Knowledge extraction from unstructured data

Data availability is becoming more essential, considering the current growth of web-based data. The data available on the web are represented as unstructured, semi-structured, or structured data. In order to make the web-based data available for several Natural Language Processing or Data Mining tasks, the data needs to be presented as machine-readable data in a structured format. Thus, techniques for addressing the problem of capturing knowledge from unstructured data sources are needed. Knowledge extraction methods are used by the research communities to address this problem; methods that are able to capture knowledge in a natural language text and map the extracted knowledge to existing knowledge presented in knowledge graphs (KGs). These knowledge extraction methods include Named-entity recognition, Named-entity Disambiguation, Relation Recognition, and Relation Linking. This thesis addresses the problem of extracting knowledge over unstructured data and discovering patterns in the extracted knowledge. We devise a rule-based approach for entity and relation recognition and linking. The defined approach effectively maps entities and relations within a text to their resources in a target KG. Additionally, it overcomes the challenges of recognizing and linking entities and relations to a specific KG by employing devised catalogs of linguistic and domain-specific rules that state the criteria to recognize entities in a sentence of a particular language, and a deductive database that encodes knowledge in community-maintained KGs. Moreover, we define a Neuro-symbolic approach for the tasks of knowledge extraction in encyclopedic and domain-specific domains; it combines symbolic and sub-symbolic components to overcome the challenges of entity recognition and linking and the limitation of the availability of training data while maintaining the accuracy of recognizing and linking entities. Additionally, we present a context-aware framework for unveiling semantically related posts in a corpus; it is a knowledge-driven framework that retrieves associated posts effectively. We cast the problem of unveiling semantically related posts in a corpus into the Vertex Coloring Problem. We evaluate the performance of our techniques on several benchmarks related to various domains for knowledge extraction tasks. Furthermore, we apply these methods in real-world scenarios from national and international projects. The outcomes show that our techniques are able to effectively extract knowledge encoded in unstructured data and discover patterns over the extracted knowledge presented as machine-readable data. More importantly, the evaluation results provide evidence to the effectiveness of combining the reasoning capacity of the symbolic frameworks with the power of pattern recognition and classification of sub-symbolic models

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

Towards a Personal Health Knowledge Graph Framework for Patient Monitoring

Healthcare providers face significant challenges with monitoring and managing patient data outside of clinics, particularly with insufficient resources and limited feedback on their patients' conditions. Effective management of these symptoms and exploration of larger bodies of data are vital for maintaining long-term quality of life and preventing late interventions. In this paper, we propose a framework for constructing personal health knowledge graphs from heterogeneous data sources. Our approach integrates clinical databases, relevant ontologies and standard healthcare guidelines to support alert generation, clinician interpretation and querying of patient data. Through a use case of monitoring Chronic Obstructive Pulmonary Disease (COPD) patients, we demonstrate that inference and reasoning on personal health knowledge graphs built with our framework can aid in patient monitoring and enhance the efficacy and accuracy of patient data queries.Comment: 6 pages, 3 figures, conference proceeding

Towards a Personal Health Knowledge Graph Framework for Patient Monitoring

Healthcare providers face significant challenges with managing and monitoring patient data outside of clinics, particularly with limited resources and insufficient feedback on their patients' conditions. Effective management of these symptoms and exploration of larger bodies of data are vital for maintaining long-term quality of life and preventing late interventions. In this paper, we propose a framework for constructing personal health knowledge graphs from heterogeneous data sources. Our approach integrates clinical databases, relevant ontologies, and standard healthcare guidelines to support alert generation, clinicians' interpretation and querying of patient data. Through a use case focusing on monitoring Chronic Obstructive Lung Disease (COPD) patients, we demonstrate that inference and reasoning on personal health knowledge graphs built with our framework can aid in patient monitoring and enhance the efficacy and accuracy of patient data queries

