1. 2617-2640 of 2696 « 1 2 ... 107 108 109 110 111 112 113 »
    1. Evaluating the state-of-the-art in automatic de-identification.

      Related Articles Evaluating the state-of-the-art in automatic de-identification. J Am Med Inform Assoc. 2007 Sep-Oct;14(5):550-63 Authors: Uzuner O, Luo Y, Szolovits P To facilitate and survey studies in automatic de-identification, as a part of the i2b2 (Informatics for Integrating Biology to the Bedside) project, authors organized a Natural Language Processing (NLP) challenge on automatically removing private health information (PHI) from medical discharge records. This manuscript provides an overview of this de-identification challenge, describes the data and the annotation process, explains the evaluation metrics, discusses the nature of the systems that addressed the challenge, analyzes the results of ...
      Read Full Article
    2. Rapidly retargetable approaches to de-identification in medical records.

      Related Articles Rapidly retargetable approaches to de-identification in medical records. J Am Med Inform Assoc. 2007 Sep-Oct;14(5):564-73 Authors: Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan A, Peshkin L, Yeh A, Hitzeman J, Hirschman L OBJECTIVE: This paper describes a successful approach to de-identification that was developed to participate in a recent AMIA-sponsored challenge evaluation. METHOD: Our approach focused on rapid adaptation of existing toolkits for named entity recognition using two existing toolkits, Carafe and LingPipe. RESULTS: The "out of the box" Carafe system achieved a very good score (phrase F-measure of 0.9664) with only ...
      Read Full Article
    3. Heuristic sample selection to minimize reference standard training set for a part-of-speech tagger.

      Related Articles Heuristic sample selection to minimize reference standard training set for a part-of-speech tagger. J Am Med Inform Assoc. 2007 Sep-Oct;14(5):641-50 Authors: Liu K, Chapman W, Hwa R, Crowley RS Part-of-speech tagging represents an important first step for most medical natural language processing (NLP) systems. The majority of current statistically-based POS taggers are trained using a general English corpus. Consequently, these systems perform poorly on medical text. Annotated medical corpora are difficult to develop because of the time and labor required. We investigated a heuristic-based sample selection method to minimize annotated corpus size for retraining a ...
      Read Full Article
    4. Applying language technology to nursing documents: Pros and cons with a focus on ethics.

      Related Articles Applying language technology to nursing documents: Pros and cons with a focus on ethics. Int J Med Inform. 2007 Oct;76 Suppl 2:S293-301 Authors: Suominen H, Lehtikunnas T, Back B, Karsten H, Salakoski T, Salanterä S OBJECTIVES: The present study discusses ethics in building and using applications based on natural language processing in electronic nursing documentation. Specifically, we first focus on the question of how patient confidentiality can be ensured in developing language technology for the nursing documentation domain. Then, we identify and theoretically analyze the ethical outcomes which arise when using natural language processing to support ...
      Read Full Article
    5. A transversal approach to predict gene product networks from ontology-based similarity.

      Related Articles A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics. 2007;8:235 Authors: Chabalier J, Mosser J, Burgun A BACKGROUND: Interpretation of transcriptomic data is usually made through a "standard" approach which consists in clustering the genes according to their expression patterns and exploiting Gene Ontology (GO) annotations within each expression cluster. This approach makes it difficult to underline functional relationships between gene products that belong to different expression clusters. To address this issue, we propose a transversal analysis that aims to predict functional networks based on a combination of GO processes and data ...
      Read Full Article
    6. Extended Backus-systems for the representation and specification of the genome.

      Related Articles Extended Backus-systems for the representation and specification of the genome. J Bioinform Comput Biol. 2007 Apr;5(2B):457-66 Authors: Hofestädt R In this theoretical paper, we focus to the usage of formal languages and define an extended Backus-System which will allow an adequate representation of molecular data. Furthermore, based on this new formalization we try to define the "complexity of organisms". Our results show that this formalization is useful for the syntactical specification of the genome interpreted as a formal language. PMID: 17636855 [PubMed - indexed for MEDLINE]
      Read Full Article
    7. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.

