Virtual Cell Models Leveraging Artificial Intelligence

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</div> </div> </div> </div> </header> <main id="content" role="main" class="content-wrapper with-subnav ">  <div class="search-overlay "></div> <div class="dimmed-overlay"></div> <section class="section--alert alert-page section--border-bottom section--" data-id="30718" closable-alert-page> <div class="alert"> <a href="https://chanzuckerberg.com/rfa/ai-computing-gpu/" title="Scale and accelerate science using AI on CZI’s high-performance computing cluster." class="alert__link" aria-label="Scale and accelerate science using AI on CZI’s high-performance computing cluster." target="_self"></a> <p class="t-h6--roman">Scale and accelerate science using AI on CZI’s high-performance computing cluster.</p> <a href="https://chanzuckerberg.com/rfa/ai-computing-gpu/" target="_self" class="button-arrow button-arrow--" title="" aria-label=""> <div class="button-cta__arrow cta-arrow cta-arrow--"> <div class="cta-arrow__bkg"></div> </div> </a> <div class=" mobile-only button-cta__arrow cta-arrow 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We believe this effort will deepen our understanding of human biology at a molecular level — bringing scientists closer to curing, preventing or managing all diseases by the end of this century.</p> <p class="t-body--medium">To enable this work, we’re building a platform where biologists and machine learning researchers can more easily access curated, large AI models of cell biology and the datasets they were built on. This lowers the barriers for biologists to use AI for specific biological tasks and allows ML/AI researchers to rapidly iterate and improve the quality, utility and performance of models, which will, in turn, speed up the process of science.</p> <p class="t-body--medium">We’re prototyping in the open and the platform is now available in early access for the scientific community.</p> <a class="cta-square " href="https://virtualcellmodels.cziscience.com/?utm_source=czi&utm_campaign=MVP_launch&utm_medium=website" target="_blank"> <div class="cta-square__text">Visit the Platform</div> </a> </div> </div> </div> <div class="hero__wrapper section--border-bottom"> <div class="hero__block--img "> <div class="hero__image hero__image--row-first frame frame--red"> <div class="fit-photo fit-photo "> <img src="https://chanzuckerberg.com/wp-content/uploads/2024/03/illustration-of-a-cell-on-a-computer-screen.jpg" alt="A black computer illustration with a pink cell on the screen." object-fit-polyfill loading="lazy" /> </div> </div> </div> </div> </section> </div> <div style="position: relative;" fixed-button-section> <div class="sticky-back mobile-only" fixed-button data-offset="111"> <a class="sticky-back-btn" href="#introduction">Back to Top <svg xmlns="http://www.w3.org/2000/svg" width="12" height="9" viewBox="0 0 12 9" fill="none"> <path d="M0.248535 8.63574L11.3596 8.63574L5.80409 0.635741L0.248535 8.63574Z" fill="#FF414B"/> </svg> </a> </div> <div class="section--connected-illustrations-tablet section--padding-b-4 section--padding-t-4"> <div class="thumbnail-list__header"> <div class="hero-text hero-text--white-bg hero-text--small-title hero-text--left"> <div class="hero-text__container"> <h2 class="hero-text__title color--black"> Our Approach </h2> </div> </div> </div> <div class="connected-illustrations__columns"> <div class="connected-illustrations__desktop-icon above-tablet" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/03/approach-icons.png)"></div> <div class="connected-illustrations__column"> <div class="connected-illustrations__icon-box"> <h3 class="t-h5--semibold">Biological Data</h3> <div class="connected-illustrations__icon desktop-only tablet-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/biological-data-models-applications.png)"></div> <div class="connected-illustrations__icon mobile-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/biological-data-illustration.png)"></div> </div> <div class="connected-illustrations__single-content t-body--large"> <p>Building virtual cells will require vast amounts of diverse and multimodal biological data. CZI supports these datasets by building open source software tools like <a href="https://cellxgene.cziscience.com/" target="_blank" rel="noopener">Chan Zuckerberg CELLxGENE</a> (CZ CELLxGENE) to make machine-learning-ready, high-quality data more accessible for scientific research, <a href="https://chanzuckerberg.com/science/programs-resources/cell-science/" target="_blank" rel="noopener">funding single-cell data generation</a>, and <a href="https://www.czbiohub.org/" target="_blank" rel="noopener">creating scientific institutes</a> that also generate data to advance cell biology.