/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lib/__init__.py:32: UserWarning: JAX on Mac ARM machines is experimental and minimally tested. Please see https://github.com/google/jax/issues/5501 in the event of problems.
+ warnings.warn("JAX on Mac ARM machines is experimental and minimally tested. "
+
+
---------------------------------------------------------------------------
-ModuleNotFoundErrorTraceback (most recent call last)
+AttributeErrorTraceback (most recent call last)
Input In [4], in <cell line: 1>()----> 1fromtensorflow.kerasimportdatasets,layers,models2fromtensorflow.keras.layersimportInput
@@ -1216,14 +1247,122 @@ labels = (n_inputs) = (1797,)
30fromtensorflow.lite.pythonimportwrap_toco31fromtensorflow.lite.python.convert_phaseimportComponent
-File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:26,in<module>
-23importsix
-24fromsix.movesimportrange
----> 26importflatbuffers
-27fromtensorflow.core.protobufimportconfig_pb2as_config_pb2
-28fromtensorflow.core.protobufimportgraph_debug_info_pb2
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:51,in<module>
+47# Jax functions used by TFLite
+48# pylint: disable=g-import-not-at-top
+49# pylint: disable=unused-import
+50try:
+---> 51fromjaximportxla_computationas_xla_computation
+52exceptImportError:
+53_xla_computation=None
-ModuleNotFoundError: No module named 'flatbuffers'
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/__init__.py:116,in<module>
+40from._src.configimport(
+41configasconfig,
+42enable_checksasenable_checks,
+ (...)
+51numpy_rank_promotionasnumpy_rank_promotion,
+52)
+53from._src.apiimport(
+54ad,# TODO(phawkins): update users to avoid this.
+55checkpointascheckpoint,
+ (...)
+114xla_computationasxla_computation,
+115)
+--> 116from.experimental.mapsimportsoft_pmapassoft_pmap
+117from.versionimport__version__as__version__
+119# These submodules are separate because they are in an import cycle with
+120# jax and rely on the names imported above.
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/experimental/maps.py:26,in<module>
+23fromfunctoolsimportwraps,partial,partialmethod
+24fromenumimportEnum
+---> 26from..importnumpyasjnp
+27from..importcore
+28from..importlinear_utilaslu
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/__init__.py:19,in<module>
+1# Copyright 2018 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+17
+18# flake8: noqa: F401
+---> 19from.importfftasfft
+20from.importlinalgaslinalg
+22fromjax.interpreters.xlaimportDeviceArrayasDeviceArray
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/fft.py:17,in<module>
+1# Copyright 2020 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+14
+15# flake8: noqa: F401
+---> 17fromjax._src.numpy.fftimport(
+18ifftasifft,
+19ifft2asifft2,
+20ifftnasifftn,
+21ifftshiftasifftshift,
+22ihfftasihfft,
+23irfftasirfft,
+24irfft2asirfft2,
+25irfftnasirfftn,
+26fftasfft,
+27fft2asfft2,
+28fftfreqasfftfreq,
+29fftnasfftn,
+30fftshiftasfftshift,
+31hfftashfft,
+32rfftasrfft,
+33rfft2asrfft2,
+34rfftfreqasrfftfreq,
+35rfftnasrfftn,
+36)
+38# Module initialization is encapsulated in a function to avoid accidental
+39# namespace pollution.
+40_NOT_IMPLEMENTED=[]
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/numpy/fft.py:19,in<module>
+16importoperator
+17importnumpyasnp
+---> 19fromjaximportlax
+20fromjax._src.libimportxla_client
+21fromjax._src.utilimportsafe_zip
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/lax/__init__.py:332,in<module>
+299fromjax._src.lax.laximport(_reduce_sum,_reduce_max,_reduce_min,_reduce_or,
+300_reduce_and,_reduce_window_sum,_reduce_window_max,
+301_reduce_window_min,_reduce_window_prod,
+ (...)
+306_upcast_fp16_for_computation,_broadcasting_shape_rule,
+307_eye,_tri,_delta,_ones,_zeros,_dilate_shape)
+308fromjax._src.lax.control_flowimport(
+309associative_scanasassociative_scan,
+310condascond,
+ (...)
+330while_paswhile_p,
+331)
+--> 332fromjax._src.lax.fftimport(
+333fftasfft,
+334fft_pasfft_p,
+335)
+336fromjax._src.lax.parallelimport(
+337all_gatherasall_gather,
+338all_to_allasall_to_all,
+ (...)
+355xeinsumasxeinsum,
+356)
+357fromjax._src.lax.otherimport(
+358conv_general_dilated_patchesasconv_general_dilated_patches
+359)
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lax/fft.py:145,in<module>
+143batching.primitive_batchers[fft_p]=fft_batching_rule
+144ifpocketfft:
+--> 145xla.backend_specific_translations['cpu'][fft_p]=pocketfft.pocketfft
+
+AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
@@ -538,8 +566,12 @@ systems such as automatic translation and speech-to-text.
+
/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lib/__init__.py:32: UserWarning: JAX on Mac ARM machines is experimental and minimally tested. Please see https://github.com/google/jax/issues/5501 in the event of problems.
+ warnings.warn("JAX on Mac ARM machines is experimental and minimally tested. "
+
+
---------------------------------------------------------------------------
-ModuleNotFoundErrorTraceback (most recent call last)
+AttributeErrorTraceback (most recent call last)
Input In [1], in <cell line: 7>()5importnumpyasnp6importmatplotlib.pyplotasplt
@@ -627,14 +659,122 @@ systems such as automatic translation and speech-to-text.
