Luz, Nuno (GECAD - Knowledge Engineering and Decision Support Research Center) | Silva, Nuno ( GECAD - Knowledge Engineering and Decision Support Research Center Institute of Engineering - Polytechnic of Porto (ISEP/IPP) ) | Maio, Paulo ( GECAD - Knowledge Engineering and Decision Support Research Center Institute of Engineering - Polytechnic of Porto (ISEP/IPP) ) | Novais, Paulo ( CCTC - Computer Science and Technology Center University of Minho )
Currently, the majority of matchers are able to establish simple correspondences between entities, but are not able to provide complex alignments. Furthermore, the resulting alignments do not contain additional information on how they were extracted and formed. Not only it becomes hard to debug the alignment results, but it is also difficult to justify correspondences. We propose a method to generate complex ontology alignments that captures the semantics of matching algorithms and human-oriented ontology alignment definition processes. Through these semantics, arguments that provide an abstraction over the specificities of the alignment process are generated and used by agents to share, negotiate and combine correspondences. After the negotiation process, the resulting arguments and their relations can be visualized by humans in order to debug and understand the given correspondences.
In domains such as biomedicine, ontologies are prominently utilized for annotating data. Consequently, aligning ontologies facilitates integrating data. Several algorithms exist for automatically aligning ontologies with diverse levels of performance. As alignment applications evolve and exhibit online run time constraints, performing the alignment in a reasonable amount of time without compromising the quality of the alignment is a crucial challenge. A large class of alignment algorithms is iterative and often consumes more time than others in delivering solutions of high quality. We present a novel and general approach for speeding up the multivariable optimization process utilized by these algorithms. Specifically, we use the technique of block-coordinate descent (BCD), which exploits the subdimensions of the alignment problem identified using a partitioning scheme. We integrate this approach into multiple well-known alignment algorithms and show that the enhanced algorithms generate similar or improved alignments in significantly less time on a comprehensive testbed of ontology pairs. Because BCD does not overly constrain how we partition or order the parts, we vary the partitioning and ordering schemes in order to empirically determine the best schemes for each of the selected algorithms. As biomedicine represents a key application domain for ontologies, we introduce a comprehensive biomedical ontology testbed for the community in order to evaluate alignment algorithms. Because biomedical ontologies tend to be large, default iterative techniques find it difficult to produce a good quality alignment within a reasonable amount of time. We align a significant number of ontology pairs from this testbed using BCD-enhanced algorithms. Our contributions represent an important step toward making a significant class of alignment techniques computationally feasible.
Ontology alignment (also called ontology matching) is the process of identifying correspondences between entities in different, possibly heterogeneous, ontologies. Traditional ontology alignment techniques rely on the full disclosure of the ontological models; however, within open and opportunistic environments, such approaches may not always be pragmatic or even acceptable (due to privacy concerns). Several studies have focussed on collaborative, decentralised approaches to ontology alignment, where agents negotiate the acceptability of single correspondences acquired from past encounters, or try to ascertain novel correspondences on the fly. However, such approaches can lead to logical violations that may undermine their utility. In this paper, we extend a dialogical approach to correspondence negotiation, whereby agents not only exchange details of possible correspondences, but also identify potential violations to the consistency and conservativity principles. We present a formal model of the dialogue, and show how agents can repair logical violations during the dialogue by invoking a correspondence repair, thus negotiating and exchanging repair plans. We illustrate this opportunistic alignment mechanism with an example and we empirically show that allowing agents to strategically reject or weaken correspondences when these cause violations does not degrade the effectiveness of the alignment computed, whilst reducing the number of residual violations.
Ontology alignment is widely-used to find the correspondences between different ontologies in diverse fields.After discovering the alignments,several performance scores are available to evaluate them.The scores typically require the identified alignment and a reference containing the underlying actual correspondences of the given ontologies.The current trend in the alignment evaluation is to put forward a new score(e.g., precision, weighted precision, etc.)and to compare various alignments by juxtaposing the obtained scores. However,it is substantially provocative to select one measure among others for comparison.On top of that, claiming if one system has a better performance than one another cannot be substantiated solely by comparing two scalars.In this paper,we propose the statistical procedures which enable us to theoretically favor one system over one another.The McNemar's test is the statistical means by which the comparison of two ontology alignment systems over one matching task is drawn.The test applies to a 2x2 contingency table which can be constructed in two different ways based on the alignments,each of which has their own merits/pitfalls.The ways of the contingency table construction and various apposite statistics from the McNemar's test are elaborated in minute detail.In the case of having more than two alignment systems for comparison, the family-wise error rate is expected to happen. Thus, the ways of preventing such an error are also discussed.A directed graph visualizes the outcome of the McNemar's test in the presence of multiple alignment systems.From this graph, it is readily understood if one system is better than one another or if their differences are imperceptible.The proposed statistical methodologies are applied to the systems participated in the OAEI 2016 anatomy track, and also compares several well-known similarity metrics for the same matching problem.
When ontologies cover overlapping topics, the overlap can be represented using ontology alignments. These alignments need to be continuously adapted to changing ontologies. Especially for large ontologies this is a costly task often consisting of manual work. Finding changes that do not lead to an adaption of the alignment can potentially make this process significantly easier. This work presents an approach to finding these changes based on RDF embeddings and common classification techniques. To examine the feasibility of this approach, an evaluation on a real-world dataset is presented. In this evaluation, the best classifiers reached a precision of 0.8.