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<title>Botanic1 | Genomic language models for land plants</title>
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<header class="topbar"><div class="inner"><a class="lockup" href="index.html"><div class="wordmark" aria-label="BOTANIC-1"><span class="cell">B</span><span class="cell">O</span><span class="cell">T</span><span class="cell">A</span><span class="cell">N</span><span class="cell">I</span><span class="cell">C</span><span class="cell tok" data-state="masked"><span class="probs"><i></i><i class="top"></i><i></i><i></i></span>?</span></div><span class="org"><svg class="living-models-mark" width="18" height="20" fill="currentColor" aria-hidden="true" focusable="false" xmlns="http://www.w3.org/2000/svg" version="1.1" viewBox="0 0 85.90 91.50"><rect x="55.1000" y="2.1000" width="3.2000" height="53.2000" /><rect x="55.1000" y="61.3000" width="3.2000" height="28.1000" /><rect x="68.9000" y="9.2000" width="3.2000" height="15.5000" /><rect x="68.9000" y="30.6000" width="3.2000" height="51.7000" /><rect x="82.7000" y="24.7000" width="3.2000" height="42.2000" /><rect x="41.4000" y="0.0000" width="3.2000" height="11.6000" /><rect x="41.4000" y="17.5000" width="3.2000" height="74.0000" /><rect x="27.6000" y="2.1000" width="3.2000" height="70.7000" /><rect x="27.6000" y="78.7000" width="3.2000" height="10.6000" /><rect x="13.8000" y="9.2000" width="3.2000" height="25.0000" /><rect x="13.8000" y="40.2000" width="3.2000" height="42.2000" /><rect x="0.0000" y="24.7000" width="3.2000" height="42.2000" /></svg>Living Models</span></a><nav aria-label="Pages"><a href="index.html" aria-current="page">Overview</a><a href="factory.html">Model factory</a><a href="leaderboard.html">Leaderboard</a><a href="causal-variants.html">Causal variants</a><a href="sae-features.html">SAE features</a><a href="use-case.html">Use case</a><a href="corpus.html">Corpus</a><a class="ext" href="https://huggingface.co/collections/living-models/botanic1-6a97f4e3c33f3d109a75057d" target="_blank" rel="noopener">Models</a></nav></div></header>

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        <h1 id="intro-title">Genomic language models<br>for land plants.</h1>
        <div class="chips">
          <a class="primary" href="https://huggingface.co/collections/living-models/botanic1-6a97f4e3c33f3d109a75057d" target="_blank" rel="noopener">Model cards <span aria-hidden="true">↗</span></a>
          <a href="https://www.biorxiv.org/content/10.64898/2026.09.04.749355v2" target="_blank" rel="noopener">Technical report <span class="ext">bioRxiv</span></a>
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  <nav class="landing-tabs" aria-label="About Botanic1">
    <a id="tab-overview" href="#overview">Overview</a>
    <a id="tab-use" href="#use">Use the model</a>
    <a id="tab-models" href="#models">Models &amp; data</a>
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  <section class="landing-panel" id="overview" aria-labelledby="tab-overview">
    <div class="facts">
      <article class="fact">
        <p class="fact-label">Model size</p>
        <h2>318M to 3.2B parameters</h2>
        <p>Botanic1-S scores 0.758 on the aggregate benchmark across nine task families. PlantCAD2-L scores 0.752, Carbon-8B 0.723, and Evo&nbsp;2-7B 0.716.</p>
        <figure class="overview-plot" id="overview-benchmark" aria-label="Model benchmark comparison" hidden></figure>
        <p class="fact-note">Frozen models · aggregate test score (S<sub>bal</sub><sup>test</sup>) · whiskers are 95% CIs</p>
        <a class="text-link" href="leaderboard.html">Scores by task and species <span aria-hidden="true">↗</span></a>
      </article>
      <article class="fact">
        <p class="fact-label">Species coverage</p>
        <h2>320 land plant species</h2>
        <p>Pre-training spans bryophytes, vascular spore plants, gymnosperms, and flowering plants.</p>
        <figure class="overview-plot" id="overview-corpus" aria-label="Training corpus by plant family" hidden></figure>
        <a class="text-link" href="corpus.html">Explore the training species <span aria-hidden="true">↗</span></a>
      </article>
      <article class="fact">
        <p class="fact-label">Zero-shot scoring</p>
        <h2>Variant prioritisation</h2>
        <p>Botanic1-XL recovers 49.9% of validated causal variants within the top 1% of candidates (~60 variants out of a median of 5,904 per locus), across 545 studies in 14 species, from the sequence and mutation allele alone.</p>
        <figure class="overview-plot" id="overview-causal" aria-label="Causal-variant recall curves" hidden></figure>
        <a class="text-link" href="causal-variants.html">Explore the variant benchmark <span aria-hidden="true">↗</span></a>
      </article>
      <article class="fact">
        <p class="fact-label">Fine-tuning</p>
        <h2>Molecular phenotype predictions</h2>
        <p>Easier and better fine-tuning for promoter and terminator strength, poly(A) sites, lncRNA classification, chromatin accessibility, and TF-family binding.</p>
        <figure class="overview-plot" id="overview-finetune" aria-label="Fine-tuning results across six experiments" hidden></figure>
        <p class="fact-note">Full fine-tuning · LoRA · IA³</p>
        <a class="text-link" href="https://www.biorxiv.org/content/10.64898/2026.09.04.749355v2" target="_blank" rel="noopener">Methods and results in the report <span aria-hidden="true">↗</span></a>
      </article>
    </div>
