On the Suitability of Genetic-Based Algorithms for Data Mining

Data mining has as goal to extract knowledge from large databases. A database may be considered as a search space consisting of an enormous number of elements, and a mining algorithm as a search strategy. In general, an exhaustive search of the space is infeasible. Therefore, efficient search strategies are of vital importance. Search strategies on genetic-based algorithms have been applied successfully in a wide range of applications. We focus on the suitability of genetic-based algorithms for data mining. We discuss the design and implementation of a genetic-based algorithm for data mining and illustrate its potentials

Spatio-temporal Functional Regression on Paleo-ecological Data

The influence of climate on biodiversity is an important ecological question. Various theories try to link climate change to allelic richness and therefore to predict the impact of global warming on genetic diversity. We model the relationship between genetic diversity in the European beech forests and curves of temperature and precipitation reconstructed from pollen databases. Our model links the genetic measure to the climate curves through a linear functional regression. The interaction in climate variables is assumed to be bilinear. Since the data are georeferenced, our methodology accounts for the spatial dependence among the observations. The practical issues of these extensions are discussed

Guilt By Genetic Association: The Fourth Amendment and the Search of Private Genetic Databases by Law Enforcement

Over the course of 2018, a number of suspects in unsolved crimes have been identified through the use of GEDMatch, a public online genetic database. Law enforcement’s use of GEDMatch to identify suspects in cold cases likely does not constitute a search under the Fourth Amendment because the genetic information hosted on the website is publicly available. Transparency reports from direct-to-consumer (DTC) genetic testing providers like 23andMe and Ancestry suggest that federal and state officials may now be requesting access to private genetic databases as well. Whether law enforcement’s use of private DTC genetic databases to search for familial relatives of a suspect’s genetic profile constitutes a search within the meaning of the Fourth Amendment is far less clear. A strict application of the third-party doctrine suggests that individuals have no expectation of privacy in genetic information that they voluntarily disclose to third parties, including DTC providers. This Note, however, contends that the U.S. Supreme Court’s recent decision in Carpenter v. United States overwhelmingly supports the proposition that genetic information disclosed to third-party DTC providers is subject to Fourth Amendment protection. Approximately fifteen million individuals in the United States have already submitted their genetic information to DTC providers. The genetic information held by these providers can reveal a host of highly intimate details about consumers’ medical conditions, behavioral traits, genetic health risks, ethnic background, and familial relationships. Allowing law enforcement warrantless access to investigate third-party DTC genetic databases circumvents their consumers’ reasonable expectations of privacy by exposing this sensitive genetic information to law enforcement without any meaningful oversight. Furthermore, individuals likely reasonably expect that they retain ownership over their uniquely personal genetic information despite their disclosure of that information to a thirdparty provider. This Note therefore asserts that the third-party doctrine does not permit law enforcement to conduct warrantless searches for suspects on private DTC genetics databases under the Fourth Amendment

The role of the genetic counsellor: a systematic review of research evidence

In Europe, genetic counsellors are employed in specialist genetic centres or other specialist units. According to the European Board of Medical Genetics, the genetic counsellor must fulfil a range of roles, including provision of information and facilitation of psychosocial adjustment of the client to their genetic status and situation. To evaluate the extent to which genetic counsellors fulfil their prescribed roles, we conducted a systematic review of the published relevant scientific evidence. We searched five relevant electronic databases (Medline, CINAHL, SocIndex, AMED and PsychInfo) using relevant search terms and handsearched four subject-specific journals for research-based papers published in English between 1 January 2000 and 30 June 2013. Of 419 potential papers identified initially, seven satisfied the inclusion criteria for the review. Themes derived from the thematic analysis of the data were: (i) rationale for genetic counsellors to provide care, (ii) appropriate roles and responsibilities and (iii) the types of conditions included in the genetic counsellor caseload. The findings of this systematic review indicate that where genetic counsellors are utilised in specialist genetic settings, they undertake a significant workload associated with direct patient care and this appears to be acceptable to patients. With the burden on genetic services, there is an argument for the increased use of genetic counsellors in countries where they are under-utilised. In addition, roles undertaken by genetic counsellors in specialist genetic settings could be adapted to integrate genetic counsellors into multi-disciplinary teams in other specialisms

