A hidden Markov model for detecting confinement in single particle tracking trajectories

State-of-the-art single-particle tracking (SPT) techniques can generate long trajectories with high temporal and spatial resolution. This offers the possibility of mechanistically interpreting particle movements and behavior in membranes. To this end, a number of statistical techniques have been developed that partition SPT trajectories into states with distinct diffusion signatures, allowing a statistical analysis of diffusion state dynamics and switching behavior. Here, we develop a confinement model, within a hidden Markov framework, that switches between phases of free diffusion and confinement in a harmonic potential well. By using a Markov chain Monte Carlo algorithm to fit this model, automated partitioning of individual SPT trajectories into these two phases is achieved, which allows us to analyze confinement events. We demonstrate the utility of this algorithm on a previously published interferometric scattering microscopy data set, in which gold-nanoparticle-tagged ganglioside GM1 lipids were tracked in model membranes. We performed a comprehensive analysis of confinement events, demonstrating that there is heterogeneity in the lifetime, shape, and size of events, with confinement size and shape being highly conserved within trajectories. Our observations suggest that heterogeneity in confinement events is caused by both individual nanoparticle characteristics and the binding-site environment. The individual nanoparticle heterogeneity ultimately limits the ability of interferometric scattering microscopy to resolve molecule dynamics to the order of the tag size; homogeneous tags could potentially allow the resolution to be taken below this limit by deconvolution methods. In a wider context, the presented harmonic potential well confinement model has the potential to detect and characterize a wide variety of biological phenomena, such as hop diffusion, receptor clustering, and lipid rafts

Langevin and Hamiltonian based Sequential MCMC for Efficient Bayesian Filtering in High-dimensional Spaces

Nonlinear non-Gaussian state-space models arise in numerous applications in statistics and signal processing. In this context, one of the most successful and popular approximation techniques is the Sequential Monte Carlo (SMC) algorithm, also known as particle filtering. Nevertheless, this method tends to be inefficient when applied to high dimensional problems. In this paper, we focus on another class of sequential inference methods, namely the Sequential Markov Chain Monte Carlo (SMCMC) techniques, which represent a promising alternative to SMC methods. After providing a unifying framework for the class of SMCMC approaches, we propose novel efficient strategies based on the principle of Langevin diffusion and Hamiltonian dynamics in order to cope with the increasing number of high-dimensional applications. Simulation results show that the proposed algorithms achieve significantly better performance compared to existing algorithms

Subgradient-Based Markov Chain Monte Carlo Particle Methods for Discrete-Time Nonlinear Filtering

This work shows how a carefully designed instrumental distribution can improve the performance of a Markov chain Monte Carlo (MCMC) filter for systems with a high state dimension. We propose a special subgradient-based kernel from which candidate moves are drawn. This facilitates the implementation of the filtering algorithm in high dimensional settings using a remarkably small number of particles. We demonstrate our approach in solving a nonlinear non-Gaussian high-dimensional problem in comparison with a recently developed block particle filter and over a dynamic compressed sensing (l1 constrained) algorithm. The results show high estimation accuracy

Random finite sets in multi-target tracking - efficient sequential MCMC implementation

Over the last few decades multi-target tracking (MTT) has proved to be a challenging and attractive research topic. MTT applications span a wide variety of disciplines, including robotics, radar/sonar surveillance, computer vision and biomedical research. The primary focus of this dissertation is to develop an effective and efficient multi-target tracking algorithm dealing with an unknown and time-varying number of targets. The emerging and promising Random Finite Set (RFS) framework provides a rigorous foundation for optimal Bayes multi-target tracking. In contrast to traditional approaches, the collection of individual targets is treated as a set-valued state. The intent of this dissertation is two-fold; first to assert that the RFS framework not only is a natural, elegant and rigorous foundation, but also leads to practical, efficient and reliable algorithms for Bayesian multi-target tracking, and second to provide several novel RFS based tracking algorithms suitable for the specific Track-Before-Detect (TBD) surveillance application. One main contribution of this dissertation is a rigorous derivation and practical implementation of a novel algorithm well suited to deal with multi-target tracking problems for a given cardinality. The proposed Interacting Population-based MCMC-PF algorithm makes use of several Metropolis-Hastings samplers running in parallel, which interact through genetic variation. Another key contribution concerns the design and implementation of two novel algorithms to handle a varying number of targets. The first approach exploits Reversible Jumps. The second approach is built upon the concepts of labeled RFSs and multiple cardinality hypotheses. The performance of the proposed algorithms is also demonstrated in practical scenarios, and shown to significantly outperform conventional multi-target PF in terms of track accuracy and consistency. The final contribution seeks to exploit external information to increase the performance of the surveillance system. In multi-target scenarios, kinematic constraints from the interaction of targets with their environment or other targets can restrict target motion. Such motion constraint information is integrated by using a fixed-lag smoothing procedure, named Knowledge-Based Fixed-Lag Smoother (KB-Smoother). The proposed combination IP-MCMC-PF/KB-Smoother yields enhanced tracking

Ensemble Transport Adaptive Importance Sampling

Markov chain Monte Carlo methods are a powerful and commonly used family of numerical methods for sampling from complex probability distributions. As applications of these methods increase in size and complexity, the need for efficient methods increases. In this paper, we present a particle ensemble algorithm. At each iteration, an importance sampling proposal distribution is formed using an ensemble of particles. A stratified sample is taken from this distribution and weighted under the posterior, a state-of-the-art ensemble transport resampling method is then used to create an evenly weighted sample ready for the next iteration. We demonstrate that this ensemble transport adaptive importance sampling (ETAIS) method outperforms MCMC methods with equivalent proposal distributions for low dimensional problems, and in fact shows better than linear improvements in convergence rates with respect to the number of ensemble members. We also introduce a new resampling strategy, multinomial transformation (MT), which while not as accurate as the ensemble transport resampler, is substantially less costly for large ensemble sizes, and can then be used in conjunction with ETAIS for complex problems. We also focus on how algorithmic parameters regarding the mixture proposal can be quickly tuned to optimise performance. In particular, we demonstrate this methodology's superior sampling for multimodal problems, such as those arising from inference for mixture models, and for problems with expensive likelihoods requiring the solution of a differential equation, for which speed-ups of orders of magnitude are demonstrated. Likelihood evaluations of the ensemble could be computed in a distributed manner, suggesting that this methodology is a good candidate for parallel Bayesian computations

Extended Object Tracking: Introduction, Overview and Applications

This article provides an elaborate overview of current research in extended object tracking. We provide a clear definition of the extended object tracking problem and discuss its delimitation to other types of object tracking. Next, different aspects of extended object modelling are extensively discussed. Subsequently, we give a tutorial introduction to two basic and well used extended object tracking approaches - the random matrix approach and the Kalman filter-based approach for star-convex shapes. The next part treats the tracking of multiple extended objects and elaborates how the large number of feasible association hypotheses can be tackled using both Random Finite Set (RFS) and Non-RFS multi-object trackers. The article concludes with a summary of current applications, where four example applications involving camera, X-band radar, light detection and ranging (lidar), red-green-blue-depth (RGB-D) sensors are highlighted.Comment: 30 pages, 19 figure