</p> </div> </div> <div class="connected-illustrations__column"> <div class="connected-illustrations__icon-box"> <h3 class="t-h5--semibold">Models & Applications</h3> <div class="connected-illustrations__icon mobile-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/models-applications-illustration.png)"></div> </div> <div class="connected-illustrations__single-content t-body--large"> <p>Our science technology team will partner with leading AI experts and academic researchers to build models that will help unlock the mysteries of cells and how cells interact within systems. These models and their outputs will be openly accessible to the scientific community through a <a href="https://virtualcellmodels.cziscience.com/?utm_source=czi&utm_campaign=MVP_launch&utm_medium=website" target="_blank" rel="noopener">centralized platform</a>.</p> </div> </div> <div class="connected-illustrations__column"> <div class="connected-illustrations__icon-box"> <h3 class="t-h5--semibold">Compute Infrastructure</h3> <div class="connected-illustrations__icon desktop-only tablet-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/compute-infrastructure-collaborative-open-science.png)"></div> <div class="connected-illustrations__icon mobile-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/compute-infrastructure-illustration.png)"></div> </div> <div class="connected-illustrations__single-content t-body--large"> <p>Training AI on enormous amounts of biological data will require a high-powered computing system. We’re <a href="https://chanzuckerberg.com/newsroom/czscience-builds-ai-gpu-cluster-predictive-cell-models/" target="_blank" rel="noopener">building and funding</a> one of the largest computing systems for nonprofit life science research, which will power the next generation of AI modeling for cell biology.</p> </div> </div> <div class="connected-illustrations__column"> <div class="connected-illustrations__icon-box"> <h3 class="t-h5--semibold">Collaboration</h3> <div class="connected-illustrations__icon mobile-only" style="background-image: url(https://chanzuckerberg.com/wp-content/uploads/2024/12/collaborative-open-science-illustration.png)"></div> </div> <div class="connected-illustrations__single-content t-body--large"> <p>Enabling AI at scale for research will require close collaboration with the scientific community. With our <a href="https://chanzuckerberg.com/science/programs-resources/" target="_blank" rel="noopener">network of grantees</a> and collaborative <a href="https://www.czbiohub.org/" target="_blank" rel="noopener">research institutes</a>, we have a history of bringing together experts across disciplines to pursue some of the toughest, riskiest scientific challenges that can’t be done elsewhere. We’re also committed to making data, models and applications open source for research.</p> </div> </div> </div> </div> <section class="section--focus-areas"> <img class="focus-areas-cols-bg desktop-only" src="https://chanzuckerberg.com/wp-content/uploads/2024/12/initial-research-areas-bg-scaled.jpg" alt=""> <h2 class="t-h3--semibold color--black">Initial Research Areas</h2> <div class="focus-areas-cols"> <div class="focus-areas-col theme-light"> <figure> <picture> <source media="(max-width: 768px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/visual-representation-of-cell-embeddings-mobile.jpg"> <source media="(min-width: 769px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/visual-representation-of-cell-embeddings.jpg"> <img src="https://chanzuckerberg.com/wp-content/uploads/2024/12/visual-representation-of-cell-embeddings.jpg" alt="A cluster of multi-colored spots forming a misshapen circle." /> </picture> <figcaption> <span>Visual representation of universal cell embeddings. Photograph courtesy of Leskovec Lab</span> </figcaption> </figure> <div class="focus-areas-col__text-wrap"> <h3 class="t-h6--semibold">scGenePT</h3> <p class="focus-areas-col__subtitle t-body--medium">Model Developer: Chan Zuckerberg Initiative</p> <div class="focus-areas-col__copy t-body--medium"> <p>scGenePT is a collection of single-cell models for perturbation prediction. It leverages the scGPT foundation model for scRNAseq data by injecting language embeddings at the gene level into the model architecture. The language gene embeddings are obtained by embedding gene-level information from different knowledge sources using LLMs. The knowledge sources used include NCBI gene descriptions, UniProt protein summaries for protein-coding genes — as inspired by the genePT approach — and GO (Gene Ontology) Gene Molecular Annotations, across three different axes: molecular function, biological process and cellular component.