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Pull Request Overview
This PR adds support for modality‐specific CLS tokens and updates reserved token naming in the Ume tokenizer implementations. Key changes include renaming latent generator tokens to coordinates 3D tokens, adding modality‐specific CLS tokens across tokenizers, and updating tests and asset JSON files accordingly.
Reviewed Changes
Copilot reviewed 16 out of 16 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| tests/lobster/tokenization/test__ume_tokenizers.py | Updates to reserved token names and test expectations; renamed test_ume_amino_acid_tokenizer for clarity. |
| src/lobster/tokenization/_ume_tokenizers.py | Modifications to special token definitions, reserved token generation, and post processor configuration; renaming functions and parameters to support modality-specific tokens. |
| src/lobster/assets/ume_tokenizers/* | Updates to tokenizer configuration and special tokens map files to reflect new CLS token names and reserved token ordering. |
Comments suppressed due to low confidence (1)
src/lobster/tokenization/_ume_tokenizers.py:334
- The function was renamed to _make_3d_coordinates_tokenizer_fast while the class remains named UmeLatentGenerator3DCoordTokenizerFast. Consider renaming the class to maintain a consistent naming convention for 3D coordinate tokenizers.
def _make_3d_coordinates_tokenizer_fast(vocab: list[str]) -> PreTrainedTokenizerFast:
ncfrey
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May 7, 2025
taylormjs
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May 14, 2025
* add <cls_modality> tokens * add <cls_modality> tokens * docstring
karinazad
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May 14, 2025
* peer fixes, add evaluate method * dataloader checkpoint callback (#60) * dataloader callback * utils * ume * gitignore dev * tests * update flash attention wheels (#61) * lock * torch 2.5 * torch 2.5 * part * .env * unpin flash attn (#62) * fix scheduler params (#64) * scheduler * fix scheduler * fix scheduler * Add AtomicaDataset (#63) Processed Atomica interactions dataset * Ume conversion/interaction tokenizer + fix SMILES and nucleotide tokenizers (#65) add two special tokens: <convert> and <interact> for later stages of Ume training: will be used as this: (or something like that) [CLS] PROT_SEQ [SEP] <convert> PROT_STRUCT(masked) [SEP] [CLS] PROT_SEQ [SEP] <interact> SMILES(masked) [SEP] extend functionality of UmeTokenizerTransform to handle dual modalities change the name of Ume embedding method and allow embedding from existing input_ids fix existing tokenizers: add lowercase normalized to nucleotide tokenizer (OG2 dataset contains a mix of upper and lowercase letters) BPE handled SMILES tokenization incorrectly, switch to WordLevel * Ume SMILES tokenizer fix (#66) * tokenizer * fix tests * lowercase normalizer for nt * tests * remove mod conv dataset * embed * Test * merge 2mod into UmeTokenizerTransform * fix tests * all * type hints * docstrings * tests * fix SMILES tokenizer * switch all tokenizer to BPE * Revert "switch all tokenizer to BPE" This reverts commit 367e77d. * tok * fix SMILES tokenizer * remove print statement * Ume perplexity logging (#67) * pplx * tests * src * ignore torchmetrics warnings * docstrings * docstrings * Update README.md (#69) * Ume fix perplexity device (#68) * pplx as attr * pplx as attr * pplx * comments * on step * comment * update tests, fix ruff * ruff * ruff ruff * Add <cls_modality> to Ume tokenizers (#71) * add <cls_modality> tokens * add <cls_modality> tokens * docstring * RNS metric implementation (#73) * add <cls_modality> tokens * add <cls_modality> tokens * modality embeddings * module dict * embeddings * tests * modality and device * rank zero only * rank zero * fix back modality mask * sync dist * RNS implementation * restore from main * restore * docstrings * docstrings * review * test * Ume modality-specific embeddings (#72) * add <cls_modality> tokens * add <cls_modality> tokens * modality embeddings * module dict * embeddings * tests * modality and device * rank zero only * rank zero * fix back modality mask * sync dist * add conversion transforms (#74) * add initial smiles to peptide and peptide to smiles transforms * remove smiles -> * transforms and touch up conversion functions * rename * add option to randomize smiles and caps --------- Co-authored-by: Colin Grambow <grambowc@gene.com> * fix def pad token, replace process_and_embed w/ ume.embed * update tests w -100 pad token --------- 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: Colin Grambow <17198155+cgrambow@users.noreply.github.com> Co-authored-by: Colin Grambow <grambowc@gene.com>
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For single modality tracks:
For conversion/interaction tasks: