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1.132-3.368.397-.406.89-.717 1.474-.952 1.399-1.136 3.392-2.093 6.122-2.093 2.731 0 4.767.957 6.166 2.093.584.235 1.077.546 1.474.952.85.869 1.132 2.037 1.132 3.368 0 .368-.014.733-.052 1.086.23.462.477 1.088.644 1.517 1.258.364 2.233 1.721 2.605 2.656a.832.832 0 0 1 .053.22v2.869a.641.641 0 0 1-.078.256ZM12.172 11h-.344a4.323 4.323 0 0 1-.355.508C10.703 12.455 9.555 13 7.965 13c-1.725 0-2.989-.359-3.782-1.259a2.005 2.005 0 0 1-.085-.104L4 11.741v6.585c1.435.779 4.514 2.179 8 2.179 3.486 0 6.565-1.4 8-2.179v-6.585l-.098-.104s-.033.045-.085.104c-.793.9-2.057 1.259-3.782 1.259-1.59 0-2.738-.545-3.508-1.492a4.323 4.323 0 0 1-.355-.508h-.016.016Zm.641-2.935c.136 1.057.403 1.913.878 2.497.442.544 1.134.938 2.344.938 1.573 0 2.292-.337 2.657-.751.384-.435.558-1.15.558-2.361 0-1.14-.243-1.847-.705-2.319-.477-.488-1.319-.862-2.824-1.025-1.487-.161-2.192.138-2.533.529-.269.307-.437.808-.438 1.578v.021c0 .265.021.562.063.893Zm-1.626 0c.042-.331.063-.628.063-.894v-.02c-.001-.77-.169-1.271-.438-1.578-.341-.391-1.046-.69-2.533-.529-1.505.163-2.347.537-2.824 1.025-.462.472-.705 1.179-.705 2.319 0 1.211.175 1.926.558 2.361.365.414 1.084.751 2.657.751 1.21 0 1.902-.394 2.344-.938.475-.584.742-1.44.878-2.497Z"></path><path d="M14.5 14.25a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path> </svg> <div> <div class="color-fg-default h4">GitHub Copilot</div> Write better code with AI </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"security","context":"product","tag":"link","label":"security_link_product_navbar"}" href="https://github.com/features/security"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon 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href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2"> Search syntax tips </a> <div class="d-flex flex-1"></div> </div> </div> </div> </div> </modal-dialog></div> </div> <div data-action="click:qbsearch-input#retract" class="dark-backdrop position-fixed" hidden data-target="qbsearch-input.darkBackdrop"></div> <div class="color-fg-default"> <dialog-helper> <dialog data-target="qbsearch-input.feedbackDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="feedback-dialog" aria-modal="true" aria-labelledby="feedback-dialog-title" aria-describedby="feedback-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header"> <div class="Overlay-headerContentWrap"> <div 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method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="NeSMvzW/nzQaqJ3GeK4TX+qhqhvb9iPUV/MBkSIQJx8BrT7FROkrOy5aWQfeBnF5cSpEGNK543XxnvVQjqcrfw==" /> <p>We read every piece of feedback, and take your input very seriously.</p> <textarea name="feedback" class="form-control width-full mb-2" style="height: 120px" id="feedback"></textarea> <input name="include_email" id="include_email" aria-label="Include my email address so I can be contacted" class="form-control mr-2" type="checkbox"> <label for="include_email" style="font-weight: normal">Include my email address so I can be contacted</label> </form></div> </scrollable-region> <div data-view-component="true" class="Overlay-footer Overlay-footer--alignEnd"> <button data-close-dialog-id="feedback-dialog" type="button" data-view-component="true" class="btn"> Cancel </button> <button form="code-search-feedback-form" data-action="click:qbsearch-input#submitFeedback" type="submit" data-view-component="true" class="btn-primary btn"> Submit feedback </button> </div> </dialog></dialog-helper> <custom-scopes data-target="qbsearch-input.customScopesManager"> <dialog-helper> <dialog data-target="custom-scopes.customScopesModalDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="custom-scopes-dialog" aria-modal="true" aria-labelledby="custom-scopes-dialog-title" aria-describedby="custom-scopes-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header Overlay-header--divided"> <div class="Overlay-headerContentWrap"> <div class="Overlay-titleWrap"> <h1 class="Overlay-title " id="custom-scopes-dialog-title"> Saved searches </h1> <h2 id="custom-scopes-dialog-description" class="Overlay-description">Use saved searches to filter your results more quickly</h2> </div> <div class="Overlay-actionWrap"> 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rel=\"nofollow\"\u003e\n \u003cimg src=\"/helicalAI/helical/raw/release/docs/assets/logo_and_text_v2.png\" alt=\"Helical Logo\" width=\"400\" style=\"max-width: 100%;\"\u003e\n \u003c/a\u003e\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eWhat is Helical ?\u003c/h1\u003e\u003ca id=\"user-content-what-is-helical-\" class=\"anchor\" aria-label=\"Permalink: What is Helical ?