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Clustering4Ever

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C4E, a JVM friendly library written in Scala for both local and distributed (Spark) Clustering.

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# Clustering :four: Ever  [ ![Download](https://api.bintray.com/packages/clustering4ever/C4E/clustering4ever/images/download.svg) ](https://bintray.com/clustering4ever/C4E/clustering4ever/_latestVersion) [![Maven Central](https://img.shields.io/maven-central/v/org.clustering4ever/clustering4ever_2.11.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22org.clustering4ever%22%20AND%20a:%22clustering4ever_2.11%22) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Clustering4Ever/Notebooks/master)

**Welcome** to Clustering:four:Ever, a Big Data Clustering Library gathering clustering, unsupervised algorithms, and quality indices. Don't hesitate to check our **[Wiki](https://github.com/Clustering4Ever/Clustering4Ever/wiki)**, ask questions or make recommendations in our **[Gitter](https://gitter.im/Clustering4Ever/Lobby)**.

## [API documentation](http://www.clustering4ever.org/API%20Documentation/)

## Include it in your project

Add following line in your build.sbt :

* `"org.clustering4ever" % "clustering4ever_2.11" % "0.11.0"` to your `libraryDependencies`

Eventually add one of these resolvers :

* `resolvers += Resolver.bintrayRepo("clustering4ever", "C4E")`
  * `resolvers += "mvnrepository" at "http://mvnrepository.com/artifact/"`

You can also take specifics parts (Core, ScalaClustering, ...) from [Bintray](https://bintray.com/clustering4ever/C4E) or [Maven](https://mvnrepository.com/artifact/org.clustering4ever).

## Available algorithms

* _emphasized algorithms_ are in Scala.
  * **bold algorithms** are implemented in Spark.
  * They can be available in **_both versions_**

### Clustering algorithms

* _Jenks Natural Breaks_
  * **_Epsilon Proximity_**`*`
    * **_Scalar Epsilon Proximity_**`*`, _Binary Epsilon Proximity_`*`, _Mixed Epsilon Proximity_`*`, _Any Object Epsilon Proximity_`*`
  * **_K-Centers_**`*`
    * **_K-Means_**`*`, **_K-Modes_**`*`, **_K-Prototypes_**`*`, **_Any Object K-Centers_**`*`
  * _Gaussian Mixture_ 
  * **Self Organizing Maps** ([Original project](https://github.com/TugdualSarazin/spark-clustering))
  * **G-Stream** ([Original project](https://github.com/Spark-clustering-notebook/G-stream))
  * **PatchWork** ([Original project](https://github.com/crim-ca/patchwork))
  * _Random Local Area_ `*`
  * _OPTICS_ `*`
  * **Clusterwize** 
  * _Tensor Biclustering algorithms_ ([Original project](https://github.com/SoheilFeizi/Tensor-Biclustering))
    * _Folding-Spectral_, _Unfolding-Spectral_, _Thresholding Sum Of Squared Trajectory Length_, _Thresholding Individuals Trajectory Length_, _Recursive Biclustering_, _Multiple Biclustering_
  * _Ant-Tree_ `*`
    * _Continuous Ant-Tree_, _Binary Ant-Tree_, _Mixed Ant-Tree_
  * **DC-DPM** ([Original project](https://github.com/khadidjaM/DC-DPM)) - Distributed Clustering based on Dirichlet Process Mixture
  * **SG2Stream**
 
Algorithm followed with a `*` can be executed by benchmarking classes.

### Preprocessing

* _UMAP_
  * **_Gradient Ascent_** (Mean-Shift related)
    * **_Scalar Gradient Ascent_**, _Binary Gradient Ascent_, _Mixed Gradient Ascent_, _Any Object Gradient Ascent_
  * **_Rough Set Features Selection_**

### Quality Indices

You can realize manually your quality measures with dedicated class for local or distributed collection. Helpers _ClustersIndicesAnalysisLocal_ and _ClustersIndicesAnalysisDistributed_ allow you to test indices on multiple clustering at once.