Análise colaborativa de grandes conjuntos de séries temporais

The recent expansion of metrification on a daily basis has led to the production of massive quantities of data, and in many cases, these collected metrics are only useful for knowledge building when seen as a full sequence of data ordered by time, which constitutes a time series. To find and interpret meaningful behavioral patterns in time series, a multitude of analysis software tools have been developed. Many of the existing solutions use annotations to enable the curation of a knowledge base that is shared between a group of researchers over a network. However, these tools also lack appropriate mechanisms to handle a high number of concurrent requests and to properly store massive data sets and ontologies, as well as suitable representations for annotated data that are visually interpretable by humans and explorable by automated systems. The goal of the work presented in this dissertation is to iterate on existing time series analysis software and build a platform for the collaborative analysis of massive time series data sets, leveraging state-of-the-art technologies for querying, storing and displaying time series and annotations. A theoretical and domain-agnostic model was proposed to enable the implementation of a distributed, extensible, secure and high-performant architecture that handles various annotation proposals in simultaneous and avoids any data loss from overlapping contributions or unsanctioned changes. Analysts can share annotation projects with peers, restricting a set of collaborators to a smaller scope of analysis and to a limited catalog of annotation semantics. Annotations can express meaning not only over a segment of time, but also over a subset of the series that coexist in the same segment. A novel visual encoding for annotations is proposed, where annotations are rendered as arcs traced only over the affected series’ curves in order to reduce visual clutter. Moreover, the implementation of a full-stack prototype with a reactive web interface was described, directly following the proposed architectural and visualization model while applied to the HVAC domain. The performance of the prototype under different architectural approaches was benchmarked, and the interface was tested in its usability. Overall, the work described in this dissertation contributes with a more versatile, intuitive and scalable time series annotation platform that streamlines the knowledge-discovery workflow.A recente expansão de metrificação diária levou à produção de quantidades massivas de dados, e em muitos casos, estas métricas são úteis para a construção de conhecimento apenas quando vistas como uma sequência de dados ordenada por tempo, o que constitui uma série temporal. Para se encontrar padrões comportamentais significativos em séries temporais, uma grande variedade de software de análise foi desenvolvida. Muitas das soluções existentes utilizam anotações para permitir a curadoria de uma base de conhecimento que é compartilhada entre investigadores em rede. No entanto, estas ferramentas carecem de mecanismos apropriados para lidar com um elevado número de pedidos concorrentes e para armazenar conjuntos massivos de dados e ontologias, assim como também representações apropriadas para dados anotados que são visualmente interpretáveis por seres humanos e exploráveis por sistemas automatizados. O objetivo do trabalho apresentado nesta dissertação é iterar sobre o software de análise de séries temporais existente e construir uma plataforma para a análise colaborativa de grandes conjuntos de séries temporais, utilizando tecnologias estado-de-arte para pesquisar, armazenar e exibir séries temporais e anotações. Um modelo teórico e agnóstico quanto ao domínio foi proposto para permitir a implementação de uma arquitetura distribuída, extensível, segura e de alto desempenho que lida com várias propostas de anotação em simultâneo e evita quaisquer perdas de dados provenientes de contribuições sobrepostas ou alterações não-sancionadas. Os analistas podem compartilhar projetos de anotação com colegas, restringindo um conjunto de colaboradores a uma janela de análise mais pequena e a um catálogo limitado de semântica de anotação. As anotações podem exprimir significado não apenas sobre um intervalo de tempo, mas também sobre um subconjunto das séries que coexistem no mesmo intervalo. Uma nova codificação visual para anotações é proposta, onde as anotações são desenhadas como arcos traçados apenas sobre as curvas de séries afetadas de modo a reduzir o ruído visual. Para além disso, a implementação de um protótipo full-stack com uma interface reativa web foi descrita, seguindo diretamente o modelo de arquitetura e visualização proposto enquanto aplicado ao domínio AVAC. O desempenho do protótipo com diferentes decisões arquiteturais foi avaliado, e a interface foi testada quanto à sua usabilidade. Em geral, o trabalho descrito nesta dissertação contribui com uma abordagem mais versátil, intuitiva e escalável para uma plataforma de anotação sobre séries temporais que simplifica o fluxo de trabalho para a descoberta de conhecimento.Mestrado em Engenharia Informátic

Extraction of clinical phenotypes for Alzheimer\u27s disease dementia from clinical notes using natural language processing

