diff --git a/docs/_config.yml b/docs/_config.yml index 60b485868..6d8ef26aa 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -9,7 +9,9 @@ theme: # Force re-execution of notebooks on each build. # See https://jupyterbook.org/content/execute.html execute: - execute_notebooks: force + execute_notebooks: 'off' + exclude_tags: + - skip-execution # Define the name of the latex output file for PDF builds latex: diff --git a/docs/tutorials/02_speed.ipynb b/docs/tutorials/02_speed.ipynb index c88c75240..e47012e0c 100644 --- a/docs/tutorials/02_speed.ipynb +++ b/docs/tutorials/02_speed.ipynb @@ -27,16 +27,7 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/mstoffel/turing/projects/autoemulate/autoemulate/compare.py:8: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n", - " from tqdm.autonotebook import tqdm\n" - ] - } - ], + "outputs": [], "source": [ "from sklearn.datasets import make_regression\n", "from autoemulate.compare import AutoEmulate" @@ -126,11 +117,23 @@ "
| \n", + " | preprocessing | \n", + "model | \n", + "short | \n", + "fold | \n", + "rmse | \n", + "r2 | \n", + "
|---|---|---|---|---|---|---|
| 0 | \n", + "None | \n", + "SupportVectorMachines | \n", + "svm | \n", + "2 | \n", + "8.720925 | \n", + "0.997536 | \n", + "
| 1 | \n", + "None | \n", + "SupportVectorMachines | \n", + "svm | \n", + "0 | \n", + "7.939373 | \n", + "0.997482 | \n", + "
| 2 | \n", + "None | \n", + "SupportVectorMachines | \n", + "svm | \n", + "1 | \n", + "9.151469 | \n", + "0.997225 | \n", + "
| 3 | \n", + "None | \n", + "SupportVectorMachines | \n", + "svm | \n", + "3 | \n", + "9.114729 | \n", + "0.997204 | \n", + "
| 4 | \n", + "None | \n", + "SupportVectorMachines | \n", + "svm | \n", + "4 | \n", + "8.731051 | \n", + "0.997105 | \n", + "
| \n", + " | model | \n", + "short | \n", + "preprocessing | \n", + "rmse | \n", + "r2 | \n", + "
|---|---|---|---|---|---|
| 0 | \n", + "GaussianProcess | \n", + "gp | \n", + "None | \n", + "4.4152 | \n", + "0.9952 | \n", + "
| \n", + " | ao.r | \n", + "ao.c | \n", + "art.r | \n", + "art.c | \n", + "ven.r | \n", + "ven.c | \n", + "av.r | \n", + "mv.r | \n", + "la.E_pas | \n", + "la.E_act | \n", + "la.v_ref | \n", + "la.k_pas | \n", + "lv.E_pas | \n", + "lv.E_act | \n", + "lv.v_ref | \n", + "lv.k_pas | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "296.440885 | \n", + "0.396672 | \n", + "1015.055683 | \n", + "1.988679 | \n", + "6.507542 | \n", + "167.642001 | \n", + "5.485211 | \n", + "3.162309 | \n", + "0.233027 | \n", + "0.326324 | \n", + "12.565421 | \n", + "0.022142 | \n", + "1.443565 | \n", + "3.103660 | \n", + "7.226351 | \n", + "0.025244 | \n", + "
| 1 | \n", + "170.936176 | \n", + "0.430408 | \n", + "810.882333 | \n", + "2.385469 | \n", + "10.865371 | \n", + "147.729601 | \n", + "5.217009 | \n", + "5.843980 | \n", + "0.254431 | \n", + "0.435555 | \n", + "14.803089 | \n", + "0.035664 | \n", + "0.854612 | \n", + "2.958498 | \n", + "8.912569 | \n", + "0.039591 | \n", + "
| 2 | \n", + "224.910382 | \n", + "0.215161 | \n", + "1669.192723 | \n", + "1.551490 | \n", + "10.593887 | \n", + "88.536086 | \n", + "4.763047 | \n", + "3.939957 | \n", + "0.516216 | \n", + "0.304267 | \n", + "6.212975 | \n", + "0.020790 | \n", + "1.461334 | \n", + "4.461589 | \n", + "8.717625 | \n", + "0.031072 | \n", + "
| 3 | \n", + "315.206213 | \n", + "0.151029 | \n", + "1201.130539 | \n", + "3.547849 | \n", + "6.280902 | \n", + "139.960518 | \n", + "4.016971 | \n", + "5.931769 | \n", + "0.629961 | \n", + "0.387896 | \n", + "14.515793 | \n", + "0.048657 | \n", + "1.499412 | \n", + "3.940640 | \n", + "14.773632 | \n", + "0.010744 | \n", + "
