Local matching learning of large scale biomedical ontologies

Les larges ontologies biomédicales décrivent généralement le même domaine d'intérêt, mais en utilisant des modèles de modélisation et des vocabulaires différents. Aligner ces ontologies qui sont complexes et hétérogènes est une tâche fastidieuse. Les systèmes de matching doivent fournir des résultats de haute qualité en tenant compte de la grande taille de ces ressources. Les systèmes de matching d'ontologies doivent résoudre deux problèmes: (i) intégrer la grande taille d'ontologies, (ii) automatiser le processus d'alignement. Le matching d'ontologies est une tâche difficile en raison de la large taille des ontologies. Les systèmes de matching d'ontologies combinent différents types de matcher pour résoudre ces problèmes. Les principaux problèmes de l'alignement de larges ontologies biomédicales sont: l'hétérogénéité conceptuelle, l'espace de recherche élevé et la qualité réduite des alignements résultants. Les systèmes d'alignement d'ontologies combinent différents matchers afin de réduire l'hétérogénéité. Cette combinaison devrait définir le choix des matchers à combiner et le poids. Différents matchers traitent différents types d'hétérogénéité. Par conséquent, le paramétrage d'un matcher devrait être automatisé par les systèmes d'alignement d'ontologies afin d'obtenir une bonne qualité de correspondance. Nous avons proposé une approche appele "local matching learning" pour faire face à la fois à la grande taille des ontologies et au problème de l'automatisation. Nous divisons un gros problème d'alignement en un ensemble de problèmes d'alignement locaux plus petits. Chaque problème d'alignement local est indépendamment aligné par une approche d'apprentissage automatique. Nous réduisons l'énorme espace de recherche en un ensemble de taches de recherche de corresondances locales plus petites. Nous pouvons aligner efficacement chaque tache de recherche de corresondances locale pour obtenir une meilleure qualité de correspondance. Notre approche de partitionnement se base sur une nouvelle stratégie à découpes multiples générant des partitions non volumineuses et non isolées. Par conséquence, nous pouvons surmonter le problème de l'hétérogénéité conceptuelle. Le nouvel algorithme de partitionnement est basé sur le clustering hiérarchique par agglomération (CHA). Cette approche génère un ensemble de tâches de correspondance locale avec un taux de couverture suffisant avec aucune partition isolée. Chaque tâche d'alignement local est automatiquement alignée en se basant sur les techniques d'apprentissage automatique. Un classificateur local aligne une seule tâche d'alignement local. Les classificateurs locaux sont basés sur des features élémentaires et structurelles. L'attribut class de chaque set de donne d'apprentissage " training set" est automatiquement étiqueté à l'aide d'une base de connaissances externe. Nous avons appliqué une technique de sélection de features pour chaque classificateur local afin de sélectionner les matchers appropriés pour chaque tâche d'alignement local. Cette approche réduit la complexité d'alignement et augmente la précision globale par rapport aux méthodes d'apprentissage traditionnelles. Nous avons prouvé que l'approche de partitionnement est meilleure que les approches actuelles en terme de précision, de taux de couverture et d'absence de partitions isolées. Nous avons évalué l'approche d'apprentissage d'alignement local à l'aide de diverses expériences basées sur des jeux de données d'OAEI 2018. Nous avons déduit qu'il est avantageux de diviser une grande tâche d'alignement d'ontologies en un ensemble de tâches d'alignement locaux. L'espace de recherche est réduit, ce qui réduit le nombre de faux négatifs et de faux positifs. L'application de techniques de sélection de caractéristiques à chaque classificateur local augmente la valeur de rappel pour chaque tâche d'alignement local.Although a considerable body of research work has addressed the problem of ontology matching, few studies have tackled the large ontologies used in the biomedical domain. We introduce a fully automated local matching learning approach that breaks down a large ontology matching task into a set of independent local sub-matching tasks. This approach integrates a novel partitioning algorithm as well as a set of matching learning techniques. The partitioning method is based on hierarchical clustering and does not generate isolated partitions. The matching learning approach employs different techniques: (i) local matching tasks are independently and automatically aligned using their local classifiers, which are based on local training sets built from element level and structure level features, (ii) resampling techniques are used to balance each local training set, and (iii) feature selection techniques are used to automatically select the appropriate tuning parameters for each local matching context. Our local matching learning approach generates a set of combined alignments from each local matching task, and experiments show that a multiple local classifier approach outperforms conventional, state-of-the-art approaches: these use a single classifier for the whole ontology matching task. In addition, focusing on context-aware local training sets based on local feature selection and resampling techniques significantly enhances the obtained results

Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences Among Ontologies

An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'sability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the networks. The output of one network in response to a stimulus to another network can be interpreted as an analogical mapping. In a similar fashion, the networks can be explicitly trained to mapspecific items in one domain to specific items in another domain. Representation layer helpsthe network learn relationship mapping with direct training method.The OMNN approach is tested on family tree test cases. Node mapping, relationshipmapping, unequal structure mapping, and scalability test are performed. Results showthat OMNN is able to learn and infer correspondences in tree-like structures. Furthermore, OMNN is applied to several OAEI benchmark test cases to test its performance on ontologymapping. Results show that OMNN approach is competitive to the top performing systems that participated in OAEI 2009

