Text Mining and Gene Expression Analysis Towards Combined Interpretation of High Throughput Data

Microarrays can capture gene expression activity for thousands of genes simultaneously and thus make it possible to analyze cell physiology and disease processes on molecular level. The interpretation of microarray gene expression experiments profits from knowledge on the analyzed genes and proteins and the biochemical networks in which they play a role. The trend is towards the development of data analysis methods that integrate diverse data types. Currently, the most comprehensive biomedical knowledge source is a large repository of free text articles. Text mining makes it possible to automatically extract and use information from texts. This thesis addresses two key aspects, biomedical text mining and gene expression data analysis, with the focus on providing high-quality methods and data that contribute to the development of integrated analysis approaches. The work is structured in three parts. Each part begins by providing the relevant background, and each chapter describes the developed methods as well as applications and results. Part I deals with biomedical text mining: Chapter 2 summarizes the relevant background of text mining; it describes text mining fundamentals, important text mining tasks, applications and particularities of text mining in the biomedical domain, and evaluation issues. In Chapter 3, a method for generating high-quality gene and protein name dictionaries is described. The analysis of the generated dictionaries revealed important properties of individual nomenclatures and the used databases (Fundel and Zimmer, 2006). The dictionaries are publicly available via a Wiki, a web service, and several client applications (Szugat et al., 2005). In Chapter 4, methods for the dictionary-based recognition of gene and protein names in texts and their mapping onto unique database identifiers are described. These methods make it possible to extract information from texts and to integrate text-derived information with data from other sources. Three named entity identification systems have been set up, two of them building upon the previously existing tool ProMiner (Hanisch et al., 2003). All of them have shown very good performance in the BioCreAtIvE challenges (Fundel et al., 2005a; Hanisch et al., 2005; Fundel and Zimmer, 2007). In Chapter 5, a new method for relation extraction (Fundel et al., 2007) is presented. It was applied on the largest collection of biomedical literature abstracts, and thus a comprehensive network of human gene and protein relations has been generated. A classification approach (Küffner et al., 2006) can be used to specify relation types further; e. g., as activating, direct physical, or gene regulatory relation. Part II deals with gene expression data analysis: Gene expression data needs to be processed so that differentially expressed genes can be identified. Gene expression data processing consists of several sequential steps. Two important steps are normalization, which aims at removing systematic variances between measurements, and quantification of differential expression by p-value and fold change determination. Numerous methods exist for these tasks. Chapter 6 describes the relevant background of gene expression data analysis; it presents the biological and technical principles of microarrays and gives an overview of the most relevant data processing steps. Finally, it provides a short introduction to osteoarthritis, which is in the focus of the analyzed gene expression data sets. In Chapter 7, quality criteria for the selection of normalization methods are described, and a method for the identification of differentially expressed genes is proposed, which is appropriate for data with large intensity variances between spots representing the same gene (Fundel et al., 2005b). Furthermore, a system is described that selects an appropriate combination of feature selection method and classifier, and thus identifies genes which lead to good classification results and show consistent behavior in different sample subgroups (Davis et al., 2006). The analysis of several gene expression data sets dealing with osteoarthritis is described in Chapter 8. This chapter contains the biomedical analysis of relevant disease processes and distinct disease stages (Aigner et al., 2006a), and a comparison of various microarray platforms and osteoarthritis models. Part III deals with integrated approaches and thus provides the connection between parts I and II: Chapter 9 gives an overview of different types of integrated data analysis approaches, with a focus on approaches that integrate gene expression data with manually compiled data, large-scale networks, or text mining. In Chapter 10, a method for the identification of genes which are consistently regulated and have a coherent literature background (Küffner et al., 2005) is described. This method indicates how gene and protein name identification and gene expression data can be integrated to return clusters which contain genes that are relevant for the respective experiment together with literature information that supports interpretation. Finally, in Chapter 11 ideas on how the described methods can contribute to current research and possible future directions are presented

Improving the Representation and Conversion of Mathematical Formulae by Considering their Textual Context

