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Pull Request Overview
This PR addresses modifications in the UME model to change how perplexity metrics are stored and accessed during training and validation. Key changes include replacing the metrics dictionary with dynamic attributes using setattr, and adjusting the logging of perplexity metrics accordingly.
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src/lobster/model/_ume.py:146
- [nitpick] Using attribute names with a slash (e.g., "train_perplexity/{modality.value}") is unconventional and may lead to confusion when accessing these attributes. Consider using a valid identifier format, such as replacing the slash with an underscore.
setattr(self, f"train_perplexity/{modality.value}", Perplexity(ignore_index=-100))
| metric = getattr(self, metric_name) | ||
| metric(logits_reshaped[mask], labels_reshaped[mask]) | ||
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| self.log(metric_name, metric, sync_dist=True) |
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The updated logging call no longer specifies the on_step parameter, which changes the logging behavior compared to previous implementations. If this change is intentional, please document the rationale to ensure consistent logging.
Suggested change
| self.log(metric_name, metric, sync_dist=True) | |
| self.log(metric_name, metric, on_step=True, sync_dist=True) |
ncfrey
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May 2, 2025
ncfrey
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May 2, 2025
taylormjs
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May 6, 2025
* pplx as attr * pplx as attr * pplx * comments * on step * comment
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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