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<span class="md-ellipsis"> Models </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_1_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_1"> <span class="md-nav__icon md-icon"></span> Models </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_1_1" > <label class="md-nav__link" for="__nav_1_1" id="__nav_1_1_label" tabindex="0"> <span class="md-ellipsis"> Geneformer </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_1_1_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_1_1"> <span class="md-nav__icon md-icon"></span> Geneformer </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="model_cards/geneformer/" class="md-nav__link"> <span class="md-ellipsis"> Model Card </span> </a> </li> <li class="md-nav__item"> <a href="configs/geneformer_config/" class="md-nav__link"> <span class="md-ellipsis"> Config </span> </a> </li> <li class="md-nav__item"> <a href="models/geneformer/" class="md-nav__link"> <span class="md-ellipsis"> Model </span> </a> </li> <li class="md-nav__item"> <a href="fine_tuning_models/geneformer_fine_tune/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tuning Model </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_1_2" > <label class="md-nav__link" for="__nav_1_2" id="__nav_1_2_label" tabindex="0"> <span class="md-ellipsis"> scGPT </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_1_2_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_1_2"> <span class="md-nav__icon md-icon"></span> scGPT </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="model_cards/scgpt/" class="md-nav__link"> <span class="md-ellipsis"> Model Card </span> </a> </li> <li class="md-nav__item"> <a href="configs/scgpt_config/" class="md-nav__link"> <span class="md-ellipsis"> Config </span> </a> </li> <li class="md-nav__item"> <a href="models/scgpt/" class="md-nav__link"> <span class="md-ellipsis"> Model </span> </a> </li> <li class="md-nav__item"> <a href="fine_tuning_models/scgpt_fine_tune/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tuning Model </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_1_3" > <label class="md-nav__link" for="__nav_1_3" id="__nav_1_3_label" tabindex="0"> <span class="md-ellipsis"> HyenaDNA </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_1_3_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_1_3"> <span class="md-nav__icon md-icon"></span> HyenaDNA </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="model_cards/hyenadna/" class="md-nav__link"> <span class="md-ellipsis"> Model Card </span> </a> </li> <li class="md-nav__item"> <a href="configs/hyenadna_config/" class="md-nav__link"> <span class="md-ellipsis"> Config </span> </a> </li> <li class="md-nav__item"> <a href="models/hyenadna/" class="md-nav__link"> <span class="md-ellipsis"> Model </span> </a> </li> <li class="md-nav__item"> <a href="fine_tuning_models/hyenadna_fine_tune/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tuning Model </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_1_4" > <label class="md-nav__link" for="__nav_1_4" id="__nav_1_4_label" tabindex="0"> <span class="md-ellipsis"> UCE </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_1_4_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_1_4"> <span class="md-nav__icon md-icon"></span> UCE </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="model_cards/uce/" class="md-nav__link"> <span class="md-ellipsis"> Model Card </span> </a> </li> <li class="md-nav__item"> <a href="configs/uce_config/" class="md-nav__link"> <span class="md-ellipsis"> Config </span> </a> </li> <li class="md-nav__item"> <a href="models/uce/" class="md-nav__link"> <span class="md-ellipsis"> Model </span> </a> </li> <li class="md-nav__item"> <a href="fine_tuning_models/uce_fine_tune/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tuning Model </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="models/base_models/" class="md-nav__link"> <span class="md-ellipsis"> Helical Base Models </span> </a> </li> <li class="md-nav__item"> <a href="models/fine_tuning_heads/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tuning Heads </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" > <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0"> <span class="md-ellipsis"> Example Notebooks </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_2"> <span class="md-nav__icon md-icon"></span> Example Notebooks </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="notebooks/Quick-Start-Tutorial/" class="md-nav__link"> <span class="md-ellipsis"> Helical Quick Start Tutorial </span> </a> </li> <li class="md-nav__item"> <a href="notebooks/Cell-Type-Annotation/" class="md-nav__link"> <span class="md-ellipsis"> Cell type annotation prediction </span> </a> </li> <li class="md-nav__item"> <a href="notebooks/Cell-Type-Classification-Fine-Tuning/" class="md-nav__link"> <span class="md-ellipsis"> Classification fine-tuning using Helical </span> </a> </li> <li class="md-nav__item"> <a href="notebooks/Geneformer-vs-UCE/" class="md-nav__link"> <span class="md-ellipsis"> Comparing Geneformer & UCE for cell-type classification </span> </a> </li> <li class="md-nav__item"> <a href="notebooks/Hyena-DNA-Inference/" class="md-nav__link"> <span class="md-ellipsis"> Downstream prediction </span> </a> </li> <li class="md-nav__item"> <a href="notebooks/HyenaDNA-Fine-Tuning/" class="md-nav__link"> <span class="md-ellipsis"> Fine-Tune HyenaDNA On A Downstream Classification Task </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="benchmarking/description/" class="md-nav__link"> <span