A Novel Algorithm for Local Network Alignment Based on Network Embedding
Networks are widely used in bioinformatics and biomedicine to represent associations across a large class of biological entities. Network alignment refers to the set of approaches that aim to reveal similarities among networks. Local Network Alignment (LNA) algorithms find (relatively small) local r...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | Applied Sciences |
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| Online Access: | https://www.mdpi.com/2076-3417/12/11/5403 |
| _version_ | 1797494269052715008 |
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| author | Pietro Hiram Guzzi Giuseppe Tradigo Pierangelo Veltri |
| author_facet | Pietro Hiram Guzzi Giuseppe Tradigo Pierangelo Veltri |
| author_sort | Pietro Hiram Guzzi |
| collection | DOAJ |
| description | Networks are widely used in bioinformatics and biomedicine to represent associations across a large class of biological entities. Network alignment refers to the set of approaches that aim to reveal similarities among networks. Local Network Alignment (LNA) algorithms find (relatively small) local regions of similarity between two or more networks. Such algorithms are in general based on a set of seed nodes that are used to build the alignment incrementally. A large fraction of LNA algorithms uses a set of vertices based on context information as seed nodes, even if this may cause a bias or a data-circularity problem. Moreover, using topology information to choose seed nodes improves overall alignment. Finally, similarities among nodes can be identified by network embedding methods (or representation learning). Given there are two networks, we propose to use network embedding to capture structural similarity among nodes, which can also be used to improve LNA effectiveness. We present an algorithm and experimental tests on real and syntactic graph data to find LNAs. |
| first_indexed | 2024-03-10T01:31:56Z |
| format | Article |
| id | doaj.art-b7d4f89ddaa84bdd95440efd657a9aba |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-10T01:31:56Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-b7d4f89ddaa84bdd95440efd657a9aba2023-11-23T13:40:59ZengMDPI AGApplied Sciences2076-34172022-05-011211540310.3390/app12115403A Novel Algorithm for Local Network Alignment Based on Network EmbeddingPietro Hiram Guzzi0Giuseppe Tradigo1Pierangelo Veltri2Department of Surgical and Medical Science, University Magna Graecia of Catanzaro, 88100 Catanzaro, ItalyUniversity eCampus Novedrate (CO), 22060 Novedrate, ItalyDepartment of Surgical and Medical Science, University Magna Graecia of Catanzaro, 88100 Catanzaro, ItalyNetworks are widely used in bioinformatics and biomedicine to represent associations across a large class of biological entities. Network alignment refers to the set of approaches that aim to reveal similarities among networks. Local Network Alignment (LNA) algorithms find (relatively small) local regions of similarity between two or more networks. Such algorithms are in general based on a set of seed nodes that are used to build the alignment incrementally. A large fraction of LNA algorithms uses a set of vertices based on context information as seed nodes, even if this may cause a bias or a data-circularity problem. Moreover, using topology information to choose seed nodes improves overall alignment. Finally, similarities among nodes can be identified by network embedding methods (or representation learning). Given there are two networks, we propose to use network embedding to capture structural similarity among nodes, which can also be used to improve LNA effectiveness. We present an algorithm and experimental tests on real and syntactic graph data to find LNAs.https://www.mdpi.com/2076-3417/12/11/5403LNALocal Network Alignmenttopologybiological entities |
| spellingShingle | Pietro Hiram Guzzi Giuseppe Tradigo Pierangelo Veltri A Novel Algorithm for Local Network Alignment Based on Network Embedding Applied Sciences LNA Local Network Alignment topology biological entities |
| title | A Novel Algorithm for Local Network Alignment Based on Network Embedding |
| title_full | A Novel Algorithm for Local Network Alignment Based on Network Embedding |
| title_fullStr | A Novel Algorithm for Local Network Alignment Based on Network Embedding |
| title_full_unstemmed | A Novel Algorithm for Local Network Alignment Based on Network Embedding |
| title_short | A Novel Algorithm for Local Network Alignment Based on Network Embedding |
| title_sort | novel algorithm for local network alignment based on network embedding |
| topic | LNA Local Network Alignment topology biological entities |
| url | https://www.mdpi.com/2076-3417/12/11/5403 |
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