classification:
regression:
clustering:
geometry:
preprocessing:
misc. / other:
overview
Highquality documentation is a development goal of mlpack. mlpack’s documentation is split into two parts: documentation for the bindings, and documentation for the C++ library. Generally, working with the bindings is a good choice for simple machine learning and data science tasks, and writing C++ is a good idea when complex or custom functionality is desired.
All interfaces are heavily documented, and if you find a documentation issue, please report it.
quickstart
Just getting started with mlpack? Try these quickstart tutorials for the bindings to other languages.
Quickstart Tutorials
These tutorials give very quick “getting started” examples that you can use to get started with mlpack in different languages.
Once you’re comfortable with the quickstart guides for the language of your choice, full documentation for every binding can be found below. Quick links are in the left sidebar.
The C++ interfaces of mlpack are carefully documented and doxygen is used to provide automaticallygenerated searchable documentation.
tutorials
A number of tutorials are available covering individual algorithms and functionality inside of mlpack, both for bindings to other languages and for the C++ interface.
Introductory Tutorials
These tutorials introduce the basic concepts of working with mlpack, aimed at developers who want to use and contribute to mlpack but are not sure where to start.
 Building mlpack From Source
 Building mlpack From Source on Windows
 File formats and loading data in mlpack
 Matrices in mlpack
 Writing an mlpack binding
 mlpack Timers
 Simple Sample mlpack Programs
 Sample C++ ML App for Windows
Methodspecific Tutorials
These tutorials introduce the various methods mlpack offers, aimed at users who want to get started quickly. These tutorials start with simple examples and progress to complex, extensible uses.
 NeighborSearch tutorial (knearestneighbors)
 Linear/ridge regression tutorial (mlpack_linear_regression)
 RangeSearch tutorial (mlpack_range_search)
 Density Estimation Tree (DET) tutorial
 KMeans tutorial (kmeans)
 Fast maxkernel search tutorial (fastmks)
 EMST Tutorial
 Alternating Matrix Factorization tutorial
 Collaborative filtering tutorial
 Approximate furthest neighbor search (mlpack_approx_kfn) tutorial
 Neural Network tutorial
Advanced Tutorials
These tutorials discuss some of the more advanced functionality contained in mlpack.
Policy Class Documentation
mlpack uses templates to achieve its genericity and flexibility. Some of the template types used by mlpack are common across multiple machine learning algorithms. The links below provide documentation for some of these common types.
mlpack 3.1.0 binding documentation
data formats
mlpack bindings for CLI 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.
int
: An integer (i.e., “1”).double
: A floatingpoint number (i.e., “0.5”).flag
: A boolean flag option. If not specified, it is false; if specified, it is true.string
: A character string (i.e., “hello”).int vector
: A vector of integers, separated by commas (i.e., “1,2,3”).string vector
: A vector of strings, separated by commas (i.e., “hello”,”goodbye”).2d matrix file
: A data matrix filename. The file can be CSV (.csv), TSV (.csv), ASCII (spaceseparated values, .txt), Armadillo ASCII (.txt), PGM (.pgm), PPM (.ppm), Armadillo binary (.bin), or HDF5 (.h5, .hdf, .hdf5, or .he5), if mlpack was compiled with HDF5 support. The type of the data is detected by the extension of the filename. The storage should be such that one row corresponds to one point, and one column corresponds to one dimension (this is the typical storage format for ondisk data). All values of the matrix will be loaded as doubleprecision floating point data.2d index matrix file
: A data matrix filename, where the matrix holds only nonnegative integer values. This type is often used for labels or indices. The file can be CSV (.csv), TSV (.csv), ASCII (spaceseparated values, .txt), Armadillo ASCII (.txt), PGM (.pgm), PPM (.ppm), Armadillo binary (.bin), or HDF5 (.h5, .hdf, .hdf5, or .he5), if mlpack was compiled with HDF5 support. The type of the data is detected by the extension of the filename. The storage should be such that one row corresponds to one point, and one column corresponds to one dimension (this is the typical storage format for ondisk data). All values of the matrix will be loaded as unsigned integers.1d matrix file
: A onedimensional vector filename. This file can take the same formats as the data matrix filenames; however, it must either contain one row and many columns, or one column and many rows.1d index matrix file
: A onedimensional vector filename, where the matrix holds only nonnegative integer values. This type is typically used for labels or predictions or other indices. This file can take the same formats as the data matrix filenames; however, it must either contain one row and many columns, or one column and many rows.2d categorical matrix file
: A filename for a data matrix that can contain categorical (nonnumeric) data. If the file contains only numeric data, then the same formats for regular data matrices can be used. If the file contains strings or other values that can’t be parsed as numbers, then the type to be loaded must be CSV (.csv) or ARFF (.arff). Any nonnumeric data will be converted to an unsigned integer value, and dimensions where the data is converted will be treated as categorical dimensions. When using this format, there is no need for onehot encoding of categorical data.mlpackModel file
: A filename containing an mlpack model. These can have one of three formats: binary (.bin), text (.txt), and XML (.xml). The XML format produces the largest (but most humanreadable) files, while the binary format can be significantly more compact and quicker to load and save.
mlpack_adaboost
AdaBoost
$ mlpack_adaboost [input_model_file <string>] [iterations 1000]
[labels_file <string>] [test_file <string>] [tolerance 1e10]
[training_file <string>] [weak_learner 'decision_stump']
[output_file <string>] [output_model_file <string>]
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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
AdaBoostModel file 
Input AdaBoost model.  '' 
iterations (i) 
int 
The maximum number of boosting iterations to be run (0 will run until convergence.)  1000 
labels_file (l) 
1d index matrix file 
Labels for the training set.  '' 
test_file (T) 
2d matrix file 
Test dataset.  '' 
tolerance (e) 
double 
The tolerance for change in values of the weighted error during training.  1e10 
training_file (t) 
2d matrix file 
Dataset for training AdaBoost.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding.  
weak_learner (w) 
string 
The type of weak learner to use: ‘decision_stump’, or ‘perceptron’.  'decision_stump' 
Output options
name  type  description 

output_file (o) 
1d index matrix file 
Predicted labels for the test set. 
output_model_file (M) 
AdaBoostModel file 
Output trained AdaBoost model. 
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 ConfidenceRated 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_file (t)
option. Labels can be given with the labels_file (l)
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_file (m)
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_file (T)
parameter. The predicted classes for each point in the test dataset are output to the output_file (o)
output parameter. The AdaBoost model itself is output to the output_model_file (M)
output parameter.
For example, to run AdaBoost on an input dataset 'data.csv'
with perceptrons as the weak learner type, storing the trained model in 'model.bin'
, one could use the following command:
$ mlpack_adaboost training_file data.csv output_model_file model.bin
weak_learner perceptron
Similarly, an alreadytrained model in 'model.bin'
can be used to provide class predictions from test data 'test_data.csv'
and store the output in 'predictions.csv'
with the following command:
$ mlpack_adaboost input_model_file model.bin test_file test_data.csv
output_file predictions.csv
See also
 AdaBoost on Wikipedia
 Improved boosting algorithms using confidencerated predictions (pdf)
 Perceptron
 Decision Stump
 mlpack::adaboost::AdaBoost C++ class documentation
mlpack_approx_kfn
Approximate furthest neighbor search
$ mlpack_approx_kfn [algorithm 'ds'] [calculate_error]
[exact_distances_file <string>] [input_model_file <string>] [k 0]
[num_projections 5] [num_tables 5] [query_file <string>]
[reference_file <string>] [distances_file <string>]
[neighbors_file <string>] [output_model_file <string>]
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 (a) 
string 
Algorithm to use: ‘ds’ or ‘qdafn’.  'ds' 
calculate_error (e) 
flag 
If set, calculate the average distance error for the first furthest neighbor only.  
exact_distances_file (x) 
2d matrix file 
Matrix containing exact distances to furthest neighbors; this can be used to avoid explicit calculation when –calculate_error is set.  '' 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
ApproxKFNModel file 
File containing input model.  '' 
k (k) 
int 
Number of furthest neighbors to search for.  0 
num_projections (p) 
int 
Number of projections to use in each hash table.  5 
num_tables (t) 
int 
Number of hash tables to use.  5 
query_file (q) 
2d matrix file 
Matrix containing query points.  '' 
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
2d matrix file 
Matrix to save furthest neighbor distances to. 
neighbors_file (n) 
2d index matrix file 
Matrix to save neighbor indices to. 
output_model_file (M) 
ApproxKFNModel file 
File to save output model to. 
Detailed documentation
This program implements two strategies for furthest neighbor search. These strategies are:
 The ‘qdafn’ algorithm from “Approximate Furthest Neighbor in High Dimensions” by R. Pagh, F. Silvestri, J. Sivertsen, and M. Skala, in Similarity Search and Applications 2015 (SISAP).
 The ‘DrusillaSelect’ algorithm from “Fast approximate furthest neighbors with datadependent candidate selection”, by R.R. Curtin and A.B. Gardner, in Similarity Search and Applications 2016 (SISAP).
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_file (r)
, specify a query set with query_file (q)
, and specify algorithm parameters with num_tables (t)
and num_projections (p)
(or don’t and defaults will be used). The algorithm to be used (either ‘ds’—the default—or ‘qdafn’) may be specified with algorithm (a)
. Also specify the number of neighbors to search for with k (k)
.
If no query set is specified, the reference set will be used as the query set. The output_model_file (M)
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_file (m)
option.
Results for each query point can be stored with the neighbors_file (n)
and distances_file (d)
output parameters. Each row of these output matrices holds the k distances or neighbor indices for each query point.
For example, to find the 5 approximate furthest neighbors with 'reference_set.csv'
as the reference set and 'query_set.csv'
as the query set using DrusillaSelect, storing the furthest neighbor indices to 'neighbors.csv'
and the furthest neighbor distances to 'distances.csv'
, one could call
$ mlpack_approx_kfn query_file query_set.csv reference_file
reference_set.csv k 5 algorithm ds neighbors_file neighbors.csv
distances_file distances.csv
and to perform approximate allfurthestneighbors search with k=1 on the set 'data.csv'
storing only the furthest neighbor distances to 'distances.csv'
, one could call
$ mlpack_approx_kfn reference_file reference_set.csv k 1 distances_file
distances.csv
A trained model can be reused. If a model has been previously saved to 'model.bin'
, then we may find 3 approximate furthest neighbors on a query set 'new_query_set.csv'
using that model and store the furthest neighbor indices into 'neighbors.csv'
by calling
$ mlpack_approx_kfn input_model_file model.bin query_file
new_query_set.csv k 3 neighbors_file neighbors.csv
See also
 kfurthestneighbor search
 knearestneighbor search
 Fast approximate furthest neighbors with datadependent candidate selection (pdf)
 Approximate furthest neighbor in high dimensions (pdf)
 mlpack::neighbor::QDAFN class documentation
 mlpack::neighbor::DrusillaSelect class documentation
mlpack_cf
Collaborative Filtering
$ mlpack_cf [algorithm 'NMF'] [all_user_recommendations]
[input_model_file <string>] [interpolation 'average']
[iteration_only_termination] [max_iterations 1000] [min_residue
1e05] [neighbor_search 'euclidean'] [neighborhood 5] [query_file
<string>] [rank 0] [recommendations 5] [seed 0] [test_file
<string>] [training_file <string>] [output_file <string>]
[output_model_file <string>]
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 (a) 
string 
Algorithm used for matrix factorization.  'NMF' 
all_user_recommendations (A) 
flag 
Generate recommendations for all users.  
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
CFModel file 
Trained CF model to load.  '' 
interpolation (i) 
string 
Algorithm used for weight interpolation.  'average' 
iteration_only_termination (I) 
flag 
Terminate only when the maximum number of iterations is reached.  
max_iterations (N) 
int 
Maximum number of iterations. If set to zero, there is no limit on the number of iterations.  1000 
min_residue (r) 
double 
Residue required to terminate the factorization (lower values generally mean better fits).  1e05 
neighbor_search (S) 
string 
Algorithm used for neighbor search.  'euclidean' 
neighborhood (n) 
int 
Size of the neighborhood of similar users to consider for each query user.  5 
query_file (q) 
2d index matrix file 
List of query users for which recommendations should be generated.  '' 
rank (R) 
int 
Rank of decomposed matrices (if 0, a heuristic is used to estimate the rank).  0 
recommendations (c) 
int 
Number of recommendations to generate for each query user.  5 
seed (s) 
int 
Set the random seed (0 uses std::time(NULL)).  0 
test_file (T) 
2d matrix file 
Test set to calculate RMSE on.  '' 
training_file (t) 
2d matrix file 
Input dataset to perform CF on.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d index matrix file 
Matrix that will store output recommendations. 
output_model_file (M) 
CFModel file 
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_file (t)
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_file (m)
parameter and then use that model to provide recommendations or predict values.
The input matrix should be a 3dimensional 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_file (q)
parameter; alternately, recommendations may be generated for every user in the dataset by specifying the all_user_recommendations (A)
parameter. In addition, the number of recommendations per user to generate can be specified with the recommendations (c)
parameter, and the number of similar users (the size of the neighborhood) to be considered when generating recommendations can be specified with the neighborhood (n)
parameter.
For performing the matrix decomposition, the following optimization algorithms can be specified via the algorithm (a)
parameter:
 ‘RegSVD’ – Regularized SVD using a SGD optimizer
 ‘NMF’ – Nonnegative matrix factorization with alternating least squares update rules
 ‘BatchSVD’ – SVD batch learning
 ‘SVDIncompleteIncremental’ – SVD incomplete incremental learning
 ‘SVDCompleteIncremental’ – SVD complete incremental learning
 ‘BiasSVD’ – Bias SVD using a SGD optimizer
 ‘SVDPP’ – SVD++ using a SGD optimizer
The following neighbor search algorithms can be specified via the neighbor_search (S)
parameter:
 ‘cosine’ – Cosine Search Algorithm
 ‘euclidean’ – Euclidean Search Algorithm
 ‘pearson’ – Pearson Search Algorithm
The following weight interpolation algorithms can be specified via the interpolation (i)
parameter:
 ‘average’ – Average Interpolation Algorithm
 ‘regression’ – Regression Interpolation Algorithm
 ‘similarity’ – Similarity Interpolation Algorithm
A trained model may be saved to with the output_model_file (M)
output parameter.
To train a CF model on a dataset 'training_set.csv'
using NMF for decomposition and saving the trained model to 'model.bin'
, one could call:
$ mlpack_cf training_file training_set.csv algorithm NMF
output_model_file model.bin
Then, to use this model to generate recommendations for the list of users in the query set 'users.csv'
, storing 5 recommendations in 'recommendations.csv'
, one could call
$ mlpack_cf input_model_file model.bin query_file users.csv
recommendations 5 output_file recommendations.csv
See also
 Collaborative filtering tutorial
 Alternating Matrix Factorization tutorial
 Collaborative Filtering on Wikipedia
 Matrix factorization on Wikipedia
 Matrix factorization techniques for recommender systems (pdf)
 mlpack::cf::CFType class documentation
mlpack_dbscan
DBSCAN clustering
$ mlpack_dbscan [epsilon 1] input_file <string> [min_size 5]
[naive] [selection_type 'ordered'] [single_mode] [tree_type
'kd'] [assignments_file <string>] [centroids_file <string>]
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 