30fromtensorflow.lite.pythonimportwrap_toco31fromtensorflow.lite.python.convert_phaseimportComponent
-File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:26,in<module>
-23importsix
-24fromsix.movesimportrange
----> 26importflatbuffers
-27fromtensorflow.core.protobufimportconfig_pb2as_config_pb2
-28fromtensorflow.core.protobufimportgraph_debug_info_pb2
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:51,in<module>
+47# Jax functions used by TFLite
+48# pylint: disable=g-import-not-at-top
+49# pylint: disable=unused-import
+50try:
+---> 51fromjaximportxla_computationas_xla_computation
+52exceptImportError:
+53_xla_computation=None
-ModuleNotFoundError: No module named 'flatbuffers'
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/__init__.py:116,in<module>
+40from._src.configimport(
+41configasconfig,
+42enable_checksasenable_checks,
+ (...)
+51numpy_rank_promotionasnumpy_rank_promotion,
+52)
+53from._src.apiimport(
+54ad,# TODO(phawkins): update users to avoid this.
+55checkpointascheckpoint,
+ (...)
+114xla_computationasxla_computation,
+115)
+--> 116from.experimental.mapsimportsoft_pmapassoft_pmap
+117from.versionimport__version__as__version__
+119# These submodules are separate because they are in an import cycle with
+120# jax and rely on the names imported above.
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/experimental/maps.py:26,in<module>
+23fromfunctoolsimportwraps,partial,partialmethod
+24fromenumimportEnum
+---> 26from..importnumpyasjnp
+27from..importcore
+28from..importlinear_utilaslu
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/__init__.py:19,in<module>
+1# Copyright 2018 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+17
+18# flake8: noqa: F401
+---> 19from.importfftasfft
+20from.importlinalgaslinalg
+22fromjax.interpreters.xlaimportDeviceArrayasDeviceArray
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/fft.py:17,in<module>
+1# Copyright 2020 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+14
+15# flake8: noqa: F401
+---> 17fromjax._src.numpy.fftimport(
+18ifftasifft,
+19ifft2asifft2,
+20ifftnasifftn,
+21ifftshiftasifftshift,
+22ihfftasihfft,
+23irfftasirfft,
+24irfft2asirfft2,
+25irfftnasirfftn,
+26fftasfft,
+27fft2asfft2,
+28fftfreqasfftfreq,
+29fftnasfftn,
+30fftshiftasfftshift,
+31hfftashfft,
+32rfftasrfft,
+33rfft2asrfft2,
+34rfftfreqasrfftfreq,
+35rfftnasrfftn,
+36)
+38# Module initialization is encapsulated in a function to avoid accidental
+39# namespace pollution.
+40_NOT_IMPLEMENTED=[]
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/numpy/fft.py:19,in<module>
+16importoperator
+17importnumpyasnp
+---> 19fromjaximportlax
+20fromjax._src.libimportxla_client
+21fromjax._src.utilimportsafe_zip
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/lax/__init__.py:332,in<module>
+299fromjax._src.lax.laximport(_reduce_sum,_reduce_max,_reduce_min,_reduce_or,
+300_reduce_and,_reduce_window_sum,_reduce_window_max,
+301_reduce_window_min,_reduce_window_prod,
+ (...)
+306_upcast_fp16_for_computation,_broadcasting_shape_rule,
+307_eye,_tri,_delta,_ones,_zeros,_dilate_shape)
+308fromjax._src.lax.control_flowimport(
+309associative_scanasassociative_scan,
+310condascond,
+ (...)
+330while_paswhile_p,
+331)
+--> 332fromjax._src.lax.fftimport(
+333fftasfft,
+334fft_pasfft_p,
+335)
+336fromjax._src.lax.parallelimport(
+337all_gatherasall_gather,
+338all_to_allasall_to_all,
+ (...)
+355xeinsumasxeinsum,
+356)
+357fromjax._src.lax.otherimport(
+358conv_general_dilated_patchesasconv_general_dilated_patches
+359)
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lax/fft.py:145,in<module>
+143batching.primitive_batchers[fft_p]=fft_batching_rule
+144ifpocketfft:
+--> 145xla.backend_specific_translations['cpu'][fft_p]=pocketfft.pocketfft
+
+AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
Polynomial degree: 11
Error: 0.07160048164232538
Bias^2: 0.014436800088896381
Var: 0.05716368155342902
@@ -1508,12 +1535,12 @@ Mean squared error on test data: 0.17446471
Degree of polynomial: 13
Mean squared error on training data: 0.00759119
Mean squared error on test data: 1.08131003
-
-
-
Degree of polynomial: 14
+Degree of polynomial: 14
Mean squared error on training data: 0.00472199
Mean squared error on test data: 0.81333804
-Degree of polynomial: 15
+
+
+
Degree of polynomial: 15
Mean squared error on training data: 0.00410478
Mean squared error on test data: 92.09172409
Degree of polynomial: 16
@@ -1528,12 +1555,12 @@ Mean squared error on test data: 108.27092910
Degree of polynomial: 19
Mean squared error on training data: 0.00156376
Mean squared error on test data: 1371.99051150
-
-
-
Degree of polynomial: 20
+Degree of polynomial: 20
Mean squared error on training data: 0.00137818
Mean squared error on test data: 1887.86252988
-Degree of polynomial: 21
+
+
+
Degree of polynomial: 21
Mean squared error on training data: 0.00118508
Mean squared error on test data: 14859.69908626
Degree of polynomial: 22
@@ -1548,12 +1575,12 @@ Mean squared error on test data: 1277.61702282
Degree of polynomial: 25
Mean squared error on training data: 0.00079129
Mean squared error on test data: 128664.31650694
-
-
-
Degree of polynomial: 26
+Degree of polynomial: 26
Mean squared error on training data: 0.00076905
Mean squared error on test data: 19003.94822514
-Degree of polynomial: 27
+
+
+
Degree of polynomial: 27
Mean squared error on training data: 0.00068946
Mean squared error on test data: 2379.66219404
Degree of polynomial: 28
@@ -1564,9 +1591,9 @@ Mean squared error on training data: 0.00060705
Mean squared error on test data: 3250.17647619
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/626635268.py:73: RuntimeWarning: divide by zero encountered in log10
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/626635268.py:73: RuntimeWarning: divide by zero encountered in log10
plt.plot(polynomial, np.log10(trainingerror), label='Training Error')
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/626635268.py:74: RuntimeWarning: divide by zero encountered in log10
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/626635268.py:74: RuntimeWarning: divide by zero encountered in log10
plt.plot(polynomial, np.log10(testerror), label='Test Error')
@@ -1800,7 +1827,7 @@ cross-validation (LOOCV).
