Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.3.2] - 2025-12-16#

Added#

  • tutorial for regression

  • support for sample-covariate embeddings, experimental, only one-hot

Changed#

  • removed muon from dependencies for tutorials

  • changed the classification tutorial to include training across 3 CV folds

Fixed#

  • fixed a bug in regression which was caused by a wrong key when accessing the continuous covariates registered with scvi-tools

[0.3.1] - 2025-07-14#

Fixed#

  • Fixed a bug in score_top_cells that didn’t set the specified key_added column in .obs to True.

  • Fixed a bug in score_top_cells that set the key_added to be categorical, which resulted in wrong indexing in get_sample_representations.

[0.3.0] - 2025-07-13#

Added#

  • Utility functions: Added score_top_cells and get_sample_representations to utils module

  • score_top_cells: Function to identify and score top cells based on attention weights

  • get_sample_representations: Function to aggregate cell-level data to sample-level representations

Changed#

  • Major refactoring: Removed MultiVAE and MultiVAE_MIL models, keeping only MIL classifier

  • Code cleanup: Removed MLP attention weight learning from Aggregator class

  • Parameter consistency: Fixed default values between model and module classes

  • Dynamic z_dim: Automatically infer z_dim from input data shape instead of hardcoded value

Fixed#

  • Make categorical covariates categorical: Ensure the correct type in setup_anndata.

  • Improved error handling: If the prediction covariate hasn’t been registered with setup_anndata, throw an error.

  • Dead links to API and changelog: Fixed in README.

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