epsilon (e) 
double 
Radius of each range search.  1 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to cluster.  required 
min_size (m) 
int 
Minimum number of points for a cluster.  5 
naive (N) 
flag 
If set, bruteforce range search (not treebased) will be used.  
selection_type (s) 
string 
If using point selection policy, the type of selection to use (‘ordered’, ‘random’).  'ordered' 
single_mode (S) 
flag 
If set, singletree range search (not dualtree) will be used.  
tree_type (t) 
string 
If using singletree or dualtree search, the type of tree to use (‘kd’, ‘r’, ‘rstar’, ‘x’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘cover’, ‘ball’).  'kd' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

assignments_file (a) 
1d index matrix file 
Output matrix for assignments of each point. 
centroids_file (C) 
2d matrix file 
Matrix to save output centroids to. 
Detailed documentation
This program implements the DBSCAN algorithm for clustering using accelerated treebased range search. The type of tree that is used may be parameterized, or bruteforce range search may also be used.
The input dataset to be clustered may be specified with the input_file (i)
parameter; the radius of each range search may be specified with the epsilon (e)
parameters, and the minimum number of points in a cluster may be specified with the min_size (m)
parameter.
The assignments_file (a)
and centroids_file (C)
output parameters may be used to save the output of the clustering. assignments_file (a)
contains the cluster assignments of each point, and centroids_file (C)
contains the centroids of each cluster.
The range search may be controlled with the tree_type (t)
, single_mode (S)
, and naive (N)
parameters. tree_type (t)
can control the type of tree used for range search; this can take a variety of values: ‘kd’, ‘r’, ‘rstar’, ‘x’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘cover’, ‘ball’. The single_mode (S)
parameter will force singletree search (as opposed to the default dualtree search), and ‘naive (N)
will force bruteforce range search.
An example usage to run DBSCAN on the dataset in 'input.csv'
with a radius of 0.5 and a minimum cluster size of 5 is given below:
$ mlpack_dbscan input_file input.csv epsilon 0.5 min_size 5
See also
 DBSCAN on Wikipedia
 A densitybased algorithm for discovering clusters in large spatial databases with noise (pdf)
 mlpack::dbscan::DBSCAN class documentation
mlpack_decision_stump
Decision Stump
$ mlpack_decision_stump [bucket_size 6] [input_model_file <string>]
[labels_file <string>] [test_file <string>] [training_file
<string>] [output_model_file <string>] [predictions_file <string>]
An implementation of a decision stump, which is a singlelevel decision tree. Given labeled data, a new decision stump can be trained; or, an existing decision stump can be used to classify points. Detailed documentation.
Input options
name  type  description  default 

bucket_size (b) 
int 
The minimum number of training points in each decision stump bucket.  6 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
DSModel file 
Decision stump model to load.  '' 
labels_file (l) 
1d index matrix file 
Labels for the training set. If not specified, the labels are assumed to be the last row of the training data.  '' 
test_file (T) 
2d matrix file 
A dataset to calculate predictions for.  '' 
training_file (t) 
2d matrix file 
The dataset to train on.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
DSModel file 
Output decision stump model to save. 
predictions_file (p) 
1d index matrix file 
The output matrix that will hold the predicted labels for the test set. 
Detailed documentation
This program implements a decision stump, which is a singlelevel decision tree. The decision stump will split on one dimension of the input data, and will split into multiple buckets. The dimension and bins are selected by maximizing the information gain of the split. Optionally, the minimum number of training points in each bin can be specified with the bucket_size (b)
parameter.
The decision stump is parameterized by a splitting dimension and a vector of values that denote the splitting values of each bin.
This program enables several applications: a decision tree may be trained or loaded, and then that decision tree may be used to classify a given set of test points. The decision tree may also be saved to a file for later usage.
To train a decision stump, training data should be passed with the training_file (t)
parameter, and their corresponding labels should be passed with the labels_file (l)
option. Optionally, if labels_file (l)
is not specified, the labels are assumed to be the last dimension of the training dataset. The bucket_size (b)
parameter controls the minimum number of training points in each decision stump bucket.
For classifying a test set, a decision stump may be loaded with the input_model_file (m)
parameter (useful for the situation where a stump has already been trained), and a test set may be specified with the test_file (T)
parameter. The predicted labels can be saved with the predictions_file (p)
output parameter.
Because decision stumps are trained in batch, retraining does not make sense and thus it is not possible to pass both training_file (t)
and input_model_file (m)
; instead, simply build a new decision stump with the training data.
After training, a decision stump can be saved with the output_model_file (M)
output parameter. That stump may later be reused in subsequent calls to this program (or others).
See also
 Decision tree
 Decision stumps on Wikipedia
 mlpack::decision_stump::DecisionStump class documentation
mlpack_decision_tree
Decision tree
$ mlpack_decision_tree [input_model_file <string>] [labels_file
<string>] [minimum_gain_split 1e07] [minimum_leaf_size 20]
[print_training_error] [test_file <string>] [test_labels_file
<string>] [training_file <string>] [weights_file <string>]
[output_model_file <string>] [predictions_file <string>]
[probabilities_file <string>]
An implementation of an ID3style 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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
DecisionTreeModel file 
Pretrained decision tree, to be used with test points.  '' 
labels_file (l) 
1d index matrix file 
Training labels.  '' 
minimum_gain_split (g) 
double 
Minimum gain for node splitting.  1e07 
minimum_leaf_size (n) 
int 
Minimum number of points in a leaf.  20 
print_training_error (e) 
flag 
Print the training error.  
test_file (T) 
2d categorical matrix file 
Testing dataset (may be categorical).  '' 
test_labels_file (L) 
2d index matrix file 
Test point labels, if accuracy calculation is desired.  '' 
training_file (t) 
2d categorical matrix file 
Training dataset (may be categorical).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding.  
weights_file (w) 
2d matrix file 
The weight of labels  '' 
Output options
name  type  description 

output_model_file (M) 
DecisionTreeModel file 
Output for trained decision tree. 
predictions_file (p) 
1d index matrix file 
Class predictions for each test point. 
probabilities_file (P) 
2d matrix file 
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_file (t)
and labels_file (l)
parameters, respectively. The labels should be in the range [0, num_classes  1]. Optionally, if labels_file (l)
is not specified, the labels are assumed to be the last dimension of the training dataset.
When a model is trained, the output_model_file (M)
output parameter may be used to save the trained model. A model may be loaded for predictions with the input_model_file (m)
parameter. The input_model_file (m)
parameter may not be specified when the training_file (t)
parameter is specified. The minimum_leaf_size (n)
parameter specifies the minimum number of training points that must fall into each leaf for it to be split. The minimum_gain_split (g)
parameter specifies the minimum gain that is needed for the node to split. If print_training_error (e)
is specified, the training error will be printed.
Test data may be specified with the test_file (T)
parameter, and if performance numbers are desired for that test set, labels may be specified with the test_labels_file (L)
parameter. Predictions for each test point may be saved via the predictions_file (p)
output parameter. Class probabilities for each prediction may be saved with the probabilities_file (P)
output parameter.
For example, to train a decision tree with a minimum leaf size of 20 on the dataset contained in 'data.csv'
with labels 'labels.csv'
, saving the output model to 'tree.bin'
and printing the training error, one could call
$ mlpack_decision_tree training_file data.arff labels_file labels.csv
output_model_file tree.bin minimum_leaf_size 20 minimum_gain_split 0.001
print_training_error
Then, to use that model to classify points in 'test_set.csv'
and print the test error given the labels 'test_labels.csv'
using that model, while saving the predictions for each point to 'predictions.csv'
, one could call
$ mlpack_decision_tree input_model_file tree.bin test_file test_set.arff
test_labels_file test_labels.csv predictions_file predictions.csv
See also
 Decision stump
 Random forest
 Decision trees on Wikipedia
 Induction of Decision Trees (pdf)
 mlpack::tree::DecisionTree class documentation
mlpack_det
Density Estimation With Density Estimation Trees
$ mlpack_det [folds 10] [input_model_file <string>] [max_leaf_size
10] [min_leaf_size 5] [path_format 'lr'] [skip_pruning]
[test_file <string>] [training_file <string>] [output_model_file
<string>] [tag_counters_file <string>] [tag_file <string>]
[test_set_estimates_file <string>] [training_set_estimates_file
<string>] [vi_file <string>]
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 

folds (f) 
int 
The number of folds of crossvalidation to perform for the estimation (0 is LOOCV)  10 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
DTree<> file 
Trained density estimation tree to load.  '' 
max_leaf_size (L) 
int 
The maximum size of a leaf in the unpruned, fully grown DET.  10 
min_leaf_size (l) 
int 
The minimum size of a leaf in the unpruned, fully grown DET.  5 
path_format (p) 
string 
The format of path printing: ‘lr’, ‘idlr’, or ‘lrid’.  'lr' 
skip_pruning (s) 
flag 
Whether to bypass the pruning process and output the unpruned tree only.  
test_file (T) 
2d matrix file 
A set of test points to estimate the density of.  '' 
training_file (t) 
2d matrix file 
The data set on which to build a density estimation tree.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
DTree<> file 
Output to save trained density estimation tree to. 
tag_counters_file (c) 
string 
The file to output the number of points that went to each leaf. 
tag_file (g) 
string 
The file to output the tags (and possibly paths) for each sample in the test set. 
test_set_estimates_file (E) 
2d matrix file 
The output estimates on the test set from the final optimally pruned tree. 
training_set_estimates_file (e) 
2d matrix file 
The output density estimates on the training set from the final optimally pruned tree. 
vi_file (i) 
2d matrix file 
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_file (t)
) using crossvalidation (with number of folds specified with the folds (f)
parameter). This trained density estimation tree may then be saved with the output_model_file (M)
output parameter.
The variable importances (that is, the feature importance values for each dimension) may be saved with the vi_file (i)
output parameter, and the density estimates for each training point may be saved with the training_set_estimates_file (e)
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 ‘lrid’ or ‘idlr’ are given as the path_format (p)
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_file (T)
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_file (m)
. The density estimates for the test points may be saved using the test_set_estimates_file (E)
output parameter.
See also
 Density estimation tree (DET) tutorial
 Density estimation on Wikipedia
 Density estimation trees (pdf)
 mlpack::tree::DTree class documentation
mlpack_emst
Fast Euclidean Minimum Spanning Tree
$ mlpack_emst input_file <string> [leaf_size 1] [naive]
[output_file <string>]
An implementation of the DualTree Boruvka algorithm for computing the Euclidean minimum spanning tree of a set of input points. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input data matrix.  required 
leaf_size (l) 
int 
Leaf size in the kdtree. Oneelement leaves give the empirically best performance, but at the cost of greater memory requirements.  1 
naive (n) 
flag 
Compute the MST using O(n^2) naive algorithm.  
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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 dualtree Boruvka algorithm.
The set to calculate the minimum spanning tree of is specified with the input_file (i)
parameter, and the output may be saved with the output_file (o)
output parameter.
The leaf_size (l)
parameter controls the leaf size of the kdtree that is used to calculate the minimum spanning tree, and if the naive (n)
option is given, then bruteforce 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.
For example, the minimum spanning tree of the input dataset 'data.csv'
can be calculated with a leaf size of 20 and stored as 'spanning_tree.csv'
using the following command:
$ mlpack_emst input_file data.csv leaf_size 20 output_file
spanning_tree.csv
The output matrix is a threedimensional 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
 EMST Tutorial
 Minimum spanning tree on Wikipedia
 Fast Euclidean Minimum Spanning Tree: Algorithm, Analysis, and Applications (pdf)
 mlpack::emst::DualTreeBoruvka class documentation
mlpack_fastmks
FastMKS (Fast MaxKernel Search)
$ mlpack_fastmks [bandwidth 1] [base 2] [degree 2]
[input_model_file <string>] [k 0] [kernel 'linear'] [naive]
[offset 0] [query_file <string>] [reference_file <string>]
[scale 1] [single] [indices_file <string>] [kernels_file
<string>] [output_model_file <string>]
An implementation of the singletree and dualtree fast maxkernel 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 (w) 
double 
Bandwidth (for Gaussian, Epanechnikov, and triangular kernels).  1 
base (b) 
double 
Base to use during cover tree construction.  2 
degree (d) 
double 
Degree of polynomial kernel.  2 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
FastMKSModel file 
Input FastMKS model to use.  '' 
k (k) 
int 
Number of maximum kernels to find.  0 
kernel (K) 
string 
Kernel type to use: ‘linear’, ‘polynomial’, ‘cosine’, ‘gaussian’, ‘epanechnikov’, ‘triangular’, ‘hyptan’.  'linear' 
naive (N) 
flag 
If true, O(n^2) naive mode is used for computation.  
offset (o) 
double 
Offset of kernel (for polynomial and hyptan kernels).  0 
query_file (q) 
2d matrix file 
The query dataset.  '' 
reference_file (r) 
2d matrix file 
The reference dataset.  '' 
scale (s) 
double 
Scale of kernel (for hyptan kernel).  1 
single (S) 
flag 
If true, singletree search is used (as opposed to dualtree search.  
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