\" href=\"#what-is-helical-\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eHelical provides a framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eHelical simplifies the entire application lifecycle when building with bio foundation models. You will be able to:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eLeverage the latest bio foundation models through our easy-to-use python package\u003c/li\u003e\n\u003cli\u003eRun example notebooks on key downstream tasks from examples\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eWe will update this repo on a regular basis with new models, benchmarks, modalities and functions - so stay tuned.\nLet’s build the most exciting AI-for-Bio community together!\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstallation\u003c/h2\u003e\u003ca id=\"user-content-installation\" class=\"anchor\" aria-label=\"Permalink: Installation\" href=\"#installation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eWe recommend installing Helical within a conda environment with the commands below (run them in your terminal) - this step is optional:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"conda create --name helical-package python=3.11.8\nconda activate helical-package\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003econda create --name helical-package python=3.11.8\nconda activate helical-package\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo install the latest pip release of our Helical package, you can run the command below:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"pip install helical\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003epip install helical\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo install the latest Helical package, you can run the command below:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"pip install --upgrade git+https://github.com/helicalAI/helical.git\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003epip install --upgrade git+https://github.com/helicalAI/helical.git\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSingularity (Optional)\u003c/h3\u003e\u003ca id=\"user-content-singularity-optional\" class=\"anchor\" aria-label=\"Permalink: Singularity (Optional)\" href=\"#singularity-optional\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you desire to run your code in a singularity file, you can use the \u003ca href=\"/helicalAI/helical/blob/release/singularity.def\"\u003esingularity.def\u003c/a\u003e file and build an apptainer with it:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"apptainer build --sandbox singularity/helical singularity.def\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eapptainer build --sandbox singularity/helical singularity.def\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eand then shell into the sandbox container (use the --nv flag if you have a GPU available):\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"apptainer shell --nv --fakeroot singularity/helical/\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eapptainer shell --nv --fakeroot singularity/helical/\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstallation\u003c/h2\u003e\u003ca id=\"user-content-installation-1\" class=\"anchor\" aria-label=\"Permalink: Installation\" href=\"#installation-1\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRNA models:\u003c/h3\u003e\u003ca id=\"user-content-rna-models\" class=\"anchor\" aria-label=\"Permalink: RNA models:\" href=\"#rna-models\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"https://helical.readthedocs.io/en/latest/docs/Geneformer.html\" rel=\"nofollow\"\u003eGeneformer\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://helical.readthedocs.io/en/latest/docs/scGPT.html\" rel=\"nofollow\"\u003escGPT\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://helical.readthedocs.io/en/latest/docs/UCE.html\" rel=\"nofollow\"\u003eUniversal Cell Embedding (UCE)\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDNA models:\u003c/h3\u003e\u003ca id=\"user-content-dna-models\" class=\"anchor\" aria-label=\"Permalink: DNA models:\" href=\"#dna-models\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"https://helical.readthedocs.io/en/latest/docs/hyena_dna.html\" rel=\"nofollow\"\u003eHyenaDNA\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDemo \u0026amp; Use Cases\u003c/h2\u003e\u003ca id=\"user-content-demo--use-cases\" class=\"anchor\" aria-label=\"Permalink: Demo \u0026amp; Use Cases\" href=\"#demo--use-cases\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eTo run examples, be sure to have installed the Helical package (see Installation) and that it is up-to-date.