37 research outputs found
HYDRA: a Java library for Markov Chain Monte Carlo
Hydra is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use, extend, and integrate with other software tools. In this paper, we describe the problem that motivated our work, outline our goals for the Hydra pro ject, and describe the current features of the Hydra library. We then provide a step-by-step example of using Hydra to simulate from a mixture model drawn from cancer genetics, first using a variable-at-a-time Metropolis sampler and then a Normal Kernel Coupler. We conclude with a discussion of future directions for Hydra.
License GPL-2 NeedsCompilation No Repository CRAN
Description Various R programming tools for plotting dat
Side-Payments and the Costs of Conflict
Conflict and competition often impose costs on both winners and losers, and conflicting parties may prefer to resolve the dispute before it occurs. The equilibrium of a conflict game with side-payments predicts that with binding offers, proposers make and responders accept side-payments, generating settlements that strongly favor proposers. When side-payments are non-binding, proposers offer nothing and conflicts always arise. Laboratory experiments confirm that binding side-payments reduce conflicts. However, 30 % of responders reject binding offers, and offers are more egalitarian than predicted. Surprisingly, non-binding side-payments also improve efficiency, although less than binding. With binding side-payments, 87 % of efficiency gains come from avoided conflicts. However, with non-binding side-payments, only 39 % of gains come from avoided conflicts and 61 % from reduced conflict expenditures
Transcriptome Analysis of the Arabidopsis Megaspore Mother Cell Uncovers the Importance of RNA Helicases for Plant Germline Development
Germ line specification is a crucial step in the life cycle of all organisms. For sexual plant reproduction, the megaspore mother cell (MMC) is of crucial importance: it marks the first cell of the plant “germline” lineage that gets committed to undergo meiosis. One of the meiotic products, the functional megaspore, subsequently gives rise to the haploid, multicellular female gametophyte that harbours the female gametes. The MMC is formed by selection and differentiation of a single somatic, sub-epidermal cell in the ovule. The transcriptional network underlying MMC specification and differentiation is largely unknown. We provide the first transcriptome analysis of an MMC using the model plant Arabidopsis thaliana with a combination of laser-assisted microdissection and microarray hybridizations. Statistical analyses identified an over-representation of translational regulation control pathways and a significant enrichment of DEAD/DEAH-box helicases in the MMC transcriptome, paralleling important features of the animal germline. Analysis of two independent T-DNA insertion lines suggests an important role of an enriched helicase, MNEME (MEM), in MMC differentiation and the restriction of the germline fate to only one cell per ovule primordium. In heterozygous mem mutants, additional enlarged MMC-like cells, which sometimes initiate female gametophyte development, were observed at higher frequencies than in the wild type. This closely resembles the phenotype of mutants affected in the small RNA and DNA-methylation pathways important for epigenetic regulation. Importantly, the mem phenotype shows features of apospory, as female gametophytes initiate from two non-sister cells in these mutants. Moreover, in mem gametophytic nuclei, both higher order chromatin structure and the distribution of LIKE HETEROCHROMATIN PROTEIN1 were affected, indicating epigenetic perturbations. In summary, the MMC transcriptome sets the stage for future functional characterization as illustrated by the identification of MEM, a novel gene involved in the restriction of germline fate
Sample Size Estimation for Microarray Experiments
mRNA Expression Microarray technology is widely applied in biomedical and pharmaceutical research. The huge number of mRNA concentrations estimated for each sample make it difficult to apply traditional sample size calculation techniques and has left most practitioners to rely on rule-of-thumb techniques. In this paper, we briefly describe and then demonstrate a simple method for performing and visualizing sample size calculations for microarray experiments as implemented in the ssize R package
Hydra: A java library for markov chain monte carlo
Hydra is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use, extend, and integrate with other software tools. In this paper, we describe the problem that motivated our work, outline our goals for the Hydra project, and describe the current features of the Hydra library. We then provide a step-by-step example of using Hydra to simulate from a mixture model drawn from cancer genetics, first using a variable-at-a-time Metropolis sampler and then a Normal Kernel Coupler. We conclude wit
The normal kernel coupler: an adaptive Markov Chain Monte Carlo method for efficiently sampling from multi-modal distributions
Thesis (Ph. D.)--University of Washington, 2000The Normal Kernel Coupler (NKC) is an adaptive Markov Chain Monte Carlo (MCMC) method which maintains a set of current state vectors. At each iteration one state vector is updated using a density estimate formed by applying a normal kernel to the full set of states.We give proofs showing that this sampler is ergodic (irreducible, Harris recurrent and aperiodic) for any continuous distribution on d-dimensional Euclidean space. We also show that the NKC outperforms standard MCMC methods on a variety of uni-modal and bimodal problems in low to moderate dimensions.Further, we address practical issues in using the NKC by giving direction for the selection of various parameters and by providing a run-length diagnostic. Using these we give a systematic method for initializing the NKC, selecting the kernel variance, and determining the number of MCMC iterations.We demonstrate the utility of the NKC on a problem of current interest in cancer genetics which has two distinct and dissimilar modes and show that the results are consistent with current scientific understanding.Finally, we introduce Hydra, a software library for MCMC. We show how to use Hydra to implement both a variable-at-a-time Metropolis sampler and the NKC for our example problem