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| <title>NTv3 — Foundation Models for Long-Range Genomics</title> | |
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| <h1>NTv3 — Foundation Models for Long-Range Genomics</h1> | |
| <p> | |
| This Space is the companion hub for <strong>NTv3</strong> models: runnable notebooks for inference, fine-tuning, interpretation, and sequence generation. | |
| </p> | |
| <div class="pillrow"> | |
| <span class="pill">Long-context genomics</span> | |
| <span class="pill">Torch notebooks</span> | |
| <span class="pill">Inference • Fine-tune • Interpret • Generate</span> | |
| </div> | |
| </div> | |
| <div class="grid"> | |
| <div class="card"> | |
| <h2>Notebooks</h2> | |
| <ul> | |
| <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/tree/main/notebooks" target="_blank" rel="noopener">Browse notebooks folder</a></li> | |
| <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks/00_quickstart_inference.ipynb" target="_blank" rel="noopener">00 — Quickstart inference</a></li> | |
| <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks/01_tracks_prediction.ipynb" target="_blank" rel="noopener">01 — Tracks prediction</a></li> | |
| <li>02 — Genome annotation / segmentation</li> | |
| <li>03 — Fine-tune a head</li> | |
| <li>04 — Model interpretation</li> | |
| <li>05 — Sequence generation</li> | |
| </ul> | |
| </div> | |
| <div class="card"> | |
| <h2>Models</h2> | |
| <ul> | |
| <li>Pretrained checkpoints: | |
| <div style="margin-top: 8px; margin-left: 0;"> | |
| <div><a href="https://huggingface.co/InstaDeepAI/ntv3_8M_7downsample_pretrained_le_1mb"><code>InstaDeepAI/ntv3_8M_7downsample_pretrained_le_1mb</code></a></div> | |
| <div><a href="https://huggingface.co/InstaDeepAI/ntv3_106M_7downsample_pretrained_le_1mb"><code>InstaDeepAI/ntv3_106M_7downsample_pretrained_le_1mb</code></a></div> | |
| <div><a href="https://huggingface.co/InstaDeepAI/ntv3_650M_7downsample_pretrained_le_1mb"><code>InstaDeepAI/ntv3_650M_7downsample_pretrained_le_1mb</code></a></div> | |
| </div> | |
| </li> | |
| <li>Post-trained checkpoints: | |
| <div style="margin-top: 8px; margin-left: 0;"> | |
| <div><a href="https://huggingface.co/InstaDeepAI/ntv3_650M_7downsample_post_trained_1mb"><code>InstaDeepAI/ntv3_650M_7downsample_post_trained_1mb</code></a></div> | |
| <div><a href="https://huggingface.co/InstaDeepAI/ntv3_106M_7downsample_post_trained_1mb"><code>InstaDeepAI/ntv3_106M_7downsample_post_trained_1mb</code></a></div> | |
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| </li> | |
| </ul> | |
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| <div class="card"> | |
| <h2>Model usage (to update)</h2> | |
| <p>Here is a quick example of how to use NTv3 models.</p> | |
| <div class="code"><code>from transformers import pipeline | |
| pipe = pipeline( | |
| task="ntv3-tracks", | |
| model="InstaDeepAI/ntv3_106M_7downsample_post_trained_1mb", | |
| trust_remote_code=True, | |
| device="cuda", | |
| torch_dtype=torch.bfloat16, | |
| )</code></div> | |
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| <h2>Links</h2> | |
| <ul> | |
| <li>Paper: (add link)</li> | |
| <li><a href="https://github.com/instadeepai/nucleotide-transformer">JAX training code</a></li> | |
| </ul> | |
| </div> | |
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| <p class="footer"> | |
| © instadeep-ai — NTv3 companion Space. | |
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