scholarly journals DAEOM: A Deep Attentional Embedding Approach for Biomedical Ontology Matching

2020 ◽  
Vol 10 (21) ◽  
pp. 7909
Author(s):  
Jifang Wu ◽  
Jianghua Lv ◽  
Haoming Guo ◽  
Shilong Ma
Keyword(s):  
Network Structure ◽  
Threshold Value ◽  
Representation Learning ◽  
Biomedical Ontology ◽  
Semantic Integration ◽  
Ontology Matching ◽  
Matching Process ◽  
Learning Techniques ◽  
Expert User ◽  
Final Alignment

Ontology Matching (OM) is performed to find semantic correspondences between the entity elements of different ontologies to enable semantic integration, reuse, and interoperability. Representation learning techniques have been introduced to the field of OM with the development of deep learning. However, there still exist two limitations. Firstly, these methods only focus on the terminological-based features to learn word vectors for discovering mappings, ignoring the network structure of ontology. Secondly, the final alignment threshold is usually determined manually within these methods. It is difficult for an expert to adjust the threshold value and even more so for a non-expert user. To address these issues, we propose an alternative ontology matching framework called Deep Attentional Embedded Ontology Matching (DAEOM), which models the matching process by embedding techniques with jointly encoding ontology terminological description and network structure. We propose a novel inter-intra negative sampling skill tailored for the structural relations asserted in ontologies, and further improve our iterative final alignment method by introducing an automatic adjustment of the final alignment threshold. The preliminary result on real-world biomedical ontologies indicates that DAEOM is competitive with several OAEI top-ranked systems in terms of F-measure.

scholarly journals Using decision trees for inductively driven semantic integration and ontology matching

2021 ◽  
Author(s):  
Bart Gajderowicz
Keyword(s):  
Decision Trees ◽  
Real World ◽  
Semantic Integration ◽  
Use Cases ◽  
Ontology Matching ◽  
Bottom Up ◽  
Matching Algorithm ◽  
Matching Process ◽  
Narrow Context

The popularity of ontologies for representing the semantics behind many real-world domains has created a growing pool of ontologies on various topics. While different ontologists, experts, and organizations create the vast majority of ontologies, often for internal use of for use in a narrow context, their domains frequently overlap in a wider context, specifically for complementary domains. To assist in the reuse of ontologies, this thesis proposes a bottom-up technique for creating concept anchors that are used for ontology matching. Anchors are ontology concepts that have been matched to concepts in an eternal ontology. The matching process is based on inductively derived decision trees rules for an ontology that are compared with rules derived for external ontologies. The matching algorithm is intended to match taxomonies, ontologies which define subsumption relations between concepts, with an associated database used to derive the decision trees. This thesis also introduces several algorithm evolution measures, and presents a set of use cases that demonstrate the strengths and weaknesses of the matching process.

scholarly journals Using decision trees for inductively driven semantic integration and ontology matching

2021 ◽  
Author(s):  
Bart Gajderowicz
Keyword(s):  
Decision Trees ◽  
Real World ◽  
Semantic Integration ◽  
Use Cases ◽  
Ontology Matching ◽  
Bottom Up ◽  
Matching Algorithm ◽  
Matching Process ◽  
Narrow Context

The popularity of ontologies for representing the semantics behind many real-world domains has created a growing pool of ontologies on various topics. While different ontologists, experts, and organizations create the vast majority of ontologies, often for internal use of for use in a narrow context, their domains frequently overlap in a wider context, specifically for complementary domains. To assist in the reuse of ontologies, this thesis proposes a bottom-up technique for creating concept anchors that are used for ontology matching. Anchors are ontology concepts that have been matched to concepts in an eternal ontology. The matching process is based on inductively derived decision trees rules for an ontology that are compared with rules derived for external ontologies. The matching algorithm is intended to match taxomonies, ontologies which define subsumption relations between concepts, with an associated database used to derive the decision trees. This thesis also introduces several algorithm evolution measures, and presents a set of use cases that demonstrate the strengths and weaknesses of the matching process.

scholarly journals An Iterative Automatic Final Alignment Method in the Ontology Matching System

2018 ◽  
Vol 42 (1) ◽  
pp. 39-61 ◽  
Author(s):  
Marko Gulić ◽  
Marin Vuković
Keyword(s):  
Heterogeneous Data ◽  
Data Sources ◽  
Ontology Matching ◽  
Alignment Method ◽  
Automatic Adjustment ◽  
Matching Process ◽  
Heterogeneous Data Sources ◽  
Final Alignment

Ontology matching plays an important role in the integration of heterogeneous data sources that are described by ontologies. In order to determine correspondences between ontologies, a set of matchers can be used. After the execution of these matchers and the aggregation of the results obtained by these matchers, a final alignment method is executed in order to select appropriate correspondences between entities of compared ontologies. The final alignment method is an important part of the ontology matching process because it directly determines the output result of this process. In this paper we improve our iterative final alignment method by introducing an automatic adjustment of final alignment threshold as well as a new rule for determining false correspondences with similarity values greater than adjusted threshold. An evaluation of the method is performed on the test ontologies of the OAEI evaluation contest and a comparison with other final alignment methods is given.

scholarly journals Representation Learning for Fine-Grained Change Detection

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4486
Author(s):  
Niall O’Mahony ◽  
Sean Campbell ◽  
Lenka Krpalkova ◽  
Anderson Carvalho ◽  
Joseph Walsh ◽  
...  
Keyword(s):  
Deep Learning ◽  
Change Detection ◽  
Model Calibration ◽  
State Of The Art ◽  
Representation Learning ◽  
Machine Intelligence ◽  
The State ◽  
Sensor Data ◽  
Fine Grained ◽  
Learning Techniques

Fine-grained change detection in sensor data is very challenging for artificial intelligence though it is critically important in practice. It is the process of identifying differences in the state of an object or phenomenon where the differences are class-specific and are difficult to generalise. As a result, many recent technologies that leverage big data and deep learning struggle with this task. This review focuses on the state-of-the-art methods, applications, and challenges of representation learning for fine-grained change detection. Our research focuses on methods of harnessing the latent metric space of representation learning techniques as an interim output for hybrid human-machine intelligence. We review methods for transforming and projecting embedding space such that significant changes can be communicated more effectively and a more comprehensive interpretation of underlying relationships in sensor data is facilitated. We conduct this research in our work towards developing a method for aligning the axes of latent embedding space with meaningful real-world metrics so that the reasoning behind the detection of change in relation to past observations may be revealed and adjusted. This is an important topic in many fields concerned with producing more meaningful and explainable outputs from deep learning and also for providing means for knowledge injection and model calibration in order to maintain user confidence.

scholarly journals Community Detection Based on Graph Representation Learning in Evolutionary Networks

2021 ◽  
Vol 11 (10) ◽  
pp. 4497
Author(s):  
Dongming Chen ◽  
Mingshuo Nie ◽  
Jie Wang ◽  
Yun Kong ◽  
Dongqi Wang ◽  
...  
Keyword(s):  
Community Detection ◽  
Network Structure ◽  
Clustering Algorithm ◽  
Laplacian Matrix ◽  
Representation Learning ◽  
Detection Algorithm ◽  
Graph Representation ◽  
Time Slice ◽  
Current Time ◽  
Evolutionary Networks

Aiming at analyzing the temporal structures in evolutionary networks, we propose a community detection algorithm based on graph representation learning. The proposed algorithm employs a Laplacian matrix to obtain the node relationship information of the directly connected edges of the network structure at the previous time slice, the deep sparse autoencoder learns to represent the network structure under the current time slice, and the K-means clustering algorithm is used to partition the low-dimensional feature matrix of the network structure under the current time slice into communities. Experiments on three real datasets show that the proposed algorithm outperformed the baselines regarding effectiveness and feasibility.

A Semantic-Based Ontology Matching Process for PDMS

2009 ◽  
pp. 124-135 ◽  
Author(s):  
Carlos Eduardo Pires ◽  
Damires Souza ◽  
Thiago Pachêco ◽  
Ana Carolina Salgado
Keyword(s):  
Ontology Matching ◽  
Matching Process

Continual representation learning for evolving biomedical bipartite networks

2021 ◽  
Author(s):  
Kishlay Jha ◽  
Guangxu Xun ◽  
Aidong Zhang
Keyword(s):  
Network Structure ◽  
Learning Strategy ◽  
Structure Learning ◽  
Fundamental Problem ◽  
Representation Learning ◽  
Research Area ◽  
Bipartite Network ◽  
Bipartite Networks ◽  
Straightforward Application ◽  
Low Dimensional

Abstract Motivation Many real-world biomedical interactions such as ‘gene-disease’, ‘disease-symptom’ and ‘drug-target’ are modeled as a bipartite network structure. Learning meaningful representations for such networks is a fundamental problem in the research area of Network Representation Learning (NRL). NRL approaches aim to translate the network structure into low-dimensional vector representations that are useful to a variety of biomedical applications. Despite significant advances, the existing approaches still have certain limitations. First, a majority of these approaches do not model the unique topological properties of bipartite networks. Consequently, their straightforward application to the bipartite graphs yields unsatisfactory results. Second, the existing approaches typically learn representations from static networks. This is limiting for the biomedical bipartite networks that evolve at a rapid pace, and thus necessitate the development of approaches that can update the representations in an online fashion. Results In this research, we propose a novel representation learning approach that accurately preserves the intricate bipartite structure, and efficiently updates the node representations. Specifically, we design a customized autoencoder that captures the proximity relationship between nodes participating in the bipartite bicliques (2 × 2 sub-graph), while preserving both the global and local structures. Moreover, the proposed structure-preserving technique is carefully interleaved with the central tenets of continual machine learning to design an incremental learning strategy that updates the node representations in an online manner. Taken together, the proposed approach produces meaningful representations with high fidelity and computational efficiency. Extensive experiments conducted on several biomedical bipartite networks validate the effectiveness and rationality of the proposed approach.

