mlpack

mlpack R binding documentation

🔗 mlpack overview

mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It aims to provide fast, lightweight implementations of both common and cutting-edge machine learning algorithms.

This reference page details mlpack’s bindings to R.

Further useful mlpack documentation links are given below.

See also the quickstart guide for R:

🔗 Data Formats

mlpack bindings for R take and return a restricted set of types, for simplicity. These include primitive types, matrix/vector types, categorical matrix types, and model types. Each type is detailed below.

🔗 approx_kfn()

Approximate furthest neighbor search

R> library(mlpack)
R> d <- approx_kfn(algorithm="ds", calculate_error=FALSE,
        exact_distances=matrix(numeric(), 0, 0), input_model=NA, k=0,
        num_projections=5, num_tables=5, query=matrix(numeric(), 0, 0),
        reference=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> distances <- d$distances
R> neighbors <- d$neighbors
R> output_model <- d$output_model

An implementation of two strategies for furthest neighbor search. This can be used to compute the furthest neighbor of query point(s) from a set of points; furthest neighbor models can be saved and reused with future query point(s). Detailed documentation.

🔗 Input options

name type description default
algorithm character Algorithm to use: ‘ds’ or ‘qdafn’. "ds"
calculate_error logical If set, calculate the average distance error for the first furthest neighbor only. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
exact_distances numeric matrix Matrix containing exact distances to furthest neighbors; this can be used to avoid explicit calculation when –calculate_error is set. matrix(numeric(), 0, 0)
input_model ApproxKFNModel File containing input model. NA
k integer Number of furthest neighbors to search for. 0
num_projections integer Number of projections to use in each hash table. 5
num_tables integer Number of hash tables to use. 5
query numeric matrix Matrix containing query points. matrix(numeric(), 0, 0)
reference numeric matrix Matrix containing the reference dataset. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
distances numeric matrix Matrix to save furthest neighbor distances to.
neighbors integer matrix Matrix to save neighbor indices to.
output_model ApproxKFNModel File to save output model to.

🔗 Detailed documentation

This program implements two strategies for furthest neighbor search. These strategies are:

These two strategies give approximate results for the furthest neighbor search problem and can be used as fast replacements for other furthest neighbor techniques such as those found in the mlpack_kfn program. Note that typically, the ‘ds’ algorithm requires far fewer tables and projections than the ‘qdafn’ algorithm.

Specify a reference set (set to search in) with reference, specify a query set with query, and specify algorithm parameters with num_tables and num_projections (or don’t and defaults will be used). The algorithm to be used (either ‘ds’—the default—or ‘qdafn’) may be specified with algorithm. Also specify the number of neighbors to search for with k.

Note that for ‘qdafn’ in lower dimensions, num_projections may need to be set to a high value in order to return results for each query point.

If no query set is specified, the reference set will be used as the query set. The output_model output parameter may be used to store the built model, and an input model may be loaded instead of specifying a reference set with the input_model option.

Results for each query point can be stored with the neighbors and distances output parameters. Each row of these output matrices holds the k distances or neighbor indices for each query point.

🔗 Example

For example, to find the 5 approximate furthest neighbors with "reference_set" as the reference set and "query_set" as the query set using DrusillaSelect, storing the furthest neighbor indices to "neighbors" and the furthest neighbor distances to "distances", one could call

R> output <- approx_kfn(query=query_set, reference=reference_set, k=5,
  algorithm="ds")
R> neighbors <- output$neighbors
R> distances <- output$distances

and to perform approximate all-furthest-neighbors search with k=1 on the set "data" storing only the furthest neighbor distances to "distances", one could call

R> output <- approx_kfn(reference=reference_set, k=1)
R> distances <- output$distances

A trained model can be re-used. If a model has been previously saved to "model", then we may find 3 approximate furthest neighbors on a query set "new_query_set" using that model and store the furthest neighbor indices into "neighbors" by calling

R> output <- approx_kfn(input_model=model, query=new_query_set, k=3)
R> neighbors <- output$neighbors

🔗 See also

🔗 bayesian_linear_regression()

BayesianLinearRegression

R> library(mlpack)
R> d <- bayesian_linear_regression(center=FALSE, input=matrix(numeric(),
        0, 0), input_model=NA, responses=matrix(numeric(), 0, 0), scale=FALSE,
        test=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> stds <- d$stds

An implementation of the bayesian linear regression. Detailed documentation.

🔗 Input options

name type description default
center logical Center the data and fit the intercept if enabled. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Matrix of covariates (X). matrix(numeric(), 0, 0)
input_model BayesianLinearRegression Trained BayesianLinearRegression model to use. NA
responses numeric vector Matrix of responses/observations (y). matrix(numeric(), 0, 0)
scale logical Scale each feature by their standard deviations if enabled. FALSE
test numeric matrix Matrix containing points to regress on (test points). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model BayesianLinearRegression Output BayesianLinearRegression model.
predictions numeric matrix If –test_file is specified, this file is where the predicted responses will be saved.
stds numeric matrix If specified, this is where the standard deviations of the predictive distribution will be saved.

🔗 Detailed documentation

An implementation of the bayesian linear regression. This model is a probabilistic view and implementation of the linear regression. The final solution is obtained by computing a posterior distribution from gaussian likelihood and a zero mean gaussian isotropic prior distribution on the solution. Optimization is AUTOMATIC and does not require cross validation. The optimization is performed by maximization of the evidence function. Parameters are tuned during the maximization of the marginal likelihood. This procedure includes the Ockham’s razor that penalizes over complex solutions.

This program is able to train a Bayesian linear regression model or load a model from file, output regression predictions for a test set, and save the trained model to a file.

To train a BayesianLinearRegression model, the input and responsesparameters must be given. The centerand scale parameters control the centering and the normalizing options. A trained model can be saved with the output_model. If no training is desired at all, a model can be passed via the input_model parameter.

The program can also provide predictions for test data using either the trained model or the given input model. Test points can be specified with the test parameter. Predicted responses to the test points can be saved with the predictions output parameter. The corresponding standard deviation can be save by precising the stds parameter.

🔗 Example

For example, the following command trains a model on the data "data" and responses "responses"with center set to true and scale set to false (so, Bayesian linear regression is being solved, and then the model is saved to "blr_model":

R> output <- bayesian_linear_regression(input=data, responses=responses,
  center=1, scale=0)
R> blr_model <- output$output_model

The following command uses the "blr_model" to provide predicted responses for the data "test" and save those responses to "test_predictions":

R> output <- bayesian_linear_regression(input_model=blr_model, test=test)
R> test_predictions <- output$predictions

Because the estimator computes a predictive distribution instead of a simple point estimate, the stds parameter allows one to save the prediction uncertainties:

R> output <- bayesian_linear_regression(input_model=blr_model, test=test)
R> test_predictions <- output$predictions
R> stds <- output$stds

🔗 See also

🔗 cf()

Collaborative Filtering

R> library(mlpack)
R> d <- cf(algorithm="NMF", all_user_recommendations=FALSE,
        input_model=NA, interpolation="average",
        iteration_only_termination=FALSE, max_iterations=1000,
        min_residue=1e-05, neighbor_search="euclidean", neighborhood=5,
        normalization="none", query=matrix(integer(), 0, 0), rank=0,
        recommendations=5, seed=0, test=matrix(numeric(), 0, 0),
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output <- d$output
R> output_model <- d$output_model

An implementation of several collaborative filtering (CF) techniques for recommender systems. This can be used to train a new CF model, or use an existing CF model to compute recommendations. Detailed documentation.

🔗 Input options

name type description default
algorithm character Algorithm used for matrix factorization. "NMF"
all_user_recommendations logical Generate recommendations for all users. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model CFModel Trained CF model to load. NA
interpolation character Algorithm used for weight interpolation. "average"
iteration_only_termination logical Terminate only when the maximum number of iterations is reached. FALSE
max_iterations integer Maximum number of iterations. If set to zero, there is no limit on the number of iterations. 1000
min_residue numeric Residue required to terminate the factorization (lower values generally mean better fits). 1e-05
neighbor_search character Algorithm used for neighbor search. "euclidean"
neighborhood integer Size of the neighborhood of similar users to consider for each query user. 5
normalization character Normalization performed on the ratings. "none"
query integer matrix List of query users for which recommendations should be generated. matrix(integer(), 0, 0)
rank integer Rank of decomposed matrices (if 0, a heuristic is used to estimate the rank). 0
recommendations integer Number of recommendations to generate for each query user. 5
seed integer Set the random seed (0 uses std::time(NULL)). 0
test numeric matrix Test set to calculate RMSE on. matrix(numeric(), 0, 0)
training numeric matrix Input dataset to perform CF on. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output integer matrix Matrix that will store output recommendations.
output_model CFModel Output for trained CF model.

🔗 Detailed documentation

This program performs collaborative filtering (CF) on the given dataset. Given a list of user, item and preferences (the training parameter), the program will perform a matrix decomposition and then can perform a series of actions related to collaborative filtering. Alternately, the program can load an existing saved CF model with the input_model parameter and then use that model to provide recommendations or predict values.

The input matrix should be a 3-dimensional matrix of ratings, where the first dimension is the user, the second dimension is the item, and the third dimension is that user’s rating of that item. Both the users and items should be numeric indices, not names. The indices are assumed to start from 0.

A set of query users for which recommendations can be generated may be specified with the query parameter; alternately, recommendations may be generated for every user in the dataset by specifying the all_user_recommendations parameter. In addition, the number of recommendations per user to generate can be specified with the recommendations parameter, and the number of similar users (the size of the neighborhood) to be considered when generating recommendations can be specified with the neighborhood parameter.

For performing the matrix decomposition, the following optimization algorithms can be specified via the algorithm parameter:

The following neighbor search algorithms can be specified via the neighbor_search parameter:

The following weight interpolation algorithms can be specified via the interpolation parameter:

The following ranking normalization algorithms can be specified via the normalization parameter:

A trained model may be saved to with the output_model output parameter.

🔗 Example

To train a CF model on a dataset "training_set" using NMF for decomposition and saving the trained model to "model", one could call:

R> output <- cf(training=training_set, algorithm="NMF")
R> model <- output$output_model

Then, to use this model to generate recommendations for the list of users in the query set "users", storing 5 recommendations in "recommendations", one could call

R> output <- cf(input_model=model, query=users, recommendations=5)
R> recommendations <- output$output

🔗 See also

🔗 dbscan()

DBSCAN clustering

R> library(mlpack)
R> d <- dbscan(epsilon=1, input=matrix(numeric(), 0, 0), min_size=5,
        naive=FALSE, selection_type="ordered", single_mode=FALSE,
        tree_type="kd", verbose=getOption("mlpack.verbose", FALSE))
R> assignments <- d$assignments
R> centroids <- d$centroids

An implementation of DBSCAN clustering. Given a dataset, this can compute and return a clustering of that dataset. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
epsilon numeric Radius of each range search. 1
input numeric matrix Input dataset to cluster. **--**
min_size integer Minimum number of points for a cluster. 5
naive logical If set, brute-force range search (not tree-based) will be used. FALSE
selection_type character If using point selection policy, the type of selection to use (‘ordered’, ‘random’). "ordered"
single_mode logical If set, single-tree range search (not dual-tree) will be used. FALSE
tree_type character If using single-tree or dual-tree search, the type of tree to use (‘kd’, ‘r’, ‘r-star’, ‘x’, ‘hilbert-r’, ‘r-plus’, ‘r-plus-plus’, ‘cover’, ‘ball’). "kd"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
assignments integer vector Output matrix for assignments of each point.
centroids numeric matrix Matrix to save output centroids to.

🔗 Detailed documentation

This program implements the DBSCAN algorithm for clustering using accelerated tree-based range search. The type of tree that is used may be parameterized, or brute-force range search may also be used.

The input dataset to be clustered may be specified with the input parameter; the radius of each range search may be specified with the epsilon parameters, and the minimum number of points in a cluster may be specified with the min_size parameter.

The assignments and centroids output parameters may be used to save the output of the clustering. assignments contains the cluster assignments of each point, and centroids contains the centroids of each cluster.

The range search may be controlled with the tree_type, single_mode, and naive parameters. tree_type can control the type of tree used for range search; this can take a variety of values: ‘kd’, ‘r’, ‘r-star’, ‘x’, ‘hilbert-r’, ‘r-plus’, ‘r-plus-plus’, ‘cover’, ‘ball’. The single_mode parameter will force single-tree search (as opposed to the default dual-tree search), and ‘naive will force brute-force range search.

🔗 Example

An example usage to run DBSCAN on the dataset in "input" with a radius of 0.5 and a minimum cluster size of 5 is given below:

R> dbscan(input=input, epsilon=0.5, min_size=5)

🔗 See also

🔗 decision_tree()

Decision tree

R> library(mlpack)
R> d <- decision_tree(input_model=NA, labels=matrix(integer(), 0, 0),
        maximum_depth=0, minimum_gain_split=1e-07, minimum_leaf_size=20,
        print_training_accuracy=FALSE, test=matrix(numeric(), 0, 0),
        test_labels=matrix(integer(), 0, 0), training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE), weights=matrix(numeric(), 0,
        0))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of an ID3-style decision tree for classification, which supports categorical data. Given labeled data with numeric or categorical features, a decision tree can be trained and saved; or, an existing decision tree can be used for classification on new points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model DecisionTreeModel Pre-trained decision tree, to be used with test points. NA
labels integer vector Training labels. matrix(integer(), 0, 0)
maximum_depth integer Maximum depth of the tree (0 means no limit). 0
minimum_gain_split numeric Minimum gain for node splitting. 1e-07
minimum_leaf_size integer Minimum number of points in a leaf. 20
print_training_accuracy logical Print the training accuracy. FALSE
test categorical matrix/data.frame Testing dataset (may be categorical). matrix(numeric(), 0, 0)
test_labels integer vector Test point labels, if accuracy calculation is desired. matrix(integer(), 0, 0)
training categorical matrix/data.frame Training dataset (may be categorical). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
weights numeric matrix The weight of labels matrix(numeric(), 0, 0)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model DecisionTreeModel Output for trained decision tree.
predictions integer vector Class predictions for each test point.
probabilities numeric matrix Class probabilities for each test point.

🔗 Detailed documentation

Train and evaluate using a decision tree. Given a dataset containing numeric or categorical features, and associated labels for each point in the dataset, this program can train a decision tree on that data.

The training set and associated labels are specified with the training and labels parameters, respectively. The labels should be in the range [0, num_classes - 1]. Optionally, if labels is not specified, the labels are assumed to be the last dimension of the training dataset.

When a model is trained, the output_model output parameter may be used to save the trained model. A model may be loaded for predictions with the input_model parameter. The input_model parameter may not be specified when the training parameter is specified. The minimum_leaf_size parameter specifies the minimum number of training points that must fall into each leaf for it to be split. The minimum_gain_split parameter specifies the minimum gain that is needed for the node to split. The maximum_depth parameter specifies the maximum depth of the tree. If print_training_accuracy is specified, the training accuracy will be printed.

Test data may be specified with the test parameter, and if performance numbers are desired for that test set, labels may be specified with the test_labels parameter. Predictions for each test point may be saved via the predictions output parameter. Class probabilities for each prediction may be saved with the probabilities output parameter.

