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broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
https://cellbender.rtfd.io
BSD 3-Clause "New" or "Revised" License
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Add soft constraints to the model for semi-supervision of cell probabilities #202

Closed sjfleming closed 1 year ago

sjfleming commented 1 year ago

For the droplets that are "surely cells" or "surely empties", use a soft constraint to ensure that the cell probability encoder does not get off-track.

sjfleming commented 1 year ago

The soft constraint is implemented as a pyro.factor penalty that is grows exponentially if the output starts to deviate from the known truth.