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eYou can look directly into the example folder above and download the script of your choice, look into our \u003ca href=\"https://helical.readthedocs.io/\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e for step-by-step guides or directly clone the repository using:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/helicalAI/helical.git\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003egit clone https://github.com/helicalAI/helical.git\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eWithin the \u003ccode\u003eexamples/notebooks\u003c/code\u003e folder, open the notebook of your choice. We recommend starting with \u003ccode\u003eQuick-Start-Tutorial.ipynb\u003c/code\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eCurrent Examples:\u003c/h3\u003e\u003ca id=\"user-content-current-examples\" class=\"anchor\" aria-label=\"Permalink: Current Examples:\" href=\"#current-examples\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cmarkdown-accessiblity-table\u003e\u003ctable\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth\u003eExample\u003c/th\u003e\n\u003cth\u003eDescription\u003c/th\u003e\n\u003cth\u003eColab\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"/helicalAI/helical/blob/release/examples/notebooks/Quick-Start-Tutorial.ipynb\"\u003eQuick-Start-Tutorial.ipynb\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eA tutorial to quickly get used to the helical package and environment.\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Quick-Start-Tutorial.ipynb\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667\" alt=\"Open In Colab\" data-canonical-src=\"https://colab.research.google.com/assets/colab-badge.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"/helicalAI/helical/blob/release/examples/notebooks/Geneformer-vs-UCE.ipynb\"\u003eGeneformer-vs-UCE.ipynb\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eZero-Shot Reference Mapping with Geneformer \u0026amp; UCE and compare the outcomes.\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Geneformer-vs-UCE.ipynb\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667\" alt=\"Open In Colab\" data-canonical-src=\"https://colab.research.google.com/assets/colab-badge.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"/helicalAI/helical/blob/release/examples/notebooks/Hyena-DNA-Inference.ipynb\"\u003eHyena-DNA-Inference.ipynb\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eAn example how to do probing with HyenaDNA by training a neural network on 18 downstream classification tasks.\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Hyena-Dna-Inference.ipynb\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667\" alt=\"Open In Colab\" data-canonical-src=\"https://colab.research.google.com/assets/colab-badge.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003e\u003ca href=\"/helicalAI/helical/blob/release/examples/notebooks/Cell-Type-Annotation.ipynb\"\u003eCell-Type-Annotation.ipynb\u003c/a\u003e\u003c/td\u003e\n\u003ctd\u003eAn example how to do probing with scGPT by training a neural network to predict cell type annotations.\u003c/td\u003e\n\u003ctd\u003e\u003ca href=\"https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Type-Annotation.ipynb\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667\" alt=\"Open In Colab\" data-canonical-src=\"https://colab.research.google.com/assets/colab-badge.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eComing Soon\u003c/td\u003e\n\u003ctd\u003eNew models such as SCimilarity, scVI; benchmarking scripts; new use cases; others\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\u003c/markdown-accessiblity-table\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eStuck somewhere ? Other ideas ?\u003c/h2\u003e\u003ca id=\"user-content-stuck-somewhere--other-ideas-\" class=\"anchor\" aria-label=\"Permalink: Stuck somewhere ? Other ideas ?\" href=\"#stuck-somewhere--other-ideas-\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eWe are eager to help you and interact with you. Reach out via \u003ca href=\"mailto:support@helical-ai.com\"\u003esupport@helical-ai.com\u003c/a\u003e.\nYou can also open github issues here.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eWhy should I use Helical \u0026amp; what to expect in the future?\u003c/h2\u003e\u003ca id=\"user-content-why-should-i-use-helical--what-to-expect-in-the-future\" class=\"anchor\" aria-label=\"Permalink: Why should I use Helical \u0026amp; what to expect in the future?\" href=\"#why-should-i-use-helical--what-to-expect-in-the-future\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you are (or plan to) working with bio foundation models s.a. Geneformer or UCE on RNA and DNA data, Helical will be your best buddy! We provide and improve on:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eUp-to-date model library\u003c/li\u003e\n\u003cli\u003eA unified API for all models\u003c/li\u003e\n\u003cli\u003eUser-facing abstractions tailored to computational biologists, researchers \u0026amp; AI developers\u003c/li\u003e\n\u003cli\u003eInnovative use case and application examples and ideas\u003c/li\u003e\n\u003cli\u003eEfficient data processing \u0026amp; code-base\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eWe will continuously upload the latest model, publish benchmarks and make our code more efficient.