| 4 | \n", + "220.269324 | \n", + "0.387451 | \n", + "933.723349 | \n", + "3.972825 | \n", + "5.981294 | \n", + "165.658227 | \n", + "6.785018 | \n", + "3.791956 | \n", + "0.381240 | \n", + "0.458787 | \n", + "11.295892 | \n", + "0.064039 | \n", + "0.929570 | \n", + "3.532311 | \n", + "9.808989 | \n", + "0.010605 | \n", + "
| \n", + " | 0 | \n", + "1 | \n", + "2 | \n", + "3 | \n", + "4 | \n", + "5 | \n", + "6 | \n", + "7 | \n", + "
|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "15.168249 | \n", + "20.161629 | \n", + "18.472553 | \n", + "4.993380 | \n", + "15.168249 | \n", + "20.161629 | \n", + "18.472553 | \n", + "4.993380 | \n", + "
| 1 | \n", + "36.019994 | \n", + "39.135503 | \n", + "37.573478 | \n", + "3.115509 | \n", + "36.019994 | \n", + "39.135503 | \n", + "37.573478 | \n", + "3.115509 | \n", + "
| 2 | \n", + "26.756008 | \n", + "26.886811 | \n", + "26.814212 | \n", + "0.130803 | \n", + "26.756008 | \n", + "26.886811 | \n", + "26.814212 | \n", + "0.130803 | \n", + "
| 3 | \n", + "2.411396 | \n", + "7.086565 | \n", + "5.246729 | \n", + "4.675169 | \n", + "2.411396 | \n", + "7.086565 | \n", + "5.246729 | \n", + "4.675169 | \n", + "
| 4 | \n", + "1.594468 | \n", + "5.884158 | \n", + "4.283615 | \n", + "4.289690 | \n", + "1.594468 | \n", + "5.884158 | \n", + "4.283615 | \n", + "4.289690 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 95 | \n", + "4.781580 | \n", + "15.237328 | \n", + "13.694896 | \n", + "10.455748 | \n", + "4.781580 | \n", + "15.237328 | \n", + "13.694896 | \n", + "10.455748 | \n", + "
| 96 | \n", + "11.317115 | \n", + "20.156449 | \n", + "18.979320 | \n", + "8.839334 | \n", + "11.317115 | \n", + "20.156449 | \n", + "18.979320 | \n", + "8.839334 | \n", + "
| 97 | \n", + "18.666848 | \n", + "23.334430 | \n", + "21.667915 | \n", + "4.667582 | \n", + "18.666848 | \n", + "23.334430 | \n", + "21.667915 | \n", + "4.667582 | \n", + "
| 98 | \n", + "12.985272 | \n", + "24.617342 | \n", + "23.214435 | \n", + "11.632069 | \n", + "12.985272 | \n", + "24.617342 | \n", + "23.214435 | \n", + "11.632069 | \n", + "
| 99 | \n", + "9.713965 | \n", + "15.335051 | \n", + "14.554911 | \n", + "5.621086 | \n", + "9.713965 | \n", + "15.335051 | \n", + "14.554911 | \n", + "5.621086 | \n", + "
100 rows × 8 columns
\n", + "AutoEmulate is set up with the following settings:
" + ], + "text/plain": [ + "| \n", + " | Values | \n", + "
|---|---|
| Simulation input shape (X) | \n", + "(100, 16) | \n", + "
| Simulation output shape (y) | \n", + "(100, 8) | \n", + "
| Proportion of data for testing (test_set_size) | \n", + "0.2 | \n", + "
| Scale input data (scale) | \n", + "True | \n", + "
| Scaler (scaler) | \n", + "StandardScaler | \n", + "
| Scale output data (scale_output) | \n", + "True | \n", + "
| Scaler output (scaler_output) | \n", + "StandardScaler | \n", + "
| Do hyperparameter search (param_search) | \n", + "False | \n", + "
| Reduce input dimensionality (reduce_dim) | \n", + "False | \n", + "
| Reduce output dimensionality (reduce_dim_output) | \n", + "True | \n", + "
| Dimensionality output reduction methods (dim_reducer_output) | \n", + "PCA | \n", + "
| Cross validator (cross_validator) | \n", + "KFold | \n", + "
| Parallel jobs (n_jobs) | \n", + "1 | \n", + "
| \n", + " | preprocessing | \n", + "model | \n", + "short | \n", + "fold | \n", + "rmse | \n", + "r2 | \n", + "
|---|---|---|---|---|---|---|
| 0 | \n", + "PCA | \n", + "GaussianProcess | \n", + "gp | \n", + "4 | \n", + "1.640022 | \n", + "0.916621 | \n", + "
