# 7 Markov-modulated (marked) Poisson processes

#### Jan-Ole Fischer

> Before diving into this vignette, we recommend reading the vignettes Introduction to LaMa, Automatic differentiation via RTMB, and Continuous-time HMMs.

    library(LaMa)

In a continuous-time HMM, observation values carry information about the latent state while the observation times are treated as fixed or uninformative (the snapshot property). The Markov-modulated Poisson process (MMPP) reverses this: the arrival times themselves are the observations, and their spacing carries information about the hidden state process.

The key idea is that an unobserved continuous-time Markov chain (CTMC) modulates the rate of a Poisson process. While the chain stays in state \(j\), events arrive at a constant, state-specific rate \(\lambda_j\). A high-rate state produces rapid bursts of closely spaced arrivals; a low-rate state produces sparse events. By fitting the model to the observed arrival times alone, we can infer both the Poisson rates and the dynamics of the hidden CTMC (described by its generator matrix \(Q\), as in the continuous-time HMM vignette).

A natural extension, the Markov-modulated marked Poisson process (MMMPP), additionally associates a random mark \(y_i\) with each arrival. Marks are drawn from a state-dependent distribution at the moment of arrival, providing a second source of information about the latent state alongside the timing. For more background see Meier-Hellstern (1987) and Langrock et al. (2013).

## Likelihood

### MMPP

For \(n\) arrivals at times \(t_1 < \dots < t_n\), let \(\Delta t_i = t_{i+1} - t_i\) be the inter-arrival waiting times and \(\Lambda = \text{diag}(\lambda_1, \dots, \lambda_N)\) the diagonal matrix of state-dependent rates. The likelihood of a stationary MMPP is

\[ L(\theta) = \pi \Bigl(\prod_{i=1}^{n-1} \exp\bigl((Q - \Lambda)\,\Delta t_i\bigr)\,\Lambda\Bigr)\,\mathbf{1}^\top, \]

where \(\pi\) is the stationary distribution of the CTMC and \(\mathbf{1}\) is a column vector of ones. The matrix \(\exp((Q - \Lambda)\,\Delta t_i)\) propagates the state distribution through gap \(\Delta t_i\) while accounting for the fact that no event occurred during this interval; \(\Lambda\) then contributes the instantaneous rate of the event that does occur at the end of the gap.

This has exactly the same structure as the regular HMM likelihood, so `forward()` applies directly. We construct the `allprobs` matrix with \(n\) rows: the first row is all ones (pure initialisation with \(\pi\), no density contribution), and rows \(2, \dots, n\) all equal \((\lambda_1, \dots, \lambda_N)\) — the instantaneous arrival-rate density at each observed event.

### MMMPP

When each arrival \(i\) also carries a mark \(y_i\), the likelihood gains one additional factor per event:

\[ L(\theta) = \pi\,P(y_1) \Bigl(\prod_{i=1}^{n-1} \exp\bigl((Q - \Lambda)\,\Delta t_i\bigr)\,\Lambda\,P(y_{i+1})\Bigr)\,\mathbf{1}^\top, \]

where \(P(y_i)\) is a diagonal matrix of state-dependent densities evaluated at mark \(y_i\). In practice we fold \(\Lambda\) into the `allprobs` matrix: after filling in the mark densities for all \(n\) rows, rows \(2, \dots, n\) are multiplied element-wise by \((\lambda_1, \dots, \lambda_N)\), so the same `forward()` call handles everything.

## Example 1: Markov-modulated Poisson processes

### Setting parameters

We use a 2-state model. State 2 has a much higher arrival rate and shorter mean sojourn time — it is the bursty state.

    lambda = c(2, 15)  # state-dependent Poisson rates
    Q = matrix(c(-0.5, 0.5,
                  2.0, -2.0), nrow = 2, byrow = TRUE)

The mean sojourn time in state 1 is \(1/0.5 = 2\) time units; in state 2 it is \(1/2 = 0.5\) time units.