🔗 Example

For example, to train a decision tree with a minimum leaf size of 20 on the dataset contained in "data" with labels "labels", saving the output model to "tree" and printing the training error, one could call

R> output <- decision_tree(training=data, labels=labels, minimum_leaf_size=20,
  minimum_gain_split=0.001, print_training_accuracy=TRUE)
R> tree <- output$output_model

Then, to use that model to classify points in "test_set" and print the test error given the labels "test_labels" using that model, while saving the predictions for each point to "predictions", one could call

R> output <- decision_tree(input_model=tree, test=test_set,
  test_labels=test_labels)
R> predictions <- output$predictions

🔗 See also

🔗 det()

Density Estimation With Density Estimation Trees

R> library(mlpack)
R> d <- det(folds=10, input_model=NA, max_leaf_size=10, min_leaf_size=5,
        path_format="lr", skip_pruning=FALSE, test=matrix(numeric(), 0, 0),
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> tag_counters_file <- d$tag_counters_file
R> tag_file <- d$tag_file
R> test_set_estimates <- d$test_set_estimates
R> training_set_estimates <- d$training_set_estimates
R> vi <- d$vi

An implementation of density estimation trees for the density estimation task. Density estimation trees can be trained or used to predict the density at locations given by query points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
folds integer The number of folds of cross-validation to perform for the estimation (0 is LOOCV) 10
input_model DTree Trained density estimation tree to load. NA
max_leaf_size integer The maximum size of a leaf in the unpruned, fully grown DET. 10
min_leaf_size integer The minimum size of a leaf in the unpruned, fully grown DET. 5
path_format character The format of path printing: ‘lr’, ‘id-lr’, or ‘lr-id’. "lr"
skip_pruning logical Whether to bypass the pruning process and output the unpruned tree only. FALSE
test numeric matrix A set of test points to estimate the density of. matrix(numeric(), 0, 0)
training numeric matrix The data set on which to build a density estimation tree. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model DTree Output to save trained density estimation tree to.
tag_counters_file character The file to output the number of points that went to each leaf.
tag_file character The file to output the tags (and possibly paths) for each sample in the test set.
test_set_estimates numeric matrix The output estimates on the test set from the final optimally pruned tree.
training_set_estimates numeric matrix The output density estimates on the training set from the final optimally pruned tree.
vi numeric matrix The output variable importance values for each feature.

🔗 Detailed documentation

This program performs a number of functions related to Density Estimation Trees. The optimal Density Estimation Tree (DET) can be trained on a set of data (specified by training) using cross-validation (with number of folds specified with the folds parameter). This trained density estimation tree may then be saved with the output_model output parameter.

The variable importances (that is, the feature importance values for each dimension) may be saved with the vi output parameter, and the density estimates for each training point may be saved with the training_set_estimates output parameter.

Enabling path printing for each node outputs the path from the root node to a leaf for each entry in the test set, or training set (if a test set is not provided). Strings like ‘LRLRLR’ (indicating that traversal went to the left child, then the right child, then the left child, and so forth) will be output. If ‘lr-id’ or ‘id-lr’ are given as the path_format parameter, then the ID (tag) of every node along the path will be printed after or before the L or R character indicating the direction of traversal, respectively.

This program also can provide density estimates for a set of test points, specified in the test parameter. The density estimation tree used for this task will be the tree that was trained on the given training points, or a tree given as the parameter input_model. The density estimates for the test points may be saved using the test_set_estimates output parameter.

🔗 See also

🔗 emst()

Fast Euclidean Minimum Spanning Tree

R> library(mlpack)
R> d <- emst(input=matrix(numeric(), 0, 0), leaf_size=1, naive=FALSE,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

An implementation of the Dual-Tree Boruvka algorithm for computing the Euclidean minimum spanning tree of a set of input points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Input data matrix. **--**
leaf_size integer Leaf size in the kd-tree. One-element leaves give the empirically best performance, but at the cost of greater memory requirements. 1
naive logical Compute the MST using O(n^2) naive algorithm. FALSE
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Output data. Stored as an edge list.

🔗 Detailed documentation

This program can compute the Euclidean minimum spanning tree of a set of input points using the dual-tree Boruvka algorithm.

The set to calculate the minimum spanning tree of is specified with the input parameter, and the output may be saved with the output output parameter.

The leaf_size parameter controls the leaf size of the kd-tree that is used to calculate the minimum spanning tree, and if the naive option is given, then brute-force search is used (this is typically much slower in low dimensions). The leaf size does not affect the results, but it may have some effect on the runtime of the algorithm.

🔗 Example

For example, the minimum spanning tree of the input dataset "data" can be calculated with a leaf size of 20 and stored as "spanning_tree" using the following command:

R> output <- emst(input=data, leaf_size=20)
R> spanning_tree <- output$output

The output matrix is a three-dimensional matrix, where each row indicates an edge. The first dimension corresponds to the lesser index of the edge; the second dimension corresponds to the greater index of the edge; and the third column corresponds to the distance between the two points.

🔗 See also

🔗 fastmks()

FastMKS (Fast Max-Kernel Search)

R> library(mlpack)
R> d <- fastmks(bandwidth=1, base=2, degree=2, input_model=NA, k=0,
        kernel="linear", naive=FALSE, offset=0, query=matrix(numeric(), 0, 0),
        reference=matrix(numeric(), 0, 0), scale=1, single=FALSE,
        verbose=getOption("mlpack.verbose", FALSE))
R> indices <- d$indices
R> kernels <- d$kernels
R> output_model <- d$output_model

An implementation of the single-tree and dual-tree fast max-kernel search (FastMKS) algorithm. Given a set of reference points and a set of query points, this can find the reference point with maximum kernel value for each query point; trained models can be reused for future queries. Detailed documentation.

🔗 Input options

name type description default
bandwidth numeric Bandwidth (for Gaussian, Epanechnikov, and triangular kernels). 1
base numeric Base to use during cover tree construction. 2
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
degree numeric Degree of polynomial kernel. 2
input_model FastMKSModel Input FastMKS model to use. NA
k integer Number of maximum kernels to find. 0
kernel character Kernel type to use: ‘linear’, ‘polynomial’, ‘cosine’, ‘gaussian’, ‘epanechnikov’, ‘triangular’, ‘hyptan’. "linear"
naive logical If true, O(n^2) naive mode is used for computation. FALSE
offset numeric Offset of kernel (for polynomial and hyptan kernels). 0
query numeric matrix The query dataset. matrix(numeric(), 0, 0)
reference numeric matrix The reference dataset. matrix(numeric(), 0, 0)
scale numeric Scale of kernel (for hyptan kernel). 1
single logical If true, single-tree search is used (as opposed to dual-tree search. FALSE
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
indices integer matrix Output matrix of indices.
kernels numeric matrix Output matrix of kernels.
output_model FastMKSModel Output for FastMKS model.

🔗 Detailed documentation

This program will find the k maximum kernels of a set of points, using a query set and a reference set (which can optionally be the same set). More specifically, for each point in the query set, the k points in the reference set with maximum kernel evaluations are found. The kernel function used is specified with the kernel parameter.

🔗 Example

For example, the following command will calculate, for each point in the query set "query", the five points in the reference set "reference" with maximum kernel evaluation using the linear kernel. The kernel evaluations may be saved with the "kernels" output parameter and the indices may be saved with the "indices" output parameter.

R> output <- fastmks(k=5, reference=reference, query=query, kernel="linear")
R> indices <- output$indices
R> kernels <- output$kernels

The output matrices are organized such that row i and column j in the indices matrix corresponds to the index of the point in the reference set that has j’th largest kernel evaluation with the point in the query set with index i. Row i and column j in the kernels matrix corresponds to the kernel evaluation between those two points.

This program performs FastMKS using a cover tree. The base used to build the cover tree can be specified with the base parameter.

🔗 See also

🔗 gmm_train()

Gaussian Mixture Model (GMM) Training

R> library(mlpack)
R> d <- gmm_train(diagonal_covariance=FALSE, gaussians=0,
        input=matrix(numeric(), 0, 0), input_model=NA,
        kmeans_max_iterations=1000, max_iterations=250, no_force_positive=FALSE,
        noise=0, percentage=0.02, refined_start=FALSE, samplings=100, seed=0,
        tolerance=1e-10, trials=1, verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model

An implementation of the EM algorithm for training Gaussian mixture models (GMMs). Given a dataset, this can train a GMM for future use with other tools. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
diagonal_covariance logical Force the covariance of the Gaussians to be diagonal. This can accelerate training time significantly. FALSE
gaussians integer Number of Gaussians in the GMM. **--**
input numeric matrix The training data on which the model will be fit. **--**
input_model GMM Initial input GMM model to start training with. NA
kmeans_max_iterations integer Maximum number of iterations for the k-means algorithm (used to initialize EM). 1000
max_iterations integer Maximum number of iterations of EM algorithm (passing 0 will run until convergence). 250
no_force_positive logical Do not force the covariance matrices to be positive definite. FALSE
noise numeric Variance of zero-mean Gaussian noise to add to data. 0
percentage numeric If using –refined_start, specify the percentage of the dataset used for each sampling (should be between 0.0 and 1.0). 0.02
refined_start logical During the initialization, use refined initial positions for k-means clustering (Bradley and Fayyad, 1998). FALSE
samplings integer If using –refined_start, specify the number of samplings used for initial points. 100
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
tolerance numeric Tolerance for convergence of EM. 1e-10
trials integer Number of trials to perform in training GMM. 1
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model GMM Output for trained GMM model.

🔗 Detailed documentation

This program takes a parametric estimate of a Gaussian mixture model (GMM) using the EM algorithm to find the maximum likelihood estimate. The model may be saved and reused by other mlpack GMM tools.

The input data to train on must be specified with the input parameter, and the number of Gaussians in the model must be specified with the gaussians parameter. Optionally, many trials with different random initializations may be run, and the result with highest log-likelihood on the training data will be taken. The number of trials to run is specified with the trials parameter. By default, only one trial is run.

The tolerance for convergence and maximum number of iterations of the EM algorithm are specified with the tolerance and max_iterations parameters, respectively. The GMM may be initialized for training with another model, specified with the input_model parameter. Otherwise, the model is initialized by running k-means on the data. The k-means clustering initialization can be controlled with the kmeans_max_iterations, refined_start, samplings, and percentage parameters. If refined_start is specified, then the Bradley-Fayyad refined start initialization will be used. This can often lead to better clustering results.

The ‘diagonal_covariance’ flag will cause the learned covariances to be diagonal matrices. This significantly simplifies the model itself and causes training to be faster, but restricts the ability to fit more complex GMMs.

If GMM training fails with an error indicating that a covariance matrix could not be inverted, make sure that the no_force_positive parameter is not specified. Alternately, adding a small amount of Gaussian noise (using the noise parameter) to the entire dataset may help prevent Gaussians with zero variance in a particular dimension, which is usually the cause of non-invertible covariance matrices.

The no_force_positive parameter, if set, will avoid the checks after each iteration of the EM algorithm which ensure that the covariance matrices are positive definite. Specifying the flag can cause faster runtime, but may also cause non-positive definite covariance matrices, which will cause the program to crash.

🔗 Example

As an example, to train a 6-Gaussian GMM on the data in "data" with a maximum of 100 iterations of EM and 3 trials, saving the trained GMM to "gmm", the following command can be used:

R> output <- gmm_train(input=data, gaussians=6, trials=3)
R> gmm <- output$output_model

To re-train that GMM on another set of data "data2", the following command may be used:

R> output <- gmm_train(input_model=gmm, input=data2, gaussians=6)
R> new_gmm <- output$output_model

🔗 See also

🔗 gmm_generate()

GMM Sample Generator

R> library(mlpack)
R> d <- gmm_generate(input_model=NA, samples=0, seed=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

A sample generator for pre-trained GMMs. Given a pre-trained GMM, this can sample new points randomly from that distribution. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model GMM Input GMM model to generate samples from. **--**
samples integer Number of samples to generate. **--**
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save output samples in.

🔗 Detailed documentation

This program is able to generate samples from a pre-trained GMM (use gmm_train to train a GMM). The pre-trained GMM must be specified with the input_model parameter. The number of samples to generate is specified by the samples parameter. Output samples may be saved with the output output parameter.

🔗 Example

The following command can be used to generate 100 samples from the pre-trained GMM "gmm" and store those generated samples in "samples":

R> output <- gmm_generate(input_model=gmm, samples=100)
R> samples <- output$output

🔗 See also

🔗 gmm_probability()

GMM Probability Calculator

R> library(mlpack)
R> d <- gmm_probability(input=matrix(numeric(), 0, 0), input_model=NA,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

A probability calculator for GMMs. Given a pre-trained GMM and a set of points, this can compute the probability that each point is from the given GMM. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Input matrix to calculate probabilities of. **--**
input_model GMM Input GMM to use as model. **--**
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to store calculated probabilities in.

🔗 Detailed documentation

This program calculates the probability that given points came from a given GMM (that is, P(X | gmm)). The GMM is specified with the input_model parameter, and the points are specified with the input parameter. The output probabilities may be saved via the output output parameter.

🔗 Example

So, for example, to calculate the probabilities of each point in "points" coming from the pre-trained GMM "gmm", while storing those probabilities in "probs", the following command could be used:

R> output <- gmm_probability(input_model=gmm, input=points)
R> probs <- output$output

🔗 See also

🔗 hmm_train()

Hidden Markov Model (HMM) Training

R> library(mlpack)
R> d <- hmm_train(batch=FALSE, gaussians=0, input_file="",
        input_model=NA, labels_file="", seed=0, states=0, tolerance=1e-05,
        type="gaussian", verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model

An implementation of training algorithms for Hidden Markov Models (HMMs). Given labeled or unlabeled data, an HMM can be trained for further use with other mlpack HMM tools. Detailed documentation.

🔗 Input options

name type description default
batch logical If true, input_file (and if passed, labels_file) are expected to contain a list of files to use as input observation sequences (and label sequences). FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
gaussians integer Number of gaussians in each GMM (necessary when type is ‘gmm’). 0
input_file character File containing input observations. **--**
input_model HMMModel Pre-existing HMM model to initialize training with. NA
labels_file character Optional file of hidden states, used for labeled training. ""
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
states integer Number of hidden states in HMM (necessary, unless model_file is specified). 0
tolerance numeric Tolerance of the Baum-Welch algorithm. 1e-05
type character Type of HMM: discrete | gaussian | diag_gmm | gmm. "gaussian"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model HMMModel Output for trained HMM.

🔗 Detailed documentation

This program allows a Hidden Markov Model to be trained on labeled or unlabeled data. It supports four types of HMMs: Discrete HMMs, Gaussian HMMs, GMM HMMs, or Diagonal GMM HMMs

Either one input sequence can be specified (with input_file), or, a file containing files in which input sequences can be found (when input_fileandbatch are used together). In addition, labels can be provided in the file specified by labels_file, and if batch is used, the file given to labels_file should contain a list of files of labels corresponding to the sequences in the file given to input_file.

The HMM is trained with the Baum-Welch algorithm if no labels are provided. The tolerance of the Baum-Welch algorithm can be set with the toleranceoption. By default, the transition matrix is randomly initialized and the emission distributions are initialized to fit the extent of the data.

Optionally, a pre-created HMM model can be used as a guess for the transition matrix and emission probabilities; this is specifiable with output_model.

🔗 See also

🔗 hmm_generate()

Hidden Markov Model (HMM) Sequence Generator

R> library(mlpack)
R> d <- hmm_generate(length=0, model=NA, seed=0, start_state=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output
R> state <- d$state

A utility to generate random sequences from a pre-trained Hidden Markov Model (HMM). The length of the desired sequence can be specified, and a random sequence of observations is returned. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
length integer Length of sequence to generate. **--**
model HMMModel Trained HMM to generate sequences with. **--**
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
start_state integer Starting state of sequence. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save observation sequence to.
state integer matrix Matrix to save hidden state sequence to.

🔗 Detailed documentation

This utility takes an already-trained HMM, specified as the model parameter, and generates a random observation sequence and hidden state sequence based on its parameters. The observation sequence may be saved with the output output parameter, and the internal state sequence may be saved with the state output parameter.

The state to start the sequence in may be specified with the start_state parameter.

🔗 Example

For example, to generate a sequence of length 150 from the HMM "hmm" and save the observation sequence to "observations" and the hidden state sequence to "states", the following command may be used:

R> output <- hmm_generate(model=hmm, length=150)
R> observations <- output$output
R> states <- output$state

🔗 See also

🔗 hmm_loglik()

Hidden Markov Model (HMM) Sequence Log-Likelihood

R> library(mlpack)
R> d <- hmm_loglik(input=matrix(numeric(), 0, 0), input_model=NA,
        verbose=getOption("mlpack.verbose", FALSE))
R> log_likelihood <- d$log_likelihood

A utility for computing the log-likelihood of a sequence for Hidden Markov Models (HMMs). Given a pre-trained HMM and an observation sequence, this computes and returns the log-likelihood of that sequence being observed from that HMM. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix File containing observations, **--**
input_model HMMModel File containing HMM. **--**
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
log_likelihood numeric Log-likelihood of the sequence.