indices_file (i) 
2d index matrix file 
Output matrix of indices. 
kernels_file (p) 
2d matrix file 
Output matrix of kernels. 
output_model_file (M) 
FastMKSModel file 
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 (K)
parameter.
For example, the following command will calculate, for each point in the query set 'query.csv'
, the five points in the reference set 'reference.csv'
with maximum kernel evaluation using the linear kernel. The kernel evaluations may be saved with the 'kernels.csv'
output parameter and the indices may be saved with the 'indices.csv'
output parameter.
$ mlpack_fastmks k 5 reference_file reference.csv query_file query.csv
indices_file indices.csv kernels_file kernels.csv kernel linear
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 (b)
parameter.
See also
 Fast maxkernel search tutorial (fastmks)
 knearestneighbor search
 Dualtree Fast Exact MaxKernel Search (pdf)
 mlpack::fastmks::FastMKS class documentation
mlpack_gmm_train
Gaussian Mixture Model (GMM) Training
$ mlpack_gmm_train [diagonal_covariance] gaussians 0 input_file
<string> [input_model_file <string>] [max_iterations 250]
[no_force_positive] [noise 0] [percentage 0.02] [refined_start]
[samplings 100] [seed 0] [tolerance 1e10] [trials 1]
[output_model_file <string>]
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 

diagonal_covariance (d) 
flag 
Force the covariance of the Gaussians to be diagonal. This can accelerate training time significantly.  
gaussians (g) 
int 
Number of Gaussians in the GMM.  required 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
The training data on which the model will be fit.  required 
input_model_file (m) 
GMM file 
Initial input GMM model to start training with.  '' 
max_iterations (n) 
int 
Maximum number of iterations of EM algorithm (passing 0 will run until convergence).  250 
no_force_positive (P) 
flag 
Do not force the covariance matrices to be positive definite.  
noise (N) 
double 
Variance of zeromean Gaussian noise to add to data.  0 
percentage (p) 
double 
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 (r) 
flag 
During the initialization, use refined initial positions for kmeans clustering (Bradley and Fayyad, 1998).  
samplings (S) 
int 
If using –refined_start, specify the number of samplings used for initial points.  100 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
tolerance (T) 
double 
Tolerance for convergence of EM.  1e10 
trials (t) 
int 
Number of trials to perform in training GMM.  1 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
GMM file 
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_file (i)
parameter, and the number of Gaussians in the model must be specified with the gaussians (g)
parameter. Optionally, many trials with different random initializations may be run, and the result with highest loglikelihood on the training data will be taken. The number of trials to run is specified with the trials (t)
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 (T)
and max_iterations (n)
parameters, respectively. The GMM may be initialized for training with another model, specified with the input_model_file (m)
parameter. Otherwise, the model is initialized by running kmeans on the data. The kmeans clustering initialization can be controlled with the refined_start (r)
, samplings (S)
, and percentage (p)
parameters. If refined_start (r)
is specified, then the BradleyFayyad 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 (P)
parameter is not specified. Alternately, adding a small amount of Gaussian noise (using the noise (N)
parameter) to the entire dataset may help prevent Gaussians with zero variance in a particular dimension, which is usually the cause of noninvertible covariance matrices.
The no_force_positive (P)
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 nonpositive definite covariance matrices, which will cause the program to crash.
As an example, to train a 6Gaussian GMM on the data in 'data.csv'
with a maximum of 100 iterations of EM and 3 trials, saving the trained GMM to 'gmm.bin'
, the following command can be used:
$ mlpack_gmm_train input_file data.csv gaussians 6 trials 3
output_model_file gmm.bin
To retrain that GMM on another set of data 'data2.csv'
, the following command may be used:
$ mlpack_gmm_train input_model_file gmm.bin input_file data2.csv
gaussians 6 output_model_file new_gmm.bin
See also
 mlpack_gmm_generate
 mlpack_gmm_probability
 Gaussian Mixture Models on Wikipedia
 mlpack::gmm::GMM class documentation
mlpack_gmm_generate
GMM Sample Generator
$ mlpack_gmm_generate input_model_file <string> samples 0 [seed 0]
[output_file <string>]
A sample generator for pretrained GMMs. Given a pretrained GMM, this can sample new points randomly from that distribution. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
GMM file 
Input GMM model to generate samples from.  required 
samples (n) 
int 
Number of samples to generate.  required 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
Matrix to save output samples in. 
Detailed documentation
This program is able to generate samples from a pretrained GMM (use gmm_train to train a GMM). The pretrained GMM must be specified with the input_model_file (m)
parameter. The number of samples to generate is specified by the samples (n)
parameter. Output samples may be saved with the output_file (o)
output parameter.
The following command can be used to generate 100 samples from the pretrained GMM 'gmm.bin'
and store those generated samples in 'samples.csv'
:
$ mlpack_gmm_generate input_model_file gmm.bin samples 100 output_file
samples.csv
See also
 mlpack_gmm_train
 mlpack_gmm_probability
 Gaussian Mixture Models on Wikipedia
 mlpack::gmm::GMM class documentation
mlpack_gmm_probability
GMM Probability Calculator
$ mlpack_gmm_probability input_file <string> input_model_file
<string> [output_file <string>]
A probability calculator for GMMs. Given a pretrained 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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input matrix to calculate probabilities of.  required 
input_model_file (m) 
GMM file 
Input GMM to use as model.  required 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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_file (m) parameter, and the points are specified with the input_file (i) parameter. The output probabilities may be saved via the output_file (o) output parameter. 
So, for example, to calculate the probabilities of each point in 'points.csv'
coming from the pretrained GMM 'gmm.bin'
, while storing those probabilities in 'probs.csv'
, the following command could be used:
$ mlpack_gmm_probability input_model_file gmm.bin input_file points.csv
output_file probs.csv
See also
 mlpack_gmm_train
 mlpack_gmm_generate
 Gaussian Mixture Models on Wikipedia
 mlpack::gmm::GMM class documentation
mlpack_hmm_train
Hidden Markov Model (HMM) Training
$ mlpack_hmm_train [batch] [gaussians 0] input_file <string>
[input_model_file <string>] [labels_file <string>] [seed 0]
[states 0] [tolerance 1e05] [type 'gaussian']
[output_model_file <string>]
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 (b) 
flag 
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).  
gaussians (g) 
int 
Number of gaussians in each GMM (necessary when type is ‘gmm’).  0 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 

input_file (i) 
string 
File containing input observations.  required  
input_model_file (m) 
HMMModel file 
Preexisting HMM model to initialize training with.  '' 

labels_file (l) 
string 
Optional file of hidden states, used for labeled training.  '' 

seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 

states (n) 
int 
Number of hidden states in HMM (necessary, unless model_file is specified).  0 

tolerance (T) 
double 
Tolerance of the BaumWelch algorithm.  1e05 

type (t) 
string 
Type of HMM: discrete  gaussian  diag_gmm  gmm.  'gaussian' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
HMMModel file 
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_file and –batch 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 BaumWelch algorithm if no labels are provided. The tolerance of the BaumWelch algorithm can be set with the –tolerance option. By default, the transition matrix is randomly initialized and the emission distributions are initialized to fit the extent of the data.
Optionally, a precreated HMM model can be used as a guess for the transition matrix and emission probabilities; this is specifiable with –model_file.
See also
 mlpack_hmm_generate
 mlpack_hmm_loglik
 mlpack_hmm_viterbi
 Hidden Mixture Models on Wikipedia
 mlpack::hmm::HMM class documentation
mlpack_hmm_loglik
Hidden Markov Model (HMM) Sequence LogLikelihood
$ mlpack_hmm_loglik input_file <string> input_model_file <string>
[log_likelihood 0]
A utility for computing the loglikelihood of a sequence for Hidden Markov Models (HMMs). Given a pretrained HMM and an observation sequence, this computes and returns the loglikelihood of that sequence being observed from that HMM. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
File containing observations,  required 
input_model_file (m) 
HMMModel file 
File containing HMM.  required 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

log_likelihood 
double 
Loglikelihood of the sequence. 
Detailed documentation
This utility takes an alreadytrained HMM, specified with the input_model_file (m)
parameter, and evaluates the loglikelihood of a sequence of observations, given with the input_file (i)
parameter. The computed loglikelihood is given as output.
For example, to compute the loglikelihood of the sequence 'seq.csv'
with the pretrained HMM 'hmm.bin'
, the following command may be used:
$ mlpack_hmm_loglik input_file seq.csv input_model_file hmm.bin
See also
 mlpack_hmm_train
 mlpack_hmm_generate
 mlpack_hmm_viterbi
 Hidden Mixture Models on Wikipedia
 mlpack::hmm::HMM class documentation
mlpack_hmm_viterbi
Hidden Markov Model (HMM) Viterbi State Prediction
$ mlpack_hmm_viterbi input_file <string> input_model_file <string>
[output_file <string>]
A utility for computing the most probable hidden state sequence for Hidden Markov Models (HMMs). Given a pretrained 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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Matrix containing observations,  required 
input_model_file (m) 
HMMModel file 
Trained HMM to use.  required 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d index matrix file 
File to save predicted state sequence to. 
Detailed documentation
This utility takes an alreadytrained HMM, specified as input_model_file (m)
, and evaluates the most probable hidden state sequence of a given sequence of observations (specified as ‘input_file (i)
, using the Viterbi algorithm. The computed state sequence may be saved using the output_file (o)
output parameter.
For example, to predict the state sequence of the observations 'obs.csv'
using the HMM 'hmm.bin'
, storing the predicted state sequence to 'states.csv'
, the following command could be used:
$ mlpack_hmm_viterbi input_file obs.csv input_model_file hmm.bin
output_file states.csv
See also
 mlpack_hmm_train
 mlpack_hmm_generate
 mlpack_hmm_loglik
 Hidden Mixture Models on Wikipedia
 mlpack::hmm::HMM class documentation
mlpack_hmm_generate
Hidden Markov Model (HMM) Sequence Generator
$ mlpack_hmm_generate length 0 model_file <string> [seed 0]
[start_state 0] [output_file <string>] [state_file <string>]
A utility to generate random sequences from a pretrained 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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
length (l) 
int 
Length of sequence to generate.  required 
model_file (m) 
HMMModel file 
Trained HMM to generate sequences with.  required 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
start_state (t) 
int 
Starting state of sequence.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
Matrix to save observation sequence to. 
state_file (S) 
2d index matrix file 
Matrix to save hidden state sequence to. 
Detailed documentation
This utility takes an alreadytrained HMM, specified as the model_file (m)
parameter, and generates a random observation sequence and hidden state sequence based on its parameters. The observation sequence may be saved with the output_file (o)
output parameter, and the internal state sequence may be saved with the state_file (S)
output parameter.
The state to start the sequence in may be specified with the start_state (t)
parameter.
For example, to generate a sequence of length 150 from the HMM 'hmm.bin'
and save the observation sequence to 'observations.csv'
and the hidden state sequence to 'states.csv'
, the following command may be used:
$ mlpack_hmm_generate model_file hmm.bin length 150 output_file
observations.csv state_file states.csv
See also
 mlpack_hmm_train
 mlpack_hmm_loglik
 mlpack_hmm_viterbi
 Hidden Mixture Models on Wikipedia
 mlpack::hmm::HMM class documentation
mlpack_hoeffding_tree
Hoeffding trees
$ mlpack_hoeffding_tree [batch_mode] [bins 10] [confidence 0.95]
[info_gain] [input_model_file <string>] [labels_file <string>]
[max_samples 5000] [min_samples 100] [numeric_split_strategy
'binary'] [observations_before_binning 100] [passes 1] [test_file
<string>] [test_labels_file <string>] [training_file <string>]
[output_model_file <string>] [predictions_file <string>]
[probabilities_file <string>]
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 pretrained Hoeffding tree can be used for predicting the classifications of new points. Detailed documentation.
Input options
name  type  description  default 

