From a78fa86014dc8d56a18a59b197afc794f9ab9a6e Mon Sep 17 00:00:00 2001 From: "Kevin M. Jablonka" Date: Sun, 25 Oct 2020 22:27:14 +0100 Subject: [PATCH] docs: adding description of tutorials --- docs/_build/doctrees/environment.pickle | Bin 145582 -> 146528 bytes docs/_build/doctrees/getting_started.doctree | Bin 61955 -> 61721 bytes docs/_build/doctrees/tutorials.doctree | Bin 5696 -> 13063 bytes docs/_build/html/.buildinfo | 2 +- docs/_build/html/_modules/index.html | 2 +- .../html/_modules/pypal/models/gpr.html | 2 +- docs/_build/html/_modules/pypal/pal/core.html | 2 +- .../html/_modules/pypal/pal/pal_base.html | 2 +- .../pypal/pal/pal_coregionalized.html | 2 +- .../html/_modules/pypal/pal/pal_gbdt.html | 2 +- .../html/_modules/pypal/pal/pal_gpy.html | 2 +- .../html/_modules/pypal/pal/pal_sklearn.html | 2 +- .../html/_modules/pypal/pal/schedules.html | 2 +- .../_build/html/_modules/pypal/pal/utils.html | 2 +- .../_modules/pypal/pal/validate_inputs.html | 2 +- docs/_build/html/_modules/pypal/plotting.html | 2 +- .../html/_sources/getting_started.rst.txt | 2 +- docs/_build/html/_sources/tutorials.rst.txt | 21 ++++++++- .../html/_static/documentation_options.js | 2 +- docs/_build/html/api.html | 2 +- docs/_build/html/background.html | 2 +- docs/_build/html/developer_notes.html | 2 +- docs/_build/html/genindex.html | 2 +- docs/_build/html/getting_started.html | 4 +- docs/_build/html/index.html | 12 +++-- docs/_build/html/objects.inv | Bin 2130 -> 2147 bytes docs/_build/html/py-modindex.html | 2 +- docs/_build/html/search.html | 2 +- docs/_build/html/searchindex.js | 2 +- docs/_build/html/tutorials.html | 42 ++++++++++++++++-- docs/getting_started.rst | 2 +- docs/tutorials.rst | 21 ++++++++- 32 files changed, 112 insertions(+), 34 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 85bbcdf6565310798504bda4c0a0065a3663a5b9..77bfc57a0035076d05a46f3650588a01cbac9b56 100644 GIT binary patch delta 20260 zcmcg!d0Z4n_O}O>V>m=Plygv2kXu0sA__uKNr(q(4iyF%VOj(NgXbD_H&N7yqHhvB zqDGBTF&Ygf81IXy(Wr5MQFr}p?wHd=WA@4>*?m1VwVPRrY(^XZh8&?NUkBrvUz@{3HkzO3u zbTa6ilea7)wpd?fm}`O&VLnZJHG!^bw?b{vjFPH~n(|^;HLyo7qm#B$Z!&h#mlx~i zn2fH58bd{uURze(q#E#ps&;(jre(j6-sf*XDj9$gMS-P@{N?lccd4)k& zZEiCD`*VvpM!VtcUpcvEs#p4aAf8fn>O@IKjk;_ zVhcsYGkAel27WC>!HPk#LOdK9)L)2&F9zuYVw^g4idoB}dH9`8YpqLsln^26R6ylHAv)D!-j|>hT zNc-^0w2Xp=jRNavG8JaR1|n8_jDm9kT8RU@I*^!fo z@f#c?jV4j=AyUv0ZNy*pLlgd<)gLa8>l{s7W8}JFjN23$YgtSiy^AVlR%(k3`IXu# zZAq23vefMPO_Wt!ix+#j6d`U@YUvdJhCX79sw_= z`1GYwaS-X4&1V%k%r=WBB-$2A+W{lRd$G~VL?;l31||^D=sB{YN~f7#Q(k1ySCm(q zUH+Y-<~Ym|uyS-aa7%Tww)bmAuKwnEOSbo>BCRDJTuHR&>kYb@W~Dx(EQ+JuAxE(J zw_2wuD$`b1n@H3rSY~T7GfOROM7=w=83SW8{Tn_~3tcSc%Aw$?$Y`OJU87c{wSF7wY8HJIc%++ph){*taZ-_;-)QIW&e+VzUG z560RRS#jJDufV-BUC>(;)k34Qtqne@NNsEIF-6)3WAK!0-ryNKMcM~r^!KB}F{ZyC6=aTSk1lO4SSv>dSX=9+$YE=(vm)(-v3Av%5R$=T z{LI!SDC$GUwqH(PYinZ_Ic%+sYM0h}Nz&Q5g^M?DcU$f0*&4(4fcBVd7ygrNZ-yc| zx*O`ASE@6w`WoDg&(N0Wa91=`zK1p1qhR_MDmsX|f6Al&*6z<&Di+?qmmv#fNNr#QSFj&!#Sm^7|Cz2_IlqK?dCXBEAR z#LY_`!Gawgd9XFpfu zvc!^{tDh*++Aa(qGM^~j#CODU*pT-SXZVJ^6lS=(Ya6Q}8C-8jnwV@oz%GhhwuX0U zmsU;;W_VjkBqtmToVI9XxyKZpZwW|q!qMYHrC7ZG3Fnmw;|Ke*gqtQMT&AMOXfWnZ z^(LoE)?<>c$Yrrn4#qS}tGI9|CtZi87Fe$j=3;NXK7_?yk)p`00^LH8LxoSoh?%*SNUDrzj*xp;=nQQ0CzF54V?Mv>Oy6FC>=GoReg$ps_V zs2)4lP+C#0DZ=9sdT7MXjH0cZ*qX9KQDMm?J~O*nhxj%{E?bvuQKYqR&dk4{sGMZ}+H!Ae^Uo=A*_!{3BJBf<2#?H)qMDhya)Xwf zqslQsy<*kK+;Uq{X^UHic=jo7CDnZLB_Au^Qj}rqq;J}#wN9J1mK%9#V$+U2THDxr zlIoziv~*-5g2tx@;6}ai>E7m>K#g;oi+t|X?l8H^=HMz=k;~ST0qxSto@5r=^NvNX z>`AszwM8q-9jZ8*mXJ3u^7L_&(jtGK*FG{eM!>+N$kvaK%B02q2}RG*m@g={yVy@s zR*@7zziR!7d{!$_<$K(kVH8)XTvv-RCG8VK%)x1U%tkJqy+- za#@l~HodAH)3=b}amL4shAN%n(?8p1&T3;6tV|RDZqzy1t#h35|Zgo2+8{p31PEQ ztX*%2!;x&N$=JE53)$Fe!F!