-time HMM to the data

par = c(mu = c(5, 10, 25), # state-dependent means
        logsigma = c(log(2), log(2), log(6)), # state-dependent sds
        qs = rep(0, 6)) # off-diagonals of Q

timediff = diff(obs_times)

system.time(
  mod2 <- nlm(nll, par, timediff = timediff, x = x, N = 3, stepmax = 10)
)
#>    user  system elapsed 
#>   2.012   2.751   1.589
# without restricting stepmax, we run into numerical problems

Results

N = 3
# mu
round(mod2$estimate[1:N],2)
#> [1]  4.90 15.45 29.10
# sigma
round(exp(mod2$estimate[N+1:N]),2)
#> [1] 1.80 2.58 5.06
Q = generator(mod2$estimate[2*N+1:(N*(N-1))])
round(Q, 3)
#>        [,1]   [,2]   [,3]
#> [1,] -0.888  0.565  0.323
#> [2,]  2.821 -3.469  0.647
#> [3,]  0.000  0.770 -0.770

References

Dobrow, Robert P. 2016. Introduction to Stochastic Processes with r. John Wiley & Sons.
Glennie, Richard, Timo Adam, Vianey Leos-Barajas, Théo Michelot, Theoni Photopoulou, and Brett T McClintock. 2023. “Hidden Markov Models: Pitfalls and Opportunities in Ecology.” Methods in Ecology and Evolution 14 (1): 43–56.