batch_mode (b) 
flag 
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.  
bins (B) 
int 
If the ‘domingos’ split strategy is used, this specifies the number of bins for each numeric split.  10 
confidence (c) 
double 
Confidence before splitting (between 0 and 1).  0.95 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
info_gain (i) 
flag 
If set, information gain is used instead of Gini impurity for calculating Hoeffding bounds.  
input_model_file (m) 
HoeffdingTreeModel file 
Input trained Hoeffding tree model.  '' 
labels_file (l) 
1d index matrix file 
Labels for training dataset.  '' 
max_samples (n) 
int 
Maximum number of samples before splitting.  5000 
min_samples (I) 
int 
Minimum number of samples before splitting.  100 
numeric_split_strategy (N) 
string 
The splitting strategy to use for numeric features: ‘domingos’ or ‘binary’.  'binary' 
observations_before_binning (o) 
int 
If the ‘domingos’ split strategy is used, this specifies the number of samples observed before binning is performed.  100 
passes (s) 
int 
Number of passes to take over the dataset.  1 
test_file (T) 
2d categorical matrix file 
Testing dataset (may be categorical).  '' 
test_labels_file (L) 
1d index matrix file 
Labels of test data.  '' 
training_file (t) 
2d categorical matrix file 
Training dataset (may be categorical).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
HoeffdingTreeModel file 
Output for trained Hoeffding tree model. 
predictions_file (p) 
1d index matrix file 
Matrix to output label predictions for test data into. 
probabilities_file (P) 
2d matrix file 
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_file (t)
and labels_file (l)
parameters, respectively. Optionally, if labels_file (l)
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 (b)
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_file (M)
output parameter. A model may be loaded from file for further training or testing with the input_model_file (m)
parameter.
Test data may be specified with the test_file (T)
parameter, and if performance statistics are desired for that test set, labels may be specified with the test_labels_file (L)
parameter. Predictions for each test point may be saved with the predictions_file (p)
output parameter, and class probabilities for each prediction may be saved with the probabilities_file (P)
output parameter.
For example, to train a Hoeffding tree with confidence 0.99 with data 'dataset.csv'
, saving the trained tree to 'tree.bin'
, the following command may be used:
$ mlpack_hoeffding_tree training_file dataset.arff confidence 0.99
output_model_file tree.bin
Then, this tree may be used to make predictions on the test set 'test_set.csv'
, saving the predictions into 'predictions.csv'
and the class probabilities into 'class_probs.csv'
with the following command:
$ mlpack_hoeffding_tree input_model_file tree.bin test_file test_set.arff
predictions_file predictions.csv probabilities_file class_probs.csv
See also
 mlpack_decision_tree
 mlpack_random_forest
 Mining HighSpeed Data Streams (pdf)
 mlpack::tree::HoeffdingTree class documentation
mlpack_kernel_pca
Kernel Principal Components Analysis
$ mlpack_kernel_pca [bandwidth 1] [center] [degree 1] input_file
<string> kernel <string> [kernel_scale 1] [new_dimensionality 0]
[nystroem_method] [offset 0] [sampling 'kmeans'] [output_file
<string>]
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 (b) 
double 
Bandwidth, for ‘gaussian’ and ‘laplacian’ kernels.  1 
center (c) 
flag 
If set, the transformed data will be centered about the origin.  
degree (D) 
double 
Degree of polynomial, for ‘polynomial’ kernel.  1 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to perform KPCA on.  required 
kernel (k) 
string 
The kernel to use; see the above documentation for the list of usable kernels.  required 
kernel_scale (S) 
double 
Scale, for ‘hyptan’ kernel.  1 
new_dimensionality (d) 
int 
If not 0, reduce the dimensionality of the output dataset by ignoring the dimensions with the smallest eigenvalues.  0 
nystroem_method (n) 
flag 
If set, the Nystroem method will be used.  
offset (O) 
double 
Offset, for ‘hyptan’ and ‘polynomial’ kernels.  0 
sampling (s) 
string 
Sampling scheme to use for the Nystroem method: ‘kmeans’, ‘random’, ‘ordered’  'kmeans' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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.
For example, the following command will perform KPCA on the dataset 'input.csv'
using the Gaussian kernel, and saving the transformed data to 'transformed.csv'
:
$ mlpack_kernel_pca input_file input.csv kernel gaussian output_file
transformed.csv
The kernels that are supported are listed below:

‘linear’: the standard linear dot product (same as normal PCA): K(x, y) = x^T y

‘gaussian’: a Gaussian kernel; requires bandwidth: K(x, y) = exp(( x  y  ^ 2) / (2 * (bandwidth ^ 2)))

‘polynomial’: polynomial kernel; requires offset and degree: K(x, y) = (x^T y + offset) ^ degree

‘hyptan’: hyperbolic tangent kernel; requires scale and offset: K(x, y) = tanh(scale * (x^T y) + offset)

‘laplacian’: Laplacian kernel; requires bandwidth: K(x, y) = exp(( x  y ) / bandwidth)

‘epanechnikov’: Epanechnikov kernel; requires bandwidth: K(x, y) = max(0, 1   x  y ^2 / bandwidth^2)

‘cosine’: cosine distance: K(x, y) = 1  (x^T y) / ( x  *  y )
The parameters for each of the kernels should be specified with the options bandwidth (b)
, kernel_scale (S)
, offset (O)
, or degree (D)
(or a combination of those parameters).
Optionally, the Nyström method (“Using the Nystroem method to speed up kernel machines”, 2001) can be used to calculate the kernel matrix by specifying the nystroem_method (n)
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 (s)
parameter is used. The sampling scheme for the Nyström method can be chosen from the following list: ‘kmeans’, ‘random’, ‘ordered’.
See also
 Kernel principal component analysis on Wikipedia
 Kernel Principal Component Analysis (pdf)
 mlpack::kpca::KernelPCA class documentation
mlpack_kmeans
KMeans Clustering
$ mlpack_kmeans [algorithm 'naive'] [allow_empty_clusters]
clusters 0 [in_place] [initial_centroids_file <string>]
input_file <string> [kill_empty_clusters] [labels_only]
[max_iterations 1000] [percentage 0.02] [refined_start]
[samplings 100] [seed 0] [centroid_file <string>] [output_file
<string>]
An implementation of several strategies for efficient kmeans clustering. Given a dataset and a value of k, this computes and returns a kmeans clustering on that data. Detailed documentation.
Input options
name  type  description  default 

algorithm (a) 
string 
Algorithm to use for the Lloyd iteration (‘naive’, ‘pellegmoore’, ‘elkan’, ‘hamerly’, ‘dualtree’, or ‘dualtreecovertree’).  'naive' 
allow_empty_clusters (e) 
flag 
Allow empty clusters to be persist.  
clusters (c) 
int 
Number of clusters to find (0 autodetects from initial centroids).  required 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
in_place (P) 
flag 
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.)  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
initial_centroids_file (I) 
2d matrix file 
Start with the specified initial centroids.  '' 
input_file (i) 
2d matrix file 
Input dataset to perform clustering on.  required 
kill_empty_clusters (E) 
flag 
Remove empty clusters when they occur.  
labels_only (l) 
flag 
Only output labels into output file.  
max_iterations (m) 
int 
Maximum number of iterations before kmeans terminates.  1000 
percentage (p) 
double 
Percentage of dataset to use for each refined start sampling (use when –refined_start is specified).  0.02 
refined_start (r) 
flag 
Use the refined initial point strategy by Bradley and Fayyad to choose initial points.  
samplings (S) 
int 
Number of samplings to perform for refined start (use when –refined_start is specified).  100 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

centroid_file (C) 
2d matrix file 
If specified, the centroids of each cluster will be written to the given file. 
output_file (o) 
2d matrix file 
Matrix to store output labels or labeled data to. 
Detailed documentation
This program performs KMeans 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 Bradley and Fayyad approach (“Refining initial points for kmeans clustering”, 1998) can be used to select initial points by specifying the refined_start (r)
parameter. This approach works by taking random samplings of the dataset; to specify the number of samplings, the samplings (S)
parameter is used, and to specify the percentage of the dataset to be used in each sample, the percentage (p)
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 (a)
option. The standard O(kN) approach can be used (‘naive’). Other options include the PellegMoore treebased algorithm (‘pellegmoore’), Elkan’s triangleinequality based algorithm (‘elkan’), Hamerly’s modification to Elkan’s algorithm (‘hamerly’), the dualtree kmeans algorithm (‘dualtree’), and the dualtree kmeans algorithm using the cover tree (‘dualtreecovertree’).
The behavior for when an empty cluster is encountered can be modified with the allow_empty_clusters (e)
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 (E)
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 timeconsuming to calculate; therefore, specifying either of these parameters will often accelerate runtime.
Initial clustering assignments may be specified using the initial_centroids_file (I)
parameter, and the maximum number of iterations may be specified with the max_iterations (m)
parameter.
As an example, to use Hamerly’s algorithm to perform kmeans clustering with k=10 on the dataset 'data.csv'
, saving the centroids to 'centroids.csv'
and the assignments for each point to 'assignments.csv'
, the following command could be used:
$ mlpack_kmeans input_file data.csv clusters 10 output_file
assignments.csv centroid_file centroids.csv
To run kmeans on that same dataset with initial centroids specified in 'initial.csv'
with a maximum of 500 iterations, storing the output centroids in 'final.csv'
the following command may be used:
$ mlpack_kmeans input_file data.csv initial_centroids_file initial.csv
clusters 10 max_iterations 500 centroid_file final.csv
See also
 KMeans tutorial
 mlpack_dbscan
 Using the triangle inequality to accelerate kmeans (pdf)
 Making kmeans even faster (pdf)
 Accelerating exact kmeans algorithms with geometric reasoning (pdf)
 A dualtree algorithm for fast kmeans clustering with large k (pdf)
 mlpack::kmeans::KMeans class documentation
mlpack_lars
LARS
$ mlpack_lars [input_file <string>] [input_model_file <string>]
[lambda1 0] [lambda2 0] [responses_file <string>] [test_file
<string>] [use_cholesky] [output_model_file <string>]
[output_predictions_file <string>]
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 pretrained model to output regression predictions for a test set. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Matrix of covariates (X).  '' 
input_model_file (m) 
LARS file 
Trained LARS model to use.  '' 
lambda1 (l) 
double 
Regularization parameter for l1norm penalty.  0 
lambda2 (L) 
double 
Regularization parameter for l2norm penalty.  0 
responses_file (r) 
2d matrix file 
Matrix of responses/observations (y).  '' 
test_file (t) 
2d matrix file 
Matrix containing points to regress on (test points).  '' 
use_cholesky (c) 
flag 
Use Cholesky decomposition during computation rather than explicitly computing the full Gram matrix.  
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
LARS file 
Output LARS model. 
output_predictions_file (o) 
2d matrix file 
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 stagewise homotopybased algorithm for L1regularized linear regression (LASSO) and L1+L2regularized 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 (l)
= 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_file (i)
and responses_file (r)
parameters must be given. The lambda1 (l)
, lambda2 (L)
, and use_cholesky (c)
parameters control the training options. A trained model can be saved with the output_model_file (M)
. If no training is desired at all, a model can be passed via the input_model_file (m)
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_file (t)
parameter. Predicted responses to the test points can be saved with the output_predictions_file (o)
output parameter.
For example, the following command trains a model on the data 'data.csv'
and responses 'responses.csv'
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.bin'
:
$ mlpack_lars input_file data.csv responses_file responses.csv lambda1
0.4 lambda2 0 output_model_file lasso_model.bin
The following command uses the 'lasso_model.bin'
to provide predicted responses for the data 'test.csv'
and save those responses to 'test_predictions.csv'
:
$ mlpack_lars input_model_file lasso_model.bin test_file test.csv
output_predictions_file test_predictions.csv
See also
 mlpack_linear_regression
 Least angle regression (pdf)
 mlpack::regression::LARS C++ class documentation
mlpack_linear_regression
Simple Linear Regression and Prediction
$ mlpack_linear_regression [input_model_file <string>] [lambda 0]
[test_file <string>] [training_file <string>]
[training_responses_file <string>] [output_model_file <string>]
[output_predictions_file <string>]
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 pretrained model can be used to output regression predictions for a test set. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
LinearRegression file 
Existing LinearRegression model to use.  '' 
lambda (l) 
double 
Tikhonov regularization for ridge regression. If 0, the method reduces to linear regression.  0 
test_file (T) 
2d matrix file 
Matrix containing X’ (test regressors).  '' 
training_file (t) 
2d matrix file 
Matrix containing training set X (regressors).  '' 
training_responses_file (r) 
1d matrix file 
Optional vector containing y (responses). If not given, the responses are assumed to be the last row of the input file.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
LinearRegression file 
Output LinearRegression model. 
output_predictions_file (o) 
1d matrix file 
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_file (t)
) and y (specified either as the last column of the input matrix training_file (t)
or via the training_responses_file (r)
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 (l)
) greater than 0, which will regularize the covariance matrix to make it invertible. The calculated b may be saved with the output_predictions_file (o)
output parameter.
Optionally, the calculated value of b is used to predict the responses for another matrix X’ (specified by the test_file (T)
parameter):
y’ = X’ * b
and the predicted responses y’ may be saved with the output_predictions_file (o)
output parameter. This type of regression is related to leastangle regression, which mlpack implements as the ‘lars’ program.
For example, to run a linear regression on the dataset 'X.csv'
with responses 'y.csv'
, saving the trained model to 'lr_model.bin'
, the following command could be used:
$ mlpack_linear_regression training_file X.csv training_responses_file
y.csv output_model_file lr_model.bin
Then, to use 'lr_model.bin'
to predict responses for a test set 'X_test.csv'
, saving the predictions to 'X_test_responses.csv'
, the following command could be used:
$ mlpack_linear_regression input_model_file lr_model.bin test_file
X_test.csv output_predictions_file X_test_responses.csv
See also
 Linear/ridge regression tutorial
 mlpack_lars
 Linear regression on Wikipedia
 mlpack::regression::LinearRegression C++ class documentation
mlpack_lmnn
Large Margin Nearest Neighbors (LMNN)
$ mlpack_lmnn [batch_size 50] [center] [distance_file <string>]
input_file <string> [k 1] [labels_file <string>] [linear_scan]
[max_iterations 100000] [normalize] [optimizer 'amsgrad']
[passes 50] [print_accuracy] [range 1] [rank 0]
[regularization 0.5] [seed 0] [step_size 0.01] [tolerance 1e07]
[centered_data_file <string>] [output_file <string>]
[transformed_data_file <string>]
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 knearestneighbor performance; this can be useful as a preprocessing step. Detailed documentation.
Input options
name  type  description  default 