</p> </div> <div class="focus-areas-col__links t-body--medium"> <a href="https://www.biorxiv.org/content/10.1101/2024.10.23.619972v1.full" target="_blank"> Read the Preprint </a> <a href="https://virtualcellmodels.cziscience.com/model/01936eb7-dba3-7f2e-b71a-463a7b173120?utm_source=czi&utm_campaign=MVP_launch&utm_medium=website" target="_blank"> View Model Details </a> </div> </div> </div> <div class="focus-areas-col theme-dark"> <figure> <picture> <source media="(max-width: 768px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/virtual-images-of-proteins-expressions-over-pre-existing-reference-markers-mobile.jpg"> <source media="(min-width: 769px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/virtual-images-of-proteins-expressions-over-pre-existing-reference-markers.png"> <img src="https://chanzuckerberg.com/wp-content/uploads/2024/12/virtual-images-of-proteins-expressions-over-pre-existing-reference-markers.png" alt="An irregular red and green shape with blue ovals throughout, taking up most of a black background." /> </picture> <figcaption> <span>Visual representation of protein expressions over pre-existing reference markers. | Photograph courtesy of Emma Lundberg, Human Protein Atlas</span> </figcaption> </figure> <div class="focus-areas-col__text-wrap"> <h3 class="t-h6--semibold">SubCell</h3> <p class="focus-areas-col__subtitle t-body--medium">Model Developer: Ankit Gupta, The Lundberg Lab (Stanford University) and Chan Zuckerberg Initiative</p> <div class="focus-areas-col__copy t-body--medium"> <p><span>The SubCell models are Vision Transformer or ViT models pre-trained on the single-cell images of the Human Protein Atlas dataset containing protein expression and spatiotemporal distribution of more than 13,000 genes in 37 cell lines. The models generate feature embeddings that encode the protein localization patterns in the immunofluorescence images and can be used in downstream tasks such as protein localization classification or morphology-based profiling of the cells. </span></p> </div> <div class="focus-areas-col__links t-body--medium"> <a href="https://www.biorxiv.org/content/10.1101/2024.12.06.627299v1" target="_blank"> Read the preprint </a> <a href="https://virtualcellmodels.cziscience.com/model/0193323e-ebd5-727c-bb32-87ed8f737213?utm_source=czi&utm_campaign=MVP_launch&utm_medium=website" target="_blank"> View model details </a> </div> </div> </div> </div> <div class="focus-areas-sign-up" id="sign-up"> <div class="inline-sign-up "> <div class="inline-sign-up__copy"> <div class="t-smallcaps-plain--med">Sign up for updates</div> <p>Join our mailing list to stay updated on the latest virtual cell news, collaboration opportunities, and more. You can unsubscribe at any time.</p> </div> <p id="hubspot-inline-signup"><em>Sorry, marketing cookies are required to view this form.</em></p> <script> window.addEventListener('hubspotLoaded', () => { hbspt.forms.create({ region: "na1", portalId: "7272273", formId: "4c2f85ee-bb76-418e-aced-80b5880863c1", formInstanceId: "2" }); document.getElementById('hubspot-inline-signup').remove(); }); </script> </div> <img class="mobile-only" src="https://chanzuckerberg.com/wp-content/themes/czi/img/virtual-cells-form-mobile.png" alt=""> </div> </section> <section class="section--image-text-split section--image-text-split--inverted section--image-text-split--compact section--border-bottom " id=""> <div class="image-text-split__background"></div> <div class="image-text-split__image"> <div class="image-text-split__image-inner "> <div class="fit-photo fit-photo "> <img src="https://chanzuckerberg.com/wp-content/uploads/2024/03/AI-residents-at-CZI.jpg" alt="A group of individuals standing together at an office. Most wear red lanyards and an art installation is in the background." object-fit-polyfill loading="lazy" /> <div class="caption--overlay t-caption "></div> <figcaption class="caption t-caption "> AI Residents at CZI | Photograph courtesy of Donghui Li</figcaption> </div> <div class="caption--overlay t-caption is-left color--white "></div> <figcaption class="caption t-caption is-left color--white "> AI Residents at CZI | Photograph courtesy of Donghui Li</figcaption> </div> </div> <div class="image-text-split__text"> <div class="content-block content-block--demo-class-content" > <h2 class="content-block__heading t-h2--semibold color--black">Building Virtual Cells With the Scientific Community</h2> <div class="content-block__body t-body--large"> <p class="content-block__text">We’re introducing a new AI residency program to coalesce AI/machine-learning leaders from the academic research community. In collaboration with CZI scientists and engineers, the projects spearheaded by these residents will lay the foundation for virtual cell models that will allow researchers to explore the molecular underpinnings of human health and disease.