mllib-data-types.md

layout: global
title: Data Types - RDD-based API
displayTitle: Data Types - RDD-based API

• Table of contents {:toc}

MLlib supports local vectors and matrices stored on a single machine, as well as distributed matrices backed by one or more RDDs. Local vectors and local matrices are simple data models that serve as public interfaces. The underlying linear algebra operations are provided by Breeze. A training example used in supervised learning is called a "labeled point" in MLlib.

Local vector

A local vector has integer-typed and 0-based indices and double-typed values, stored on a single machine. MLlib supports two types of local vectors: dense and sparse. A dense vector is backed by a double array representing its entry values, while a sparse vector is backed by two parallel arrays: indices and values. For example, a vector (1.0, 0.0, 3.0) can be represented in dense format as [1.0, 0.0, 3.0] or in sparse format as (3, [0, 2], [1.0, 3.0]), where 3 is the size of the vector.

The base class of local vectors is Vector, and we provide two implementations: DenseVector and SparseVector. We recommend using the factory methods implemented in Vectors to create local vectors.

Refer to the Vector Scala docs and Vectors Scala docs for details on the API.

{% highlight scala %} import org.apache.spark.mllib.linalg.{Vector, Vectors}

// Create a dense vector (1.0, 0.0, 3.0). val dv: Vector = Vectors.dense(1.0, 0.0, 3.0) // Create a sparse vector (1.0, 0.0, 3.0) by specifying its indices and values corresponding to nonzero entries. val sv1: Vector = Vectors.sparse(3, Array(0, 2), Array(1.0, 3.0)) // Create a sparse vector (1.0, 0.0, 3.0) by specifying its nonzero entries. val sv2: Vector = Vectors.sparse(3, Seq((0, 1.0), (2, 3.0))) {% endhighlight %}

Note: Scala imports scala.collection.immutable.Vector by default, so you have to import org.apache.spark.mllib.linalg.Vector explicitly to use MLlib's Vector.

The base class of local vectors is Vector, and we provide two implementations: DenseVector and SparseVector. We recommend using the factory methods implemented in Vectors to create local vectors.

Refer to the Vector Java docs and Vectors Java docs for details on the API.

{% highlight java %} import org.apache.spark.mllib.linalg.Vector; import org.apache.spark.mllib.linalg.Vectors;

// Create a dense vector (1.0, 0.0, 3.0). Vector dv = Vectors.dense(1.0, 0.0, 3.0); // Create a sparse vector (1.0, 0.0, 3.0) by specifying its indices and values corresponding to nonzero entries. Vector sv = Vectors.sparse(3, new int[] {0, 2}, new double[] {1.0, 3.0}); {% endhighlight %}

MLlib recognizes the following types as dense vectors:

• NumPy's array
• Python's list, e.g., [1, 2, 3]

and the following as sparse vectors:

• MLlib's SparseVector.
• SciPy's csc_matrix with a single column

We recommend using NumPy arrays over lists for efficiency, and using the factory methods implemented in Vectors to create sparse vectors.

Refer to the Vectors Python docs for more details on the API.

{% highlight python %} import numpy as np import scipy.sparse as sps from pyspark.mllib.linalg import Vectors

Use a NumPy array as a dense vector.

dv1 = np.array([1.0, 0.0, 3.0])

Use a Python list as a dense vector.

dv2 = [1.0, 0.0, 3.0]

Create a SparseVector.

sv1 = Vectors.sparse(3, [0, 2], [1.0, 3.0])

Use a single-column SciPy csc_matrix as a sparse vector.

sv2 = sps.csc_matrix((np.array([1.0, 3.0]), np.array([0, 2]), np.array([0, 2])), shape = (3, 1)) {% endhighlight %}

Labeled point

A labeled point is a local vector, either dense or sparse, associated with a label/response. In MLlib, labeled points are used in supervised learning algorithms. We use a double to store a label, so we can use labeled points in both regression and classification. For binary classification, a label should be either 0 (negative) or 1 (positive). For multiclass classification, labels should be class indices starting from zero: 0, 1, 2, ....

