Recognition of Gene Names from Gene Pathway Figures Using Siamese Network

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Gene Pathway Figures Using Siamese Network</title> <meta name="description" content="Recognition of Gene Names from Gene Pathway Figures Using Siamese Network"> <meta name="keywords" content="Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group."> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <meta name="citation_title" content="Recognition of Gene Names from Gene Pathway Figures Using Siamese Network"> <meta name="citation_author" content="Muhammad Azam"> <meta name="citation_author" content="Micheal Olaolu Arowolo"> <meta name="citation_author" content="Fei He"> <meta name="citation_author" content="Mihail Popescu"> <meta name="citation_author" content="Dong Xu"> <meta name="citation_publication_date" content="2023/05/23"> <meta name="citation_journal_title" content="International Journal of Bioengineering and Life 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href="https://publications.waset.org/search?q=Muhammad%20Azam">Muhammad Azam</a>, <a href="https://publications.waset.org/search?q=Micheal%20Olaolu%20Arowolo"> Micheal Olaolu Arowolo</a>, <a href="https://publications.waset.org/search?q=Fei%20He"> Fei He</a>, <a href="https://publications.waset.org/search?q=Mihail%20Popescu"> Mihail Popescu</a>, <a href="https://publications.waset.org/search?q=Dong%20Xu"> Dong Xu</a> </p> <p class="card-text"><strong>Abstract:</strong></p> <p>The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.</p> <iframe src="https://publications.waset.org/10013091.pdf" style="width:100%; height:400px;" frameborder="0"></iframe> <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/search?q=Biological%20pathway" title="Biological pathway">Biological pathway</a>, <a href="https://publications.waset.org/search?q=image%20understanding" title=" image understanding"> image understanding</a>, <a href="https://publications.waset.org/search?q=gene%20name%20recognition" title=" gene name recognition"> gene name recognition</a>, <a href="https://publications.waset.org/search?q=object%20detection" title=" object detection"> object detection</a>, <a href="https://publications.waset.org/search?q=Siamese%20network" title=" Siamese network"> Siamese network</a>, <a href="https://publications.waset.org/search?q=Visual%20Geometry%20Group." title=" Visual Geometry Group."> Visual Geometry Group.</a> </p> <a href="https://publications.waset.org/10013091/recognition-of-gene-names-from-gene-pathway-figures-using-siamese-network" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/10013091/apa" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">APA</a> <a href="https://publications.waset.org/10013091/bibtex" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">BibTeX</a> <a href="https://publications.waset.org/10013091/chicago" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">Chicago</a> <a href="https://publications.waset.org/10013091/endnote" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">EndNote</a> <a href="https://publications.waset.org/10013091/harvard" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">Harvard</a> <a href="https://publications.waset.org/10013091/json" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">JSON</a> <a href="https://publications.waset.org/10013091/mla" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">MLA</a> <a href="https://publications.waset.org/10013091/ris" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">RIS</a> <a href="https://publications.waset.org/10013091/xml" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">XML</a> <a href="https://publications.waset.org/10013091/iso690" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">ISO 690</a> <a href="https://publications.waset.org/10013091.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">676</span> </span> <p class="card-text"><strong>References:</strong></p> <br>[1] D. 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Recognition of Gene Names from Gene Pathway Figures Using Siamese Network