Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Strategies for Managing Linked Enterprise Data

Data, information and knowledge become key assets of our 21st century economy. As a result, data and knowledge management become key tasks with regard to sustainable development and business success. Often, knowledge is not explicitly represented residing in the minds of people or scattered among a variety of data sources. Knowledge is inherently associated with semantics that conveys its meaning to a human or machine agent. The Linked Data concept facilitates the semantic integration of heterogeneous data sources. However, we still lack an effective knowledge integration strategy applicable to enterprise scenarios, which balances between large amounts of data stored in legacy information systems and data lakes as well as tailored domain specific ontologies that formally describe real-world concepts. In this thesis we investigate strategies for managing linked enterprise data analyzing how actionable knowledge can be derived from enterprise data leveraging knowledge graphs. Actionable knowledge provides valuable insights, supports decision makers with clear interpretable arguments, and keeps its inference processes explainable. The benefits of employing actionable knowledge and its coherent management strategy span from a holistic semantic representation layer of enterprise data, i.e., representing numerous data sources as one, consistent, and integrated knowledge source, to unified interaction mechanisms with other systems that are able to effectively and efficiently leverage such an actionable knowledge. Several challenges have to be addressed on different conceptual levels pursuing this goal, i.e., means for representing knowledge, semantic data integration of raw data sources and subsequent knowledge extraction, communication interfaces, and implementation. In order to tackle those challenges we present the concept of Enterprise Knowledge Graphs (EKGs), describe their characteristics and advantages compared to existing approaches. We study each challenge with regard to using EKGs and demonstrate their efficiency. In particular, EKGs are able to reduce the semantic data integration effort when processing large-scale heterogeneous datasets. Then, having built a consistent logical integration layer with heterogeneity behind the scenes, EKGs unify query processing and enable effective communication interfaces for other enterprise systems. The achieved results allow us to conclude that strategies for managing linked enterprise data based on EKGs exhibit reasonable performance, comply with enterprise requirements, and ensure integrated data and knowledge management throughout its life cycle

Génération automatique d'alignements complexes d'ontologies

Le web de données liées (LOD) est composé de nombreux entrepôts de données. Ces données sont décrites par différents vocabulaires (ou ontologies). Chaque ontologie a une terminologie et une modélisation propre ce qui les rend hétérogènes. Pour lier et rendre les données du web de données liées interopérables, les alignements d'ontologies établissent des correspondances entre les entités desdites ontologies. Il existe de nombreux systèmes d'alignement qui génèrent des correspondances simples, i.e., ils lient une entité à une autre entité. Toutefois, pour surmonter l'hétérogénéité des ontologies, des correspondances plus expressives sont parfois nécessaires. Trouver ce genre de correspondances est un travail fastidieux qu'il convient d'automatiser. Dans le cadre de cette thèse, une approche d'alignement complexe basée sur des besoins utilisateurs et des instances communes est proposée. Le domaine des alignements complexes est relativement récent et peu de travaux adressent la problématique de leur évaluation. Pour pallier ce manque, un système d'évaluation automatique basé sur de la comparaison d'instances est proposé. Ce système est complété par un jeu de données artificiel sur le domaine des conférences.The Linked Open Data (LOD) cloud is composed of data repositories. The data in the repositories are described by vocabularies also called ontologies. Each ontology has its own terminology and model. This leads to heterogeneity between them. To make the ontologies and the data they describe interoperable, ontology alignments establish correspondences, or links between their entities. There are many ontology matching systems which generate simple alignments, i.e., they link an entity to another. However, to overcome the ontology heterogeneity, more expressive correspondences are sometimes needed. Finding this kind of correspondence is a fastidious task that can be automated. In this thesis, an automatic complex matching approach based on a user's knowledge needs and common instances is proposed. The complex alignment field is still growing and little work address the evaluation of such alignments. To palliate this lack, we propose an automatic complex alignment evaluation system. This system is based on instances. A famous alignment evaluation dataset has been extended for this evaluation

Using natural language processing for question answering in closed and open domains

