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Documented how to speed up AUC calculation for region-based database.
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bramvds committed Apr 28, 2018
1 parent 85ff01f commit ca620bb
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions src/pyscenic/regions.py
Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,10 @@ class RegionRankingDatabase(InvertedRankingDatabase):
# signature). Potential mitigation challenges are:
# - Recoding the decompression of the inverted design using C++ and its standard template library. Impact will only
# be a constant factor while personal investment will be substantial.
# - Break the clean interface between database storage and AUC and recovery curve calculation. The exact order of
# the genes is not really required for AUC calculation so decompression times could be significantly reduced.
# - Break the clean interface between database storage and AUC and recovery curve calculation. The name of the
# genes that are at the top of a feature ranking is not necessary to calculate the AUC for enrichment of this
# feature. This fact can be used so that decompression times could be significantly reduced.
#
def __init__(self, fname: str, name: str):
super().__init__(fname, name)

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