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The model

We begin by describing the simplest version of our model. Later on, we will introduce several modifications, in order to deal with time dependent parameters.

Consider a hidden process (the non-observable actual number of counts in the phenomenon under study) X_n with Po-INAR(1) structure:

(1)   \begin{equation*}X_n=\alpha \circ X_{n-1}+W_n(\lambda),\end{equation*}

 where 0<\alpha<1 is a fixed parameter, W_n \sim Poisson(\lambda), i.i.d., independent of X_n are the innovations, and \circ is the binomial thinning operator: \alpha \circ X_{n-1}=\sum_{i=1}^{X_{n-1}}Z_i with Z_i i.i.d Bernoulli(\alpha) random variables. Later on, we shall introduce time dependence, and hence we will be considering that \lambda is a funtion of n.

The INAR(1) process is a homogeneous Markov chain with transition probabilities

    \[\mbox{\bf P}(X_n = i | X_{n-1} = j) = \sum_{k=0}^{i\wedge j} {j \choose k} \alpha^k (1-\alpha)^{j-k}\mbox{\bf P}(W_n=i-m)\]

The expectation and variance of the  binomial thinning operator are

    \[\textrm{{\bf E}}\left(\alpha \circ X_{n-1}|X_{n-1}=x_{n-1}\right)=\alpha x_{n-1}\]

    \[\textrm{{\bf Var}}\left(\alpha \circ X_{n-1}|X_{n-1}=x_{n-1}\right)=\alpha (1-\alpha)x_{n-1}\]

A simple under-reporting scheme

The under-reported phenomenon is modeled by assuming that the observed counts are

(2)   \begin{equation*}Y_n = \left\{ \begin{array}{ll} X_n & \text{with probability } 1-\omega\\ q \circ X_n & \text{with probability } \omega, \end{array} \right.\end{equation*}

where \omega and q represent the frequency and intensity of the under-reporting process, respectively. We will eventually be interested in considering that q is time dependent: q_n. That is, for each n, we observe X_n with probability 1-\omega, and a q-thinning of X_n with probability \omega, independently of the past \{X_j: j \leq n\}.

Hence, what we observe (the reported counts) are

    \[Y_n = (1- \mbox{\bf 1}_n)X_n + \mbox{\bf 1}_n \sum_{j=1}^{X_n} \xi_j \quad\quad \mbox{\bf 1}_n\sim\mbox{Bern}(\omega), \quad \xi_j\sim\mbox{Bern}(q)\]

Properties of the model

The mean and the variance of a stationary INAR(1) process X_n with Poisson(\lambda) innovations are \mu_X=\sigma_X^2=\frac{\lambda}{1-\alpha}.
Its auto-covariance and auto-correlation functions are \gamma_X(k)=\alpha^{|k|}\lambda and \rho_{X}(k)=\alpha^{|k|} respectively.

(3)   \begin{equation*} \mbox{\bf E} Y_n =\mbox{\bf E} X_n (1-\omega(1-q)).\end{equation*}

The auto-covariance function of the observed process Y_n is


Hence, the auto-correlation function of Y_n is a multiple of \rho_{X}(k):


Parameter estimation

The marginal probability distribution of Y_n is a \textbf{mixture of two Poisson distributions}

(4)   \begin{align*}Y_n &\sim\begin{cases}\textrm{Poisson}\left(\frac{\lambda}{1-\alpha}\right) &\quad\mbox{with probability } 1-\omega,\\\textrm{Poisson}\left(\frac{q\lambda}{1-\alpha}\right) &\quad\mbox{with probability } \omega.\nonumber\end{cases}\end{align*}

When q=0 the distribution of the observed process \{Y_n\} is a zero-inflated Poisson distribution.

From the mixture we derive initial estimations for \alpha, \lambda, \omega and q, to be used in a maximum likelihood estimation procedure.

The likelihood function of Y is quite cumbersome to compute,


hence the  forward algorithm (Lystig and Hughes (2002)),  used in the context of HMC is a suitable option.

