Paper Co-citation Analysis Using Semantic Similarity Measures

2020 ◽  
pp. 264-277
Author(s):  
Mohamed Ali Hadj Taieb ◽  
Mohamed Ben Aouicha ◽  
Houcemeddine Turki
Keyword(s):  
Citation Analysis ◽  
Semantic Similarity ◽  
Similarity Measures

Document- and Keyword-based Author Co-citation Analysis

2018 ◽  
Vol 2 (2) ◽  
pp. 70-82 ◽  
Author(s):  
Binglu Wang ◽  
Yi Bu ◽  
Win-bin Huang
Keyword(s):  
Citation Analysis ◽  
Semantic Similarity ◽  
Method Validation ◽  
New Method ◽  
Global Network ◽  
Network Visualization ◽  
Knowledge Domain ◽  
Knowledge Domains ◽  
Domain Mapping ◽  
The Relationship

AbstractIn the field of scientometrics, the principal purpose for author co-citation analysis (ACA) is to map knowledge domains by quantifying the relationship between co-cited author pairs. However, traditional ACA has been criticized since its input is insufficiently informative by simply counting authors’ co-citation frequencies. To address this issue, this paper introduces a new method that reconstructs the raw co-citation matrices by regarding document unit counts and keywords of references, named as Document- and Keyword-Based Author Co-Citation Analysis (DKACA). Based on the traditional ACA, DKACA counted co-citation pairs by document units instead of authors from the global network perspective. Moreover, by incorporating the information of keywords from cited papers, DKACA captured their semantic similarity between co-cited papers. In the method validation part, we implemented network visualization and MDS measurement to evaluate the effectiveness of DKACA. Results suggest that the proposed DKACA method not only reveals more insights that are previously unknown but also improves the performance and accuracy of knowledge domain mapping, representing a new basis for further studies.

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 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.

scholarly journals Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures

2019 ◽  
Vol 2019 ◽  
pp. 1-20 ◽  
Author(s):  
Ameera M. Almasoud ◽  
Hend S. Al-Khalifa ◽  
Abdulmalik S. Al-Salman
Keyword(s):  
Big Data ◽  
Semantic Similarity ◽  
Data Clustering ◽  
Input Data ◽  
Distributed Processing ◽  
Clustering Algorithms ◽  
Similarity Measures ◽  
Parallel And Distributed Processing ◽  
Time Reduction ◽  
Improved Performance

In the field of biology, researchers need to compare genes or gene products using semantic similarity measures (SSM). Continuous data growth and diversity in data characteristics comprise what is called big data; current biological SSMs cannot handle big data. Therefore, these measures need the ability to control the size of big data. We used parallel and distributed processing by splitting data into multiple partitions and applied SSM measures to each partition; this approach helped manage big data scalability and computational problems. Our solution involves three steps: split gene ontology (GO), data clustering, and semantic similarity calculation. To test this method, split GO and data clustering algorithms were defined and assessed for performance in the first two steps. Three of the best SSMs in biology [Resnik, Shortest Semantic Differentiation Distance (SSDD), and SORA] are enhanced by introducing threaded parallel processing, which is used in the third step. Our results demonstrate that introducing threads in SSMs reduced the time of calculating semantic similarity between gene pairs and improved performance of the three SSMs. Average time was reduced by 24.51% for Resnik, 22.93%, for SSDD, and 33.68% for SORA. Total time was reduced by 8.88% for Resnik, 23.14% for SSDD, and 39.27% for SORA. Using these threaded measures in the distributed system, combined with using split GO and data clustering algorithms to split input data based on their similarity, reduced the average time more than did the approach of equally dividing input data. Time reduction increased with increasing number of splits. Time reduction percentage was 24.1%, 39.2%, and 66.6% for Threaded SSDD; 33.0%, 78.2%, and 93.1% for Threaded SORA in the case of 2, 3, and 4 slaves, respectively; and 92.04% for Threaded Resnik in the case of four slaves.

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