Supervised Typing of Big Graphs using Semantic Embeddings

We propose a supervised algorithm for generating type embeddings in the same semantic vector space as a given set of entity embeddings. The algorithm is agnostic to the derivation of the underlying entity embeddings. It does not require any manual feature engineering, generalizes well to hundreds of types and achieves near-linear scaling on Big Graphs containing many millions of triples and instances by virtue of an incremental execution. We demonstrate the utility of the embeddings on a type recommendation task, outperforming a non-parametric feature-agnostic baseline while achieving 15x speedup and near-constant memory usage on a full partition of DBpedia. Using state-of-the-art visualization, we illustrate the agreement of our extensionally derived DBpedia type embeddings with the manually curated domain ontology. Finally, we use the embeddings to probabilistically cluster about 4 million DBpedia instances into 415 types in the DBpedia ontology.Comment: 6 pages, to be published in Semantic Big Data Workshop at ACM, SIGMOD 2017; extended version in preparation for Open Journal of Semantic Web (OJSW

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results