🔗 Detailed documentation

This utility takes an already-trained HMM, specified with the input_model parameter, and evaluates the log-likelihood of a sequence of observations, given with the input parameter. The computed log-likelihood is given as output.

🔗 Example

For example, to compute the log-likelihood of the sequence "seq" with the pre-trained HMM "hmm", the following command may be used:

R> hmm_loglik(input=seq, input_model=hmm)

🔗 See also

🔗 hmm_viterbi()

Hidden Markov Model (HMM) Viterbi State Prediction

R> library(mlpack)
R> d <- hmm_viterbi(input=matrix(numeric(), 0, 0), input_model=NA,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

A utility for computing the most probable hidden state sequence for Hidden Markov Models (HMMs). Given a pre-trained HMM and an observed sequence, this uses the Viterbi algorithm to compute and return the most probable hidden state sequence. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Matrix containing observations, **--**
input_model HMMModel Trained HMM to use. **--**
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output integer matrix File to save predicted state sequence to.

🔗 Detailed documentation

This utility takes an already-trained HMM, specified as input_model, and evaluates the most probable hidden state sequence of a given sequence of observations (specified as ‘input, using the Viterbi algorithm. The computed state sequence may be saved using the output output parameter.

🔗 Example

For example, to predict the state sequence of the observations "obs" using the HMM "hmm", storing the predicted state sequence to "states", the following command could be used:

R> output <- hmm_viterbi(input=obs, input_model=hmm)
R> states <- output$output

🔗 See also

🔗 hoeffding_tree()

Hoeffding trees

R> library(mlpack)
R> d <- hoeffding_tree(batch_mode=FALSE, bins=10, confidence=0.95,
        info_gain=FALSE, input_model=NA, labels=matrix(integer(), 0, 0),
        max_samples=5000, min_samples=100, numeric_split_strategy="binary",
        observations_before_binning=100, passes=1, test=matrix(numeric(), 0, 0),
        test_labels=matrix(integer(), 0, 0), training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of Hoeffding trees, a form of streaming decision tree for classification. Given labeled data, a Hoeffding tree can be trained and saved for later use, or a pre-trained Hoeffding tree can be used for predicting the classifications of new points. Detailed documentation.

🔗 Input options

name type description default
batch_mode logical If true, samples will be considered in batch instead of as a stream. This generally results in better trees but at the cost of memory usage and runtime. FALSE
bins integer If the ‘domingos’ split strategy is used, this specifies the number of bins for each numeric split. 10
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
confidence numeric Confidence before splitting (between 0 and 1). 0.95
info_gain logical If set, information gain is used instead of Gini impurity for calculating Hoeffding bounds. FALSE
input_model HoeffdingTreeModel Input trained Hoeffding tree model. NA
labels integer vector Labels for training dataset. matrix(integer(), 0, 0)
max_samples integer Maximum number of samples before splitting. 5000
min_samples integer Minimum number of samples before splitting. 100
numeric_split_strategy character The splitting strategy to use for numeric features: ‘domingos’ or ‘binary’. "binary"
observations_before_binning integer If the ‘domingos’ split strategy is used, this specifies the number of samples observed before binning is performed. 100
passes integer Number of passes to take over the dataset. 1
test categorical matrix/data.frame Testing dataset (may be categorical). matrix(numeric(), 0, 0)
test_labels integer vector Labels of test data. matrix(integer(), 0, 0)
training categorical matrix/data.frame Training dataset (may be categorical). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model HoeffdingTreeModel Output for trained Hoeffding tree model.
predictions integer vector Matrix to output label predictions for test data into.
probabilities numeric matrix In addition to predicting labels, provide rediction probabilities in this matrix.

🔗 Detailed documentation

This program implements Hoeffding trees, a form of streaming decision tree suited best for large (or streaming) datasets. This program supports both categorical and numeric data. Given an input dataset, this program is able to train the tree with numerous training options, and save the model to a file. The program is also able to use a trained model or a model from file in order to predict classes for a given test set.

The training file and associated labels are specified with the training and labels parameters, respectively. Optionally, if labels is not specified, the labels are assumed to be the last dimension of the training dataset.

The training may be performed in batch mode (like a typical decision tree algorithm) by specifying the batch_mode option, but this may not be the best option for large datasets.

When a model is trained, it may be saved via the output_model output parameter. A model may be loaded from file for further training or testing with the input_model parameter.

Test data may be specified with the test parameter, and if performance statistics are desired for that test set, labels may be specified with the test_labels parameter. Predictions for each test point may be saved with the predictions output parameter, and class probabilities for each prediction may be saved with the probabilities output parameter.

🔗 Example

For example, to train a Hoeffding tree with confidence 0.99 with data "dataset", saving the trained tree to "tree", the following command may be used:

R> output <- hoeffding_tree(training=dataset, confidence=0.99)
R> tree <- output$output_model

Then, this tree may be used to make predictions on the test set "test_set", saving the predictions into "predictions" and the class probabilities into "class_probs" with the following command:

R> output <- hoeffding_tree(input_model=tree, test=test_set)
R> predictions <- output$predictions
R> class_probs <- output$probabilities

🔗 See also

🔗 kde()

Kernel Density Estimation

R> library(mlpack)
R> d <- kde(abs_error=0, algorithm="dual-tree", bandwidth=1,
        initial_sample_size=100, input_model=NA, kernel="gaussian",
        mc_break_coef=0.4, mc_entry_coef=3, mc_probability=0.95,
        monte_carlo=FALSE, query=matrix(numeric(), 0, 0),
        reference=matrix(numeric(), 0, 0), rel_error=0.05, tree="kd-tree",
        verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions

An implementation of kernel density estimation with dual-tree algorithms. Given a set of reference points and query points and a kernel function, this can estimate the density function at the location of each query point using trees; trees that are built can be saved for later use. Detailed documentation.

🔗 Input options

name type description default
abs_error numeric Relative error tolerance for the prediction. 0
algorithm character Algorithm to use for the prediction.(‘dual-tree’, ‘single-tree’). "dual-tree"
bandwidth numeric Bandwidth of the kernel. 1
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
initial_sample_size integer Initial sample size for Monte Carlo estimations. 100
input_model KDEModel Contains pre-trained KDE model. NA
kernel character Kernel to use for the prediction.(‘gaussian’, ‘epanechnikov’, ‘laplacian’, ‘spherical’, ‘triangular’). "gaussian"
mc_break_coef numeric Controls what fraction of the amount of node’s descendants is the limit for the sample size before it recurses. 0.4
mc_entry_coef numeric Controls how much larger does the amount of node descendants has to be compared to the initial sample size in order to be a candidate for Monte Carlo estimations. 3
mc_probability numeric Probability of the estimation being bounded by relative error when using Monte Carlo estimations. 0.95
monte_carlo logical Whether to use Monte Carlo estimations when possible. FALSE
query numeric matrix Query dataset to KDE on. matrix(numeric(), 0, 0)
reference numeric matrix Input reference dataset use for KDE. matrix(numeric(), 0, 0)
rel_error numeric Relative error tolerance for the prediction. 0.05
tree character Tree to use for the prediction.(‘kd-tree’, ‘ball-tree’, ‘cover-tree’, ‘octree’, ‘r-tree’). "kd-tree"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model KDEModel If specified, the KDE model will be saved here.
predictions numeric vector Vector to store density predictions.

🔗 Detailed documentation

This program performs a Kernel Density Estimation. KDE is a non-parametric way of estimating probability density function. For each query point the program will estimate its probability density by applying a kernel function to each reference point. The computational complexity of this is O(N^2) where there are N query points and N reference points, but this implementation will typically see better performance as it uses an approximate dual or single tree algorithm for acceleration.

Dual or single tree optimization avoids many barely relevant calculations (as kernel function values decrease with distance), so it is an approximate computation. You can specify the maximum relative error tolerance for each query value with rel_error as well as the maximum absolute error tolerance with the parameter abs_error. This program runs using an Euclidean metric. Kernel function can be selected using the kernel option. You can also choose what which type of tree to use for the dual-tree algorithm with tree. It is also possible to select whether to use dual-tree algorithm or single-tree algorithm using the algorithm option.

Monte Carlo estimations can be used to accelerate the KDE estimate when the Gaussian Kernel is used. This provides a probabilistic guarantee on the the error of the resulting KDE instead of an absolute guarantee.To enable Monte Carlo estimations, the monte_carlo flag can be used, and success probability can be set with the mc_probability option. It is possible to set the initial sample size for the Monte Carlo estimation using initial_sample_size. This implementation will only consider a node, as a candidate for the Monte Carlo estimation, if its number of descendant nodes is bigger than the initial sample size. This can be controlled using a coefficient that will multiply the initial sample size and can be set using mc_entry_coef. To avoid using the same amount of computations an exact approach would take, this program recurses the tree whenever a fraction of the amount of the node’s descendant points have already been computed. This fraction is set using mc_break_coef.

🔗 Example

For example, the following will run KDE using the data in "ref_data" for training and the data in "qu_data" as query data. It will apply an Epanechnikov kernel with a 0.2 bandwidth to each reference point and use a KD-Tree for the dual-tree optimization. The returned predictions will be within 5% of the real KDE value for each query point.

R> output <- kde(reference=ref_data, query=qu_data, bandwidth=0.2,
  kernel="epanechnikov", tree="kd-tree", rel_error=0.05)
R> out_data <- output$predictions

the predicted density estimations will be stored in "out_data". If no query is provided, then KDE will be computed on the reference dataset. It is possible to select either a reference dataset or an input model but not both at the same time. If an input model is selected and parameter values are not set (e.g. bandwidth) then default parameter values will be used.

In addition to the last program call, it is also possible to activate Monte Carlo estimations if a Gaussian kernel is used. This can provide faster results, but the KDE will only have a probabilistic guarantee of meeting the desired error bound (instead of an absolute guarantee). The following example will run KDE using a Monte Carlo estimation when possible. The results will be within a 5% of the real KDE value with a 95% probability. Initial sample size for the Monte Carlo estimation will be 200 points and a node will be a candidate for the estimation only when it contains 700 (i.e. 3.5200) points. If a node contains 700 points and 420 (i.e. 0.6700) have already been sampled, then the algorithm will recurse instead of keep sampling.

R> output <- kde(reference=ref_data, query=qu_data, bandwidth=0.2,
  kernel="gaussian", tree="kd-tree", rel_error=0.05, monte_carlo=,
  mc_probability=0.95, initial_sample_size=200, mc_entry_coef=3.5,
  mc_break_coef=0.6)
R> out_data <- output$predictions

🔗 See also

🔗 kernel_pca()

Kernel Principal Components Analysis

R> library(mlpack)
R> d <- kernel_pca(bandwidth=1, center=FALSE, degree=1,
        input=matrix(numeric(), 0, 0), kernel="", kernel_scale=1,
        new_dimensionality=0, nystroem_method=FALSE, offset=0,
        sampling="kmeans", verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

An implementation of Kernel Principal Components Analysis (KPCA). This can be used to perform nonlinear dimensionality reduction or preprocessing on a given dataset. Detailed documentation.

🔗 Input options

name type description default
bandwidth numeric Bandwidth, for ‘gaussian’ and ‘laplacian’ kernels. 1
center logical If set, the transformed data will be centered about the origin. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
degree numeric Degree of polynomial, for ‘polynomial’ kernel. 1
input numeric matrix Input dataset to perform KPCA on. **--**
kernel character The kernel to use; see the above documentation for the list of usable kernels. **--**
kernel_scale numeric Scale, for ‘hyptan’ kernel. 1
new_dimensionality integer If not 0, reduce the dimensionality of the output dataset by ignoring the dimensions with the smallest eigenvalues. 0
nystroem_method logical If set, the Nystroem method will be used. FALSE
offset numeric Offset, for ‘hyptan’ and ‘polynomial’ kernels. 0
sampling character Sampling scheme to use for the Nystroem method: ‘kmeans’, ‘random’, ‘ordered’ "kmeans"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save modified dataset to.

🔗 Detailed documentation

This program performs Kernel Principal Components Analysis (KPCA) on the specified dataset with the specified kernel. This will transform the data onto the kernel principal components, and optionally reduce the dimensionality by ignoring the kernel principal components with the smallest eigenvalues.

For the case where a linear kernel is used, this reduces to regular PCA.

The kernels that are supported are listed below:

The parameters for each of the kernels should be specified with the options bandwidth, kernel_scale, offset, or degree (or a combination of those parameters).

Optionally, the Nystroem method (“Using the Nystroem method to speed up kernel machines”, 2001) can be used to calculate the kernel matrix by specifying the nystroem_method parameter. This approach works by using a subset of the data as basis to reconstruct the kernel matrix; to specify the sampling scheme, the sampling parameter is used. The sampling scheme for the Nystroem method can be chosen from the following list: ‘kmeans’, ‘random’, ‘ordered’.

🔗 Example

For example, the following command will perform KPCA on the dataset "input" using the Gaussian kernel, and saving the transformed data to "transformed":

R> output <- kernel_pca(input=input, kernel="gaussian")
R> transformed <- output$output

🔗 See also

🔗 kmeans()

K-Means Clustering

R> library(mlpack)
R> d <- kmeans(algorithm="naive", allow_empty_clusters=FALSE,
        clusters=0, in_place=FALSE, initial_centroids=matrix(numeric(), 0, 0),
        input=matrix(numeric(), 0, 0), kill_empty_clusters=FALSE,
        kmeans_plus_plus=FALSE, labels_only=FALSE, max_iterations=1000,
        percentage=0.02, refined_start=FALSE, samplings=100, seed=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> centroid <- d$centroid
R> output <- d$output

An implementation of several strategies for efficient k-means clustering. Given a dataset and a value of k, this computes and returns a k-means clustering on that data. Detailed documentation.

🔗 Input options

name type description default
algorithm character Algorithm to use for the Lloyd iteration (‘naive’, ‘pelleg-moore’, ‘elkan’, ‘hamerly’, ‘dualtree’, or ‘dualtree-covertree’). "naive"
allow_empty_clusters logical Allow empty clusters to be persist. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
clusters integer Number of clusters to find (0 autodetects from initial centroids). **--**
in_place logical If specified, a column containing the learned cluster assignments will be added to the input dataset file. In this case, –output_file is overridden. (Do not use in Python.) FALSE
initial_centroids numeric matrix Start with the specified initial centroids. matrix(numeric(), 0, 0)
input numeric matrix Input dataset to perform clustering on. **--**
kill_empty_clusters logical Remove empty clusters when they occur. FALSE
kmeans_plus_plus logical Use the k-means++ initialization strategy to choose initial points. FALSE
labels_only logical Only output labels into output file. FALSE
max_iterations integer Maximum number of iterations before k-means terminates. 1000
percentage numeric Percentage of dataset to use for each refined start sampling (use when –refined_start is specified). 0.02
refined_start logical Use the refined initial point strategy by Bradley and Fayyad to choose initial points. FALSE
samplings integer Number of samplings to perform for refined start (use when –refined_start is specified). 100
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
centroid numeric matrix If specified, the centroids of each cluster will be written to the given file.
output numeric matrix Matrix to store output labels or labeled data to.

🔗 Detailed documentation

This program performs K-Means clustering on the given dataset. It can return the learned cluster assignments, and the centroids of the clusters. Empty clusters are not allowed by default; when a cluster becomes empty, the point furthest from the centroid of the cluster with maximum variance is taken to fill that cluster.

