A Survey on Particle Swarm Optimization for Association Rule Mining

Association rule mining (ARM) is one of the core techniques of data mining to discover potentially valuable association relationships from mixed datasets. In the current research, various heuristic algorithms have been introduced into ARM to address the high computation time of traditional ARM. Although a more detailed review of the heuristic algorithms based on ARM is available, this paper differs from the existing reviews in that we expected it to provide a more comprehensive and multi-faceted survey of emerging research, which could provide a reference for researchers in the field to help them understand the state-of-the-art PSO-based ARM algorithms. In this paper, we review the existing research results. Heuristic algorithms for ARM were divided into three main groups, including biologically inspired, physically inspired, and other algorithms. Additionally, different types of ARM and their evaluation metrics are described in this paper, and the current status of the improvement in PSO algorithms is discussed in stages, including swarm initialization, algorithm parameter optimization, optimal particle update, and velocity and position updates. Furthermore, we discuss the applications of PSO-based ARM algorithms and propose further research directions by exploring the existing problems.publishedVersio

Computational Methods for the Analysis of Genomic Data and Biological Processes

In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality

Who wrote this scientific text?

The IEEE bibliographic database contains a number of proven duplications with indication of the original paper(s) copied. This corpus is used to test a method for the detection of hidden intertextuality (commonly named "plagiarism"). The intertextual distance, combined with the sliding window and with various classification techniques, identifies these duplications with a very low risk of error. These experiments also show that several factors blur the identity of the scientific author, including variable group authorship and the high levels of intertextuality accepted, and sometimes desired, in scientific papers on the same topic

Code smells detection and visualization: A systematic literature review

Context: Code smells (CS) tend to compromise software quality and also demand more effort by developers to maintain and evolve the application throughout its life-cycle. They have long been catalogued with corresponding mitigating solutions called refactoring operations. Objective: This SLR has a twofold goal: the first is to identify the main code smells detection techniques and tools discussed in the literature, and the second is to analyze to which extent visual techniques have been applied to support the former. Method: Over 83 primary studies indexed in major scientific repositories were identified by our search string in this SLR. Then, following existing best practices for secondary studies, we applied inclusion/exclusion criteria to select the most relevant works, extract their features and classify them. Results: We found that the most commonly used approaches to code smells detection are search-based (30.1%), and metric-based (24.1%). Most of the studies (83.1%) use open-source software, with the Java language occupying the first position (77.1%). In terms of code smells, God Class (51.8%), Feature Envy (33.7%), and Long Method (26.5%) are the most covered ones. Machine learning techniques are used in 35% of the studies. Around 80% of the studies only detect code smells, without providing visualization techniques. In visualization-based approaches several methods are used, such as: city metaphors, 3D visualization techniques. Conclusions: We confirm that the detection of CS is a non trivial task, and there is still a lot of work to be done in terms of: reducing the subjectivity associated with the definition and detection of CS; increasing the diversity of detected CS and of supported programming languages; constructing and sharing oracles and datasets to facilitate the replication of CS detection and visualization techniques validation experiments.Comment: submitted to ARC

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

A systems-based approach for detecting molecular interactions across tissues.

Current high-throughput gene expression experiments have a straightforward design of examining the gene expression of one group or condition relative to that of another. The data is typically analyzed as if they represent strictly intracellular events, and often treats genes as coming from a homogeneous population. Although intracellular events are crucial to nearly all biological processes, cell-cell interactions are often just as important, especially when gene expression data is generated from heterogeneous cell populations, such as from whole tissues. Cell-cell molecular interactions are generally lost in the available analytical procedures and as a result, are not examined experimentally, at least not accurately or with efficiency. Most importantly, this imposes major limitations when studying gene expression changes in multiple samples that interact with one another. In order to addresses the limitations of current techniques, we have developed a novel systems-based approach that expands the traditional analysis of gene expression in two stages. This includes a novel sequence-based meta-analytic tool, AbsIDconvert, that allows for conversion of annotated features using an interval tree for storing and querying absolute genomic coordinates for comparison of multi-scale macro-molecule identifiers across platforms and/or organisms. In addition, a systems-based heuristic algorithm is developed to find intercellular interactions between two sets of genes, potentially from different tissues by utilizing location information of each gene along with the information available in the secondary databases in the form of interactions, pathways and signaling. AbsIDconvert is shown to provide a high accuracy in identifier conversion as compared to other available methodologies (typically at an average rate of 84%) while maintaining a higher efficiency (O(n*log(n)). Our intercellular interaction approach and underlying visualization shows promise in allowing researchers to uncover novel signaling pathways in an intercellular fashion that to this point has not been possible

L'intertextualité dans les publications scientifiques

La base de données bibliographiques de l'IEEE contient un certain nombre de duplications avérées avec indication des originaux copiés. Ce corpus est utilisé pour tester une méthode d'attribution d'auteur. La combinaison de la distance intertextuelle avec la fenêtre glissante et diverses techniques de classification permet d'identifier ces duplications avec un risque d'erreur très faible. Cette expérience montre également que plusieurs facteurs brouillent l'identité de l'auteur scientifique, notamment des collectifs de chercheurs à géométrie variable et une forte dose d'intertextualité acceptée voire recherchée

Emerging Vaccine Informatics

Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions and improve vaccine production and vaccination protocols. Computational methods have also been used for development of immunization registries or immunization information systems, assessment of vaccine safety and efficacy, and immunization modeling. Computational literature mining and databases effectively process, mine, and store large amounts of vaccine literature and data. Vaccine Ontology (VO) has been initiated to integrate various vaccine data and support automated reasoning