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Data Science with Apache Spark
  • Preface
  • Contents
  • Basic Prerequisite Skills
  • Computer needed for this course
  • Spark Environment Setup
  • Dev environment setup, task list
  • JDK setup
  • Download and install Anaconda Python and create virtual environment with Python 3.6
  • Download and install Spark
  • Eclipse, the Scala IDE
  • Install findspark, add spylon-kernel for scala
  • ssh and scp client
  • Summary
  • Development environment on MacOS
  • Production Spark Environment Setup
  • VirtualBox VM
  • VirtualBox only shows 32bit on AMD CPU
  • Configure VirtualBox NAT as Network Adapter on Guest VM and Allow putty ssh Through Port Forwarding
  • Docker deployment of Spark Cluster
  • Create customized Apache Spark Docker container
  • Dockerfile
  • docker-compose and docker-compose.yml
  • Launch custom built Docker container with docker-compose
  • Entering Docker Container
  • Setup Hadoop, Hive and Spark on Linux without docker
  • Hadoop Preparation
  • Hadoop setup
  • Configure $HADOOP_HOME/etc/hadoop
  • HDFS
  • Start and stop Hadoop
  • Work with Hadoop and HDFS file system
  • Connect to Hadoop web interface port 50070 and 8088
  • Install Hive
  • hive home
  • Initialize hive schema
  • Start hive metastore service.
  • hive-site.xml
  • Hive client
  • Setup Apache Spark
  • Spark Home
  • Jupyter-notebook server
  • Python 3 Warm Up
  • Basics
  • Iterables/Collections
  • Strings
  • List
  • Tuple
  • Dictionary
  • Set
  • Conditional statement
  • for loop
  • while loop
  • Functions and methods
  • map and filter
  • map and filter takes function as input
  • lambda
  • Python Class
  • Input and if statement
  • Input from a file
  • Output to a file
  • try except
  • Python coding exercise
  • Scala Warm Up
  • Start Spylon-kernel on Jupyter-notebook
  • Type of Variable: Mutable or immutable
  • Block statement
  • Scala Data Type
  • Array in Scala
  • Methods
  • Functions
  • Anonymous function
  • Scala map and filter methods
  • Class
  • Objects
  • Trait
  • Tuple in Scala
  • List/Seq
  • Set in Scala
  • Scala Map
  • Scala if statement
  • Scala for loop
  • Scala While Loop
  • Scala Exceptions + try catch finally
  • Scala coding exercise
  • Run a program to estimate pi
  • Common Spark command line
  • Run Scala code with spark-submit
  • Python with Apache Spark using Jupyter notebook
  • Spark Core Introduction
  • Spark and Scala Version
  • Basic Spark Package
  • Resilient Distributed Datasets (RDDs)
  • RDD Operations
  • Passing Function to Spark
  • Printing elements of an RDD
  • Working with key value pair
  • RDD Transformation Functions
  • RDD Action Functions
  • SPARK SQL
  • SQL
  • Datasets and DataFrames
  • SparkSession
  • Creating DataFrames
  • Running SQL Queries Programmatically
  • Issue from running Cartesian Join Query
  • Creating Datasets
  • Interoperating with RDD
  • Untyped User-Defined Aggregate Functions
  • Generic Load/Save Functions
  • Manually specify file option
  • Run SQL on files directly
  • Save Mode
  • Saving to Persistent Tables
  • Bucketing, Sorting and Partitioning
  • Apache Arrow
  • Install Python Arrow Module PyArrow
  • Issue might happen import PyArrow
  • Enabling for Conversion to/from Pandas in Python
  • Connect to any data source the same consistent way
  • Spark SQL Implementation Example in Scala
  • Run scala code in Eclipse IDE
  • Hive Integration, run SQL or HiveQL queries on existing warehouses.
  • Example: Enrich JSON
  • Integrate Tableau Data Visualization with Hive Data Warehouse and Apache Spark SQL
  • Connect Tableau to Spark SQL running in VM with VirtualBox with NAT
  • Issues with connecting from Tableau to Spark SQL
  • SPARK Streaming
  • Discretized Streams (DStreams)
  • Transformations on DStreams
  • map(func)
  • filter(func)
  • repartition(numPartitions)
  • union(otherStream)
  • reduce(func)
  • count()
  • countByValue()
  • reduceByKey(func, [numTasks])
  • join(otherStream, [numTasks])
  • cogroup(otherStream, [numTasks])
  • transform(func)
  • updateStateByKey(func)
  • Scala Tips for updateStateByKey
  • repartition(numPartitions)
  • DStream Window Operations
  • DStream Window Transformation
  • countByWindow(windowLength, slideInterval)