Optionally, the strategy to choose initial centroids can be specified. The k-means++ algorithm can be used to choose initial centroids with the kmeans_plus_plus parameter. The Bradley and Fayyad approach (“Refining initial points for k-means clustering”, 1998) can be used to select initial points by specifying the refined_start parameter. This approach works by taking random samplings of the dataset; to specify the number of samplings, the samplings parameter is used, and to specify the percentage of the dataset to be used in each sample, the percentage parameter is used (it should be a value between 0.0 and 1.0).

There are several options available for the algorithm used for each Lloyd iteration, specified with the algorithm option. The standard O(kN) approach can be used (‘naive’). Other options include the Pelleg-Moore tree-based algorithm (‘pelleg-moore’), Elkan’s triangle-inequality based algorithm (‘elkan’), Hamerly’s modification to Elkan’s algorithm (‘hamerly’), the dual-tree k-means algorithm (‘dualtree’), and the dual-tree k-means algorithm using the cover tree (‘dualtree-covertree’).

The behavior for when an empty cluster is encountered can be modified with the allow_empty_clusters option. When this option is specified and there is a cluster owning no points at the end of an iteration, that cluster’s centroid will simply remain in its position from the previous iteration. If the kill_empty_clusters option is specified, then when a cluster owns no points at the end of an iteration, the cluster centroid is simply filled with DBL_MAX, killing it and effectively reducing k for the rest of the computation. Note that the default option when neither empty cluster option is specified can be time-consuming to calculate; therefore, specifying either of these parameters will often accelerate runtime.

Initial clustering assignments may be specified using the initial_centroids parameter, and the maximum number of iterations may be specified with the max_iterations parameter.

🔗 Example

As an example, to use Hamerly’s algorithm to perform k-means clustering with k=10 on the dataset "data", saving the centroids to "centroids" and the assignments for each point to "assignments", the following command could be used:

R> output <- kmeans(input=data, clusters=10)
R> assignments <- output$output
R> centroids <- output$centroid

To run k-means on that same dataset with initial centroids specified in "initial" with a maximum of 500 iterations, storing the output centroids in "final" the following command may be used:

R> output <- kmeans(input=data, initial_centroids=initial, clusters=10,
  max_iterations=500)
R> final <- output$centroid

🔗 See also

🔗 lars()

LARS

R> library(mlpack)
R> d <- lars(input=matrix(numeric(), 0, 0), input_model=NA, lambda1=0,
        lambda2=0, no_intercept=FALSE, no_normalize=FALSE,
        responses=matrix(numeric(), 0, 0), test=matrix(numeric(), 0, 0),
        use_cholesky=FALSE, verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model
R> output_predictions <- d$output_predictions

An implementation of Least Angle Regression (Stagewise/laSso), also known as LARS. This can train a LARS/LASSO/Elastic Net model and use that model or a pre-trained model to output regression predictions for a test set. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Matrix of covariates (X). matrix(numeric(), 0, 0)
input_model LARS Trained LARS model to use. NA
lambda1 numeric Regularization parameter for l1-norm penalty. 0
lambda2 numeric Regularization parameter for l2-norm penalty. 0
no_intercept logical Do not fit an intercept in the model. FALSE
no_normalize logical Do not normalize data to unit variance before modeling. FALSE
responses numeric matrix Matrix of responses/observations (y). matrix(numeric(), 0, 0)
test numeric matrix Matrix containing points to regress on (test points). matrix(numeric(), 0, 0)
use_cholesky logical Use Cholesky decomposition during computation rather than explicitly computing the full Gram matrix. FALSE
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model LARS Output LARS model.
output_predictions numeric matrix If –test_file is specified, this file is where the predicted responses will be saved.

🔗 Detailed documentation

An implementation of LARS: Least Angle Regression (Stagewise/laSso). This is a stage-wise homotopy-based algorithm for L1-regularized linear regression (LASSO) and L1+L2-regularized linear regression (Elastic Net).

This program is able to train a LARS/LASSO/Elastic Net model or load a model from file, output regression predictions for a test set, and save the trained model to a file. The LARS algorithm is described in more detail below:

Let X be a matrix where each row is a point and each column is a dimension, and let y be a vector of targets.

The Elastic Net problem is to solve

min_beta 0.5 || X * beta - y ||_2^2 + lambda_1 ||beta||_1 + 0.5 lambda_2 ||beta||_2^2

If lambda1 > 0 and lambda2 = 0, the problem is the LASSO. If lambda1 > 0 and lambda2 > 0, the problem is the Elastic Net. If lambda1 = 0 and lambda2 > 0, the problem is ridge regression. If lambda1 = 0 and lambda2 = 0, the problem is unregularized linear regression.

For efficiency reasons, it is not recommended to use this algorithm with lambda1 = 0. In that case, use the ‘linear_regression’ program, which implements both unregularized linear regression and ridge regression.

To train a LARS/LASSO/Elastic Net model, the input and responses parameters must be given. The lambda1, lambda2, and use_cholesky parameters control the training options. A trained model can be saved with the output_model. If no training is desired at all, a model can be passed via the input_model parameter.

The program can also provide predictions for test data using either the trained model or the given input model. Test points can be specified with the test parameter. Predicted responses to the test points can be saved with the output_predictions output parameter.

🔗 Example

For example, the following command trains a model on the data "data" and responses "responses" with lambda1 set to 0.4 and lambda2 set to 0 (so, LASSO is being solved), and then the model is saved to "lasso_model":

R> output <- lars(input=data, responses=responses, lambda1=0.4, lambda2=0)
R> lasso_model <- output$output_model

The following command uses the "lasso_model" to provide predicted responses for the data "test" and save those responses to "test_predictions":

R> output <- lars(input_model=lasso_model, test=test)
R> test_predictions <- output$output_predictions

🔗 See also

🔗 linear_svm()

Linear SVM is an L2-regularized support vector machine.

R> library(mlpack)
R> d <- linear_svm(delta=1, epochs=50, input_model=NA,
        labels=matrix(integer(), 0, 0), lambda=0.0001, max_iterations=10000,
        no_intercept=FALSE, num_classes=0, optimizer="lbfgs", seed=0,
        shuffle=FALSE, step_size=0.01, test=matrix(numeric(), 0, 0),
        test_labels=matrix(integer(), 0, 0), tolerance=1e-10,
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of linear SVM for multiclass classification. Given labeled data, a model can be trained and saved for future use; or, a pre-trained model can be used to classify new points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
delta numeric Margin of difference between correct class and other classes. 1
epochs integer Maximum number of full epochs over dataset for psgd 50
input_model LinearSVMModel Existing model (parameters). NA
labels integer vector A matrix containing labels (0 or 1) for the points in the training set (y). matrix(integer(), 0, 0)
lambda numeric L2-regularization parameter for training. 0.0001
max_iterations integer Maximum iterations for optimizer (0 indicates no limit). 10000
no_intercept logical Do not add the intercept term to the model. FALSE
num_classes integer Number of classes for classification; if unspecified (or 0), the number of classes found in the labels will be used. 0
optimizer character Optimizer to use for training (‘lbfgs’ or ‘psgd’). "lbfgs"
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
shuffle logical Don’t shuffle the order in which data points are visited for parallel SGD. FALSE
step_size numeric Step size for parallel SGD optimizer. 0.01
test numeric matrix Matrix containing test dataset. matrix(numeric(), 0, 0)
test_labels integer vector Matrix containing test labels. matrix(integer(), 0, 0)
tolerance numeric Convergence tolerance for optimizer. 1e-10
training numeric matrix A matrix containing the training set (the matrix of predictors, X). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model LinearSVMModel Output for trained linear svm model.
predictions integer vector If test data is specified, this matrix is where the predictions for the test set will be saved.
probabilities numeric matrix If test data is specified, this matrix is where the class probabilities for the test set will be saved.

🔗 Detailed documentation

An implementation of linear SVMs that uses either L-BFGS or parallel SGD (stochastic gradient descent) to train the model.

This program allows loading a linear SVM model (via the input_model parameter) or training a linear SVM model given training data (specified with the training parameter), or both those things at once. In addition, this program allows classification on a test dataset (specified with the test parameter) and the classification results may be saved with the predictions output parameter. The trained linear SVM model may be saved using the output_model output parameter.

The training data, if specified, may have class labels as its last dimension. Alternately, the labels parameter may be used to specify a separate vector of labels.

When a model is being trained, there are many options. L2 regularization (to prevent overfitting) can be specified with the lambda option, and the number of classes can be manually specified with the num_classesand if an intercept term is not desired in the model, the no_intercept parameter can be specified.Margin of difference between correct class and other classes can be specified with the delta option.The optimizer used to train the model can be specified with the optimizer parameter. Available options are ‘psgd’ (parallel stochastic gradient descent) and ‘lbfgs’ (the L-BFGS optimizer). There are also various parameters for the optimizer; the max_iterations parameter specifies the maximum number of allowed iterations, and the tolerance parameter specifies the tolerance for convergence. For the parallel SGD optimizer, the step_size parameter controls the step size taken at each iteration by the optimizer and the maximum number of epochs (specified with epochs). If the objective function for your data is oscillating between Inf and 0, the step size is probably too large. There are more parameters for the optimizers, but the C++ interface must be used to access these.

Optionally, the model can be used to predict the labels for another matrix of data points, if test is specified. The test parameter can be specified without the training parameter, so long as an existing linear SVM model is given with the input_model parameter. The output predictions from the linear SVM model may be saved with the predictions parameter.

🔗 Example

As an example, to train a LinaerSVM on the data ‘"data"’ with labels ‘"labels"’ with L2 regularization of 0.1, saving the model to ‘"lsvm_model"’, the following command may be used:

R> output <- linear_svm(training=data, labels=labels, lambda=0.1, delta=1,
  num_classes=0)
R> lsvm_model <- output$output_model

Then, to use that model to predict classes for the dataset ‘"test"’, storing the output predictions in ‘"predictions"’, the following command may be used:

R> output <- linear_svm(input_model=lsvm_model, test=test)
R> predictions <- output$predictions

🔗 See also

🔗 lmnn()

Large Margin Nearest Neighbors (LMNN)

R> library(mlpack)
R> d <- lmnn(batch_size=50, center=FALSE, distance=matrix(numeric(), 0,
        0), input=matrix(numeric(), 0, 0), k=1, labels=matrix(integer(), 0, 0),
        linear_scan=FALSE, max_iterations=100000, normalize=FALSE,
        optimizer="amsgrad", passes=50, print_accuracy=FALSE, rank=0,
        regularization=0.5, seed=0, step_size=0.01, tolerance=1e-07,
        update_interval=1, verbose=getOption("mlpack.verbose", FALSE))
R> centered_data <- d$centered_data
R> output <- d$output
R> transformed_data <- d$transformed_data

An implementation of Large Margin Nearest Neighbors (LMNN), a distance learning technique. Given a labeled dataset, this learns a transformation of the data that improves k-nearest-neighbor performance; this can be useful as a preprocessing step. Detailed documentation.

🔗 Input options

name type description default
batch_size integer Batch size for mini-batch SGD. 50
center logical Perform mean-centering on the dataset. It is useful when the centroid of the data is far from the origin. FALSE
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
distance numeric matrix Initial distance matrix to be used as starting point matrix(numeric(), 0, 0)
input numeric matrix Input dataset to run LMNN on. **--**
k integer Number of target neighbors to use for each datapoint. 1
labels integer vector Labels for input dataset. matrix(integer(), 0, 0)
linear_scan logical Don’t shuffle the order in which data points are visited for SGD or mini-batch SGD. FALSE
max_iterations integer Maximum number of iterations for L-BFGS (0 indicates no limit). 100000
normalize logical Use a normalized starting point for optimization. Itis useful for when points are far apart, or when SGD is returning NaN. FALSE
optimizer character Optimizer to use; ‘amsgrad’, ‘bbsgd’, ‘sgd’, or ‘lbfgs’. "amsgrad"
passes integer Maximum number of full passes over dataset for AMSGrad, BB_SGD and SGD. 50
print_accuracy logical Print accuracies on initial and transformed dataset FALSE
rank integer Rank of distance matrix to be optimized. 0
regularization numeric Regularization for LMNN objective function 0.5
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
step_size numeric Step size for AMSGrad, BB_SGD and SGD (alpha). 0.01
tolerance numeric Maximum tolerance for termination of AMSGrad, BB_SGD, SGD or L-BFGS. 1e-07
update_interval integer Number of iterations after which impostors need to be recalculated. 1
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
centered_data numeric matrix Output matrix for mean-centered dataset.
output numeric matrix Output matrix for learned distance matrix.
transformed_data numeric matrix Output matrix for transformed dataset.

🔗 Detailed documentation

This program implements Large Margin Nearest Neighbors, a distance learning technique. The method seeks to improve k-nearest-neighbor classification on a dataset. The method employes the strategy of reducing distance between similar labeled data points (a.k.a target neighbors) and increasing distance between differently labeled points (a.k.a impostors) using standard optimization techniques over the gradient of the distance between data points.

To work, this algorithm needs labeled data. It can be given as the last row of the input dataset (specified with input), or alternatively as a separate matrix (specified with labels). Additionally, a starting point for optimization (specified with distancecan be given, having (r x d) dimensionality. Here r should satisfy 1 <= r <= d, Consequently a Low-Rank matrix will be optimized. Alternatively, Low-Rank distance can be learned by specifying the rankparameter (A Low-Rank matrix with uniformly distributed values will be used as initial learning point).

The program also requires number of targets neighbors to work with ( specified with k), A regularization parameter can also be passed, It acts as a trade of between the pulling and pushing terms (specified with regularization), In addition, this implementation of LMNN includes a parameter to decide the interval after which impostors must be re-calculated (specified with update_interval).

Output can either be the learned distance matrix (specified with output), or the transformed dataset (specified with transformed_data), or both. Additionally mean-centered dataset (specified with centered_data) can be accessed given mean-centering (specified with center) is performed on the dataset. Accuracy on initial dataset and final transformed dataset can be printed by specifying the print_accuracyparameter.

This implementation of LMNN uses AdaGrad, BigBatch_SGD, stochastic gradient descent, mini-batch stochastic gradient descent, or the L_BFGS optimizer.

AdaGrad, specified by the value ‘adagrad’ for the parameter optimizer, uses maximum of past squared gradients. It primarily on six parameters: the step size (specified with step_size), the batch size (specified with batch_size), the maximum number of passes (specified with passes). Inaddition, a normalized starting point can be used by specifying the normalize parameter.

BigBatch_SGD, specified by the value ‘bbsgd’ for the parameter optimizer, depends primarily on four parameters: the step size (specified with step_size), the batch size (specified with batch_size), the maximum number of passes (specified with passes). In addition, a normalized starting point can be used by specifying the normalize parameter.

Stochastic gradient descent, specified by the value ‘sgd’ for the parameter optimizer, depends primarily on three parameters: the step size (specified with step_size), the batch size (specified with batch_size), and the maximum number of passes (specified with passes). In addition, a normalized starting point can be used by specifying the normalize parameter. Furthermore, mean-centering can be performed on the dataset by specifying the centerparameter.

The L-BFGS optimizer, specified by the value ‘lbfgs’ for the parameter optimizer, uses a back-tracking line search algorithm to minimize a function. The following parameters are used by L-BFGS: max_iterations, tolerance(the optimization is terminated when the gradient norm is below this value). For more details on the L-BFGS optimizer, consult either the mlpack L-BFGS documentation (in lbfgs.hpp) or the vast set of published literature on L-BFGS. In addition, a normalized starting point can be used by specifying the normalize parameter.

By default, the AMSGrad optimizer is used.

