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Log ei change #259

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merged 13 commits into from
Jan 8, 2025
Merged

Log ei change #259

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e0f545b
change expected improvement to log expected improvement
roussel-ryan Jan 7, 2025
4a3ed0f
formatting
roussel-ryan Jan 7, 2025
49c25e5
remove ucb log validator
roussel-ryan Jan 7, 2025
af8bfdc
Merge branch 'main' into log-ei-change
roussel-ryan Jan 7, 2025
326e83b
correct import
roussel-ryan Jan 7, 2025
33422ad
fix tests + remove old test
roussel-ryan Jan 7, 2025
e49a6f2
formatting
roussel-ryan Jan 7, 2025
ad5ce76
update examples
roussel-ryan Jan 7, 2025
6275620
remove outputs
roussel-ryan Jan 7, 2025
826f098
remove magic command
roussel-ryan Jan 7, 2025
94356b8
fix bugs in notebooks
roussel-ryan Jan 7, 2025
f6f8c42
clear notebook outputs
roussel-ryan Jan 8, 2025
3c9bc66
formatting
roussel-ryan Jan 8, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -127,3 +127,4 @@ private_tests/*

# Don't include JupyterLab language server (LSP) files:
/.virtual_documents
*.csv
34 changes: 1 addition & 33 deletions docs/examples/bayes_exp/bayesian_exploration.ipynb
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Expand Up @@ -33,10 +33,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:51.865697700Z",
"start_time": "2023-09-19T18:54:48.783739700Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:35.830514Z",
"iopub.status.busy": "2024-09-13T15:49:35.830266Z",
Expand Down Expand Up @@ -99,10 +95,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:51.916698600Z",
"start_time": "2023-09-19T18:54:51.867698800Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:37.522962Z",
"iopub.status.busy": "2024-09-13T15:49:37.522764Z",
Expand All @@ -122,10 +114,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:55.212579300Z",
"start_time": "2023-09-19T18:54:51.897698400Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:37.531732Z",
"iopub.status.busy": "2024-09-13T15:49:37.531635Z",
Expand All @@ -147,10 +135,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:55.227580Z",
"start_time": "2023-09-19T18:54:55.212579300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:39.056947Z",
"iopub.status.busy": "2024-09-13T15:49:39.056826Z",
Expand All @@ -171,10 +155,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:55.947579900Z",
"start_time": "2023-09-19T18:54:55.230580300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:39.062334Z",
"iopub.status.busy": "2024-09-13T15:49:39.062246Z",
Expand Down Expand Up @@ -238,10 +218,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:58.766007500Z",
"start_time": "2023-09-19T18:54:58.724008300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:40.599399Z",
"iopub.status.busy": "2024-09-13T15:49:40.599290Z",
Expand All @@ -258,7 +234,7 @@
"for name, val in X.generator.model.named_parameters():\n",
" print(f\"{name}:{val}\")\n",
"\n",
"X.generator.model.models[2].covar_module.base_kernel.lengthscale"
"X.generator.model.models[2].covar_module.lengthscale"
]
},
{
Expand All @@ -279,10 +255,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:54:58.776010Z",
"start_time": "2023-09-19T18:54:58.746008900Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:40.605375Z",
"iopub.status.busy": "2024-09-13T15:49:40.605292Z",
Expand All @@ -302,10 +274,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-19T18:55:02.760921Z",
"start_time": "2023-09-19T18:54:58.766007500Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:49:40.611135Z",
"iopub.status.busy": "2024-09-13T15:49:40.611035Z",
Expand Down
2 changes: 1 addition & 1 deletion docs/examples/bayes_exp/bayesian_exploration_w_interpolation.ipynb
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Expand Up @@ -264,7 +264,7 @@
"for name, val in X.generator.model.named_parameters():\n",
" print(f\"{name}:{val}\")\n",
"\n",
"X.generator.model.models[2].covar_module.base_kernel.lengthscale"