With regard to the growth in the amount of social, environmental, and biomedical information available digitally, there is a growing need for Question Answering (QA) systems that can empower users to master this new wealth of information. Despite recent progress in QA, the quality of interpretation and extraction of the desired answer is not adequate. We believe that striving for higher accuracy in QA systems is subject to on-going research, i.e., it is better to have no answer is better than wrong answers. However, there are diverse queries, which the state of the art QA systems cannot interpret and answer properly. The problem of interpreting a question in a way that could preserve its syntactic-semantic structure is considered as one of the most important challenges in this area. In this work we focus on the problems of semantic-based QA systems and analyzing the effectiveness of NLP techniques, query mapping, and answer inferencing both in closed (first scenario) and open (second scenario) domains. For this purpose, the architecture of Semantic-based closed and open domain Question Answering System (hereafter “ScoQAS”) over ontology resources is presented with two different prototyping: Ontology-based closed domain and an open domain under Linked Open Data (LOD) resource. The ScoQAS is based on NLP techniques combining semantic-based structure-feature patterns for question classification and creating a question syntactic-semantic information structure (QSiS). The QSiS provides an actual potential by building constraints to formulate the related terms on syntactic-semantic aspects and generating a question graph (QGraph) which facilitates making inference for getting a precise answer in the closed domain. In addition, our approach provides a convenient method to map the formulated comprehensive information into SPARQL query template to crawl in the LOD resources in the open domain. The main contributions of this dissertation are as follows: 1. Developing ScoQAS architecture integrated with common and specific components compatible with closed and open domain ontologies. 2. Analysing user’s question and building a question syntactic-semantic information structure (QSiS), which is constituted by several processes of the methodology: question classification, Expected Answer Type (EAT) determination, and generated constraints. 3. Presenting an empirical semantic-based structure-feature pattern for question classification and generalizing heuristic constraints to formulate the relations between the features in the recognized pattern in terms of syntactical and semantical. 4. Developing a syntactic-semantic QGraph for representing core components of the question. 5. Presenting an empirical graph-based answer inference in the closed domain. In a nutshell, a semantic-based QA system is presented which provides some experimental results over the closed and open domains. The efficiency of the ScoQAS is evaluated using measures such as precision, recall, and F-measure on LOD challenges in the open domain. We focus on quantitative evaluation in the closed domain scenario. Due to the lack of predefined benchmark(s) in the first scenario, we define measures that demonstrate the actual complexity of the problem and the actual efficiency of the solutions. The results of the analysis corroborate the performance and effectiveness of our approach to achieve a reasonable accuracy.Con respecto al crecimiento en la cantidad de información social, ambiental y biomédica disponible digitalmente, existe una creciente necesidad de sistemas de la búsqueda de la respuesta (QA) que puedan ofrecer a los usuarios la gestión de esta nueva cantidad de información. A pesar del progreso reciente en QA, la calidad de interpretación y extracción de la respuesta deseada no es la adecuada. Creemos que trabajar para lograr una mayor precisión en los sistemas de QA es todavía un campo de investigación abierto. Es decir, es mejor no tener respuestas que tener respuestas incorrectas. Sin embargo, existen diversas consultas que los sistemas de QA en el estado del arte no pueden interpretar ni responder adecuadamente. El problema de interpretar una pregunta de una manera que podría preservar su estructura sintáctica-semántica es considerado como uno de los desafíos más importantes en esta área. En este trabajo nos centramos en los problemas de los sistemas de QA basados en semántica y en el análisis de la efectividad de las técnicas de PNL, y la aplicación de consultas e inferencia respuesta tanto en dominios cerrados (primer escenario) como abiertos (segundo escenario). Para este propósito, la arquitectura del sistema de búsqueda de respuestas en dominios cerrados y abiertos basado en semántica (en adelante "ScoQAS") sobre ontologías se presenta con dos prototipos diferentes: en dominio cerrado basado en el uso de ontologías y un dominio abierto dirigido a repositorios de Linked Open Data (LOD). El ScoQAS se basa en técnicas de PNL que combinan patrones de características de estructura semánticas para la clasificación de preguntas y la creación de una estructura de información sintáctico-semántica de preguntas (QSiS). El QSiS proporciona una manera la construcción de restricciones para formular los términos relacionados en aspectos sintáctico-semánticos y generar un grafo de preguntas (QGraph) el cual facilita derivar inferencias para obtener una respuesta precisa en el dominio cerrado. Además, nuestro enfoque proporciona un método adecuado para aplicar la información integral formulada en la plantilla de consulta SPARQL para navegar en los recursos LOD en el dominio abierto. Las principales contribuciones de este trabajo son los siguientes: 1. El desarrollo de la arquitectura ScoQAS integrada con componentes comunes y específicos compatibles con ontologías de dominio cerrado y abierto. 2. El análisis de la pregunta del usuario y la construcción de una estructura de información sintáctico-semántica de las preguntas (QSiS), que está constituida por varios procesos de la metodología: clasificación de preguntas, determinación del Tipo de Respuesta Esperada (EAT) y las restricciones generadas. 3. La presentación de un patrón empírico basado en la estructura semántica para clasificar las preguntas y generalizar las restricciones heurísticas para formular las relaciones entre las características en el patrón reconocido en términos sintácticos y semánticos. 4. El desarrollo de un QGraph sintáctico-semántico para representar los componentes centrales de la pregunta. 5. La presentación de la respuesta inferida a partir de un grafo empírico en el dominio cerrado. En pocas palabras, se presenta un sistema semántico de QA que proporciona algunos resultados experimentales sobre los dominios cerrados y abiertos. La eficiencia del ScoQAS se evalúa utilizando medidas tales como una precisión, cobertura y la medida-F en desafíos LOD para el dominio abierto. Para el dominio cerrado, nos centramos en la evaluación cuantitativa; su precisión se analiza en una ontología empresarial. La falta de un banco la pruebas predefinidas es uno de los principales desafíos de la evaluación en el primer escenario. Por lo tanto, definimos medidas que demuestran la complejidad real del problema y la eficiencia real de las soluciones. Los resultados del análisis corroboran el rendimient