🔗 Example

Example - Let’s say we want to learn distance on iris dataset with number of targets as 3 using BigBatch_SGD optimizer. A simple call for the same will look like:

R> output <- lmnn(input=iris, labels=iris_labels, k=3, optimizer="bbsgd")
R> output <- output$output

Another program call making use of update interval & regularization parameter with dataset having labels as last column can be made as:

R> output <- lmnn(input=letter_recognition, k=5, update_interval=10,
  regularization=0.4)
R> output <- output$output

🔗 See also

🔗 local_coordinate_coding()

Local Coordinate Coding

R> library(mlpack)
R> d <- local_coordinate_coding(atoms=0,
        initial_dictionary=matrix(numeric(), 0, 0), input_model=NA, lambda=0,
        max_iterations=0, normalize=FALSE, seed=0, test=matrix(numeric(), 0, 0),
        tolerance=0.01, training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> codes <- d$codes
R> dictionary <- d$dictionary
R> output_model <- d$output_model

An implementation of Local Coordinate Coding (LCC), a data transformation technique. Given input data, this transforms each point to be expressed as a linear combination of a few points in the dataset; once an LCC model is trained, it can be used to transform points later also. Detailed documentation.

🔗 Input options

name type description default
atoms integer Number of atoms in the dictionary. 0
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
initial_dictionary numeric matrix Optional initial dictionary. matrix(numeric(), 0, 0)
input_model LocalCoordinateCoding Input LCC model. NA
lambda numeric Weighted l1-norm regularization parameter. 0
max_iterations integer Maximum number of iterations for LCC (0 indicates no limit). 0
normalize logical If set, the input data matrix will be normalized before coding. FALSE
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
test numeric matrix Test points to encode. matrix(numeric(), 0, 0)
tolerance numeric Tolerance for objective function. 0.01
training numeric matrix Matrix of training data (X). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
codes numeric matrix Output codes matrix.
dictionary numeric matrix Output dictionary matrix.
output_model LocalCoordinateCoding Output for trained LCC model.

🔗 Detailed documentation

An implementation of Local Coordinate Coding (LCC), which codes data that approximately lives on a manifold using a variation of l1-norm regularized sparse coding. Given a dense data matrix X with n points and d dimensions, LCC seeks to find a dense dictionary matrix D with k atoms in d dimensions, and a coding matrix Z with n points in k dimensions. Because of the regularization method used, the atoms in D should lie close to the manifold on which the data points lie.

The original data matrix X can then be reconstructed as D * Z. Therefore, this program finds a representation of each point in X as a sparse linear combination of atoms in the dictionary D.

The coding is found with an algorithm which alternates between a dictionary step, which updates the dictionary D, and a coding step, which updates the coding matrix Z.

To run this program, the input matrix X must be specified (with -i), along with the number of atoms in the dictionary (-k). An initial dictionary may also be specified with the initial_dictionary parameter. The l1-norm regularization parameter is specified with the lambda parameter.

🔗 Example

For example, to run LCC on the dataset "data" using 200 atoms and an l1-regularization parameter of 0.1, saving the dictionary dictionary and the codes into codes, use

R> output <- local_coordinate_coding(training=data, atoms=200, lambda=0.1)
R> dict <- output$dictionary
R> codes <- output$codes

The maximum number of iterations may be specified with the max_iterations parameter. Optionally, the input data matrix X can be normalized before coding with the normalize parameter.

An LCC model may be saved using the output_model output parameter. Then, to encode new points from the dataset "points" with the previously saved model "lcc_model", saving the new codes to "new_codes", the following command can be used:

R> output <- local_coordinate_coding(input_model=lcc_model, test=points)
R> new_codes <- output$codes

🔗 See also

🔗 logistic_regression()

L2-regularized Logistic Regression and Prediction

R> library(mlpack)
R> d <- logistic_regression(batch_size=64, decision_boundary=0.5,
        input_model=NA, labels=matrix(integer(), 0, 0), lambda=0,
        max_iterations=10000, optimizer="lbfgs", print_training_accuracy=FALSE,
        step_size=0.01, test=matrix(numeric(), 0, 0), tolerance=1e-10,
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of L2-regularized logistic regression for two-class classification. Given labeled data, a model can be trained and saved for future use; or, a pre-trained model can be used to classify new points. Detailed documentation.

🔗 Input options

name type description default
batch_size integer Batch size for SGD. 64
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
decision_boundary numeric Decision boundary for prediction; if the logistic function for a point is less than the boundary, the class is taken to be 0; otherwise, the class is 1. 0.5
input_model LogisticRegression Existing model (parameters). NA
labels integer vector A matrix containing labels (0 or 1) for the points in the training set (y). matrix(integer(), 0, 0)
lambda numeric L2-regularization parameter for training. 0
max_iterations integer Maximum iterations for optimizer (0 indicates no limit). 10000
optimizer character Optimizer to use for training (‘lbfgs’ or ‘sgd’). "lbfgs"
print_training_accuracy logical If set, then the accuracy of the model on the training set will be printed (verbose must also be specified). FALSE
step_size numeric Step size for SGD optimizer. 0.01
test numeric matrix Matrix containing test dataset. matrix(numeric(), 0, 0)
tolerance numeric Convergence tolerance for optimizer. 1e-10
training numeric matrix A matrix containing the training set (the matrix of predictors, X). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model LogisticRegression Output for trained logistic regression model.
predictions integer vector If test data is specified, this matrix is where the predictions for the test set will be saved.
probabilities numeric matrix If test data is specified, this matrix is where the class probabilities for the test set will be saved.

🔗 Detailed documentation

An implementation of L2-regularized logistic regression using either the L-BFGS optimizer or SGD (stochastic gradient descent). This solves the regression problem

y = (1 / 1 + e^-(X * b)).

In this setting, y corresponds to class labels and X corresponds to data.

This program allows loading a logistic regression model (via the input_model parameter) or training a logistic regression model given training data (specified with the training parameter), or both those things at once. In addition, this program allows classification on a test dataset (specified with the test parameter) and the classification results may be saved with the predictions output parameter. The trained logistic regression model may be saved using the output_model output parameter.

The training data, if specified, may have class labels as its last dimension. Alternately, the labels parameter may be used to specify a separate matrix of labels.

When a model is being trained, there are many options. L2 regularization (to prevent overfitting) can be specified with the lambda option, and the optimizer used to train the model can be specified with the optimizer parameter. Available options are ‘sgd’ (stochastic gradient descent) and ‘lbfgs’ (the L-BFGS optimizer). There are also various parameters for the optimizer; the max_iterations parameter specifies the maximum number of allowed iterations, and the tolerance parameter specifies the tolerance for convergence. For the SGD optimizer, the step_size parameter controls the step size taken at each iteration by the optimizer. The batch size for SGD is controlled with the batch_size parameter. If the objective function for your data is oscillating between Inf and 0, the step size is probably too large. There are more parameters for the optimizers, but the C++ interface must be used to access these.

For SGD, an iteration refers to a single point. So to take a single pass over the dataset with SGD, max_iterations should be set to the number of points in the dataset.

Optionally, the model can be used to predict the responses for another matrix of data points, if test is specified. The test parameter can be specified without the training parameter, so long as an existing logistic regression model is given with the input_model parameter. The output predictions from the logistic regression model may be saved with the predictions parameter.

This implementation of logistic regression does not support the general multi-class case but instead only the two-class case. Any labels must be either 0 or 1. For more classes, see the softmax regression implementation.

🔗 Example

As an example, to train a logistic regression model on the data ‘"data"’ with labels ‘"labels"’ with L2 regularization of 0.1, saving the model to ‘"lr_model"’, the following command may be used:

R> output <- logistic_regression(training=data, labels=labels, lambda=0.1,
  print_training_accuracy=TRUE)
R> lr_model <- output$output_model

Then, to use that model to predict classes for the dataset ‘"test"’, storing the output predictions in ‘"predictions"’, the following command may be used:

R> output <- logistic_regression(input_model=lr_model, test=test)
R> predictions <- output$predictions

🔗 See also

🔗 lsh()

K-Approximate-Nearest-Neighbor Search with LSH

R> library(mlpack)
R> d <- lsh(bucket_size=500, hash_width=0, input_model=NA, k=0,
        num_probes=0, projections=10, query=matrix(numeric(), 0, 0),
        reference=matrix(numeric(), 0, 0), second_hash_size=99901, seed=0,
        tables=30, true_neighbors=matrix(integer(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> distances <- d$distances
R> neighbors <- d$neighbors
R> output_model <- d$output_model

An implementation of approximate k-nearest-neighbor search with locality-sensitive hashing (LSH). Given a set of reference points and a set of query points, this will compute the k approximate nearest neighbors of each query point in the reference set; models can be saved for future use. Detailed documentation.

🔗 Input options

name type description default
bucket_size integer The size of a bucket in the second level hash. 500
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
hash_width numeric The hash width for the first-level hashing in the LSH preprocessing. By default, the LSH class automatically estimates a hash width for its use. 0
input_model LSHSearch Input LSH model. NA
k integer Number of nearest neighbors to find. 0
num_probes integer Number of additional probes for multiprobe LSH; if 0, traditional LSH is used. 0
projections integer The number of hash functions for each table 10
query numeric matrix Matrix containing query points (optional). matrix(numeric(), 0, 0)
reference numeric matrix Matrix containing the reference dataset. matrix(numeric(), 0, 0)
second_hash_size integer The size of the second level hash table. 99901
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
tables integer The number of hash tables to be used. 30
true_neighbors integer matrix Matrix of true neighbors to compute recall with (the recall is printed when -v is specified). matrix(integer(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
distances numeric matrix Matrix to output distances into.
neighbors integer matrix Matrix to output neighbors into.
output_model LSHSearch Output for trained LSH model.

🔗 Detailed documentation

This program will calculate the k approximate-nearest-neighbors of a set of points using locality-sensitive hashing. You may specify a separate set of reference points and query points, or just a reference set which will be used as both the reference and query set.

🔗 Example

For example, the following will return 5 neighbors from the data for each point in "input" and store the distances in "distances" and the neighbors in "neighbors":

R> output <- lsh(k=5, reference=input)
R> distances <- output$distances
R> neighbors <- output$neighbors

The output is organized such that row i and column j in the neighbors output corresponds to the index of the point in the reference set which is the j’th nearest neighbor from the point in the query set with index i. Row j and column i in the distances output file corresponds to the distance between those two points.

Because this is approximate-nearest-neighbors search, results may be different from run to run. Thus, the seed parameter can be specified to set the random seed.

This program also has many other parameters to control its functionality; see the parameter-specific documentation for more information.

🔗 See also

🔗 mean_shift()

Mean Shift Clustering

R> library(mlpack)
R> d <- mean_shift(force_convergence=FALSE, in_place=FALSE,
        input=matrix(numeric(), 0, 0), labels_only=FALSE, max_iterations=1000,
        radius=0, verbose=getOption("mlpack.verbose", FALSE))
R> centroid <- d$centroid
R> output <- d$output

A fast implementation of mean-shift clustering using dual-tree range search. Given a dataset, this uses the mean shift algorithm to produce and return a clustering of the data. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
force_convergence logical If specified, the mean shift algorithm will continue running regardless of max_iterations until the clusters converge. FALSE
in_place logical If specified, a column containing the learned cluster assignments will be added to the input dataset file. In this case, –output_file is overridden. (Do not use with Python.) FALSE
input numeric matrix Input dataset to perform clustering on. **--**
labels_only logical If specified, only the output labels will be written to the file specified by –output_file. FALSE
max_iterations integer Maximum number of iterations before mean shift terminates. 1000
radius numeric If the distance between two centroids is less than the given radius, one will be removed. A radius of 0 or less means an estimate will be calculated and used for the radius. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
centroid numeric matrix If specified, the centroids of each cluster will be written to the given matrix.
output numeric matrix Matrix to write output labels or labeled data to.

🔗 Detailed documentation

This program performs mean shift clustering on the given dataset, storing the learned cluster assignments either as a column of labels in the input dataset or separately.

The input dataset should be specified with the input parameter, and the radius used for search can be specified with the radius parameter. The maximum number of iterations before algorithm termination is controlled with the max_iterations parameter.

The output labels may be saved with the output output parameter and the centroids of each cluster may be saved with the centroid output parameter.

🔗 Example

For example, to run mean shift clustering on the dataset "data" and store the centroids to "centroids", the following command may be used:

R> output <- mean_shift(input=data)
R> centroids <- output$centroid

🔗 See also

🔗 nbc()

Parametric Naive Bayes Classifier

R> library(mlpack)
R> d <- nbc(incremental_variance=FALSE, input_model=NA,
        labels=matrix(integer(), 0, 0), test=matrix(numeric(), 0, 0),
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of the Naive Bayes Classifier, used for classification. Given labeled data, an NBC model can be trained and saved, or, a pre-trained model can be used for classification. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
incremental_variance logical The variance of each class will be calculated incrementally. FALSE
input_model NBCModel Input Naive Bayes model. NA
labels integer vector A file containing labels for the training set. matrix(integer(), 0, 0)
test numeric matrix A matrix containing the test set. matrix(numeric(), 0, 0)
training numeric matrix A matrix containing the training set. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model NBCModel File to save trained Naive Bayes model to.
predictions integer vector The matrix in which the predicted labels for the test set will be written.
probabilities numeric matrix The matrix in which the predicted probability of labels for the test set will be written.

🔗 Detailed documentation

This program trains the Naive Bayes classifier on the given labeled training set, or loads a model from the given model file, and then may use that trained model to classify the points in a given test set.

The training set is specified with the training parameter. Labels may be either the last row of the training set, or alternately the labels parameter may be specified to pass a separate matrix of labels.

If training is not desired, a pre-existing model may be loaded with the input_model parameter.

The incremental_variance parameter can be used to force the training to use an incremental algorithm for calculating variance. This is slower, but can help avoid loss of precision in some cases.

If classifying a test set is desired, the test set may be specified with the test parameter, and the classifications may be saved with the predictionspredictions parameter. If saving the trained model is desired, this may be done with the output_model output parameter.

🔗 Example

For example, to train a Naive Bayes classifier on the dataset "data" with labels "labels" and save the model to "nbc_model", the following command may be used:

R> output <- nbc(training=data, labels=labels)
R> nbc_model <- output$output_model

Then, to use "nbc_model" to predict the classes of the dataset "test_set" and save the predicted classes to "predictions", the following command may be used:

R> output <- nbc(input_model=nbc_model, test=test_set)
R> predictions <- output$predictions

🔗 See also

🔗 nca()

Neighborhood Components Analysis (NCA)

R> library(mlpack)
R> d <- nca(armijo_constant=0.0001, batch_size=50,
        input=matrix(numeric(), 0, 0), labels=matrix(integer(), 0, 0),
        linear_scan=FALSE, max_iterations=500000, max_line_search_trials=50,
        max_step=1e+20, min_step=1e-20, normalize=FALSE, num_basis=5,
        optimizer="sgd", seed=0, step_size=0.01, tolerance=1e-07,
        verbose=getOption("mlpack.verbose", FALSE), wolfe=0.9)
R> output <- d$output

An implementation of neighborhood components analysis, a distance learning technique that can be used for preprocessing. Given a labeled dataset, this uses NCA, which seeks to improve the k-nearest-neighbor classification, and returns the learned distance metric. Detailed documentation.

🔗 Input options

name type description default
armijo_constant numeric Armijo constant for L-BFGS. 0.0001
batch_size integer Batch size for mini-batch SGD. 50
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Input dataset to run NCA on. **--**
labels integer vector Labels for input dataset. matrix(integer(), 0, 0)
linear_scan logical Don’t shuffle the order in which data points are visited for SGD or mini-batch SGD. FALSE
max_iterations integer Maximum number of iterations for SGD or L-BFGS (0 indicates no limit). 500000
max_line_search_trials integer Maximum number of line search trials for L-BFGS. 50
max_step numeric Maximum step of line search for L-BFGS. 1e+20
min_step numeric Minimum step of line search for L-BFGS. 1e-20
normalize logical Use a normalized starting point for optimization. This is useful for when points are far apart, or when SGD is returning NaN. FALSE
num_basis integer Number of memory points to be stored for L-BFGS. 5
optimizer character Optimizer to use; ‘sgd’ or ‘lbfgs’. "sgd"
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
step_size numeric Step size for stochastic gradient descent (alpha). 0.01
tolerance numeric Maximum tolerance for termination of SGD or L-BFGS. 1e-07
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
wolfe numeric Wolfe condition parameter for L-BFGS. 0.9

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Output matrix for learned distance matrix.