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3817475779.py:63: RuntimeWarning: divide by zero encountered in log10
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3817475779.py:63: RuntimeWarning: divide by zero encountered in log10
plt.plot(polynomial, np.log10(estimated_mse_sklearn), label='Test Error')
@@ -2689,9 +2716,9 @@ linear system as an equation would reduce this down to
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/4162706317.py:6: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/4162706317.py:6: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
cb = fig.colorbar(im)
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/4162706317.py:7: UserWarning: FixedFormatter should only be used together with FixedLocator
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/4162706317.py:7: UserWarning: FixedFormatter should only be used together with FixedLocator
cb.ax.set_yticklabels(cb.ax.get_yticklabels(), fontsize=18)
@@ -2835,9 +2862,9 @@ with the form utilized in linear regression, viz.
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3777801602.py:6: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3777801602.py:6: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
cb = fig.colorbar(im)
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3777801602.py:7: UserWarning: FixedFormatter should only be used together with FixedLocator
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3777801602.py:7: UserWarning: FixedFormatter should only be used together with FixedLocator
cb.ax.set_yticklabels(cb.ax.get_yticklabels(), fontsize=18)
@@ -2877,9 +2904,9 @@ cost function is given by
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/438060758.py:9: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/438060758.py:9: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
cb = fig.colorbar(im)
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/438060758.py:10: UserWarning: FixedFormatter should only be used together with FixedLocator
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/438060758.py:10: UserWarning: FixedFormatter should only be used together with FixedLocator
cb.ax.set_yticklabels(cb.ax.get_yticklabels(), fontsize=18)
@@ -2914,9 +2941,9 @@ cost function is given by
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3544313922.py:8: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3544313922.py:8: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
cb = fig.colorbar(im)
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3544313922.py:9: UserWarning: FixedFormatter should only be used together with FixedLocator
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3544313922.py:9: UserWarning: FixedFormatter should only be used together with FixedLocator
cb.ax.set_yticklabels(cb.ax.get_yticklabels(), fontsize=18)
@@ -2969,43 +2996,43 @@ constant as opposed to ridge and OLS. We get a sparse solution with
-
0%| | 0/10 [00:00<?, ?it/s]
+
0%| | 0/10 [00:00<?, ?it/s]
/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/sklearn/linear_model/_coordinate_descent.py:647: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.924e+00, tolerance: 1.797e+00
model = cd_fast.enet_coordinate_descent(
- 10%|███████████▉ | 1/10 [00:00<00:06, 1.50it/s]
+ 10%|██████████████▋ | 1/10 [00:00<00:05, 1.53it/s]
@@ -3152,9 +3179,9 @@ which polynomial fits the data best.
-
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3980313467.py:9: MatplotlibDeprecationWarning: Calling gca() with keyword arguments was deprecated in Matplotlib 3.4. Starting two minor releases later, gca() will take no keyword arguments. The gca() function should only be used to get the current axes, or if no axes exist, create new axes with default keyword arguments. To create a new axes with non-default arguments, use plt.axes() or plt.subplot().
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3980313467.py:9: MatplotlibDeprecationWarning: Calling gca() with keyword arguments was deprecated in Matplotlib 3.4. Starting two minor releases later, gca() will take no keyword arguments. The gca() function should only be used to get the current axes, or if no axes exist, create new axes with default keyword arguments. To create a new axes with non-default arguments, use plt.axes() or plt.subplot().
ax = fig.gca(projection='3d')
-/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_41811/3980313467.py:37: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
+/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20614/3980313467.py:37: MatplotlibDeprecationWarning: Auto-removal of grids by pcolor() and pcolormesh() is deprecated since 3.5 and will be removed two minor releases later; please call grid(False) first.
fig.colorbar(surf, shrink=0.5, aspect=5)
Alternatively, the tree can also be exported in textual format with the function exporttext.
This method doesn’t require the installation of external libraries and is more compact:
@@ -999,6 +1139,17 @@ This method doesn’t require the installation of external libraries and is more
@@ -1163,6 +1314,20 @@ humidity and weak and strong for wind.
+
+
---------------------------------------------------------------------------
+FileNotFoundErrorTraceback (most recent call last)
+Input In [6], in <cell line: 37>()
+34defsave_fig(fig_id):
+35plt.savefig(image_path(fig_id)+".png",format='png')
+---> 37infile=open(data_path("rideclass.csv"),'r')
+39# Read the experimental data with Pandas
+40fromIPython.displayimportdisplay
+
+FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/rideclass.csv'
+
+
+
The above functions (gini, entropy and misclassification error) are
important components of the so-called CART algorithm. We will discuss
diff --git a/doc/LectureNotes/_build/html/chapter7.html b/doc/LectureNotes/_build/html/chapter7.html
index a4134fde8..735ae8dbe 100644
--- a/doc/LectureNotes/_build/html/chapter7.html
+++ b/doc/LectureNotes/_build/html/chapter7.html
@@ -242,6 +242,33 @@ const thebe_selector_output = ".output, .cell_output"
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_9414/483257001.py:18: MatplotlibDeprecationWarning: Calling gca() with keyword arguments was deprecated in Matplotlib 3.4. Starting two minor releases later, gca() will take no keyword arguments. The gca() function should only be used to get the current axes, or if no axes exist, create new axes with default keyword arguments. To create a new axes with non-default arguments, use plt.axes() or plt.subplot().