Ontology-driven International Maize Information System (IMIS) for Phenotypic and Genotypic Data Exchange

The Consultative Group on International Agricultural Research (CGIAR; http://www.cgiar.org/) centres have developed the International Crop Information System (ICIS; http://www.icis.cgiar.org) for the management and integration of global information on genetic resources, and germplasm improvement for any crop. The Maize breeding programs at CIMMYT (http://beta.cimmyt.org/) have different software tools to manage phenotypic, genotypic, and environmental information for their experiments generated worldwide. These tools have the capacity of collecting information in the field, wet lab, and store it into different relational databases. The IMIS (http://imis.cimmyt.org/confluence/display/IMIS/Crop+Finder) is an implementation of the ICIS, which is a computerized database system for general, integrated management and utilization of genealogy, nomenclature, genetic, phenotypic and characterization data for maize. Data exchange within and between databases as well as retrieving information are often hampered by the variability of terms used to describe comparable objects. To overcome this problem, the Crop Ontology (CO) database (http://cropontology.org/) is developed. It provides controlled vocabulary sets for several economically important plant species and facilitates biocurators working in genebanks of plant genetic resources (PGR) and crop breeding data curation and annotation. The maize trait ontology is developed as one of subclasses of CO trait ontology providing standardized trait descriptions, scales and scale values implemented into the IMIS. This ontology-driven IMIS will allow researchers who wish to exploit comparative phenotypic and genotypic information of maize to elucidate functional aspects of each trait

An Ontology Based Method to Solve Query Identifier Heterogeneity in Post-Genomic Clinical Trials

The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains—e.g. clinical and genetic data. One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases. In this work, we describe an approach to overcome heterogeneities in identifiers inside queries. We present an ontology classifying the most common identifier semantic heterogeneities, and a service that makes use of it to cope with the problem using the described approach. Finally, we illustrate the solution by analysing a set of real queries

An investigation of genetic algorithm-based feature selection techniques applied to keystroke dynamics biometrics

Due to the continuous use of social networks, users can be vulnerable to online situations such as paedophilia treats. One of the ways to do the investigation of an alleged pedophile is to verify the legitimacy of the genre that it claims. One possible technique to adopt is keystroke dynamics analysis. However, this technique can extract many attributes, causing a negative impact on the accuracy of the classifier due to the presence of redundant and irrelevant attributes. Thus, this work using the wrapper approach in features selection using genetic algorithms and as KNN, SVM and Naive Bayes classifiers. Bringing as best result the SVM classifier with 90% accuracy, identifying what is most suitable for both bases

Pl@ntNote: a flexible software for the management and share of data on plants

A key issue for biodiversity, agronomy and ecological studies is the availability of large and reliable databases on plants. Today, internet tools provide several services that allow the aggregation of various kinds of data into large databases. However, the preliminary and fundamental work of collecting and synthesizing data still relies on individual scientists or amateurs-each often with distinct objectives, tools and methods-who manage their data by themselves, rather than through network databases. The resulting multiplicity of database and data file formats impedes data standardization and exchange. Furthermore, large collective databases are usually made by aggregating duplicates of individual datasets, yet often lack reliability because any control of data quality is made in the original dataset, but not in the duplicate. Pl@ntNote is a free, easy-access and powerful solution to these problems, allowing the individual management of potentially any kind of botanical data. Its core includes generic methods independent from data type, such as editing, viewing, exporting, sharing, mapping, and searching. The user freely designs a database structure according to his/her own requirements. In a second step, structures and/or data can be exchanged within a community of users. The distinction between structure and methods makes Pl@ntNote particularly well suited to meet the needs of scientists from various disciplines. Indeed, this tool is now in current use for the management of herbarium specimens, pictures, plant descriptions, growth surveys, weeds surveys, field inventories, living collections, genetic resources as well as palaeobotanic records. It is available in a stable beta version. (Texte intégral