}{viZDH>R)U|@8pVa(~?uuUig>?q&vKz9cDeXh1pes zyyap$AR){VN&})8c^%8z(VdJQc@>rVBHZ84!j~nATf5P!jXCsjMQhAH@JTWdkuesL zHhZ~=iV|#-dwjdJa&kY`F0H%+VSctZlGAM_%s?tv(e)ij`Ure2>QG@i?&f|i9LzGH zj&%})7w+8;qnA1At7nwyv{mI+k?(AVTMwIrvH`2N>lSkch$$|Z2{iuunhj4wdfU)9 z>z4>W6!{LIdwpliGjrArBe3UDDL1N$ZF1u|yUN+mjXzRa$9FsrE;o)ST4V7+Oy@rO z;sldTP8?L^w9Sd;c4_6D*xxR#oD`Ujudnu?C08gXR-`i@WneLyR2ZBdUjb2x3dD__Mhlxg}qO>16!D& zK8^^Y^318TRT810A{3{E)_a(zkWGF$wIgqop-*>}%yM?~m(85<-Qr!p7c&%;HCpB>2U1mkB1G1uuGQCD)^uGzh; 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pypal.pal.pal_gbdt — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.pal_gbdt — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/pal/pal_gpy.html b/docs/_build/html/_modules/pypal/pal/pal_gpy.html index 36c65f9..9860e8c 100644 --- a/docs/_build/html/_modules/pypal/pal/pal_gpy.html +++ b/docs/_build/html/_modules/pypal/pal/pal_gpy.html @@ -5,7 +5,7 @@ - pypal.pal.pal_gpy — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.pal_gpy — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/pal/pal_sklearn.html b/docs/_build/html/_modules/pypal/pal/pal_sklearn.html index 5339bdf..86a52bc 100644 --- a/docs/_build/html/_modules/pypal/pal/pal_sklearn.html +++ b/docs/_build/html/_modules/pypal/pal/pal_sklearn.html @@ -5,7 +5,7 @@ - pypal.pal.pal_sklearn — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.pal_sklearn — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/pal/schedules.html b/docs/_build/html/_modules/pypal/pal/schedules.html index e53fc8d..970dbd8 100644 --- a/docs/_build/html/_modules/pypal/pal/schedules.html +++ b/docs/_build/html/_modules/pypal/pal/schedules.html @@ -5,7 +5,7 @@ - pypal.pal.schedules — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.schedules — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/pal/utils.html b/docs/_build/html/_modules/pypal/pal/utils.html index 57c3a7b..7643d43 100644 --- a/docs/_build/html/_modules/pypal/pal/utils.html +++ b/docs/_build/html/_modules/pypal/pal/utils.html @@ -5,7 +5,7 @@ - pypal.pal.utils — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.utils — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/pal/validate_inputs.html b/docs/_build/html/_modules/pypal/pal/validate_inputs.html index 0cc43d3..fe4c658 100644 --- a/docs/_build/html/_modules/pypal/pal/validate_inputs.html +++ b/docs/_build/html/_modules/pypal/pal/validate_inputs.html @@ -5,7 +5,7 @@ - pypal.pal.validate_inputs — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.pal.validate_inputs — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_modules/pypal/plotting.html b/docs/_build/html/_modules/pypal/plotting.html index feac2ad..e6a7a36 100644 --- a/docs/_build/html/_modules/pypal/plotting.html +++ b/docs/_build/html/_modules/pypal/plotting.html @@ -5,7 +5,7 @@ - pypal.plotting — pypal 0+untagged.212.g4af8189.dirty documentation + pypal.plotting — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt index 86a70c4..122ffc0 100644 --- a/docs/_build/html/_sources/getting_started.rst.txt +++ b/docs/_build/html/_sources/getting_started.rst.txt @@ -193,7 +193,7 @@ By default, the code will run a simple cross-validation only on the first iterat This behavior can changed with the cross-validation test being performed more frequently by overriding the :code:`should_run_crossvalidation` function. -Another way to detect overfitting is to use :py:func:`pypal.plotting.make_jointplot`function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted. +Another way to detect overfitting is to use :py:func:`pypal.plotting.make_jointplot` function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted. .. code-block:: python diff --git a/docs/_build/html/_sources/tutorials.rst.txt b/docs/_build/html/_sources/tutorials.rst.txt index dfc2f3e..359b4fd 100644 --- a/docs/_build/html/_sources/tutorials.rst.txt +++ b/docs/_build/html/_sources/tutorials.rst.txt @@ -2,7 +2,8 @@ Tutorials ============ To explore different use cases of PyPAL, we recommend checking out the `example notebooks `_. -All notebooks can be run without installation on MyBinder. +All notebooks can be run without installation on MyBinder. In the folder, you find the notebooks with the output cells, if you rerun them, the execution +should not take more than a few minutes. 