A labeled point is represented by the case class LabeledPoint.

Refer to the LabeledPoint Scala docs for details on the API.

{% highlight scala %} import org.apache.spark.mllib.linalg.Vectors import org.apache.spark.mllib.regression.LabeledPoint

// Create a labeled point with a positive label and a dense feature vector. val pos = LabeledPoint(1.0, Vectors.dense(1.0, 0.0, 3.0))

// Create a labeled point with a negative label and a sparse feature vector. val neg = LabeledPoint(0.0, Vectors.sparse(3, Array(0, 2), Array(1.0, 3.0))) {% endhighlight %}

A labeled point is represented by LabeledPoint.

Refer to the LabeledPoint Java docs for details on the API.

{% highlight java %} import org.apache.spark.mllib.linalg.Vectors; import org.apache.spark.mllib.regression.LabeledPoint;

// Create a labeled point with a positive label and a dense feature vector. LabeledPoint pos = new LabeledPoint(1.0, Vectors.dense(1.0, 0.0, 3.0));

// Create a labeled point with a negative label and a sparse feature vector. LabeledPoint neg = new LabeledPoint(0.0, Vectors.sparse(3, new int[] {0, 2}, new double[] {1.0, 3.0})); {% endhighlight %}

A labeled point is represented by LabeledPoint.

Refer to the LabeledPoint Python docs for more details on the API.

{% highlight python %} from pyspark.mllib.linalg import SparseVector from pyspark.mllib.regression import LabeledPoint

Create a labeled point with a positive label and a dense feature vector.

pos = LabeledPoint(1.0, [1.0, 0.0, 3.0])

Create a labeled point with a negative label and a sparse feature vector.

neg = LabeledPoint(0.0, SparseVector(3, [0, 2], [1.0, 3.0])) {% endhighlight %}

Sparse data

It is very common in practice to have sparse training data. MLlib supports reading training examples stored in LIBSVM format, which is the default format used by LIBSVM and LIBLINEAR. It is a text format in which each line represents a labeled sparse feature vector using the following format:

label index1:value1 index2:value2 ...

where the indices are one-based and in ascending order. After loading, the feature indices are converted to zero-based.

MLUtils.loadLibSVMFile reads training examples stored in LIBSVM format.

Refer to the MLUtils Scala docs for details on the API.

{% highlight scala %} import org.apache.spark.mllib.regression.LabeledPoint import org.apache.spark.mllib.util.MLUtils import org.apache.spark.rdd.RDD

val examples: RDD[LabeledPoint] = MLUtils.loadLibSVMFile(sc, "data/mllib/sample_libsvm_data.txt") {% endhighlight %}

MLUtils.loadLibSVMFile reads training examples stored in LIBSVM format.

Refer to the MLUtils Java docs for details on the API.

{% highlight java %} import org.apache.spark.mllib.regression.LabeledPoint; import org.apache.spark.mllib.util.MLUtils; import org.apache.spark.api.java.JavaRDD;

JavaRDD examples = MLUtils.loadLibSVMFile(jsc.sc(), "data/mllib/sample_libsvm_data.txt").toJavaRDD(); {% endhighlight %}

MLUtils.loadLibSVMFile reads training examples stored in LIBSVM format.

Refer to the MLUtils Python docs for more details on the API.

{% highlight python %} from pyspark.mllib.util import MLUtils

examples = MLUtils.loadLibSVMFile(sc, "data/mllib/sample_libsvm_data.txt") {% endhighlight %}

Local matrix

A local matrix has integer-typed row and column indices and double-typed values, stored on a single machine. MLlib supports dense matrices, whose entry values are stored in a single double array in column-major order, and sparse matrices, whose non-zero entry values are stored in the Compressed Sparse Column (CSC) format in column-major order. For example, the following dense matrix \[ \begin{pmatrix} 1.0 & 2.0 \\ 3.0 & 4.0 \\ 5.0 & 6.0 \end{pmatrix} \] is stored in a one-dimensional array [1.0, 3.0, 5.0, 2.0, 4.0, 6.0] with the matrix size (3, 2).

