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Fix reaction-diffusion example and update GP predictive #639

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Merged
sgreenbury merged 8 commits into from
Jul 22, 2025
Merged

Fix reaction-diffusion example and update GP predictive #639

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3e8aeb2
Add notebook for v0 version and update hyperparams
sgreenbury Jul 14, 2025
3fb62c0
Revise to current GP default params, update comparison
sgreenbury Jul 21, 2025
6ade997
Add notebook comparison with observation noise
sgreenbury Jul 21, 2025
561e8ad
Fix lint
sgreenbury Jul 21, 2025
5b5b091
Add posterior_predictive to GP API and predict
sgreenbury Jul 21, 2025
5f11066
Update example
sgreenbury Jul 21, 2025
be3bb5e
Remove obsolete notebooks
sgreenbury Jul 21, 2025
877776b
Remove obsolete notebook, update revised notebook
sgreenbury Jul 21, 2025
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Remove obsolete notebook, update revised notebook
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@sgreenbury
sgreenbury committed Jul 21, 2025
commit 877776b89487286d32eb0fdea2471f52e0dec261
348 changes: 0 additions & 348 deletions docs/experimental/tutorials/05_reaction_diffusion_experimental.ipynb
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21 changes: 16 additions & 5 deletions docs/experimental/tutorials/emulation/03_reaction_diffusion_experimental.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,6 @@
"import warnings\n",
"warnings.filterwarnings(\"ignore\")\n",
"\n",
"from autoemulate.experimental.compare import AutoEmulate\n",
"from autoemulate.experimental.simulations.reaction_diffusion import ReactionDiffusion\n",
"from autoemulate.experimental.datasets import fetch_data\n",
"\n",
Expand Down Expand Up @@ -149,21 +148,33 @@
"metadata": {},
"outputs": [],
"source": [
"from autoemulate.experimental.emulators import GaussianProcessExact\n",
"from autoemulate.experimental.emulators.gaussian_process.exact import GaussianProcessExact\n",
"from autoemulate.experimental.emulators.gaussian_process.kernel import rbf_plus_constant\n",
"from autoemulate.experimental.emulators.gaussian_process.mean import constant_mean\n",
"from autoemulate.experimental.emulators.transformed.base import TransformedEmulator\n",
"from autoemulate.experimental.transforms import *\n",
"import torch \n",
"\n",
"# Convert to tensors\n",
"x, y = torch.Tensor(X).float(), torch.Tensor(Y).float()\n",
"\n",
"# Create a TransformedEmulator\n",
"em = TransformedEmulator(\n",
" x,\n",
" y,\n",
" model= GaussianProcessExact,\n",
" x_transforms=[StandardizeTransform()],\n",
" y_transforms=[\n",
" PCATransform(n_components=16)\n",
" StandardizeTransform(),\n",
" PCATransform(n_components=16),\n",
" StandardizeTransform()\n",
" ],\n",
")\n"
" epochs=50,\n",
" lr=0.2,\n",
" mean_module_fn=constant_mean,\n",
" covar_module_fn=rbf_plus_constant,\n",
" posterior_predictive=True\n",
")"
]
},
{
Expand Down Expand Up @@ -271,7 +282,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
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