Computational and human-based methods for knowledge discovery over knowledge graphs

The modern world has evolved, accompanied by the huge exploitation of data and information. Daily, increasing volumes of data from various sources and formats are stored, resulting in a challenging strategy to manage and integrate them to discover new knowledge. The appropriate use of data in various sectors of society, such as education, healthcare, e-commerce, and industry, provides advantages for decision support in these areas. However, knowledge discovery becomes challenging since data may come from heterogeneous sources with important information hidden. Thus, new approaches that adapt to the new challenges of knowledge discovery in such heterogeneous data environments are required. The semantic web and knowledge graphs (KGs) are becoming increasingly relevant on the road to knowledge discovery. This thesis tackles the problem of knowledge discovery over KGs built from heterogeneous data sources. We provide a neuro-symbolic artificial intelligence system that integrates symbolic and sub-symbolic frameworks to exploit the semantics encoded in a KG and its structure. The symbolic system relies on existing approaches of deductive databases to make explicit, implicit knowledge encoded in a KG. The proposed deductive database $DS$ can derive new statements to ego networks given an abstract target prediction. Thus, $DS$ minimizes data sparsity in KGs. In addition, a sub-symbolic system relies on knowledge graph embedding (KGE) models. KGE models are commonly applied in the KG completion task to represent entities in a KG in a low-dimensional vector space. However, KGE models are known to suffer from data sparsity, and a symbolic system assists in overcoming this fact. The proposed approach discovers knowledge given a target prediction in a KG and extracts unknown implicit information related to the target prediction. As a proof of concept, we have implemented the neuro-symbolic system on top of a KG for lung cancer to predict polypharmacy treatment effectiveness. The symbolic system implements a deductive system to deduce pharmacokinetic drug-drug interactions encoded in a set of rules through the Datalog program. Additionally, the sub-symbolic system predicts treatment effectiveness using a KGE model, which preserves the KG structure. An ablation study on the components of our approach is conducted, considering state-of-the-art KGE methods. The observed results provide evidence for the benefits of the neuro-symbolic integration of our approach, where the neuro-symbolic system for an abstract target prediction exhibits improved results. The enhancement of the results occurs because the symbolic system increases the prediction capacity of the sub-symbolic system. Moreover, the proposed neuro-symbolic artificial intelligence system in Industry 4.0 (I4.0) is evaluated, demonstrating its effectiveness in determining relatedness among standards and analyzing their properties to detect unknown relations in the I4.0KG. The results achieved allow us to conclude that the proposed neuro-symbolic approach for an abstract target prediction improves the prediction capability of KGE models by minimizing data sparsity in KGs

Knowledge graph exploration for natural language understanding in web information retrieval

