MINDWALC : mining interpretable, discriminative walks for classification of nodes in a knowledge graph

Background Leveraging graphs for machine learning tasks can result in more expressive power as extra information is added to the data by explicitly encoding relations between entities. Knowledge graphs are multi-relational, directed graph representations of domain knowledge. Recently, deep learning-based techniques have been gaining a lot of popularity. They can directly process these type of graphs or learn a low-dimensional numerical representation. While it has been shown empirically that these techniques achieve excellent predictive performances, they lack interpretability. This is of vital importance in applications situated in critical domains, such as health care. Methods We present a technique that mines interpretable walks from knowledge graphs that are very informative for a certain classification problem. The walks themselves are of a specific format to allow for the creation of data structures that result in very efficient mining. We combine this mining algorithm with three different approaches in order to classify nodes within a graph. Each of these approaches excels on different dimensions such as explainability, predictive performance and computational runtime. Results We compare our techniques to well-known state-of-the-art black-box alternatives on four benchmark knowledge graph data sets. Results show that our three presented approaches in combination with the proposed mining algorithm are at least competitive to the black-box alternatives, even often outperforming them, while being interpretable. Conclusions The mining of walks is an interesting alternative for node classification in knowledge graphs. Opposed to the current state-of-the-art that uses deep learning techniques, it results in inherently interpretable or transparent models without a sacrifice in terms of predictive performance

Exploiting semantic web knowledge graphs in data mining

Data Mining and Knowledge Discovery in Databases (KDD) is a research field concerned with deriving higher-level insights from data. The tasks performed in that field are knowledge intensive and can often benefit from using additional knowledge from various sources. Therefore, many approaches have been proposed in this area that combine Semantic Web data with the data mining and knowledge discovery process. Semantic Web knowledge graphs are a backbone of many information systems that require access to structured knowledge. Such knowledge graphs contain factual knowledge about real word entities and the relations between them, which can be utilized in various natural language processing, information retrieval, and any data mining applications. Following the principles of the Semantic Web, Semantic Web knowledge graphs are publicly available as Linked Open Data. Linked Open Data is an open, interlinked collection of datasets in machine-interpretable form, covering most of the real world domains. In this thesis, we investigate the hypothesis if Semantic Web knowledge graphs can be exploited as background knowledge in different steps of the knowledge discovery process, and different data mining tasks. More precisely, we aim to show that Semantic Web knowledge graphs can be utilized for generating valuable data mining features that can be used in various data mining tasks. Identifying, collecting and integrating useful background knowledge for a given data mining application can be a tedious and time consuming task. Furthermore, most data mining tools require features in propositional form, i.e., binary, nominal or numerical features associated with an instance, while Linked Open Data sources are usually graphs by nature. Therefore, in Part I, we evaluate unsupervised feature generation strategies from types and relations in knowledge graphs, which are used in different data mining tasks, i.e., classification, regression, and outlier detection. As the number of generated features grows rapidly with the number of instances in the dataset, we provide a strategy for feature selection in hierarchical feature space, in order to select only the most informative and most representative features for a given dataset. Furthermore, we provide an end-to-end tool for mining the Web of Linked Data, which provides functionalities for each step of the knowledge discovery process, i.e., linking local data to a Semantic Web knowledge graph, integrating features from multiple knowledge graphs, feature generation and selection, and building machine learning models. However, we show that such feature generation strategies often lead to high dimensional feature vectors even after dimensionality reduction, and also, the reusability of such feature vectors across different datasets is limited. In Part II, we propose an approach that circumvents the shortcomings introduced with the approaches in Part I. More precisely, we develop an approach that is able to embed complete Semantic Web knowledge graphs in a low dimensional feature space, where each entity and relation in the knowledge graph is represented as a numerical vector. Projecting such latent representations of entities into a lower dimensional feature space shows that semantically similar entities appear closer to each other. We use several Semantic Web knowledge graphs to show that such latent representation of entities have high relevance for different data mining tasks. Furthermore, we show that such features can be easily reused for different datasets and different tasks. In Part III, we describe a list of applications that exploit Semantic Web knowledge graphs, besides the standard data mining tasks, like classification and regression. We show that the approaches developed in Part I and Part II can be used in applications in various domains. More precisely, we show that Semantic Web graphs can be exploited for analyzing statistics, building recommender systems, entity and document modeling, and taxonomy induction. %In Part III, we focus on semantic annotations in HTML pages, which are another realization of the Semantic Web vision. Semantic annotations are integrated into the code of HTML pages using markup languages, like Microformats, RDFa, and Microdata. While such data covers various domains and topics, and can be useful for developing various data mining applications, additional steps of cleaning and integrating the data need to be performed. In this thesis, we describe a set of approaches for processing long literals and images extracted from semantic annotations in HTML pages. We showcase the approaches in the e-commerce domain. Such approaches contribute in building and consuming Semantic Web knowledge graphs

{UNIQORN}: {U}nified Question Answering over {RDF} Knowledge Graphs and Natural Language Text

