{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T22:52:23Z","timestamp":1770331943146,"version":"3.49.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:00:00Z","timestamp":1663286400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61725302"],"award-info":[{"award-number":["61725302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62073219"],"award-info":[{"award-number":["62073219"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62272300"],"award-info":[{"award-number":["62272300"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972251"],"award-info":[{"award-number":["61972251"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Guangdong Province of China","award":["2022A1515011436"],"award-info":[{"award-number":["2022A1515011436"]}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["22511104100"],"award-info":[{"award-number":["22511104100"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Recognition of protein subcellular distribution patterns and identification of location biomarker proteins in cancer tissues are important for understanding protein functions and related diseases. Immunohistochemical (IHC) images enable visualizing the distribution of proteins at the tissue level, providing an important resource for the protein localization studies. In the past decades, several image-based protein subcellular location prediction methods have been developed, but the prediction accuracies still have much space to improve due to the complexity of protein patterns resulting from multi-label proteins and the variation of location patterns across cell types or states.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose a multi-label multi-instance model based on deep graph convolutional neural networks, GraphLoc, to recognize protein subcellular location patterns. GraphLoc builds a graph of multiple IHC images for one protein, learns protein-level representations by graph convolutions and predicts multi-label information by a dynamic threshold method. Our results show that GraphLoc is a promising model for image-based protein subcellular location prediction with model interpretability. Furthermore, we apply GraphLoc to the identification of candidate location biomarkers and potential members for protein networks. A large portion of the predicted results have supporting evidence from the existing literatures and the new candidates also provide guidance for further experimental screening.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The dataset and code are available at: www.csbio.sjtu.edu.cn\/bioinf\/GraphLoc.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac634","type":"journal-article","created":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T15:30:52Z","timestamp":1663342252000},"page":"4941-4948","source":"Crossref","is-referenced-by-count":8,"title":["GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images"],"prefix":"10.1093","volume":"38","author":[{"given":"Jin-Xian","family":"Hu","sequence":"first","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5720-773X","authenticated-orcid":false,"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Center for Brain-Like Computing and Machine Intelligence, Shanghai Jiao Tong University , Shanghai 200240, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3185-811X","authenticated-orcid":false,"given":"Ying-Ying","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University , Guangzhou 510515, China"},{"name":"Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University , Guangzhou 510515, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4029-3325","authenticated-orcid":false,"given":"Hong-Bin","family":"Shen","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240, China"}]}],"member":"286","published-online":{"date-parts":[[2022,9,16]]},"reference":[{"key":"2022103112485691600_btac634-B1","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.artint.2013.06.003","article-title":"Multiple instance classification: review, taxonomy and comparative study","volume":"201","author":"Amores","year":"2013","journal-title":"Artif. 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