Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

<p>Abstract</p> <p>Background</p> <p>A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level.</p> <p>Results</p> <p>This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context written in the surrounding text. MEDLINE abstract texts have been processed to identify protein mentions in combination with taxonomic species and protein residues (F1-measure 0.52). The identified protein-species-residue triplets have been validated and benchmarked against reference data resources (UniProtKb, average F1-measure of 0.54). Then, contextual features were extracted through shallow and deep parsing and the features have been classified into predefined categories (F1-measure ranges from 0.15 to 0.67). Furthermore, the feature sets have been aligned with annotation types in UniProtKb to assess the relevance of the annotations for ongoing curation projects. Altogether, the annotations have been assessed automatically and manually against reference data resources.</p> <p>Conclusion</p> <p>This work proposes a solution for the automatic extraction of functional annotation for protein residues from biomedical articles. The presented approach is an extension to other existing systems in that a wider range of residue entities are considered and that features of residues are extracted as annotations.</p

Arabic named entity recognition

En esta tesis doctoral se describen las investigaciones realizadas con el objetivo de determinar las mejores tecnicas para construir un Reconocedor de Entidades Nombradas en Arabe. Tal sistema tendria la habilidad de identificar y clasificar las entidades nombradas que se encuentran en un texto arabe de dominio abierto. La tarea de Reconocimiento de Entidades Nombradas (REN) ayuda a otras tareas de Procesamiento del Lenguaje Natural (por ejemplo, la Recuperacion de Informacion, la Busqueda de Respuestas, la Traduccion Automatica, etc.) a lograr mejores resultados gracias al enriquecimiento que a~nade al texto. En la literatura existen diversos trabajos que investigan la tarea de REN para un idioma especifico o desde una perspectiva independiente del lenguaje. Sin embargo, hasta el momento, se han publicado muy pocos trabajos que estudien dicha tarea para el arabe. El arabe tiene una ortografia especial y una morfologia compleja, estos aspectos aportan nuevos desafios para la investigacion en la tarea de REN. Una investigacion completa del REN para elarabe no solo aportaria las tecnicas necesarias para conseguir un alto rendimiento, sino que tambien proporcionara un analisis de los errores y una discusion sobre los resultados que benefician a la comunidad de investigadores del REN. El objetivo principal de esta tesis es satisfacer esa necesidad. Para ello hemos: 1. Elaborado un estudio de los diferentes aspectos del arabe relacionados con dicha tarea; 2. Analizado el estado del arte del REN; 3. Llevado a cabo una comparativa de los resultados obtenidos por diferentes tecnicas de aprendizaje automatico; 4. Desarrollado un metodo basado en la combinacion de diferentes clasificadores, donde cada clasificador trata con una sola clase de entidades nombradas y emplea el conjunto de caracteristicas y la tecnica de aprendizaje automatico mas adecuados para la clase de entidades nombradas en cuestion. Nuestros experimentos han sido evaluados sobre nueve conjuntos de test.Benajiba, Y. (2009). Arabic named entity recognition [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8318Palanci