"X.generator.model.models[2].covar_module.lengthscale"
]
},
{
Expand Down
6 changes: 3 additions & 3 deletions docs/examples/cnsga/cnsga_tnk.ipynb
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Expand Up @@ -260,7 +260,7 @@
"strict: False\n",
"generator:\n",
" name: cnsga\n",
" population_size: 64\n",
" population_size: 32\n",
" population_file: test.csv\n",
" output_path: .\n",
"\n",
Expand Down Expand Up @@ -613,14 +613,14 @@
"strict: False\n",
"generator:\n",
" name: cnsga\n",
" population_size: 64\n",
" population_size: 32\n",
"\n",
"evaluator:\n",
" function: __main__.evaluate_TNK2\n",
" function_kwargs:\n",
" raise_probability: 0.1\n",
" vectorized: True\n",
" max_workers: 100 \n",
" max_workers: 32\n",
"\n",
"vocs:\n",
" variables:\n",
Expand Down
41 changes: 25 additions & 16 deletions docs/examples/gp_model_creation/model_creation.ipynb
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Expand Up @@ -22,8 +22,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:45:11.242373800Z",
"start_time": "2024-04-24T14:45:05.850560800Z"
"end_time": "2025-01-07T21:01:37.888221500Z",
"start_time": "2025-01-07T21:01:33.895927300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:57.465196Z",
Expand Down Expand Up @@ -84,8 +84,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:45:11.261375100Z",
"start_time": "2024-04-24T14:45:11.244374300Z"
"end_time": "2025-01-07T21:01:37.891750100Z",
"start_time": "2025-01-07T21:01:37.890225800Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:59.042358Z",
Expand All @@ -104,8 +104,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:45:13.955823900Z",
"start_time": "2024-04-24T14:45:11.260373200Z"
"end_time": "2025-01-07T21:01:38.729744700Z",
"start_time": "2025-01-07T21:01:37.892751300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:59.045209Z",
Expand Down Expand Up @@ -148,8 +148,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:45:13.998821Z",
"start_time": "2024-04-24T14:45:13.958825500Z"
"end_time": "2025-01-07T21:01:38.736745Z",
"start_time": "2025-01-07T21:01:38.731745300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:59.303297Z",
Expand All @@ -172,8 +172,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:45:14.007821800Z",
"start_time": "2024-04-24T14:45:13.974821300Z"
"end_time": "2025-01-07T21:06:12.904773200Z",
"start_time": "2025-01-07T21:06:12.899686500Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:59.307614Z",
Expand All @@ -185,10 +185,23 @@
"outputs": [],
"source": [
"# print real values - note that these are in normalized coordinates\n",
"print(\"outputscale:\", objective_model.covar_module.outputscale.data)\n",
"print(\"prior mean:\", objective_model.mean_module.constant.data)\n",
"print(\"noise:\", objective_model.likelihood.noise_covar.noise.data)\n",
"print(\"lengthscales\", objective_model.covar_module.base_kernel.lengthscale.data)"
"print(\"lengthscales\", objective_model.covar_module.lengthscale.data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2025-01-07T21:02:08.637731400Z",
"start_time": "2025-01-07T21:02:08.632699900Z"
}
},
"outputs": [],
"source": [
"objective_model"
]
},
{
Expand All @@ -207,10 +220,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2024-04-24T14:49:36.001389300Z",
"start_time": "2024-04-24T14:49:35.410177700Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:59.311380Z",
"iopub.status.busy": "2024-09-13T15:56:59.311290Z",
Expand Down
17 changes: 0 additions & 17 deletions docs/examples/multi_objective_bayes_opt/mobo.ipynb
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Expand Up @@ -242,23 +242,6 @@
"print(candidate[[\"x1\", \"x2\"]].to_numpy())\n",
"ax.plot(*candidate[[\"x1\", \"x2\"]].to_numpy()[0], \"o\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-13T15:57:37.628734Z",
"iopub.status.busy": "2024-09-13T15:57:37.628594Z",
"iopub.status.idle": "2024-09-13T15:57:37.935451Z",
"shell.execute_reply": "2024-09-13T15:57:37.935103Z"
}