🔗 Detailed documentation

This program implements Neighborhood Components Analysis, both a linear dimensionality reduction technique and a distance learning technique. The method seeks to improve k-nearest-neighbor classification on a dataset by scaling the dimensions. The method is nonparametric, and does not require a value of k. It works by using stochastic (“soft”) neighbor assignments and using optimization techniques over the gradient of the accuracy of the neighbor assignments.

To work, this algorithm needs labeled data. It can be given as the last row of the input dataset (specified with input), or alternatively as a separate matrix (specified with labels).

This implementation of NCA uses stochastic gradient descent, mini-batch stochastic gradient descent, or the L_BFGS optimizer. These optimizers do not guarantee global convergence for a nonconvex objective function (NCA’s objective function is nonconvex), so the final results could depend on the random seed or other optimizer parameters.

Stochastic gradient descent, specified by the value ‘sgd’ for the parameter optimizer, depends primarily on three parameters: the step size (specified with step_size), the batch size (specified with batch_size), and the maximum number of iterations (specified with max_iterations). In addition, a normalized starting point can be used by specifying the normalize parameter, which is necessary if many warnings of the form ‘Denominator of p_i is 0!’ are given. Tuning the step size can be a tedious affair. In general, the step size is too large if the objective is not mostly uniformly decreasing, or if zero-valued denominator warnings are being issued. The step size is too small if the objective is changing very slowly. Setting the termination condition can be done easily once a good step size parameter is found; either increase the maximum iterations to a large number and allow SGD to find a minimum, or set the maximum iterations to 0 (allowing infinite iterations) and set the tolerance (specified by tolerance) to define the maximum allowed difference between objectives for SGD to terminate. Be careful—setting the tolerance instead of the maximum iterations can take a very long time and may actually never converge due to the properties of the SGD optimizer. Note that a single iteration of SGD refers to a single point, so to take a single pass over the dataset, set the value of the max_iterations parameter equal to the number of points in the dataset.

The L-BFGS optimizer, specified by the value ‘lbfgs’ for the parameter optimizer, uses a back-tracking line search algorithm to minimize a function. The following parameters are used by L-BFGS: num_basis (specifies the number of memory points used by L-BFGS), max_iterations, armijo_constant, wolfe, tolerance (the optimization is terminated when the gradient norm is below this value), max_line_search_trials, min_step, and max_step (which both refer to the line search routine). For more details on the L-BFGS optimizer, consult either the mlpack L-BFGS documentation (in lbfgs.hpp) or the vast set of published literature on L-BFGS.

By default, the SGD optimizer is used.

🔗 See also

🔗 knn()

k-Nearest-Neighbors Search

R> library(mlpack)
R> d <- knn(algorithm="dual_tree", epsilon=0, input_model=NA, k=0,
        leaf_size=20, query=matrix(numeric(), 0, 0), random_basis=FALSE,
        reference=matrix(numeric(), 0, 0), rho=0.7, seed=0, tau=0,
        tree_type="kd", true_distances=matrix(numeric(), 0, 0),
        true_neighbors=matrix(integer(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> distances <- d$distances
R> neighbors <- d$neighbors
R> output_model <- d$output_model

An implementation of k-nearest-neighbor search using single-tree and dual-tree algorithms. Given a set of reference points and query points, this can find the k nearest neighbors in the reference set of each query point using trees; trees that are built can be saved for future use. Detailed documentation.

🔗 Input options

name type description default
algorithm character Type of neighbor search: ‘naive’, ‘single_tree’, ‘dual_tree’, ‘greedy’. "dual_tree"
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
epsilon numeric If specified, will do approximate nearest neighbor search with given relative error. 0
input_model KNNModel Pre-trained kNN model. NA
k integer Number of nearest neighbors to find. 0
leaf_size integer Leaf size for tree building (used for kd-trees, vp trees, random projection trees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, spill trees, and octrees). 20
query numeric matrix Matrix containing query points (optional). matrix(numeric(), 0, 0)
random_basis logical Before tree-building, project the data onto a random orthogonal basis. FALSE
reference numeric matrix Matrix containing the reference dataset. matrix(numeric(), 0, 0)
rho numeric Balance threshold (only valid for spill trees). 0.7
seed integer Random seed (if 0, std::time(NULL) is used). 0
tau numeric Overlapping size (only valid for spill trees). 0
tree_type character Type of tree to use: ‘kd’, ‘vp’, ‘rp’, ‘max-rp’, ‘ub’, ‘cover’, ‘r’, ‘r-star’, ‘x’, ‘ball’, ‘hilbert-r’, ‘r-plus’, ‘r-plus-plus’, ‘spill’, ‘oct’. "kd"
true_distances numeric matrix Matrix of true distances to compute the effective error (average relative error) (it is printed when -v is specified). matrix(numeric(), 0, 0)
true_neighbors integer matrix Matrix of true neighbors to compute the recall (it is printed when -v is specified). matrix(integer(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
distances numeric matrix Matrix to output distances into.
neighbors integer matrix Matrix to output neighbors into.
output_model KNNModel If specified, the kNN model will be output here.

🔗 Detailed documentation

This program will calculate the k-nearest-neighbors of a set of points using kd-trees or cover trees (cover tree support is experimental and may be slow). You may specify a separate set of reference points and query points, or just a reference set which will be used as both the reference and query set.

🔗 Example

For example, the following command will calculate the 5 nearest neighbors of each point in "input" and store the distances in "distances" and the neighbors in "neighbors":

R> output <- knn(k=5, reference=input)
R> neighbors <- output$neighbors
R> distances <- output$distances

The output is organized such that row i and column j in the neighbors output matrix corresponds to the index of the point in the reference set which is the j’th nearest neighbor from the point in the query set with index i. Row j and column i in the distances output matrix corresponds to the distance between those two points.

🔗 See also

🔗 kfn()

k-Furthest-Neighbors Search

R> library(mlpack)
R> d <- kfn(algorithm="dual_tree", epsilon=0, input_model=NA, k=0,
        leaf_size=20, percentage=1, query=matrix(numeric(), 0, 0),
        random_basis=FALSE, reference=matrix(numeric(), 0, 0), seed=0,
        tree_type="kd", true_distances=matrix(numeric(), 0, 0),
        true_neighbors=matrix(integer(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> distances <- d$distances
R> neighbors <- d$neighbors
R> output_model <- d$output_model

An implementation of k-furthest-neighbor search using single-tree and dual-tree algorithms. Given a set of reference points and query points, this can find the k furthest neighbors in the reference set of each query point using trees; trees that are built can be saved for future use. Detailed documentation.

🔗 Input options

name type description default
algorithm character Type of neighbor search: ‘naive’, ‘single_tree’, ‘dual_tree’, ‘greedy’. "dual_tree"
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
epsilon numeric If specified, will do approximate furthest neighbor search with given relative error. Must be in the range [0,1). 0
input_model KFNModel Pre-trained kFN model. NA
k integer Number of furthest neighbors to find. 0
leaf_size integer Leaf size for tree building (used for kd-trees, vp trees, random projection trees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, and octrees). 20
percentage numeric If specified, will do approximate furthest neighbor search. Must be in the range (0,1] (decimal form). Resultant neighbors will be at least (p*100) % of the distance as the true furthest neighbor. 1
query numeric matrix Matrix containing query points (optional). matrix(numeric(), 0, 0)
random_basis logical Before tree-building, project the data onto a random orthogonal basis. FALSE
reference numeric matrix Matrix containing the reference dataset. matrix(numeric(), 0, 0)
seed integer Random seed (if 0, std::time(NULL) is used). 0
tree_type character Type of tree to use: ‘kd’, ‘vp’, ‘rp’, ‘max-rp’, ‘ub’, ‘cover’, ‘r’, ‘r-star’, ‘x’, ‘ball’, ‘hilbert-r’, ‘r-plus’, ‘r-plus-plus’, ‘oct’. "kd"
true_distances numeric matrix Matrix of true distances to compute the effective error (average relative error) (it is printed when -v is specified). matrix(numeric(), 0, 0)
true_neighbors integer matrix Matrix of true neighbors to compute the recall (it is printed when -v is specified). matrix(integer(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
distances numeric matrix Matrix to output distances into.
neighbors integer matrix Matrix to output neighbors into.
output_model KFNModel If specified, the kFN model will be output here.

🔗 Detailed documentation

This program will calculate the k-furthest-neighbors of a set of points. You may specify a separate set of reference points and query points, or just a reference set which will be used as both the reference and query set.

🔗 Example

For example, the following will calculate the 5 furthest neighbors of eachpoint in "input" and store the distances in "distances" and the neighbors in "neighbors":

R> output <- kfn(k=5, reference=input)
R> distances <- output$distances
R> neighbors <- output$neighbors

The output files are organized such that row i and column j in the neighbors output matrix corresponds to the index of the point in the reference set which is the j’th furthest neighbor from the point in the query set with index i. Row i and column j in the distances output file corresponds to the distance between those two points.

🔗 See also

🔗 nmf()

Non-negative Matrix Factorization

R> library(mlpack)
R> d <- nmf(initial_h=matrix(numeric(), 0, 0),
        initial_w=matrix(numeric(), 0, 0), input=matrix(numeric(), 0, 0),
        max_iterations=10000, min_residue=1e-05, rank=0, seed=0,
        update_rules="multdist", verbose=getOption("mlpack.verbose", FALSE))
R> h <- d$h
R> w <- d$w

An implementation of non-negative matrix factorization. This can be used to decompose an input dataset into two low-rank non-negative components. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
initial_h numeric matrix Initial H matrix. matrix(numeric(), 0, 0)
initial_w numeric matrix Initial W matrix. matrix(numeric(), 0, 0)
input numeric matrix Input dataset to perform NMF on. **--**
max_iterations integer Number of iterations before NMF terminates (0 runs until convergence. 10000
min_residue numeric The minimum root mean square residue allowed for each iteration, below which the program terminates. 1e-05
rank integer Rank of the factorization. **--**
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
update_rules character Update rules for each iteration; ( multdist | multdiv | als ). "multdist"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
h numeric matrix Matrix to save the calculated H to.
w numeric matrix Matrix to save the calculated W to.

🔗 Detailed documentation

This program performs non-negative matrix factorization on the given dataset, storing the resulting decomposed matrices in the specified files. For an input dataset V, NMF decomposes V into two matrices W and H such that

V = W * H

where all elements in W and H are non-negative. If V is of size (n x m), then W will be of size (n x r) and H will be of size (r x m), where r is the rank of the factorization (specified by the rank parameter).

Optionally, the desired update rules for each NMF iteration can be chosen from the following list:

The maximum number of iterations is specified with max_iterations, and the minimum residue required for algorithm termination is specified with the min_residue parameter.

🔗 Example

For example, to run NMF on the input matrix "V" using the ‘multdist’ update rules with a rank-10 decomposition and storing the decomposed matrices into "W" and "H", the following command could be used:

R> output <- nmf(input=V, rank=10, update_rules="multdist")
R> W <- output$w
R> H <- output$h

🔗 See also

🔗 pca()

Principal Components Analysis

R> library(mlpack)
R> d <- pca(decomposition_method="exact", input=matrix(numeric(), 0, 0),
        new_dimensionality=0, scale=FALSE, var_to_retain=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

An implementation of several strategies for principal components analysis (PCA), a common preprocessing step. Given a dataset and a desired new dimensionality, this can reduce the dimensionality of the data using the linear transformation determined by PCA. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
decomposition_method character Method used for the principal components analysis: ‘exact’, ‘randomized’, ‘randomized-block-krylov’, ‘quic’. "exact"
input numeric matrix Input dataset to perform PCA on. **--**
new_dimensionality integer Desired dimensionality of output dataset. If 0, no dimensionality reduction is performed. 0
scale logical If set, the data will be scaled before running PCA, such that the variance of each feature is 1. FALSE
var_to_retain numeric Amount of variance to retain; should be between 0 and 1. If 1, all variance is retained. Overrides -d. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save modified dataset to.

🔗 Detailed documentation

This program performs principal components analysis on the given dataset using the exact, randomized, randomized block Krylov, or QUIC SVD method. It will transform the data onto its principal components, optionally performing dimensionality reduction by ignoring the principal components with the smallest eigenvalues.

Use the input parameter to specify the dataset to perform PCA on. A desired new dimensionality can be specified with the new_dimensionality parameter, or the desired variance to retain can be specified with the var_to_retain parameter. If desired, the dataset can be scaled before running PCA with the scale parameter.

Multiple different decomposition techniques can be used. The method to use can be specified with the decomposition_method parameter, and it may take the values ‘exact’, ‘randomized’, or ‘quic’.

🔗 Example

For example, to reduce the dimensionality of the matrix "data" to 5 dimensions using randomized SVD for the decomposition, storing the output matrix to "data_mod", the following command can be used:

R> output <- pca(input=data, new_dimensionality=5,
  decomposition_method="randomized")
R> data_mod <- output$output

🔗 See also

🔗 perceptron()

Perceptron

R> library(mlpack)
R> d <- perceptron(input_model=NA, labels=matrix(integer(), 0, 0),
        max_iterations=1000, test=matrix(numeric(), 0, 0),
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions

An implementation of a perceptron—a single level neural network–=for classification. Given labeled data, a perceptron can be trained and saved for future use; or, a pre-trained perceptron can be used for classification on new points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model PerceptronModel Input perceptron model. NA
labels integer vector A matrix containing labels for the training set. matrix(integer(), 0, 0)
max_iterations integer The maximum number of iterations the perceptron is to be run 1000
test numeric matrix A matrix containing the test set. matrix(numeric(), 0, 0)
training numeric matrix A matrix containing the training set. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model PerceptronModel Output for trained perceptron model.
predictions integer vector The matrix in which the predicted labels for the test set will be written.

🔗 Detailed documentation

This program implements a perceptron, which is a single level neural network. The perceptron makes its predictions based on a linear predictor function combining a set of weights with the feature vector. The perceptron learning rule is able to converge, given enough iterations (specified using the max_iterations parameter), if the data supplied is linearly separable. The perceptron is parameterized by a matrix of weight vectors that denote the numerical weights of the neural network.

This program allows loading a perceptron from a model (via the input_model parameter) or training a perceptron given training data (via the training parameter), or both those things at once. In addition, this program allows classification on a test dataset (via the test parameter) and the classification results on the test set may be saved with the predictions output parameter. The perceptron model may be saved with the output_model output parameter.

🔗 Example

The training data given with the training option may have class labels as its last dimension (so, if the training data is in CSV format, labels should be the last column). Alternately, the labels parameter may be used to specify a separate matrix of labels.

All these options make it easy to train a perceptron, and then re-use that perceptron for later classification. The invocation below trains a perceptron on "training_data" with labels "training_labels", and saves the model to "perceptron_model".

R> output <- perceptron(training=training_data, labels=training_labels)
R> perceptron_model <- output$output_model

Then, this model can be re-used for classification on the test data "test_data". The example below does precisely that, saving the predicted classes to "predictions".

R> output <- perceptron(input_model=perceptron_model, test=test_data)
R> predictions <- output$predictions

Note that all of the options may be specified at once: predictions may be calculated right after training a model, and model training can occur even if an existing perceptron model is passed with the input_model parameter. However, note that the number of classes and the dimensionality of all data must match. So you cannot pass a perceptron model trained on 2 classes and then re-train with a 4-class dataset. Similarly, attempting classification on a 3-dimensional dataset with a perceptron that has been trained on 8 dimensions will cause an error.

🔗 See also

🔗 preprocess_split()

Split Data

R> library(mlpack)
R> d <- preprocess_split(input=matrix(numeric(), 0, 0),
        input_labels=matrix(integer(), 0, 0), no_shuffle=FALSE, seed=0,
        stratify_data=FALSE, test_ratio=0.2, verbose=getOption("mlpack.verbose",
        FALSE))
R> test <- d$test
R> test_labels <- d$test_labels
R> training <- d$training
R> training_labels <- d$training_labels

A utility to split data into a training and testing dataset. This can also split labels according to the same split. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Matrix containing data. **--**
input_labels integer matrix Matrix containing labels. matrix(integer(), 0, 0)
no_shuffle logical Avoid shuffling the data before splitting. FALSE
seed integer Random seed (0 for std::time(NULL)). 0
stratify_data logical Stratify the data according to labels FALSE
test_ratio numeric Ratio of test set; if not set,the ratio defaults to 0.2 0.2
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
test numeric matrix Matrix to save test data to.
test_labels integer matrix Matrix to save test labels to.
training numeric matrix Matrix to save training data to.
training_labels integer matrix Matrix to save train labels to.

🔗 Detailed documentation

This utility takes a dataset and optionally labels and splits them into a training set and a test set. Before the split, the points in the dataset are randomly reordered. The percentage of the dataset to be used as the test set can be specified with the test_ratio parameter; the default is 0.2 (20%).

The output training and test matrices may be saved with the training and test output parameters.

Optionally, labels can also be split along with the data by specifying the input_labels parameter. Splitting labels works the same way as splitting the data. The output training and test labels may be saved with the training_labels and test_labels output parameters, respectively.

🔗 Example

So, a simple example where we want to split the dataset "X" into "X_train" and "X_test" with 60% of the data in the training set and 40% of the dataset in the test set, we could run

R> output <- preprocess_split(input=X, test_ratio=0.4)
R> X_train <- output$training
R> X_test <- output$test

Also by default the dataset is shuffled and split; you can provide the no_shuffle option to avoid shuffling the data; an example to avoid shuffling of data is:

R> output <- preprocess_split(input=X, test_ratio=0.4, no_shuffle=TRUE)
R> X_train <- output$training
R> X_test <- output$test

If we had a dataset "X" and associated labels "y", and we wanted to split these into "X_train", "y_train", "X_test", and "y_test", with 30% of the data in the test set, we could run

R> output <- preprocess_split(input=X, input_labels=y, test_ratio=0.3)
R> X_train <- output$training
R> y_train <- output$training_labels
R> X_test <- output$test
R> y_test <- output$test_labels

To maintain the ratio of each class in the train and test sets, thestratify_data option can be used.

R> output <- preprocess_split(input=X, test_ratio=0.4, stratify_data=TRUE)
R> X_train <- output$training
R> X_test <- output$test

🔗 See also

🔗 preprocess_binarize()

Binarize Data

R> library(mlpack)
R> d <- preprocess_binarize(dimension=0, input=matrix(numeric(), 0, 0),
        threshold=0, verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output

A utility to binarize a dataset. Given a dataset, this utility converts each value in the desired dimension(s) to 0 or 1; this can be a useful preprocessing step. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
dimension integer Dimension to apply the binarization. If not set, the program will binarize every dimension by default. 0
input numeric matrix Input data matrix. **--**
threshold numeric Threshold to be applied for binarization. If not set, the threshold defaults to 0.0. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix in which to save the output.

🔗 Detailed documentation

This utility takes a dataset and binarizes the variables into either 0 or 1 given threshold. User can apply binarization on a dimension or the whole dataset. The dimension to apply binarization to can be specified using the dimension parameter; if left unspecified, every dimension will be binarized. The threshold for binarization can also be specified with the threshold parameter; the default threshold is 0.0.

The binarized matrix may be saved with the output output parameter.

🔗 Example

For example, if we want to set all variables greater than 5 in the dataset "X" to 1 and variables less than or equal to 5.0 to 0, and save the result to "Y", we could run

R> output <- preprocess_binarize(input=X, threshold=5)
R> Y <- output$output

But if we want to apply this to only the first (0th) dimension of "X", we could instead run

R> output <- preprocess_binarize(input=X, threshold=5, dimension=0)
R> Y <- output$output

🔗 See also

🔗 preprocess_describe()

Descriptive Statistics

R> library(mlpack)
R> preprocess_describe(dimension=0, input=matrix(numeric(), 0, 0),
        population=FALSE, precision=4, row_major=FALSE,
        verbose=getOption("mlpack.verbose", FALSE), width=8)

A utility for printing descriptive statistics about a dataset. This prints a number of details about a dataset in a tabular format. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
dimension integer Dimension of the data. Use this to specify a dimension 0
input numeric matrix Matrix containing data, **--**
population logical If specified, the program will calculate statistics assuming the dataset is the population. By default, the program will assume the dataset as a sample. FALSE
precision integer Precision of the output statistics. 4
row_major logical If specified, the program will calculate statistics across rows, not across columns. (Remember that in mlpack, a column represents a point, so this option is generally not necessary.) FALSE
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
width integer Width of the output table. 8

🔗 Detailed documentation

This utility takes a dataset and prints out the descriptive statistics of the data. Descriptive statistics is the discipline of quantitatively describing the main features of a collection of information, or the quantitative description itself. The program does not modify the original file, but instead prints out the statistics to the console. The printed result will look like a table.

Optionally, width and precision of the output can be adjusted by a user using the width and precision parameters. A user can also select a specific dimension to analyze if there are too many dimensions. The population parameter can be specified when the dataset should be considered as a population. Otherwise, the dataset will be considered as a sample.

🔗 Example

So, a simple example where we want to print out statistical facts about the dataset "X" using the default settings, we could run

R> preprocess_describe(input=X, verbose=TRUE)

If we want to customize the width to 10 and precision to 5 and consider the dataset as a population, we could run

R> preprocess_describe(input=X, width=10, precision=5, verbose=TRUE)

🔗 See also

🔗 preprocess_scale()

Scale Data

R> library(mlpack)
R> d <- preprocess_scale(epsilon=1e-06, input=matrix(numeric(), 0, 0),
        input_model=NA, inverse_scaling=FALSE, max_value=1, min_value=0,
        scaler_method="standard_scaler", seed=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> output <- d$output
R> output_model <- d$output_model

A utility to perform feature scaling on datasets using one of sixtechniques. Both scaling and inverse scaling are supported, andscalers can be saved and then applied to other datasets. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
epsilon numeric regularization Parameter for pcawhitening, or zcawhitening, should be between -1 to 1. 1e-06
input numeric matrix Matrix containing data. **--**
input_model ScalingModel Input Scaling model. NA
inverse_scaling logical Inverse Scaling to get original dataset FALSE
max_value integer Ending value of range for min_max_scaler. 1
min_value integer Starting value of range for min_max_scaler. 0
scaler_method character method to use for scaling, the default is standard_scaler. "standard_scaler"
seed integer Random seed (0 for std::time(NULL)). 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save scaled data to.
output_model ScalingModel Output scaling model.

🔗 Detailed documentation

This utility takes a dataset and performs feature scaling using one of the six scaler methods namely: ‘max_abs_scaler’, ‘mean_normalization’, ‘min_max_scaler’ ,’standard_scaler’, ‘pca_whitening’ and ‘zca_whitening’. The function takes a matrix as input and a scaling method type which you can specify using scaler_method parameter; the default is standard scaler, and outputs a matrix with scaled feature.

The output scaled feature matrix may be saved with the output output parameters.

The model to scale features can be saved using output_model and later can be loaded back usinginput_model.

🔗 Example

So, a simple example where we want to scale the dataset "X" into "X_scaled" with standard_scaler as scaler_method, we could run

R> output <- preprocess_scale(input=X, scaler_method="standard_scaler")
R> X_scaled <- output$output

A simple example where we want to whiten the dataset "X" into "X_whitened" with PCA as whitening_method and use 0.01 as regularization parameter, we could run

R> output <- preprocess_scale(input=X, scaler_method="pca_whitening",
  epsilon=0.01)
R> X_scaled <- output$output

You can also retransform the scaled dataset back usinginverse_scaling. An example to rescale : "X_scaled" into "X"using the saved model input_model is:

R> output <- preprocess_scale(input=X_scaled, inverse_scaling=TRUE,
  input_model=saved)
R> X <- output$output

Another simple example where we want to scale the dataset "X" into "X_scaled" with min_max_scaler as scaler method, where scaling range is 1 to 3 instead of default 0 to 1. We could run

R> output <- preprocess_scale(input=X, scaler_method="min_max_scaler",
  min_value=1, max_value=3)
R> X_scaled <- output$output

🔗 See also

🔗 preprocess_one_hot_encoding()

One Hot Encoding

R> library(mlpack)
R> d <- preprocess_one_hot_encoding(dimensions=c(),
        input=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE))
R> output <- d$output

A utility to do one-hot encoding on features of dataset. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
dimensions vector of integers Index of dimensions that need to be one-hot encoded (if unspecified, all categorical dimensions are one-hot encoded). c()
input categorical matrix/data.frame Matrix containing data. **--**
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save one-hot encoded features data to.

🔗 Detailed documentation

This utility takes a dataset and a vector of indices and does one-hot encoding of the respective features at those indices. Indices represent the IDs of the dimensions to be one-hot encoded.

If no dimensions are specified with dimensions, then all categorical-type dimensions will be one-hot encoded. Otherwise, only the dimensions given in dimensions will be one-hot encoded.

The output matrix with encoded features may be saved with the output parameters.

🔗 Example

So, a simple example where we want to encode 1st and 3rd feature from dataset "X" into "X_output" would be

R> output <- preprocess_one_hot_encoding(input=X, dimensions=1, dimensions=3)
R> X_ouput <- output$output

🔗 See also

🔗 radical()

RADICAL

R> library(mlpack)
R> d <- radical(angles=150, input=matrix(numeric(), 0, 0),
        noise_std_dev=0.175, objective=FALSE, replicates=30, seed=0, sweeps=0,
        verbose=getOption("mlpack.verbose", FALSE))
R> output_ic <- d$output_ic
R> output_unmixing <- d$output_unmixing

An implementation of RADICAL, a method for independent component analysis (ICA). Given a dataset, this can decompose the dataset into an unmixing matrix and an independent component matrix; this can be useful for preprocessing. Detailed documentation.

🔗 Input options

name type description default
angles integer Number of angles to consider in brute-force search during Radical2D. 150
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input numeric matrix Input dataset for ICA. **--**
noise_std_dev numeric Standard deviation of Gaussian noise. 0.175
objective logical If set, an estimate of the final objective function is printed. FALSE
replicates integer Number of Gaussian-perturbed replicates to use (per point) in Radical2D. 30
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
sweeps integer Number of sweeps; each sweep calls Radical2D once for each pair of dimensions. 0
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_ic numeric matrix Matrix to save independent components to.
output_unmixing numeric matrix Matrix to save unmixing matrix to.

🔗 Detailed documentation

An implementation of RADICAL, a method for independent component analysis (ICA). Assuming that we have an input matrix X, the goal is to find a square unmixing matrix W such that Y = W * X and the dimensions of Y are independent components. If the algorithm is running particularly slowly, try reducing the number of replicates.

The input matrix to perform ICA on should be specified with the input parameter. The output matrix Y may be saved with the output_ic output parameter, and the output unmixing matrix W may be saved with the output_unmixing output parameter.

🔗 Example

For example, to perform ICA on the matrix "X" with 40 replicates, saving the independent components to "ic", the following command may be used:

R> output <- radical(input=X, replicates=40)
R> ic <- output$output_ic

🔗 See also

🔗 random_forest()

Random forests

R> library(mlpack)
R> d <- random_forest(input_model=NA, labels=matrix(integer(), 0, 0),
        maximum_depth=0, minimum_gain_split=0, minimum_leaf_size=1,
        num_trees=10, print_training_accuracy=FALSE, seed=0, subspace_dim=0,
        test=matrix(numeric(), 0, 0), test_labels=matrix(integer(), 0, 0),
        training=matrix(numeric(), 0, 0), verbose=getOption("mlpack.verbose",
        FALSE), warm_start=FALSE)
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of the standard random forest algorithm by Leo Breiman for classification. Given labeled data, a random forest can be trained and saved for future use; or, a pre-trained random forest can be used for classification. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model RandomForestModel Pre-trained random forest to use for classification. NA
labels integer vector Labels for training dataset. matrix(integer(), 0, 0)
maximum_depth integer Maximum depth of the tree (0 means no limit). 0
minimum_gain_split numeric Minimum gain needed to make a split when building a tree. 0
minimum_leaf_size integer Minimum number of points in each leaf node. 1
num_trees integer Number of trees in the random forest. 10
print_training_accuracy logical If set, then the accuracy of the model on the training set will be predicted (verbose must also be specified). FALSE
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
subspace_dim integer Dimensionality of random subspace to use for each split. ‘0’ will autoselect the square root of data dimensionality. 0
test numeric matrix Test dataset to produce predictions for. matrix(numeric(), 0, 0)
test_labels integer vector Test dataset labels, if accuracy calculation is desired. matrix(integer(), 0, 0)
training numeric matrix Training dataset. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
warm_start logical If true and passed along with training and input_model then trains more trees on top of existing model. FALSE

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model RandomForestModel Model to save trained random forest to.
predictions integer vector Predicted classes for each point in the test set.
probabilities numeric matrix Predicted class probabilities for each point in the test set.

🔗 Detailed documentation

This program is an implementation of the standard random forest classification algorithm by Leo Breiman. A random forest can be trained and saved for later use, or a random forest may be loaded and predictions or class probabilities for points may be generated.

The training set and associated labels are specified with the training and labels parameters, respectively. The labels should be in the range [0, num_classes - 1]. Optionally, if labels is not specified, the labels are assumed to be the last dimension of the training dataset.

When a model is trained, the output_model output parameter may be used to save the trained model. A model may be loaded for predictions with the input_modelparameter. The input_model parameter may not be specified when the training parameter is specified. The minimum_leaf_size parameter specifies the minimum number of training points that must fall into each leaf for it to be split. The num_trees controls the number of trees in the random forest. The minimum_gain_split parameter controls the minimum required gain for a decision tree node to split. Larger values will force higher-confidence splits. The maximum_depth parameter specifies the maximum depth of the tree. The subspace_dim parameter is used to control the number of random dimensions chosen for an individual node’s split. If print_training_accuracy is specified, the calculated accuracy on the training set will be printed.

Test data may be specified with the test parameter, and if performance measures are desired for that test set, labels for the test points may be specified with the test_labels parameter. Predictions for each test point may be saved via the predictionsoutput parameter. Class probabilities for each prediction may be saved with the probabilities output parameter.

🔗 Example

For example, to train a random forest with a minimum leaf size of 20 using 10 trees on the dataset contained in "data"with labels "labels", saving the output random forest to "rf_model" and printing the training error, one could call

R> output <- random_forest(training=data, labels=labels, minimum_leaf_size=20,
  num_trees=10, print_training_accuracy=TRUE)
R> rf_model <- output$output_model

Then, to use that model to classify points in "test_set" and print the test error given the labels "test_labels" using that model, while saving the predictions for each point to "predictions", one could call

R> output <- random_forest(input_model=rf_model, test=test_set,
  test_labels=test_labels)
R> predictions <- output$predictions

🔗 See also

🔗 krann()

K-Rank-Approximate-Nearest-Neighbors (kRANN)

R> library(mlpack)
R> d <- krann(alpha=0.95, first_leaf_exact=FALSE, input_model=NA, k=0,
        leaf_size=20, naive=FALSE, query=matrix(numeric(), 0, 0),
        random_basis=FALSE, reference=matrix(numeric(), 0, 0),
        sample_at_leaves=FALSE, seed=0, single_mode=FALSE,
        single_sample_limit=20, tau=5, tree_type="kd",
        verbose=getOption("mlpack.verbose", FALSE))
R> distances <- d$distances
R> neighbors <- d$neighbors
R> output_model <- d$output_model

An implementation of rank-approximate k-nearest-neighbor search (kRANN) using single-tree and dual-tree algorithms. Given a set of reference points and query points, this can find the k nearest neighbors in the reference set of each query point using trees; trees that are built can be saved for future use. Detailed documentation.