Mathematical formulae represent complex semantic information in a concise form. Especially in Science, Technology, Engineering, and Mathematics, mathematical formulae are crucial to communicate information, e.g., in scientific papers, and to perform computations using computer algebra systems. Enabling computers to access the information encoded in mathematical formulae requires machine-readable formats that can represent both the presentation and content, i.e., the semantics, of formulae. Exchanging such information between systems additionally requires conversion methods for mathematical representation formats. We analyze how the semantic enrichment of formulae improves the format conversion process and show that considering the textual context of formulae reduces the error rate of such conversions. Our main contributions are: (1) providing an openly available benchmark dataset for the mathematical format conversion task consisting of a newly created test collection, an extensive, manually curated gold standard and task-specific evaluation metrics; (2) performing a quantitative evaluation of state-of-the-art tools for mathematical format conversions; (3) presenting a new approach that considers the textual context of formulae to reduce the error rate for mathematical format conversions. Our benchmark dataset facilitates future research on mathematical format conversions as well as research on many problems in mathematical information retrieval. Because we annotated and linked all components of formulae, e.g., identifiers, operators and other entities, to Wikidata entries, the gold standard can, for instance, be used to train methods for formula concept discovery and recognition. Such methods can then be applied to improve mathematical information retrieval systems, e.g., for semantic formula search, recommendation of mathematical content, or detection of mathematical plagiarism.Comment: 10 pages, 4 figure

Underwater image restoration: super-resolution and deblurring via sparse representation and denoising by means of marine snow removal

Underwater imaging has been widely used as a tool in many fields, however, a major issue is the quality of the resulting images/videos. Due to the light's interaction with water and its constituents, the acquired underwater images/videos often suffer from a significant amount of scatter (blur, haze) and noise. In the light of these issues, this thesis considers problems of low-resolution, blurred and noisy underwater images and proposes several approaches to improve the quality of such images/video frames. Quantitative and qualitative experiments validate the success of proposed algorithms

Multilingual sentiment analysis in social media.

252 p.This thesis addresses the task of analysing sentiment in messages coming from social media. The ultimate goal was to develop a Sentiment Analysis system for Basque. However, because of the socio-linguistic reality of the Basque language a tool providing only analysis for Basque would not be enough for a real world application. Thus, we set out to develop a multilingual system, including Basque, English, French and Spanish.The thesis addresses the following challenges to build such a system:- Analysing methods for creating Sentiment lexicons, suitable for less resourced languages.- Analysis of social media (specifically Twitter): Tweets pose several challenges in order to understand and extract opinions from such messages. Language identification and microtext normalization are addressed.- Research the state of the art in polarity classification, and develop a supervised classifier that is tested against well known social media benchmarks.- Develop a social media monitor capable of analysing sentiment with respect to specific events, products or organizations

D7.1. Criteria for evaluation of resources, technology and integration.

This deliverable defines how evaluation is carried out at each integration cycle in the PANACEA project. As PANACEA aims at producing large scale resources, evaluation becomes a critical and challenging issue. Critical because it is important to assess the quality of the results that should be delivered to users. Challenging because we prospect rather new areas, and through a technical platform: some new methodologies will have to be explored or old ones to be adapted

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)

The TXM Portal Software giving access to Old French Manuscripts Online

Texte intégral en ligne : http://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdfInternational audiencehttp://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdf This paper presents the new TXM software platform giving online access to Old French Text Manuscripts images and tagged transcriptions for concordancing and text mining. This platform is able to import medieval sources encoded in XML according to the TEI Guidelines for linking manuscript images to transcriptions, encode several diplomatic levels of transcription including abbreviations and word level corrections. It includes a sophisticated tokenizer able to deal with TEI tags at different levels of linguistic hierarchy. Words are tagged on the fly during the import process using IMS TreeTagger tool with a specific language model. Synoptic editions displaying side by side manuscript images and text transcriptions are automatically produced during the import process. Texts are organized in a corpus with their own metadata (title, author, date, genre, etc.) and several word properties indexes are produced for the CQP search engine to allow efficient word patterns search to build different type of frequency lists or concordances. For syntactically annotated texts, special indexes are produced for the Tiger Search engine to allow efficient syntactic concordances building. The platform has also been tested on classical Latin, ancient Greek, Old Slavonic and Old Hieroglyphic Egyptian corpora (including various types of encoding and annotations)

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