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kernels working on a given set of features #476

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merged 45 commits into from
Jan 16, 2025
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ac7de64
kernels working on a given set of features
e-dorigatti Dec 4, 2024
a806dc0
pre-commit
e-dorigatti Dec 4, 2024
c3f1899
test map singletaskgp with additive kernel
R-M-Lee Dec 4, 2024
86b6ad6
test active_dims of mapped kernels
R-M-Lee Dec 4, 2024
b4458fb
add features_to_idx_mapper to outlier detection tutorial
R-M-Lee Dec 4, 2024
d243ad0
correctly handling categorical mol features
e-dorigatti Dec 4, 2024
842797f
validating mol features transforms
e-dorigatti Dec 4, 2024
22c4382
verifying proper type
e-dorigatti Dec 6, 2024
17d8350
custom hamming kernel enabling single task gp on categorical features
e-dorigatti Dec 19, 2024
6ad1dfd
removed unnecessary parameter from data model
e-dorigatti Dec 19, 2024
4a2a547
testing equivalence of mixed gp and single gp with custom kernel
e-dorigatti Dec 19, 2024
3750827
(temporary) running on all py versions
e-dorigatti Dec 19, 2024
7162983
(temporary) debug github actions by printing
e-dorigatti Dec 19, 2024
01a01e1
more printing
e-dorigatti Dec 19, 2024
1cd2776
Revert "testing equivalence of mixed gp and single gp with custom ker…
e-dorigatti Dec 19, 2024
8400fdb
Revert "removed unnecessary parameter from data model"
e-dorigatti Dec 19, 2024
2e29852
Revert "custom hamming kernel enabling single task gp on categorical …
e-dorigatti Dec 19, 2024
7e455b7
Revert "Revert "custom hamming kernel enabling single task gp on cate…
e-dorigatti Dec 19, 2024
25f947b
Revert "Revert "testing equivalence of mixed gp and single gp with cu…
e-dorigatti Dec 19, 2024
2c145b6
removed test debug and restored to latest implemented features
e-dorigatti Dec 19, 2024
30dd123
pinning compatible version of formulaic
e-dorigatti Dec 19, 2024
065824f
Merge branch 'main' into 474-kernels-on-feature-subsets
e-dorigatti Dec 19, 2024
b53d3bb
pinning compatible version of formulaic
e-dorigatti Dec 19, 2024
8d47cbd
removed old code
e-dorigatti Dec 19, 2024
ce38428
lint
e-dorigatti Dec 19, 2024
16bdc1f
removed scratch file
e-dorigatti Dec 19, 2024
e306d16
removed old code again
e-dorigatti Dec 19, 2024
9d5dfc6
silencing pyright false positive
e-dorigatti Dec 19, 2024
62ba2c2
compatibility with py39
e-dorigatti Dec 19, 2024
d2c1f5d
pin compatible version of formulaic
e-dorigatti Dec 19, 2024
966bf8b
restored old code
e-dorigatti Dec 19, 2024
231f9f6
pinning sklearn
e-dorigatti Dec 19, 2024
6a7c9d7
pinning sklearn
e-dorigatti Dec 19, 2024
6576547
pinning scikit everywhere
e-dorigatti Dec 19, 2024
3e79e31
Merge branch '488-tests-failing-with-formulaic=11' into 474-kernels-o…
e-dorigatti Dec 19, 2024
e70cc16
not testing for prediction quality
e-dorigatti Dec 20, 2024
54b3c7f
matching lengthscale constraints in hamming kernel
e-dorigatti Dec 20, 2024
9b32536
removed equivalence test
e-dorigatti Dec 20, 2024
831a03e
testing hamming kernel
e-dorigatti Dec 20, 2024
561ac20
added test for mol features in single task gp
e-dorigatti Jan 13, 2025
1867e7b
categorical onehot kernel uses the right lengthscale for multiple fea…
e-dorigatti Jan 13, 2025
f30ed6d
removed redundant check
e-dorigatti Jan 13, 2025
7afcd7c
more descriptive name for base kernel
e-dorigatti Jan 13, 2025
d6e2957
updated docstring
e-dorigatti Jan 13, 2025
16d831c
improved tests and comments
e-dorigatti Jan 14, 2025
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removed scratch file
e-dorigatti committed Dec 19, 2024
commit 16bdc1f26a467250ded294d0b745b76b44739a4b
132 changes: 0 additions & 132 deletions scratch.py

This file was deleted.


Unchanged files with check annotations Beta

) -> GpytorchKernel:
active_dims = _compute_active_dims(data_model, active_dims, features_to_idx_mapper)
if data_model.with_one_hots is None:

Check failure on line 222 in bofire/kernels/mapper.py

GitHub Actions / lint

Cannot access member "with_one_hots" for type "HammingDistanceKernel"   Member "with_one_hots" is unknown (reportGeneralTypeIssues)
with_one_hots = data_model.features is not None and len(active_dims) > 1
else:
with_one_hots = data_model.with_one_hots

Check failure on line 225 in bofire/kernels/mapper.py

GitHub Actions / lint

Cannot access member "with_one_hots" for type "HammingDistanceKernel"   Member "with_one_hots" is unknown (reportGeneralTypeIssues)
if with_one_hots and len(active_dims) == 1:
raise RuntimeError(
elif isinstance(feature, CategoricalMolecularInput):
preproc = self.input_preprocessing_specs[feat]
if not isinstance(preproc, AnyMolFeatures):

Check failure on line 659 in bofire/strategies/predictives/botorch.py

GitHub Actions / lint

Argument of type "AnyMolFeatures" cannot be assigned to parameter "__class_or_tuple" of type "_ClassInfo" in function "isinstance"   Type "object" cannot be assigned to type "_ClassInfo"     "object" is incompatible with "type"     "object" is incompatible with "tuple[_ClassInfo, ...]" (reportGeneralTypeIssues)
raise ValueError(
f"preprocessing for {feat} must be of type AnyMolFeatures"
)