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20669/483257001.py:18: MatplotlibDeprecationWarning: Calling gca() with keyword arguments was deprecated in Matplotlib 3.4. Starting two minor releases later, gca() will take no keyword arguments. The gca() function should only be used to get the current axes, or if no axes exist, create new axes with default keyword arguments. To create a new axes with non-default arguments, use plt.axes() or plt.subplot().
ax = fig.gca(projection="3d")
-
<mpl_toolkits.mplot3d.art3d.Poly3DCollection at 0x13b240850>
+
<mpl_toolkits.mplot3d.art3d.Poly3DCollection at 0x1336a6040>
@@ -1000,7 +1027,7 @@ which equals
-
[<matplotlib.lines.Line2D at 0x13b8c72e0>]
+
[<matplotlib.lines.Line2D at 0x133c2e1c0>]
@@ -1257,11 +1284,11 @@ when \(||\nabla_\beta C(\beta_k) || \
/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lib/__init__.py:32: UserWarning: JAX on Mac ARM machines is experimental and minimally tested. Please see https://github.com/google/jax/issues/5501 in the event of problems.
+ warnings.warn("JAX on Mac ARM machines is experimental and minimally tested. "
+
+
---------------------------------------------------------------------------
-ModuleNotFoundErrorTraceback (most recent call last)
+AttributeErrorTraceback (most recent call last)
Input In [1], in <cell line: 5>()3importtime4importnumpyasnp
@@ -581,14 +612,122 @@ Gaussian distribution.
30fromtensorflow.lite.pythonimportwrap_toco31fromtensorflow.lite.python.convert_phaseimportComponent
-File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:26,in<module>
-23importsix
-24fromsix.movesimportrange
----> 26importflatbuffers
-27fromtensorflow.core.protobufimportconfig_pb2as_config_pb2
-28fromtensorflow.core.protobufimportgraph_debug_info_pb2
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:51,in<module>
+47# Jax functions used by TFLite
+48# pylint: disable=g-import-not-at-top
+49# pylint: disable=unused-import
+50try:
+---> 51fromjaximportxla_computationas_xla_computation
+52exceptImportError:
+53_xla_computation=None
-ModuleNotFoundError: No module named 'flatbuffers'
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/__init__.py:116,in<module>
+40from._src.configimport(
+41configasconfig,
+42enable_checksasenable_checks,
+ (...)
+51numpy_rank_promotionasnumpy_rank_promotion,
+52)
+53from._src.apiimport(
+54ad,# TODO(phawkins): update users to avoid this.
+55checkpointascheckpoint,
+ (...)
+114xla_computationasxla_computation,
+115)
+--> 116from.experimental.mapsimportsoft_pmapassoft_pmap
+117from.versionimport__version__as__version__
+119# These submodules are separate because they are in an import cycle with
+120# jax and rely on the names imported above.
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/experimental/maps.py:26,in<module>
+23fromfunctoolsimportwraps,partial,partialmethod
+24fromenumimportEnum
+---> 26from..importnumpyasjnp
+27from..importcore
+28from..importlinear_utilaslu
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/__init__.py:19,in<module>
+1# Copyright 2018 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+17
+18# flake8: noqa: F401
+---> 19from.importfftasfft
+20from.importlinalgaslinalg
+22fromjax.interpreters.xlaimportDeviceArrayasDeviceArray
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/fft.py:17,in<module>
+1# Copyright 2020 Google LLC
+2#
+3# Licensed under the Apache License, Version 2.0 (the "License");
+ (...)
+14
+15# flake8: noqa: F401
+---> 17fromjax._src.numpy.fftimport(
+18ifftasifft,
+19ifft2asifft2,
+20ifftnasifftn,
+21ifftshiftasifftshift,
+22ihfftasihfft,
+23irfftasirfft,
+24irfft2asirfft2,
+25irfftnasirfftn,
+26fftasfft,
+27fft2asfft2,
+28fftfreqasfftfreq,
+29fftnasfftn,
+30fftshiftasfftshift,
+31hfftashfft,
+32rfftasrfft,
+33rfft2asrfft2,
+34rfftfreqasrfftfreq,
+35rfftnasrfftn,
+36)
+38# Module initialization is encapsulated in a function to avoid accidental
+39# namespace pollution.
+40_NOT_IMPLEMENTED=[]
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/numpy/fft.py:19,in<module>
+16importoperator
+17importnumpyasnp
+---> 19fromjaximportlax
+20fromjax._src.libimportxla_client
+21fromjax._src.utilimportsafe_zip
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/lax/__init__.py:332,in<module>
+299fromjax._src.lax.laximport(_reduce_sum,_reduce_max,_reduce_min,_reduce_or,
+300_reduce_and,_reduce_window_sum,_reduce_window_max,
+301_reduce_window_min,_reduce_window_prod,
+ (...)
+306_upcast_fp16_for_computation,_broadcasting_shape_rule,
+307_eye,_tri,_delta,_ones,_zeros,_dilate_shape)
+308fromjax._src.lax.control_flowimport(
+309associative_scanasassociative_scan,
+310condascond,
+ (...)
+330while_paswhile_p,
+331)
+--> 332fromjax._src.lax.fftimport(
+333fftasfft,
+334fft_pasfft_p,
+335)
+336fromjax._src.lax.parallelimport(
+337all_gatherasall_gather,
+338all_to_allasall_to_all,
+ (...)
+355xeinsumasxeinsum,
+356)
+357fromjax._src.lax.otherimport(
+358conv_general_dilated_patchesasconv_general_dilated_patches
+359)
+
+File~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lax/fft.py:145,in<module>
+143batching.primitive_batchers[fft_p]=fft_batching_rule
+144ifpocketfft:
+--> 145xla.backend_specific_translations['cpu'][fft_p]=pocketfft.pocketfft
+
+AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
19.2. Exercise 1: Setting up various Python environments¶
+
Exercise 1: Setting up various Python environments¶
The first exercise here is of a mere technical art. We want you to have
git as a version control software and to establish a user account on a provider like GitHub. Other providers like GitLab etc are equally fine. You can also use the University of Oslo GitHub facilities.