scholarly journals Exponential Family Graph Embeddings

2020 ◽  
Vol 34 (04) ◽  
pp. 3357-3364
Author(s):  
Abdulkadir Celikkanat ◽  
Fragkiskos D. Malliaros
Keyword(s):  
Random Walk ◽  
Exponential Family ◽  
Representation Learning ◽  
Learning Problems ◽  
Interaction Patterns ◽  
Network Representation ◽  
Learning Tasks ◽  
Learning Techniques ◽  
Real World Datasets ◽  
Low Dimensional

Representing networks in a low dimensional latent space is a crucial task with many interesting applications in graph learning problems, such as link prediction and node classification. A widely applied network representation learning paradigm is based on the combination of random walks for sampling context nodes and the traditional Skip-Gram model to capture center-context node relationships. In this paper, we emphasize on exponential family distributions to capture rich interaction patterns between nodes in random walk sequences. We introduce the generic exponential family graph embedding model, that generalizes random walk-based network representation learning techniques to exponential family conditional distributions. We study three particular instances of this model, analyzing their properties and showing their relationship to existing unsupervised learning models. Our experimental evaluation on real-world datasets demonstrates that the proposed techniques outperform well-known baseline methods in two downstream machine learning tasks.

scholarly journals Using a Convolutional Siamese Network for Image-Based Plant Species Identification with Small Datasets

Biomimetics ◽  
2020 ◽  
Vol 5 (1) ◽  
pp. 8 ◽  
Author(s):  
Geovanni Figueroa-Mata ◽  
Erick Mata-Montero
Keyword(s):  
Plant Species ◽  
Euclidean Distance ◽  
Threshold Value ◽  
Costa Rican ◽  
Similarity Function ◽  
Siamese Network ◽  
Learning Techniques ◽  
Dataset Size ◽  
Plant Species Identification ◽  
Siamese Networks

The application of deep learning techniques may prove difficult when datasets are small. Recently, techniques such as one-shot learning, few-shot learning, and Siamese networks have been proposed to address this problem. In this paper, we propose the use a convolutional Siamese network (CSN) that learns a similarity metric that discriminates between plant species based on images of leaves. Once the CSN has learned the similarity function, its discriminatory power is generalized to classify not just new pictures of the species used during training but also entirely new species for which only a few images are available. This is achieved by exposing the network to pairs of similar and dissimilar observations and minimizing the Euclidean distance between similar pairs while simultaneously maximizing it between dissimilar pairs. We conducted experiments to study two different scenarios. In the first one, the CSN was trained and validated with datasets that comprise 5, 10, 15, 20, 25, and 30 pictures per species, extracted from the well-known Flavia dataset. Then, the trained model was tested with another dataset composed of 320 images (10 images per species) also from Flavia. The obtained accuracy was compared with the results of feeding the same training, validation, and testing datasets to a convolutional neural network (CNN) in order to determine if there is a threshold value t for dataset size that defines the intervals for which either the CSN or the CNN has better accuracy. In the second studied scenario, the accuracy of both the CSN and the CNN—both trained and validated with the same datasets extracted from Flavia—were compared when tested on a set of images of leaves of 20 Costa Rican tree species that are not represented in Flavia.

scholarly journals Alin: improving interactive ontology matching by interactively revising mapping suggestions

2020 ◽  
Vol 35 ◽  
Author(s):  
Jomar Da Silva ◽  
Kate Revoredo ◽  
Fernanda Baião ◽  
Jérôme Euzenat
Keyword(s):  
State Of The Art ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Ontology Matching ◽  
New Techniques ◽  
Domain Experts ◽  
Matching Process ◽  
Heterogeneous Data Sources ◽  
Expert Answer ◽  
Comparable Quality

Abstract Ontology matching aims at discovering mappings between the entities of two ontologies. It plays an important role in the integration of heterogeneous data sources that are described by ontologies. Interactive ontology matching involves domain experts in the matching process. In some approaches, the expert provides feedback about mappings between ontology entities, that is, these approaches select mappings to present to the expert who replies which of them should be accepted or rejected, so taking advantage of the knowledge of domain experts towards finding an alignment. In this paper, we present Alin, an interactive ontology matching approach which uses expert feedback not only to approve or reject selected mappings but also to dynamically improve the set of selected mappings, that is, to interactively include and to exclude mappings from it. This additional use for expert answers aims at increasing in the benefit brought by each expert answer. For this purpose, Alin uses four techniques. Two techniques were used in the previous versions of Alin to dynamically select concept and attribute mappings. Two new techniques are introduced in this paper: one to dynamically select relationship mappings and another one to dynamically reject inconsistent selected mappings using anti-patterns. We compared Alin with state-of-the-art tools, showing that it generates alignment of comparable quality.

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