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remove-background version 0.2.0 #71

Merged
merged 3 commits into from
Oct 16, 2020
Merged

remove-background version 0.2.0 #71

merged 3 commits into from
Oct 16, 2020

Commits on Oct 16, 2020

  1. Initial commit of v2 model 

    Added swapping model back in

Intermediate commit

Produces poster results for v2

Updates to include epsilon inference

Working status as of 20200114

Still a bug working with some v3 chem v2 cellranger input files where genes seem to get re-ordered?  Still slow.

Faster and improved log prob, learning rate schedule

Rho as a latent variable, epsilon set to 1

Approx log_prob = big speedup; better cell prob encoder

Big speedup from an approximate log_prob computation.
 Important changes with the encoder and regularizers lead to better performance on difficult test data.

Prevent NaNs late in training

It was noticed that (presumably due to underflow) late in training, alpha can include zero values, which become NaN.  Also put tougher constraints on rho params.

Solid on benchmarks

Code to include gene_ids, feature_types, antibodies

Data reading and writing

Write to cellranger format matching input file.  Include gene_ids.  Include all the things in v3 needed for scanpy to read it using sc.read_10x_h5()

Fix "simple" model errors

Add z to latent encoder, and fixes for "simple" model

Stale import, and a gene_ids MTX fix

Output dataset in same format (v2 or v3) as input

Fix typo

Fix gene_id parse error for CellRanger v2 h5

Extend the range of epsilon, correct an error in lam

Calculation of lambda had an error in its use of epsilon.  Epsilon previously had very limited range.  Most of the responsibility was on d.  Now most of the responsibility is shifted back to epsilon.  This improves noise removal especially in the case of swapping.

Update posterior inference to FPR calculation

updates to lambda multiplier handling

global overdispersion, no Dirichlet

Eliminate use of deprecated scheduler epoch param, preclude lambda infinite loop

Remove cooldown from LR scheduler, as it is deprecated

Code cleanup, no substance changes

Default learning rate 1e-4

Minor logging tweak

Tiny change: make a constant

Cosmetic code cleanup

More code cleanup

Move values to consts
    @sjfleming
    sjfleming committed Oct 16, 2020
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  2. Documentation updates 

    Update README.rst
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    sjfleming committed Oct 16, 2020
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  3. Update cellbender_remove_background.wdl

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    sjfleming committed Oct 16, 2020
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