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C2s attention returns genenames and optimisation#329

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martinaoliver merged 21 commits intomainfrom
c2s_attention_genenames
Feb 10, 2026
Merged

C2s attention returns genenames and optimisation#329
martinaoliver merged 21 commits intomainfrom
c2s_attention_genenames

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@martinaoliver martinaoliver commented Feb 6, 2026

Three updates for optimisation and compatibility with attention map analysis

  1. get_embeddings function now also returns gene_names_list (order of gene names ranked by tokenizer).
  2. _aggregate_token_to_word_attention has GPU implementation for speedup
  3. Only process layer selected with emb_layer
    ***NOTE: This function is not being called in bioagents for inference with c2s - is only being used to retrieve attention maps

@bputzeys bputzeys requested a review from maxiallard February 9, 2026 08:31
@martinaoliver martinaoliver changed the title C2s attention genenames C2s attention returns genenames and optimisation Feb 9, 2026
@martinaoliver martinaoliver marked this pull request as draft February 9, 2026 12:31
@martinaoliver martinaoliver marked this pull request as ready for review February 9, 2026 12:39
@martinaoliver martinaoliver merged commit 38c6574 into main Feb 10, 2026
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bputzeys added a commit that referenced this pull request Feb 11, 2026
C2s attention returns genenames and optimisation (#329)
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3 participants