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ESM2 Finetuning refactor #574

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22bb887
refactor datasets
farhadrgh Jan 6, 2025
4848f9c
refactor datasets
farhadrgh Jan 6, 2025
db955ef
add finetune script
farhadrgh Jan 6, 2025
4cac6d7
fix typing
farhadrgh Jan 6, 2025
900ef00
simplify, use 650m
farhadrgh Jan 6, 2025
d7d526b
Merge branch 'main' into farhadr/ft_refactor
farhadrgh Jan 6, 2025
5e2dd4b
executable finetune_esm2
farhadrgh Jan 8, 2025
4577bc2
typing
farhadrgh Jan 9, 2025
9154c56
resolve conflicts
farhadrgh Jan 9, 2025
8fc64a3
add finetune notebook
farhadrgh Jan 9, 2025
087341a
move test
farhadrgh Jan 9, 2025
3eb8740
deprecate old example
farhadrgh Jan 9, 2025
ca2a89a
update tests
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1efd34c
add unit tests
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884bbf9
update brev.dev link
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Merge branch 'main' into farhadr/ft_refactor
farhadrgh Jan 9, 2025
ee97688
move dataset classes
farhadrgh Jan 13, 2025
2e3d496
Merge branch 'farhadr/ft_refactor' of https://github.com/NVIDIA/bione…
farhadrgh Jan 13, 2025
5d50cfc
updated
farhadrgh Jan 13, 2025
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Merge branch 'main' into farhadr/ft_refactor
farhadrgh Jan 13, 2025
55dd32d
rm douplicate dataset
farhadrgh Jan 13, 2025
8ca52b4
update
farhadrgh Jan 13, 2025
c213cdb
test args
farhadrgh Jan 14, 2025
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Merge branch 'main' into farhadr/ft_refactor
farhadrgh Jan 14, 2025
2191c0b
fix arg type
farhadrgh Jan 14, 2025
25b3db2
Merge branch 'farhadr/ft_refactor' of https://github.com/NVIDIA/bione…
farhadrgh Jan 14, 2025
2bba40d
fix docstr
farhadrgh Jan 14, 2025
af4a612
add from_csv classmethod
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6091790
Merge branch 'main' into farhadr/ft_refactor
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Merge branch 'main' into farhadr/ft_refactor
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826 changes: 826 additions & 0 deletions docs/docs/user-guide/examples/bionemo-esm2/finetune.ipynb

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263 changes: 0 additions & 263 deletions docs/docs/user-guide/examples/bionemo-esm2/finetune.md

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2 changes: 1 addition & 1 deletion docs/docs/user-guide/getting-started/development.md
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Expand Up @@ -136,7 +136,7 @@ of the model. The fine-tuning steps will be application-specific, but a general
6. **Run inference**: Once the model is fine-tuned, use it to make predictions on new, unseen data.

For more information on fine-tuning a model, refer to the [ESM-2 Fine-tuning
Tutorial](../examples/bionemo-esm2/finetune.md).
Tutorial](../examples/bionemo-esm2/finetune.ipynb).

## Advanced Developer Documentation

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1 change: 1 addition & 0 deletions sub-packages/bionemo-esm2/pyproject.toml
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Expand Up @@ -22,6 +22,7 @@ bionemo-esm2-train= "bionemo.esm2.run.main:main"
bionemo-esm2-recipe= "bionemo.esm2.run.recipes:main"
infer_esm2 = "bionemo.esm2.scripts.infer_esm2:infer_esm2_entrypoint"
train_esm2 = "bionemo.esm2.scripts.train_esm2:train_esm2_entrypoint"
finetune_esm2 = "bionemo.esm2.scripts.finetune_esm2:finetune_esm2_entrypoint"

# Make sure that the tokenizer files are included along with the python files during installation.
[tool.setuptools.package-data]
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