class="md-ellipsis"> Benchmarking </span> </a> </li> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" > <div class="md-sidebar__scrollwrap"> <div class="md-sidebar__inner"> <nav class="md-nav md-nav--secondary" aria-label="Table of contents"> <label class="md-nav__title" for="__toc"> <span class="md-nav__icon md-icon"></span> Table of contents </label> <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix> <li class="md-nav__item"> <a href="#installation" class="md-nav__link"> <span class="md-ellipsis"> Installation </span> </a> <nav class="md-nav" aria-label="Installation"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#singularity-optional" class="md-nav__link"> <span class="md-ellipsis"> Singularity (Optional) </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="#installation_1" class="md-nav__link"> <span class="md-ellipsis"> Installation </span> </a> <nav class="md-nav" aria-label="Installation"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#rna-models" class="md-nav__link"> <span class="md-ellipsis"> RNA models: </span> </a> </li> <li class="md-nav__item"> <a href="#dna-models" class="md-nav__link"> <span class="md-ellipsis"> DNA models: </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="#demo-use-cases" class="md-nav__link"> <span class="md-ellipsis"> Demo & Use Cases </span> </a> <nav class="md-nav" aria-label="Demo & Use Cases"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#current-examples" class="md-nav__link"> <span class="md-ellipsis"> Current Examples: </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="#stuck-somewhere-other-ideas" class="md-nav__link"> <span class="md-ellipsis"> Stuck somewhere ? Other ideas ? </span> </a> </li> <li class="md-nav__item"> <a href="#why-should-i-use-helical-what-to-expect-in-the-future" class="md-nav__link"> <span class="md-ellipsis"> Why should I use Helical & what to expect in the future? </span> </a> </li> <li class="md-nav__item"> <a href="#acknowledgements" class="md-nav__link"> <span class="md-ellipsis"> Acknowledgements </span> </a> <nav class="md-nav" aria-label="Acknowledgements"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#licenses" class="md-nav__link"> <span class="md-ellipsis"> Licenses </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="#citation" class="md-nav__link"> <span class="md-ellipsis"> Citation </span> </a> </li> </ul> </nav> </div> </div> </div> <div class="md-content" data-md-component="content"> <article class="md-content__inner md-typeset"> <h1 id="what-is-helical">What is Helical ?</h1> <p>Helical provides a framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.</p> <p>Helical simplifies the entire application lifecycle when building with bio foundation models. You will be able to: - Leverage the latest bio foundation models through our easy-to-use python package - Run example notebooks on key downstream tasks from examples</p> <p>We will update this repo on a regular basis with new models, benchmarks, modalities and functions - so stay tuned. Let鈥檚 build the most exciting AI-for-Bio community together!</p> <h2 id="installation">Installation</h2> <p>We recommend installing Helical within a conda environment with the commands below (run them in your terminal) - this step is optional: <div class="language-shell highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>conda<span class="w"> </span>create<span class="w"> </span>--name<span class="w"> </span>helical-package<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.11.8 </span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>conda<span class="w"> </span>activate<span class="w"> </span>helical-package </span></code></pre></div> To install the latest pip release of our Helical package, you can run the command below: <div class="language-shell highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>pip<span class="w"> </span>install<span class="w"> </span>helical </span></code></pre></div></p> <p>To install the latest Helical package, you can run the command below: <div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>pip install --upgrade git+https://github.com/helicalAI/helical.git </span></code></pre></div></p> <h3 id="singularity-optional">Singularity (Optional)</h3> <p>If you desire to run your code in a singularity file, you can use the <a href="https://github.com/helicalAI/helical/blob/release/singularity.def" target="_blank">singularity.def</a> file and build an apptainer with it: <div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>apptainer build --sandbox singularity/helical singularity.def </span></code></pre></div></p> <p>and then shell into the sandbox container (use the --nv flag if you have a GPU available): <div class="language-text highlight"><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>apptainer shell --nv --fakeroot singularity/helical/ </span></code></pre></div></p> <h2 id="installation_1">Installation</h2> <h3 id="rna-models">RNA models:</h3> <ul> <li><a href="model_cards/geneformer/">Geneformer</a></li> <li><a href="model_cards/scgpt/">scGPT</a></li> <li><a href="model_cards/uce/">Universal Cell Embedding (UCE)</a></li> </ul> <h3 id="dna-models">DNA models:</h3> <ul> <li><a href="model_cards/hyenadna/">HyenaDNA</a></li> </ul> <h2 id="demo-use-cases">Demo & Use Cases</h2> <p>To run examples, be sure to have installed the Helical package (see Installation) and that it is up-to-date.