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Ume evaluation callbacks - switch to Ume tokenizers, expose evaluate#57

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ncfrey merged 8 commits intomainfrom
ume-callback-probes-fix
Mar 28, 2025
Merged

Ume evaluation callbacks - switch to Ume tokenizers, expose evaluate#57
ncfrey merged 8 commits intomainfrom
ume-callback-probes-fix

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@karinazad
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@karinazad karinazad commented Mar 27, 2025

  • Switches to UmeTokenizerTransform in evaluation callbacks
  • Exposes evaluate method outside of Lightning context
from lobster.callbacks import MoleculeACELinearProbeCallback

ume = Ume.load_from_checkpoint(...)

probe = MoleculeACELinearProbeCallback(
    max_length=ume.embedding_dim
)
scores = molecule_ace_probe.evaluate(ume)

  • Updates the notebook example with callback evaluations

@karinazad karinazad changed the title Switch to UmeTokenizerTransform in evaluation callbacks Switch to UmeTokenizerTransform in evaluation callbacks, expose evaluate method outside of Lightning context Mar 27, 2025
@karinazad karinazad changed the title Switch to UmeTokenizerTransform in evaluation callbacks, expose evaluate method outside of Lightning context Ume evaluation callbacks - switch to Ume tokenizers, expose evaluate Mar 27, 2025
@ncfrey
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ncfrey commented Mar 28, 2025

TODO: add a script that runs all eval callbacks

@ncfrey ncfrey merged commit 103ca15 into main Mar 28, 2025
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@ncfrey ncfrey deleted the ume-callback-probes-fix branch March 28, 2025 13:44
taylormjs pushed a commit that referenced this pull request Apr 1, 2025
#57)

* fix callbacks

* name

* fix

* callbacks

* docstrings

* fix

* notebook
taylormjs added a commit that referenced this pull request Apr 2, 2025
* add iid splits, heldout set

* ruff

* update docstring

* Ume evaluation callbacks - switch to Ume tokenizers, expose `evaluate` (#57)

* fix callbacks

* name

* fix

* callbacks

* docstrings

* fix

* notebook

* temp datamodule

* remove default caching in homefs

* update tests, fix ruff

* slurm script time interval, Ume config, ModernBERT max length (#59)

* config

* max length

* max length

* beignet

* configs (#55)

Co-authored-by: freyn6 <freyn6@gene.com>

* make iid test set, fix heldout to combine all species, update all supported splits

* fix iterable split getting

---------

Co-authored-by: Taylor Joren <joren.taylor@gene.com>
Co-authored-by: Karina Zadorozhny <karina.zadorozhny@gmail.com>
Co-authored-by: Nathan Frey <ncfrey@users.noreply.github.com>
Co-authored-by: freyn6 <freyn6@gene.com>
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2 participants