The base class of local matrices is Matrix, and we provide two implementations: DenseMatrix, and SparseMatrix. We recommend using the factory methods implemented in Matrices to create local matrices. Remember, local matrices in MLlib are stored in column-major order.

Refer to the Matrix Scala docs and Matrices Scala docs for details on the API.

{% highlight scala %} import org.apache.spark.mllib.linalg.{Matrix, Matrices}

// Create a dense matrix ((1.0, 2.0), (3.0, 4.0), (5.0, 6.0)) val dm: Matrix = Matrices.dense(3, 2, Array(1.0, 3.0, 5.0, 2.0, 4.0, 6.0))

// Create a sparse matrix ((9.0, 0.0), (0.0, 8.0), (0.0, 6.0)) val sm: Matrix = Matrices.sparse(3, 2, Array(0, 1, 3), Array(0, 2, 1), Array(9, 6, 8)) {% endhighlight %}

The base class of local matrices is Matrix, and we provide two implementations: DenseMatrix, and SparseMatrix. We recommend using the factory methods implemented in Matrices to create local matrices. Remember, local matrices in MLlib are stored in column-major order.

Refer to the Matrix Java docs and Matrices Java docs for details on the API.

{% highlight java %} import org.apache.spark.mllib.linalg.Matrix; import org.apache.spark.mllib.linalg.Matrices;

// Create a dense matrix ((1.0, 2.0), (3.0, 4.0), (5.0, 6.0)) Matrix dm = Matrices.dense(3, 2, new double[] {1.0, 3.0, 5.0, 2.0, 4.0, 6.0});

// Create a sparse matrix ((9.0, 0.0), (0.0, 8.0), (0.0, 6.0)) Matrix sm = Matrices.sparse(3, 2, new int[] {0, 1, 3}, new int[] {0, 2, 1}, new double[] {9, 6, 8}); {% endhighlight %}

The base class of local matrices is Matrix, and we provide two implementations: DenseMatrix, and SparseMatrix. We recommend using the factory methods implemented in Matrices to create local matrices. Remember, local matrices in MLlib are stored in column-major order.

Refer to the Matrix Python docs and Matrices Python docs for more details on the API.

{% highlight python %} from pyspark.mllib.linalg import Matrix, Matrices

Create a dense matrix ((1.0, 2.0), (3.0, 4.0), (5.0, 6.0))

dm2 = Matrices.dense(3, 2, [1, 2, 3, 4, 5, 6])

Create a sparse matrix ((9.0, 0.0), (0.0, 8.0), (0.0, 6.0))

sm = Matrices.sparse(3, 2, [0, 1, 3], [0, 2, 1], [9, 6, 8]) {% endhighlight %}

Distributed matrix

A distributed matrix has long-typed row and column indices and double-typed values, stored distributively in one or more RDDs. It is very important to choose the right format to store large and distributed matrices. Converting a distributed matrix to a different format may require a global shuffle, which is quite expensive. Four types of distributed matrices have been implemented so far.

The basic type is called RowMatrix. A RowMatrix is a row-oriented distributed matrix without meaningful row indices, e.g., a collection of feature vectors. It is backed by an RDD of its rows, where each row is a local vector. We assume that the number of columns is not huge for a RowMatrix so that a single local vector can be reasonably communicated to the driver and can also be stored / operated on using a single node. An IndexedRowMatrix is similar to a RowMatrix but with row indices, which can be used for identifying rows and executing joins. A CoordinateMatrix is a distributed matrix stored in coordinate list (COO) format, backed by an RDD of its entries. A BlockMatrix is a distributed matrix backed by an RDD of MatrixBlock which is a tuple of (Int, Int, Matrix).