  We propose a new framework to estimate the evolution of an ensemble of
indistinguishable agents on a hidden Markov chain using only aggregate output
data. This work can be viewed as an extension of the recent developments in
optimal mass transport and Schr\"odinger bridges to the finite state space
hidden Markov chain setting. The flow of the ensemble is estimated by solving a
maximum likelihood problem, which has a convex formulation at the
infinite-particle limit, and we develop a fast numerical algorithm for it. We
illustrate in two numerical examples how this framework can be used to track
the flow of identical and indistinguishable dynamical systems.