In this thesis, we study methods to leverage information from fully-structured knowledge bases (KBs), in particular the encyclopedic knowledge graph (KG) DBpedia, for different text-related tasks from the area of information retrieval (IR) and natural language processing (NLP). The key idea is to apply entity linking (EL) methods that identify mentions of KB entities in text, and then exploit the structured information within KGs. Developing entity-centric methods for text understanding using KG exploration is the focus of this work. We aim to show that structured background knowledge is a means for improving performance in different IR and NLP tasks that traditionally only make use of the unstructured text input itself. Thereby, the KB entities mentioned in text act as connection between the unstructured text and the structured KG. We focus in particular on how to best leverage the knowledge as contained in such fully-structured (RDF) KGs like DBpedia with their labeled edges/predicates – which is in contrast to previous work on Wikipedia-based approaches we build upon, which typically relies on unlabeled graphs only. The contribution of this thesis can be structured along its three parts: In Part I, we apply EL and semantify short text snippets with KB entities. While only retrieving types and categories from DBpedia for each entity, we are able to leverage this information to create semantically coherent clusters of text snippets. This pipeline of connecting text to background knowledge via the mentioned entities will be reused in all following chapters. In Part II, we focus on semantic similarity and extend the idea of semantifying text with entities by proposing in Chapter 5 a model that represents whole documents by their entities. In this model, comparing documents semantically with each other is viewed as the task of comparing the semantic relatedness of the respective entities, which we address in Chapter 4. We propose an unsupervised graph weighting schema and show that weighting the DBpedia KG leads to better results on an existing entity ranking dataset. The exploration of weighted KG paths turns out to be also useful when trying to disambiguate the entities from an open information extraction (OIE) system in Chapter 6. With this weighting schema, the integration of KG information for computing semantic document similarity in Chapter 5 becomes the task of comparing the two KG subgraphs with each other, which we address by an approximate subgraph matching. Based on a well-established evaluation dataset for semantic document similarity, we show that our unsupervised method achieves competitive performance similar to other state-of-the-art methods. Our results from this part indicate that KGs can contain helpful background knowledge, in particular when exploring KG paths, but that selecting the relevant parts of the graph is an important yet difficult challenge. In Part III, we shift to the task of relevance ranking and first study in Chapter 7 how to best retrieve KB entities for a given keyword query. Combining again text with KB information, we extract entities from the top-k retrieved, query-specific documents and then link the documents to two different KBs, namely Wikipedia and DBpedia. In a learning-to-rank setting, we study extensively which features from the text, theWikipedia KB, and the DBpedia KG can be helpful for ranking entities with respect to the query. Experimental results on two datasets, which build upon existing TREC document retrieval collections, indicate that the document-based mention frequency of an entity and the Wikipedia-based query-to-entity similarity are both important features for ranking. The KG paths in contrast play only a minor role in this setting, even when integrated with a semantic kernel extension. In Chapter 8, we further extend the integration of query-specific text documents and KG information, by extracting not only entities, but also relations from text. In this exploratory study based on a self-created relevance dataset, we find that not all extracted relations are relevant with respect to the query, but that they often contain information not contained within the DBpedia KG. The main insight from the research presented in this part is that in a query-specific setting, established IR methods for document retrieval provide an important source of information even for entity-centric tasks, and that a close integration of relevant text document and background knowledge is promising. Finally, in the concluding chapter we argue that future research should further address the integration of KG information with entities and relations extracted from (specific) text documents, as their potential seems to be not fully explored yet. The same holds also true for a better KG exploration, which has gained some scientific interest in recent years. It seems to us that both aspects will remain interesting problems in the next years, also because of the growing importance of KGs for web search and knowledge modeling in industry and academia

Workshop NotesInternational Workshop ``What can FCA do for Artificial Intelligence?'' (FCA4AI 2015)

International audienceThis volume includes the proceedings of the fourth edition of the FCA4AI --What can FCA do for Artificial Intelligence?-- Workshop co-located with the IJCAI 2015 Conference in Buenos Aires (Argentina). Formal Concept Analysis (FCA) is a mathematically well-founded theory aimed at data analysis and classification. FCA allows one to build a concept lattice and a system of dependencies (implications) which can be used for many AI needs, e.g. knowledge discovery, learning, knowledge representation, reasoning, ontology engineering, as well as information retrieval and text processing. There are many ``natural links'' between FCA and AI, and the present workshop is organized for discussing about these links and more generally for improving the links between knowledge discovery based on FCA and knowledge management in artificial intelligence