Development of a Knowledge Graph Embeddings Model for Pain

Pain is a complex concept that can interconnect with other concepts such as a disorder that might cause pain, a medication that might relieve pain, and so on. To fully understand the context of pain experienced by either an individual or across a population, we may need to examine all concepts related to pain and the relationships between them. This is especially useful when modeling pain that has been recorded in electronic health records. Knowledge graphs represent concepts and their relations by an interlinked network, enabling semantic and context-based reasoning in a computationally tractable form. These graphs can, however, be too large for efficient computation. Knowledge graph embeddings help to resolve this by representing the graphs in a low-dimensional vector space. These embeddings can then be used in various downstream tasks such as classification and link prediction. The various relations associated with pain which are required to construct such a knowledge graph can be obtained from external medical knowledge bases such as SNOMED CT, a hierarchical systematic nomenclature of medical terms. A knowledge graph built in this way could be further enriched with real-world examples of pain and its relations extracted from electronic health records. This paper describes the construction of such knowledge graph embedding models of pain concepts, extracted from the unstructured text of mental health electronic health records, combined with external knowledge created from relations described in SNOMED CT, and their evaluation on a subject-object link prediction task. The performance of the models was compared with other baseline models.Comment: Accepted at AMIA 2023, New Orlean

Triplétoile: Extraction of knowledge from microblogging text

Numerous methods and pipelines have recently emerged for the automatic extraction of knowledge graphs from documents such as scientific publications and patents. However, adapting these methods to incorporate alternative text sources like micro-blogging posts and news has proven challenging as they struggle to model open-domain entities and relations, typically found in these sources. In this paper, we propose an enhanced information extraction pipeline tailored to the extraction of a knowledge graph comprising open-domain entities from micro-blogging posts on social media platforms. Our pipeline leverages dependency parsing and classifies entity relations in an unsupervised manner through hierarchical clustering over word embeddings. We provide a use case on extracting semantic triples from a corpus of 100 thousand tweets about digital transformation and publicly release the generated knowledge graph. On the same dataset, we conduct two experimental evaluations, showing that the system produces triples with precision over 95% and outperforms similar pipelines of around 5% in terms of precision, while generating a comparatively higher number of triples

Short Text Categorization using World Knowledge

The content of the World Wide Web is drastically multiplying, and thus the amount of available online text data is increasing every day. Today, many users contribute to this massive global network via online platforms by sharing information in the form of a short text. Such an immense amount of data covers subjects from all the existing domains (e.g., Sports, Economy, Biology, etc.). Further, manually processing such data is beyond human capabilities. As a result, Natural Language Processing (NLP) tasks, which aim to automatically analyze and process natural language documents have gained significant attention. Among these tasks, due to its application in various domains, text categorization has become one of the most fundamental and crucial tasks. However, the standard text categorization models face major challenges while performing short text categorization, due to the unique characteristics of short texts, i.e., insufficient text length, sparsity, ambiguity, etc. In other words, the conventional approaches provide substandard performance, when they are directly applied to the short text categorization task. Furthermore, in the case of short text, the standard feature extraction techniques such as bag-of-words suffer from limited contextual information. Hence, it is essential to enhance the text representations with an external knowledge source. Moreover, the traditional models require a significant amount of manually labeled data and obtaining labeled data is a costly and time-consuming task. Therefore, although recently proposed supervised methods, especially, deep neural network approaches have demonstrated notable performance, the requirement of the labeled data remains the main bottleneck of these approaches. In this thesis, we investigate the main research question of how to perform \textit{short text categorization} effectively \textit{without requiring any labeled data} using knowledge bases as an external source. In this regard, novel short text categorization models, namely, Knowledge-Based Short Text Categorization (KBSTC) and Weakly Supervised Short Text Categorization using World Knowledge (WESSTEC) have been introduced and evaluated in this thesis. The models do not require any hand-labeled data to perform short text categorization, instead, they leverage the semantic similarity between the short texts and the predefined categories. To quantify such semantic similarity, the low dimensional representation of entities and categories have been learned by exploiting a large knowledge base. To achieve that a novel entity and category embedding model has also been proposed in this thesis. The extensive experiments have been conducted to assess the performance of the proposed short text categorization models and the embedding model on several standard benchmark datasets

Federated Query Processing over Heterogeneous Data Sources in a Semantic Data Lake

Data provides the basis for emerging scientific and interdisciplinary data-centric applications with the potential of improving the quality of life for citizens. Big Data plays an important role in promoting both manufacturing and scientific development through industrial digitization and emerging interdisciplinary research. Open data initiatives have encouraged the publication of Big Data by exploiting the decentralized nature of the Web, allowing for the availability of heterogeneous data generated and maintained by autonomous data providers. Consequently, the growing volume of data consumed by different applications raise the need for effective data integration approaches able to process a large volume of data that is represented in different format, schema and model, which may also include sensitive data, e.g., financial transactions, medical procedures, or personal data. Data Lakes are composed of heterogeneous data sources in their original format, that reduce the overhead of materialized data integration. Query processing over Data Lakes require the semantic description of data collected from heterogeneous data sources. A Data Lake with such semantic annotations is referred to as a Semantic Data Lake. Transforming Big Data into actionable knowledge demands novel and scalable techniques for enabling not only Big Data ingestion and curation to the Semantic Data Lake, but also for efficient large-scale semantic data integration, exploration, and discovery. Federated query processing techniques utilize source descriptions to find relevant data sources and find efficient execution plan that minimize the total execution time and maximize the completeness of answers. Existing federated query processing engines employ a coarse-grained description model where the semantics encoded in data sources are ignored. Such descriptions may lead to the erroneous selection of data sources for a query and unnecessary retrieval of data, affecting thus the performance of query processing engine. In this thesis, we address the problem of federated query processing against heterogeneous data sources in a Semantic Data Lake. First, we tackle the challenge of knowledge representation and propose a novel source description model, RDF Molecule Templates, that describe knowledge available in a Semantic Data Lake. RDF Molecule Templates (RDF-MTs) describes data sources in terms of an abstract description of entities belonging to the same semantic concept. Then, we propose a technique for data source selection and query decomposition, the MULDER approach, and query planning and optimization techniques, Ontario, that exploit the characteristics of heterogeneous data sources described using RDF-MTs and provide a uniform access to heterogeneous data sources. We then address the challenge of enforcing privacy and access control requirements imposed by data providers. We introduce a privacy-aware federated query technique, BOUNCER, able to enforce privacy and access control regulations during query processing over data sources in a Semantic Data Lake. In particular, BOUNCER exploits RDF-MTs based source descriptions in order to express privacy and access control policies as well as their automatic enforcement during source selection, query decomposition, and planning. Furthermore, BOUNCER implements query decomposition and optimization techniques able to identify query plans over data sources that not only contain the relevant entities to answer a query, but also are regulated by policies that allow for accessing these relevant entities. Finally, we tackle the problem of interest based update propagation and co-evolution of data sources. We present a novel approach for interest-based RDF update propagation that consistently maintains a full or partial replication of large datasets and deal with co-evolution