batch_size (b) 
int 
Batch size for minibatch SGD.  50 
center (C) 
flag 
Perform meancentering on the dataset. It is useful when the centroid of the data is far from the origin.  
distance_file (d) 
2d matrix file 
Initial distance matrix to be used as starting point  '' 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to run LMNN on.  required 
k (k) 
int 
Number of target neighbors to use for each datapoint.  1 
labels_file (l) 
1d index matrix file 
Labels for input dataset.  '' 
linear_scan (L) 
flag 
Don’t shuffle the order in which data points are visited for SGD or minibatch SGD.  
max_iterations (n) 
int 
Maximum number of iterations for LBFGS (0 indicates no limit).  100000 
normalize (N) 
flag 
Use a normalized starting point for optimization. Itis useful for when points are far apart, or when SGD is returning NaN.  
optimizer (O) 
string 
Optimizer to use; ‘amsgrad’, ‘bbsgd’, ‘sgd’, or ‘lbfgs’.  'amsgrad' 
passes (p) 
int 
Maximum number of full passes over dataset for AMSGrad, BB_SGD and SGD.  50 
print_accuracy (P) 
flag 
Print accuracies on initial and transformed dataset  
range (R) 
int 
Number of iterations after which impostors needs to be recalculated  1 
rank (A) 
int 
Rank of distance matrix to be optimized.  0 
regularization (r) 
double 
Regularization for LMNN objective function  0.5 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
step_size (a) 
double 
Step size for AMSGrad, BB_SGD and SGD (alpha).  0.01 
tolerance (t) 
double 
Maximum tolerance for termination of AMSGrad, BB_SGD, SGD or LBFGS.  1e07 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

centered_data_file (c) 
2d matrix file 
Output matrix for meancentered dataset. 
output_file (o) 
2d matrix file 
Output matrix for learned distance matrix. 
transformed_data_file (D) 
2d matrix file 
Output matrix for transformed dataset. 
Detailed documentation
This program implements Large Margin Nearest Neighbors, a distance learning technique. The method seeks to improve knearestneighbor 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_file (i)
), or alternatively as a separate matrix (specified with labels_file (l)
). Additionally, a starting point for optimization (specified with distance_file (d)
can be given, having (r x d) dimensionality. Here r should satisfy 1 <= r <= d, Consequently a LowRank matrix will be optimized. Alternatively, LowRank distance can be learned by specifying the rank (A)
parameter (A LowRank 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 (k)
), A regularization parameter can also be passed, It acts as a trade of between the pulling and pushing terms (specified with regularization (r)
), In addition, this implementation of LMNN includes a parameter to decide the interval after which impostors must be recalculated (specified with range (R)
).
Output can either be the learned distance matrix (specified with output_file (o)
), or the transformed dataset (specified with transformed_data_file (D)
), or both. Additionally meancentered dataset (specified with centered_data_file (c)
) can be accessed given meancentering (specified with center (C)
) is performed on the dataset. Accuracy on initial dataset and final transformed dataset can be printed by specifying the print_accuracy (P)
parameter.
This implementation of LMNN uses AdaGrad, BigBatch_SGD, stochastic gradient descent, minibatch stochastic gradient descent, or the L_BFGS optimizer.
AdaGrad, specified by the value ‘adagrad’ for the parameter optimizer (O)
, uses maximum of past squared gradients. It primarily on six parameters: the step size (specified with step_size (a)
), the batch size (specified with batch_size (b)
), the maximum number of passes (specified with passes (p)
). Inaddition, a normalized starting point can be used by specifying the normalize (N)
parameter.
BigBatch_SGD, specified by the value ‘bbsgd’ for the parameter optimizer (O)
, depends primarily on four parameters: the step size (specified with step_size (a)
), the batch size (specified with batch_size (b)
), the maximum number of passes (specified with passes (p)
). In addition, a normalized starting point can be used by specifying the normalize (N)
parameter.
Stochastic gradient descent, specified by the value ‘sgd’ for the parameter optimizer (O)
, depends primarily on three parameters: the step size (specified with step_size (a)
), the batch size (specified with batch_size (b)
), and the maximum number of passes (specified with passes (p)
). In addition, a normalized starting point can be used by specifying the normalize (N)
parameter. Furthermore, meancentering can be performed on the dataset by specifying the center (C)
parameter.
The LBFGS optimizer, specified by the value ‘lbfgs’ for the parameter optimizer (O)
, uses a backtracking line search algorithm to minimize a function. The following parameters are used by LBFGS: max_iterations (n)
, tolerance (t)
(the optimization is terminated when the gradient norm is below this value). For more details on the LBFGS optimizer, consult either the mlpack LBFGS documentation (in lbfgs.hpp) or the vast set of published literature on LBFGS. In addition, a normalized starting point can be used by specifying the normalize (N)
parameter.
By default, the AMSGrad optimizer is used.
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:
$ mlpack_mlpack_lmnn input_file iris.csv labels_file iris_labels.csv k 3
optimizer bbsgd output_file output.csv
An another program call making use of range & regularization parameter with dataset having labels as last column can be made as:
$ mlpack_mlpack_lmnn input_file letter_recognition.csv k 5 range 10
regularization 0.4 output_file output.csv
See also
 mlpack_nca
 Large margin nearest neighbor on Wikipedia
 Distance metric learning for large margin nearest neighbor classification (pdf)
 mlpack::lmnn::LMNN C++ class documentation
mlpack_local_coordinate_coding
Local Coordinate Coding
$ mlpack_local_coordinate_coding [atoms 0] [initial_dictionary_file
<string>] [input_model_file <string>] [lambda 0] [max_iterations
0] [normalize] [seed 0] [test_file <string>] [tolerance 0.01]
[training_file <string>] [codes_file <string>] [dictionary_file
<string>] [output_model_file <string>]
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 (k) 
int 
Number of atoms in the dictionary.  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
initial_dictionary_file (i) 
2d matrix file 
Optional initial dictionary.  '' 
input_model_file (m) 
LocalCoordinateCoding file 
Input LCC model.  '' 
lambda (l) 
double 
Weighted l1norm regularization parameter.  0 
max_iterations (n) 
int 
Maximum number of iterations for LCC (0 indicates no limit).  0 
normalize (N) 
flag 
If set, the input data matrix will be normalized before coding.  
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
test_file (T) 
2d matrix file 
Test points to encode.  '' 
tolerance (o) 
double 
Tolerance for objective function.  0.01 
training_file (t) 
2d matrix file 
Matrix of training data (X).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

codes_file (c) 
2d matrix file 
Output codes matrix. 
dictionary_file (d) 
2d matrix file 
Output dictionary matrix. 
output_model_file (M) 
LocalCoordinateCoding file 
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 l1norm 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_file (i)
parameter. The l1norm regularization parameter is specified with the lambda (l)
parameter. For example, to run LCC on the dataset 'data.csv'
using 200 atoms and an l1regularization parameter of 0.1, saving the dictionary dictionary_file (d)
and the codes into codes_file (c)
, use
$ mlpack_local_coordinate_coding training_file data.csv atoms 200 lambda
0.1 dictionary_file dict.csv codes_file codes.csv
The maximum number of iterations may be specified with the max_iterations (n)
parameter. Optionally, the input data matrix X can be normalized before coding with the normalize (N)
parameter.
An LCC model may be saved using the output_model_file (M)
output parameter. Then, to encode new points from the dataset 'points.csv'
with the previously saved model 'lcc_model.bin'
, saving the new codes to 'new_codes.csv'
, the following command can be used:
$ mlpack_local_coordinate_coding input_model_file lcc_model.bin test_file
points.csv codes_file new_codes.csv
See also
 mlpack_sparse_coding
 Nonlinear learning using local coordinate coding (pdf)
 mlpack::lcc::LocalCoordinateCoding C++ class documentation
mlpack_logistic_regression
L2regularized Logistic Regression and Prediction
$ mlpack_logistic_regression [batch_size 64] [decision_boundary 0.5]
[input_model_file <string>] [labels_file <string>] [lambda 0]
[max_iterations 10000] [optimizer 'lbfgs'] [step_size 0.01]
[test_file <string>] [tolerance 1e10] [training_file <string>]
[output_file <string>] [output_model_file <string>]
[output_probabilities_file <string>] [predictions_file <string>]
[probabilities_file <string>]
An implementation of L2regularized logistic regression for twoclass classification. Given labeled data, a model can be trained and saved for future use; or, a pretrained model can be used to classify new points. Detailed documentation.
Input options
name  type  description  default 