      Related Articles Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics. 2007;8:243 Authors: Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I BACKGROUND: Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more ...
      Read Full Article
      Mentions: Rockville
    8. Learning to extract relations for protein annotation.

      Related Articles Learning to extract relations for protein annotation. Bioinformatics. 2007 Jul 1;23(13):i256-63 Authors: Kim JH, Mitchell A, Attwood TK, Hilario M MOTIVATION: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this ...
      Read Full Article
    9. Negation of protein-protein interactions: analysis and extraction.

      Related Articles Negation of protein-protein interactions: analysis and extraction. Bioinformatics. 2007 Jul 1;23(13):i424-32 Authors: Sanchez-Graillet O, Poesio M MOTIVATION: Negative information about protein-protein interactions--from uncertainty about the occurrence of an interaction to knowledge that it did not occur--is often of great use to biologists and could lead to important discoveries. Yet, to our knowledge, no proposals focusing on extracting such information have been proposed in the text mining literature. RESULTS: In this work, we present an analysis of the types of negative information that is reported, and a heuristic-based system using a full dependency parser to extract ...
      Read Full Article
    10. Identification of new drug classification terms in textual resources.

      Related Articles Identification of new drug classification terms in textual resources. Bioinformatics. 2007 Jul 1;23(13):i264-72 Authors: Kolárik C, Hofmann-Apitius M, Zimmermann M, Fluck J Knowledge about biological effects of small molecules helps in the understanding of biological processes and supports the development of new therapeutic agents. DrugBank is a high quality database providing such information about drugs that contains annotation of drug effects and classification of therapeutic effects. However, to broaden the scope of such a database in classifying and annotating drugs, systems for automatic extraction of classification terms and the corresponding annotation of drugs are ...
      Read Full Article
    11. Annotating gene function by combining expression data with a modular gene network.

      Related Articles Annotating gene function by combining expression data with a modular gene network. Bioinformatics. 2007 Jul 1;23(13):i468-78 Authors: Shiga M, Takigawa I, Mamitsuka H MOTIVATION: A promising and reliable approach to annotate gene function is clustering genes not only by using gene expression data but also literature information, especially gene networks. RESULTS: We present a systematic method for gene clustering by combining these totally different two types of data, particularly focusing on network modularity, a global feature of gene networks. Our method is based on learning a probabilistic model, which we call a hidden modular random ...
      Read Full Article
    12. Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

      Related Articles Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007;8:264 Authors: Fan JW, Xu H, Friedman C BACKGROUND: Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous ...
      Read Full Article
      Mentions: New York Xu H
    13. Semantic integration to identify overlapping functional modules in protein interaction networks.

      Related Articles Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics. 2007;8:265 Authors: Cho YR, Hwang W, Ramanathan M, Zhang A BACKGROUND: The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module ...
      Read Full Article
    14. Automating document classification for the Immune Epitope Database.

      Related Articles Automating document classification for the Immune Epitope Database. BMC Bioinformatics. 2007;8:269 Authors: Wang P, Morgan AA, Zhang Q, Sette A, Peters B BACKGROUND: The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose. RESULTS: We here report our experience in automating this process using Naïve Bayes classifiers trained on 20,910 abstracts classified by domain experts. Improvements on the basic classifier performance were made by a) utilizing information stored in ...
      Read Full Article
    15. Compression of annotated nucleotide sequences.

      Related Articles Compression of annotated nucleotide sequences. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):447-57 Authors: Korodi G, Tabus I This article introduces an algorithm for the lossless compression of DNA files, which contain annotation text besides the nucleotide sequence. First a grammar is specifically designed to capture the regularities of the annotation text. A revertible transformation uses the grammar rules in order to equivalently represent the original file as a collection of parsed segments and a sequence of decisions made by the grammar parser. This decomposition enables the efficient use of state-of-the-art encoders for processing the ...
      Read Full Article
      Mentions: Finland Tampere
    16. A field theoretical approach to medical natural language processing.