@@ -465,7 +475,7 @@ license.
We recommend using Anaconda if you are not too familiar with setting paths in a terminal environment.
-
19.3. Exercise 2: making your own data and exploring scikit-learn¶
+
Exercise 2: making your own data and exploring scikit-learn¶
We will generate our own dataset for a function \(y(x)\) where \(x \in [0,1]\) and defined by random numbers computed with the uniform distribution. The function \(y\) is a quadratic polynomial in \(x\) with added stochastic noise according to the normal distribution \(\cal {N}(0,1)\).
The following simple Python instructions define our \(x\) and \(y\) values (with 100 data points).
@@ -512,7 +522,7 @@ R^2(\boldsymbol{y}, \tilde{\boldsymbol{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i
Discuss the meaning of these results. Try also to vary the coefficient in front of the added stochastic noise term and discuss the quality of the fits.
-
19.4. Exercise 3: Split data in test and training data¶
In this exercise we want you to to compute the MSE for the training
data and the test data as function of the complexity of a polynomial,
that is the degree of a given polynomial.
@@ -575,7 +585,7 @@ Add now a model which allows you to make polynomials up to degree
next
-
20. Week 34: Introduction to the course, Logistics and Practicalities
+
Week 34: Introduction to the course, Logistics and Practicalities
diff --git a/doc/LectureNotes/_build/html/searchindex.js b/doc/LectureNotes/_build/html/searchindex.js
index 72d2d5d61..b2905d4d1 100644
--- a/doc/LectureNotes/_build/html/searchindex.js
+++ b/doc/LectureNotes/_build/html/searchindex.js
@@ -1 +1 @@
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Linear Regression","14. Building a Feed Forward Neural Network","15. Solving Differential Equations with Deep Learning","16. Convolutional Neural Networks","17. Recurrent neural networks: Overarching view","4. Ridge and Lasso Regression","5. Resampling Methods","6. Logistic Regression","8. Support Vector Machines, overarching aims","9. Decision trees, overarching aims","10. Ensemble Methods: From a Single Tree to Many Trees and Extreme Boosting, Meet the Jungle of Methods","11. Basic ideas of the Principal Component Analysis (PCA)","13. Neural networks","7. Optimization, the central part of any Machine Learning algortithm","12. Clustering and Unsupervised Learning","Exercises week 34","Exercises week 35","Applied Data Analysis and Machine Learning","2. Linear Algebra, Handling of Arrays and more Python Features","Teaching schedule with links to material","1. Elements of Probability Theory and Statistical Data Analysis","Teachers and Grading","Textbooks","Week 34: Introduction to the course, Logistics and Practicalities","Week 35: From Ordinary Linear Regression to Ridge and Lasso 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diff --git a/doc/LectureNotes/_build/html/statistics.html b/doc/LectureNotes/_build/html/statistics.html
index a88abd420..ba447d4b5 100644
--- a/doc/LectureNotes/_build/html/statistics.html
+++ b/doc/LectureNotes/_build/html/statistics.html
@@ -242,6 +242,33 @@ const thebe_selector_output = ".output, .cell_output"
20. Week 34: Introduction to the course, Logistics and Practicalities¶
+
Week 34: Introduction to the course, Logistics and Practicalities¶
Morten Hjorth-Jensen, Department of Physics and Center for Computing in Science Education, University of Oslo, Norway and Department of Physics and Astronomy and Facility for Rare Isotope Beams, Michigan State University, USA
The sessions on Tuesdays and Wednesdays last four hours for each group (four groups in total) and will include lectures in a flipped mode (promoting active learning) and work on exercices and projects.
The sessions will begin with lectures, discussions, questions and answers about the material to be covered every week. Videos and teaching material will be announced in due time.
@@ -1168,7 +1179,7 @@ doconce format html week34.do.txt --no_mako -->
The labs are also available till 6pm Tuesdays and Wednesdays. Videos and learning material with reading suggestions will be made available before each week starts.
August 22: Presentation of the course, aims and content. Introduction to software and repetition of Python Programming, linear algebra and basic elements of statistics. Please select group.
August 23: Presentation of the course, aims and content. Introduction to software and repetition of Python Programming, linear algebra and basic elements of statistics. Please select group.
@@ -1176,7 +1187,7 @@ doconce format html week34.do.txt --no_mako -->
The sessions on Tuesdays and Wednesdays last four hours and will include partly lectures in a flipped mode (promoting active learning) and work on exercices and projects.
Thursdays: regular lectures (12.15pm-2pm)
@@ -1188,14 +1199,14 @@ doconce format html week34.do.txt --no_mako -->
Three compulsory projects. Electronic reports only using Canvas to hand in projects and git as version control software and GitHub for repository (or GitLab) of all your material.
Evaluation and grading: The three projects are graded and each counts 1/3 of the final mark. No final written or oral exam.
@@ -1208,7 +1219,7 @@ doconce format html week34.do.txt --no_mako -->
Project 1: October 9 (available September 4) graded with feedback)
Project 2: November 6 (available October 6, graded with feedback)
@@ -1235,7 +1246,7 @@ doconce format html week34.do.txt --no_mako -->
Extra Credit (not mandatory), weekly exercise assignments, 10 in total (due Friday same week), 10% additional score. The extra credit assignments are due each Friday and can be uploaed to Canvas in your preferred format (although we prefer jupyter-notebooks). First assignment is for week 35. Each weekly exercise set counts 1%.
Grades are awarded on a scale from A to F, where A is the best grade and F is a fail. There are three projects which are graded and each project counts 1/3 of the final grade. The total score is thus the average from all three projects.
