{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T09:43:49Z","timestamp":1781171029427,"version":"3.54.1"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T00:00:00Z","timestamp":1723161600000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institute of General Medical Sciences of the National Institutes of Health","award":["R35GM151089"],"award-info":[{"award-number":["R35GM151089"]}]},{"name":"National Library of Medicine of the National Institutes of Health","award":["R01LM013771"],"award-info":[{"award-number":["R01LM013771"]}]},{"name":"Indiana University Precision Health Initiative"},{"name":"Indiana University Melvin and Bren Simon Comprehensive Cancer Center Support Grant from the National Cancer Institute","award":["P30CA 082709"],"award-info":[{"award-number":["P30CA 082709"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multichannel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multimodal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of gradient-weighted class activation mapping component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within complex cellular interactions.<\/jats:p>","DOI":"10.1093\/bib\/bbae388","type":"journal-article","created":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T20:57:04Z","timestamp":1723237024000},"source":"Crossref","is-referenced-by-count":16,"title":["xSiGra: explainable model for single-cell spatial data elucidation"],"prefix":"10.1093","volume":"25","author":[{"given":"Aishwarya","family":"Budhkar","sequence":"first","affiliation":[{"name":"Luddy School of Informatics , Computing, and Engineering, , 107 S Indiana Ave, Bloomington, IN 47405, United States"},{"name":"Indiana University Bloomington , Computing, and Engineering, , 107 S Indiana Ave, Bloomington, IN 47405, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyang","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Technology, Purdue University , 610 Purdue Mall, West Lafayette, IN 47907, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine , 340 W 10th St, Indianapolis, IN 46202, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7563-9915","authenticated-orcid":false,"given":"Xuhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Luddy School of Informatics , Computing, and Engineering, , 107 S Indiana Ave, Bloomington, IN 47405, United States"},{"name":"Indiana University Bloomington , Computing, and Engineering, , 107 S Indiana Ave, Bloomington, IN 47405, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine , 340 W 10th St, Indianapolis, IN 46202, United States"},{"name":"Gerontology and Geriatric Medicine, Wake Forest School of Medicine , 475 Vine St, Winston-Salem, NC 27101, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4455-5302","authenticated-orcid":false,"given":"Qianqian","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Health Outcomes and Biomedical Informatics , College of Medicine, , Gainesville, FL 32611, United States"},{"name":"University of Florida , College of Medicine, , Gainesville, FL 32611, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,8,9]]},"reference":[{"key":"2024080914364289100_ref1","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","article-title":"Exploring tissue architecture using spatial transcriptomics","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"2024080914364289100_ref2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell\u2013cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat Rev Genet"},{"key":"2024080914364289100_ref3","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1038\/s41467-018-04724-5","article-title":"Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity","volume":"9","author":"Berglund","year":"2018","journal-title":"Nat Commun"},{"key":"2024080914364289100_ref4","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1038\/s41587-022-01483-z","article-title":"High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging","volume":"40","author":"He","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2024080914364289100_ref5","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1017\/S1551929521001346","article-title":"Using MERSCOPE to generate a cell atlas of the mouse brain that includes lowly expressed genes","volume":"29","author":"Emanuel","year":"2021","journal-title":"Microscopy Today"},{"key":"2024080914364289100_ref6","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaa6090","article-title":"RNA imaging. 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