1. Regarding calibration
Numerical optimization is computatinoal intensive and
prone to local max, but it is able to estimate any general model
specification. On the other hand, EM algorithms such as Baum-Welch are
more reliable in seeking global max, but they are only capable of
backing out the parameters of models with distributions that are fully
described by moments (Gaussian, Poisson, ...)
2. Problem with HMM, and extensions
As Soltan discusses in his paper, ordinary HMM is by
definition prone to instability due to the exponentiated matrix
structure. The instability dominates in the long run, meaning that state
occupancy duration estimation of ordinary HMM is usually unreliable.
There are two ways to go: 1) HSMM (a.k.a. explicit duration HMM, inhomogeneous HMM, etc.), or 2)
Treat duration as an extra degree of state space (see Soltan).
References:
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