batch_size (b) 
int 
Batch size for SGD.  64 
decision_boundary (d) 
double 
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 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
LogisticRegression<> file 
Existing model (parameters).  '' 
labels_file (l) 
1d index matrix file 
A matrix containing labels (0 or 1) for the points in the training set (y).  '' 
lambda (L) 
double 
L2regularization parameter for training.  0 
max_iterations (n) 
int 
Maximum iterations for optimizer (0 indicates no limit).  10000 
optimizer (O) 
string 
Optimizer to use for training (‘lbfgs’ or ‘sgd’).  'lbfgs' 
step_size (s) 
double 
Step size for SGD optimizer.  0.01 
test_file (T) 
2d matrix file 
Matrix containing test dataset.  '' 
tolerance (e) 
double 
Convergence tolerance for optimizer.  1e10 
training_file (t) 
2d matrix file 
A matrix containing the training set (the matrix of predictors, X).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
1d index matrix file 
If test data is specified, this matrix is where the predictions for the test set will be saved. 
output_model_file (M) 
LogisticRegression<> file 
Output for trained logistic regression model. 
output_probabilities_file (x) 
2d matrix file 
If test data is specified, this matrix is where the class probabilities for the test set will be saved. 
predictions_file (P) 
1d index matrix file 
If test data is specified, this matrix is where the predictions for the test set will be saved. 
probabilities_file (p) 
2d matrix file 
If test data is specified, this matrix is where the class probabilities for the test set will be saved. 
Detailed documentation
An implementation of L2regularized logistic regression using either the LBFGS optimizer or SGD (stochastic gradient descent). This solves the regression problem
y = (1 / 1 + e^(X * b))
where y takes values 0 or 1.
This program allows loading a logistic regression model (via the input_model_file (m)
parameter) or training a logistic regression model given training data (specified with the training_file (t)
parameter), or both those things at once. In addition, this program allows classification on a test dataset (specified with the test_file (T)
parameter) and the classification results may be saved with the predictions_file (P)
output parameter. The trained logistic regression model may be saved using the output_model_file (M)
output parameter.
The training data, if specified, may have class labels as its last dimension. Alternately, the labels_file (l)
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 (L)
option, and the optimizer used to train the model can be specified with the optimizer (O)
parameter. Available options are ‘sgd’ (stochastic gradient descent) and ‘lbfgs’ (the LBFGS optimizer). There are also various parameters for the optimizer; the max_iterations (n)
parameter specifies the maximum number of allowed iterations, and the tolerance (e)
parameter specifies the tolerance for convergence. For the SGD optimizer, the step_size (s)
parameter controls the step size taken at each iteration by the optimizer. The batch size for SGD is controlled with the batch_size (b)
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 (n)
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_file (T)
is specified. The test_file (T)
parameter can be specified without the training_file (t)
parameter, so long as an existing logistic regression model is given with the input_model_file (m)
parameter. The output predictions from the logistic regression model may be saved with the predictions_file (P)
parameter.
Note : The following parameters are deprecated and will be removed in mlpack 4: output_file (o)
, output_probabilities_file (x)
Use predictions_file (P)
instead of output_file (o)
Use probabilities_file (p)
instead of output_probabilities_file (x)
This implementation of logistic regression does not support the general multiclass case but instead only the twoclass case. Any labels must be either 0 or 1. For more classes, see the softmax_regression program.
As an example, to train a logistic regression model on the data ‘'data.csv'
’ with labels ‘'labels.csv'
’ with L2 regularization of 0.1, saving the model to ‘'lr_model.bin'
’, the following command may be used:
$ mlpack_logistic_regression training_file data.csv labels_file labels.csv
lambda 0.1 output_model_file lr_model.bin
Then, to use that model to predict classes for the dataset ‘'test.csv'
’, storing the output predictions in ‘'predictions.csv'
’, the following command may be used:
$ mlpack_logistic_regression input_model_file lr_model.bin test_file
test.csv output_file predictions.csv
See also
 mlpack_softmax_regression
 mlpack_random_forest
 Logistic regression on Wikipedia
 mlpack::regression::LogisticRegression C++ class documentation
mlpack_lsh
KApproximateNearestNeighbor Search with LSH
$ mlpack_lsh [bucket_size 500] [hash_width 0] [input_model_file
<string>] [k 0] [num_probes 0] [projections 10] [query_file
<string>] [reference_file <string>] [second_hash_size 99901] [seed
0] [tables 30] [true_neighbors_file <string>] [distances_file
<string>] [neighbors_file <string>] [output_model_file <string>]
An implementation of approximate knearestneighbor search with localitysensitive 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 (B) 
int 
The size of a bucket in the second level hash.  500 
hash_width (H) 
double 
The hash width for the firstlevel hashing in the LSH preprocessing. By default, the LSH class automatically estimates a hash width for its use.  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
LSHSearch<> file 
Input LSH model.  '' 
k (k) 
int 
Number of nearest neighbors to find.  0 
num_probes (T) 
int 
Number of additional probes for multiprobe LSH; if 0, traditional LSH is used.  0 
projections (K) 
int 
The number of hash functions for each table  10 
query_file (q) 
2d matrix file 
Matrix containing query points (optional).  '' 
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
second_hash_size (S) 
int 
The size of the second level hash table.  99901 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
tables (L) 
int 
The number of hash tables to be used.  30 
true_neighbors_file (t) 
2d index matrix file 
Matrix of true neighbors to compute recall with (the recall is printed when v is specified).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
2d matrix file 
Matrix to output distances into. 
neighbors_file (n) 
2d index matrix file 
Matrix to output neighbors into. 
output_model_file (M) 
LSHSearch<> file 
Output for trained LSH model. 
Detailed documentation
This program will calculate the k approximatenearestneighbors of a set of points using localitysensitive 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.
For example, the following will return 5 neighbors from the data for each point in 'input.csv'
and store the distances in 'distances.csv'
and the neighbors in 'neighbors.csv'
:
$ mlpack_lsh k 5 reference_file input.csv distances_file distances.csv
neighbors_file neighbors.csv
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 approximatenearestneighbors search, results may be different from run to run. Thus, the seed (s)
parameter can be specified to set the random seed.
This program also has many other parameters to control its functionality; see the parameterspecific documentation for more information.
See also
 mlpack_knn
 mlpack_krann
 Localitysensitive hashing on Wikipedia
 Localitysensitive hashing scheme based on pstable distributions (pdf)
 mlpack::neighbor::LSHSearch C++ class documentation
mlpack_mean_shift
Mean Shift Clustering
$ mlpack_mean_shift [force_convergence] [in_place] input_file
<string> [labels_only] [max_iterations 1000] [radius 0]
[centroid_file <string>] [output_file <string>]
A fast implementation of meanshift clustering using dualtree 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 

force_convergence (f) 
flag 
If specified, the mean shift algorithm will continue running regardless of max_iterations until the clusters converge.  
help (h) 
flag 
Default help info. Only exists in CLI binding.  
in_place (P) 
flag 
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.)  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to perform clustering on.  required 
labels_only (l) 
flag 
If specified, only the output labels will be written to the file specified by –output_file.  
max_iterations (m) 
int 
Maximum number of iterations before mean shift terminates.  1000 
radius (r) 
double 
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 (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

centroid_file (C) 
2d matrix file 
If specified, the centroids of each cluster will be written to the given matrix. 
output_file (o) 
2d matrix file 
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_file (i)
parameter, and the radius used for search can be specified with the radius (r)
parameter. The maximum number of iterations before algorithm termination is controlled with the max_iterations (m)
parameter.
The output labels may be saved with the output_file (o)
output parameter and the centroids of each cluster may be saved with the centroid_file (C)
output parameter.
For example, to run mean shift clustering on the dataset 'data.csv'
and store the centroids to 'centroids.csv'
, the following command may be used:
$ mlpack_mean_shift input_file data.csv centroid_file centroids.csv
See also
 mlpack_kmeans
 mlpack_dbscan
 Mean shift on Wikipedia
 Mean Shift, Mode Seeking, and Clustering (pdf)
 mlpack::mean_shift::MeanShift C++ class documentation
mlpack_nbc
Parametric Naive Bayes Classifier
$ mlpack_nbc [incremental_variance] [input_model_file <string>]
[labels_file <string>] [test_file <string>] [training_file
<string>] [output_file <string>] [output_model_file <string>]
[output_probs_file <string>] [predictions_file <string>]
[probabilities_file <string>]
An implementation of the Naive Bayes Classifier, used for classification. Given labeled data, an NBC model can be trained and saved, or, a pretrained model can be used for classification. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
incremental_variance (I) 
flag 
The variance of each class will be calculated incrementally.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
NBCModel file 
Input Naive Bayes model.  '' 
labels_file (l) 
1d index matrix file 
A file containing labels for the training set.  '' 
test_file (T) 
2d matrix file 
A matrix containing the test set.  '' 
training_file (t) 
2d matrix file 
A matrix containing the training set.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
1d index matrix file 
The matrix in which the predicted labels for the test set will be written (deprecated). 
output_model_file (M) 
NBCModel file 
File to save trained Naive Bayes model to. 
output_probs_file 
2d matrix file 
The matrix in which the predicted probability of labels for the test set will be written (deprecated). 
predictions_file (a) 
1d index matrix file 
The matrix in which the predicted labels for the test set will be written. 
probabilities_file (p) 
2d matrix file 
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_file (t)
parameter. Labels may be either the last row of the training set, or alternately the labels_file (l)
parameter may be specified to pass a separate matrix of labels.
If training is not desired, a preexisting model may be loaded with the input_model_file (m)
parameter.
The incremental_variance (I)
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_file (T)
parameter, and the classifications may be saved with the predictions_file (a)
predictions parameter. If saving the trained model is desired, this may be done with the output_model_file (M)
output parameter.
Note: the output_file (o)
and output_probs_file
parameters are deprecated and will be removed in mlpack 4.0.0. Use predictions_file (a)
and probabilities_file (p)
instead.
For example, to train a Naive Bayes classifier on the dataset 'data.csv'
with labels 'labels.csv'
and save the model to 'nbc_model.bin'
, the following command may be used:
$ mlpack_nbc training_file data.csv labels_file labels.csv
output_model_file nbc_model.bin
Then, to use 'nbc_model.bin'
to predict the classes of the dataset 'test_set.csv'
and save the predicted classes to 'predictions.csv'
, the following command may be used:
$ mlpack_nbc input_model_file nbc_model.bin test_file test_set.csv
output_file predictions.csv
See also
 mlpack_softmax_regression
 mlpack_random_forest
 Naive Bayes classifier on Wikipedia
 mlpack::naive_bayes::NaiveBayesClassifier C++ class documentation
mlpack_nca
Neighborhood Components Analysis (NCA)
$ mlpack_nca [armijo_constant 0.0001] [batch_size 50] input_file
<string> [labels_file <string>] [linear_scan] [max_iterations
500000] [max_line_search_trials 50] [max_step 1e+20] [min_step
1e20] [normalize] [num_basis 5] [optimizer 'sgd'] [seed 0]
[step_size 0.01] [tolerance 1e07] [wolfe 0.9] [output_file
<string>]
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 knearestneighbor classification, and returns the learned distance metric. Detailed documentation.
Input options
name  type  description  default 

armijo_constant (A) 
double 
Armijo constant for LBFGS.  0.0001 
batch_size (b) 
int 
Batch size for minibatch SGD.  50 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to run NCA on.  required 
labels_file (l) 
1d index matrix file 
Labels for input dataset.  '' 
linear_scan (L) 
flag 
Don’t shuffle the order in which data points are visited for SGD or minibatch SGD.  
max_iterations (n) 
int 
Maximum number of iterations for SGD or LBFGS (0 indicates no limit).  500000 
max_line_search_trials (T) 
int 
Maximum number of line search trials for LBFGS.  50 
max_step (M) 
double 
Maximum step of line search for LBFGS.  1e+20 
min_step (m) 
double 
Minimum step of line search for LBFGS.  1e20 
normalize (N) 
flag 
Use a normalized starting point for optimization. This is useful for when points are far apart, or when SGD is returning NaN.  
num_basis (B) 
int 
Number of memory points to be stored for LBFGS.  5 
optimizer (O) 
string 
Optimizer to use; ‘sgd’ or ‘lbfgs’.  'sgd' 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
step_size (a) 
double 
Step size for stochastic gradient descent (alpha).  0.01 
tolerance (t) 
double 
Maximum tolerance for termination of SGD or LBFGS.  1e07 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding.  
wolfe (w) 
double 
Wolfe condition parameter for LBFGS.  0.9 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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 knearestneighbor 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_file (i)
), or alternatively as a separate matrix (specified with labels_file (l)
).
This implementation of NCA uses stochastic gradient descent, minibatch 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 (O)
, depends primarily on three parameters: the step size (specified with step_size (a)
), the batch size (specified with batch_size (b)
), and the maximum number of iterations (specified with max_iterations (n)
). In addition, a normalized starting point can be used by specifying the normalize (N)
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 zerovalued 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 (t)
) 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 (n)
parameter equal to the number of points in the dataset.
The LBFGS optimizer, specified by the value ‘lbfgs’ for the parameter optimizer (O)
, uses a backtracking line search algorithm to minimize a function. The following parameters are used by LBFGS: num_basis (B)
(specifies the number of memory points used by LBFGS), max_iterations (n)
, armijo_constant (A)
, wolfe (w)
, tolerance (t)
(the optimization is terminated when the gradient norm is below this value), max_line_search_trials (T)
, min_step (m)
, and max_step (M)
(which both refer to the line search routine). For more details on the LBFGS optimizer, consult either the mlpack LBFGS documentation (in lbfgs.hpp) or the vast set of published literature on LBFGS.
By default, the SGD optimizer is used.
See also
 mlpack_lmnn
 Neighbourhood components analysis on Wikipedia
 Neighbourhood components analysis (pdf)
 mlpack::nca::NCA C++ class documentation
mlpack_knn
kNearestNeighbors Search
$ mlpack_knn [algorithm 'dual_tree'] [epsilon 0] [input_model_file
<string>] [k 0] [leaf_size 20] [query_file <string>]
[random_basis] [reference_file <string>] [rho 0.7] [seed 0]
[tau 0] [tree_type 'kd'] [true_distances_file <string>]
[true_neighbors_file <string>] [distances_file <string>]
[neighbors_file <string>] [output_model_file <string>]
An implementation of knearestneighbor search using singletree and dualtree 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 (a) 
string 
Type of neighbor search: ‘naive’, ‘single_tree’, ‘dual_tree’, ‘greedy’.  'dual_tree' 
epsilon (e) 
double 
If specified, will do approximate nearest neighbor search with given relative error.  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
KNNModel file 
Pretrained kNN model.  '' 
k (k) 
int 
Number of nearest neighbors to find.  0 
leaf_size (l) 
int 
Leaf size for tree building (used for kdtrees, 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_file (q) 
2d matrix file 
Matrix containing query points (optional).  '' 
random_basis (R) 
flag 
Before treebuilding, project the data onto a random orthogonal basis.  
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
rho (b) 
double 
Balance threshold (only valid for spill trees).  0.7 
seed (s) 
int 
Random seed (if 0, std::time(NULL) is used).  0 
tau (u) 
double 
Overlapping size (only valid for spill trees).  0 
tree_type (t) 
string 
Type of tree to use: ‘kd’, ‘vp’, ‘rp’, ‘maxrp’, ‘ub’, ‘cover’, ‘r’, ‘rstar’, ‘x’, ‘ball’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘spill’, ‘oct’.  'kd' 
true_distances_file (D) 
2d matrix file 
Matrix of true distances to compute the effective error (average relative error) (it is printed when v is specified).  '' 
true_neighbors_file (T) 
2d index matrix file 
Matrix of true neighbors to compute the recall (it is printed when v is specified).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
2d matrix file 
Matrix to output distances into. 
neighbors_file (n) 
2d index matrix file 
Matrix to output neighbors into. 
output_model_file (M) 
KNNModel file 
If specified, the kNN model will be output here. 
Detailed documentation
This program will calculate the knearestneighbors of a set of points using kdtrees 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.
For example, the following command will calculate the 5 nearest neighbors of each point in 'input.csv'
and store the distances in 'distances.csv'
and the neighbors in 'neighbors.csv'
:
$ mlpack_knn k 5 reference_file input.csv neighbors_file neighbors.csv
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
 mlpack_lsh
 mlpack_krann
 mlpack_kfn
 NeighborSearch tutorial (knearestneighbors)
 Treeindependent dualtree algorithms (pdf)
 mlpack::neighbor::NeighborSearch C++ class documentation
mlpack_kfn
kFurthestNeighbors Search
$ mlpack_kfn [algorithm 'dual_tree'] [epsilon 0] [input_model_file
<string>] [k 0] [leaf_size 20] [percentage 1] [query_file
<string>] [random_basis] [reference_file <string>] [seed 0]
[tree_type 'kd'] [true_distances_file <string>]
[true_neighbors_file <string>] [distances_file <string>]
[neighbors_file <string>] [output_model_file <string>]
An implementation of kfurthestneighbor search using singletree and dualtree 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 (a) 
string 
Type of neighbor search: ‘naive’, ‘single_tree’, ‘dual_tree’, ‘greedy’.  'dual_tree' 
epsilon (e) 
double 
If specified, will do approximate furthest neighbor search with given relative error. Must be in the range [0,1).  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
KFNModel file 
Pretrained kFN model.  '' 
k (k) 
int 
Number of furthest neighbors to find.  0 
leaf_size (l) 
int 
Leaf size for tree building (used for kdtrees, vp trees, random projection trees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, and octrees).  20 
percentage (p) 
double 
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_file (q) 
2d matrix file 
Matrix containing query points (optional).  '' 
random_basis (R) 
flag 
Before treebuilding, project the data onto a random orthogonal basis.  
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
seed (s) 
int 
Random seed (if 0, std::time(NULL) is used).  0 
tree_type (t) 
string 
Type of tree to use: ‘kd’, ‘vp’, ‘rp’, ‘maxrp’, ‘ub’, ‘cover’, ‘r’, ‘rstar’, ‘x’, ‘ball’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘oct’.  'kd' 
true_distances_file (D) 
2d matrix file 
Matrix of true distances to compute the effective error (average relative error) (it is printed when v is specified).  '' 
true_neighbors_file (T) 
2d index matrix file 
Matrix of true neighbors to compute the recall (it is printed when v is specified).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
2d matrix file 
Matrix to output distances into. 
neighbors_file (n) 
2d index matrix file 
Matrix to output neighbors into. 
output_model_file (M) 
KFNModel file 
If specified, the kFN model will be output here. 
Detailed documentation
This program will calculate the kfurthestneighbors 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.
For example, the following will calculate the 5 furthest neighbors of eachpoint in 'input.csv'
and store the distances in 'distances.csv'
and the neighbors in 'neighbors.csv'
:
$ mlpack_kfn k 5 reference_file input.csv distances_file distances.csv
neighbors_file neighbors.csv
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
 mlpack_approx_kfn
 mlpack_knn
 Treeindependent dualtree algorithms (pdf)
 mlpack::neighbor::NeighborSearch C++ class documentation
mlpack_nmf
Nonnegative Matrix Factorization
$ mlpack_nmf [initial_h_file <string>] [initial_w_file <string>]
input_file <string> [max_iterations 10000] [min_residue 1e05]
rank 0 [seed 0] [update_rules 'multdist'] [h_file <string>]
[w_file <string>]
An implementation of nonnegative matrix factorization. This can be used to decompose an input dataset into two lowrank nonnegative components. Detailed documentation.
Input options
name  type  description  default  

