Search results for "Algorithm"

1127P Correlation of BRAF mutation status in circulating tumour DNA (ctDNA) with tumour biopsy and clinical outcomes in COLUMBUS

2020

PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment

2017

The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art a…

Erratum to “New time-dependent Monte Carlo algorithm designed to model three-phase batch reactor processes: applications on 2,4-dinitro-toluene hydro…

2003

Erratum to “New time-dependent Monte Carlo algorithm designed to model three-phase batch reactor processes: applications on 2,4-dinitro-toluene hydrogenation on Pd/C catalysts” [Chem. Eng. J. 91 (2003) 133–142] Giampaolo Barone a,b, Dario Duca a,b,∗ a Dipartimento di Chimica Inorganica ed Analitica, Universita di Palermo, Viale delle Scienze, I-90128 Palermo, Italy b Dipartimento di Scienze Farmaceutiche, Universita di Salerno, Via Ponte don Melillo, I-84084 Fisciano, Salerno, Italy

A New pH-Dependent Macrocyclic Rhodamine B-Based Fluorescent Probe for Copper Detection in White Wine

2019

For efficiently measuring copper (II) ions in the acidic media of white wine, a new chemosensor based on rhodamine B coupled to a tetraazamacrocyclic ring (13aneN4CH2NH2) was designed and synthesized by a one-pot reaction using ethanol as a green solvent. The obtained chemosensor was characterized via NMR, UV and fluorescent spectra. It was marked with no color emission under neutral pH conditions, with a pink color emission under acidic conditions, and a magenta color emission under acidic conditions where copper (II) ions were present. The sensitivity towards copper (II) ions was tested and verified over Ca2+, Ag+, Zn2+, Mg2+, Co2+, Ni2+, Fe2+, Pb2+, Cd2+, Fe3+, and Mn2+, with a detection…

Evaluation of Hybrid Models to Estimate Chlorophyll and Nitrogen Content of Maize Crops in the Framework of the Future CHIME Mission

2022

In the next few years, the new Copernicus Hyperspectral Imaging Mission (CHIME) is foreseen to be launched by the European Space Agency (ESA). This mission will provide an unprecedented amount of hyperspectral data, enabling new research possibilities within several fields of natural resources, including the “agriculture and food security” domain. In order to efficiently exploit this upcoming hyperspectral data stream, new processing methods and techniques need to be studied and implemented. In this work, the hybrid approach (HYB) and its variant, featuring sampling dimensionality reduction through active learning heuristics (HAL), were applied to CHIME-like data to evaluate the…

Classification in point patterns on linear networks under clutter

2022

The problem of features detection under present of clutter in point process on linear networks establishes a methodological and computational challenge with multiple kind of applications as traffic accidents among other. Previous works related to the same topical but developed in more simpler geometries tackles the issue of the clutter removal through the distance of nearest-neighbour and show good results with high classification rates. We extend this procedure to the linear networks motivated by the classification of the traffic accidents on the road network of a city. Simulations demonstrate the performance of the method.

GPU accelerated Monte Carlo simulations of lattice spin models

2011

We consider Monte Carlo simulations of classical spin models of statistical mechanics using the massively parallel architecture provided by graphics processing units (GPUs). We discuss simulations of models with discrete and continuous variables, and using an array of algorithms ranging from single-spin flip Metropolis updates over cluster algorithms to multicanonical and Wang-Landau techniques to judge the scope and limitations of GPU accelerated computation in this field. For most simulations discussed, we find significant speed-ups by two to three orders of magnitude as compared to single-threaded CPU implementations.

The Three Steps of Clustering in the Post-Genomic Era: A Synopsis

2011

Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from Statistics to Computer Science. Following Handl et al., it can be summarized as a three step process: (a) choice of a distance function; (b) choice of a clustering algorithm; (c) choice of a validation method. Although such a purist approach to clustering is hardly seen in many areas of science, genomic data require that level of attention, if inferences made from cluster analysis have to be of some relevance to biomedical research. Unfortunately, the high dimensionality of the data and their noisy nature makes cluster analysis of genomic data particul…

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…

2008

Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…

The pedagogy of multiliteracies as a code breaker : A suggestion for a transversal approach to computing education in basic education

2021

While computing has been (re)introduced into the basic education curricula in various countries, its actual implementation appears to be inconsistent. There are schools in which computing education is commonplace, while the implementation seems to be lagging behind in others. There is emerging evidence that some teachers do not consider computing education relevant, meaningful and important and, thus, intentionally neglect its provision. This is problematic as understanding the principles of code and computing is crucial for agentic citizenship in the post-digital era. This paper argues that one main reason for these teachers' reluctance is the economy-driven discursive framing of computing…