### Simulating an MMPP

The simulation mirrors the CTMC simulation from the continuous-time HMM vignette. The only difference is that instead of drawing observation values during each sojourn, we draw Poisson arrival times. Within each sojourn of length `dwell`, the number of arrivals is Poisson with mean `lambda * dwell`, and their positions are uniform over the sojourn interval.

    set.seed(123)

    k = 200              # number of state switches to simulate
    s = rep(NA, k)       # latent state sequence
    trans_times = rep(NA, k)  # cumulative transition times

    # initialise
    s[1] = sample(1:2, 1)
    dwell = rexp(1, -Q[s[1], s[1]])
    trans_times[1] = dwell

    n_arrivals = rpois(1, lambda[s[1]] * dwell)
    arrival_times = sort(runif(n_arrivals, 0, dwell))

    for (t in 2:k) {
      # 2-state chain: always switches to the other state
      s[t] = 3 - s[t-1]

      dwell = rexp(1, -Q[s[t], s[t]])
      trans_times[t] = trans_times[t-1] + dwell

      t_start = trans_times[t-1]
      t_end   = trans_times[t]

      # Poisson arrivals uniformly distributed within sojourn
      n_arrivals = rpois(1, lambda[s[t]] * dwell)
      arrival_times = c(arrival_times, sort(runif(n_arrivals, t_start, t_end)))
    }

The cumulative arrivals plot is the clearest way to see how the Poisson rate changes with the hidden state: the slope of the curve equals the current arrival rate, so steep segments correspond to the bursty state and shallow segments to the slow state.

    color = LaMaColors(2)
    n = length(arrival_times)
    plot(c(0, arrival_times), 0:n, type = "l", bty = "n",
         xlab = "time", ylab = "cumulative arrivals",
         ylim = c(-n * 0.05, n))
    segments(x0 = c(0, trans_times[-k]), x1 = trans_times,
             y0 = rep(-n * 0.05, k), y1 = rep(-n * 0.05, k),
             col = color[s], lwd = 4)
    legend("topleft", lwd = 2, col = color, legend = paste("state", 1:2), box.lwd = 0)

### Writing the negative log-likelihood function

The `allprobs` matrix has `length(timediff) + 1` rows (one per arrival, plus one for initialisation). Row 1 is all ones; the remaining rows carry the state-dependent rates \(\lambda_j\). The transition matrices are computed via `tpm_ct(Q, timediff, lambda)`, where the optional `lambda` argument internally subtracts \(\Lambda\) from \(Q\) before the matrix exponential — simultaneously propagating the state distribution and accounting for the absence of arrivals during each gap.

    nll = function(par) {
      getAll(par, dat)
      lambda = exp(log_lambda); REPORT(lambda)
      Q = generator(log_qs); REPORT(Q)
      Pi = stationary_ct(Q); REPORT(Pi)
      Qube = tpm_ct(Q, timediff, lambda)
      allprobs = matrix(rep(lambda, length(timediff) + 1),
                        nrow = length(timediff) + 1, ncol = N, byrow = TRUE)
      allprobs[1,] = 1
      -forward(Pi, Qube, allprobs)
    }

### Fitting the model

    N = 2
    timediff = diff(arrival_times)

    par = list(
      log_lambda = log(c(2, 15)),
      log_qs     = log(c(2, 0.5))
    )
    dat = list(
      timediff = timediff,
      N = N
    )

    obj = MakeADFun(nll, par, silent = TRUE)
    system.time(
      opt <- nlminb(obj$par, obj$fn, obj$gr)
    )
    #>    user  system elapsed
    #>   0.580   0.003   0.583
    mod = report(obj)

### Results

    mod$lambda           # true: 2, 15
    #> [1]  1.950361 15.056559
    round(mod$Q, 3)      # true: Q as defined above
    #>        S1     S2
    #> S1 -0.399  0.399
    #> S2  1.883 -1.883
    round(1 / diag(-mod$Q), 2)  # mean dwell times; true: 2, 0.5
    #>   S1   S2
    #> 2.51 0.53
    mod$Pi               # stationary distribution of the CTMC
    #>        S1        S2
    #> 0.8251464 0.1748536

We can decode the most probable state sequence with `viterbi()` and colour each arrival by its inferred state.

    states = viterbi(mod = mod)

    plot(arrival_times[1:100], rep(0.5, 100), type = "h", bty = "n",
         ylim = c(0, 1), yaxt = "n", col = color[states[1:100]],
         xlab = "arrival times", ylab = "")
    legend("top", lwd = 2, col = color, legend = paste("state", 1:N), box.lwd = 0)

## Example 2: Markov-modulated marked Poisson processes

Adding marks to each arrival provides a second channel of information about the latent state. Here we use three states with well-separated mark distributions so the model is clearly identifiable.