},
"outputs": [],
"source": [
"%%time\n",
"candidate = X.generator.generate(1)"
]
}
],
"metadata": {
Expand Down
24 changes: 12 additions & 12 deletions docs/examples/single_objective_bayes_opt/constrained_bo_tutorial.ipynb
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Expand Up @@ -32,8 +32,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-05T19:42:57.249481900Z",
"start_time": "2023-09-05T19:42:54.284575600Z"
"end_time": "2025-01-07T20:55:57.751261500Z",
"start_time": "2025-01-07T20:55:53.793271Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:22.206398Z",
Expand Down Expand Up @@ -74,8 +74,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-05T19:42:57.265086500Z",
"start_time": "2023-09-05T19:42:57.251814200Z"
"end_time": "2025-01-07T20:55:57.766139300Z",
"start_time": "2025-01-07T20:55:57.738794400Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:23.776855Z",
Expand Down Expand Up @@ -115,8 +115,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-05T19:42:57.283085300Z",
"start_time": "2023-09-05T19:42:57.267088500Z"
"end_time": "2025-01-07T20:55:57.766682400Z",
"start_time": "2025-01-07T20:55:57.751261500Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:23.780319Z",
Expand Down Expand Up @@ -157,8 +157,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-05T19:42:57.323085Z",
"start_time": "2023-09-05T19:42:57.284084500Z"
"end_time": "2025-01-07T20:55:57.767710800Z",
"start_time": "2025-01-07T20:55:57.766139300Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:23.786867Z",
Expand Down Expand Up @@ -199,8 +199,8 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2023-09-05T19:44:14.815598300Z",
"start_time": "2023-09-05T19:43:54.788355100Z"
"end_time": "2025-01-07T20:57:47.398979200Z",
"start_time": "2025-01-07T20:57:37.742437900Z"
},
"execution": {
"iopub.execute_input": "2024-09-13T15:56:23.870983Z",
Expand All @@ -227,8 +227,8 @@
"\n",
" # add ground truth functions to plots\n",
" out = test_function({\"x\": test_x})\n",
" ax[0].plot(test_x, out[\"f\"], \"C0-.\")\n",
" ax[1].plot(test_x, out[\"c\"], \"C2-.\")\n",
" ax[0, 0].plot(test_x, out[\"f\"], \"C0-.\")\n",
" ax[1, 0].plot(test_x, out[\"c\"], \"C2-.\")\n",
"\n",
" # do the optimization step\n",
" X.step()"
Expand Down
8 changes: 4 additions & 4 deletions docs/examples/single_objective_bayes_opt/custom_model.ipynb
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Expand Up @@ -155,8 +155,8 @@
"\n",
"fig, ax = generator.visualize_model(n_grid=len(test_x))\n",
"# plot ground truth\n",
"ax[0].plot(test_x, y(test_x), \"C0-.\")\n",
"ax[1].plot(test_x, c(test_x), \"C2-.\");"
"ax[0, 0].plot(test_x, y(test_x), \"C0-.\")\n",
"ax[1, 0].plot(test_x, c(test_x), \"C2-.\");"
]
},
{
Expand Down Expand Up @@ -260,8 +260,8 @@
"\n",
"fig, ax = generator.visualize_model(n_grid=len(test_x))\n",
"# plot ground truth\n",
"ax[0].plot(test_x, y(test_x), \"C0-.\")\n",
"ax[1].plot(test_x, c(test_x), \"C2-.\");"
"ax[0, 0].plot(test_x, y(test_x), \"C0-.\")\n",
"ax[1, 0].plot(test_x, c(test_x), \"C2-.\");"
]
},
{
Expand Down
1 change: 0 additions & 1 deletion docs/examples/single_objective_bayes_opt/custom_objective.ipynb
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Expand Up @@ -132,7 +132,6 @@
"generator = ExpectedImprovementGenerator(\n",
" vocs=vocs,\n",
" custom_objective=MyObjective(vocs),\n",
" log_transform_acquisition_function=True,\n",
")\n",
"X = Xopt(evaluator=evaluator, generator=generator, vocs=vocs)\n",
"print(X)\n",
Expand Down
2 changes: 1 addition & 1 deletion docs/examples/single_objective_bayes_opt/heteroskedastic_noise_tutorial.ipynb
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Expand Up @@ -234,7 +234,7 @@
"\n",
" # plot true function\n",
" true_f = sin_function({\"x\": test_x})[\"f\"]\n",
" ax[0].plot(test_x, true_f, \"C1--\")\n",
" ax[0, 0].plot(test_x, true_f, \"C1--\")\n",
"\n",
" # do the optimization step\n",
" X.step()"
Expand Down
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