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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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FP-Growth

The FP-growth algorithm is described in the paper Han et al., Mining frequent patterns without candidate generation, where ā€œFPā€ stands for frequent pattern. Given a dataset of transactions, the first step of FP-growth is to calculate item frequencies and identify frequent items. Different from Apriori-like algorithms designed for the same purpose, the second step of FP-growth uses a suffix tree (FP-tree) structure to encode transactions without generating candidate sets explicitly, which are usually expensive to generate. After the second step, the frequent itemsets can be extracted from the FP-tree. In spark.mllib, we implemented a parallel version of FP-growth called PFP, as described in Li et al., PFP: Parallel FP-growth for query recommendation. PFP distributes the work of growing FP-trees based on the suffixes of transactions, and hence is more scalable than a single-machine implementation. We refer users to the papers for more details.

spark.ml's FP-growth implementation takes the following (hyper-)parameters:

minSupport: the minimum support for an itemset to be identified as frequent. For example, if an item appears 3 out of 5 transactions, it has a support of 3/5=0.6.

minConfidence: minimum confidence for generating Association Rule. Confidence is an indication of how often an association rule has been found to be true. For example, if in the transactions itemset X appears 4 times, X and Y co-occur only 2 times, the confidence for the rule X => Y is then 2/4 = 0.5. The parameter will not affect the mining for frequent itemsets, but specify the minimum confidence for generating association rules from frequent itemsets.

numPartitions: the number of partitions used to distribute the work. By default the param is not set, and number of partitions of the input dataset is used. The FPGrowthModel provides:

freqItemsets: frequent itemsets in the format of DataFrame("items"[Array], "freq"[Long]) associationRules: association rules generated with confidence above minConfidence, in the format of DataFrame("antecedent"[Array], "consequent"[Array], "confidence"[Double]).

transform: For each transaction in itemsCol, the transform method will compare its items against the antecedents of each association rule. If the record contains all the antecedents of a specific association rule, the rule will be considered as applicable and its consequents will be added to the prediction result. The transform method will summarize the consequents from all the applicable rules as prediction. The prediction column has the same data type as itemsCol and does not contain existing items in the itemsCol.

import org.apache.spark.ml.fpm.FPGrowth

val dataset = spark.createDataset(Seq(
  "1 2 5",
  "1 2 3 5",
  "1 2")
).map(t => t.split(" ")).toDF("items")

val fpgrowth = new FPGrowth().setItemsCol("items").setMinSupport(0.5).setMinConfidence(0.6)
val model = fpgrowth.fit(dataset)

// Display frequent itemsets.
model.freqItemsets.show()

// Display generated association rules.
model.associationRules.show()

// transform examines the input items against all the association rules and summarize the
// consequents as prediction
model.transform(dataset).show()
/*
Output:
+---------+----+
|    items|freq|
+---------+----+
|      [1]|   3|
|      [2]|   3|
|   [2, 1]|   3|
|      [5]|   2|
|   [5, 2]|   2|
|[5, 2, 1]|   2|
|   [5, 1]|   2|
+---------+----+

+----------+----------+------------------+----+
|antecedent|consequent|        confidence|lift|
+----------+----------+------------------+----+
|    [2, 1]|       [5]|0.6666666666666666| 1.0|
|    [5, 1]|       [2]|               1.0| 1.0|
|       [2]|       [1]|               1.0| 1.0|
|       [2]|       [5]|0.6666666666666666| 1.0|
|       [5]|       [2]|               1.0| 1.0|
|       [5]|       [1]|               1.0| 1.0|
|       [1]|       [2]|               1.0| 1.0|
|       [1]|       [5]|0.6666666666666666| 1.0|
|    [5, 2]|       [1]|               1.0| 1.0|
+----------+----------+------------------+----+

+------------+----------+
|       items|prediction|
+------------+----------+
|   [1, 2, 5]|        []|
|[1, 2, 3, 5]|        []|
|      [1, 2]|       [5]|
+------------+----------+



*/
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