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eAcknowledgements\u003c/h2\u003e\u003ca id=\"user-content-acknowledgements\" class=\"anchor\" aria-label=\"Permalink: Acknowledgements\" href=\"#acknowledgements\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eA lot of our models have been published by talend authors developing these exciting technologies. We sincerely thank the authors of the following open-source projects:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/bowang-lab/scGPT/\"\u003escGPT\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://huggingface.co/ctheodoris/Geneformer\" rel=\"nofollow\"\u003eGeneformer\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/snap-stanford/UCE\"\u003eUCE\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/HazyResearch/hyena-dna\"\u003eHyenaDNA\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/scverse/anndata\"\u003eanndata\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/scverse/scanpy\"\u003escanpy\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/huggingface/transformers\"\u003etransformers\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/scikit-learn/scikit-learn\"\u003escikit-learn\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eLicenses\u003c/h3\u003e\u003ca id=\"user-content-licenses\" class=\"anchor\" aria-label=\"Permalink: Licenses\" href=\"#licenses\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eYou can find the Licenses for each model implementation in the model repositories:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"/helicalAI/helical/blob/release/helical/models/scgpt/LICENSE\"\u003escGPT\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"/helicalAI/helical/blob/release/helical/models/geneformer/LICENSE\"\u003eGeneformer\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"/helicalAI/helical/blob/release/helical/models/uce/LICENSE\"\u003eUCE\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"/helicalAI/helical/blob/release/helical/models/hyena_dna/LICENSE\"\u003eHyenaDNA\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch2 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eCitation\u003c/h2\u003e\u003ca id=\"user-content-citation\" class=\"anchor\" aria-label=\"Permalink: Citation\" href=\"#citation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePlease use this BibTeX to cite this repository in your publications:\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"@software{allard_2024_13135902,\n author = {Helical Team},\n title = {helicalAI/helical: v0.0.1-alpha3},\n month = jul,\n year = 2024,\n publisher = {Zenodo},\n version = {0.0.1a5},\n doi = {10.5281/zenodo.13135902},\n url = {https://doi.org/10.5281/zenodo.13135902}\n}\n\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003e@software{allard_2024_13135902,\n author = {Helical Team},\n title = {helicalAI/helical: v0.0.1-alpha3},\n month = jul,\n year = 2024,\n publisher = {Zenodo},\n version = {0.0.1a5},\n doi = {10.5281/zenodo.13135902},\n url = {https://doi.org/10.5281/zenodo.13135902}\n}\n\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":1,"text":"What is Helical ?","anchor":"what-is-helical-","htmlText":"What is Helical ?"},{"level":2,"text":"Installation","anchor":"installation","htmlText":"Installation"},{"level":3,"text":"Singularity (Optional)","anchor":"singularity-optional","htmlText":"Singularity (Optional)"},{"level":2,"text":"Installation","anchor":"installation-1","htmlText":"Installation"},{"level":3,"text":"RNA models:","anchor":"rna-models","htmlText":"RNA models:"},{"level":3,"text":"DNA models:","anchor":"dna-models","htmlText":"DNA models:"},{"level":2,"text":"Demo \u0026 Use Cases","anchor":"demo--use-cases","htmlText":"Demo \u0026amp; Use Cases"},{"level":3,"text":"Current Examples:","anchor":"current-examples","htmlText":"Current Examples:"},{"level":2,"text":"Stuck somewhere ? Other ideas ?","anchor":"stuck-somewhere--other-ideas-","htmlText":"Stuck somewhere ? Other ideas ?"},{"level":2,"text":"Why should I use Helical \u0026 what to expect in the future?","anchor":"why-should-i-use-helical--what-to-expect-in-the-future","htmlText":"Why should I use Helical \u0026amp; what to expect in the future?"},{"level":2,"text":"Acknowledgements","anchor":"acknowledgements","htmlText":"Acknowledgements"},{"level":3,"text":"Licenses","anchor":"licenses","htmlText":"Licenses"},{"level":2,"text":"Citation","anchor":"citation","htmlText":"Citation"}],"siteNavLoginPath":"/login?return_to=https%3A%2F%2Fgithub.com%2FhelicalAI%2Fhelical"}},{"displayName":"LICENSE","repoName":"helical","refName":"release","path":"LICENSE","preferredFileType":"license","tabName":"AGPL-3.0","richText":null,"loaded":false,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":null,"siteNavLoginPath":"/login?return_to=https%3A%2F%2Fgithub.com%2FhelicalAI%2Fhelical"}}],"overviewFilesProcessingTime":0}},"appPayload":{"helpUrl":"https://docs.github.com","findFileWorkerPath":"/assets-cdn/worker/find-file-worker-1583894afd38.js","findInFileWorkerPath":"/assets-cdn/worker/find-in-file-worker-67668e8c2caa.js","githubDevUrl":null,"enabled_features":{"code_nav_ui_events":false,"overview_shared_code_dropdown_button":false,"react_blob_overlay":false,"copilot_conversational_ux_embedding_update":false,"copilot_smell_icebreaker_ux":true,"copilot_workspace":false,"blob_edit_unsaved_changes_storage":true,"accessible_code_button":true}}}}</script> 