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From m...@apache.org
Subject spark git commit: [SPARK-10689][ML][DOC] User guide and example code for AFTSurvivalRegression
Date Mon, 09 Nov 2015 16:57:33 GMT
Repository: spark
Updated Branches:
  refs/heads/branch-1.6 029e931da -> a85a9122f


[SPARK-10689][ML][DOC] User guide and example code for AFTSurvivalRegression

Add user guide and example code for ```AFTSurvivalRegression```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9491 from yanboliang/spark-10689.

(cherry picked from commit d50a66cc04bfa1c483f04daffe465322316c745e)
Signed-off-by: Xiangrui Meng <meng@databricks.com>


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/a85a9122
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/a85a9122
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/a85a9122

Branch: refs/heads/branch-1.6
Commit: a85a9122fb9390aa589da0eb7eacdbf949662600
Parents: 029e931
Author: Yanbo Liang <ybliang8@gmail.com>
Authored: Mon Nov 9 08:57:29 2015 -0800
Committer: Xiangrui Meng <meng@databricks.com>
Committed: Mon Nov 9 08:57:36 2015 -0800

----------------------------------------------------------------------
 docs/ml-guide.md                                |  1 +
 docs/ml-survival-regression.md                  | 96 ++++++++++++++++++++
 .../ml/JavaAFTSurvivalRegressionExample.java    | 71 +++++++++++++++
 .../main/python/ml/aft_survival_regression.py   | 51 +++++++++++
 .../ml/AFTSurvivalRegressionExample.scala       | 62 +++++++++++++
 5 files changed, 281 insertions(+)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/a85a9122/docs/ml-guide.md
----------------------------------------------------------------------
diff --git a/docs/ml-guide.md b/docs/ml-guide.md
index fd3a616..c293e71 100644
--- a/docs/ml-guide.md
+++ b/docs/ml-guide.md
@@ -44,6 +44,7 @@ provide class probabilities, and linear models provide model summaries.
 * [Ensembles](ml-ensembles.html)
 * [Linear methods with elastic net regularization](ml-linear-methods.html)
 * [Multilayer perceptron classifier](ml-ann.html)
+* [Survival Regression](ml-survival-regression.html)
 
 
 # Main concepts in Pipelines

http://git-wip-us.apache.org/repos/asf/spark/blob/a85a9122/docs/ml-survival-regression.md
----------------------------------------------------------------------
diff --git a/docs/ml-survival-regression.md b/docs/ml-survival-regression.md
new file mode 100644
index 0000000..ab27521
--- /dev/null
+++ b/docs/ml-survival-regression.md
@@ -0,0 +1,96 @@
+---
+layout: global
+title: Survival Regression - ML
+displayTitle: <a href="ml-guide.html">ML</a> - Survival Regression
+---
+
+
+`\[
+\newcommand{\R}{\mathbb{R}}
+\newcommand{\E}{\mathbb{E}}
+\newcommand{\x}{\mathbf{x}}
+\newcommand{\y}{\mathbf{y}}
+\newcommand{\wv}{\mathbf{w}}
+\newcommand{\av}{\mathbf{\alpha}}
+\newcommand{\bv}{\mathbf{b}}
+\newcommand{\N}{\mathbb{N}}
+\newcommand{\id}{\mathbf{I}}
+\newcommand{\ind}{\mathbf{1}}
+\newcommand{\0}{\mathbf{0}}
+\newcommand{\unit}{\mathbf{e}}
+\newcommand{\one}{\mathbf{1}}
+\newcommand{\zero}{\mathbf{0}}
+\]`
+
+
+In `spark.ml`, we implement the [Accelerated failure time (AFT)](https://en.wikipedia.org/wiki/Accelerated_failure_time_model)

+model which is a parametric survival regression model for censored data. 
+It describes a model for the log of survival time, so it's often called 
+log-linear model for survival analysis. Different from 
+[Proportional hazards](https://en.wikipedia.org/wiki/Proportional_hazards_model) model
+designed for the same purpose, the AFT model is more easily to parallelize 
+because each instance contribute to the objective function independently.
+
+Given the values of the covariates $x^{'}$, for random lifetime $t_{i}$ of 
+subjects i = 1, ..., n, with possible right-censoring, 
+the likelihood function under the AFT model is given as:
+`\[
+L(\beta,\sigma)=\prod_{i=1}^n[\frac{1}{\sigma}f_{0}(\frac{\log{t_{i}}-x^{'}\beta}{\sigma})]^{\delta_{i}}S_{0}(\frac{\log{t_{i}}-x^{'}\beta}{\sigma})^{1-\delta_{i}}
+\]`
+Where $\delta_{i}$ is the indicator of the event has occurred i.e. uncensored or not.
+Using $\epsilon_{i}=\frac{\log{t_{i}}-x^{'}\beta}{\sigma}$, the log-likelihood function
+assumes the form:
+`\[
+\iota(\beta,\sigma)=\sum_{i=1}^{n}[-\delta_{i}\log\sigma+\delta_{i}\log{f_{0}}(\epsilon_{i})+(1-\delta_{i})\log{S_{0}(\epsilon_{i})}]
+\]`
+Where $S_{0}(\epsilon_{i})$ is the baseline survivor function,
+and $f_{0}(\epsilon_{i})$ is corresponding density function.
+
+The most commonly used AFT model is based on the Weibull distribution of the survival time.

