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48 lines
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ReStructuredText
48 lines
2.0 KiB
ReStructuredText
Data
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====
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Trained Models
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--------------
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- `Bepler & Berger language model <http://cb.csail.mit.edu/cb/dscript/data/models/lm_v1.sav>`_
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- `Human TT3D model <http://cb.csail.mit.edu/cb/dscript/data/models/tt3d_v1.sav>`_
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- `Human Topsy-Turvy model <http://cb.csail.mit.edu/cb/dscript/data/models/topsy_turvy_v1.sav>`_ **(recommended)**
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- `Human D-SCRIPT model <http://cb.csail.mit.edu/cb/dscript/data/models/human_v1.sav>`_ (from original D-SCRIPT paper)
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Pre-trained models can be loaded in the prediction script from HuggingFace hub by specifying the model name. For example, to load the Topsy-Turvy model, use `samsl/topsy_turvy_v1`.
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Sample Data
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-----------
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Sequences
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~~~~~~~~~
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- `Human`_
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- `Mouse`_
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- `Fly`_
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- `Yeast`_
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- `Worm`_
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- `E.coli`_
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Interactions
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~~~~~~~~~~~~
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- `Human Train`_
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- `Human Test`_
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- `Mouse Test`_
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- `Fly Test`_
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- `Yeast Test`_
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- `Worm Test`_
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- `E. coli Test`_
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.. _`Human`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/human.fasta
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.. _`Mouse`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/mouse.fasta
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.. _`Fly`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/fly.fasta
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.. _`Yeast`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/yeast.fasta
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.. _`Worm`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/worm.fasta
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.. _`E.coli`: https://github.com/samsledje/D-SCRIPT/blob/main/data/seqs/ecoli.fasta
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.. _`Human Train`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/human_train.tsv
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.. _`Human Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/human_test.tsv
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.. _`Mouse Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/mouse_test.tsv
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.. _`Fly Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/fly_test.tsv
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.. _`Yeast Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/yeast_test.tsv
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.. _`Worm Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/worm_test.tsv
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.. _`E. coli Test`: https://github.com/samsledje/D-SCRIPT/blob/main/data/pairs/ecoli_test.tsv
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