{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T13:44:35Z","timestamp":1776692675889,"version":"3.51.2"},"posted":{"date-parts":[[2026,4,17]]},"group-title":"Bioinformatics","reference-count":63,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["U54CA268083"],"award-info":[{"award-number":["U54CA268083"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The Johns Hopkins University Oncology Tissue & Imaging Services"},{"DOI":"10.13039\/100017989","name":"Rolfe Pancreatic Cancer Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017989","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Lustgarten Foundation-AACR Career development award for pancreatic cancer research in honor of Ruth Bader Ginsburg"},{"DOI":"10.13039\/100018560","name":"The Joseph C. Monastra Foundation for Pancreatic Cancer Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018560","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The Carl Nale Fund for Pancreatic Cancer Research"},{"name":"The Sol Goldman Pancreatic Cancer Research Center"},{"name":"Susan Wojcicki and Denis Troper"},{"name":"The Carol and Robert Long Fund for Pancreatic Cancer Research"},{"name":"Fight Cancer Stay Positive"},{"name":"The Stringer Foundation"},{"name":"Break Through Cancer Data Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Classical hematoxylin and eosin (H&amp;E) staining enables review of tissue morphology but lacks information regarding the molecular state of cells. Immunohistochemical (IHC) techniques label specific proteins in tissue, allowing differentiation of relevant structures that may go undetectable in H&amp;E. However, the IHC process is complex, expensive, and time-consuming, especially for multiplex IHC (mIHC) limiting its use in large cohorts. Stain conversion of H&amp;E to IHC using generative artificial intelligence models such as generative adversarial networks (GANs) represent one solution to this problem. However, GANs are unstable during out of distribution sampling and are prone to hallucinations or mode collapse, limiting their accuracy in challenging image conversion tasks. To address this, the field has recently turned to diffusion models. Here, we introduce Schr\u00f6dinger-bridge for Multiplex ImmunoLabel Estimation (SMILE). Unlike conventional diffusion models that map from source to target through an intermediate Gaussian noise, Schr\u00f6dinger-bridge diffusion models skip this step and have been shown to better preserve structures during image translation.<\/jats:p>\n                <jats:p>To test the performance of SMILE, we generated a large cohort of high-fidelity H&amp;E-mIHC image pairs from pancreatic organ donors, targeting insulin, glucagon, and CD3. Our dataset well-sampled across type-1 diabetes status, pancreas anatomical location, age, and sex. Using this cohort, we demonstrate the superiority of SMILE compared to GANs via a comprehensive evaluation framework incorporating texture, distribution, and antibody-specific metrics, as well as blinded pathologist reviews. We further confirmed the ability of SMILE to generate accurate mIHC images from H&amp;Es generated at an external site, to perform whole slide image conversion, and to generate realistic three-dimensional maps of the pancreatic islets in non-diabetic, auto-antibody positive, and type-1 diabetic donor tissue. Finally, we performed stain conversion of paired H&amp;E to HER2 and Ki67 images in breast cancer, confirming the superiority of SMILE in diverse stain conversion applications. Collectively, this framework provides a scalable pipeline for high-throughput proteomic inference from archival H&amp;Es, providing transformative potential for pancreatic research and digital pathology.<\/jats:p>","DOI":"10.64898\/2026.04.14.718559","type":"posted-content","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T19:55:15Z","timestamp":1776455715000},"source":"Crossref","is-referenced-by-count":0,"title":["Virtual multiplex staining of the pancreatic islets across type 1 diabetes progression using a Schr\u00f6dinger bridge"],"prefix":"10.64898","author":[{"given":"Yu","family":"Shen","sequence":"first","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Won June","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saurabh","family":"Joshi","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Wen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Swarnagouri","family":"Naganathanhalli","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Beery","sequence":"additional","affiliation":[{"name":"Network for Pancreatic Organ Donors with Diabetes, University of Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casey","family":"Grubel","sequence":"additional","affiliation":[{"name":"Network for Pancreatic Organ Donors with Diabetes, University of Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arrun","family":"Sivasubramanian","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre","family":"Forjaz","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mia P.","family":"Grahn","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucie","family":"Dequiedt","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yichen","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5115-2293","authenticated-orcid":false,"given":"Kyu Sang","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fan","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD"},{"name":"Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian A.","family":"Pedro","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura D.","family":"Wood","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine"},{"name":"Department of Oncology, Johns Hopkins University School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiane","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4554-5672","authenticated-orcid":false,"given":"Ralph H.","family":"Hruban","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine"},{"name":"Department of Oncology, Johns Hopkins University School of 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