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GPU support and optimizations for posterior model #156

Merged
merged 24 commits into from
Nov 7, 2024
Merged

GPU support and optimizations for posterior model #156

merged 24 commits into from
Nov 7, 2024

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davidbenjamin
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Continuing in the spirit of recent work by @fatsmcgee

@davidbenjamin
inference batch size argument added to training and pruning WDLs
b150017
@davidbenjamin
artifact model and data don't carry around the ref_alt_seq embeddings
ce55c7e
@davidbenjamin
consolidate IntTensors in ArtifactBatch
2d365a9
@davidbenjamin
same for the ArtifactBatch's is_labeled_mask
771e704
@davidbenjamin
variants, counts_and_seq_lks, are stored as np arrays in ArtifactBatch
465049e
@davidbenjamin
get rid of a coupe pesky warnings
cb05115
@davidbenjamin
hoping to fix the pesky no artists warning by adding label= to all pl…
7fbe302 
…otting
@davidbenjamin
increase LR scheduler patience to 5 since we have introduced ramped-u…
431aa59 
…p adversarial losses
@davidbenjamin
PosteriorBatch no longer keeps original_data -- everything is tensors
bdeab02
@davidbenjamin
GPU in call variants WDL
3d8b136
@davidbenjamin
using torch.inference_mode() in filter_variants (except for learning …
2cafcae 
…spectra etc)
@davidbenjamin
randn had to be created on the right device
9ee8a20
@davidbenjamin
more device carefulness
ebef11f
@davidbenjamin
whoops
d3797dd
@davidbenjamin
whoops same
ea8a60e
@davidbenjamin
CPU / GPU consistency in spectra plotting method
80426e2
@davidbenjamin
more of same
b4d8f08
@davidbenjamin
and still more CPU / GPU
f1de432
@davidbenjamin
same -- they keep coming
8f4a329
@davidbenjamin
MORE OF SAME
3a82bd1
@davidbenjamin
whoops, but getting closer to no bugs
1293bda
@davidbenjamin
quick bug fix edge case
55e3745
@davidbenjamin
pseudocounts to avoid divide by zero
3074c25
@davidbenjamin
whoops, totally wrong logic for posterior batch get variants due to m…
089d72e 
…issing colon
@davidbenjamin davidbenjamin merged commit 6a8919a into master Nov 7, 2024
@davidbenjamin davidbenjamin deleted the db_followup branch November 7, 2024 02:21
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@davidbenjamin