The final number of points is based on the average of all projects and the grade follows the following table:
@@ -1249,12 +1260,12 @@ doconce format html week34.do.txt --no_mako -->
In addition you can get an extra 10% score for weekly assignments (10 in total and due each Friday). Each weekly assignment counts 1%.
In addition to the lecture notes, we recommend the books of Bishop, Hastie et al, Murphy and Goodfellow et al. We will follow these texts closely and the weekly reading assignments refer to these texts. The text by Hastie et al is also widely used in the Machine Learning community. Finally, we also recommend the hands-on text by Geron, see next slide for links.
Basic knowledge in programming and mathematics, with an emphasis on
linear algebra. Knowledge of Python or/and C++ as programming
languages is strongly recommended and experience with Jupiter notebook
@@ -1280,7 +1291,7 @@ offer nowadays a basic programming course (often compulsory) where
Python is the recurring programming language.
-
20.13. Topics covered in this course: Statistical analysis and optimization of data¶
+
Topics covered in this course: Statistical analysis and optimization of data¶
The course has two central parts
Statistical analysis and optimization of data
@@ -1289,7 +1300,7 @@ Python is the recurring programming language.
These topics will be scattered thorughout the course and may not necessarily be taught separately. Rather, we will often take an approach (during the lectures and project/exercise sessions) where say elements from statistical data analysis are mixed with specific Machine Learning algorithms.
-
20.14. Statistical analysis and optimization of data¶
This course aims at giving you insights and knowledge about many of
the central algorithms used in Data Analysis and Machine Learning.
The course is project based and through various numerical projects,
@@ -1382,7 +1393,7 @@ specifically, after this course you will
Our emphasis throughout this series of lectures
is on understanding the mathematical aspects of
different algorithms used in the fields of data analysis and machine learning.
@@ -1414,7 +1425,7 @@ well as allowing you to set up models and produce your own data and
get started with programming.
-
20.21. AI/ML and some statements you may have heard (and what do they mean?)¶
+
AI/ML and some statements you may have heard (and what do they mean?)¶
Statistics, data science and machine learning form important fields of
research in modern science. They describe how to learn and make
predictions from data, as well as allowing us to extract important
@@ -1485,7 +1496,7 @@ Carlo methods are central elements in a proper understanding of many
of algorithms and methods we will discuss.
The approaches to machine learning are many, but are often split into
two main categories. In supervised learning we know the answer to a
problem, and let the computer deduce the logic behind it. On the other
@@ -1504,7 +1515,7 @@ desired output of a system. Some of the most common tasks are:
At the heart of basically all Machine Learning algorithms we will encounter so-called minimization or optimization algorithms. A large family of such methods are so-called gradient methods.
When you hear phrases like predictions and estimations and
correlations and causations, what do you think of? May be you think
of the difference between classifying new data points and generating
@@ -1543,7 +1554,7 @@ used in turn to make estimations and find causations such as given \(B\).
In science and engineering we often end up in situations where we want to infer (or learn) a
quantitative model \(M\) for a given set of sample points \(\boldsymbol{X} \in [x_1, x_2,\dots x_N]\).
As we will see repeatedely in these lectures, we could try to fit these data points to a model given by a
@@ -1561,7 +1572,7 @@ is that if we are not specific about what we mean by a correct model, t
could easily be many different models that fit the given data set equally well.
The central question is this: what leads us to say that a model is correct or
optimal for a given data set? To make the model inference problem well posed, i.e.,
to guarantee that there is a unique optimal model for the given data, we need to
@@ -1582,7 +1593,7 @@ may first try the simplest class of models, namely linear models, followed obvio
How to evaluate which model fits best the data is something we will come back to over and over again in these sets of lectures.
We will make extensive use of Python as programming language and its
myriad of available libraries. You will find
Jupyter notebooks invaluable in your work. You can run R
@@ -1611,7 +1622,7 @@ you can use pip as well and simply install Python as
If you don’t want to perform these operations separately and venture
into the hassle of exploring how to set up dependencies and paths, we
recommend two widely used distrubutions which set up all relevant
@@ -1635,7 +1646,7 @@ license.
no setup and runs entirely in the cloud. Try it out!
Here we list several useful Python libraries we strongly recommend (if you use anaconda many of these are already there)
NumPy is a highly popular library for large, multi-dimensional arrays and matrices, along with a large collection of high-level mathematical functions to operate on these arrays
@@ -1653,7 +1664,7 @@ no setup and runs entirely in the cloud. Try it out!
You will also find it convenient to utilize R. We will mainly
use Python during our lectures and in various projects and exercises.
Those of you
@@ -1668,7 +1679,7 @@ lectures.
For the C++ aficionados, Jupyter/IPython notebook allows you also to
install C++ and run codes written in this language interactively in
the browser. Since we will emphasize writing many of the algorithms
@@ -1691,7 +1702,7 @@ further processing. For example, convert to latex as
Finally, we recommend strongly using Autograd or JAX for automatic differentiation.
-
20.34. Numpy examples and Important Matrix and vector handling packages¶
+
Numpy examples and Important Matrix and vector handling packages¶
There are several central software libraries for linear algebra and eigenvalue problems. Several of the more
popular ones have been wrapped into ofter software packages like those from the widely used text Numerical Recipes. The original source codes in many of the available packages are often taken from the widely used
software package LAPACK, which follows two other popular packages
@@ -1703,7 +1714,7 @@ developed in the 1970s, namely EISPACK and LINPACK. We describe them shortly he
Having defined vectors, we are now ready to try out matrices. We can
define a \(3 \times 3 \) real matrix \(\boldsymbol{A}\) as (recall that we user
lowercase letters for vectors and uppercase letters for matrices)
@@ -1948,26 +1959,26 @@ lowercase letters for vectors and uppercase letters for matrices)
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_65914/1326197715.py:6: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
+
/var/folders/td/3yk470mj5p931p9dtkk0y6jw0000gn/T/ipykernel_20702/1326197715.py:6: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
data_pandas=data_pandas.append(pd.DataFrame(new_hobbit, index=['Pippin']))
@@ -2766,7 +2777,7 @@ most operations are vectorized, achieving thereby a high performance when dealin
As we will see below it leads also to a very concice code close to the mathematical operations we may be interested in.