  • reduceByWindow(func, windowLength, slideInterval)
  • reduceByKeyAndWindow(func, windowLength, slideInterval, [numTasks])
  • reduceByKeyAndWindow(func, invFunc, windowLength, slideInterval, [numTasks])
  • countByValueAndWindow(windowLength, slideInterval, [numTasks])
  • window(windowLength, slideInterval)
  • Window DStream print(n)
  • saveAsTextFiles(prefix, [suffix])
  • saveAsObjectFiles(prefix, [suffix])
  • saveAsHadoopFiles(prefix, [suffix])
  • foreachRDD(func)
  • Build Twitter Scala API Library for Spark Streaming using sbt
  • Spark Streaming with Twitter, you can get public tweets by using Twitter API.
  • Spark streaming use case with Python
  • Spark Graph Computing
  • Spark Graph Computing Continue
  • Graphx
  • Package org.apache.spark.graphx
  • Edge Class
  • EdgeContext Class
  • EdgeDirection Class
  • EdgeRDD Class
  • EdgeTriplet Class
  • Graph Class
  • GraphLoader Object
  • GraphOps Class
  • GraphXUtils Object
  • PartitionStrategy Trait
  • Pregel Object
  • TripletFields Class
  • VertexRDD Class
  • Package org.apache.spark.graphx.impl
  • AggregatingEdgeContext Class
  • EdgeRDDImpl Class
  • Class GraphImpl<VD,ED>
  • Class VertexRDDImpl<VD>
  • Package org.apache.spark.graphx.lib
  • Class ConnectedComponents
  • Class LabelPropagation
  • Class PageRank
  • Class ShortestPaths
  • Class StronglyConnectedComponents
  • Class SVDPlusPlus
  • Class SVDPlusPlus.Conf
  • Class TriangleCount
  • Package org.apache.spark.graphx.util
  • Class BytecodeUtils
  • Class GraphGenerators
  • Graphx Example 1
  • Graphx Example 2
  • Graphx Example 3
  • Spark Graphx Describes Organization Chart Easy and Fast
  • Page Rank with Apache Spark Graphx
  • bulk synchronous parallel with Google Pregel Graphx Implementation Use Cases
  • Tree and Graph Traversal with and without Spark Graphx
  • Graphx Graph Traversal with Pregel Explained
  • Spark Machine Learning
  • Binary Classification
  • Multiclass Classification
  • Regression
  • Correlation
  • Image Data Source
  • ML DataFrame is SQL DataFrame
  • ML Transformer
  • ML Estimator
  • ML Pipeline
  • Transformer/Estimator Parameters
  • Extracting, transforming and selecting features
  • TF-IDF
  • Word2Vec
  • FeatureHasher
  • Tokenizer
  • CountVectorizer
  • StopWordRemover
  • n-gram
  • Binarizer
  • PCA
  • PolynomialExpansion
  • StringIndexer
  • Discrete Cosine Transform (DCT)
  • One-hot encoding
  • StandardScaler
  • IndexToString
  • VectorIndexer
  • Interaction
  • Normalizer
  • MinMaxScaler
  • MaxAbScaler
  • Bucketizer
  • ElementwiseProduct
  • SQLTransformer
  • VectorAssembler
  • VectorSizeHint
  • QuantileDiscretizer
  • Imputer
  • VectorSlicer
  • RFormula
  • ChiSqSelector
  • Locality Sensitive Hashing
  • MinHash for Jaccard Distance
  • Classification and Regression
  • LogisticRegression
  • OneVsRest
  • Naive Bayes classifiers
  • Decision trees
  • Random forests
  • Gradient-boosted trees (GBTs)
  • Multilayer perceptron classifier
  • Linear Support Vector Machine
  • Linear Regression
  • Generalized linear regression
  • Isotonic regression
  • Decision Tree Regression
  • Random Forest Regression
  • Gradient-boosted tree regression
  • Survival regression
  • Clustering
  • k-means
  • Latent Dirichlet allocation or LDA
  • Bisecting k-means
  • A Gaussian Mixture Model
  • Collaborative filtering
  • Frequent Pattern Mining
  • FP-Growth
  • PrefixSpan
  • ML Tuning: model selection and hyperparameter tuning
  • Model selection (a.k.a. hyperparameter tuning)
  • Cross-Validation
  • Train-Validation Split
  • Spark Machine Learning Applications
  • Apache Spark SQL & Machine Learning on Genetic Variant Classifications
  • Data Visualization with Vegas Viz and Scala with Spark ML
  • Apache Spark Machine Learning with Dremio Data Lake Engine
  • Dremio Data Lake Engine Apache Arrow Flight Connector with Spark Machine Learning
  • Neural Network with Apache Spark Machine Learning Multilayer Perceptron Classifier
  • Setup TensorFlow, Keras, Theano, Pytorch/torchvision on the CentOS VM
  • Virus Xray Image Classification with Tensorflow Keras Python and Apache Spark Scala
  • Appendix -- Video Presentations
  • References
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Generalized linear regression