* Internal Indices
    * **_Davies Bouldin_**
    * **_Ball Hall_**
  * External Indices
    * **_Multiple Classification_**
      * **_Mutual Information_**, **_Normalized Mutual Information_**
      * **_Purity_**
      * **_Accuracy_**, **_Precision_**, **_Recall_**, **_fBeta_**, **_f1_**, **_RAND_**, **_ARAND_**, **_Matthews correlation coefficient_**, **_CzekanowskiDice_**, **_RogersTanimoto_**, **_FolkesMallows_**, **_Jaccard_**, **_Kulcztnski_**, **_McNemar_**, **_RusselRao_**, **_SokalSneath1_**, **_SokalSneath2_**
    * **_Binary Classification_**
      * **_Accuracy_**, **_Precision_**, **_Recall_**, **_fBeta_**, **_f1_**

### Clustering benchmarking and analysis

Using classes _ClusteringChainingLocal_, _BigDataClusteringChaining_, _DistributedClusteringChaining_, and _ChainingOneAlgorithm_ descendants you have the possibility to run multiple clustering algorithms respectively **locally and parallel**, **in a sequentially distributed way**, and **parallel on a distributed system**, **locally and parallel**, generate much vectorization of the data whilst keeping active information on each clustering including **used vectorization, clustering model, clustering number and clustering arguments**.

Classes _ClustersIndicesAnalysisLocal_ and _ClustersIndicesAnalysisDistributed_ are devoted for clustering indices analysis.

Classes _ClustersAnalysisLocal_ and _ClustersAnalysisDistributed_ will be used to describe obtained clustering in terms of distributions, proportions of categorical features...

### Incoming soon (developped by our team)
  
  * **[DESOM:Deep Embedded Self-Organizing Map: Joint Representation Learning and Self-Organization](https://github.com/FlorentF9/DESOM)**
  * **[SOM:Kohonen self-organizing map](https://github.com/FlorentF9/sparkml-som)**
  * **[SOMperf: SOM performance metrics and quality indices](https://github.com/FlorentF9/SOMperf/)**
  * **[skstab is a module for clustering stability analysis in Python with a scikit-learn compatible API](https://github.com/FlorentF9/skstab)**
  * **[FunCLBM: Functional Conditional Latent Block Model](https://github.com/EtienneGof/FunCLBM)**
  * **[Spark Time Series Set data analysis](https://github.com/spark-tss/spark-tss)**
  * **[UMAP](https://github.com/lmcinnes/umap)**
  * **Gaussian Mixture**
  * _DBScan_
  * **[Bayesian Optimization for AutoML](https://github.com/YazidJanati/bayestuner-scala)**

## Citation

If you publish material based on information obtained from this repository, then, in your acknowledgements, please note the assistance you received by using this community work. This will help others to obtain the same information and **replicate your experiments**, because having results is cool but being able to compare to others is better.
Citation: `@misc{C4E, url = “https://github.com/Clustering4Ever/Clustering4Ever“, institution = “Paris 13 University, LIPN UMR CNRS 7030”}`

## C4E-Notebooks examples

Basic usages of implemented algorithms are exposed with **BeakerX and Jupyter notebook** through binder :arrow_right:
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Clustering4Ever/Notebooks/master).

They also can be downloaded directly from our [Notebooks](https://github.com/Clustering4Ever/Notebooks) repository under different format as **Jupyter** or **SparkNotebook**.

## Miscellaneous

### Helper functions to generate Clusterizable collections

You can easily generate your collections with basic `Clusterizable` using helpers in `org.clustering4ever.util.{ArrayAndSeqTowardGVectorImplicit, ScalaCollectionImplicits, SparkImplicits}` or explore `Clusterizable` and `EasyClusterizable` for more advanced usages.

### [References](https://github.com/Clustering4Ever/Clustering4Ever/wiki/5.-References)

### What data structures are recommended for best performances

ArrayBuffer or ParArray as vector containers are recommended for local applications, if data is bigger don't hesitate to pass to RDD.

Clustering4Ever

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