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TensorFlow 2 model fitting for negative binomial noise#88

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picciama wants to merge 142 commits intodevelopmentfrom
tf2
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TensorFlow 2 model fitting for negative binomial noise#88
picciama wants to merge 142 commits intodevelopmentfrom
tf2

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@picciama
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@picciama picciama commented Oct 22, 2019

Adds tensorflow 2 specific code at batchglm/train/tf2/.
Includes negative binomial noise model.
No changes in other folders were made.
To import, we will need to apply changes to api/models/glm_nb.py, so that it can import from batchglm/train/tf2/ instead of batchglm/train/tf/

@davidsebfischer davidsebfischer changed the title Eager executing TensorFlow 2 training with negative binomial noise TensorFlow 2 model fitting for negative binomial noise Oct 23, 2019
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picciama commented Nov 5, 2019 •
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Branch tf2_compatibility merged into tf2. Tf2 can now be merged with dev.
tf2 api has been added on the tf2_compatibility branch before, but doesn't affect tf1.

@picciama picciama self-assigned this Nov 5, 2019
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davidsebfischer commented Nov 8, 2019

Checking locally:

git diff --name-status tf2..tf2_compatibility
D batchglm/train/tf2/init.py
D batchglm/train/tf2/base/init.py
D batchglm/train/tf2/base/estimator.py
D batchglm/train/tf2/base/external.py
D batchglm/train/tf2/base/model.py
D batchglm/train/tf2/base/optim.py
D batchglm/train/tf2/base_glm/README.md
D batchglm/train/tf2/base_glm/init.py
D batchglm/train/tf2/base_glm/estimator.py
D batchglm/train/tf2/base_glm/external.py
D batchglm/train/tf2/base_glm/layers.py
D batchglm/train/tf2/base_glm/layers_gradients.py
D batchglm/train/tf2/base_glm/model.py
D batchglm/train/tf2/base_glm/optim.py
D batchglm/train/tf2/base_glm/processModel.py
D batchglm/train/tf2/base_glm/training_strategies.py
D batchglm/train/tf2/base_glm/vars.py
D batchglm/train/tf2/glm_beta/init.py
D batchglm/train/tf2/glm_beta/estimator.py
D batchglm/train/tf2/glm_beta/external.py
D batchglm/train/tf2/glm_beta/layers.py
D batchglm/train/tf2/glm_beta/layers_gradients.py
D batchglm/train/tf2/glm_beta/model.py
D batchglm/train/tf2/glm_beta/processModel.py
D batchglm/train/tf2/glm_beta/vars.py
D batchglm/train/tf2/glm_nb/init.py
D batchglm/train/tf2/glm_nb/estimator.py
D batchglm/train/tf2/glm_nb/external.py
D batchglm/train/tf2/glm_nb/layers.py
D batchglm/train/tf2/glm_nb/layers_gradients.py
D batchglm/train/tf2/glm_nb/model.py
D batchglm/train/tf2/glm_nb/processModel.py
D batchglm/train/tf2/glm_nb/vars.py

All changes are in tf2, that looks fine.

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davidsebfischer commented Nov 8, 2019

waiting for #92

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picciama commented Nov 13, 2019

refactoring finished. The arguments for the training_method are not identical to the ones in train/tf1 which allows to access the method from within diffxpy.

picciama added 27 commits April 22, 2020 18:41
@picciama
Merge branch 'dev' into linesearch_tf2
2407938
@picciama
Merge branch 'dev' into tf2
4a3491c
@picciama
make TRTOL same as XTOL
bece862
@picciama
cleanup train/base, rm Loss class
20e7188
@picciama
rm layers as args, Loss + add layers in base class
83648d2
@picciama
cleanup glm_norm folder, rm Loss
dc4fd93
@picciama
cleanup glm_beta folder, rm Loss
1a46283
@picciama
ll_dtype->self.dtype in likelihood
ae9d864
@picciama
rm Loss
3fc33b5
@picciama
add support for irls(_tr)_gd_tr, cleanup
7ab343e
@picciama
cleanup, revert updates not only if tr_mode
98d3fe6
@picciama
pass dtype to keras superclass for all layers
75ed5b8
@picciama
jumpt to scale update if loc already converged
2e1557c
@picciama
add support for irls(_tr)_gd_tr
a61b0dd
@picciama
rm Loss
7264bf8
@picciama
alpha0 addet for armijo line search
a7539b0
@picciama
bugfix: scale grads zero if b_update_freq change
b0e6bd4
@picciama
updated known optimizer strings
7c8c0ba
@picciama
style issue fix
0082b82
@picciama
rm IRLS_LS strategy
621083d
@picciama
bugfix: NaNs in armijo steplength
fd7ca8c
@picciama
Merge branch 'linesearch_tf2' into tf2
e848d00
@picciama
default b_update-freq set to 1
ba7e1a9
@picciama
bugfix for #44: fisher_inv not saved in property
64f46c6
@picciama
removed TODO after bugfix #44
5d03ee0
@picciama
simplify masking
699d26d
@picciama
cleanup
e85a881
@ilan-gold ilan-gold mentioned this pull request Jan 27, 2022
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@picciama picciama mentioned this pull request Feb 1, 2022
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@picciama picciama changed the base branch from dev to development September 23, 2022 14:49
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