Factoid question answering for spoken documents

In this dissertation, we present a factoid question answering system, specifically tailored for Question Answering (QA) on spoken documents. This work explores, for the first time, which techniques can be robustly adapted from the usual QA on written documents to the more difficult spoken documents scenario. More specifically, we study new information retrieval (IR) techniques designed for speech, and utilize several levels of linguistic information for the speech-based QA task. These include named-entity detection with phonetic information, syntactic parsing applied to speech transcripts, and the use of coreference resolution. Our approach is largely based on supervised machine learning techniques, with special focus on the answer extraction step, and makes little use of handcrafted knowledge. Consequently, it should be easily adaptable to other domains and languages. In the work resulting of this Thesis, we have impulsed and coordinated the creation of an evaluation framework for the task of QA on spoken documents. The framework, named QAst, provides multi-lingual corpora, evaluation questions, and answers key. These corpora have been used in the QAst evaluation that was held in the CLEF workshop for the years 2007, 2008 and 2009, thus helping the developing of state-of-the-art techniques for this particular topic. The presentend QA system and all its modules are extensively evaluated on the European Parliament Plenary Sessions English corpus composed of manual transcripts and automatic transcripts obtained by three different Automatic Speech Recognition (ASR) systems that exhibit significantly different word error rates. This data belongs to the CLEF 2009 track for QA on speech transcripts. The main results confirm that syntactic information is very useful for learning to rank question candidates, improving results on both manual and automatic transcripts unless the ASR quality is very low. Overall, the performance of our system is comparable or better than the state-of-the-art on this corpus, confirming the validity of our approach.En aquesta Tesi, presentem un sistema de Question Answering (QA) factual, especialment ajustat per treballar amb documents orals. En el desenvolupament explorem, per primera vegada, quines tècniques de les habitualment emprades en QA per documents escrit són suficientment robustes per funcionar en l'escenari més difícil de documents orals. Amb més especificitat, estudiem nous mètodes de Information Retrieval (IR) dissenyats per tractar amb la veu, i utilitzem diversos nivells d'informació linqüística. Entre aquests s'inclouen, a saber: detecció de Named Entities utilitzant informació fonètica, "parsing" sintàctic aplicat a transcripcions de veu, i també l'ús d'un sub-sistema de detecció i resolució de la correferència. La nostra aproximació al problema es recolza en gran part en tècniques supervisades de Machine Learning, estant aquestes enfocades especialment cap a la part d'extracció de la resposta, i fa servir la menor quantitat possible de coneixement creat per humans. En conseqüència, tot el procés de QA pot ser adaptat a altres dominis o altres llengües amb relativa facilitat. Un dels resultats addicionals de la feina darrere d'aquesta Tesis ha estat que hem impulsat i coordinat la creació d'un marc d'avaluació de la taska de QA en documents orals. Aquest marc de treball, anomenat QAst (Question Answering on Speech Transcripts), proporciona un corpus de documents orals multi-lingüe, uns conjunts de preguntes d'avaluació, i les respostes correctes d'aquestes. Aquestes dades han estat utilitzades en les evaluacionis QAst que han tingut lloc en el si de les conferències CLEF en els anys 2007, 2008 i 2009; d'aquesta manera s'ha promogut i ajudat a la creació d'un estat-de-l'art de tècniques adreçades a aquest problema en particular. El sistema de QA que presentem i tots els seus particulars sumbòduls, han estat avaluats extensivament utilitzant el corpus EPPS (transcripcions de les Sessions Plenaries del Parlament Europeu) en anglès, que cónté transcripcions manuals de tots els discursos i també transcripcions automàtiques obtingudes mitjançant tres reconeixedors automàtics de la parla (ASR) diferents. Els reconeixedors tenen característiques i resultats diferents que permetes una avaluació quantitativa i qualitativa de la tasca. Aquestes dades pertanyen a l'avaluació QAst del 2009. Els resultats principals de la nostra feina confirmen que la informació sintàctica és mol útil per aprendre automàticament a valorar la plausibilitat de les respostes candidates, millorant els resultats previs tan en transcripcions manuals com transcripcions automàtiques, descomptat que la qualitat de l'ASR sigui molt baixa. En general, el rendiment del nostre sistema és comparable o millor que els altres sistemes pertanyents a l'estat-del'art, confirmant així la validesa de la nostra aproximació

Sensor-based datasets for human activity recognition - a systematic review of literature

The research area of ambient assisted living has led to the development of activity recognition systems (ARS) based on human activity recognition (HAR). These systems improve the quality of life and the health care of the elderly and dependent people. However, before making them available to end users, it is necessary to evaluate their performance in recognizing activities of daily living, using data set benchmarks in experimental scenarios. For that reason, the scientific community has developed and provided a huge amount of data sets for HAR. Therefore, identifying which ones to use in the evaluation process and which techniques are the most appropriate for prediction of HAR in a specific context is not a trivial task and is key to further progress in this area of research. This work presents a systematic review of the literature of the sensor-based data sets used to evaluate ARS. On the one hand, an analysis of different variables taken from indexed publications related to this field was performed. The sources of information are journals, proceedings, and books located in specialized databases. The analyzed variables characterize publications by year, database, type, quartile, country of origin, and destination, using scientometrics, which allowed identification of the data set most used by researchers. On the other hand, the descriptive and functional variables were analyzed for each of the identified data sets: occupation, annotation, approach, segmentation, representation, feature selection, balancing and addition of instances, and classifier used for recognition. This paper provides an analysis of the sensor-based data sets used in HAR to date, identifying the most appropriate dataset to evaluate ARS and the classification techniques that generate better results

Sensor-based datasets for human activity recognition - a systematic review of literature

The research area of ambient assisted living has led to the development of activity recognition systems (ARS) based on human activity recognition (HAR). These systems improve the quality of life and the health care of the elderly and dependent people. However, before making them available to end users, it is necessary to evaluate their performance in recognizing activities of daily living, using data set benchmarks in experimental scenarios. For that reason, the scientific community has developed and provided a huge amount of data sets for HAR. Therefore, identifying which ones to use in the evaluation process and which techniques are the most appropriate for prediction of HAR in a specific context is not a trivial task and is key to further progress in this area of research. This work presents a systematic review of the literature of the sensor-based data sets used to evaluate ARS. On the one hand, an analysis of different variables taken from indexed publications related to this field was performed. The sources of information are journals, proceedings, and books located in specialized databases. The analyzed variables characterize publications by year, database, type, quartile, country of origin, and destination, using scientometrics, which allowed identification of the data set most used by researchers. On the other hand, the descriptive and functional variables were analyzed for each of the identified data sets: occupation, annotation, approach, segmentation, representation, feature selection, balancing and addition of instances, and classifier used for recognition. This paper provides an analysis of the sensor-based data sets used in HAR to date, identifying the most appropriate dataset to evaluate ARS and the classification techniques that generate better results

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This work explores the potential of using textual patterns for Information Extraction from the World Wide Web

Automatic text filtering using limited supervision learning for epidemic intelligence

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