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Refactor: add transforms and transformed emulator #474
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9698fbf
Add transformed emulator and transform class, add PCA transform
sgreenbury 944bd32
Add kwargs
sgreenbury 77c1b32
Add example notebook
sgreenbury 81321e3
Add _inverse_sample method
sgreenbury 844ff56
Add refit placeholder
sgreenbury 50394e0
Add initial test for transformed emulator
sgreenbury cdc404b
Add check for whether fitted
sgreenbury a6d2de2
Initial reimpl of VAE for refactor
sgreenbury 7a9d501
Assert transform ops on TensorLike
sgreenbury 372190b
Update poetry.lock
sgreenbury 4f08241
Add utils and apply make_positive_definite
sgreenbury 725ce86
Fix missing VAE init
sgreenbury 80107c0
Add delta method for VAE
sgreenbury fe8c0fe
Add tests for transforms
sgreenbury 2555143
Make transforms optional
sgreenbury 37f0906
Add spectral approach, generalize test
sgreenbury d5bb502
Fix _inverse_sample shapes
sgreenbury 6c4b8b3
Add test for inverse for gaussians
sgreenbury 31c4a4b
Add fallback to sample if delta method fails
sgreenbury 29ac348
Begin standardize transform
sgreenbury 66647ba
Merge remote-tracking branch 'origin/main' into 348-refactor-preproce…
sgreenbury 8325738
Fix import
sgreenbury e40da06
Initial standardize transform
sgreenbury 8ec6c1b
Refactor common functionality to base class for transforms
sgreenbury 0746610
Split basis_matrix and expanded_basis_matrix
sgreenbury 333a5ba
Add kwargs to init for transformed emulator
sgreenbury f97748b
Update example notebook
sgreenbury 904efc3
Add _cast, implement refit
sgreenbury f92be14
Add StandardizeTransform to init
sgreenbury 754d208
Fix error msg, remove todo
sgreenbury f539acb
Fix case when elements of std are 0
sgreenbury 5152b21
Extend tests
sgreenbury 261faa7
Increase default number of retries
sgreenbury 1c5644d
Update example notebook
sgreenbury f95abf5
Remove CNPModule from emulators
sgreenbury 5843c68
Extend test to all emulators
sgreenbury 06ccaa0
Add fixture with many targets
sgreenbury f9a925f
Ensure finite std
sgreenbury f34ca3a
Revise make_positive_definite fn
sgreenbury 09d7151
Add tests for large number of targets
sgreenbury 97b1aa8
Remove test with VAE transform without standardize
sgreenbury d930a5b
Fix pre-commit
sgreenbury 4720548
Refactors
sgreenbury 3c84ead
Update test cases for large number of targets
sgreenbury 0a89d2e
Add niter to PCA
sgreenbury 4962183
Add test for PCA
sgreenbury 2964d18
Fix sample method
sgreenbury 8ab2b95
Add initial tests comparing sample and basis transform
sgreenbury 08c5cbd
Add prediction with sampled outputs for transformed emulator
sgreenbury 986fd6a
Add required fields
sgreenbury fde4a10
Initial reaction diffusion with experimental
sgreenbury cd524f6
Fixing the sampling approaches, use linear ops for large cov matrix
sgreenbury e00d498
Only test cases with reduction for 100 targets
sgreenbury bff4e45
Add tests for 1000 targets, add todo
sgreenbury 9ba545a
Update notebooks
sgreenbury 585a624
Add device
sgreenbury dd770ed
Revise function defaults, add warnings and docstring
sgreenbury c9ba448
Remove retain_graph argument
sgreenbury b7a08bf
Add comments
sgreenbury 3f87bee
Merge remote-tracking branch 'origin/main' into 348-refactor-preproce…
sgreenbury e99b7c8
Move transforms notebook to exploratory
sgreenbury fcccf07
Extend examples in notebook and explore error rate
sgreenbury 7baedb9
Extend tests for transforms
sgreenbury 3f763ac
Refine test for VAE inv transforms
sgreenbury bf1ef40
Merge branch 'main' into 348-refactor-preprocessing
sgreenbury 3a5a617
Fix condition to retrain transforms
sgreenbury b723a8b
Refactor attribute aassignment
sgreenbury c7749a8
Revise docstrings
sgreenbury 63025a5
Fix lints
sgreenbury bb5dc25
Refactor variable names and docstrings
sgreenbury 1926abf
Update default device argument
sgreenbury ebf7dff
Revise TransformedEmulator API variable names and docstrings
sgreenbury f9bfc3a
Add docstring and refactor VAETrasnform
sgreenbury 499fb4c
Move experimental reaction diffusion to experimental docs
sgreenbury 1cc4d70
Update and extend _inverse_sample docstring
sgreenbury f886b7c
Update and extend docstrings
sgreenbury fc2f886
Add issue number for todo
sgreenbury ad52543
Add mixins to base transform
sgreenbury 57d37f0
Add check_matrix call in StandardizeTransform
sgreenbury a75a24b
Remove niter in PCA test
sgreenbury d68894c
Update init and remove cache from API
sgreenbury 98fd93e
Update fit with check, move comments, add type hints
sgreenbury 2902587
Revise cache_size in API, add docstrings
sgreenbury 3323ca9
Refactor with _convert_to_dataloader method
sgreenbury 64e71b8
Add diagram for fitting
sgreenbury 28dcbf1
Add and revise docstrings for clarity and completeness
sgreenbury 062686d
Revise method for compatibility with base
sgreenbury 9d299bb
Rename methods for clarity
sgreenbury e04ee4f
Merge branch 'main' into 348-refactor-preprocessing
sgreenbury 31f16d0
Rename to random_seed, add todo
sgreenbury ef26951
Fix docstring
sgreenbury File filter
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,13 +1,14 @@ | ||
from .gaussian_process.exact import GaussianProcessExact | ||
from .lightgbm import LightGBM | ||
from .neural_processes.conditional_neural_process import CNPModule | ||
|
||
# from .neural_processes.conditional_neural_process import CNPModule | ||
from .random_forest import RandomForest | ||
from .svm import SupportVectorMachine | ||
|
||
ALL_EMULATORS = [ | ||
GaussianProcessExact, | ||
LightGBM, | ||
CNPModule, | ||
# CNPModule, | ||
SupportVectorMachine, | ||
RandomForest, | ||
] |
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