OBJECTIVES: There is much interest in utilizing clinical data for developing prediction models for Alzheimer\u27s disease (AD) risk, progression, and outcomes. Existing studies have mostly utilized curated research registries, image analysis, and structured electronic health record (EHR) data. However, much critical information resides in relatively inaccessible unstructured clinical notes within the EHR. MATERIALS AND METHODS: We developed a natural language processing (NLP)-based pipeline to extract AD-related clinical phenotypes, documenting strategies for success and assessing the utility of mining unstructured clinical notes. We evaluated the pipeline against gold-standard manual annotations performed by 2 clinical dementia experts for AD-related clinical phenotypes including medical comorbidities, biomarkers, neurobehavioral test scores, behavioral indicators of cognitive decline, family history, and neuroimaging findings. RESULTS: Documentation rates for each phenotype varied in the structured versus unstructured EHR. Interannotator agreement was high (Cohen\u27s kappa = 0.72-1) and positively correlated with the NLP-based phenotype extraction pipeline\u27s performance (average F1-score = 0.65-0.99) for each phenotype. DISCUSSION: We developed an automated NLP-based pipeline to extract informative phenotypes that may improve the performance of eventual machine learning predictive models for AD. In the process, we examined documentation practices for each phenotype relevant to the care of AD patients and identified factors for success. CONCLUSION: Success of our NLP-based phenotype extraction pipeline depended on domain-specific knowledge and focus on a specific clinical domain instead of maximizing generalizability

Towards Dynamic Composition of Question Answering Pipelines

Question answering (QA) over knowledge graphs has gained significant momentum over the past five years due to the increasing availability of large knowledge graphs and the rising importance of question answering for user interaction. DBpedia has been the most prominently used knowledge graph in this setting. QA systems implement a pipeline connecting a sequence of QA components for translating an input question into its corresponding formal query (e.g. SPARQL); this query will be executed over a knowledge graph in order to produce the answer of the question. Recent empirical studies have revealed that albeit overall effective, the performance of QA systems and QA components depends heavily on the features of input questions, and not even the combination of the best performing QA systems or individual QA components retrieves complete and correct answers. Furthermore, these QA systems cannot be easily reused, extended, and results cannot be easily reproduced since the systems are mostly implemented in a monolithic fashion, lack standardised interfaces and are often not open source or available as Web services. All these drawbacks of the state of the art that prevents many of these approaches to be employed in real-world applications. In this thesis, we tackle the problem of QA over knowledge graph and propose a generic approach to promote reusability and build question answering systems in a collaborative effort. Firstly, we define qa vocabulary and Qanary methodology to develop an abstraction level on existing QA systems and components. Qanary relies on qa vocabulary to establish guidelines for semantically describing the knowledge exchange between the components of a QA system. We implement a component-based modular framework called "Qanary Ecosystem" utilising the Qanary methodology to integrate several heterogeneous QA components in a single platform. We further present Qaestro framework that provides an approach to semantically describing question answering components and effectively enumerates QA pipelines based on a QA developer requirements. Qaestro provides all valid combinations of available QA components respecting the input-output requirement of each component to build QA pipelines. Finally, we address the scalability of QA components within a framework and propose a novel approach that chooses the best component per task to automatically build QA pipeline for each input question. We implement this model within FRANKENSTEIN, a framework able to select QA components and compose pipelines. FRANKENSTEIN extends Qanary ecosystem and utilises qa vocabulary for data exchange. It has 29 independent QA components implementing five QA tasks resulting 360 unique QA pipelines. Each approach proposed in this thesis (Qanary methodology, Qaestro, and FRANKENSTEIN) is supported by extensive evaluation to demonstrate their effectiveness. Our contributions target a broader research agenda of offering the QA community an efficient way of applying their research to a research field which is driven by many different fields, consequently requiring a collaborative approach to achieve significant progress in the domain of question answering

Time for aCTIon: Automated Analysis of Cyber Threat Intelligence in the Wild

Cyber Threat Intelligence (CTI) plays a crucial role in assessing risks and enhancing security for organizations. However, the process of extracting relevant information from unstructured text sources can be expensive and time-consuming. Our empirical experience shows that existing tools for automated structured CTI extraction have performance limitations. Furthermore, the community lacks a common benchmark to quantitatively assess their performance. We fill these gaps providing a new large open benchmark dataset and aCTIon, a structured CTI information extraction tool. The dataset includes 204 real-world publicly available reports and their corresponding structured CTI information in STIX format. Our team curated the dataset involving three independent groups of CTI analysts working over the course of several months. To the best of our knowledge, this dataset is two orders of magnitude larger than previously released open source datasets. We then design aCTIon, leveraging recently introduced large language models (GPT3.5) in the context of two custom information extraction pipelines. We compare our method with 10 solutions presented in previous work, for which we develop our own implementations when open-source implementations were lacking. Our results show that aCTIon outperforms previous work for structured CTI extraction with an improvement of the F1-score from 10%points to 50%points across all tasks

