{"id":1822,"date":"2025-07-12T15:56:24","date_gmt":"2025-07-12T15:56:24","guid":{"rendered":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/?p=1822"},"modified":"2025-07-12T15:58:39","modified_gmt":"2025-07-12T15:58:39","slug":"c2s-scale-language-models-for-single-cell-biological-analysis-%f0%9f%94%ac","status":"publish","type":"post","link":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/?p=1822","title":{"rendered":"C2S-Scale: Language Models for Single-Cell Biological Analysis \ud83d\udd2c"},"content":{"rendered":"\n<figure class=\"wp-block-audio\"><audio controls src=\"http:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/C2S-Scale_-Language-Models-for-Single-Cell-Biological-Analysis.mp3\"><\/audio><\/figure>\n\n\n\n<p><\/p>\n\n\n\n<p>PODCAST: explore <strong>Cell2Sentence-Scale (C2S-Scale)<\/strong>, an innovative application of <strong>large language models (LLMs)<\/strong> specifically designed to interpret and analyze <strong>single-cell biological data<\/strong>. The core concept involves transforming complex gene expression profiles of individual cells into <strong>&#8220;cell sentences,&#8221;<\/strong> allowing LLMs to process biological information in a familiar language-based format. This approach facilitates <strong>conversational analysis<\/strong> of biological data, enables the <strong>automatic generation of biological summaries<\/strong>, and demonstrates the potential to <strong>predict cellular responses to perturbations<\/strong>, accelerating fields like drug discovery. The project emphasizes the <strong>scalability of biological LLMs<\/strong> and provides open-source access to models for the research community.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img data-opt-id=264421696  fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"614\" src=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:614\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png\" alt=\"\" class=\"wp-image-1824\" srcset=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:614\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png 1024w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:300\/h:180\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png 300w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:768\/h:460\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png 768w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1536\/h:921\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png 1536w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1920\/h:1151\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-288.png 2048w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>Cell2Sentence models and resources are now available on platforms such as&nbsp;<a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fhuggingface.co%2Fcollections%2Fvandijklab%2Fcell2sentence-models-66d71f690a7b77558a36b9ef\" rel=\"noreferrer noopener\">HuggingFace<\/a>&nbsp;and&nbsp;<a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fgithub.com%2Fvandijklab%2Fcell2sentence\" rel=\"noreferrer noopener\">GitHub<\/a>. We invite you to explore these tools, experiment with your own single-cell data, and see how far we can go when we teach machines to understand the language of life \u2014 one cell at a time.<\/p>\n\n\n\n<p>Acknowledgements<\/p>\n\n\n\n<p><em>Key contributors to this project include: Syed Rizvi<\/em>1,2<em>, Daniel Levine<\/em>2<em>, Aakash Patel<\/em>2<em>, Shiyang Zhang<\/em>2<em>, Eric Wang<\/em>3<em>, Sizhuang He<\/em>2<em>, David Zhang<\/em>2<em>, Cerise Tang<\/em>2<em>, Zhuoyang Lyu<\/em>4<em>, Rayyan Darji<\/em>2<em>, Chang Li<\/em>2<em>, Emily Sun<\/em>2<em>, David Jeong<\/em>2<em>, Lawrence Zhao<\/em>2<em>, Jennifer Kwan<\/em>2<em>, David Braun<\/em>2<em>, Brian Hafler<\/em>2<em>, Jeffrey Ishizuka<\/em>2<em>, Rahul M. Dhodapkar<\/em>5<em>, Hattie Chung<\/em>2<em>, Shekoofeh Azizi<\/em>3<em>, Bryan Perozzi<\/em>1<em>, and David van Dijk<\/em>2<em>.<\/em><\/p>\n\n\n\n<p><em>Affiliations:<\/em><\/p>\n\n\n\n<p><em>Google Research,<\/em><em>Graph Mining Team<\/em><\/p>\n\n\n\n<p><em>Yale University<\/em><\/p>\n\n\n\n<p><em>Google DeepMind<\/em><\/p>\n\n\n\n<p><em>Brown University<\/em><\/p>\n\n\n\n<p><em>University of Southern California<\/em><\/p>\n\n\n\n<p>Labels:&nbsp;<a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fresearch.google%2Fblog%2Flabel%2Fhealth-bioscience\" rel=\"noreferrer noopener\">Health &amp; Bioscience<\/a><\/p>\n\n\n\n<p><a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fresearch.google%2Fblog%2Flabel%2Fhealth-bioscience\" rel=\"noreferrer noopener\">Natural Language Processing<\/a><\/p>\n\n\n\n<p><a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fresearch.google%2Fblog%2Flabel%2Fhealth-bioscience\" rel=\"noreferrer noopener\">Paper<\/a><\/p>\n\n\n\n<p><a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fresearch.google%2Fblog%2Flabel%2Fhealth-bioscience\" rel=\"noreferrer noopener\">GitHub<\/a><\/p>\n\n\n\n<p><a target=\"_blank\" href=\"https:\/\/www.google.com\/url?sa=E&amp;q=https%3A%2F%2Fresearch.google%2Fblog%2Flabel%2Fhealth-bioscience\" rel=\"noreferrer noopener\">HuggingFace<\/a><\/p>\n\n\n\n<p>Natural Language Processing April 2, 2025 ECLeKTic: A novel benchmark for evaluating cross-lingual knowledge transfer in LLMs<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img data-opt-id=570125479  fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"550\" src=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:550\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-289.png\" alt=\"\" class=\"wp-image-1826\" srcset=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:550\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-289.png 1024w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:300\/h:161\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-289.png 300w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:768\/h:413\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-289.png 768w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1200\/h:645\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-289.png 1200w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/www.google.com\/url?sa=i&amp;url=https%3A%2F%2Fwww.hawkdive.com%2Fintroducing-c2s-scale-enabling-dialogue-between-researchers-and-cells%2F&amp;psig=AOvVaw3-iAYEmxVbYcr6H2cDCFeq&amp;ust=1752422140945000&amp;source=images&amp;cd=vfe&amp;opi=89978449&amp;ved=0CBcQjhxqFwoTCMin3qvXt44DFQAAAAAdAAAAABAU\"><img data-opt-id=1966127485  data-opt-src=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:550\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-290.png\"  decoding=\"async\" width=\"1024\" height=\"550\" src=\"data:image/svg+xml,%3Csvg%20viewBox%3D%220%200%201024%20550%22%20width%3D%221024%22%20height%3D%22550%22%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%3E%3Crect%20width%3D%221024%22%20height%3D%22550%22%20fill%3D%22transparent%22%2F%3E%3C%2Fsvg%3E\" alt=\"\" class=\"wp-image-1827\" old-srcset=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:550\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-290.png 1024w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:300\/h:161\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-290.png 300w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:768\/h:412\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-290.png 768w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1440\/h:773\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-290.png 1440w\" \/><\/a><\/figure>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/www.google.com\/url?sa=i&amp;url=https%3A%2F%2Fwww.vandijklab.org%2Fc2s-scale&amp;psig=AOvVaw3-iAYEmxVbYcr6H2cDCFeq&amp;ust=1752422140945000&amp;source=images&amp;cd=vfe&amp;opi=89978449&amp;ved=0CBcQjhxqFwoTCMin3qvXt44DFQAAAAAdAAAAABAd\"><img data-opt-id=760186729  data-opt-src=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:850\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png\"  decoding=\"async\" width=\"1024\" height=\"850\" src=\"data:image/svg+xml,%3Csvg%20viewBox%3D%220%200%201024%20850%22%20width%3D%221024%22%20height%3D%22850%22%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%3E%3Crect%20width%3D%221024%22%20height%3D%22850%22%20fill%3D%22transparent%22%2F%3E%3C%2Fsvg%3E\" alt=\"\" class=\"wp-image-1829\" old-srcset=\"https:\/\/ml6vmqguit1n.i.optimole.com\/w:1024\/h:850\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png 1024w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:300\/h:249\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png 300w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:768\/h:637\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png 768w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1536\/h:1275\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png 1536w, https:\/\/ml6vmqguit1n.i.optimole.com\/w:1920\/h:1593\/q:mauto\/f:best\/https:\/\/172-234-197-23.ip.linodeusercontent.com\/wp-content\/uploads\/2025\/07\/image-291.png 2048w\" \/><\/a><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>PODCAST: explore Cell2Sentence-Scale (C2S-Scale), an innovative application of large language models (LLMs) specifically designed to interpret and analyze single-cell biological data. The core concept involves transforming complex gene expression profiles of individual cells into &#8220;cell sentences,&#8221; allowing LLMs to process biological information in a familiar language-based format. This approach facilitates conversational analysis of biological data,&hellip;&nbsp;<a href=\"https:\/\/172-234-197-23.ip.linodeusercontent.com\/?p=1822\" rel=\"bookmark\"><span class=\"screen-reader-text\">C2S-Scale: Language Models for Single-Cell Biological Analysis \ud83d\udd2c<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":1829,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"categories":[14,7],"tags":[],"class_list":["post-1822","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-podcast","category-the-truben-show"],"_links":{"self":[{"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/posts\/1822","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1822"}],"version-history":[{"count":2,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/posts\/1822\/revisions"}],"predecessor-version":[{"id":1830,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/posts\/1822\/revisions\/1830"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=\/wp\/v2\/media\/1829"}],"wp:attachment":[{"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1822"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1822"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/172-234-197-23.ip.linodeusercontent.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1822"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}