[doc] Display survival demos in sphinx doc. [skip ci] (dmlc#8328)

Author: trivialfis

demo/aft_survival/README.rst

@@ -0,0 +1,5 @@
+Survival Analysis Walkthrough
+=============================
+
+This is a collection of examples for using the XGBoost Python package for training
+survival models. For an introduction, see :doc:`/tutorials/aft_survival_analysis`

demo/aft_survival/aft_survival_demo.py

@@ -1,6 +1,10 @@
 """
-Demo for survival analysis (regression) using Accelerated Failure Time (AFT) model
+Demo for survival analysis (regression).
+========================================
+
+Demo for survival analysis (regression). using Accelerated Failure Time (AFT) model.
 """
+
 import os
 from sklearn.model_selection import ShuffleSplit
 import pandas as pd

demo/aft_survival/aft_survival_demo_with_optuna.py

@@ -1,6 +1,10 @@
 """
-Demo for survival analysis (regression) using Accelerated Failure Time (AFT) model, using Optuna
-to tune hyperparameters
+Demo for survival analysis (regression) with Optuna.
+====================================================
+
+Demo for survival analysis (regression) using Accelerated Failure Time (AFT) model,
+using Optuna to tune hyperparameters
+
 """
 from sklearn.model_selection import ShuffleSplit
 import pandas as pd
@@ -45,7 +49,7 @@ def objective(trial):
     params.update(base_params)
     pruning_callback = optuna.integration.XGBoostPruningCallback(trial, 'valid-aft-nloglik')
     bst = xgb.train(params, dtrain, num_boost_round=10000,
-                    evals=[(dtrain, 'train'), (dvalid, 'valid')], 
+                    evals=[(dtrain, 'train'), (dvalid, 'valid')],
                     early_stopping_rounds=50, verbose_eval=False, callbacks=[pruning_callback])
     if bst.best_iteration >= 25:
         return bst.best_score
@@ -63,7 +67,7 @@ def objective(trial):
 # Re-run training with the best hyperparameter combination
 print('Re-running the best trial... params = {}'.format(params))
 bst = xgb.train(params, dtrain, num_boost_round=10000,
-                evals=[(dtrain, 'train'), (dvalid, 'valid')], 
+                evals=[(dtrain, 'train'), (dvalid, 'valid')],
                 early_stopping_rounds=50)
 
 # Run prediction on the validation set

demo/aft_survival/aft_survival_viz_demo.py

@@ -1,9 +1,10 @@
 """
 Visual demo for survival analysis (regression) with Accelerated Failure Time (AFT) model.
+=========================================================================================
 
-This demo uses 1D toy data and visualizes how XGBoost fits a tree ensemble. The ensemble model
-starts out as a flat line and evolves into a step function in order to account for all ranged
-labels.
+This demo uses 1D toy data and visualizes how XGBoost fits a tree ensemble. The ensemble
+model starts out as a flat line and evolves into a step function in order to account for
+all ranged labels.
 """
 import numpy as np
 import xgboost as xgb
@@ -57,7 +58,7 @@ def plot_intermediate_model_callback(env):
     #              the corresponding predicted label (y_pred)
     acc = np.sum(np.logical_and(y_pred >= y_lower, y_pred <= y_upper)/len(X) * 100)
     accuracy_history.append(acc)
-    
+
     # Plot ranged labels as well as predictions by the model
     plt.subplot(5, 3, env.iteration + 1)
     plot_censored_labels(X, y_lower, y_upper)

doc/conf.py

@@ -93,9 +93,9 @@
 
 sphinx_gallery_conf = {
     # path to your example scripts
-    "examples_dirs": ["../demo/guide-python", "../demo/dask"],
+    "examples_dirs": ["../demo/guide-python", "../demo/dask", "../demo/aft_survival"],
     # path to where to save gallery generated output
-    "gallery_dirs": ["python/examples", "python/dask-examples"],
+    "gallery_dirs": ["python/examples", "python/dask-examples", "python/survival-examples"],
     "matplotlib_animations": True,
 }
 

doc/python/.gitignore

@@ -1,2 +1,3 @@
 examples
-dask-examples
+dask-examples
+survival-examples

doc/python/index.rst

@@ -15,3 +15,4 @@ Contents
   model
   examples/index
   dask-examples/index
+  survival-examples/index

doc/tutorials/aft_survival_analysis.rst

@@ -98,7 +98,7 @@ Collect the lower bound numbers in one array (let's call it ``y_lower_bound``) a
   # 4-by-2 Data matrix
   X = np.array([[1, -1], [-1, 1], [0, 1], [1, 0]])
   dtrain = xgb.DMatrix(X)
-  
+
   # Associate ranged labels with the data matrix.
   # This example shows each kind of censored labels.
   #                         uncensored    right     left  interval
@@ -109,7 +109,7 @@ Collect the lower bound numbers in one array (let's call it ``y_lower_bound``) a
 
 .. code-block:: r
   :caption: R
-  
+
   library(xgboost)
 
   # 4-by-2 Data matrix
@@ -165,4 +165,4 @@ Currently, you can choose from three probability distributions for ``aft_loss_di
 ``extreme``               :math:`e^z e^{-\exp{z}}`
 ========================= ===========================================
 
-Note that it is not yet possible to set the ranged label using the scikit-learn interface (e.g. :class:`xgboost.XGBRegressor`). For now, you should use :class:`xgboost.train` with :class:`xgboost.DMatrix`.
+Note that it is not yet possible to set the ranged label using the scikit-learn interface (e.g. :class:`xgboost.XGBRegressor`). For now, you should use :class:`xgboost.train` with :class:`xgboost.DMatrix`. For a collection of Python examples, see :doc:`/python/survival-examples/index`