Knowledge discovery with CRF-based clustering of named entities without a priori classes

International audienceKnowledge discovery aims at bringing out coherent groups of entities. It is usually based on clustering which necessitates defining a notion of similarity between the relevant entities. In this paper, we propose to divert a supervised machine learning technique (namely Conditional Random Fields, widely used for supervised labeling tasks) in order to calculate, indirectly and without supervision, similarities among text sequences. Our approach consists in generating artificial labeling problems on the data to reveal regularities between entities through their labeling. We describe how this framework can be implemented and experiment it on two information extraction/discovery tasks. The results demonstrate the usefulness of this unsupervised approach, and open many avenues for defining similarities for complex representations of textual data

Approaches for enriching and improving textual knowledge bases

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Unsupervised Information Extraction From Text Extraction and Clustering of Relations between Entities

L'extraction d'information non supervisée en domaine ouvert est une évolution récente de l'extraction d'information adaptée à des contextes dans lesquels le besoin informationnel est faiblement spécifié. Dans ce cadre, la thèse se concentre plus particulièrement sur l'extraction et le regroupement de relations entre entités en se donnant la possibilité de traiter des volumes importants de données.L'extraction de relations se fixe plus précisément pour objectif de faire émerger des relations de type non prédéfini à partir de textes. Ces relations sont de nature semi-structurée : elles associent des éléments faisant référence à des structures de connaissance définies a priori, dans le cas présent les entités qu elles relient, et des éléments donnés uniquement sous la forme d une caractérisation linguistique, en l occurrence leur type. Leur extraction est réalisée en deux temps : des relations candidates sont d'abord extraites sur la base de critères simples mais efficaces pour être ensuite filtrées selon des critères plus avancés. Ce filtrage associe lui-même deux étapes : une première étape utilise des heuristiques pour éliminer rapidement les fausses relations en conservant un bon rappel tandis qu'une seconde étape se fonde sur des modèles statistiques pour raffiner la sélection des relations candidates.Le regroupement de relations a quant à lui un double objectif : d une part, organiser les relations extraites pour en caractériser le type au travers du regroupement des relations sémantiquement équivalentes et d autre part, en offrir une vue synthétique. Il est réalisé dans le cas présent selon une stratégie multiniveau permettant de prendre en compte à la fois un volume important de relations et des critères de regroupement élaborés. Un premier niveau de regroupement, dit de base, réunit des relations proches par leur expression linguistique grâce à une mesure de similarité vectorielle appliquée à une représentation de type sac-de-mots pour former des clusters fortement homogènes. Un second niveau de regroupement est ensuite appliqué pour traiter des phénomènes plus sémantiques tels que la synonymie et la paraphrase et fusionner des clusters de base recouvrant des relations équivalentes sur le plan sémantique. Ce second niveau s'appuie sur la définition de mesures de similarité au niveau des mots, des relations et des clusters de relations en exploitant soit des ressources de type WordNet, soit des thésaurus distributionnels. Enfin, le travail illustre l intérêt de la mise en œuvre d un clustering des relations opéré selon une dimension thématique, en complément de la dimension sémantique des regroupements évoqués précédemment. Ce clustering est réalisé de façon indirecte au travers du regroupement des contextes thématiques textuels des relations. Il offre à la fois un axe supplémentaire de structuration des relations facilitant leur appréhension globale mais également le moyen d invalider certains regroupements sémantiques fondés sur des termes polysémiques utilisés avec des sens différents. La thèse aborde également le problème de l'évaluation de l'extraction d'information non supervisée par l'entremise de mesures internes et externes. Pour les mesures externes, une méthode interactive est proposée pour construire manuellement un large ensemble de clusters de référence. Son application sur un corpus journalistique de grande taille a donné lieu à la construction d'une référence vis-à-vis de laquelle les différentes méthodes de regroupement proposées dans la thèse ont été évaluées.Unsupervised information extraction in open domain gains more and more importance recently by loosening the constraints on the strict definition of the extracted information and allowing to design more open information extraction systems. In this new domain of unsupervised information extraction, this thesis focuses on the tasks of extraction and clustering of relations between entities at a large scale. The objective of relation extraction is to discover unknown relations from texts. A relation prototype is first defined, with which candidates of relation instances are initially extracted with a minimal criterion. To guarantee the validity of the extracted relation instances, a two-step filtering procedures is applied: the first step with filtering heuristics to remove efficiently large amount of false relations and the second step with statistical models to refine the relation candidate selection. The objective of relation clustering is to organize extracted relation instances into clusters so that their relation types can be characterized by the formed clusters and a synthetic view can be offered to end-users. A multi-level clustering procedure is design, which allows to take into account the massive data and diverse linguistic phenomena at the same time. First, the basic clustering groups similar relation instances by their linguistic expressions using only simple similarity measures on a bag-of-word representation for relation instances to form high-homogeneous basic clusters. Second, the semantic clustering aims at grouping basic clusters whose relation instances share the same semantic meaning, dealing with more particularly phenomena such as synonymy or more complex paraphrase. Different similarities measures, either based on resources such as WordNet or distributional thesaurus, at the level of words, relation instances and basic clusters are analyzed. Moreover, a topic-based relation clustering is proposed to consider thematic information in relation clustering so that more precise semantic clusters can be formed. Finally, the thesis also tackles the problem of clustering evaluation in the context of unsupervised information extraction, using both internal and external measures. For the evaluations with external measures, an interactive and efficient way of building reference of relation clusters proposed. The application of this method on a newspaper corpus results in a large reference, based on which different clustering methods are evaluated.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts