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Last updated 5 years ago

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Contrasted with linear regression where the output is assumed to follow a Gaussian distribution, generalized linear models (GLMs) are specifications of linear models where the response variable Yi follows some distribution from the exponential family of distributions. Spark’s GeneralizedLinearRegression interface allows for flexible specification of GLMs which can be used for various types of prediction problems including linear regression, Poisson regression, logistic regression, and others. Currently in spark.ml, only a subset of the exponential family distributions are supported and they are listed below.

NOTE: Spark currently only supports up to 4096 features through its GeneralizedLinearRegression interface, and will throw an exception if this constraint is exceeded.

Spark’s generalized linear regression interface also provides summary statistics for diagnosing the fit of GLM models, including residuals, p-values, deviances, the Akaike information criterion, and others.

import org.apache.spark.ml.regression.GeneralizedLinearRegression

// Load training data
val dataset = spark.read.format("libsvm")
  .load("data/mllib/sample_linear_regression_data.txt")

val glr = new GeneralizedLinearRegression()
  .setFamily("gaussian")
  .setLink("identity")
  .setMaxIter(10)
  .setRegParam(0.3)

// Fit the model
val model = glr.fit(dataset)

// Print the coefficients and intercept for generalized linear regression model
println(s"Coefficients: ${model.coefficients}")
println(s"Intercept: ${model.intercept}")

// Summarize the model over the training set and print out some metrics
val summary = model.summary
println(s"Coefficient Standard Errors: ${summary.coefficientStandardErrors.mkString(",")}")
println(s"T Values: ${summary.tValues.mkString(",")}")
println(s"P Values: ${summary.pValues.mkString(",")}")
println(s"Dispersion: ${summary.dispersion}")
println(s"Null Deviance: ${summary.nullDeviance}")
println(s"Residual Degree Of Freedom Null: ${summary.residualDegreeOfFreedomNull}")
println(s"Deviance: ${summary.deviance}")
println(s"Residual Degree Of Freedom: ${summary.residualDegreeOfFreedom}")
println(s"AIC: ${summary.aic}")
println("Deviance Residuals: ")
summary.residuals().show()

/*
Output:
Coefficients: [0.010541828081257216,0.8003253100560949,-0.7845165541420371,2.3679887171421914,0.5010002089857577,1.1222351159753026,-0.2926824398623296,-0.49837174323213035,-0.6035797180675657,0.6725550067187461]
Intercept: 0.14592176145232041
Coefficient Standard Errors: 0.7950428434287478,0.8049713176546897,0.7975916824772489,0.8312649247659919,0.7945436200517938,0.8118992572197593,0.7919506385542777,0.7973378214726764,0.8300714999626418,0.7771333489686802,0.463930109648428
T Values: 0.013259446542269243,0.9942283563442594,-0.9836067393599172,2.848657084633759,0.6305509179635714,1.382234441029355,-0.3695715687490668,-0.6250446546128238,-0.7271418403049983,0.8654306337661122,0.31453393176593286
P Values: 0.989426199114056,0.32060241580811044,0.3257943227369877,0.004575078538306521,0.5286281628105467,0.16752945248679119,0.7118614002322872,0.5322327097421431,0.467486325282384,0.3872259825794293,0.753249430501097
Dispersion: 105.60988356821714
Null Deviance: 53229.3654338832
Residual Degree Of Freedom Null: 500
Deviance: 51748.8429484264
Residual Degree Of Freedom: 490
AIC: 3769.1895871765314
Deviance Residuals: 
+-------------------+
|  devianceResiduals|
+-------------------+
|-10.974359174246889|
| 0.8872320138420559|
| -4.596541837478908|
|-20.411667435019638|
|-10.270419345342642|
|-6.0156058956799905|
|-10.663939415849267|
| 2.1153960525024713|
| 3.9807132379137675|
|-17.225218272069533|
| -4.611647633532147|
| 6.4176669407698546|
| 11.407137945300537|
| -20.70176540467664|
| -2.683748540510967|
|-16.755494794232536|
|  8.154668342638725|
|-1.4355057987358848|
|-0.6435058688185704|
|  -1.13802589316832|
+-------------------+
only showing top 20 rows


*/