scholarly journals An Efficient Parallelized Ontology Network-Based Semantic Similarity Measure for Big Biomedical Document Clustering

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Meijing Li ◽  
Tianjie Chen ◽  
Keun Ho Ryu ◽  
Cheng Hao Jin
Keyword(s):  
Semantic Similarity ◽  
Clustering Algorithms ◽  
Semantic Features ◽  
Text Data ◽  
Semantic Similarity Measure ◽  
Document Similarity ◽  
Hadoop Mapreduce ◽  
Semantic Mining ◽  
Semantic Similarity Measurement ◽  
Open Datasets

Semantic mining is always a challenge for big biomedical text data. Ontology has been widely proved and used to extract semantic information. However, the process of ontology-based semantic similarity calculation is so complex that it cannot measure the similarity for big text data. To solve this problem, we propose a parallelized semantic similarity measurement method based on Hadoop MapReduce for big text data. At first, we preprocess and extract the semantic features from documents. Then, we calculate the document semantic similarity based on ontology network structure under MapReduce framework. Finally, based on the generated semantic document similarity, document clusters are generated via clustering algorithms. To validate the effectiveness, we use two kinds of open datasets. The experimental results show that the traditional methods can hardly work for more than ten thousand biomedical documents. The proposed method keeps efficient and accurate for big dataset and is of high parallelism and scalability.

scholarly journals A state-of-the-art survey on semantic similarity for document clustering using GloVe and density-based algorithms

2021 ◽  
Vol 22 (1) ◽  
pp. 552
Author(s):  
Shapol M. Mohammed ◽  
Karwan Jacksi ◽  
Subhi R. M. Zeebaree
Keyword(s):  
Semantic Similarity ◽  
State Of The Art ◽  
Clustering Algorithms ◽  
Document Clustering ◽  
Accuracy Evaluation ◽  
Similar Data ◽  
Document Similarity ◽  
Density Based Clustering ◽  
Data Points ◽  
The Common

<p><span>Semantic similarity is the process of identifying relevant data semantically. The traditional way of identifying document similarity is by using synonymous keywords and syntactician. In comparison, semantic similarity is to find similar data using meaning of words and semantics. Clustering is a concept of grouping objects that have the same features and properties as a cluster and separate from those objects that have different features and properties. In semantic document clustering, documents are clustered using semantic similarity techniques with similarity measurements. One of the common techniques to cluster documents is the density-based clustering algorithms using the density of data points as a main strategic to measure the similarity between them. In this paper, a state-of-the-art survey is presented to analyze the density-based algorithms for clustering documents. Furthermore, the similarity and evaluation measures are investigated with the selected algorithms to grasp the common ones. The delivered review revealed that the most used density-based algorithms in document clustering are DBSCAN and DPC. The most effective similarity measurement has been used with density-based algorithms, specifically DBSCAN and DPC, is Cosine similarity with F-measure for performance and accuracy evaluation.</span></p>

An Approach of Semantic Similarity Measure between Documents Based on Big Data

2016 ◽  
Vol 6 (5) ◽  
pp. 2454 ◽  
Author(s):  
Mohammed Erritali ◽  
Abderrahim Beni-Hssane ◽  
Marouane Birjali ◽  
Youness Madani
Keyword(s):  
Big Data ◽  
Semantic Similarity ◽  
Retrieval System ◽  
Programming Model ◽  
State Of The Art ◽  
Distributed Processing ◽  
Similarity Measures ◽  
The State ◽  
Semantic Similarity Measure ◽  
Document Similarity

<p>Semantic indexing and document similarity is an important information retrieval system problem in Big Data with broad applications. In this paper, we investigate MapReduce programming model as a specific framework for managing distributed processing in a large of amount documents. Then we study the state of the art of different approaches for computing the similarity of documents. Finally, we propose our approach of semantic similarity measures using WordNet as an external network semantic resource. For evaluation, we compare the proposed approach with other approaches previously presented by using our new MapReduce algorithm. Experimental results review that our proposed approach outperforms the state of the art ones on running time performance and increases the measurement of semantic similarity.</p>

scholarly journals An Approach of Semantic Similarity Measure between Documents Based on Big Data

2016 ◽  
Vol 6 (5) ◽  
pp. 2454 ◽  
Author(s):  
Mohammed Erritali ◽  
Abderrahim Beni-Hssane ◽  
Marouane Birjali ◽  
Youness Madani
Keyword(s):  
Big Data ◽  
Semantic Similarity ◽  
Retrieval System ◽  
Programming Model ◽  
State Of The Art ◽  
Distributed Processing ◽  
Similarity Measures ◽  
The State ◽  
Semantic Similarity Measure ◽  
Document Similarity