Ontology Mapping Tools, Methods and Approaches – Analytical Survey

In this paper we present the results of browsing, analyzing and comparing many ontology mapping tools, approaches and methods. We extract and classify valuable parameters for strict and unambiguous tool or method description. Every mapping tool, algorithm or approach must have such a description, practically usable for both human and software agents and sufficient for easy checking if it suitable or not for a given task. We will use our classifications for developing ontology, conceptualizing all valuable metadata for semantic machine-processable mapping tools description

Clustering documents with active learning using Wikipedia

Wikipedia has been applied as a background knowledge base to various text mining problems, but very few attempts have been made to utilize it for document clustering. In this paper we propose to exploit the semantic knowledge in Wikipedia for clustering, enabling the automatic grouping of documents with similar themes. Although clustering is intrinsically unsupervised, recent research has shown that incorporating supervision improves clustering performance, even when limited supervision is provided. The approach presented in this paper applies supervision using active learning. We first utilize Wikipedia to create a concept-based representation of a text document, with each concept associated to a Wikipedia article. We then exploit the semantic relatedness between Wikipedia concepts to find pair-wise instance-level constraints for supervised clustering, guiding clustering towards the direction indicated by the constraints. We test our approach on three standard text document datasets. Empirical results show that our basic document representation strategy yields comparable performance to previous attempts; and adding constraints improves clustering performance further by up to 20%

Unsupervised Learning of Semantic Audio Representations

Even in the absence of any explicit semantic annotation, vast collections of audio recordings provide valuable information for learning the categorical structure of sounds. We consider several class-agnostic semantic constraints that apply to unlabeled nonspeech audio: (i) noise and translations in time do not change the underlying sound category, (ii) a mixture of two sound events inherits the categories of the constituents, and (iii) the categories of events in close temporal proximity are likely to be the same or related. Without labels to ground them, these constraints are incompatible with classification loss functions. However, they may still be leveraged to identify geometric inequalities needed for triplet loss-based training of convolutional neural networks. The result is low-dimensional embeddings of the input spectrograms that recover 41% and 84% of the performance of their fully-supervised counterparts when applied to downstream query-by-example sound retrieval and sound event classification tasks, respectively. Moreover, in limited-supervision settings, our unsupervised embeddings double the state-of-the-art classification performance.Comment: Submitted to ICASSP 201

Machine Learning-Based Ontology Mapping Tool to Enable Interoperability in Coastal Sensor Networks

In today’s world, ontologies are being widely used for data integration tasks and solving information heterogeneity problems on the web because of their capability in providing explicit meaning to the information. The growing need to resolve the heterogeneities between different information systems within a domain of interest has led to the rapid development of individual ontologies by different organizations. These ontologies designed for a particular task could be a unique representation of their project needs. Thus, integrating distributed and heterogeneous ontologies by finding semantic correspondences between their concepts has become the key point to achieve interoperability among different representations. In this thesis, an advanced instance-based ontology matching algorithm has been proposed to enable data integration tasks in ocean sensor networks, whose data are highly heterogeneous in syntax, structure, and semantics. This provides a solution to the ontology mapping problem in such systems based on machine-learning methods and string-based methods

Ontology matching: state of the art and future challenges

shvaiko2013aInternational audienceAfter years of research on ontology matching, it is reasonable to consider several questions: is the field of ontology matching still making progress? Is this progress significant enough to pursue some further research? If so, what are the particularly promising directions? To answer these questions, we review the state of the art of ontology matching and analyze the results of recent ontology matching evaluations. These results show a measurable improvement in the field, the speed of which is albeit slowing down. We conjecture that significant improvements can be obtained only by addressing important challenges for ontology matching. We present such challenges with insights on how to approach them, thereby aiming to direct research into the most promising tracks and to facilitate the progress of the field

Survey on Techniques for Ontology Interoperability in Semantic Web

Ontology is a shared conceptualization of knowledge representation of particular domain. These are used for the enhancement of semantic information explicitly. It is considered as a key element in semantic web development. Creation of global web data sources is impossible because of the dynamic nature of the web. Ontology Interoperability provides the reusability of ontologies. Different domain experts and ontology engineers create different ontologies for the same or similar domain depending on their data modeling requirements. These cause ontology heterogeneity and inconsistency problems. For more better and precise results ontology mapping is the solution. As their use has increased, providing means of resolving semantic differences has also become very important. Papers on ontology interoperability report the results on different frameworks and this makes their comparison almost impossible. Therefore, the main focus of this paper will be on providing some basics of ontology interoperability and briefly introducing its different approaches. In this paper we survey the approaches that have been proposed for providing interoperability among domain ontologies and its related techniques and tools