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5h8.5a.75.75 0 0 1 0 1.5h-8.5a.75.75 0 0 1 0-1.5ZM2 14a1 1 0 1 1 0-2 1 1 0 0 1 0 2Zm1-6a1 1 0 1 1-2 0 1 1 0 0 1 2 0ZM2 4a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path></svg></button></div><div class="Box-sc-g0xbh4-0 QkQOb js-snippet-clipboard-copy-unpositioned" data-hpc="true"><article class="markdown-body entry-content container-lg" itemprop="text"><div align="center" dir="auto"> <p dir="auto"><a href="https://helical.readthedocs.io/" rel="nofollow"> <img src="/helicalAI/helical/raw/release/docs/assets/logo_and_text_v2.png" alt="Helical Logo" width="400" style="max-width: 100%;"> </a></p> </div> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">What is Helical ?</h1><a id="user-content-what-is-helical-" class="anchor" aria-label="Permalink: What is Helical ?" href="#what-is-helical-"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Helical provides a framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.</p> <p dir="auto">Helical simplifies the entire application lifecycle when building with bio foundation models. You will be able to:</p> <ul dir="auto"> <li>Leverage the latest bio foundation models through our easy-to-use python package</li> <li>Run example notebooks on key downstream tasks from examples</li> </ul> <p dir="auto">We will update this repo on a regular basis with new models, benchmarks, modalities and functions - so stay tuned. Let’s build the most exciting AI-for-Bio community together!</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Installation</h2><a id="user-content-installation" class="anchor" aria-label="Permalink: Installation" href="#installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">We recommend installing Helical within a conda environment with the commands below (run them in your terminal) - this step is optional:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="conda create --name helical-package python=3.11.8 conda activate helical-package"><pre class="notranslate"><code>conda create --name helical-package python=3.11.8 conda activate helical-package </code></pre></div> <p dir="auto">To install the latest pip release of our Helical package, you can run the command below:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="pip install helical"><pre class="notranslate"><code>pip install helical </code></pre></div> <p dir="auto">To install the latest Helical package, you can run the command below:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="pip install --upgrade git+https://github.com/helicalAI/helical.git"><pre class="notranslate"><code>pip install --upgrade git+https://github.com/helicalAI/helical.git </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Singularity (Optional)</h3><a id="user-content-singularity-optional" class="anchor" aria-label="Permalink: Singularity (Optional)" href="#singularity-optional"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If you desire to run your code in a singularity file, you can use the <a href="/helicalAI/helical/blob/release/singularity.def">singularity.def</a> file and build an apptainer with it:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="apptainer build --sandbox singularity/helical singularity.def"><pre class="notranslate"><code>apptainer build --sandbox singularity/helical singularity.def </code></pre></div> <p dir="auto">and then shell into the sandbox container (use the --nv flag if you have a GPU available):</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="apptainer shell --nv --fakeroot singularity/helical/"><pre class="notranslate"><code>apptainer shell --nv --fakeroot singularity/helical/ </code></pre></div> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Installation</h2><a id="user-content-installation-1" class="anchor" aria-label="Permalink: Installation" href="#installation-1"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">RNA models:</h3><a id="user-content-rna-models" class="anchor" aria-label="Permalink: RNA models:" href="#rna-models"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li><a href="https://helical.readthedocs.io/en/latest/docs/Geneformer.html" rel="nofollow">Geneformer</a></li> <li><a href="https://helical.readthedocs.io/en/latest/docs/scGPT.html" rel="nofollow">scGPT</a></li> <li><a href="https://helical.readthedocs.io/en/latest/docs/UCE.html" rel="nofollow">Universal Cell Embedding (UCE)</a></li> </ul> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">DNA models:</h3><a id="user-content-dna-models" class="anchor" aria-label="Permalink: DNA models:" href="#dna-models"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li><a href="https://helical.readthedocs.io/en/latest/docs/hyena_dna.html" rel="nofollow">HyenaDNA</a></li> </ul> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Demo & Use Cases</h2><a id="user-content-demo--use-cases" class="anchor" aria-label="Permalink: Demo & Use Cases" href="#demo--use-cases"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">To run examples, be sure to have installed the Helical package (see Installation) and that it is up-to-date.