For multidimensional arrays, we recommend strongly xarray. xarray has much of the same flexibility as pandas, but allows for the extension to higher dimensions than two. We will see examples later of the usage of both pandas and xarray.
-
20.37.1. Simple linear regression model using scikit-learn¶
+
Simple linear regression model using scikit-learn¶
We start with perhaps our simplest possible example, using Scikit-Learn to perform linear regression analysis on a data set produced by us.
What follows is a simple Python code where we have defined a function
\(y\) in terms of the variable \(x\). Both are defined as vectors with \(100\) entries.
@@ -3031,7 +3042,7 @@ H_{\delta}(\boldsymbol{a})=\left\{\begin{array}{cc}\frac{1}{2} \boldsymbol{a}^{2
various lectures and lab sessions.
-
20.37.2. To our real data: nuclear binding energies. Brief reminder on masses and binding energies¶
+
To our real data: nuclear binding energies. Brief reminder on masses and binding energies¶
Let us now dive into nuclear physics and remind ourselves briefly about some basic features about binding
energies. A basic quantity which can be measured for the ground
states of nuclei is the atomic mass \(M(N, Z)\) of the neutral atom with
@@ -3094,7 +3105,7 @@ arises from the tendency of proton pairs and neutron pairs to
occur. An even number of particles is more stable than an odd number.
Let us start with reading and organizing our data.
We start with the compilation of masses and binding energies from 2016.
After having downloaded this file to our own computer, we are now ready to read the file and start structuring our data.
@@ -3320,7 +3331,7 @@ Now we can print measures of how our fit is doing, the coefficients from the fit
The seaborn package allows us to visualize data in an efficient way. Note that we use scikit-learn’s multi-layer perceptron (or feed forward neural network)
functionality.
The aim behind these introductory words was to present to you various
Python libraries and their functionalities, in particular libraries like
numpy, pandas, xarray and matplotlib and other that make our life much easier
@@ -3372,7 +3383,7 @@ Machine Learning algorithms for supervised learning. Later we will meet
Now it is time to dive more into the details of various methods. We will start with linear regression and try to take a deeper look at what it entails.
-
20.39. Why Linear Regression (aka Ordinary Least Squares and family)¶
+
Why Linear Regression (aka Ordinary Least Squares and family)¶
Fitting a continuous function with linear parameterization in terms of the parameters \(\boldsymbol{\beta}\).
Method of choice for fitting a continuous function!
@@ -3389,7 +3400,7 @@ Now it is time to dive more into the details of various methods. We will start w
Similarly, Mehta et al’s article is also recommended.
Regression modeling deals with the description of the sampling distribution of a given random variable \(y\) and how it varies as function of another variable or a set of such variables \(\boldsymbol{x} =[x_0, x_1,\dots, x_{n-1}]^T\).
The first variable is called the dependent, the outcome or the response variable while the set of variables \(\boldsymbol{x}\) is called the independent variable, or the predictor variable or the explanatory variable, or simply just the inputs.
A regression model aims at finding a likelihood function \(p(\boldsymbol{y}\vert \boldsymbol{x})\) or in the more traditional sense a function \(\boldsymbol{y}(\boldsymbol{x})\), that is the conditional distribution for \(\boldsymbol{y}\) with a given \(\boldsymbol{x}\). The estimation of \(p(\boldsymbol{y}\vert \boldsymbol{x})\) is made using a data set with
@@ -3401,7 +3412,7 @@ The first variable is called the dependent, the outcome
The goal of the regression analysis is to extract/exploit relationship between \(\boldsymbol{y}\) and \(\boldsymbol{x}\) in order to infer specific dependencies, approximations to the likelihood functions, functional relationships and to make predictions, making fits and many other things.
Consider an experiment in which \(p\) characteristics/features of \(n\) samples are
measured. The data from this experiment, for various explanatory variables \(p\) are normally represented by a matrix \(\mathbf{X}\).
@@ -3419,7 +3430,7 @@ the linear regression model where \(\beta_j\).
In order to understand the relation among the predictors (or features or properties) \(p\), the set of data \(n\) and the target (outcome, output etc) \(\boldsymbol{y}\),
consider the model we discussed for describing nuclear binding energies.
There we assumed that we could parametrize the data using a polynomial approximation based on the liquid drop model.
@@ -3435,7 +3446,7 @@ This gives \(p=0,1,2,3,4\). Fu
so-called credit card default data from Taiwan. The data set contains data on \(n=30000\) credit card holders with predictors like gender, marital status, age, profession, education, etc. In total there are \(24\) such predictors or attributes leading to a design matrix of dimensionality \(24 \times 30000\). This is however a classification problem and we will come back to it when we discuss Logistic Regression.
Before we proceed let us study a case where we aim at fitting a set of data \(\boldsymbol{y}=[y_0,y_1,\dots,y_{n-1}]\). We could think of these data as a result of an experiment or a complicated numerical experiment. These data are functions of a series of variables \(\boldsymbol{x}=[x_0,x_1,\dots,x_{n-1}]\), that is \(y_i = y(x_i)\) with \(i=0,1,2,\dots,n-1\). The variables \(x_i\) could represent physical quantities like time, temperature, position etc. We assume that \(y(x)\) is a smooth function.