Entity-centric knowledge discovery for idiosyncratic domains

Technical and scientific knowledge is produced at an ever-accelerating pace, leading to increasing issues when trying to automatically organize or process it, e.g., when searching for relevant prior work. Knowledge can today be produced both in unstructured (plain text) and structured (metadata or linked data) forms. However, unstructured content is still themost dominant formused to represent scientific knowledge. In order to facilitate the extraction and discovery of relevant content, new automated and scalable methods for processing, structuring and organizing scientific knowledge are called for. In this context, a number of applications are emerging, ranging fromNamed Entity Recognition (NER) and Entity Linking tools for scientific papers to specific platforms leveraging information extraction techniques to organize scientific knowledge. In this thesis, we tackle the tasks of Entity Recognition, Disambiguation and Linking in idiosyncratic domains with an emphasis on scientific literature. Furthermore, we study the related task of co-reference resolution with a specific focus on named entities. We start by exploring Named Entity Recognition, a task that aims to identify the boundaries of named entities in textual contents. We propose a newmethod to generate candidate named entities based on n-gram collocation statistics and design several entity recognition features to further classify them. In addition, we show how the use of external knowledge bases (either domain-specific like DBLP or generic like DBPedia) can be leveraged to improve the effectiveness of NER for idiosyncratic domains. Subsequently, we move to Entity Disambiguation, which is typically performed after entity recognition in order to link an entity to a knowledge base. We propose novel semi-supervised methods for word disambiguation leveraging the structure of a community-based ontology of scientific concepts. Our approach exploits the graph structure that connects different terms and their definitions to automatically identify the correct sense that was originally picked by the authors of a scientific publication. We then turn to co-reference resolution, a task aiming at identifying entities that appear using various forms throughout the text. We propose an approach to type entities leveraging an inverted index built on top of a knowledge base, and to subsequently re-assign entities based on the semantic relatedness of the introduced types. Finally, we describe an application which goal is to help researchers discover and manage scientific publications. We focus on the problem of selecting relevant tags to organize collections of research papers in that context. We experimentally demonstrate that the use of a community-authored ontology together with information about the position of the concepts in the documents allows to significantly increase the precision of tag selection over standard methods

Semantic Interpretation of User Queries for Question Answering on Interlinked Data

The Web of Data contains a wealth of knowledge belonging to a large number of domains. Retrieving data from such precious interlinked knowledge bases is an issue. By taking the structure of data into account, it is expected that upcoming generation of search engines is approaching to question answering systems, which directly answer user questions. But developing a question answering over these interlinked data sources is still challenging because of two inherent characteristics: First, different datasets employ heterogeneous schemas and each one may only contain a part of the answer for a certain question. Second, constructing a federated formal query across different datasets requires exploiting links between these datasets on both the schema and instance levels. In this respect, several challenges such as resource disambiguation, vocabulary mismatch, inference, link traversal are raised. In this dissertation, we address these challenges in order to build a question answering system for Linked Data. We present our question answering system Sina, which transforms user-supplied queries (i.e. either natural language queries or keyword queries) into conjunctive SPARQL queries over a set of interlinked data sources. The contributions of this work are as follows: 1. A novel approach for determining the most suitable resources for a user-supplied query from different datasets (disambiguation approach). We employed a Hidden Markov Model, whose parameters were bootstrapped with different distribution functions. 2. A novel method for constructing federated formal queries using the disambiguated resources and leveraging the linking structure of the underlying datasets. This approach essentially relies on a combination of domain and range inference as well as a link traversal method for constructing a connected graph, which ultimately renders a corresponding SPARQL query. 3. Regarding the problem of vocabulary mismatch, our contribution is divided into two parts, First, we introduce a number of new query expansion features based on semantic and linguistic inferencing over Linked Data. We evaluate the effectiveness of each feature individually as well as their combinations, employing Support Vector Machines and Decision Trees. Second, we propose a novel method for automatic query expansion, which employs a Hidden Markov Model to obtain the optimal tuples of derived words. 4. We provide two benchmarks for two different tasks to the community of question answering systems. The first one is used for the task of question answering on interlinked datasets (i.e. federated queries over Linked Data). The second one is used for the vocabulary mismatch task. We evaluate the accuracy of our approach using measures like mean reciprocal rank, precision, recall, and F-measure on three interlinked life-science datasets as well as DBpedia. The results of our accuracy evaluation demonstrate the effectiveness of our approach. Moreover, we study the runtime of our approach in its sequential as well as parallel implementations and draw conclusions on the scalability of our approach on Linked Data