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.

[Unreleased]#

Added#

[0.2.5] - 2026-04-21#

Added#

  • latent stat (n_vanished) logs during training

  • Disentanglement metric logs during training

  • Relax upper bounds of all dependencies

[0.2.4] - 2026-03-02#

Added#

  • Allow sparse input as X

  • Allow generating memory efficient sparse tensors as latent

[0.2.3] - 2026-02-27#

Added#

  • Added within distribution interpretability

  • An efficient implementation of out-of-distribution interpretability is added

  • plotting and getting relevant genes is now possible in DRVI model interface.

  • Setting latent dimension stats is now done in model interface. Previous util functions still work, but will show a deprecation warning.

  • Add tutorial for query to reference mapping

Changed#

  • The default value for vanished threshold in new the interface of set_latent_dimension_stats is 0.5 (previously 0.1).

  • Interpretability scores for the other direction of a non-vanished dimension is not shown if that direction is meaningless.

  • Main tutorial updated with the new interpretability interface

[0.2.2] - 2026-02-11#

Added#

  • Added “tutorials” optional dependency that was accidentally removed.

  • Code to allow loading models from previous versions with no problem

  • Add dispersion parameter to allow modeling batch dependent dispersion

Removed#

  • Removed “x_loglib”, “div_lib_x_loglib”, “x_loglib_all” library normalization techniques

  • Removed Vamp prior and GMM prior

  • Removed Legacy likelihood functions. Will raise error if used.

Changed#

  • gene_likelihood parameter now accepts different values compared to before. gene_likelihood parameter from old models will be mapped properly, but new users should look into the docs.

[0.2.1] - 2025-12-29#

Added#

  • Add support for Python 3.13

  • Allow subset reconstruction

  • Allow gradient scaling in the last layer

  • Allow setting vector size after mapping in “split_map@k” and “power@k” splitting functions.

  • Add support for Python 3.14

Removed#

  • Remove restrict dependencies. To ensure compatibility with old packages run for example: uvx --exclude-newer 2024-01-01 hatch run pytest

Changed#

  • Minor code improvements

  • Update to scverse template version 0.7.0

[0.2.0] - 2025-11-24#

Changed#

  • Update upper bound of all dependencies

  • Align with the latest changes of scvi-tools

Added#

  • Use cruft for scverse template management

[0.1.11] - 2025-11-19#

Added#

  • Add RnaSeqMixin from scvi-tools for RNA-seq specific methods (get_normalized_expression, differential_expression, posterior_predictive_sample, get_likelihood_parameters)

Fixed#

  • Fix bug in decode space handling where library size was not considered (issue #46)

  • Update decode_latent_samples logic (decode in log space by default)

  • Code improvements and bug fixes

[0.1.10] - 2025-11-18#

Removed#

  • Remove merlin data support and all related code

  • Remove merlin-dataloader dependency

Added#

  • Add dependabot for dependency update notification (not used now, for next releases)

[0.1.9] - 2025-07-01#

Added#

  • Add DRVI-APnoEXP baseline

Fixed#

  • Imorove documnetation for all classes and functions in repository

[0.1.8] - 2025-06-22#

Changed#

  • Discretize latent dimension values in MI for benchmarking due to this bug.

Fixed#

  • Fix a minor issue with drvi.utils.tl.traverse_latent

[0.1.7] - 2025-05-30#

Fixed#

  • Fix categorical lookup for reconstruction

[0.1.6] - 2025-05-22#

Changed#

  • Allow kwargs to pass through in plot_relevant_genes_on_umap

  • Update project CI structure

  • Extract tutorial notebooks to another repo to keep this repo clean

[0.1.5] - 2025-05-09#

Changed#

  • Refactor benchmarking code for better reusability

  • Revert callable for mean and var activation

[0.1.4] - 2025-04-17#

Fixed#

  • Limit anndata version for compatibility with old scvi-tools

[0.1.3] - 2025-02-12#

Added#

  • Introduce mean activation to make non-negative latents possible (docs will come later)

Fixed#

  • Better communication when Merlin is not installed

  • Raise error when interpretability is called on model with continues covariates

[0.1.2] - 2024-11-11#

Fixed#

  • No change in DRVI code

  • Fix github workflow, tests, docs, and pypi publishing pipelines

[0.1.0] - 2024-08-21#

Added#

  • Moved all files from repo to scverse cookiecutter project template