{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,11,8]],"date-time":"2026-11-08T08:47:22Z","timestamp":1794127642205,"version":"4.8.0"},"posted":{"date-parts":[[2025,11,26]]},"group-title":"Bioinformatics","reference-count":116,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T00:00:00Z","timestamp":1764115200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,11,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Biology emerges from interactions across physical scales, where molecular interactions drive cellular states, which in turn orchestrate multicellular tissue functions that collectively define health and disease. However, current computational models are often constrained to single scales in isolation, failing to integrate the biology that emerges from lower to higher levels [1]. Here we present PULSAR (\n                  <jats:bold>P<\/jats:bold>\n                  atient\n                  <jats:bold>U<\/jats:bold>\n                  nderstanding\n                  <jats:bold>L<\/jats:bold>\n                  everaging\n                  <jats:bold>S<\/jats:bold>\n                  ingle-cell univers\n                  <jats:bold>A<\/jats:bold>\n                  l\n                  <jats:bold>R<\/jats:bold>\n                  epresentation), a multi-scale and multicellular foundation model architecture that explicitly enables information flow from genes to cells to multicellular systems. Applied to the human peripheral immune system, PULSAR extracts a unified donor representation that supports rapid disease classification, biomarker prediction, and forecasting of future clinical events, such as Rheumatoid arthritis onset. As a generative model, PULSAR enables the simulation of cytokine perturbation response across physical resolutions, while its interpretability reveals the key cell types driving disease. Overall, PULSAR opens new avenues for precision medicine by enabling computational reasoning that connects molecular biology to clinical phenotypes.\n                <\/jats:p>","DOI":"10.1101\/2025.11.24.685470","type":"posted-content","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T15:50:13Z","timestamp":1764172213000},"source":"Crossref","is-referenced-by-count":11,"title":["PULSAR: a Foundation Model for Multi-scale and Multicellular Biology"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3338-1738","authenticated-orcid":false,"given":"Kuan","family":"Pang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1129-9645","authenticated-orcid":false,"given":"Yanay","family":"Rosen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasia","family":"Kedzierska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3556-8248","authenticated-orcid":false,"given":"Ziyuan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abhejit","family":"Rajagopal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1437-6709","authenticated-orcid":false,"given":"Claire E.","family":"Gustafson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace","family":"Huynh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5411-923X","authenticated-orcid":false,"given":"Jure","family":"Leskovec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025112819001376000_2025.11.24.685470v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.11.015"},{"key":"2025112819001376000_2025.11.24.685470v1.2","first-page":"e27041","article-title":"The human cell atlas","volume":"6","year":"2017","journal-title":"In: elife"},{"issue":"17","key":"2025112819001376000_2025.11.24.685470v1.3","first-page":"4488","article-title":"Spatiotemporal omics for biology and medicine","volume":"187","year":"2024","journal-title":"In: Cell"},{"issue":"7","key":"2025112819001376000_2025.11.24.685470v1.4","first-page":"725","article-title":"Systems immunology: just getting started","volume":"18","year":"2017","journal-title":"In: Nature immunology"},{"key":"2025112819001376000_2025.11.24.685470v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.03.031"},{"issue":"12","key":"2025112819001376000_2025.11.24.685470v1.6","first-page":"602","article-title":"Immunological Genome Project and systems immunology","volume":"34","year":"2013","journal-title":"In: Trends in immunology"},{"issue":"3638","key":"2025112819001376000_2025.11.24.685470v1.7","first-page":"1315","article-title":"Genetic studies on the mixed leukocyte reaction","volume":"145","year":"1964","journal-title":"In: Science"},{"issue":"3","key":"2025112819001376000_2025.11.24.685470v1.8","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.4049\/jimmunol.155.3.1151","article-title":"Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor alpha-chains (CD25). 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