6,551 research outputs found
The Time Machine: A Simulation Approach for Stochastic Trees
In the following paper we consider a simulation technique for stochastic
trees. One of the most important areas in computational genetics is the
calculation and subsequent maximization of the likelihood function associated
to such models. This typically consists of using importance sampling (IS) and
sequential Monte Carlo (SMC) techniques. The approach proceeds by simulating
the tree, backward in time from observed data, to a most recent common ancestor
(MRCA). However, in many cases, the computational time and variance of
estimators are often too high to make standard approaches useful. In this paper
we propose to stop the simulation, subsequently yielding biased estimates of
the likelihood surface. The bias is investigated from a theoretical point of
view. Results from simulation studies are also given to investigate the balance
between loss of accuracy, saving in computing time and variance reduction.Comment: 22 Pages, 5 Figure
Probabilistic Graphical Model Representation in Phylogenetics
Recent years have seen a rapid expansion of the model space explored in
statistical phylogenetics, emphasizing the need for new approaches to
statistical model representation and software development. Clear communication
and representation of the chosen model is crucial for: (1) reproducibility of
an analysis, (2) model development and (3) software design. Moreover, a
unified, clear and understandable framework for model representation lowers the
barrier for beginners and non-specialists to grasp complex phylogenetic models,
including their assumptions and parameter/variable dependencies.
Graphical modeling is a unifying framework that has gained in popularity in
the statistical literature in recent years. The core idea is to break complex
models into conditionally independent distributions. The strength lies in the
comprehensibility, flexibility, and adaptability of this formalism, and the
large body of computational work based on it. Graphical models are well-suited
to teach statistical models, to facilitate communication among phylogeneticists
and in the development of generic software for simulation and statistical
inference.
Here, we provide an introduction to graphical models for phylogeneticists and
extend the standard graphical model representation to the realm of
phylogenetics. We introduce a new graphical model component, tree plates, to
capture the changing structure of the subgraph corresponding to a phylogenetic
tree. We describe a range of phylogenetic models using the graphical model
framework and introduce modules to simplify the representation of standard
components in large and complex models. Phylogenetic model graphs can be
readily used in simulation, maximum likelihood inference, and Bayesian
inference using, for example, Metropolis-Hastings or Gibbs sampling of the
posterior distribution
Hybrid automated reliability predictor integrated work station (HiREL)
The Hybrid Automated Reliability Predictor (HARP) integrated reliability (HiREL) workstation tool system marks another step toward the goal of producing a totally integrated computer aided design (CAD) workstation design capability. Since a reliability engineer must generally graphically represent a reliability model before he can solve it, the use of a graphical input description language increases productivity and decreases the incidence of error. The captured image displayed on a cathode ray tube (CRT) screen serves as a documented copy of the model and provides the data for automatic input to the HARP reliability model solver. The introduction of dependency gates to a fault tree notation allows the modeling of very large fault tolerant system models using a concise and visually recognizable and familiar graphical language. In addition to aiding in the validation of the reliability model, the concise graphical representation presents company management, regulatory agencies, and company customers a means of expressing a complex model that is readily understandable. The graphical postprocessor computer program HARPO (HARP Output) makes it possible for reliability engineers to quickly analyze huge amounts of reliability/availability data to observe trends due to exploratory design changes
Projecting Ising Model Parameters for Fast Mixing
Inference in general Ising models is difficult, due to high treewidth making
tree-based algorithms intractable. Moreover, when interactions are strong,
Gibbs sampling may take exponential time to converge to the stationary
distribution. We present an algorithm to project Ising model parameters onto a
parameter set that is guaranteed to be fast mixing, under several divergences.
We find that Gibbs sampling using the projected parameters is more accurate
than with the original parameters when interaction strengths are strong and
when limited time is available for sampling.Comment: Advances in Neural Information Processing Systems 201
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