{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T14:32:37Z","timestamp":1780410757812,"version":"3.54.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,7,17]],"date-time":"2022-07-17T00:00:00Z","timestamp":1658016000000},"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\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFB0204803"],"award-info":[{"award-number":["2020YFB0204803"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12126610"],"award-info":[{"award-number":["12126610"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangdong Key Field R&D Plan","award":["2019B020228001"],"award-info":[{"award-number":["2019B020228001"]}]},{"name":"Guangdong Key Field R&D Plan","award":["2018B010109006"],"award-info":[{"award-number":["2018B010109006"]}]},{"name":"Introducing Innovative and Entrepreneurial Teams","award":["2016ZT06D211"],"award-info":[{"award-number":["2016ZT06D211"]}]},{"name":"Guangzhou Science and Technology Research Plan","award":["202007030010"],"award-info":[{"award-number":["202007030010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The rapid development of spatial transcriptomics allows the measurement of RNA abundance at a high spatial resolution, making it possible to simultaneously profile gene expression, spatial locations of cells or spots, and the corresponding hematoxylin and eosin-stained histology images. It turns promising to predict gene expression from histology images that are relatively easy and cheap to obtain. For this purpose, several methods are devised, but they have not fully captured the internal relations of the 2D vision features or spatial dependency between spots. Here, we developed Hist2ST, a deep learning-based model to predict RNA-seq expression from histology images. Around each sequenced spot, the corresponding histology image is cropped into an image patch and fed into a convolutional module to extract 2D vision features. Meanwhile, the spatial relations with the whole image and neighbored patches are captured through Transformer and graph neural network modules, respectively. These learned features are then used to predict the gene expression by following the zero-inflated negative binomial distribution. To alleviate the impact by the small spatial transcriptomics data, a self-distillation mechanism is employed for efficient learning of the model. By comprehensive tests on cancer and normal datasets, Hist2ST was shown to outperform existing methods in terms of both gene expression prediction and spatial region identification. Further pathway analyses indicated that our model could reserve biological information. Thus, Hist2ST enables generating spatial transcriptomics data from histology images for elucidating molecular signatures of tissues.<\/jats:p>","DOI":"10.1093\/bib\/bbac297","type":"journal-article","created":{"date-parts":[[2022,7,18]],"date-time":"2022-07-18T11:11:57Z","timestamp":1658142717000},"source":"Crossref","is-referenced-by-count":187,"title":["Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3145-430X","authenticated-orcid":false,"given":"Yuansong","family":"Zeng","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-sen University , Guangzhou 510000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuoyi","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-sen University , Guangzhou 510000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weijiang","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-sen University , Guangzhou 510000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Yin","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Sun Yat-sen University , Guangzhou 510000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchen","family":"Yuan","sequence":"additional","affiliation":[{"name":"Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou 510080, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingling","family":"Li","sequence":"additional","affiliation":[{"name":"Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou 510080, 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