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In many ultrasound measurement situations, deriving models for the acoustic wave propagation through the system being studied is complicated. In such cases, we are often limited to study correlations between observed acoustic properties and the underlying physical properties. Sometimes this can be automated by use of statistical or empirical models. However, this often requires extensive calibration, and it does not provide as much understanding of the underlying system as we would like. In this paper we present a general methodology for estimation of parameters of physical models based on indirect observations. The principle is demonstrated for a system where the kinetic behavior of a chemical reaction is modeled, and where measurements of ultrasound attenuation are used to estimate the model parameters. Experimental results show that we can use ultrasound to measure mass fractions of the different constituents as a function of the reaction time.