1. One active learning step using GPR models built with :code:`GPy` @@ -12,6 +13,13 @@ All notebooks can be run without installation on MyBinder. :width: 400px :align: center +Topic covered +................ + +- building a pal_coregionalized GPR model using :py:meth:`pypal.pal.models.gpr.build_coregionalized_model` +- using coregionalized models with :py:obj:`pypal.pal.pal_coregionalized.PALCoregionalized` +- attributes of the :code:`PAL` instance +- :py:meth:`pypal.pal.utils.exhaust_loop` 2. Active learning with "measure" function and :code:`sklearn` models @@ -21,6 +29,13 @@ All notebooks can be run without installation on MyBinder. :width: 400px :align: center +Topic covered +................ + +- using :code:`sklearn` models with :py:obj:`pypal.pal.pal_sklearn.PALSklearn` +- selecting an initial set with :py:meth:`pypal.pal.utils.get_maxmin_samples` +- plotting with :py:meth:`pypal.plotting.make_jointplot` + 3. Quantile regression @@ -29,3 +44,7 @@ All notebooks can be run without installation on MyBinder. .. image:: _static/quantile_regression_screenshot.png :width: 400px :align: center + + +- Using LightGBM models with quantile loss with :py:obj:`pypal.pal.pal_gbdt.PALGBDT` +- selecting an initial set with :py:meth:`pypal.pal.utils.get_kmeans_samples` diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js index f9689e1..13fd9d2 100644 --- a/docs/_build/html/_static/documentation_options.js +++ b/docs/_build/html/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0+untagged.212.g4af8189.dirty', + VERSION: '0+untagged.213.g6cabb45.dirty', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_build/html/api.html b/docs/_build/html/api.html index fa6e0bb..29e2793 100644 --- a/docs/_build/html/api.html +++ b/docs/_build/html/api.html @@ -5,7 +5,7 @@ - The PyPAL API reference — pypal 0+untagged.212.g4af8189.dirty documentation + The PyPAL API reference — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/background.html b/docs/_build/html/background.html index a69faad..ef1cc16 100644 --- a/docs/_build/html/background.html +++ b/docs/_build/html/background.html @@ -5,7 +5,7 @@ - Background — pypal 0+untagged.212.g4af8189.dirty documentation + Background — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/developer_notes.html b/docs/_build/html/developer_notes.html index 4db0b9e..05be424 100644 --- a/docs/_build/html/developer_notes.html +++ b/docs/_build/html/developer_notes.html @@ -5,7 +5,7 @@ - Developer notes — pypal 0+untagged.212.g4af8189.dirty documentation + Developer notes — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 6d74ca4..09d9891 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -5,7 +5,7 @@ - Index — pypal 0+untagged.212.g4af8189.dirty documentation + Index — pypal 0+untagged.213.g6cabb45.dirty documentation diff --git a/docs/_build/html/getting_started.html b/docs/_build/html/getting_started.html index d6e93b9..bb34673 100644 --- a/docs/_build/html/getting_started.html +++ b/docs/_build/html/getting_started.html @@ -5,7 +5,7 @@ - Getting Started — pypal 0+untagged.212.g4af8189.dirty documentation + Getting Started — pypal 0+untagged.213.g6cabb45.dirty documentation @@ -371,7 +371,7 @@

