Genetic Programming Techniques in Engineering Applications

2012/2013Machine learning is a suite of techniques that allow developing algorithms for performing tasks by generalizing from examples. Machine learning systems, thus, may automatically synthesize programs from data. This approach is often feasible and cost-effective where manual programming or manual algorithm design is not. In the last decade techniques based on machine learning have spread in a broad range of application domains. In this thesis, we will present several novel applications of a specific machine Learning technique, called Genetic Programming, to a wide set of engineering applications grounded in real world problems. The problems treated in this work range from the automatic synthesis of regular expressions, to the generation of electricity price forecast, to the synthesis of a model for the tracheal pressure in mechanical ventilation. The results demonstrate that Genetic Programming is indeed a suitable tool for solving complex problems of practical interest. Furthermore, several results constitute a significant improvement over the existing state-of-the-art. The main contribution of this thesis is the design and implementation of a framework for the automatic inference of regular expressions from examples based on Genetic Programming. First, we will show the ability of such a framework to cope with the generation of regular expressions for solving text-extraction tasks from examples. We will experimentally assess our proposal comparing our results with previous proposals on a collection of real-world datasets. The results demonstrate a clear superiority of our approach. We have implemented the approach in a web application that has gained considerable interest and has reached peaks of more 10000 daily accesses. Then, we will apply the framework to a popular "regex golf" challenge, a competition for human players that are required to generate the shortest regular expression solving a given set of problems. Our results rank in the top 10 list of human players worldwide and outperform those generated by the only existing algorithm specialized to this purpose. Hence, we will perform an extensive experimental evaluation in order to compare our proposal to the state-of-the-art proposal in a very close and long-established research field: the generation of a Deterministic Finite Automata (DFA) from a labelled set of examples. Our results demonstrate that the existing state-of-the-art in DFA learning is not suitable for text extraction tasks. We will also show a variant of our framework designed for solving text processing tasks of the search-and-replace form. A common way to automate search-and-replace is to describe the region to be modified and the desired changes through a regular expression and a replacement expression. We will propose a solution to automatically produce both those expressions based only on examples provided by user. We will experimentally assess our proposal on real-word search-and-replace tasks. The results indicate that our proposal is indeed feasible. Finally, we will study the applicability of our framework to the generation of schema based on a sample of the eXtensible Markup Language documents. The eXtensible Markup Language documents are largely used in machine-to-machine interactions and such interactions often require that some constraints are applied to the contents of the documents. These constraints are usually specified in a separate document which is often unavailable or missing. In order to generate a missing schema, we will apply and will evaluate experimentally our framework to solve this problem. In the final part of this thesis we will describe two significant applications from different domains. We will describe a forecasting system for producing estimates of the next day electricity price. The system is based on a combination of a predictor based on Genetic Programming and a classifier based on Neural Networks. Key feature of this system is the ability of handling outliers-i.e., values rarely seen during the learning phase. We will compare our results with a challenging baseline representative of the state-of-the-art. We will show that our proposal exhibits smaller prediction error than the baseline. Finally, we will move to a biomedical problem: estimating tracheal pressure in a patient treated with high-frequency percussive ventilation. High-frequency percussive ventilation is a new and promising non-conventional mechanical ventilatory strategy. In order to avoid barotrauma and volutrauma in patience, the pressure of air insufflated must be monitored carefully. Since measuring the tracheal pressure is difficult, a model for accurately estimating the tracheal pressure is required. We will propose a synthesis of such model by means of Genetic Programming and we will compare our results with the state-of-the-art.XXVI Ciclo198

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

WormBook: the online review of Caenorhabditis elegans biology

WormBook () is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

Background: Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Methodology: Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. Conclusions: A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.Peer reviewe