Search results for "Computation"
showing 10 items of 7362 documents
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…
Modelling residuals dependence in dynamic life tables: A geostatistical approach
2008
The problem of modelling dynamic mortality tables is considered. In this context, the influence of age on data graduation needs to be properly assessed through a dynamic model, as mortality progresses over the years. After detrending the raw data, the residuals dependence structure is analysed, by considering them as a realisation of a homogeneous Gaussian random field defined on R × R. This setting allows for the implementation of geostatistical techniques for the estimation of the dependence and further interpolation in the domain of interest. In particular, a complex form of interaction between age and time is considered, by taking into account a zonally anisotropic component embedded in…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
On the usage of joint diagonalization in multivariate statistics
2022
Scatter matrices generalize the covariance matrix and are useful in many multivariate data analysis methods, including well-known principal component analysis (PCA), which is based on the diagonalization of the covariance matrix. The simultaneous diagonalization of two or more scatter matrices goes beyond PCA and is used more and more often. In this paper, we offer an overview of many methods that are based on a joint diagonalization. These methods range from the unsupervised context with invariant coordinate selection and blind source separation, which includes independent component analysis, to the supervised context with discriminant analysis and sliced inverse regression. They also enco…
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
2015
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
Multiple sequence editing by spreadsheet.
1990
Spreadsheets have several functions and facilities that make them good candidates to be used as multiple sequence editors. They can be easily programmed (even by non-programmers) with macros that allow them to fit the needs of the user, free of the restrictions that programs written by other people have. Here I present a sheet containing a set of macros written for Lotus 1-2-3
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…
Long read alignment based on maximal exact match seeds
2012
Abstract Motivation: The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger. Results: We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 an…
DRUDIT: Web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets
2019
Abstract Motivation New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tool…
Estimating growth charts via nonparametric quantile regression: a practical framework with application in ecology.
2013
We discuss a practical and effective framework to estimate reference growth charts via regression quantiles. Inequality constraints are used to ensure both monotonicity and non-crossing of the estimated quantile curves and penalized splines are employed to model the nonlinear growth patterns with respect to age. A companion R package is presented and relevant code discussed to favour spreading and application of the proposed methods.