      Related Articles A field theoretical approach to medical natural language processing. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):364-75 Authors: Taira RK, Bashyam V, Kangarloo H A parser for medical free text reports has been developed that is based on a chemistry/physics inspired "field theory" for word-word sentence-level dependencies. The transition from the linguistic world to the world of interacting particles with potential energies is guided by a psycholinguistics thought experiment related to the amount of "work" required to bring a reference word into an anchored configuration of words. Calibration experiments involving four and five grams were ...
      Read Full Article
    17. Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice.

      Related Articles Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):376-85 Authors: Masseroli M The growing available genomic information provides new opportunities for novel research approaches and original biomedical applications that can provide effective data management and analysis support. In fact, integration and comprehensive evaluation of available controlled data can highlight information patterns leading to unveil new biomedical knowledge. Here, we describe Genome Function INtegrated Discover (GFINDer), a Web-accessible three-tier multidatabase system we developed to automatically enrich lists of user-classified genes with several ...
      Read Full Article
    18. Modeling drug mechanism knowledge using evidence and truth maintenance.

      Related Articles Modeling drug mechanism knowledge using evidence and truth maintenance. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):386-97 Authors: Boyce RD, Collins C, Horn J, Kalet I To protect the safety of patients, it is vital that researchers find methods for representing drug mechanism knowledge that support making clinically relevant drug-drug interaction (DDI) predictions. Our research aims to identify the challenges of representing and reasoning with drug mechanism knowledge and to evaluate potential informatics solutions to these challenges through the process of developing a knowledge-based system capable of predicting clinically relevant DDIs that occur via metabolic mechanisms ...
      Read Full Article
    19. Psychiatric consultation record retrieval using scenario-based representation and multilevel mixture model.

      Related Articles Psychiatric consultation record retrieval using scenario-based representation and multilevel mixture model. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):415-27 Authors: Yu LC, Wu CH, Jang FL Psychiatric consultation record retrieval attempts to help people to efficiently and effectively locate the consultation records relevant to their depressive problems. Consultation records can also make people aware that they are not alone, because many individuals have suffered from the same or similar problems. Additionally, people can understand how to alleviate their depressive symptoms according to recommendations from health professionals. To achieve this goal, this paper proposes the use of ...
      Read Full Article
    20. An Infrastructure For Application Integration And Knowledge Discovery In Bioinformatics.

      Related Articles BAAQ: an infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):428-34 Authors: Gong X, Nakamura K, Yu H, Yura K, Go N The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public databases, computational tools as well as their analysis workflows. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments, standards and high-level services. Here, we present a system, which we named Bioinformatics: Ask ...
      Read Full Article
    21. PepBank--a database of peptides based on sequence text mining and public peptide data sources.

      Related Articles PepBank--a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics. 2007;8:280 Authors: Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R BACKGROUND: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. DESCRIPTION: We have constructed a new database (PepBank), which at the time of writing contains a total of ...
      Read Full Article
    22. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing.

      Related Articles Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics. 2007;8:293 Authors: Rodríguez-Penagos C, Salgado H, Martínez-Flores I, Collado-Vides J BACKGROUND: Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Language Processing system that creates computer-readable networks of regulatory interactions directly from different collections of abstracts and full-text papers. Our major aim is to understand how automatic annotation using Text-Mining techniques can complement manual curation of biological databases. We implemented a rule-based ...
      Read Full Article
    23. Text extraction and document image segmentation using matched wavelets and MRF model.

      Related Articles Text extraction and document image segmentation using matched wavelets and MRF model. IEEE Trans Image Process. 2007 Aug;16(8):2117-28 Authors: Kumar S, Gupta R, Khanna N, Chaudhury S, Joshi SD In this paper, we have proposed a novel scheme for the extraction of textual areas of an image using globally matched wavelet filters. A clustering-based technique has been devised for estim ating globally matched wavelet filters using a collection of groundtruth images. We have extended our text extraction scheme for the segmentation of document images into text, background, and picture components (which include graphics and continuous ...
      Read Full Article
    2617-2640 of 2696 « 1 2 ... 107 108 109 110 111 112 113 »
  1. Categories

    1. Default:

      Discourse, Entailment, Machine Translation, NER, Parsing, Segmentation, Semantic, Sentiment, Summarization, WSD