Caveats and tricks with Gaussian processesshould_run_crossvalidation function.

-

Another way to detect overfitting is to use :py:func:`pypal.plotting.make_jointplot`function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted.

+

Another way to detect overfitting is to use pypal.plotting.make_jointplot() function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted.

from pypal.plotting import make_jointplot
 
 # palinstance is a instance of a PAL class after
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index d804087..1d30717 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -5,7 +5,7 @@
   
     
     
-    PyPAL: Pareto active learning for Python — pypal 0+untagged.212.g4af8189.dirty documentation
+    PyPAL: Pareto active learning for Python — pypal 0+untagged.213.g6cabb45.dirty documentation
 
   
 
@@ -203,8 +203,14 @@ 
ContentsTutorials
 
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
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diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html
index c757356..c073037 100644
--- a/docs/_build/html/py-modindex.html
+++ b/docs/_build/html/py-modindex.html
@@ -5,7 +5,7 @@
   
     
     
-    Python Module Index — pypal 0+untagged.212.g4af8189.dirty documentation
+    Python Module Index — pypal 0+untagged.213.g6cabb45.dirty documentation
 
   
 
diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html
index 888333b..a0c0e7b 100644
--- a/docs/_build/html/search.html
+++ b/docs/_build/html/search.html
@@ -5,7 +5,7 @@
   
     
     
-    Search — pypal 0+untagged.212.g4af8189.dirty documentation
+    Search — pypal 0+untagged.213.g6cabb45.dirty documentation
 
   
 
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index abb2cdf..661b49d 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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diff --git a/docs/_build/html/tutorials.html b/docs/_build/html/tutorials.html
index e48023b..14d3de9 100644
--- a/docs/_build/html/tutorials.html
+++ b/docs/_build/html/tutorials.html
@@ -5,7 +5,7 @@
   