Question answering over knowledge graphs and other RDF data has been greatly advanced, with a number of good systems providing crisp answers for natural language questions or telegraphic queries. Some of these systems incorporate textual sources as additional evidence for the answering process, but cannot compute answers that are present in text alone. Conversely, systems from the IR and NLP communities have addressed QA over text, but barely utilize semantic data and knowledge. This paper presents the first QA system that can seamlessly operate over RDF datasets and text corpora, or both together, in a unified framework. Our method, called UNIQORN, builds a context graph on the fly, by retrieving question-relevant triples from the RDF data and/or the text corpus, where the latter case is handled by automatic information extraction. The resulting graph is typically rich but highly noisy. UNIQORN copes with this input by advanced graph algorithms for Group Steiner Trees, that identify the best answer candidates in the context graph. Experimental results on several benchmarks of complex questions with multiple entities and relations, show that UNIQORN, an unsupervised method with only five parameters, produces results comparable to the state-of-the-art on KGs, text corpora, and heterogeneous sources. The graph-based methodology provides user-interpretable evidence for the complete answering process

Matching Biomedical Knowledge Graphs with Neural Embeddings

Tese de mestrado, Ciência de Dados, Universidade de Lisboa, Faculdade de Ciências, 2020Os grafos de conhecimento são estruturas que se tornaram fundamentais para a organização dos dados biomédicos que têm sido produzidos a um ritmo exponencial nos últimos anos. A abrangente adoção desta forma de estruturar e descrever dados levou ao desenvolvimento de abordagens de prospeção de dados que tirassem partido desta informação com o intuito de auxiliar o progresso do conhecimento científico. Porém, devido à impossibilidade de isolamento de domínios de conhecimento e à idiossincrasia humana, grafos de conhecimento construídos por diferentes indivíduos contêm muitas vezes conceitos equivalentes descritos de forma diferente, dificultando uma análise integrada de dados de diferentes grafos de conhecimento. Vários sistemas de alinhamento de grafos de conhecimento têm focado a resolução deste desafio. Contudo, o desempenho destes sistemas no alinhamento de grafos de conhecimento biomédicos estagnou nos últimos quatro anos com algoritmos e recursos externos bastante trabalhados para aprimorar os resultados. Nesta dissertação, apresentamos duas novas abordagens de alinhamento de grafos de conhecimento empregando Neural Embeddings: uma utilizando semelhança simples entre embeddings à base de palavras e de entidades de grafos; outra treinando um modelo mais complexo que refinasse a informação proveniente de embeddings baseados em palavras. A metodologia proposta visa integrar estas abordagens no processo regular de alinhamento, utilizando como infraestrutura o sistema AgreementMakerLight. Estas novas componentes permitem extender os algoritmos de alinhamento do sistema, descobrindo novos mapeamentos, e criar uma abordagem de alinhamento mais generalizável e menos dependente de ontologias biomédicas externas. Esta nova metodologia foi avaliada em três casos de teste de alinhamento de ontologias biomédicas, provenientes da Ontology Alignment Evaluation Initiative. Os resultados demonstraram que apesar de ambas as abordagens não excederem o estado da arte, estas obtiveram um desempenho benéfico nas tarefas de alinhamento, superando a performance de todos os sistemas que não usam ontologias externas e inclusive alguns que tiram proveito das mesmas, o que demonstra o valor das técnicas de Neural Embeddings na tarefa de alinhamento de grafos do conhecimento biomédicos.Knowledge graphs are data structures which became essential to organize biomedical data produced at an exponential rate in the last few years. The broad adoption of this method of structuring and describing data resulted in the increased interest to develop data mining approaches which took advantage of these information structures in order to improve scientific knowledge. However, due to human idiosyncrasy and also the impossibility to isolate knowledge domains in separate pieces, knowledge graphs constructed by different individuals often contain equivalent concepts described differently. This obstructs the path to an integrated analysis of data described by multiple knowledge graphs. Multiple knowledge graph matching systems have been developed to address this challenge. Nevertheless, the performance of these systems has stagnated in the last four years, despite the fact that they were provided with highly tailored algorithms and external resources to tackle this task. In this dissertation, we present two novel knowledge graph matching approaches employing neural embeddings: one using plain embedding similarity based on word and graph models; the other one using a more complex word-based model which requires training data to refine embeddings. The proposed methodology aims to integrate these approaches in the regular matching process, using the AgreementMakerLight system as a foundation. These new components enable the extension of the system’s current matching algorithms, discovering new mappings, and developing a more generalizable and less dependent on external biomedical ontologies matching procedure. This new methodology was evaluated on three biomedical ontology matching test cases provided by the Ontology Alignment Evaluation Initiative. The results showed that despite both embedding approaches don’t exceed state of the art results, they still produce better results than any other matching systems which do not make use of external ontologies and also surpass some that do benefit from them. This shows that Neural Embeddings are a valuable technique to tackle the challenge of biomedical knowledge graph matching