+The Weibull distribution for lifetime corresponding to extreme value distribution for 
+log of the lifetime, and the $S_{0}(\epsilon)$ function is:
+`\[   
+S_{0}(\epsilon_{i})=\exp(-e^{\epsilon_{i}})
+\]`
+the $f_{0}(\epsilon_{i})$ function is:
+`\[
+f_{0}(\epsilon_{i})=e^{\epsilon_{i}}\exp(-e^{\epsilon_{i}})
+\]`
+The log-likelihood function for AFT model with Weibull distribution of lifetime is:
+`\[
+\iota(\beta,\sigma)= -\sum_{i=1}^n[\delta_{i}\log\sigma-\delta_{i}\epsilon_{i}+e^{\epsilon_{i}}]
+\]`
+Due to minimizing the negative log-likelihood equivalent to maximum a posteriori probability,
+the loss function we use to optimize is $-\iota(\beta,\sigma)$.
+The gradient functions for $\beta$ and $\log\sigma$ respectively are:
+`\[   
+\frac{\partial (-\iota)}{\partial \beta}=\sum_{1=1}^{n}[\delta_{i}-e^{\epsilon_{i}}]\frac{x_{i}}{\sigma}
+\]`
+`\[ 
+\frac{\partial (-\iota)}{\partial (\log\sigma)}=\sum_{i=1}^{n}[\delta_{i}+(\delta_{i}-e^{\epsilon_{i}})\epsilon_{i}]
+\]`
+
+The AFT model can be formulated as a convex optimization problem, 
+i.e. the task of finding a minimizer of a convex function $-\iota(\beta,\sigma)$ 
+that depends coefficients vector $\beta$ and the log of scale parameter $\log\sigma$.
+The optimization algorithm underlying the implementation is L-BFGS.
+The implementation matches the result from R's survival function 
+[survreg](https://stat.ethz.ch/R-manual/R-devel/library/survival/html/survreg.html)
+
+## Example:
+
+<div class="codetabs">
+
+<div data-lang="scala" markdown="1">
+{% include_example scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
%}
+</div>
+
+<div data-lang="java" markdown="1">
+{% include_example java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
%}
+</div>
+
+<div data-lang="python" markdown="1">
+{% include_example python/ml/aft_survival_regression.py %}
+</div>
+
+</div>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/spark/blob/a85a9122/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
----------------------------------------------------------------------
diff --git a/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
b/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
new file mode 100644
index 0000000..69a1745
--- /dev/null
+++ b/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
@@ -0,0 +1,71 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.spark.examples.ml;
+
+// $example on$
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.ml.regression.AFTSurvivalRegression;
+import org.apache.spark.ml.regression.AFTSurvivalRegressionModel;
+import org.apache.spark.mllib.linalg.*;
+import org.apache.spark.sql.DataFrame;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.RowFactory;
+import org.apache.spark.sql.SQLContext;
+import org.apache.spark.sql.types.*;
+// $example off$
+
+public class JavaAFTSurvivalRegressionExample {
+  public static void main(String[] args) {
+    SparkConf conf = new SparkConf().setAppName("JavaAFTSurvivalRegressionExample");
+    JavaSparkContext jsc = new JavaSparkContext(conf);
+    SQLContext jsql = new SQLContext(jsc);
+
+    // $example on$
+    List<Row> data = Arrays.asList(
+      RowFactory.create(1.218, 1.0, Vectors.dense(1.560, -0.605)),
+      RowFactory.create(2.949, 0.0, Vectors.dense(0.346, 2.158)),
+      RowFactory.create(3.627, 0.0, Vectors.dense(1.380, 0.231)),
+      RowFactory.create(0.273, 1.0, Vectors.dense(0.520, 1.151)),
+      RowFactory.create(4.199, 0.0, Vectors.dense(0.795, -0.226))
+    );
+    StructType schema = new StructType(new StructField[]{
+      new StructField("label", DataTypes.DoubleType, false, Metadata.empty()),
+      new StructField("censor", DataTypes.DoubleType, false, Metadata.empty()),
+      new StructField("features", new VectorUDT(), false, Metadata.empty())
+    });
+    DataFrame training = jsql.createDataFrame(data, schema);
+    double[] quantileProbabilities = new double[]{0.3, 0.6};
+    AFTSurvivalRegression aft = new AFTSurvivalRegression()
+      .setQuantileProbabilities(quantileProbabilities)
+      .setQuantilesCol("quantiles");
+
+    AFTSurvivalRegressionModel model = aft.fit(training);
+
+    // Print the coefficients, intercept and scale parameter for AFT survival regression
+    System.out.println("Coefficients: " + model.coefficients() + " Intercept: "
+      + model.intercept() + " Scale: " + model.scale());
+    model.transform(training).show(false);
+    // $example off$
+
+    jsc.stop();
+  }
+}