</p> <p>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/">documentation</a> for step-by-step guides or directly clone the repository using: <div class="language-text highlight"><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>git clone https://github.com/helicalAI/helical.git </span></code></pre></div> Within the <code>example/notebooks</code> folder, open the notebook of your choice. We recommend starting with <code>Quick-Start-Tutorial.ipynb</code>.</p> <h3 id="current-examples">Current Examples:</h3> <table> <thead> <tr> <th>Example</th> <th>Description</th> <th>Colab</th> </tr> </thead> <tbody> <tr> <td><a href="https://github.com/helicalAI/helical/blob/main/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"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></td> </tr> <tr> <td><a href="https://github.com/helicalAI/helical/blob/main/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"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></td> </tr> <tr> <td><a href="https://github.com/helicalAI/helical/blob/main/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"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></td> </tr> <tr> <td><a href="https://github.com/helicalAI/helical/blob/main/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"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></td> </tr> <tr> <td><a href="./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb">Cell-Type-Classification-Fine-Tuning.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-Classification-Fine-Tuning.ipynb"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></a></td> </tr> <tr> <td><a href="./examples/notebooks/HyenaDNA-Fine-Tuning.ipynb">HyenaDNA-Fine-Tuning.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/HyenaDNA-Fine-Tuning.ipynb"><img alt="Open In Colab" src="https://colab.research.google.com/assets/colab-badge.svg" /></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> <h2 id="stuck-somewhere-other-ideas">Stuck somewhere ? Other ideas ?</h2> <p>We are eager to help you and interact with you. Reach out via support@helical-ai.com. You can also open github issues here.</p> <h2 id="why-should-i-use-helical-what-to-expect-in-the-future">Why should I use Helical & what to expect in the future?</h2> <p>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: - Up-to-date model library - A unified API for all models - User-facing abstractions tailored to computational biologists, researchers & AI developers - Innovative use case and application examples and ideas - Efficient data processing & code-base</p> <p>We will continuously upload the latest model, publish benchmarks and make our code more efficient.</p> <h2 id="acknowledgements">Acknowledgements</h2> <p>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> <li><a href="https://github.com/bowang-lab/scGPT/">scGPT</a></li> <li><a href="https://huggingface.co/ctheodoris/Geneformer">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> </ul> <h3 id="licenses">Licenses</h3> <p>You can find the Licenses for each model implementation in the model repositories:</p> <ul> <li><a href="helical/models/scgpt/LICENSE">scGPT</a></li> <li><a href="helical/models/geneformer/LICENSE">Geneformer</a></li> <li><a href="helical/models/uce/LICENSE">UCE</a></li> <li><a href="helical/models/hyena_dna/LICENSE">HyenaDNA</a></li> </ul> <h2 id="citation">Citation</h2> <p>Please use this BibTeX to cite this repository in your publications:</p> <div class="language-bibtex highlight"><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="nc">@software</span><span class="p">{</span><span class="nl">allard_2024_13135902</span><span class="p">,</span> </span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="w"> </span><span class="na">author</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Helical Team}</span><span class="p">,</span> </span><span id="__span-6-3"><a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w"> </span><span class="na">title</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{helicalAI/helical: v0.0.1-alpha}</span><span class="p">,</span> </span><span id="__span-6-4"><a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="w"> </span><span class="na">month</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="nv">jul</span><span class="p">,</span> </span><span id="__span-6-5"><a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="w"> </span><span class="na">year</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="m">2024</span><span class="p">,</span> </span><span id="__span-6-6"><a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="w"> </span><span class="na">publisher</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{Zenodo}</span><span class="p">,</span> </span><span id="__span-6-7"><a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w"> </span><span class="na">version</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{0.0.1a5}</span><span class="p">,</span> </span><span id="__span-6-8"><a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="w"> </span><span class="na">doi</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{10.5281/zenodo.13135902}</span><span class="p">,</span> </span><span id="__span-6-9"><a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="w"> </span><span class="na">url</span><span class="w"> </span><span class="p">=</span><span class="w"> </span><span class="s">{https://doi.org/10.5281/zenodo.13135902}</span> </span><span id="__span-6-10"><a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="p">}</span> </span></code></pre></div> </article> </div> <script>var 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