Search results for "correction"
showing 10 items of 601 documents
Improvements and Modifications of Tarone's Multiple Test Procedure for Discrete Data
1998
Tarone (1990, Biometrics 46, 515-522) proposed a multiple test procedure for discrete test statistics improving the usual Bonferroni procedure. However, Tarone's procedure is not monotone depending on the predetermined multiple level a. Roth (1998, Journal of Statistical Planning and Inference, in press) developed a monotone version of Tarone's procedure. We present a similar procedure that is both monotone and an improvement of Tarone's proposal. Based on this extension, we derive a step-down procedure that is a corresponding improvement of Holm's (1979, Scandinavian Journal of Statistics 6, 65-70) sequentially rejective procedure. It is shown how adjusted p-values can be computed for the …
CARE: context-aware sequencing read error correction.
2020
Abstract Motivation Error correction is a fundamental pre-processing step in many Next-Generation Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing error correction methods either suffer from high false-positive rates since they break reads into independent k-mers or do not scale efficiently to large amounts of sequencing reads and complex genomes. Results We present CARE—an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors ar…
Spatial data of Ixodes ricinus instar abundance and nymph pathogen prevalence, Scandinavia, 2016-2017.
2020
ticks carry pathogens that can cause disease in both animals and humans, and there is a need to monitor the distribution and abundance of ticks and the pathogens they carry to pinpoint potential high risk areas for tick-borne disease transmission. In a joint Scandinavian study, we measured Ixodes ricinus instar abundance at 159 sites in southern Scandinavia in August-September, 2016, and collected 29,440 tick nymphs at 50 of these sites. We additionally measured abundance at 30 sites in August-September, 2017. We tested the 29,440 tick nymphs in pools of 10 in a Fluidigm real-time PCR chip to screen for 17 different tick-associated pathogens, 2 pathogen groups and 3 tick species. We present…
Efficient Simulation of Multivariate Binomial and Poisson Distributions
1998
Power investigations, for example, in statistical procedures for the assessment of agreement among multiple raters often require the simultaneous simulation of several dependent binomial or Poisson distributions to appropriately model the stochastical dependencies between the raters' results. Regarding the rather large dimensions of the random vectors to be generated and the even larger number of interactions to be introduced into the simulation scenarios to determine all necessary information on their distributions' dependence stucture, one needs efficient and fast algorithms for the simulation of multivariate Poisson and binomial distributions. Therefore two equivalent models for the mult…
A simple comparative analysis of exact and approximate quantum error correction
2014
We present a comparative analysis of exact and approximate quantum error correction by means of simple unabridged analytical computations. For the sake of clarity, using primitive quantum codes, we study the exact and approximate error correction of the two simplest unital (Pauli errors) and nonunital (non-Pauli errors) noise models, respectively. The similarities and differences between the two scenarios are stressed. In addition, the performances of quantum codes quantified by means of the entanglement fidelity for different recovery schemes are taken into consideration in the approximate case. Finally, the role of self-complementarity in approximate quantum error correction is briefly ad…
Quantum Walk Search through Potential Barriers
2015
An ideal quantum walk transitions from one vertex to another with perfect fidelity, but in physical systems, the particle may be hindered by potential energy barriers. Then the particle has some amplitude of tunneling through the barriers, and some amplitude of staying put. We investigate the algorithmic consequence of such barriers for the quantum walk formulation of Grover's algorithm. We prove that the failure amplitude must scale as $O(1/\sqrt{N})$ for search to retain its quantum $O(\sqrt{N})$ runtime; otherwise, it searches in classical $O(N)$ time. Thus searching larger "databases" requires increasingly reliable hop operations or error correction. This condition holds for both discre…
An entropic analysis of approximate quantum error correction
2013
The concept of entropy and the correct application of the Second Law of thermodynamics are essential in order to understand the reason why quantum error correction is thermodynamically possible and no violation of the Second Law occurs during its execution. We report in this work our first steps towards an entropic analysis extended to approximate quantum error correction (QEC). Special emphasis is devoted to the link among quantum state discrimination (QSD), quantum information gain, and quantum error correction in both the exact and approximate QEC scenarios.
Powerful short-cuts for multiple testing procedures with special reference to gatekeeping strategies.
2007
In this paper we present a general testing principle for a class of multiple testing problems based on weighted hypotheses. Under moderate conditions, this principle leads to powerful consonant multiple testing procedures. Furthermore, short-cut versions can be derived, which simplify substantially the implementation and interpretation of the related test procedures. It is shown that many well-known multiple test procedures turn out to be special cases of this general principle. Important examples include gatekeeping procedures, which are often applied in clinical trials when primary and secondary objectives are investigated, and multiple test procedures based on hypotheses which are comple…
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
Test and power considerations for multiple endpoint analyses using sequentially rejective graphical procedures
2009
A variety of powerful test procedures are available for the analysis of clinical trials addressing multiple objectives, such as comparing several treatments with a control, assessing the benefit of a new drug for more than one endpoint, etc. However, some of these procedures have reached a level of complexity that makes it difficult to communicate the underlying test strategies to clinical teams. Graphical approaches have been proposed instead that facilitate the derivation and communication of Bonferroni-based closed test procedures. In this paper we give a coherent description of the methodology and illustrate it with a real clinical trial example. We further discuss suitable power measur…