</p> <p dir="auto">You can look directly into the example folder above and download the script of your choice, look into our <a href="https://helical.readthedocs.io/" rel="nofollow">documentation</a> for step-by-step guides or directly clone the repository using:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="git clone https://github.com/helicalAI/helical.git"><pre class="notranslate"><code>git clone https://github.com/helicalAI/helical.git </code></pre></div> <p dir="auto">Within the <code>examples/notebooks</code> folder, open the notebook of your choice. We recommend starting with <code>Quick-Start-Tutorial.ipynb</code></p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Current Examples:</h3><a id="user-content-current-examples" class="anchor" aria-label="Permalink: Current Examples:" href="#current-examples"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <markdown-accessiblity-table><table> <thead> <tr> <th>Example</th> <th>Description</th> <th>Colab</th> </tr> </thead> <tbody> <tr> <td><a href="/helicalAI/helical/blob/release/examples/notebooks/Quick-Start-Tutorial.ipynb">Quick-Start-Tutorial.ipynb</a></td> <td>A tutorial to quickly get used to the helical package and environment.</td> <td><a href="https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Quick-Start-Tutorial.ipynb" rel="nofollow"><img src="https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667" alt="Open In Colab" data-canonical-src="https://colab.research.google.com/assets/colab-badge.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td><a href="/helicalAI/helical/blob/release/examples/notebooks/Geneformer-vs-UCE.ipynb">Geneformer-vs-UCE.ipynb</a></td> <td>Zero-Shot Reference Mapping with Geneformer & UCE and compare the outcomes.</td> <td><a href="https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Geneformer-vs-UCE.ipynb" rel="nofollow"><img src="https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667" alt="Open In Colab" data-canonical-src="https://colab.research.google.com/assets/colab-badge.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td><a href="/helicalAI/helical/blob/release/examples/notebooks/Hyena-DNA-Inference.ipynb">Hyena-DNA-Inference.ipynb</a></td> <td>An example how to do probing with HyenaDNA by training a neural network on 18 downstream classification tasks.</td> <td><a href="https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Hyena-Dna-Inference.ipynb" rel="nofollow"><img src="https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667" alt="Open In Colab" data-canonical-src="https://colab.research.google.com/assets/colab-badge.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td><a href="/helicalAI/helical/blob/release/examples/notebooks/Cell-Type-Annotation.ipynb">Cell-Type-Annotation.ipynb</a></td> <td>An example how to do probing with scGPT by training a neural network to predict cell type annotations.</td> <td><a href="https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Type-Annotation.ipynb" rel="nofollow"><img src="https://camo.githubusercontent.com/96889048f8a9014fdeba2a891f97150c6aac6e723f5190236b10215a97ed41f3/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667" alt="Open In Colab" data-canonical-src="https://colab.research.google.com/assets/colab-badge.svg" style="max-width: 100%;"></a></td> </tr> <tr> <td>Coming Soon</td> <td>New models such as SCimilarity, scVI; benchmarking scripts; new use cases; others</td> <td></td> </tr> </tbody> </table></markdown-accessiblity-table> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Stuck somewhere ? Other ideas ?</h2><a id="user-content-stuck-somewhere--other-ideas-" class="anchor" aria-label="Permalink: Stuck somewhere ? Other ideas ?" href="#stuck-somewhere--other-ideas-"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">We are eager to help you and interact with you. Reach out via <a href="mailto:support@helical-ai.com">support@helical-ai.com</a>. You can also open github issues here.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Why should I use Helical & what to expect in the future?</h2><a id="user-content-why-should-i-use-helical--what-to-expect-in-the-future" class="anchor" aria-label="Permalink: Why should I use Helical & what to expect in the future?" href="#why-should-i-use-helical--what-to-expect-in-the-future"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If you are (or plan to) working with bio foundation models s.a. Geneformer or UCE on RNA and DNA data, Helical will be your best buddy! We provide and improve on:</p> <ul dir="auto"> <li>Up-to-date model library</li> <li>A unified API for all models</li> <li>User-facing abstractions tailored to computational biologists, researchers & AI developers</li> <li>Innovative use case and application examples and ideas</li> <li>Efficient data processing & code-base</li> </ul> <p dir="auto">We will continuously upload the latest model, publish benchmarks and make our code more efficient.