</p> <p class="content-block__text">We’re launching the first phase of the AI residency program with current collaborators and partners. <a href="#sign-up">Join our mailing list</a> to stay updated on the latest virtual cell news, collaboration opportunities and more. </p> </div> </div> </div> </section> <section class="section--cards-grid section--padding-b-4 section--padding-t-1 carousel cards-grid--carousel cards-grid--latest cards-grid--highlights-carousel" carousel-container data-number-moving="1" data-stop-offset-mobile="0" data-stop-offset="2" id="" > <header class="cards-grid--latest__header cards-grid--latest__header--has-body"> <h2 class="t-h2--semibold color--black">News & Stories</h2> <p class="t-body--semibold">Interested in learning more about our work in AI? Get the latest information from the links below.</p> </header> <div class="carousel__slider highlights-carousel section-- " carousel-slider> <div class="cards-section cards-section--latest cards-section--3-cols section--"> <div class="card background-image-card card--align-top card--align-center card--button-bottom list__row is-active" carousel-item card> <div class="card__wrapper"> <a href="https://chanzuckerberg.com/blog/scientific-milestones-learnings-2024/" class="card__link" title="Watch Video - Priscilla Chan Discusses CZI’s Scientific Milestones" aria-labelledby="card-title-33814"></a> <div class="card__background "> <div class="fit-photo fit-photo "> <picture> <source media="(max-width: 768px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2025/01/25_0113-CZI-Priscilla-Chan-Discusses-CZIs-Scientific-Milestones-Mobile-BLANK.png"> <source media="(min-width: 769px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2025/01/25_0113-CZI-Priscilla-Chan-Discusses-CZIs-Scientific-Milestones-Desktop-BLANK.png"> <img src="https://chanzuckerberg.com/wp-content/uploads/2025/01/25_0113-CZI-Priscilla-Chan-Discusses-CZIs-Scientific-Milestones-Desktop-BLANK.png" alt="Priscilla Chan engaging in a discussion with Patricia Brennan and Shana Kelley at a table, against a blue background." object-fit-polyfill loading="lazy" /> </picture> </div> </div> <div class="card__container"> <div class="card__surtitle t-category-label background--green color--white">Science & Technology</div> <div class="card__title t-h4--bold color--black" id="card-title-33814">Priscilla Chan Discusses CZI’s Scientific Milestones</div> <a href="https://chanzuckerberg.com/blog/scientific-milestones-learnings-2024/" target="_self" class="button-cta button-cta-- button-cta--light-fill " title="Watch Video" aria-label="" > <div class="button-cta__text " >Watch Video</div> <div class="button-cta__arrow cta-arrow cta-arrow--red "> <div class="cta-arrow__bkg"></div> </div> </a> </div> </div> </div> <div class="card background-image-card card--align-top card--align-center card--button-bottom list__row is-active" carousel-item card> <div class="card__wrapper"> <a href="https://chanzuckerberg.com/blog/2024-look-back/" class="card__link" title="Read Story - How AI Shaped a Year of Impact at CZI" aria-labelledby="card-title-33455"></a> <div class="card__background "> <div class="fit-photo fit-photo "> <picture> <source media="(max-width: 768px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/24_1209-CZI-EOY-Moments-Mobile-BLANK.jpg"> <source media="(min-width: 769px)" srcset="https://chanzuckerberg.com/wp-content/uploads/2024/12/24_1209-CZI-EOY-Moments-Desktop-BLANK.jpg"> <img src="https://chanzuckerberg.com/wp-content/uploads/2024/12/24_1209-CZI-EOY-Moments-Desktop-BLANK.jpg" alt="A collage of moments featuring circular cutouts of Sandra Liu Huang in a classroom, researchers in a lab, a close-up of a gloved hand holding a tiny device, Priscilla Chan and Mark Zuckerberg clapping on stage, and Patricia Brennan and Theofanis Karaletsos in a keynote, all set against a vibrant red background with colorful abstract designs." object-fit-polyfill loading="lazy" /> </picture> </div> </div> <div class="card__container"> <div class="card__surtitle t-category-label background--green color--white">2024 Look Back</div> <div class="card__title t-h4--bold color--white" id="card-title-33455">How AI Shaped a Year of Impact at CZI</div> <a href="https://chanzuckerberg.com/blog/2024-look-back/" target="_self" class="button-cta button-cta-- button-cta--light-fill " title="Read Story" aria-label="" > <div class="button-cta__text " >Read Story</div> <div class="button-cta__arrow cta-arrow cta-arrow--red "> <div class="cta-arrow__bkg"></div> </div> </a> </div> </div> </div> <div class="card background-image-card card--align-top card--align-center card--button-bottom list__row is-active" carousel-item card> <div class="card__wrapper"> <a href="https://chanzuckerberg.com/blog/ai-cell-models-platform-release/" class="card__link" title="Read Story - 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