From Text to Knowledge

The global information space provided by the World Wide Web has changed dramatically the way knowledge is shared all over the world. To make this unbelievable huge information space accessible, search engines index the uploaded contents and provide efficient algorithmic machinery for ranking the importance of documents with respect to an input query. All major search engines such as Google, Yahoo or Bing are keyword-based, which is indisputable a very powerful tool for accessing information needs centered around documents. However, this unstructured, document-oriented paradigm of the World Wide Web has serious drawbacks, when searching for specific knowledge about real-world entities. When asking for advanced facts about entities, today's search engines are not very good in providing accurate answers. Hand-built knowledge bases such as Wikipedia or its structured counterpart DBpedia are excellent sources that provide common facts. However, these knowledge bases are far from being complete and most of the knowledge lies still buried in unstructured documents. Statistical machine learning methods have the great potential to help to bridge the gap between text and knowledge by (semi-)automatically transforming the unstructured representation of the today's World Wide Web to a more structured representation. This thesis is devoted to reduce this gap with Probabilistic Graphical Models. Probabilistic Graphical Models play a crucial role in modern pattern recognition as they merge two important fields of applied mathematics: Graph Theory and Probability Theory. The first part of the thesis will present a novel system called Text2SemRel that is able to (semi-)automatically construct knowledge bases from textual document collections. The resulting knowledge base consists of facts centered around entities and their relations. Essential part of the system is a novel algorithm for extracting relations between entity mentions that is based on Conditional Random Fields, which are Undirected Probabilistic Graphical Models. In the second part of the thesis, we will use the power of Directed Probabilistic Graphical Models to solve important knowledge discovery tasks in semantically annotated large document collections. In particular, we present extensions of the Latent Dirichlet Allocation framework that are able to learn in an unsupervised way the statistical semantic dependencies between unstructured representations such as documents and their semantic annotations. Semantic annotations of documents might refer to concepts originating from a thesaurus or ontology but also to user-generated informal tags in social tagging systems. These forms of annotations represent a first step towards the conversion to a more structured form of the World Wide Web. In the last part of the thesis, we prove the large-scale applicability of the proposed fact extraction system Text2SemRel. In particular, we extract semantic relations between genes and diseases from a large biomedical textual repository. The resulting knowledge base contains far more potential disease genes exceeding the number of disease genes that are currently stored in curated databases. Thus, the proposed system is able to unlock knowledge currently buried in the literature. The literature-derived human gene-disease network is subject of further analysis with respect to existing curated state of the art databases. We analyze the derived knowledge base quantitatively by comparing it with several curated databases with regard to size of the databases and properties of known disease genes among other things. Our experimental analysis shows that the facts extracted from the literature are of high quality

Content Recognition and Context Modeling for Document Analysis and Retrieval

The nature and scope of available documents are changing significantly in many areas of document analysis and retrieval as complex, heterogeneous collections become accessible to virtually everyone via the web. The increasing level of diversity presents a great challenge for document image content categorization, indexing, and retrieval. Meanwhile, the processing of documents with unconstrained layouts and complex formatting often requires effective leveraging of broad contextual knowledge. In this dissertation, we first present a novel approach for document image content categorization, using a lexicon of shape features. Each lexical word corresponds to a scale and rotation invariant local shape feature that is generic enough to be detected repeatably and is segmentation free. A concise, structurally indexed shape lexicon is learned by clustering and partitioning feature types through graph cuts. Our idea finds successful application in several challenging tasks, including content recognition of diverse web images and language identification on documents composed of mixed machine printed text and handwriting. Second, we address two fundamental problems in signature-based document image retrieval. Facing continually increasing volumes of documents, detecting and recognizing unique, evidentiary visual entities (\eg, signatures and logos) provides a practical and reliable supplement to the OCR recognition of printed text. We propose a novel multi-scale framework to detect and segment signatures jointly from document images, based on the structural saliency under a signature production model. We formulate the problem of signature retrieval in the unconstrained setting of geometry-invariant deformable shape matching and demonstrate state-of-the-art performance in signature matching and verification. Third, we present a model-based approach for extracting relevant named entities from unstructured documents. In a wide range of applications that require structured information from diverse, unstructured document images, processing OCR text does not give satisfactory results due to the absence of linguistic context. Our approach enables learning of inference rules collectively based on contextual information from both page layout and text features. Finally, we demonstrate the importance of mining general web user behavior data for improving document ranking and other web search experience. The context of web user activities reveals their preferences and intents, and we emphasize the analysis of individual user sessions for creating aggregate models. We introduce a novel algorithm for estimating web page and web site importance, and discuss its theoretical foundation based on an intentional surfer model. We demonstrate that our approach significantly improves large-scale document retrieval performance