Since obtaining these data points may not be trivial, we want to use these data to fit a function which can allow us to make predictions for values of \(y\) which are not in the present set. The perhaps simplest approach is to assume we can parametrize our function in terms of a polynomial of degree \(n-1\) with \(n\) points, that is
20.46. Generalizing the fitting procedure as a linear algebra problem¶
+
Generalizing the fitting procedure as a linear algebra problem¶
We are obviously not limited to the above polynomial expansions. We
could replace the various powers of \(x\) with elements of Fourier
series or instead of \(x_i^j\) we could have \(\cos{(j x_i)}\) or \(\sin{(j
@@ -3516,7 +3527,7 @@ y_{n-1}&=\beta_0x_{n-1,0}+\beta_1x_{n-1,2}+\beta_2x_{n-1,2}+\dots+\beta_{n-1
Note that we have \(p=n\) here. The matrix is symmetric. This is generally not the case!
-
20.47. Generalizing the fitting procedure as a linear algebra problem¶
+
Generalizing the fitting procedure as a linear algebra problem¶
We redefine in turn the matrix \(\boldsymbol{X}\) as
The left-hand side of this equation is kwown. Our error vector \(\boldsymbol{\epsilon}\) and the parameter vector \(\boldsymbol{\beta}\) are our unknow quantities. How can we obtain the optimal set of \(\beta_i\) values?
We have defined the matrix \(\boldsymbol{X}\) via the equations
\[\begin{split}
@@ -3556,7 +3567,7 @@ y_{n-1}&=\beta_0x_{n-1,0}+\beta_1x_{n-1,2}+\beta_2x_{n-1,2}+\dots+\beta_{n-1
our matrix as \(\boldsymbol{X}\in {\mathbb{R}}^{n\times p}\), with the predictors refering to the column numbers and the entries \(n\) being the row elements.
-
20.49. Our model for the nuclear binding energies¶
\[
@@ -3740,12 +3751,12 @@ allow for the usage of direct linear algebra methods such as LU
Small question: Do you think the example we have at hand here (the nuclear binding energies) can lead to problems in inverting the matrix \(\boldsymbol{X}^T\boldsymbol{X}\)? What kind of problems can we expect?
It is rather straightforward to implement the matrix inversion and obtain the parameters \(\boldsymbol{\beta}\). After having defined the matrix \(\boldsymbol{X}\) we simply need to
write
We can easily test our fit by computing the \(R2\) score that we discussed in connection with the functionality of Scikit-Learn in the introductory slides.
Since we are not using Scikit-Learn here we can define our own \(R2\) function as
@@ -3851,7 +3862,7 @@ Since we are not using Scikit-Learn here we can define our own
Normally, the response (dependent or outcome) variable \(y_i\) is the
outcome of a numerical experiment or another type of experiment and is
thus only an approximation to the true value. It is then always
@@ -3869,7 +3880,7 @@ as
where the matrix \(\boldsymbol{\Sigma}\) is a diagonal matrix with \(\sigma_i\) as matrix elements.
In order to find the parameters \(\beta_i\) we will then minimize the spread of \(\chi^2(\boldsymbol{\beta})\) by requiring
\[
@@ -3888,7 +3899,7 @@ as
where we have defined the matrix \(\boldsymbol{A} =\boldsymbol{X}/\boldsymbol{\Sigma}\) with matrix elements \(a_{ij} = x_{ij}/\sigma_i\) and the vector \(\boldsymbol{b}\) with elements \(b_i = y_i/\sigma_i\).
20.63. Fitting an Equation of State for Dense Nuclear Matter¶
+
Fitting an Equation of State for Dense Nuclear Matter¶
Before we continue, let us introduce yet another example. We are going to fit the
nuclear equation of state using results from many-body calculations.
The equation of state we have made available here, as function of
@@ -4002,7 +4013,7 @@ sneak in Ridge regression (to be discussed below) which include
hyperparameter \(\lambda\), also to be explained below.
It is normal in essentially all Machine Learning studies to split the
data in a training set and a test set (sometimes also an additional
validation set). Scikit-Learn has an own function for this. There
@@ -4184,11 +4195,11 @@ but now splitting the data into a training set and a test set.
20.67. Exercise 1: Setting up various Python environments¶
+
Exercise 1: Setting up various Python environments¶
The first exercise here is of a mere technical art. We want you to have
git as a version control software and to establish a user account on a provider like GitHub. Other providers like GitLab etc are equally fine. You can also use the University of Oslo GitHub facilities.
@@ -4244,7 +4255,7 @@ license.
We recommend using Anaconda if you are not too familiar with setting paths in a terminal environment.
-
20.68. Exercise 2: making your own data and exploring scikit-learn¶
+
Exercise 2: making your own data and exploring scikit-learn¶
We will generate our own dataset for a function \(y(x)\) where \(x \in [0,1]\) and defined by random numbers computed with the uniform distribution. The function \(y\) is a quadratic polynomial in \(x\) with added stochastic noise according to the normal distribution \(\cal {N}(0,1)\).
The following simple Python instructions define our \(x\) and \(y\) values (with 100 data points).
@@ -4280,7 +4291,7 @@ R^2(\boldsymbol{y}, \tilde{\boldsymbol{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i
Discuss the meaning of these results. Try also to vary the coefficient in front of the added stochastic noise term and discuss the quality of the fits.
-
20.69. Exercise 3: Split data in test and training data¶
In this exercise we want you to to compute the MSE for the training
data and the test data as function of the complexity of a polynomial,
that is the degree of a given polynomial.
@@ -4337,9 +4348,16 @@ Add now a model which allows you to make polynomials up to degree
This quantity defines was what is called the Hessian matrix (the second derivative of a function we want to optimize).
The Hessian matrix plays an important role and is defined in this course as
@@ -3558,7 +3558,7 @@ with a factor \(1/(n-1)\). Thi
method corrects the bias in the estimation of the population variance
and covariance. It also partially corrects the bias in the estimation
of the population standard deviation. If you use a library like
-Scikit-Learn or nunmpy’s function calculate the covariance, this
+Scikit-Learn or nunmpy’s function to calculate the covariance, this
quantity will be computed with a factor \(1/(n-1)\).