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Adding mixin classes for pyro training and posterior sampling #1059

Merged
merged 62 commits into from
Jun 19, 2021
Merged

Adding mixin classes for pyro training and posterior sampling #1059

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72b19df
added mixin classes for pyro training and sampling
vitkl May 12, 2021
3ef3404
Merge branch 'master' into pyro-mixin
vitkl May 12, 2021
78bcb47
added tests
vitkl May 12, 2021
8650427
added test with local variables
vitkl May 12, 2021
a9ad0d2
refactored posterior sampling, replaced tqdm, other minor changes
vitkl May 14, 2021
a05d658
Merge branch 'YosefLab:master' into pyro-mixin
vitkl May 14, 2021
9ff126e
using TrainRunner
vitkl May 14, 2021
276b2b3
Merge branch 'pyro-mixin' of github.com:vitkl/scvi-tools into pyro-mixin
vitkl May 14, 2021
700aff2
fixed parameter shape test
vitkl May 14, 2021
abf94ac
Merge branch 'master' into pyro-mixin
vitkl May 14, 2021
f393362
Merge branch 'master' into pyro-mixin
vitkl May 14, 2021
0fd40c4
deleted full data specific training code
vitkl May 15, 2021
d649947
posterior sampling with batch_size=None
vitkl May 15, 2021
c3da184
get rid of for loop in sampling global param
vitkl May 15, 2021
264d683
device-backed dataloader, providing batch size to sample_posterior, t…
vitkl May 16, 2021
f071f2f
clear pyro param store when initialising new model
vitkl May 17, 2021
7b34c51
Update scvi/model/base/_pyromixin.py
vitkl May 17, 2021
b020ff5
Update scvi/model/base/_pyromixin.py
vitkl May 17, 2021
cb3cae9
guide callback
vitkl May 19, 2021
ff54ecf
Merge branch 'pyro-mixin' of github.com:vitkl/scvi-tools into pyro-mixin
vitkl May 19, 2021
187019d
Merge branch 'master' into pyro-mixin
vitkl May 19, 2021
97288cb
commented guide callback
vitkl May 19, 2021
963495d
Merge branch 'master' into pyro-mixin
vitkl May 20, 2021
600649e
Merge branch 'master' into pyro-mixin
vitkl May 22, 2021
08dbe1f
list_obs_plate_vars as module property, incl default
vitkl May 22, 2021
b53b75b
updated docs
vitkl May 22, 2021
0cb9e60
guess obs plate sites without list_obs_plate_vars
vitkl May 22, 2021
ed796c0
fixed guide warmup dataloader callback;
vitkl May 24, 2021
deddaab
remove redundant dataloader in test
vitkl May 24, 2021
0621d8c
gpu None default
vitkl May 24, 2021
40146c6
consistent use GPU docs
vitkl May 24, 2021
151ccea
do not move data to device again for sampling global variables
vitkl May 24, 2021
27b3ecf
updated docs and lr interface for default optimiser
vitkl May 24, 2021
38ba6ba
updated docs
vitkl May 24, 2021
28e03fc
updated docs
vitkl May 24, 2021
7dd6d80
more flexible sample_posterior with summary_fun dict
vitkl May 24, 2021
a2a3376
add to docs
adamgayoso May 24, 2021
4406654
Merge branch 'master' into pyro-mixin
adamgayoso May 24, 2021
e830682
Update scvi/model/base/_pyromixin.py
vitkl May 28, 2021
b589016
Update scvi/train/_trainingplans.py
vitkl May 28, 2021
bfa3685
Update scvi/model/base/_pyromixin.py
vitkl May 28, 2021
580992d
Update scvi/model/base/_pyromixin.py
vitkl May 28, 2021
4a2720f
Merge branch 'YosefLab:master' into pyro-mixin
vitkl May 31, 2021
dccfd74
default batch size and doc edits
vitkl May 31, 2021
b9b57b1
updated tests and docs
vitkl May 31, 2021
ee65f57
exposed sample_kwargs
vitkl May 31, 2021
46c430f
updated docs
vitkl May 31, 2021
5a53fc9
updated docs
vitkl May 31, 2021
0eb4a16
updated docs
vitkl May 31, 2021
4bb2d5b
updated docs
vitkl May 31, 2021
9c38f00
renamed sts -> stds
vitkl Jun 1, 2021
f9652f2
fix model history issue for pyro on load
adamgayoso Jun 19, 2021
9148c5d
documentation
adamgayoso Jun 19, 2021
611448e
elbo should be average
adamgayoso Jun 19, 2021
e9b1e01
codacy
adamgayoso Jun 19, 2021
e586e9e
Merge branch 'master' into pyro-mixin
adamgayoso Jun 19, 2021
7238244
codacy/docs
adamgayoso Jun 19, 2021
e15bf39
show attrs in docs
adamgayoso Jun 19, 2021
08cc1de
sphinx copy button version
adamgayoso Jun 19, 2021
e4c3072
other doc fixes
adamgayoso Jun 19, 2021
ea05899
fix class template
adamgayoso Jun 19, 2021
52759bb
template
adamgayoso Jun 19, 2021
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4 changes: 4 additions & 0 deletions scvi/model/base/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from ._archesmixin import ArchesMixin
from ._base_model import BaseModelClass
from ._pyromixin import PyroJitGuideWarmup, PyroSampleMixin, PyroSviTrainMixin
from ._rnamixin import RNASeqMixin
from ._training_mixin import UnsupervisedTrainingMixin
from ._vaemixin import VAEMixin
Expand All @@ -10,4 +11,7 @@
"RNASeqMixin",
"VAEMixin",
"UnsupervisedTrainingMixin",
"PyroSviTrainMixin",
"PyroSampleMixin",
"PyroJitGuideWarmup",
]
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