     
     
-    Tutorials — pypal 0+untagged.212.g4af8189.dirty documentation
+    Tutorials — pypal 0+untagged.213.g6cabb45.dirty documentation
 
   
 
@@ -152,11 +152,23 @@
     
    
 
         
  • 
-            1. One active learning step using GPR models built with GPy
+            1. One active learning step using GPR models built with GPy
         
    • 
 
         
  • 
-            2. Active learning with “measure” function and sklearn models
+            2. Active learning with “measure” function and sklearn models
         
    • 
 
         
  • 
@@ -179,18 +191,40 @@
   
    
 
    Tutorials
    
 
    To explore different use cases of PyPAL, we recommend checking out the example notebooks.
-All notebooks can be run without installation on MyBinder.
    
+All notebooks can be run without installation on MyBinder. In the folder, you find the notebooks with the output cells, if you rerun them, the execution
+should not take more than a few minutes.
    
 
    
 
    1. One active learning step using GPR models built with GPy
    
 _images/basic_pypal_screenshot.png
+
    
+
    Topic covered
    
+
+
    
 
    
 
    
 
    2. Active learning with “measure” function and sklearn models
    
 _images/active_learning_screenshot.png
+
    
+
    Topic covered
    
+
+
    
 
    
 
    
 
    3. Quantile regression
    
 _images/quantile_regression_screenshot.png
+
 
    
 
    
 
diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index 86a70c4..122ffc0 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -193,7 +193,7 @@ By default, the code will run a simple cross-validation only on the first iterat
 
 This behavior can changed with the cross-validation test being performed more frequently by overriding the :code:`should_run_crossvalidation` function.
 
-Another way to detect overfitting is to use :py:func:`pypal.plotting.make_jointplot`function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted.
+Another way to detect overfitting is to use :py:func:`pypal.plotting.make_jointplot` function from the plotting subpackage. This function will plot all objectives against each other (with errorbars and different classes indicated with colors) and histograms of the objectives on the diagonal. If the majority of predicted points tend to overlap one another and get discarded by PyPAL, this may suggest that the surrogate model is overfitted.
 
 .. code-block:: python
 
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
index dfc2f3e..359b4fd 100644
--- a/docs/tutorials.rst
+++ b/docs/tutorials.rst
@@ -2,7 +2,8 @@ Tutorials
 ============
 
 To explore different use cases of PyPAL, we recommend checking out the `example notebooks `_.
-All notebooks can be run without installation on MyBinder.
+All notebooks can be run without installation on MyBinder. In the folder, you find the notebooks with the output cells, if you rerun them, the execution
+should not take more than a few minutes.
 
 
 1. One active learning step using GPR models built with :code:`GPy`
@@ -12,6 +13,13 @@ All notebooks can be run without installation on MyBinder.
     :width: 400px
     :align: center
 
+Topic covered
+................
+
+- building a pal_coregionalized GPR model using :py:meth:`pypal.pal.models.gpr.build_coregionalized_model`
+-  using coregionalized models with :py:obj:`pypal.pal.pal_coregionalized.PALCoregionalized`
+- attributes of the :code:`PAL` instance
+- :py:meth:`pypal.pal.utils.exhaust_loop`
 
 
 2. Active learning with "measure" function and :code:`sklearn` models
@@ -21,6 +29,13 @@ All notebooks can be run without installation on MyBinder.
     :width: 400px
     :align: center
 
+Topic covered
+................
+
+- using :code:`sklearn`  models with :py:obj:`pypal.pal.pal_sklearn.PALSklearn`
+- selecting an initial set with :py:meth:`pypal.pal.utils.get_maxmin_samples`
+- plotting with :py:meth:`pypal.plotting.make_jointplot`
+
 
 
 3. Quantile regression
@@ -29,3 +44,7 @@ All notebooks can be run without installation on MyBinder.
 .. image:: _static/quantile_regression_screenshot.png
     :width: 400px
     :align: center
+
+
+- Using LightGBM models with quantile loss with :py:obj:`pypal.pal.pal_gbdt.PALGBDT`
+- selecting an initial set with :py:meth:`pypal.pal.utils.get_kmeans_samples`