Consider the  forward probabilities

(5)   \begin{align*}\alpha_k(X_k)=P(Y_k|X_k)\sum_{X_{k-1}}P(X_k|X_{k-1})\alpha_{k-1}(X_{k-1}) \nonumber,\end{align*}

with \alpha_1(X_1)=P(X_1)P(Y_1|X_1).

Then, the likelihood function is


P(Y_k|X_k) and P(X_k|X_{k-1}) are the so-called emission and transition probabilities.

Transition probabilities are computed as

(6)   \begin{align*}P(X_n=x_n \mid X_{n-1}=x_{n-1})=e^{-\lambda}\sum_{j=0}^{x_n\wedge x_{n-1}}\binom{x_{n-1}}{j}\alpha^j(1-\alpha)^{x_{n-1}-j}\frac{\lambda^{x_n-j}}{(x_n-j)!} \nonumber\end{align*}

While emission probabilities are given by

(7)   \begin{align*}P(Y_i=j \mid X_i=k) & = \left\{ \begin{array}{lcc}0 & if & k < j \\(1-\omega) + \omega q^k& if & k=j\\\omega \binom{k}{j} q^j (1-q)^{k-j}& if & k > j,\end{array}\right. \nonumber\end{align*}

From this computations, a nonlinear optimization program computes the MLE estimates of the parameters.

Reconstructing the hidden chain X_n

In order to reconstruct the hidden series X_n, the  Viterbi algorithm (Viterbi, 1967) is used.

The idea is to provide the latent chain X_1^*=x_1^*,\dots, X_N^*=x_N^* that maximizes the likelyhood of the latent process given the observed series, assuming all the parameters are known.

Let P(X_{1:n}|Y_{1:n}) be the likelihood function of the model, then


Since P(Y_{1:n}) does not depend on X_n, it is enough to maximise the probability P(X_{1:n},Y_{1:n}).

The hidden series is reconstructed as:

    \[X^*=\arg\max_{X} P(X_{1:n},Y_{1:n}).\]


Having observed Y_1, \dots Y_n, we are interested in predicting Y_{n+k}, for k=1,2,\dots, and in evaluating the uncertainty of these predictions.

From equation 3, we have that \mbox{\bf E} Y_{n+k} = \mbox{\bf E} X_{n+k} (1-\omega + q\omega ), so that, if we have a good estimate for \mbox{\bf E} X_{n+k}, then we can predict Y_{n+k} by means of its expectation \mbox{\bf E} Y_{n+k}.

From (1), assuming that the expectation of the innovations depends on n, that is, the noise is Poisson(\lambda_n) it is straightforward to see that

(8)   \begin{eqnarray*}\mbox{\bf E} X_{n+1}& = &\alpha \mbox{\bf E} X_n +\lambda_n \\ \nonumber\mbox{\bf E} X_{n+2}& = &\alpha^2 \mbox{\bf E} X_n + \alpha \lambda_n+ \lambda_{n+1} \\ \nonumber\vdots & & \\ \nonumber\mbox{\bf E} X_{n+k} & =& \alpha^k \mbox{\bf E} X_n + \sum={s=1}^k \alpha^{k-s} \lambda_{n+s-1}\end{eqnarray*}

The easiest way to estimate \mbox{\bf E} X_n is by substituting \ Y_n by Y_n in (3), to get
\mbox{\bf E} X_n \approx \frac{ Y_n}{ 1-\omega + q\omega}, and then in 8 to get

(9)   \begin{eqnarray*}\mbox{\bf E} Y_{n+1}& = &\alpha Y_n +(1-\omega + q\omega) \lambda_n \\ \nonumber\mbox{\bf E} Y_{n+2}& = &\alpha^2 Y_n + (1-\omega + q\omega) (\alpha \lambda_n+ \lambda_{n+1}) \\ \nonumber\vdots & & \\ \nonumber\mbox{\bf E} Y_{n+k} & =& \alpha^k Y_n + (1-\omega + q\omega) \left( \sum={s=1}^k \alpha^{k-s} \lambda_{n+s-1}\right)\end{eqnarray*}


T.C. Lystig, J.P. Hughes (2002),  Exact computation of the observed information matrix for hidden Markov models, Jr of Comp.and Graph. Stat.

Viterbi, A.J. (1967),  Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Transactions on Information Theory, 13, 260-269

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