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 

initial_h_file (q) 
2d matrix file 
Initial H matrix.  '' 

initial_w_file (p) 
2d matrix file 
Initial W matrix.  '' 

input_file (i) 
2d matrix file 
Input dataset to perform NMF on.  required  
max_iterations (m) 
int 
Number of iterations before NMF terminates (0 runs until convergence.  10000 

min_residue (e) 
double 
The minimum root mean square residue allowed for each iteration, below which the program terminates.  1e05 

rank (r) 
int 
Rank of the factorization.  required  
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 

update_rules (u) 
string 
Update rules for each iteration; ( multdist  multdiv  als ).  'multdist' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

h_file (H) 
2d matrix file 
Matrix to save the calculated H to. 
w_file (W) 
2d matrix file 
Matrix to save the calculated W to. 
Detailed documentation
This program performs nonnegative 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 nonnegative. 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 (r)
parameter).
Optionally, the desired update rules for each NMF iteration can be chosen from the following list:
 multdist: multiplicative distancebased update rules (Lee and Seung 1999)
 multdiv: multiplicative divergencebased update rules (Lee and Seung 1999)
 als: alternating least squares update rules (Paatero and Tapper 1994)
The maximum number of iterations is specified with max_iterations (m)
, and the minimum residue required for algorithm termination is specified with the min_residue (e)
parameter.
For example, to run NMF on the input matrix 'V.csv'
using the ‘multdist’ update rules with a rank10 decomposition and storing the decomposed matrices into 'W.csv'
and 'H.csv'
, the following command could be used:
$ mlpack_nmf input_file V.csv w_file W.csv h_file H.csv rank 10
update_rules multdist
See also
 mlpack_cf
 Alternating matrix factorization tutorial
 Nonnegative matrix factorization on Wikipedia
 Algorithms for nonnegative matrix factorization (pdf)
 mlpack::amf::AMF C++ class documentation
mlpack_pca
Principal Components Analysis
$ mlpack_pca [decomposition_method 'exact'] input_file <string>
[new_dimensionality 0] [scale] [var_to_retain 0] [output_file
<string>]
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 

decomposition_method (c) 
string 
Method used for the principal components analysis: ‘exact’, ‘randomized’, ‘randomizedblockkrylov’, ‘quic’.  'exact' 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset to perform PCA on.  required 
new_dimensionality (d) 
int 
Desired dimensionality of output dataset. If 0, no dimensionality reduction is performed.  0 
scale (s) 
flag 
If set, the data will be scaled before running PCA, such that the variance of each feature is 1.  
var_to_retain (r) 
double 
Amount of variance to retain; should be between 0 and 1. If 1, all variance is retained. Overrides d.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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_file (i)
parameter to specify the dataset to perform PCA on. A desired new dimensionality can be specified with the new_dimensionality (d)
parameter, or the desired variance to retain can be specified with the var_to_retain (r)
parameter. If desired, the dataset can be scaled before running PCA with the scale (s)
parameter.
Multiple different decomposition techniques can be used. The method to use can be specified with the decomposition_method (c)
parameter, and it may take the values ‘exact’, ‘randomized’, or ‘quic’.
For example, to reduce the dimensionality of the matrix 'data.csv'
to 5 dimensions using randomized SVD for the decomposition, storing the output matrix to 'data_mod.csv'
, the following command can be used:
$ mlpack_pca input_file data.csv new_dimensionality 5
decomposition_method randomized output_file data_mod.csv
See also
mlpack_perceptron
Perceptron
$ mlpack_perceptron [input_model_file <string>] [labels_file
<string>] [max_iterations 1000] [test_file <string>]
[training_file <string>] [output_file <string>] [output_model_file
<string>]
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 pretrained perceptron can be used for classification on new points. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
PerceptronModel file 
Input perceptron model.  '' 
labels_file (l) 
1d index matrix file 
A matrix containing labels for the training set.  '' 
max_iterations (n) 
int 
The maximum number of iterations the perceptron is to be run  1000 
test_file (T) 
2d matrix file 
A matrix containing the test set.  '' 
training_file (t) 
2d matrix file 
A matrix containing the training set.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
1d index matrix file 
The matrix in which the predicted labels for the test set will be written. 
output_model_file (M) 
PerceptronModel file 
Output for trained perceptron model. 
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 (n)
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_file (m)
parameter) or training a perceptron given training data (via the training_file (t)
parameter), or both those things at once. In addition, this program allows classification on a test dataset (via the test_file (T)
parameter) and the classification results on the test set may be saved with the output_file (o)
output parameter. The perceptron model may be saved with the output_model_file (M)
output parameter.
The training data given with the training_file (t)
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_file (l)
parameter may be used to specify a separate matrix of labels.
All these options make it easy to train a perceptron, and then reuse that perceptron for later classification. The invocation below trains a perceptron on 'training_data.csv'
with labels 'training_labels.csv'
, and saves the model to 'perceptron_model.bin'
.
$ mlpack_perceptron training_file training_data.csv labels_file
training_labels.csv output_model_file perceptron_model.bin
Then, this model can be reused for classification on the test data 'test_data.csv'
. The example below does precisely that, saving the predicted classes to 'predictions.csv'
.
$ mlpack_perceptron input_model_file perceptron_model.bin test_file
test_data.csv output_file predictions.csv
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_file (m)
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 retrain with a 4class dataset. Similarly, attempting classification on a 3dimensional dataset with a perceptron that has been trained on 8 dimensions will cause an error.
See also
mlpack_preprocess_split
Split Data
$ mlpack_preprocess_split input_file <string> [input_labels_file
<string>] [seed 0] [test_ratio 0.2] [test_file <string>]
[test_labels_file <string>] [training_file <string>]
[training_labels_file <string>]
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 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Matrix containing data.  required 
input_labels_file (I) 
2d index matrix file 
Matrix containing labels.  '' 
seed (s) 
int 
Random seed (0 for std::time(NULL)).  0 
test_ratio (r) 
double 
Ratio of test set; if not set,the ratio defaults to 0.2  0.2 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

test_file (T) 
2d matrix file 
Matrix to save test data to. 
test_labels_file (L) 
2d index matrix file 
Matrix to save test labels to. 
training_file (t) 
2d matrix file 
Matrix to save training data to. 
training_labels_file (l) 
2d index matrix file 
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 (r)
parameter; the default is 0.2 (20%).
The output training and test matrices may be saved with the training_file (t)
and test_file (T)
output parameters.
Optionally, labels can be also be split along with the data by specifying the input_labels_file (I)
parameter. Splitting labels works the same way as splitting the data. The output training and test labels may be saved with the training_labels_file (l)
and test_labels_file (L)
output parameters, respectively.
So, a simple example where we want to split the dataset 'X.csv'
into 'X_train.csv'
and 'X_test.csv'
with 60% of the data in the training set and 40% of the dataset in the test set, we could run
$ mlpack_preprocess_split input_file X.csv training_file X_train.csv
test_file X_test.csv test_ratio 0.4
If we had a dataset 'X.csv'
and associated labels 'y.csv'
, and we wanted to split these into 'X_train.csv'
, 'y_train.csv'
, 'X_test.csv'
, and 'y_test.csv'
, with 30% of the data in the test set, we could run
$ mlpack_preprocess_split input_file X.csv input_labels_file y.csv
test_ratio 0.3 training_file X_train.csv training_labels_file
y_train.csv test_file X_test.csv test_labels_file y_test.csv
See also
mlpack_preprocess_binarize
Binarize Data
$ mlpack_preprocess_binarize [dimension 0] input_file <string>
[threshold 0] [output_file <string>]
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 

dimension (d) 
int 
Dimension to apply the binarization. If not set, the program will binarize every dimension by default.  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input data matrix.  required 
threshold (t) 
double 
Threshold to be applied for binarization. If not set, the threshold defaults to 0.0.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
2d matrix file 
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 (d)
parameter; if left unspecified, every dimension will be binarized. The threshold for binarization can also be specified with the threshold (t)
parameter; the default threshold is 0.0.
The binarized matrix may be saved with the output_file (o)
output parameter.
For example, if we want to set all variables greater than 5 in the dataset 'X.csv'
to 1 and variables less than or equal to 5.0 to 0, and save the result to 'Y.csv'
, we could run
$ mlpack_preprocess_binarize input_file X.csv threshold 5 output_file
Y.csv
But if we want to apply this to only the first (0th) dimension of 'X.csv'
, we could instead run
$ mlpack_preprocess_binarize input_file X.csv threshold 5 dimension 0
output_file Y.csv
See also
mlpack_preprocess_describe
Descriptive Statistics
$ mlpack_preprocess_describe [dimension 0] input_file <string>
[population] [precision 4] [row_major] [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 

dimension (d) 
int 
Dimension of the data. Use this to specify a dimension  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Matrix containing data,  required 
population (P) 
flag 
If specified, the program will calculate statistics assuming the dataset is the population. By default, the program will assume the dataset as a sample.  
precision (p) 
int 
Precision of the output statistics.  4 
row_major (r) 
flag 
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.)  
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding.  
width (w) 
int 
Width of the output table.  8 
Output options
 name  type  description  ——————————————
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 (w)
and precision (p)
parameters. A user can also select a specific dimension to analyze if there are too many dimensions. The population (P)
parameter can be specified when the dataset should be considered as a population. Otherwise, the dataset will be considered as a sample.
So, a simple example where we want to print out statistical facts about the dataset 'X.csv'
using the default settings, we could run
$ mlpack_preprocess_describe input_file X.csv verbose
If we want to customize the width to 10 and precision to 5 and consider the dataset as a population, we could run
$ mlpack_preprocess_describe input_file X.csv width 10 precision 5
verbose
See also
mlpack_preprocess_imputer
Impute Data
$ mlpack_preprocess_imputer [custom_value 0] [dimension 0]
input_file <string> missing_value <string> strategy <string>
[output_file <string>]
This utility provides several imputation strategies for missing data. Given a dataset with missing values, this can impute according to several strategies, including userdefined values. Detailed documentation.
Input options
name  type  description  default 

