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ArcInstitute / state Public

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Fork 154
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Aadduri/clean code#258

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abhinadduri wants to merge 18 commits intomainArcInstitute/state:mainfrom

aadduri/clean_codeArcInstitute/state:aadduri/clean_codeCopy head branch name to clipboard

Conversation Commits18 (18)Checks Files changed

Open

Aadduri/clean code#258
abhinadduri wants to merge 18 commits intomainfrom
aadduri/clean_code

Commits

Commits on Feb 21, 2026

remoed scgpt from code base, implementation exists in state-reproduce
abhinadduri
committed
removed cpa and scvi models from this repo as they are available in state reproduce
abhinadduri
committed
removes old neuralot model
abhinadduri
committed
removed stale vci fine tune decoder
abhinadduri
committed
removed batch token ablation as it does not work too well
abhinadduri
committed
removed confidence token which was also unused
abhinadduri
committed
removed combined loss as well as l1 regularization
abhinadduri
committed
removed the mmd chunks implementation
abhinadduri
committed

Commits on Feb 22, 2026

cleaned base perturbation model and latent to gene decoder to remove unused parameters
abhinadduri
committed
refactored wandb metrics names
abhinadduri
committed
updated to specify st training contract with cell load in readme
abhinadduri
committed
adds learning rate scheduling and choice of adam vs adamw in hydra config
abhinadduri
committed
updated residual to match main
abhinadduri
committed

Commits on Feb 23, 2026

correctly implemented nb nll loss to natively predict out counts
abhinadduri
committed
adds nb loss to config
abhinadduri
committed
chore: ruff
abhinadduri
committed
embedding output is incompatible with nb loss, also nb loss forces exp_counts from cell load
abhinadduri
committed
bump semvar and add is log1p logic for predict for metrics evaluator
abhinadduri
committed

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