Computationally efficient application of Sequential Monte Carlo expectation maximization to confined single particle tracking

Single Particle Tracking (SPT) plays a crucial role in biophysics through its ability to reveal dynamic mechanisms and physical properties of biological macromolecules moving inside living cells. Such molecules are often subject to confinement and important information can be revealed by understanding the mobility of the molecules and the size of the domain they are restricted to. In previous work, we introduced a method known as Sequential Monte Carlo-Expectation Maximization (SMCEM) to simultaneously estimate particle trajectories and model parameters. In this paper, we describe three modifications to SMC-EM aimed at improving its computationally efficiency and demonstrate it through analysis of simulated SPT data of a particle in a three dimensional confined environment. The first two modifications use approximation methods to reduce the complexity of the original motion and measurement models without significant loss of accuracy. The third modification replaces the previous SMC methods with a Gaussian particle filter combined with a backward simulation particle smoother, trading off some level of generality for improved computational performance. In addition, we take advantage of the improved efficiency to investigate the effect of data length on performance in localization and parameter estimation.