GIMIC - Smoothed Graph-Image representationof Microbiome Samples induce an optimal distance

GIMIC - Smoothed Graph-Image representationof Microbiome Samples induce an optimal distance | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article GIMIC - Smoothed Graph-Image representationof Microbiome Samples induce an optimal distance Oshrit Shtossel, Yoram Louzoun This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4762889/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 09 Oct, 2025 Read the published version in Genome Biology → Version 1 posted 11 You are reading this latest preprint version Abstract An essential tool in microbiome is the distance between samples. This serves to detect groups of similar samples. However, current methods lack interpretability. We have recently shown that combining the cladogram with the abundance of each microbe into a sorted normalized abundance tree can improve the accuracy of Machine Learning and Differential Analysis. We show that smoothing these tree-based images to produce GIMIC (Smoothed Graph IMages of the MICrobiome) leads to an interpretable visualization of microbiome sets and that the difference between the smoothed tree-based images is a better metric than the current state-of-the-art in a wide array of tasks. Smoothing metric dissimilarity image-microbiome 16S rRNA WGS meta-analysis Full Text Additional Declarations No competing interests reported. Supplementary Files SuppMat.pdf Cite Share Download PDF Status: Published Journal Publication published 09 Oct, 2025 Read the published version in Genome Biology → Version 1 posted Editorial decision: Revision requested 19 Feb, 2025 Reviews received at journal 14 Feb, 2025 Reviews received at journal 11 Feb, 2025 Reviewers agreed at journal 20 Jan, 2025 Reviewers agreed at journal 20 Jan, 2025 Reviews received at journal 21 Aug, 2024 Reviewers agreed at journal 13 Aug, 2024 Reviewers invited by journal 13 Aug, 2024 Editor assigned by journal 25 Jul, 2024 Submission checks completed at journal 19 Jul, 2024 First submitted to journal 18 Jul, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4762889","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":335236987,"identity":"21c00eff-99ae-40db-b587-5ec31ec70c30","order_by":0,"name":"Oshrit Shtossel","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA10lEQVRIiWNgGAWjYFACHgaGBBDJ3gDkGFgQqyUBSPIcAGmRIFILyBoGCRDBQIQWfv6zxz48/HFYRj7y+dUNPwokGPjbuxPwapGckZc8IyHhMI/h7Zyymz1Ah0mcObsBrxaDGzzGQL+k8RjOzkm7wQPUYiCRS0DL+TNQLTPPpN38Q5SWAzkgLTY88hLsx24TZYvkDJCWNBseA54cttsyBhI8BP3Cz3/GmPGHjYS9fPvxZzff/LGR42/vxa8FyYU8BiCahzjlICDfwP6AeNWjYBSMglEwogAA9ApCGLw5WBUAAAAASUVORK5CYII=","orcid":"","institution":"Bar-Ilan University","correspondingAuthor":true,"prefix":"","firstName":"Oshrit","middleName":"","lastName":"Shtossel","suffix":""},{"id":335236988,"identity":"9ac869a5-32f0-449b-9665-994eb3cd26cd","order_by":1,"name":"Yoram Louzoun","email":"","orcid":"","institution":"Bar-Ilan University","correspondingAuthor":false,"prefix":"","firstName":"Yoram","middleName":"","lastName":"Louzoun","suffix":""}],"badges":[],"createdAt":"2024-07-18 13:17:30","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4762889/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4762889/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s13059-025-03822-0","type":"published","date":"2025-10-09T15:56:50+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":93419407,"identity":"ac23afe1-0bee-4b4c-a858-d716e4d56bf1","added_by":"auto","created_at":"2025-10-13 15:59:37","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":9614407,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscriptfiles.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4762889/v1_covered_7f922204-ac3a-4f73-90a5-328c07c4267c.pdf"},{"id":62399602,"identity":"f83eb463-5376-42c4-bf59-927c0dd5904f","added_by":"auto","created_at":"2024-08-13 18:28:33","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":8708110,"visible":true,"origin":"","legend":"","description":"","filename":"SuppMat.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4762889/v1/f6cf3887cb236250751f101d.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"GIMIC - Smoothed Graph-Image representationof Microbiome Samples induce an optimal distance","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"genome-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gbio","sideBox":"Learn more about [Genome Biology](https://genomebiology.biomedcentral.com/)","snPcode":"13059","submissionUrl":"https://submission.springernature.com/new-submission/13059/3","title":"Genome Biology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Smoothing, metric, dissimilarity, image-microbiome, 16S rRNA, WGS, meta-analysis","lastPublishedDoi":"10.21203/rs.3.rs-4762889/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4762889/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"An essential tool in microbiome is the distance between samples. 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