🔗 Input options

name type description default
alpha numeric The desired success probability. 0.95
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
first_leaf_exact logical The flag to trigger sampling only after exactly exploring the first leaf. FALSE
input_model RAModel Pre-trained kNN model. NA
k integer Number of nearest neighbors to find. 0
leaf_size integer Leaf size for tree building (used for kd-trees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, and octrees). 20
naive logical If true, sampling will be done without using a tree. FALSE
query numeric matrix Matrix containing query points (optional). matrix(numeric(), 0, 0)
random_basis logical Before tree-building, project the data onto a random orthogonal basis. FALSE
reference numeric matrix Matrix containing the reference dataset. matrix(numeric(), 0, 0)
sample_at_leaves logical The flag to trigger sampling at leaves. FALSE
seed integer Random seed (if 0, std::time(NULL) is used). 0
single_mode logical If true, single-tree search is used (as opposed to dual-tree search. FALSE
single_sample_limit integer The limit on the maximum number of samples (and hence the largest node you can approximate). 20
tau numeric The allowed rank-error in terms of the percentile of the data. 5
tree_type character Type of tree to use: ‘kd’, ‘ub’, ‘cover’, ‘r’, ‘x’, ‘r-star’, ‘hilbert-r’, ‘r-plus’, ‘r-plus-plus’, ‘oct’. "kd"
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
distances numeric matrix Matrix to output distances into.
neighbors integer matrix Matrix to output neighbors into.
output_model RAModel If specified, the kNN model will be output here.

🔗 Detailed documentation

This program will calculate the k rank-approximate-nearest-neighbors of a set of points. You may specify a separate set of reference points and query points, or just a reference set which will be used as both the reference and query set. You must specify the rank approximation (in %) (and optionally the success probability).

🔗 Example

For example, the following will return 5 neighbors from the top 0.1% of the data (with probability 0.95) for each point in "input" and store the distances in "distances" and the neighbors in "neighbors.csv":

R> output <- krann(reference=input, k=5, tau=0.1)
R> distances <- output$distances
R> neighbors <- output$neighbors

Note that tau must be set such that the number of points in the corresponding percentile of the data is greater than k. Thus, if we choose tau = 0.1 with a dataset of 1000 points and k = 5, then we are attempting to choose 5 nearest neighbors out of the closest 1 point – this is invalid and the program will terminate with an error message.

The output matrices are organized such that row i and column j in the neighbors output file corresponds to the index of the point in the reference set which is the i’th nearest neighbor from the point in the query set with index j. Row i and column j in the distances output file corresponds to the distance between those two points.

🔗 See also

🔗 softmax_regression()

Softmax Regression

R> library(mlpack)
R> d <- softmax_regression(input_model=NA, labels=matrix(integer(), 0,
        0), lambda=0.0001, max_iterations=400, no_intercept=FALSE,
        number_of_classes=0, test=matrix(numeric(), 0, 0),
        test_labels=matrix(integer(), 0, 0), training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of softmax regression for classification, which is a multiclass generalization of logistic regression. Given labeled data, a softmax regression model can be trained and saved for future use, or, a pre-trained softmax regression model can be used for classification of new points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model SoftmaxRegression File containing existing model (parameters). NA
labels integer vector A matrix containing labels (0 or 1) for the points in the training set (y). The labels must order as a row. matrix(integer(), 0, 0)
lambda numeric L2-regularization constant 0.0001
max_iterations integer Maximum number of iterations before termination. 400
no_intercept logical Do not add the intercept term to the model. FALSE
number_of_classes integer Number of classes for classification; if unspecified (or 0), the number of classes found in the labels will be used. 0
test numeric matrix Matrix containing test dataset. matrix(numeric(), 0, 0)
test_labels integer vector Matrix containing test labels. matrix(integer(), 0, 0)
training numeric matrix A matrix containing the training set (the matrix of predictors, X). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model SoftmaxRegression File to save trained softmax regression model to.
predictions integer vector Matrix to save predictions for test dataset into.
probabilities numeric matrix Matrix to save class probabilities for test dataset into.

🔗 Detailed documentation

This program performs softmax regression, a generalization of logistic regression to the multiclass case, and has support for L2 regularization. The program is able to train a model, load an existing model, and give predictions (and optionally their accuracy) for test data.

Training a softmax regression model is done by giving a file of training points with the training parameter and their corresponding labels with the labels parameter. The number of classes can be manually specified with the number_of_classes parameter, and the maximum number of iterations of the L-BFGS optimizer can be specified with the max_iterations parameter. The L2 regularization constant can be specified with the lambda parameter and if an intercept term is not desired in the model, the no_intercept parameter can be specified.

The trained model can be saved with the output_model output parameter. If training is not desired, but only testing is, a model can be loaded with the input_model parameter. At the current time, a loaded model cannot be trained further, so specifying both input_model and training is not allowed.

The program is also able to evaluate a model on test data. A test dataset can be specified with the test parameter. Class predictions can be saved with the predictions output parameter. If labels are specified for the test data with the test_labels parameter, then the program will print the accuracy of the predictions on the given test set and its corresponding labels.

🔗 Example

For example, to train a softmax regression model on the data "dataset" with labels "labels" with a maximum of 1000 iterations for training, saving the trained model to "sr_model", the following command can be used:

R> output <- softmax_regression(training=dataset, labels=labels)
R> sr_model <- output$output_model

Then, to use "sr_model" to classify the test points in "test_points", saving the output predictions to "predictions", the following command can be used:

R> output <- softmax_regression(input_model=sr_model, test=test_points)
R> predictions <- output$predictions

🔗 See also

🔗 sparse_coding()

Sparse Coding

R> library(mlpack)
R> d <- sparse_coding(atoms=15, initial_dictionary=matrix(numeric(), 0,
        0), input_model=NA, lambda1=0, lambda2=0, max_iterations=0,
        newton_tolerance=1e-06, normalize=FALSE, objective_tolerance=0.01,
        seed=0, test=matrix(numeric(), 0, 0), training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> codes <- d$codes
R> dictionary <- d$dictionary
R> output_model <- d$output_model

An implementation of Sparse Coding with Dictionary Learning. Given a dataset, this will decompose the dataset into a sparse combination of a few dictionary elements, where the dictionary is learned during computation; a dictionary can be reused for future sparse coding of new points. Detailed documentation.

🔗 Input options

name type description default
atoms integer Number of atoms in the dictionary. 15
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
initial_dictionary numeric matrix Optional initial dictionary matrix. matrix(numeric(), 0, 0)
input_model SparseCoding File containing input sparse coding model. NA
lambda1 numeric Sparse coding l1-norm regularization parameter. 0
lambda2 numeric Sparse coding l2-norm regularization parameter. 0
max_iterations integer Maximum number of iterations for sparse coding (0 indicates no limit). 0
newton_tolerance numeric Tolerance for convergence of Newton method. 1e-06
normalize logical If set, the input data matrix will be normalized before coding. FALSE
objective_tolerance numeric Tolerance for convergence of the objective function. 0.01
seed integer Random seed. If 0, ‘std::time(NULL)’ is used. 0
test numeric matrix Optional matrix to be encoded by trained model. matrix(numeric(), 0, 0)
training numeric matrix Matrix of training data (X). matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
codes numeric matrix Matrix to save the output sparse codes of the test matrix (–test_file) to.
dictionary numeric matrix Matrix to save the output dictionary to.
output_model SparseCoding File to save trained sparse coding model to.

🔗 Detailed documentation

An implementation of Sparse Coding with Dictionary Learning, which achieves sparsity via an l1-norm regularizer on the codes (LASSO) or an (l1+l2)-norm regularizer on the codes (the Elastic Net). Given a dense data matrix X with d dimensions and n points, sparse coding seeks to find a dense dictionary matrix D with k atoms in d dimensions, and a sparse coding matrix Z with n points in k dimensions.

The original data matrix X can then be reconstructed as Z * D. Therefore, this program finds a representation of each point in X as a sparse linear combination of atoms in the dictionary D.

The sparse coding is found with an algorithm which alternates between a dictionary step, which updates the dictionary D, and a sparse coding step, which updates the sparse coding matrix.

Once a dictionary D is found, the sparse coding model may be used to encode other matrices, and saved for future usage.

To run this program, either an input matrix or an already-saved sparse coding model must be specified. An input matrix may be specified with the training option, along with the number of atoms in the dictionary (specified with the atoms parameter). It is also possible to specify an initial dictionary for the optimization, with the initial_dictionary parameter. An input model may be specified with the input_model parameter.

🔗 Example

As an example, to build a sparse coding model on the dataset "data" using 200 atoms and an l1-regularization parameter of 0.1, saving the model into "model", use

R> output <- sparse_coding(training=data, atoms=200, lambda1=0.1)
R> model <- output$output_model

Then, this model could be used to encode a new matrix, "otherdata", and save the output codes to "codes":

R> output <- sparse_coding(input_model=model, test=otherdata)
R> codes <- output$codes

🔗 See also

🔗 adaboost()

AdaBoost

R> library(mlpack)
R> d <- adaboost(input_model=NA, iterations=1000,
        labels=matrix(integer(), 0, 0), test=matrix(numeric(), 0, 0),
        tolerance=1e-10, training=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE),
        weak_learner="decision_stump")
R> output_model <- d$output_model
R> predictions <- d$predictions
R> probabilities <- d$probabilities

An implementation of the AdaBoost.MH (Adaptive Boosting) algorithm for classification. This can be used to train an AdaBoost model on labeled data or use an existing AdaBoost model to predict the classes of new points. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model AdaBoostModel Input AdaBoost model. NA
iterations integer The maximum number of boosting iterations to be run (0 will run until convergence.) 1000
labels integer vector Labels for the training set. matrix(integer(), 0, 0)
test numeric matrix Test dataset. matrix(numeric(), 0, 0)
tolerance numeric The tolerance for change in values of the weighted error during training. 1e-10
training numeric matrix Dataset for training AdaBoost. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
weak_learner character The type of weak learner to use: ‘decision_stump’, or ‘perceptron’. "decision_stump"

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model AdaBoostModel Output trained AdaBoost model.
predictions integer vector Predicted labels for the test set.
probabilities numeric matrix Predicted class probabilities for each point in the test set.

🔗 Detailed documentation

This program implements the AdaBoost (or Adaptive Boosting) algorithm. The variant of AdaBoost implemented here is AdaBoost.MH. It uses a weak learner, either decision stumps or perceptrons, and over many iterations, creates a strong learner that is a weighted ensemble of weak learners. It runs these iterations until a tolerance value is crossed for change in the value of the weighted training error.

For more information about the algorithm, see the paper “Improved Boosting Algorithms Using Confidence-Rated Predictions”, by R.E. Schapire and Y. Singer.

This program allows training of an AdaBoost model, and then application of that model to a test dataset. To train a model, a dataset must be passed with the training option. Labels can be given with the labels option; if no labels are specified, the labels will be assumed to be the last column of the input dataset. Alternately, an AdaBoost model may be loaded with the input_model option.

Once a model is trained or loaded, it may be used to provide class predictions for a given test dataset. A test dataset may be specified with the test parameter. The predicted classes for each point in the test dataset are output to the predictions output parameter. The AdaBoost model itself is output to the output_model output parameter.

🔗 Example

For example, to run AdaBoost on an input dataset "data" with labels "labels"and perceptrons as the weak learner type, storing the trained model in "model", one could use the following command:

R> output <- adaboost(training=data, labels=labels,
  weak_learner="perceptron")
R> model <- output$output_model

Similarly, an already-trained model in "model" can be used to provide class predictions from test data "test_data" and store the output in "predictions" with the following command:

R> output <- adaboost(input_model=model, test=test_data)
R> predictions <- output$predictions

🔗 See also

🔗 linear_regression()

Simple Linear Regression and Prediction

R> library(mlpack)
R> d <- linear_regression(input_model=NA, lambda=0,
        test=matrix(numeric(), 0, 0), training=matrix(numeric(), 0, 0),
        training_responses=matrix(numeric(), 0, 0),
        verbose=getOption("mlpack.verbose", FALSE))
R> output_model <- d$output_model
R> output_predictions <- d$output_predictions

An implementation of simple linear regression and ridge regression using ordinary least squares. Given a dataset and responses, a model can be trained and saved for later use, or a pre-trained model can be used to output regression predictions for a test set. Detailed documentation.

🔗 Input options

name type description default
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
input_model LinearRegression Existing LinearRegression model to use. NA
lambda numeric Tikhonov regularization for ridge regression. If 0, the method reduces to linear regression. 0
test numeric matrix Matrix containing X’ (test regressors). matrix(numeric(), 0, 0)
training numeric matrix Matrix containing training set X (regressors). matrix(numeric(), 0, 0)
training_responses numeric vector Optional vector containing y (responses). If not given, the responses are assumed to be the last row of the input file. matrix(numeric(), 0, 0)
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output_model LinearRegression Output LinearRegression model.
output_predictions numeric vector If –test_file is specified, this matrix is where the predicted responses will be saved.

🔗 Detailed documentation

An implementation of simple linear regression and simple ridge regression using ordinary least squares. This solves the problem

y = X * b + e

where X (specified by training) and y (specified either as the last column of the input matrix training or via the training_responses parameter) are known and b is the desired variable. If the covariance matrix (X’X) is not invertible, or if the solution is overdetermined, then specify a Tikhonov regularization constant (with lambda) greater than 0, which will regularize the covariance matrix to make it invertible. The calculated b may be saved with the output_predictions output parameter.

Optionally, the calculated value of b is used to predict the responses for another matrix X’ (specified by the test parameter):

y’ = X’ * b

and the predicted responses y’ may be saved with the output_predictions output parameter. This type of regression is related to least-angle regression, which mlpack implements as the ‘lars’ program.

🔗 Example

For example, to run a linear regression on the dataset "X" with responses "y", saving the trained model to "lr_model", the following command could be used:

R> output <- linear_regression(training=X, training_responses=y)
R> lr_model <- output$output_model

Then, to use "lr_model" to predict responses for a test set "X_test", saving the predictions to "X_test_responses", the following command could be used:

R> output <- linear_regression(input_model=lr_model, test=X_test)
R> X_test_responses <- output$output_predictions

🔗 See also

🔗 image_converter()

Image Converter

R> library(mlpack)
R> d <- image_converter(channels=0, dataset=matrix(numeric(), 0, 0),
        height=0, input=c(), quality=90, save=FALSE,
        verbose=getOption("mlpack.verbose", FALSE), width=0)
R> output <- d$output

A utility to load an image or set of images into a single dataset that can then be used by other mlpack methods and utilities. This can also unpack an image dataset into individual files, for instance after mlpack methods have been used. Detailed documentation.

🔗 Input options

name type description default
channels integer Number of channels in the image. 0
check_input_matrices logical If specified, the input matrix is checked for NaN and inf values; an exception is thrown if any are found. FALSE
dataset numeric matrix Input matrix to save as images. matrix(numeric(), 0, 0)
height integer Height of the images. 0
input vector of characters Image filenames which have to be loaded/saved. **--**
quality integer Compression of the image if saved as jpg (0-100). 90
save logical Save a dataset as images. FALSE
verbose logical Display informational messages and the full list of parameters and timers at the end of execution. getOption("mlpack.verbose", FALSE)
width integer Width of the image. 0

🔗 Output options

Results are returned in a R list. The keys of the list are the names of the output parameters.

name type description
output numeric matrix Matrix to save images data to, Onlyneeded if you are specifying ‘save’ option.

🔗 Detailed documentation

This utility takes an image or an array of images and loads them to a matrix. You can optionally specify the height height width width and channel channels of the images that needs to be loaded; otherwise, these parameters will be automatically detected from the image. There are other options too, that can be specified such as quality.

You can also provide a dataset and save them as images using dataset and save as an parameter.

🔗 Example

An example to load an image :

R> output <- image_converter(input=X, height=256, width=256, channels=3)
R> Y <- output$output

An example to save an image is :

R> image_converter(input=X, height=256, width=256, channels=3, dataset=Y,
  save=TRUE)

🔗 See also