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* changed to tf on ensembl * added info on genes expressed and mapped * logger * github pr rerun checks * Bump version to 1.8.1 --------- Co-authored-by: maxime <maxime@helical-ai.com>
Included embeddings for the following species: * canis_lupus_familiaris * macaca_fascicularis * rattus_norvegicus * sus_scrofa as per [Ensembl](https://ftp.ensembl.org/pub/current/fasta/)
More ESM-2 embeddings
Fixing typo in ESM-2 configs on S3 for 4 additional species
This change allows transcriptformer to accept multiple vocabularies of gene embeddings for out-of-sample species
Lists of gene vocabs for TF
add function to get all gene ranks from adata object using rve
Current implementation permutes indices of special tokens: ``` [START]: 2 -> 1 [END]: 3 -> 2 [RD]: 4 -> 3 [CELL]: 5 -> 4 [PAD]: 1 -> 5 [MASK]: 6 -> 6 ``` This fix makes sure we preserve the indices of the special tokens when performing vocabulary surgery.
Chore/version bump Conflict resolution with `release`
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Please do not squash when merging |
priyankvyas
approved these changes
Mar 13, 2026
dmiv-helical
approved these changes
Mar 13, 2026
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dmiv-helical
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This one is huge because we have to replay some of the history due to a previous squash
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