A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis

Hidden Markov models (HMMs) have been shown to be a flexible tool for modelling complex biological processes. However, choosing the number of hidden states remains an open question and the inclusion of random effects also deserves more research, as it is a recent addition to the fixed-effect HMM in many application fields. We present a Bayesian mixed HMM with an unknown number of hidden states and fixed covariates. The model is fitted using reversible-jump Markov chain Monte Carlo, avoiding the need to select the number of hidden states. We show through simulations that the estimations produced are more precise than those from a fixed-effect HMM and illustrate its practical application to the analysis of DNA copy number data, a field where HMMs are widely used.     

MODEL FORMULATION FOR FLEET SIZE ANALYSIS OF A UNIVERSITY MOTOR POOL

A GPSS/360 model was developed to investigate the behavior of a university's motor pool dispatch fleet. Time-series data were collected and frequency distributions were constructed for vehicle request patterns and trip-duration times. Regression analysis was performed to formulate trip mileage generators as functions of service time. Appropriate statistical goodness-of-fit tests were conducted to ascertain the extent of congruence between actual system behavior and expectations based on a number of theoretical distributions. Analysis of simulated response variables indicates that the model's internal structure reproduces reality to a high degree. Fifteen years of simulated experience were generated for six alternative fleet size configurations; results suggest that reductions in existing fleet capacity could be realized without effecting undue impairment in service levels.     

Prognostic accuracy for predicting ordinal competing risk outcomes using ROC surfaces

Lifetime Data Analysis - Many medical conditions are marked by a sequence of events in association with continuous changes in biomarkers. Few works have evaluated the overall accuracy of a...     

Graphon estimation via nearest-neighbour algorithm and two-dimensional fused-lasso denoising

We propose a class of methods for graphon estimation based on exploiting connections with nonparametric regression. The idea is to construct an ordering of the nodes in the network, similar in spirit to Chan & Airoldi (2014). However, rather than considering orderings based only on the empirical degree as in Chan & Airoldi (2014), we use the nearest-neighbour algorithm which is an approximative solution to the travelling salesman problem. This algorithm in turn can handle general distances $\widehat{d}$ between the nodes, allowing us to incorporate rich information from the network. Once an ordering is constructed, we formulate a two-dimensional-grid graph-denoising problem that we solve through fused-lasso regularization. For particular choices of the metric $\widehat{d}$, we show that the corresponding two-step estimator can attain competitive rates when the true model is the stochastic block model, and when the underlying graphon is piecewise Hölder or has bounded variation.