  Kalman filtering and smoothing algorithms are used in many areas, including
tracking and navigation, medical applications, and financial trend filtering.
One of the basic assumptions required to apply the Kalman smoothing framework
is that error covariance matrices are known and given. In this paper, we study
a general class of inference problems where covariance matrices can depend
functionally on unknown parameters. In the Kalman framework, this allows
modeling situations where covariance matrices may depend functionally on the
state sequence being estimated. We present an extended formulation and
generalized Gauss-Newton (GGN) algorithm for inference in this context. When
applied to dynamic systems inference, we show the algorithm can be implemented
to preserve the computational efficiency of the classic Kalman smoother. The
new approach is illustrated with a synthetic numerical example.
