Search results for "Computation"
showing 10 items of 7362 documents
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
2018
Abstract Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance perf…
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
2020
Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of…
Jump-diffusion models of German stock returns
1991
This paper discusses the statistical properties of jump-diffusion processes and reports on parameter estimates for the DAX stock index and 48 German stocks with traded options. It is found that a Poisson-type jump-diffusion process can explain the high levels of kurtosis and skewness of observed return distributions of German stocks. Furthermore, we demonstrate that the return dynamics of the DAX include a statistically significant jump component except for a few sample subperiods. This finding is seen to be inconsistent with asset pricing models assuming that the jump component of the stock's return is unsystematic and diversifiable in the market portfolio.
Quantitative characterization of antigens using monoclonal antibody reactivities
1993
A multipurpose program that empirically relates antigenic reactivities with monoclonal antibodies (MAbs) to genetic distances is presented. The program uses a set of known genetic pairwise distances to weigh each MAb depending on its capacity to define groups of taxonomically related antigens. This allows highly accurate identification and classification of unknown antigens. Also, the weights obtained constitute a quantitative measure of epitope conservation and can be used for improved vaccine design. © 1993 Oxford University Press.
Derived variables calculated from similar joint responses: some characteristics and examples
1995
Abstract A technique (Cox and Wermuth, 1992) is reviewed for finding linear combinations of a set of response variables having special relations of linear conditional independence with a set of explanatory variables. A theorem in linear algebra is used both to examine conditions in which the derived variables take a specially simple form and lead to reduced computations. Examples are discussed of medical and psychological investigations in which the method has aided interpretation.
Independent component analysis based on symmetrised scatter matrices
2007
A new method for separating the mixtures of independent sources has been proposed recently in [Oja et al. (2006). Scatter matrices and independent component analysis. Austrian J. Statist., to appear]. This method is based on two scatter matrices with the so-called independence property. The corresponding method is now further examined. Simple simulation studies are used to compare the performance of so-called symmetrised scatter matrices in solving the independence component analysis problem. The results are also compared with the classical FastICA method. Finally, the theory is illustrated by some examples. peerReviewed
Comparison of the Andersen–Gill model with poisson and negative binomial regression on recurrent event data
2008
Many generalizations of the Cox proportional hazard method have been elaborated to analyse recurrent event data. The Andersen-Gill model was proposed to handle event data following Poisson processes. This method is compared with non-survival approaches, such as Poisson and negative binomial regression. The comparison is performed on data simulated according to various event-generating processes and differing in subject heterogeneity. When robust standard error estimates are applied, for Poisson processes the Andersen-Gill approach is comparable to a negative binomial regression, whereas the poisson regression has comparable coverage probabilities of confidence intervals, but increased type …
A Bayesian analysis of classical hypothesis testing
1980
The procedure of maximizing the missing information is applied to derive reference posterior probabilities for null hypotheses. The results shed further light on Lindley’s paradox and suggest that a Bayesian interpretation of classical hypothesis testing is possible by providing a one-to-one approximate relationship between significance levels and posterior probabilities.
What Bayesians Expect of Each Other
1991
Abstract Our goal is to study general properties of one Bayesian's subjective beliefs about the behavior of another Bayesian's subjective beliefs. We consider two Bayesians, A and B, who have different subjective distributions for a parameter θ, and study Bayesian A's expectation of Bayesian B's posterior distribution for θ given some data Y. We show that when θ can take only two values, Bayesian A always expects Bayesian B's posterior distribution to lie between the prior distributions of A and B. Conditions are given under which a similar result holds for an arbitrary real-valued parameter θ. For a vector parameter θ we present useful expressions for the mean vector and covariance matrix …
An introduction to Bayesian reference analysis: inference on the ratio of multinomial parameters
1998
This paper offers an introduction to Bayesian reference analysis, often described as the more successful method to produce non-subjective, model-based, posterior distributions. The ideas are illustrated in detail with an interesting problem, the ratio of multinomial parameters, for which no model-based Bayesian analysis has been proposed. Signposts are provided to the huge related literature.