    <p class="panel-note">Evaluations, uncertainty estimates, and species-level results are detailed in the <a href="https://www.biorxiv.org/content/10.64898/2026.09.04.749355v2" target="_blank" rel="noopener">technical report</a>.</p>
    <div class="section-intro" id="cite">
      <h2>Cite</h2>
      <p>Barozet A., Cabeli V., Ogier du Terrail J., Rukhovich A., Janssoone T., Klajer G., Sheikhitarghi Z., Andrews G., Veran C., Strouk L. <em>BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era.</em> bioRxiv (2026). doi: <a href="https://doi.org/10.64898/2026.09.04.749355" target="_blank" rel="noopener">10.64898/2026.09.04.749355</a></p>
    </div>
<div class="citation-box"><button type="button" class="copy-bibtex" aria-label="Copy BibTeX to clipboard">Copy BibTeX</button>
<pre class="citation"><code>@article{Barozet2026.09.04.749355,
    author = {Barozet, Am{\'e}lie and Cabeli, Vincent and Ogier du Terrail, Jean
              and Rukhovich, Alexey and Janssoone, Thomas and Klajer, Gary
              and Sheikhitarghi, Zeinab and Andrews, Gregory and Veran, Cyril
              and Strouk, L{\'e}onard},
    title = {BOTANIC-1: a series of long-context plant genomic foundation
             models in the agentic era},
    journal = {bioRxiv},
    year = {2026},
    elocation-id = {2026.09.04.749355},
    doi = {10.64898/2026.09.04.749355},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2026/09/09/2026.09.04.749355},
    eprint = {https://www.biorxiv.org/content/early/2026/09/09/2026.09.04.749355.full.pdf},
}</code></pre></div>
  </section>

  <section class="landing-panel" id="use" aria-labelledby="tab-use">
    <div class="section-intro">
      <p>Model cards contain instructions and tutorials</p>
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    <div class="workflow-list">
      <article class="workflow">
        <div><h3>Score variants</h3><p>Provide a reference sequence, a variant position, and an alternate base. Get a likelihood ratio for each substitution, with no task-specific training.</p></div>
        <a class="text-link" href="https://huggingface.co/living-models/Botanic1-S#2-zero-shot-variant-effect-scoring-llr" target="_blank" rel="noopener">Variant-scoring example <span aria-hidden="true">↗</span></a>
      </article>
      <article class="workflow">
        <div><h3>Extract embeddings</h3><p>Provide DNA sequences. Get a representation at each nucleotide to train a probe for your task.</p></div>
        <a class="text-link" href="https://huggingface.co/living-models/Botanic1-S#1-generating-embeddings" target="_blank" rel="noopener">Embedding example <span aria-hidden="true">↗</span></a>
      </article>
      <article class="workflow">
        <div><h3>Fine-tune on your data</h3><p>Use labelled sequences to adapt the model with full fine-tuning or parameter-efficient methods.</p></div>
        <a class="text-link" href="https://huggingface.co/living-models/Botanic1-S#4-fine-tuning-lora-or-full" target="_blank" rel="noopener">Fine-tuning scripts <span aria-hidden="true">↗</span></a>
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  <section class="landing-panel" id="models" aria-labelledby="tab-models">
    <div class="section-intro">
      <h2>Models, data, and report</h2>
    </div>
    <div class="resource-list">
      <a href="https://huggingface.co/collections/living-models/botanic1-6a97f4e3c33f3d109a75057d" target="_blank" rel="noopener"><span>Model collection <span aria-hidden="true">↗</span></span><span class="small">Checkpoints, model cards, code examples, and licence.</span></a>
      <a href="https://huggingface.co/datasets/living-models/Botanic1-pretraining" target="_blank" rel="noopener"><span>Pre-training corpus <span aria-hidden="true">↗</span></span><span class="small">Sequence windows from 320 species and source assemblies.</span></a>
      <a href="https://huggingface.co/living-models/Botanic1-M-sae-k64-codebook8192" target="_blank" rel="noopener"><span>SAE model <span aria-hidden="true">↗</span></span><span class="small">Sparse autoencoder for Botanic1-M.</span></a>
      <a href="https://www.biorxiv.org/content/10.64898/2026.09.04.749355v2" target="_blank" rel="noopener"><span>Technical report <span class="small">bioRxiv</span></span><span class="small">Training, evaluation, long context, and interpretability.</span></a>
    </div>
    <div class="section-intro" id="cite-models">
      <h2>Cite</h2>
      <p>Barozet A., Cabeli V., Ogier du Terrail J., Rukhovich A., Janssoone T., Klajer G., Sheikhitarghi Z., Andrews G., Veran C., Strouk L. <em>BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era.</em> bioRxiv (2026). doi: <a href="https://doi.org/10.64898/2026.09.04.749355" target="_blank" rel="noopener">10.64898/2026.09.04.749355</a></p>
    </div>
<div class="citation-box"><button type="button" class="copy-bibtex" aria-label="Copy BibTeX to clipboard">Copy BibTeX</button>
<pre class="citation"><code>@article{Barozet2026.09.04.749355,
    author = {Barozet, Am{\'e}lie and Cabeli, Vincent and Ogier du Terrail, Jean
              and Rukhovich, Alexey and Janssoone, Thomas and Klajer, Gary
              and Sheikhitarghi, Zeinab and Andrews, Gregory and Veran, Cyril
              and Strouk, L{\'e}onard},
    title = {BOTANIC-1: a series of long-context plant genomic foundation
             models in the agentic era},
    journal = {bioRxiv},
    year = {2026},
    elocation-id = {2026.09.04.749355},
    doi = {10.64898/2026.09.04.749355},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2026/09/09/2026.09.04.749355},
    eprint = {https://www.biorxiv.org/content/early/2026/09/09/2026.09.04.749355.full.pdf},
}</code></pre></div>
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