A System for Aligning Geographical Entities from Large Heterogeneous Sources

Aligning points of interest (POIs) from heterogeneous geographical data sources is an important task that helps extend map data with information from different datasets. This task poses several challenges, including differences in type hierarchies, labels (different formats, languages, and levels of detail), and deviations in the coordinates. Scalability is another major issue, as global-scale datasets may have tens or hundreds of millions of entities. In this paper, we propose the GeographicaL Entities AligNment (GLEAN) system for efficiently matching large geographical datasets based on spatial partitioning with an adaptable margin. In particular, we introduce a text similarity measure based on the local-context relevance of tokens used in combination with sentence embeddings. We then come up with a scalable type embedding model. Finally, we demonstrate that our proposed system can efficiently handle the alignment of large datasets while improving the quality of alignments using the proposed entity similarity measure

Wikimatcher: Leveraging Wikipedia for Ontology Alignment

As the Semantic Web grows, so does the number of ontologies used to structure the data within it. Aligning these ontologies is critical to fully realizing the potential of the web. Previous work in ontology alignment has shown that even alignment systems utilizing basic string similarity metrics can produce useful matches. Researchers speculate that including semantic as well as syntactic information inherent in entity labels can further improve alignment results. This paper examines that hypothesis by exploring the utility of using Wikipedia as a source of semantic information. Various elements of Wikipedia are considered, including article content, page terms, and search snippets. The utility of each information source is analyzed and a composite system, WikiMatcher, is created based on this analysis. The performance of WikiMatcher is compared to that of a basic string-based alignment system on two established alignment benchmarks and two other real-world datasets. The extensive evaluation shows that although WikiMatcher performs similarly to that of the string metric overall, it is able to find many matches with no syntactic similarity between labels. This performance seems to be driven by Wikipedia\u27s query resolution and page redirection system, rather than by the particular information from Wikipedia that is used to compare entities

VeeAlign: Multifaceted Context Representation Using Dual Attention for Ontology Alignment

Ontology Alignment is an important research problem applied to various fields such as data integration, data transfer, data preparation, etc. State-of-the-art (SOTA) Ontology Alignment systems typically use naive domain-dependent approaches with handcrafted rules or domain-specific architectures, making them unscalable and inefficient. In this work, we propose VeeAlign, a Deep Learning based model that uses a novel dual-attention mechanism to compute the contextualized representation of a concept which, in turn, is used to discover alignments. By doing this, not only is our approach able to exploit both syntactic and semantic information encoded in ontologies, it is also, by design, flexible and scalable to different domains with minimal effort. We evaluate our model on four different datasets from different domains and languages, and establish its superiority through these results as well as detailed ablation studies. The code and datasets used are available at https://github.com/Remorax/VeeAlign.Comment: Duplicate of arXiv:2010.1172

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

Deep learning methods for knowledge base population

Knowledge bases store structured information about entities or concepts of the world and can be used in various applications, such as information retrieval or question answering. A major drawback of existing knowledge bases is their incompleteness. In this thesis, we explore deep learning methods for automatically populating them from text, addressing the following tasks: slot filling, uncertainty detection and type-aware relation extraction. Slot filling aims at extracting information about entities from a large text corpus. The Text Analysis Conference yearly provides new evaluation data in the context of an international shared task. We develop a modular system to address this challenge. It was one of the top-ranked systems in the shared task evaluations in 2015. For its slot filler classification module, we propose contextCNN, a convolutional neural network based on context splitting. It improves the performance of the slot filling system by 5.0% micro and 2.9% macro F1. To train our binary and multiclass classification models, we create a dataset using distant supervision and reduce the number of noisy labels with a self-training strategy. For model optimization and evaluation, we automatically extract a labeled benchmark for slot filler classification from the manual shared task assessments from 2012-2014. We show that results on this benchmark are correlated with slot filling pipeline results with a Pearson's correlation coefficient of 0.89 (0.82) on data from 2013 (2014). The combination of patterns, support vector machines and contextCNN achieves the best results on the benchmark with a micro (macro) F1 of 51% (53%) on test. Finally, we analyze the results of the slot filling pipeline and the impact of its components. For knowledge base population, it is essential to assess the factuality of the statements extracted from text. From the sentence "Obama was rumored to be born in Kenya", a system should not conclude that Kenya is the place of birth of Obama. Therefore, we address uncertainty detection in the second part of this thesis. We investigate attention-based models and make a first attempt to systematize the attention design space. Moreover, we propose novel attention variants: External attention, which incorporates an external knowledge source, k-max average attention, which only considers the vectors with the k maximum attention weights, and sequence-preserving attention, which allows to maintain order information. Our convolutional neural network with external k-max average attention sets the new state of the art on a Wikipedia benchmark dataset with an F1 score of 68%. To the best of our knowledge, we are the first to integrate an uncertainty detection component into a slot filling pipeline. It improves precision by 1.4% and micro F1 by 0.4%. In the last part of the thesis, we investigate type-aware relation extraction with neural networks. We compare different models for joint entity and relation classification: pipeline models, jointly trained models and globally normalized models based on structured prediction. First, we show that using entity class prediction scores instead of binary decisions helps relation classification. Second, joint training clearly outperforms pipeline models on a large-scale distantly supervised dataset with fine-grained entity classes. It improves the area under the precision-recall curve from 0.53 to 0.66. Third, we propose a model with a structured prediction output layer, which globally normalizes the score of a triple consisting of the classes of two entities and the relation between them. It improves relation extraction results by 4.4% F1 on a manually labeled benchmark dataset. Our analysis shows that the model learns correct correlations between entity and relation classes. Finally, we are the first to use neural networks for joint entity and relation classification in a slot filling pipeline. The jointly trained model achieves the best micro F1 score with a score of 22% while the neural structured prediction model performs best in terms of macro F1 with a score of 25%

{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

Multidimensional integration of RDF datasets

Data providers have been uploading RDF datasets on the web to aid researchers and analysts in finding insights. These datasets, made available by different data providers, contain common characteristics that enable their integration. However, since each provider has their own data dictionary, identifying common concepts is not trivial and we require costly and complex entity resolution and transformation rules to perform such integration. In this paper, we propose a novel method, that given a set of independent RDF datasets, provides a multidimensional interpretation of these datasets and integrates them based on a common multidimensional space (if any) identified. To do so, our method first identifies potential dimensional and factual data on the input datasets and performs entity resolution to merge common dimensional and factual concepts. As a result, we generate a common multidimensional space and identify each input dataset as a cuboid of the resulting lattice. With such output, we are able to exploit open data with OLAP operators in a richer fashion than dealing with them separately.This research has been funded by the European Commission through the Erasmus Mundus Joint Doctorate Information Technologies for Business Intelligence-Doctoral College (IT4BI-DC) program.Peer ReviewedPostprint (author's final draft