Semantic Similarity Measures for Topological Link Prediction

2020 ◽  
pp. 132-142 ◽  
Author(s):  
Giulio Biondi ◽  
Valentina Franzoni
Keyword(s):  
Semantic Similarity ◽  
Link Prediction ◽  
Similarity Measures

Denoising distant supervision for ontology lexicalization using semantic similarity measures

2021 ◽  
Vol 177 ◽  
pp. 114922
Author(s):  
Mehdi Jabalameli ◽  
Mohammadali Nematbakhsh ◽  
Reza Ramezani
Keyword(s):  
Semantic Similarity ◽  
Similarity Measures ◽  
Distant Supervision

scholarly journals An information theoretic approach to link prediction in multiplex networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Seyed Hossein Jafari ◽  
Amir Mahdi Abdolhosseini-Qomi ◽  
Masoud Asadpour ◽  
Maseud Rahgozar ◽  
Naser Yazdani
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Large Scale ◽  
Similarity Measures ◽  
Prediction Method ◽  
General Purpose ◽  
Fast Method ◽  
Theoretic Approach ◽  
Multiplex Networks ◽  
Wide Range

AbstractThe entities of real-world networks are connected via different types of connections (i.e., layers). The task of link prediction in multiplex networks is about finding missing connections based on both intra-layer and inter-layer correlations. Our observations confirm that in a wide range of real-world multiplex networks, from social to biological and technological, a positive correlation exists between connection probability in one layer and similarity in other layers. Accordingly, a similarity-based automatic general-purpose multiplex link prediction method—SimBins—is devised that quantifies the amount of connection uncertainty based on observed inter-layer correlations in a multiplex network. Moreover, SimBins enhances the prediction quality in the target layer by incorporating the effect of link overlap across layers. Applying SimBins to various datasets from diverse domains, our findings indicate that SimBins outperforms the compared methods (both baseline and state-of-the-art methods) in most instances when predicting links. Furthermore, it is discussed that SimBins imposes minor computational overhead to the base similarity measures making it a potentially fast method, suitable for large-scale multiplex networks.

scholarly journals Evolution of Semantic Similarity—A Survey

2021 ◽  
Vol 54 (2) ◽  
pp. 1-37
Author(s):  
Dhivya Chandrasekaran ◽  
Vijay Mago
Keyword(s):  
Natural Language ◽  
Semantic Similarity ◽  
Language Processing ◽  
Hybrid Methods ◽  
Research Work ◽  
Similarity Measures ◽  
Text Data ◽  
Knowledge Based ◽  
Open Research ◽  
Research Problems

Estimating the semantic similarity between text data is one of the challenging and open research problems in the field of Natural Language Processing (NLP). The versatility of natural language makes it difficult to define rule-based methods for determining semantic similarity measures. To address this issue, various semantic similarity methods have been proposed over the years. This survey article traces the evolution of such methods beginning from traditional NLP techniques such as kernel-based methods to the most recent research work on transformer-based models, categorizing them based on their underlying principles as knowledge-based, corpus-based, deep neural network–based methods, and hybrid methods. Discussing the strengths and weaknesses of each method, this survey provides a comprehensive view of existing systems in place for new researchers to experiment and develop innovative ideas to address the issue of semantic similarity.

Procedure Based on Semantic Similarity for Merging Ontologies by Non-Redundant Knowledge Enrichment

2018 ◽  
Vol 14 (2) ◽  
pp. 16-36 ◽  
Author(s):  
Carlos Ramón Rangel ◽  
Junior Altamiranda ◽  
Mariela Cerrada ◽  
Jose Aguilar
Keyword(s):  
Semantic Similarity ◽  
Similarity Measures ◽  
The Other ◽  
Other Hand ◽  
Knowledge Enrichment ◽  
Merging Algorithms

The merging procedures of two ontologies are mostly related to the enrichment of one of the input ontologies, i.e. the knowledge of the aligned concepts from one ontology are copied into the other ontology. As a consequence, the resulting new ontology extends the original knowledge of the base ontology, but the unaligned concepts of the other ontology are not considered in the new extended ontology. On the other hand, there are experts-aided semi-automatic approaches to accomplish the task of including the knowledge that is left out from the resulting merged ontology and debugging the possible concept redundancy. With the aim of facing the posed necessity of including all the knowledge of the ontologies to be merged without redundancy, this article proposes an automatic approach for merging ontologies, which is based on semantic similarity measures and exhaustive searching along of the closest concepts. The authors' approach was compared to other merging algorithms, and good results are obtained in terms of completeness, relationships and properties, without creating redundancy.

Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance

2020 ◽  
Vol 18 (06) ◽  
pp. 2050038
Author(s):  
Jorge Parraga-Alava ◽  
Mario Inostroza-Ponta
Keyword(s):  
Semantic Similarity ◽  
Clustering Algorithm ◽  
Performance Metrics ◽  
Expression Patterns ◽  
Biological Significance ◽  
Similarity Measures ◽  
Gene Clustering ◽  
Biological Knowledge ◽  
Multi Objective ◽  
Gene Similarity

Using a prior biological knowledge of relationships and genetic functions for gene similarity, from repository such as the Gene Ontology (GO), has shown good results in multi-objective gene clustering algorithms. In this scenario and to obtain useful clustering results, it would be helpful to know which measure of biological similarity between genes should be employed to yield meaningful clusters that have both similar expression patterns (co-expression) and biological homogeneity. In this paper, we studied the influence of the four most used GO-based semantic similarity measures in the performance of a multi-objective gene clustering algorithm. We used four publicly available datasets and carried out comparative studies based on performance metrics for the multi-objective optimization field and clustering performance indexes. In most of the cases, using Jiang–Conrath and Wang similarities stand in terms of multi-objective metrics. In clustering properties, Resnik similarity allows to achieve the best values of compactness and separation and therefore of co-expression of groups of genes. Meanwhile, in biological homogeneity, the Wang similarity reports greater number of significant GO terms. However, statistical, visual, and biological significance tests showed that none of the GO-based semantic similarity measures stand out above the rest in order to significantly improve the performance of the multi-objective gene clustering algorithm.

scholarly journals GSAn: an alternative to enrichment analysis for annotating gene sets

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Aaron Ayllon-Benitez ◽  
Romain Bourqui ◽  
Patricia Thébault ◽  
Fleur Mougin
Keyword(s):  
Gene Ontology ◽  
Semantic Similarity ◽  
A Priori ◽  
Similarity Measures ◽  
Enrichment Analysis ◽  
Biological Information ◽  
Underlying Structure ◽  
Gene Set ◽  
Sequencing Technologies ◽  
Gene Coverage

Abstract The revolution in new sequencing technologies is greatly leading to new understandings of the relations between genotype and phenotype. To interpret and analyze data that are grouped according to a phenotype of interest, methods based on statistical enrichment became a standard in biology. However, these methods synthesize the biological information by a priori selecting the over-represented terms and may suffer from focusing on the most studied genes that represent a limited coverage of annotated genes within a gene set. Semantic similarity measures have shown great results within the pairwise gene comparison by making advantage of the underlying structure of the Gene Ontology. We developed GSAn, a novel gene set annotation method that uses semantic similarity measures to synthesize a priori Gene Ontology annotation terms. The originality of our approach is to identify the best compromise between the number of retained annotation terms that has to be drastically reduced and the number of related genes that has to be as large as possible. Moreover, GSAn offers interactive visualization facilities dedicated to the multi-scale analysis of gene set annotations. Compared to enrichment analysis tools, GSAn has shown excellent results in terms of maximizing the gene coverage while minimizing the number of terms.

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