Search results for "algorithm"

Algoritmi viventi tra Shannon e Simondon

2023

Almost a century after Turing’s machine was theorised, a formal definition of what an algorithm is has still not been found by scholars. The reasons given are varied and it is clear that this is a problem that is not easy to solve. Nevertheless, one of the least travelled paths is the one that envisages the hypothesis of an algorithm that does not exhaust its potential in automatism. Starting from the algorithm written and implemented by the mathematician Claude Shannon in the 1950s in a machine made up of a group of relays, a mouse-shaped sensor and a maze structured in squares, the following work aims to understand whether a certain creative and evolutionary capacity can be found in…

A characterization of the simple groupM 24

1970

Computing the Arrangement of Circles on a Sphere, with Applications in Structural Biology

2009

International audience; Balls and spheres are the simplest modeling primitives after affine ones, which accounts for their ubiquitousness in Computer Science and Applied Mathematics. Amongst the many applications, we may cite their prevalence when it comes to modeling our ambient 3D space, or to handle molecular shapes using Van der Waals models. If most of the applications developed so far are based upon simple geometric tests between balls, in particular the intersection test, a number of applications would obviously benefit from finer pieces of information. Consider a sphere $S_0$ and a list of circles on it, each such circle stemming from the intersection between $S_0$ and another spher…

An efficient prototype merging strategy for the condensed 1-NN rule through class-conditional hierarchical clustering

2002

Abstract A generalized prototype-based classification scheme founded on hierarchical clustering is proposed. The basic idea is to obtain a condensed 1-NN classification rule by merging the two same-class nearest clusters, provided that the set of cluster representatives correctly classifies all the original points. Apart from the quality of the obtained sets and its flexibility which comes from the fact that different intercluster measures and criteria can be used, the proposed scheme includes a very efficient four-stage procedure which conveniently exploits geometric cluster properties to decide about each possible merge. Empirical results demonstrate the merits of the proposed algorithm t…

A mathematical approach to predicting the percutaneous absorption enhancing effect of sodium lauryl sulphate.

2003

A study has been made of the effect of sodium lauryl sulphate (SLS) at several concentrations from 0.24 to 5% (w/w) on skin permeability. Seven model drugs were selected for this study on the basis of their lipophilicity as represented by their logP(oct) values (from -0.95 to 4.2). Skin pre-treatment with aqueous solutions of SLS does not increase the permeability coefficient of the most lipophilic compounds (logP(oct)> or =3). For the other compounds assayed the increase in the permeability coefficients depends on the concentration of SLS used in the skin pre-treatment, and on the lipophilicity of the compounds tested.The correlation between the inverse of SLS efficacy as an enhancer (1/ER…

Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences

2014

In this paper, we present a GPU-accelerated Smith-Waterman (SW) algorithm with Alignment Backtracking, called GSWAB, for short DNA sequences. This algorithm performs all-to-all pairwise alignments and retrieves optimal local alignments on CUDA-enabled GPUs. To facilitate fast alignment backtracking, we have investigated a tile-based SW implementation using the CUDA programming model. This tiled computing pattern enables us to more deeply explore the powerful compute capability of GPUs. We have evaluated the performance of GSWAB on a Kepler-based GeForce GTX Titan graphics card. The results show that GSWAB can achieve a performance of up to 56.8 GCUPS on large-scale datasets. Furthermore, ou…

SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

2014

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, mul…

Algorithms for Graph and Network Analysis: Graph Alignment

2019

In this article we discuss the problem of graph alignment, which has been longly referred to for the purpose of analyzing and comparing biological networks. In particular, we describe different facets of graph alignment, according to the number of input networks, the fixed output objective, the possible heterogeneity of input data. Accordingly, we will discuss pairwise and multiple alignment, global and local alignment, etc. Moreover, we provide a comprehensive overview of the algorithms and techniques proposed in the literature to solve each of the specific considered types of graph alignment. In order to make the material presented here complete and useful to guide the reader in the use o…

GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences

2014

In this paper, we present GSWABE, a graphics processing unit GPU-accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all-to-all pairwise global, semi-global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture CUDA-enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile-based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA-enabled GPUs. The performance of GSWABE has been evaluated on a Kepler-based Tesla K40 GPU using a varie…

Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures

2015

In this paper we present new parallelization techniques for searching large-scale biological sequence databases with the Smith-Waterman algorithm on Xeon Phi-based neoheterogenous architectures. In order to make full use of the compute power of both the multi-core CPU and the many-core Xeon Phi hardware, we use a collaborative computing scheme as well as hybrid parallelism. At the CPU side, we employ SSE intrinsics and multi-threading to implement SIMD parallelism. At the Xeon Phi side, we use Knights Corner vector instructions to gain more data parallelism. We have presented two dynamic task distribution schemes (thread level and device level) in order to achieve better load balancing. Fur…