Peer-reviewed Articles

2 citations
402 downloads
2,946 views

We present a CUDA-based implementation of a decision tree construction algorithm within the gradient boosting library XGBoost. The tree construction algorithm is executed entirely on the graphics processing unit (GPU) and shows high performance with a variety of...

["Artificial Intelligence","Data Mining and Machine Learning","Data Science"]
doi:10.7717/peerj-cs.127
293 downloads
1,184 views

Background The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.124
61 downloads
803 views

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Synthetic Biology"]
doi:10.7717/peerj-cs.120
67 downloads
646 views

The unit of experimental measurement in a variety of scientific applications is the one-dimensional (1D) continuum: a dependent variable whose value is measured repeatedly, often at regular intervals, in time or space. A variety of software packages exist for computing...

["Scientific Computing and Simulation","Programming Languages"]
doi:10.7717/peerj-cs.125
152 downloads
681 views

Objects of more than three dimensions can be used to model geographic phenomena that occur in space, time and scale. For instance, a single 4D object can be used to represent the changes in a 3D object’s shape across time or all its optimal representations at various...

["Graphics","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7717/peerj-cs.123
111 downloads
880 views

Despite recent algorithmic improvements, learning the optimal structure of a Bayesian network from data is typically infeasible past a few dozen variables. Fortunately, domain knowledge can frequently be exploited to achieve dramatic computational savings, and...

["Artificial Intelligence","Data Mining and Machine Learning","Data Science","Distributed and Parallel Computing"]
doi:10.7717/peerj-cs.122
153 downloads
1,096 views

Motivation Scientists increasingly rely on intelligent information systems to help them in their daily tasks, in particular for managing research objects, like publications or datasets. The relatively young research field of Semantic Publishing has been addressing...

["Human-Computer Interaction","Artificial Intelligence","Data Mining and Machine Learning","Digital Libraries"]
doi:10.7717/peerj-cs.121
229 downloads
1,756 views

The ability to promptly recognise new research trends is strategic for many stakeholders, including universities, institutional funding bodies, academic publishers and companies. While the literature describes several approaches which aim to identify the emergence...

["Artificial Intelligence","Data Science","Digital Libraries"]
doi:10.7717/peerj-cs.119
1 citation
121 downloads
865 views

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.116
176 downloads
937 views

Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.118
147 downloads
663 views

Shotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological...

["Bioinformatics","Computational Biology","Data Science"]
doi:10.7717/peerj-cs.117
115 downloads
633 views

The ever-growing amount of data produced by and in today’s smart cities offers significant potential for novel applications created by city stakeholders as well as third parties. Current smart city application models mostly assume that data is exclusively managed...

["Distributed and Parallel Computing","Software Engineering"]
doi:10.7717/peerj-cs.115
1 citation
1,007 downloads
1,604 views

The rapid growth of small Internet connected devices, known as the Internet of Things (IoT), is creating a new set of challenges to create secure, private infrastructures. This paper reviews the current literature on the challenges and approaches to security and...

["Computer Networks and Communications","Embedded Computing","Real-Time and Embedded Systems","Security and Privacy","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.114
736 downloads
3,213 views

The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible....

["Human\u2013Computer Interaction","Computer Education","Computer Networks and Communications","Digital Libraries","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.112
2 citations
768 downloads
27,295 views

Biases against women in the workplace have been documented in a variety of studies. This paper presents a large scale study on gender bias, where we compare acceptance rates of contributions from men versus women in an open source software community. Surprisingly,...

["Human-Computer Interaction","Social Computing","Programming Languages","Software Engineering"]
doi:10.7717/peerj-cs.111

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