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Ume model, per-modality loss, UmeTokenizerTransform#52

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ncfrey merged 24 commits intomainfrom
lobster-ume-modality-loss
Mar 25, 2025
Merged

Ume model, per-modality loss, UmeTokenizerTransform#52
ncfrey merged 24 commits intomainfrom
lobster-ume-modality-loss

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@karinazad
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@karinazad karinazad commented Mar 24, 2025 •
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  • expands the Ume model with modality information and switches training configs from FlexBERT to Ume
  • Ume logs loss and perplexity per modality
  • implements UmeTokenizerTransform that adds modality information to batches
              {
                    "input_ids": tensor(...)
                    "attention_mask": tensor(...)
                    "modality": [Modality.AMINO_ACID, Modality.SMILES, ...]
                }
  • other small housekeeping: remove unused kwargs arguments from FlexBERT, remove unused imports

@karinazad karinazad changed the title [draft] Ume monitor per-modality loss Ume monitor per-modality loss Mar 24, 2025
@karinazad karinazad changed the title Ume monitor per-modality loss [draft] Ume monitor per-modality loss Mar 24, 2025
@karinazad karinazad changed the title [draft] Ume monitor per-modality loss Ume monitor per-modality loss Mar 25, 2025
@karinazad karinazad changed the title Ume monitor per-modality loss Ume model, per-modality loss, UmeTokenizerTransform Mar 25, 2025
ncfrey
ncfrey approved these changes Mar 25, 2025
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src/lobster/tokenization/_ume_tokenizers.py Outdated
----------
modality : str | Modality
The modality of the tokenizer
Can be either one of {"SMILES", "amino_acid", "nucleotide", "3d_coordinates"}
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@ncfrey ncfrey Mar 25, 2025

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reference the constants.ModalityType where these are defined

@ncfrey ncfrey merged commit 183c6c6 into main Mar 25, 2025
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@ncfrey ncfrey deleted the lobster-ume-modality-loss branch March 25, 2025 14:33
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@ncfrey ncfrey ncfrey approved these changes

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@karinazad @ncfrey