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updates to st infer, se fit/transform/eval

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@abhinadduri abhinadduri released this 19 Sep 18:51
v0.9.27
7224ef9
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Learn about vigilant mode.

several improvements in this overdue change log.

  1. infer now correctly groups control cells by shared covariates. see here for examples of running inference: https://colab.research.google.com/drive/1bq5v7hixnM-tZHwNdgPiuuDo6kuiwLKJ?authuser=1#scrollTo=ENfnF6ofAz1M

  2. the embedding model checkpoints are now completely packaged (so no more model folder is needed). we retain backwards compatibility. here is an example for running transform: https://colab.research.google.com/drive/1uJinTJLSesJeot0mP254fQpSxGuDEsZt

  3. the auxillary files to train the SE model, as well as the complete training data, are available here: https://huggingface.co/datasets/arcinstitute/SE-167M-Human

some notes on how to train SE yourself: #138 (comment)

  1. new eval scripts for SE checkpoints: use uv run state emb eval
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