### Setting parameters

    lambda = c(1, 5, 20)
    Q = matrix(c(-0.5, 0.3, 0.2,
                  0.7, -1.0, 0.3,
                  1.0,  1.0, -2.0), nrow = 3, byrow = TRUE)
    mu    = c(-5, 0, 5)
    sigma = c(2, 1, 2)

    color = LaMaColors(3)
    curve(dnorm(x, mu[2], sigma[2]), xlim = c(-10, 10), bty = "n",
          lwd = 2, col = color[2], n = 200, ylab = "density", xlab = "mark")
    curve(dnorm(x, mu[1], sigma[1]), add = TRUE, lwd = 2, col = color[1], n = 200)
    curve(dnorm(x, mu[3], sigma[3]), add = TRUE, lwd = 2, col = color[3], n = 200)
    legend("topright", lwd = 2, col = color, bty = "n", legend = paste("state", 1:3))

### Simulating an MMMPP

For three states, the conditional next-state probabilities after leaving state \(i\) are \(\omega_{ij} = q_{ij}/(-q_{ii})\). Marks are drawn independently from the state-dependent distribution at each arrival, in the same order as the arrival times.

    set.seed(123)

    k = 200
    s = rep(NA, k)
    trans_times = rep(NA, k)

    s[1] = sample(1:3, 1)
    dwell = rexp(1, -Q[s[1], s[1]])
    trans_times[1] = dwell

    n_arrivals = rpois(1, lambda[s[1]] * dwell)
    new_arrivals = sort(runif(n_arrivals, 0, dwell))
    arrival_times = new_arrivals
    marks = rnorm(n_arrivals, mu[s[1]], sigma[s[1]])

    for (t in 2:k) {
      # conditional next-state probabilities: omega_ij = q_ij / (-q_ii)
      omega = Q[s[t-1], -s[t-1]] / -Q[s[t-1], s[t-1]]
      s[t] = sample((1:3)[-s[t-1]], 1, prob = omega)

      dwell = rexp(1, -Q[s[t], s[t]])
      trans_times[t] = trans_times[t-1] + dwell

      t_start = trans_times[t-1]
      t_end   = trans_times[t]

      n_arrivals = rpois(1, lambda[s[t]] * dwell)
      new_arrivals = sort(runif(n_arrivals, t_start, t_end))
      arrival_times = c(arrival_times, new_arrivals)
      marks = c(marks, rnorm(n_arrivals, mu[s[t]], sigma[s[t]]))
    }

    n = length(arrival_times)
    plot(arrival_times[1:100], marks[1:100], pch = 16, bty = "n",
         ylim = c(-9, 9), xlab = "arrival times", ylab = "marks")
    segments(x0 = c(0, trans_times[1:98]), x1 = trans_times[1:99],
             y0 = rep(-9, 99), y1 = rep(-9, 99), col = color[s[1:99]], lwd = 4)
    legend("topright", lwd = 2, col = color,
           legend = paste("state", 1:3), box.lwd = 0)

### Writing the negative log-likelihood function

The `allprobs` matrix is built from the mark densities for all \(n\) arrivals. Rows \(2, \dots, n\) are then multiplied element-wise by the state-dependent rates \((\lambda_1, \dots, \lambda_N)\) to fold in the Poisson arrival contribution, giving the combined MMMPP likelihood.

    nll2 = function(par) {
      getAll(par, dat)
      lambda = exp(log_lambda); REPORT(lambda)
      REPORT(mu)
      sigma = exp(log_sigma); REPORT(sigma)
      Q = generator(log_qs); REPORT(Q)
      Pi = stationary_ct(Q); REPORT(Pi)
      Qube = tpm_ct(Q, timediff, lambda)
      allprobs = matrix(1, length(marks), N)
      for (j in 1:N) allprobs[, j] = dnorm(marks, mu[j], sigma[j])
      # multiply rows 2:n by lambda to fold in the arrival-rate contribution
      allprobs[-1,] = allprobs[-1,] * matrix(lambda, length(marks) - 1, N, byrow = TRUE)
      -forward(Pi, Qube, allprobs)
    }

