Matching Biomedical Ontologies through Adaptive Multi-Modal Multi-Objective Evolutionary Algorithm

To integrate massive amounts of heterogeneous biomedical data in biomedical ontologies and to provide more options for clinical diagnosis, this work proposes an adaptive Multi-modal Multi-Objective Evolutionary Algorithm (aMMOEA) to match two heterogeneous biomedical ontologies by finding the semantically identical concepts. In particular, we first propose two evaluation metrics on the alignment’s quality, which calculate the alignment’s statistical and its logical features, i.e., its f-measure and its conservativity. On this basis, we build a novel multi-objective optimization model for the biomedical ontology matching problem. By analyzing the essence of this problem, we point out that it is a large-scale Multi-modal Multi-objective Optimization Problem (MMOP) with sparse Pareto optimal solutions. Then, we propose a problem-specific aMMOEA to solve this problem, which uses the Guiding Matrix (GM) to adaptively guide the algorithm’s convergence and diversity in both objective and decision spaces. The experiment uses Ontology Alignment Evaluation Initiative (OAEI)’s biomedical tracks to test aMMOEA’s performance, and comparisons with two state-of-the-art MOEA-based matching techniques and OAEI’s participants show that aMMOEA is able to effectively determine diverse solutions for decision makers.

Matching Cyber Security Ontologies through Genetic Algorithm-Based Ontology Alignment Technique

Security ontology can be used to build a shared knowledge model for an application domain to overcome the data heterogeneity issue, but it suffers from its own heterogeneity issue. Finding identical entities in two ontologies, i.e., ontology alignment, is a solution. It is important to select an effective similarity measure (SM) to distinguish heterogeneous entities. However, due to the complex semantic relationships among concepts, no SM is ensured to be effective in all alignment tasks. The aggregation of SMs so that their advantages and disadvantages complement each other directly affects the quality of alignments. In this work, we formally define this problem, discuss its challenges, and present a problem-specific genetic algorithm (GA) to effectively address it. We experimentally test our approach on bibliographic tracks provided by OAEI and five pairs of security ontologies. The results show that GA can effectively address different heterogeneous ontology-alignment tasks and determine high-quality security ontology alignments.

Multimatcher Model to Enhance Ontology Matching Using Background Knowledge

Ontology matching is a rapidly emerging topic crucial for semantic web effort, data integration, and interoperability. Semantic heterogeneity is one of the most challenging aspects of ontology matching. Consequently, background knowledge (BK) resources are utilized to bridge the semantic gap between the ontologies. Generic BK approaches use a single matcher to discover correspondences between entities from different ontologies. However, the Ontology Alignment Evaluation Initiative (OAEI) results show that not all matchers identify the same correct mappings. Moreover, none of the matchers can obtain good results across all matching tasks. This study proposes a novel BK multimatcher approach for improving ontology matching by effectively generating and combining mappings from biomedical ontologies. Aggregation strategies to create more effective mappings are discussed. Then, a matcher path confidence measure that helps select the most promising paths using the final mapping selection algorithm is proposed. The proposed model performance is tested using the Anatomy and Large Biomed tracks offered by the OAEI 2020. Results show that higher recall levels have been obtained. Moreover, the F-measure values achieved with our model are comparable with those obtained by the state of the art matchers.

Matching sensor ontologies with unsupervised neural network with competitive learning

Sensor ontologies formally model the core concepts in the sensor domain and their relationships, which facilitates the trusted communication and collaboration of Artificial Intelligence of Things (AIoT). However, due to the subjectivity of the ontology building process, sensor ontologies might be defined by different terms, leading to the problem of heterogeneity. In order to integrate the knowledge of two heterogeneous sensor ontologies, it is necessary to determine the correspondence between two heterogeneous concepts, which is the so-called ontology matching. Recently, more and more neural networks have been considered as an effective approach to address the ontology heterogeneity problem, but they require a large number of manually labelled training samples to train the network, which poses an open challenge. In order to improve the quality of the sensor ontology alignment, an unsupervised neural network model is proposed in this work. It first models the ontology matching problem as a binary classification problem, and then uses a competitive learning strategy to efficiently cluster the ontologies to be matched, which does not require the labelled training samples. The experiment utilizes the benchmark track provided by the Ontology Alignment Evaluation Initiative (OAEI) and multiple real sensor ontology alignment tasks to test our proposal’s performance. The experimental results show that the proposed approach is able to determine higher quality alignment results compared to other matching strategies under different domain knowledge such as bibliographic and real sensor ontologies.

