Search results for "Python"
showing 10 items of 160 documents
Model building on the non-factorisable type IIA T6/(Z4×ΩR) orientifold
2016
We construct global semi-realistic supersymmetric models with intersecting D6-branes on the non-factorisable orientifold . The non-factorisable structure gives rise to differences compared to the factorisable case: additional conditions for the three-cycles to be Lagrangian and extra constraints on the wrapping numbers for building fractional cycles.
Monitoring the reproductive activity in captive bred female ball pythons (P. regius) by ultrasound evaluation and noninvasive analysis of faecal repr…
2018
The royal python (Python regius) is commonly bred in captivity. To have a successful breeding season, accurate monitoring of the reproductive activity is necessary. The use of non-invasive monitoring methods in exotics is important in order to minimize stress. For this purpose ultrasound has been anecdotally used to monitor royal python reproductive activity. However, there is limited information regarding the reproductive cycle of this species. The aim of the present study is to monitor the female reproductive cycle of the royal python using ultrasonography and gonadal steroid metabolite measurements in the faeces. The reproductive activity of one hundred twenty-nine adult female P. regius…
Moderated Redactable Blockchains: A Definitional Framework with an Efficient Construct
2020
Blockchain is a multiparty protocol to reach agreement on the order of events, and to record them consistently and immutably without centralized trust. In some cases, however, the blockchain can benefit from some controlled mutability. Examples include removing private information or unlawful content, and correcting protocol vulnerabilities which would otherwise require a hard fork. Two approaches to control the mutability are: moderation, where one or more designated administrators can use their private keys to approve a redaction, and voting, where miners can vote to endorse a suggested redaction. In this paper, we first present several attacks against existing redactable blockchain solut…
Predictive Model Markup Language (PMML) Representation of Bayesian Networks: An Application in Manufacturing
2018
International audience; Bayesian networks (BNs) represent a promising approach for the aggregation of multiple uncertainty sources in manufacturing networks and other engineering systems for the purposes of uncertainty quantification, risk analysis, and quality control. A standardized representation for BN models will aid in their communication and exchange across the web. This article presents an extension to the predictive model markup language (PMML) standard for the representation of a BN, which may consist of discrete variables, continuous variables, or their combination. The PMML standard is based on extensible markup language (XML) and used for the representation of analytical models…
Meta-heuristic Algorithms for Nesting Problem of Rectangular Pieces
2017
Abstract Nesting problems consist of placing multiple items onto larger shapes finding a good arrangement. The goal of the nesting process is to minimize the waste of material. It is common to assume, as in the present work, that the stock sheet has fixed width and infinite height, since in the real world a company may have to cut pieces from a roll of material. The complexity of such problems is often faced with a two-stage approach, so-called “hybrid algorithm”, combining a placement routine and a meta-heuristic algorithm. Starting from a given positioning sequence, the placement routine generates a non-overlapping configuration. The encoded solution is manipulated and modified by the met…
DESDEO: The Modular and Open Source Framework for Interactive Multiobjective Optimization
2021
Interactive multiobjective optimization methods incorporate preferences from a human decision maker in the optimization process iteratively. This allows the decision maker to focus on a subset of solutions, learn about the underlying trade-offs among the conflicting objective functions in the problem and adjust preferences during the solution process. Incorporating preference information allows computing only solutions that are interesting to the decision maker, decreasing computation time significantly. Thus, interactive methods have many strengths making them viable for various applications. However, there is a lack of existing software frameworks to apply and experiment with interactive …
SpCLUST: Towards a fast and reliable clustering for potentially divergent biological sequences
2019
International audience; This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master/slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed pac…
A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model.
2018
International audience; In this article, a new Python package for nucleotide sequences clustering is proposed. This package, freely available on-line, implements a Laplacian eigenmap embedding and a Gaussian Mixture Model for DNA clustering. It takes nucleotide sequences as input, and produces the optimal number of clusters along with a relevant visualization. Despite the fact that we did not optimise the computational speed, our method still performs reasonably well in practice. Our focus was mainly on data analytics and accuracy and as a result, our approach outperforms the state of the art, even in the case of divergent sequences. Furthermore, an a priori knowledge on the number of clust…
NESSie.jl – Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language
2018
Abstract The development of scientific software can be generally characterized by an initial phase of rapid prototyping and the subsequent transition to computationally efficient production code. Unfortunately, most programming languages are not well-suited for both tasks at the same time, commonly resulting in a considerable extension of the development time. The cross-platform and open-source Julia language aims at closing the gap between prototype and production code by providing a usability comparable to Python or MATLAB alongside high-performance capabilities known from C and C++ in a single programming language. In this paper, we present efficient protein electrostatics computations a…
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …