{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/exemplar-guided-deep-neural-network-for","title":"Exemplar Guided Deep Neural Network for Spatial Transcriptomics Analysis of Gene Expression Prediction","arxiv_id":"2210.16721","date":"2022-10-30","proceeding":null,"authors":["Yan Yang","Md Zakir Hossain","Eric A Stone","Shafin Rahman"],"abstract":"Spatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper proposes an Exemplar Guided Network (EGN) to accurately and efficiently predict gene expression directly from each window of a tissue slide image. We apply exemplar learning to dynamically boost gene expression prediction from nearest/similar exemplars of a given tissue slide image window. Our EGN framework composes of three main components: 1) an extractor to structure a representation space for unsupervised exemplar retrievals; 2) a vision transformer (ViT) backbone to progressively extract representations of the input window; and 3) an Exemplar Bridging (EB) block to adaptively revise the intermediate ViT representations by using the nearest exemplars. Finally, we complete the gene expression prediction task with a simple attention-based prediction block. Experiments on standard benchmark datasets indicate the superiority of our approach when comparing with the past state-of-the-art (SOTA) methods.","url_abs":"https://arxiv.org/abs/2210.16721v1","url_pdf":"https://arxiv.org/pdf/2210.16721v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"exemplar-guided-deep-neural-network-for","repo_url":"https://github.com/yan98/egn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"prediction","task_name":"Prediction"}],"methods":[{"method_slug":"attention","method_name":"Attention"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"vision-transformer","method_name":"Vision Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2210.16721","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}