http://git-wip-us.apache.org/repos/asf/spark/blob/a85a9122/examples/src/main/python/ml/aft_survival_regression.py
----------------------------------------------------------------------
diff --git a/examples/src/main/python/ml/aft_survival_regression.py b/examples/src/main/python/ml/aft_survival_regression.py
new file mode 100644
index 0000000..0ee01fd
--- /dev/null
+++ b/examples/src/main/python/ml/aft_survival_regression.py
@@ -0,0 +1,51 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from __future__ import print_function
+
+from pyspark import SparkContext
+from pyspark.sql import SQLContext
+# $example on$
+from pyspark.ml.regression import AFTSurvivalRegression
+from pyspark.mllib.linalg import Vectors
+# $example off$
+
+if __name__ == "__main__":
+    sc = SparkContext(appName="AFTSurvivalRegressionExample")
+    sqlContext = SQLContext(sc)
+
+    # $example on$
+    training = sqlContext.createDataFrame([
+        (1.218, 1.0, Vectors.dense(1.560, -0.605)),
+        (2.949, 0.0, Vectors.dense(0.346, 2.158)),
+        (3.627, 0.0, Vectors.dense(1.380, 0.231)),
+        (0.273, 1.0, Vectors.dense(0.520, 1.151)),
+        (4.199, 0.0, Vectors.dense(0.795, -0.226))], ["label", "censor", "features"])
+    quantileProbabilities = [0.3, 0.6]
+    aft = AFTSurvivalRegression(quantileProbabilities=quantileProbabilities,
+                                quantilesCol="quantiles")
+
+    model = aft.fit(training)
+
+    # Print the coefficients, intercept and scale parameter for AFT survival regression
+    print("Coefficients: " + str(model.coefficients))
+    print("Intercept: " + str(model.intercept))
+    print("Scale: " + str(model.scale))
+    model.transform(training).show(truncate=False)
+    # $example off$
+
+    sc.stop()

http://git-wip-us.apache.org/repos/asf/spark/blob/a85a9122/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
----------------------------------------------------------------------
diff --git a/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
b/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
new file mode 100644
index 0000000..5da285e
--- /dev/null
+++ b/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
@@ -0,0 +1,62 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// scalastyle:off println
+package org.apache.spark.examples.ml
+
+import org.apache.spark.sql.SQLContext
+import org.apache.spark.{SparkContext, SparkConf}
+// $example on$
+import org.apache.spark.ml.regression.AFTSurvivalRegression
+import org.apache.spark.mllib.linalg.Vectors
+// $example off$
+
+/**
+ * An example for AFTSurvivalRegression.
+ */
+object AFTSurvivalRegressionExample {
+
+  def main(args: Array[String]): Unit = {
+    val conf = new SparkConf().setAppName("AFTSurvivalRegressionExample")
+    val sc = new SparkContext(conf)
+    val sqlContext = new SQLContext(sc)
+
+    // $example on$
+    val training = sqlContext.createDataFrame(Seq(
+      (1.218, 1.0, Vectors.dense(1.560, -0.605)),
+      (2.949, 0.0, Vectors.dense(0.346, 2.158)),
+      (3.627, 0.0, Vectors.dense(1.380, 0.231)),
+      (0.273, 1.0, Vectors.dense(0.520, 1.151)),
+      (4.199, 0.0, Vectors.dense(0.795, -0.226))
+    )).toDF("label", "censor", "features")
+    val quantileProbabilities = Array(0.3, 0.6)
+    val aft = new AFTSurvivalRegression()
+      .setQuantileProbabilities(quantileProbabilities)
+      .setQuantilesCol("quantiles")
+
+    val model = aft.fit(training)
+
+    // Print the coefficients, intercept and scale parameter for AFT survival regression
+    println(s"Coefficients: ${model.coefficients} Intercept: " +
+      s"${model.intercept} Scale: ${model.scale}")
+    model.transform(training).show(false)
+    // $example off$
+
+    sc.stop()
+  }
+}
+// scalastyle:off println


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