</p> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Acknowledgements</h2><a id="user-content-acknowledgements" class="anchor" aria-label="Permalink: Acknowledgements" href="#acknowledgements"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">A lot of our models have been published by talend authors developing these exciting technologies. We sincerely thank the authors of the following open-source projects:</p> <ul dir="auto"> <li><a href="https://github.com/bowang-lab/scGPT/">scGPT</a></li> <li><a href="https://huggingface.co/ctheodoris/Geneformer" rel="nofollow">Geneformer</a></li> <li><a href="https://github.com/snap-stanford/UCE">UCE</a></li> <li><a href="https://github.com/HazyResearch/hyena-dna">HyenaDNA</a></li> <li><a href="https://github.com/scverse/anndata">anndata</a></li> <li><a href="https://github.com/scverse/scanpy">scanpy</a></li> <li><a href="https://github.com/huggingface/transformers">transformers</a></li> <li><a href="https://github.com/scikit-learn/scikit-learn">scikit-learn</a></li> </ul> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Licenses</h3><a id="user-content-licenses" class="anchor" aria-label="Permalink: Licenses" href="#licenses"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">You can find the Licenses for each model implementation in the model repositories:</p> <ul dir="auto"> <li><a href="/helicalAI/helical/blob/release/helical/models/scgpt/LICENSE">scGPT</a></li> <li><a href="/helicalAI/helical/blob/release/helical/models/geneformer/LICENSE">Geneformer</a></li> <li><a href="/helicalAI/helical/blob/release/helical/models/uce/LICENSE">UCE</a></li> <li><a href="/helicalAI/helical/blob/release/helical/models/hyena_dna/LICENSE">HyenaDNA</a></li> </ul> <div class="markdown-heading" dir="auto"><h2 tabindex="-1" class="heading-element" dir="auto">Citation</h2><a id="user-content-citation" class="anchor" aria-label="Permalink: Citation" href="#citation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Please use this BibTeX to cite this repository in your publications:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="@software{allard_2024_13135902, author = {Helical Team}, title = {helicalAI/helical: v0.0.1-alpha3}, month = jul, year = 2024, publisher = {Zenodo}, version = {0.0.1a5}, doi = {10.5281/zenodo.13135902}, url = {https://doi.org/10.5281/zenodo.13135902} } "><pre class="notranslate"><code>@software{allard_2024_13135902, author = {Helical Team}, title = {helicalAI/helical: v0.0.1-alpha3}, month = jul, year = 2024, publisher = {Zenodo}, version = {0.0.1a5}, doi = {10.5281/zenodo.13135902}, url = {https://doi.org/10.5281/zenodo.13135902} } </code></pre></div> </article></div></div></div></div></div>   <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div> </react-partial> <input type="hidden" data-csrf="true" value="BL3i1Wd7in/5YU5vd0VwvFrTAc0L40WM7JHCcPQwsSNo2ks1liDJyBCzuuzE5RJIiRvDzi70hqz/X4Gha3prbA==" /> </div> <div data-view-component="true" class="Layout-sidebar"> <div class="BorderGrid about-margin" data-pjax> <div class="BorderGrid-row"> <div class="BorderGrid-cell"> <div class="hide-sm hide-md"> <h2 class="mb-3 h4">About</h2> <p class="f4 my-3"> This repository contains the python package for Helical </p> <div class="my-3 d-flex flex-items-center"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link flex-shrink-0 mr-2"> <path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 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class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> </details-dialog> </details> </template> <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;"> <div class="Popover-message Popover-message--bottom-left Popover-message--large Box color-shadow-large" style="width:360px;"> </div> </div> <template id="snippet-clipboard-copy-button"> <div class="zeroclipboard-container position-absolute right-0 top-0"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn js-clipboard-copy m-2 p-0" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon m-2"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none m-2"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> <template id="snippet-clipboard-copy-button-unpositioned"> <div class="zeroclipboard-container"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn btn-invisible js-clipboard-copy m-2 p-0 d-flex flex-justify-center flex-items-center" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> </div> <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div> <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div> </body> </html>