| 1 | \n", + "PCA | \n", + "GaussianProcess | \n", + "gp | \n", + "2 | \n", + "3.126992 | \n", + "0.874326 | \n", + "
| 2 | \n", + "PCA | \n", + "GaussianProcess | \n", + "gp | \n", + "0 | \n", + "2.790274 | \n", + "0.864704 | \n", + "
| 3 | \n", + "PCA | \n", + "GaussianProcess | \n", + "gp | \n", + "3 | \n", + "3.622270 | \n", + "0.846636 | \n", + "
| 4 | \n", + "PCA | \n", + "GaussianProcess | \n", + "gp | \n", + "1 | \n", + "2.794191 | \n", + "0.774314 | \n", + "
InputOutputPipeline(regressor=Pipeline(steps=[('scaler', StandardScaler()),\n",
+ " ('model', GaussianProcess())]),\n",
+ " transformer=Pipeline(steps=[('scaler_output',\n",
+ " StandardScaler()),\n",
+ " ('dim_reducer_output',\n",
+ " PCA(n_components=2))]))In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. InputOutputPipeline(regressor=Pipeline(steps=[('scaler', StandardScaler()),\n",
+ " ('model', GaussianProcess())]),\n",
+ " transformer=Pipeline(steps=[('scaler_output',\n",
+ " StandardScaler()),\n",
+ " ('dim_reducer_output',\n",
+ " PCA(n_components=2))]))Pipeline(steps=[('scaler', StandardScaler()), ('model', GaussianProcess())])StandardScaler()
GaussianProcess()
Pipeline(steps=[('scaler_output', StandardScaler()),\n",
+ " ('dim_reducer_output', PCA(n_components=2))])StandardScaler()
PCA(n_components=2)
| \n", + " | model | \n", + "short | \n", + "preprocessing | \n", + "rmse | \n", + "r2 | \n", + "
|---|---|---|---|---|---|
| 0 | \n", + "GaussianProcess | \n", + "gp | \n", + "PCA | \n", + "3.9183 | \n", + "0.7697 | \n", + "
InputOutputPipeline(regressor=Pipeline(steps=[('scaler', StandardScaler()),\n",
+ " ('model', GaussianProcess())]),\n",
+ " transformer=Pipeline(steps=[('scaler_output',\n",
+ " StandardScaler()),\n",
+ " ('dim_reducer_output',\n",
+ " PCA(n_components=2))]))In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. InputOutputPipeline(regressor=Pipeline(steps=[('scaler', StandardScaler()),\n",
+ " ('model', GaussianProcess())]),\n",
+ " transformer=Pipeline(steps=[('scaler_output',\n",
+ " StandardScaler()),\n",
+ " ('dim_reducer_output',\n",
+ " PCA(n_components=2))]))Pipeline(steps=[('scaler', StandardScaler()), ('model', GaussianProcess())])StandardScaler()
GaussianProcess()
Pipeline(steps=[('scaler_output', StandardScaler()),\n",
+ " ('dim_reducer_output', PCA(n_components=2))])StandardScaler()
PCA(n_components=2)
| \n", + " | output | \n", + "parameter | \n", + "index | \n", + "value | \n", + "confidence | \n", + "
|---|---|---|---|---|---|
| 0 | \n", + "y1 | \n", + "ao.r | \n", + "S1 | \n", + "0.000054 | \n", + "0.000009 | \n", + "
| 1 | \n", + "y1 | \n", + "ao.c | \n", + "S1 | \n", + "0.000197 | \n", + "0.000032 | \n", + "
| 2 | \n", + "y1 | \n", + "art.r | \n", + "S1 | \n", + "0.000349 | \n", + "0.000040 | \n", + "
| 3 | \n", + "y1 | \n", + "art.c | \n", + "S1 | \n", + "0.000073 | \n", + "0.000011 | \n", + "
| 4 | \n", + "y1 | \n", + "ven.r | \n", + "S1 | \n", + "0.000271 | \n", + "0.000060 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 115 | \n", + "y8 | \n", + "(lv.E_pas, lv.v_ref) | \n", + "S2 | \n", + "-0.004675 | \n", + "0.050165 | \n", + "
| 116 | \n", + "y8 | \n", + "(lv.E_pas, lv.k_pas) | \n", + "S2 | \n", + "0.098837 | \n", + "0.057726 | \n", + "
| 117 | \n", + "y8 | \n", + "(lv.E_act, lv.v_ref) | \n", + "S2 | \n", + "0.005969 | \n", + "0.018428 | \n", + "
| 118 | \n", + "y8 | \n", + "(lv.E_act, lv.k_pas) | \n", + "S2 | \n", + "0.001894 | \n", + "0.022177 | \n", + "
| 119 | \n", + "y8 | \n", + "(lv.v_ref, lv.k_pas) | \n", + "S2 | \n", + "0.002823 | \n", + "0.018446 | \n", + "
1216 rows × 5 columns
\n", + "