From f20818d1c1631d43441aaf63b9bccb13aa32c0d3 Mon Sep 17 00:00:00 2001 From: Jason Vander Heiden Date: Wed, 11 Sep 2024 13:32:28 -0700 Subject: [PATCH] Update news. --- NEWS.rst | 33 ++++++++++++++++++++------------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/NEWS.rst b/NEWS.rst index 161e580..a3e09a3 100644 --- a/NEWS.rst +++ b/NEWS.rst @@ -4,28 +4,35 @@ Release Notes Version 0.3.0 pre-release notes: September 11, 2024 ------------------------------------------------------------------------------- -Exhaustive queries: +General: + + Various changes to utility functions to improve efficiency. + + Tutorials have been updated with new download links and analyses. + +Exhaustive queries: + Functionality to perform exhaustive queries has been added as the new - method `cell_query.search_exhaustive`. - + The kNN query method `cell_query.search` has been renamed to - `cell_query.search_nearest`. + method ``cell_query.search_exhaustive``. + + The kNN query method ``cell_query.search`` has been renamed to + ``cell_query.search_nearest``. Query result filtering and interpretation: + + The ``cell_query.compile_sample_metadata`` method has been expanded to + allow grouping by tissue and disease (in addition to study and sample). + + The methods ``utils.subset_by_unique_values``, + ``utils.subset_by_frequency``, and ``utils.categorize_and_sort_by_score`` + have been added to provide tools for filtering, sorting and summarizing + query results. + + The "query_stability" quality control metric has been renamed to + "query_coherence" and is now deterministic (by setting a random seed). + Results from exhaustive queries can be constrained to specific - metadata criteria (e.g. tissue, disease, in vitro vs in vivo, etc.) - using the `metadata_filter` argument to `cell_query.search_exhaustive`. + metadata criteria (e.g., tissue, disease, in vitro vs in vivo, etc). + using the ``metadata_filter`` argument to ``cell_query.search_exhaustive``. + Results from exhaustive queries can be constrained by distance-to-query - using the `max_dist` argument to `cell_query.search_exhaustive`. - + The `cell_query.compile_sample_metadata` method has been expanded to - allow grouping by tissue and disease (in addition to study and sample). - + The methods `utils.subset_by_unique_values`, `utils.subset_by_frequency`, - and `utils.categorize_and_sort_by_score` have been added to provide - tools for filtering, sorting and summarizing query results. + using the ``max_dist`` argument to ``cell_query.search_exhaustive``. Optimizations to training: + The ASW and NMSE training evaluation metrics were added to multiple methods. - + The `triplet_selector.get_asw` method was added to calculate ASW. + + The ``triplet_selector.get_asw`` method was added to calculate ASW. + Optimized sampling weights of study and cell type.