### Fitting the model

    N = 3
    timediff = diff(arrival_times)

    par = list(
      log_lambda = log(c(1, 5, 20)),
      mu         = c(-5, 0, 5),
      log_sigma  = log(c(2, 1, 2)),
      log_qs     = log(c(0.7, 1, 0.3, 1, 0.2, 0.3))
    )
    dat = list(
      marks    = marks,
      timediff = timediff,
      N = N
    )

    obj2 = MakeADFun(nll2, par, silent = TRUE)
    system.time(
      opt2 <- nlminb(obj2$par, obj2$fn, obj2$gr)
    )
    #>    user  system elapsed
    #>   1.329   0.005   1.335
    mod2 = report(obj2)

### Results

    mod2$lambda                  # true: 1, 5, 20
    #> [1]  0.9646738  4.8641071 19.5009530
    mod2$mu                      # true: -5, 0, 5
    #> [1] -5.18540494 -0.09096836  4.80540113
    mod2$sigma                   # true: 2, 1, 2
    #> [1] 1.7931070 0.9644496 2.0093249
    round(mod2$Q, 3)             # true: Q as defined above
    #>        S1     S2     S3
    #> S1 -0.591  0.279  0.312
    #> S2  0.926 -1.180  0.254
    #> S3  1.193  1.210 -2.403
    round(1 / diag(-mod2$Q), 2) # mean dwell times; true: 2, 1, 0.5
    #>   S1   S2   S3
    #> 1.69 0.85 0.42
    mod2$Pi                      # stationary distribution
    #>        S1        S2        S3
    #> 0.6297018 0.2609501 0.1093482

Overlaying the fitted state-dependent densities on a histogram of all marks provides an intuitive model check. Note that the mixture weights are not the stationary distribution \(\pi_j\) (proportion of time in state \(j\)) but the rate-weighted proportions \(w_j \propto \pi_j \lambda_j\) — states with higher arrival rates contribute disproportionately more marks.

    # marks arrive at rate lambda_j in state j, so the fraction of marks from
    # state j is proportional to Pi[j] * lambda[j], not Pi[j] alone
    w = mod2$Pi * mod2$lambda / sum(mod2$Pi * mod2$lambda)

    hist(marks, prob = TRUE, breaks = 50, border = "white", main = "",
         xlab = "mark")
    for (j in 1:N) {
      curve(w[j] * dnorm(x, mod2$mu[j], mod2$sigma[j]),
            add = TRUE, lwd = 2, col = color[j], n = 300)
    }
    curve(rowSums(sapply(1:N, function(j) w[j] * dnorm(x, mod2$mu[j], mod2$sigma[j]))),
          add = TRUE, lwd = 2, lty = 2, n = 300)
    legend("topright", lwd = 2, lty = c(1, 1, 1, 2), bty = "n",
           col = c(color, "black"), legend = c(paste("state", 1:N), "marginal"))

State decoding via `viterbi()` now colours each mark by its inferred state — combining both timing and mark information to assign the latent state.

    states2 = viterbi(mod = mod2)

    plot(arrival_times[1:100], marks[1:100], pch = 16, bty = "n",
         col = color[states2[1:100]],
         ylim = c(-9, 9), xlab = "arrival times", ylab = "marks")
    legend("topright", pch = 16, col = color,
           legend = paste("state", 1:3), box.lwd = 0)

## References

Langrock, Roland, David L Borchers, and Hans J Skaug. 2013. “Markov-Modulated Nonhomogeneous Poisson Processes for Modeling Detections in Surveys of Marine Mammal Abundance.” Journal of the American Statistical Association 108 (503): 840–51.
Meier-Hellstern, Kathleen S. 1987. “A Fitting Algorithm for Markov-Modulated Poisson Processes Having Two Arrival Rates.” European Journal of Operational Research 29 (3): 370–77.