<p>Semantic indexing and document similarity is an important information retrieval system problem in Big Data with broad applications. In this paper, we investigate MapReduce programming model as a specific framework for managing distributed processing in a large of amount documents. Then we study the state of the art of different approaches for computing the similarity of documents. Finally, we propose our approach of semantic similarity measures using WordNet as an external network semantic resource. For evaluation, we compare the proposed approach with other approaches previously presented by using our new MapReduce algorithm. Experimental results review that our proposed approach outperforms the state of the art ones on running time performance and increases the measurement of semantic similarity.</p>

Pembobotan Berdasarkan Tingkat Kesamaan Semantik pada Metode Fuzzy Semi-Supervised Co-Clustering untuk Pengelompokkan Dokumen Teks

2014 ◽  
Vol 6 (2) ◽  
pp. 46-51
Author(s):  
Galang Amanda Dwi P. ◽  
Gregorius Edwadr ◽  
Agus Zainal Arifin
Keyword(s):  
Supervised Learning ◽  
Semantic Similarity ◽  
The Other ◽  
Classification Result ◽  
Document Similarity ◽  
The Matrix ◽  
Index Terms ◽  
Membership Value ◽  
Degree Of Similarity

Nowadays, a large number of information can not be reached by the reader because of the misclassification of text-based documents. The misclassified data can also make the readers obtain the wrong information. The method which is proposed by this paper is aiming to classify the documents into the correct group.  Each document will have a membership value in several different classes. The method will be used to find the degree of similarity between the two documents is the semantic similarity. In fact, there is no document that doesn’t have a relationship with the other but their relationship might be close to 0. This method calculates the similarity between two documents by taking into account the level of similarity of words and their synonyms. After all inter-document similarity values obtained, a matrix will be created. The matrix is then used as a semi-supervised factor. The output of this method is the value of the membership of each document, which must be one of the greatest membership value for each document which indicates where the documents are grouped. Classification result computed by the method shows a good value which is 90 %. Index Terms - Fuzzy co-clustering, Heuristic, Semantica Similiarity, Semi-supervised learning.

A Semantic Similarity Measure between Ontological Concepts

2012 ◽  
Vol 38 (2) ◽  
pp. 229-235 ◽  
Author(s):  
Wen-Qing LI ◽  
Xin SUN ◽  
Chang-You ZHANG ◽  
Ye FENG
Keyword(s):  
Semantic Similarity ◽  
Similarity Measure ◽  
Semantic Similarity Measure

DISTANCE-WISE PATHWAY DISCOVERY FROM PROTEIN–PROTEIN INTERACTION NETWORKS WEIGHTED BY SEMANTIC SIMILARITY

2014 ◽  
Vol 12 (01) ◽  
pp. 1450004 ◽  
Author(s):  
SLAVKA JAROMERSKA ◽  
PETR PRAUS ◽  
YOUNG-RAE CHO
Keyword(s):  
Signaling Pathways ◽  
Semantic Similarity ◽  
Protein Interaction ◽  
Protein Pair ◽  
Semantic Analysis ◽  
Topological Analysis ◽  
Cellular Mechanisms ◽  
Semantic Similarity Measure ◽  
Protein Protein Interaction ◽  
Ppi Networks

Reconstruction of signaling pathways is crucial for understanding cellular mechanisms. A pathway is represented as a path of a signaling cascade involving a series of proteins to perform a particular function. Since a protein pair involved in signaling and response have a strong interaction, putative pathways can be detected from protein–protein interaction (PPI) networks. However, predicting directed pathways from the undirected genome-wide PPI networks has been challenging. We present a novel computational algorithm to efficiently predict signaling pathways from PPI networks given a starting protein and an ending protein. Our approach integrates topological analysis of PPI networks and semantic analysis of PPIs using Gene Ontology data. An advanced semantic similarity measure is used for weighting each interacting protein pair. Our distance-wise algorithm iteratively selects an adjacent protein from a PPI network to build a pathway based on a distance condition. On each iteration, the strength of a hypothetical path passing through a candidate edge is estimated by a local heuristic. We evaluate the performance by comparing the resultant paths to known signaling pathways on yeast. The results show that our approach has higher accuracy and efficiency than previous methods.

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