TOWARDS THE AUTOMATIC ONTOLOGY GENERATION AND ALIGNMENT OF BIM AND GIS DATA FORMATS

Establishing semantic interoperability between BIM and GIS is vital for geospatial information exchange. Semantic web have a natural ability to provide seamless semantic representation and integration among the heterogeneous domains like BIM and GIS through employing ontology. Ontology models can be defined (or generated) using domain-data representations and further aligned across other ontologies by the semantic similarity of their entities - introducing cross-domain ontologies to achieve interoperability of heterogeneous information. However, due to extensive semantic features and complex alignment (mapping) relations between BIM and GIS data formats, many approaches are far from generating semantically-rich ontologies and perform effective alignment to address geospatial interoperability. This study highlights the fundamental perspectives to be addressed for BIM and GIS interoperability and proposes a comprehensive conceptual framework for automatic ontology generation followed by ontology alignment of open-standards for BIM and GIS data formats. It presents an approach based on transformation patterns to automatically generate ontology models, and semantic-based and structure-based alignment techniques to form cross-domain ontology. Proposed two-phase framework provides ontology model generation for input XML schemas (i.e. of IFC and CityGML formats), and illustrates alignment technique to potentially develop a cross-domain ontology. The study concludes anticipated results of cross-domain ontology can provides future perspectives in knowledge-discovery applications and seamless information exchange for BIM and GIS.

Toward a systematic conflict resolution framework for ontologies

Background The ontology authoring step in ontology development involves having to make choices about what subject domain knowledge to include. This may concern sorting out ontological differences and making choices between conflicting axioms due to limitations in the logic or the subject domain semantics. Examples are dealing with different foundational ontologies in ontology alignment and OWL 2 DL’s transitive object property versus a qualified cardinality constraint. Such conflicts have to be resolved somehow. However, only isolated and fragmented guidance for doing so is available, which therefore results in ad hoc decision-making that may not be the best choice or forgotten about later. Results This work aims to address this by taking steps towards a framework to deal with the various types of modeling conflicts through meaning negotiation and conflict resolution in a systematic way. It proposes an initial library of common conflicts, a conflict set, typical steps toward resolution, and the software availability and requirements needed for it. The approach was evaluated with an actual case of domain knowledge usage in the context of epizootic disease outbreak, being avian influenza, and running examples with COVID-19 ontologies. Conclusions The evaluation demonstrated the potential and feasibility of a conflict resolution framework for ontologies.

Ontology alignment evaluation for online assessment of e-learners: a new e-learning management system

Purpose This paper aims to propose a new assessment system module for handling the comprehensive answers written through the answer interface. Design/methodology/approach The working principle is under three major phases: Preliminary semantic processing: In the pre-processing work, the keywords are extracted for each answer given by the course instructor. In fact, this answer is actually considered as the key to evaluating the answers written by the e-learners. Keyword and semantic processing of e-learners for hierarchical clustering-based ontology construction: For each answer given by each student, the keywords and the semantic information are extracted and clustered (hierarchical clustering) using a new improved rider optimization algorithm known as Rider with Randomized Overtaker Update (RR-OU). Ontology matching evaluation: Once the ontology structures are completed, a new alignment procedure is used to find out the similarity between two different documents. Moreover, the objects defined in this work focuses on “how exactly the matching process is done for evaluating the document.” Finally, the e-learners are classified based on their grades. Findings On observing the outcomes, the proposed model shows less relative mean squared error measure when weights were (0.5, 0, 0.5), and it was 71.78% and 16.92% better than the error values attained for (0, 0.5, 0.5) and (0.5, 0.5, 0). On examining the outcomes, the values of error attained for (1, 0, 0) were found to be lower than the values when weights were (0, 0, 1) and (0, 1, 0). Here, the mean absolute error (MAE) measure for weight (1, 0, 0) was 33.99% and 51.52% better than the MAE value for weights (0, 0, 1) and (0, 1, 0). On analyzing the overall error analysis, the mean absolute percentage error of the implemented RR-OU model was 3.74% and 56.53% better than k-means and collaborative filtering + Onto + sequential pattern mining models, respectively. Originality/value This paper adopts the latest optimization algorithm called RR-OU for proposing a new assessment system module for handling the comprehensive answers written through the answer interface. To the best of the authors’ knowledge, this is the first work that uses RR-OU-based optimization for developing a new ontology alignment-based online assessment of e-learners.