Semantic similarity estimation from multiple ontologies

The version of record is available online at: http://dx.doi.org/10.1007/s10489-012-0355-yPeer ReviewedPostprint (author's final draft

How do Ontology Mappings Change in the Life Sciences?

Mappings between related ontologies are increasingly used to support data integration and analysis tasks. Changes in the ontologies also require the adaptation of ontology mappings. So far the evolution of ontology mappings has received little attention albeit ontologies change continuously especially in the life sciences. We therefore analyze how mappings between popular life science ontologies evolve for different match algorithms. We also evaluate which semantic ontology changes primarily affect the mappings. We further investigate alternatives to predict or estimate the degree of future mapping changes based on previous ontology and mapping transitions.Comment: Keywords: mapping evolution, ontology matching, ontology evolutio

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

Dealing with uncertain entities in ontology alignment using rough sets

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.Ontology alignment facilitates exchange of knowledge among heterogeneous data sources. Many approaches to ontology alignment use multiple similarity measures to map entities between ontologies. However, it remains a key challenge in dealing with uncertain entities for which the employed ontology alignment measures produce conflicting results on similarity of the mapped entities. This paper presents OARS, a rough-set based approach to ontology alignment which achieves a high degree of accuracy in situations where uncertainty arises because of the conflicting results generated by different similarity measures. OARS employs a combinational approach and considers both lexical and structural similarity measures. OARS is extensively evaluated with the benchmark ontologies of the ontology alignment evaluation initiative (OAEI) 2010, and performs best in the aspect of recall in comparison with a number of alignment systems while generating a comparable performance in precision

NLSC: Unrestricted Natural Language-based Service Composition through Sentence Embeddings

Current approaches for service composition (assemblies of atomic services) require developers to use: (a) domain-specific semantics to formalize services that restrict the vocabulary for their descriptions, and (b) translation mechanisms for service retrieval to convert unstructured user requests to strongly-typed semantic representations. In our work, we argue that effort to developing service descriptions, request translations, and matching mechanisms could be reduced using unrestricted natural language; allowing both: (1) end-users to intuitively express their needs using natural language, and (2) service developers to develop services without relying on syntactic/semantic description languages. Although there are some natural language-based service composition approaches, they restrict service retrieval to syntactic/semantic matching. With recent developments in Machine learning and Natural Language Processing, we motivate the use of Sentence Embeddings by leveraging richer semantic representations of sentences for service description, matching and retrieval. Experimental results show that service composition development effort may be reduced by more than 44\% while keeping a high precision/recall when matching high-level user requests with low-level service method invocations.Comment: This paper will appear on SCC'19 (IEEE International Conference on Services Computing) on July 1

Measuring concept similarities in multimedia ontologies: analysis and evaluations

The recent development of large-scale multimedia concept ontologies has provided a new momentum for research in the semantic analysis of multimedia repositories. Different methods for generic concept detection have been extensively studied, but the question of how to exploit the structure of a multimedia ontology and existing inter-concept relations has not received similar attention. In this paper, we present a clustering-based method for modeling semantic concepts on low-level feature spaces and study the evaluation of the quality of such models with entropy-based methods. We cover a variety of methods for assessing the similarity of different concepts in a multimedia ontology. We study three ontologies and apply the proposed techniques in experiments involving the visual and semantic similarities, manual annotation of video, and concept detection. The results show that modeling inter-concept relations can provide a promising resource for many different application areas in semantic multimedia processing