custom_value (c) 
double 
Userdefined custom imputation value.  0 
dimension (d) 
int 
The dimension to apply imputation to.  0 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
string 
File containing data.  required 
missing_value (m) 
string 
User defined missing value.  required 
strategy (s) 
string 
imputation strategy to be applied. Strategies should be one of ‘custom’, ‘mean’, ‘median’, and ‘listwise_deletion’.  required 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_file (o) 
string 
File to save output into. 
Detailed documentation
This utility takes a dataset and converts a userdefined missing variable to another to provide more meaningful analysis.
The program does not modify the original file, but instead makes a separate file to save the output data; You can save the output by specifying the file name with –output_file (o).
For example, if we consider ‘NULL’ in dimension 0 to be a missing variable and want to delete whole row containing the NULL in the columnwise dataset, and save the result to result.csv, we could run
$ mlpack_preprocess_imputer i dataset.csv o result.csv m NULL d 0
s listwise_deletion
See also
mlpack_radical
RADICAL
$ mlpack_radical [angles 150] input_file <string> [noise_std_dev
0.175] [objective] [replicates 30] [seed 0] [sweeps 0]
[output_ic_file <string>] [output_unmixing_file <string>]
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 (a) 
int 
Number of angles to consider in bruteforce search during Radical2D.  150 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_file (i) 
2d matrix file 
Input dataset for ICA.  required 
noise_std_dev (n) 
double 
Standard deviation of Gaussian noise.  0.175 
objective (O) 
flag 
If set, an estimate of the final objective function is printed.  
replicates (r) 
int 
Number of Gaussianperturbed replicates to use (per point) in Radical2D.  30 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
sweeps (S) 
int 
Number of sweeps; each sweep calls Radical2D once for each pair of dimensions.  0 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_ic_file (o) 
2d matrix file 
Matrix to save independent components to. 
output_unmixing_file (u) 
2d matrix file 
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_file (i)
parameter. The output matrix Y may be saved with the output_ic_file (o)
output parameter, and the output unmixing matrix W may be saved with the output_unmixing_file (u)
output parameter.
For example, to perform ICA on the matrix 'X.csv'
with 40 replicates, saving the independent components to 'ic.csv'
, the following command may be used:
$ mlpack_radical input_file X.csv replicates 40 output_ic_file ic.csv
See also
 Independent component analysis on Wikipedia
 ICA using spacings estimates of entropy (pdf)
 mlpack::radical::Radical C++ class documentation
mlpack_random_forest
Random forests
$ mlpack_random_forest [input_model_file <string>] [labels_file
<string>] [minimum_leaf_size 20] [num_trees 10]
[print_training_accuracy] [test_file <string>] [test_labels_file
<string>] [training_file <string>] [output_model_file <string>]
[predictions_file <string>] [probabilities_file <string>]
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 pretrained random forest can be used for classification. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
RandomForestModel file 
Pretrained random forest to use for classification.  '' 
labels_file (l) 
1d index matrix file 
Labels for training dataset.  '' 
minimum_leaf_size (n) 
int 
Minimum number of points in each leaf node.  20 
num_trees (N) 
int 
Number of trees in the random forest.  10 
print_training_accuracy (a) 
flag 
If set, then the accuracy of the model on the training set will be predicted (verbose must also be specified).  
test_file (T) 
2d matrix file 
Test dataset to produce predictions for.  '' 
test_labels_file (L) 
1d index matrix file 
Test dataset labels, if accuracy calculation is desired.  '' 
training_file (t) 
2d matrix file 
Training dataset.  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
RandomForestModel file 
Model to save trained random forest to. 
predictions_file (p) 
1d index matrix file 
Predicted classes for each point in the test set. 
probabilities_file (P) 
2d matrix file 
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_file (t)
and labels_file (l)
parameters, respectively. The labels should be in the range [0, num_classes  1]. Optionally, if labels_file (l)
is not specified, the labels are assumed to be the last dimension of the training dataset.
When a model is trained, the output_model_file (M)
output parameter may be used to save the trained model. A model may be loaded for predictions with the input_model_file (m)
parameter. The input_model_file (m)
parameter may not be specified when the training_file (t)
parameter is specified. The minimum_leaf_size (n)
parameter specifies the minimum number of training points that must fall into each leaf for it to be split. The num_trees (N)
controls the number of trees in the random forest. If print_training_accuracy (a)
is specified, the calculated accuracy on the training set will be printed.
Test data may be specified with the test_file (T)
parameter, and if performance measures are desired for that test set, labels for the test points may be specified with the test_labels_file (L)
parameter. Predictions for each test point may be saved via the predictions_file (p)
output parameter. Class probabilities for each prediction may be saved with the probabilities_file (P)
output parameter.
For example, to train a random forest with a minimum leaf size of 20 using 10 trees on the dataset contained in 'data.csv'
with labels 'labels.csv'
, saving the output random forest to 'rf_model.bin'
and printing the training error, one could call
$ mlpack_random_forest training_file data.csv labels_file labels.csv
minimum_leaf_size 20 num_trees 10 output_model_file rf_model.bin
print_training_accuracy
Then, to use that model to classify points in 'test_set.csv'
and print the test error given the labels 'test_labels.csv'
using that model, while saving the predictions for each point to 'predictions.csv'
, one could call
$ mlpack_random_forest input_model_file rf_model.bin test_file
test_set.csv test_labels_file test_labels.csv predictions_file
predictions.csv
See also
 mlpack_decision_tree
 mlpack_hoeffding_tree
 mlpack_softmax_regression
 Random forest on Wikipedia
 Random forests (pdf)
 mlpack::tree::RandomForest C++ class documentation
mlpack_range_search
Range Search
$ mlpack_range_search [input_model_file <string>] [leaf_size 20]
[max 0] [min 0] [naive] [query_file <string>] [random_basis]
[reference_file <string>] [seed 0] [single_mode] [tree_type
'kd'] [distances_file <string>] [neighbors_file <string>]
[output_model_file <string>]
An implementation of range search with singletree and dualtree algorithms. Given a set of reference points and a set of query points and a range, this can find the set of reference points within the desired range for each query point, and any trees built during the computation can be saved for reuse with future range searches. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
RSModel file 
File containing pretrained range search model.  '' 
leaf_size (l) 
int 
Leaf size for tree building (used for kdtrees, vp trees, random projection trees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, and octrees).  20 
max (U) 
double 
Upper bound in range (if not specified, +inf will be used.  0 
min (L) 
double 
Lower bound in range.  0 
naive (N) 
flag 
If true, O(n^2) naive mode is used for computation.  
query_file (q) 
2d matrix file 
File containing query points (optional).  '' 
random_basis (R) 
flag 
Before treebuilding, project the data onto a random orthogonal basis.  
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
seed (s) 
int 
Random seed (if 0, std::time(NULL) is used).  0 
single_mode (S) 
flag 
If true, singletree search is used (as opposed to dualtree search).  
tree_type (t) 
string 
Type of tree to use: ‘kd’, ‘vp’, ‘rp’, ‘maxrp’, ‘ub’, ‘cover’, ‘r’, ‘rstar’, ‘x’, ‘ball’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘oct’.  'kd' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
string 
File to output distances into. 
neighbors_file (n) 
string 
File to output neighbors into. 
output_model_file (M) 
RSModel file 
If specified, the range search model will be saved to the given file. 
Detailed documentation
This program implements range search with a Euclidean distance metric. For a given query point, a given range, and a given set of reference points, the program will return all of the reference points with distance to the query point in the given range. This is performed for an entire set of query points. You may specify a separate set of reference and query points, or only a reference set – which is then used as both the reference and query set. The given range is taken to be inclusive (that is, points with a distance exactly equal to the minimum and maximum of the range are included in the results).
For example, the following will calculate the points within the range [2, 5] of each point in ‘input.csv’ and store the distances in ‘distances.csv’ and the neighbors in ‘neighbors.csv’:
$ range_search –min=2 –max=5 –reference_file=input.csv –distances_file=distances.csv –neighbors_file=neighbors.csv
The output files are organized such that line i corresponds to the points found for query point i. Because sometimes 0 points may be found in the given range, lines of the output files may be empty. The points are not ordered in any specific manner.
Because the number of points returned for each query point may differ, the resultant CSVlike files may not be loadable by many programs. However, at this time a better way to store this nonsquare result is not known. As a result, any output files will be written as CSVs in this manner, regardless of the given extension.
See also
 mlpack_knn
 Range searching on Wikipedia
 Treeindependent dualtree algorithms (pdf)
 mlpack::range::RangeSearch C++ class documentation
mlpack_krann
KRankApproximateNearestNeighbors (kRANN)
$ mlpack_krann [alpha 0.95] [first_leaf_exact] [input_model_file
<string>] [k 0] [leaf_size 20] [naive] [query_file <string>]
[random_basis] [reference_file <string>] [sample_at_leaves]
[seed 0] [single_mode] [single_sample_limit 20] [tau 5]
[tree_type 'kd'] [distances_file <string>] [neighbors_file
<string>] [output_model_file <string>]
An implementation of rankapproximate knearestneighbor search (kRANN) using singletree and dualtree 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 (a) 
double 
The desired success probability.  0.95 
first_leaf_exact (X) 
flag 
The flag to trigger sampling only after exactly exploring the first leaf.  
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
RANNModel file 
Pretrained kNN model.  '' 
k (k) 
int 
Number of nearest neighbors to find.  0 
leaf_size (l) 
int 
Leaf size for tree building (used for kdtrees, UB trees, R trees, R* trees, X trees, Hilbert R trees, R+ trees, R++ trees, and octrees).  20 
naive (N) 
flag 
If true, sampling will be done without using a tree.  
query_file (q) 
2d matrix file 
Matrix containing query points (optional).  '' 
random_basis (R) 
flag 
Before treebuilding, project the data onto a random orthogonal basis.  
reference_file (r) 
2d matrix file 
Matrix containing the reference dataset.  '' 
sample_at_leaves (L) 
flag 
The flag to trigger sampling at leaves.  
seed (s) 
int 
Random seed (if 0, std::time(NULL) is used).  0 
single_mode (S) 
flag 
If true, singletree search is used (as opposed to dualtree search.  
single_sample_limit (z) 
int 
The limit on the maximum number of samples (and hence the largest node you can approximate).  20 
tau (T) 
double 
The allowed rankerror in terms of the percentile of the data.  5 
tree_type (t) 
string 
Type of tree to use: ‘kd’, ‘ub’, ‘cover’, ‘r’, ‘x’, ‘rstar’, ‘hilbertr’, ‘rplus’, ‘rplusplus’, ‘oct’.  'kd' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

distances_file (d) 
2d matrix file 
Matrix to output distances into. 
neighbors_file (n) 
2d index matrix file 
Matrix to output neighbors into. 
output_model_file (M) 
RANNModel file 
If specified, the kNN model will be output here. 
Detailed documentation
This program will calculate the k rankapproximatenearestneighbors 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).
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.csv'
and store the distances in 'distances.csv'
and the neighbors in 'neighbors.csv.csv'
:
$ mlpack_krann reference_file input.csv k 5 distances_file distances.csv
neighbors_file neighbors.csv tau 0.1
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
 mlpack_knn
 mlpack_lsh
 Rankapproximate nearest neighbor search: Retaining meaning and speed in high dimensions (pdf)
 mlpack::neighbor::RASearch C++ class documentation
mlpack_softmax_regression
Softmax Regression
$ mlpack_softmax_regression [input_model_file <string>] [labels_file
<string>] [lambda 0.0001] [max_iterations 400] [no_intercept]
[number_of_classes 0] [test_file <string>] [test_labels_file
<string>] [training_file <string>] [output_model_file <string>]
[predictions_file <string>]
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 pretrained softmax regression model can be used for classification of new points. Detailed documentation.
Input options
name  type  description  default 

help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
input_model_file (m) 
SoftmaxRegression file 
File containing existing model (parameters).  '' 
labels_file (l) 
1d index matrix file 
A matrix containing labels (0 or 1) for the points in the training set (y). The labels must order as a row.  '' 
lambda (r) 
double 
L2regularization constant  0.0001 
max_iterations (n) 
int 
Maximum number of iterations before termination.  400 
no_intercept (N) 
flag 
Do not add the intercept term to the model.  
number_of_classes (c) 
int 
Number of classes for classification; if unspecified (or 0), the number of classes found in the labels will be used.  0 
test_file (T) 
2d matrix file 
Matrix containing test dataset.  '' 
test_labels_file (L) 
1d index matrix file 
Matrix containing test labels.  '' 
training_file (t) 
2d matrix file 
A matrix containing the training set (the matrix of predictors, X).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

output_model_file (M) 
SoftmaxRegression file 
File to save trained softmax regression model to. 
predictions_file (p) 
1d index matrix file 
Matrix to save predictions 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_file (t)
parameter and their corresponding labels with the labels_file (l)
parameter. The number of classes can be manually specified with the number_of_classes (c)
parameter, and the maximum number of iterations of the LBFGS optimizer can be specified with the max_iterations (n)
parameter. The L2 regularization constant can be specified with the lambda (r)
parameter and if an intercept term is not desired in the model, the no_intercept (N)
parameter can be specified.
The trained model can be saved with the output_model_file (M)
output parameter. If training is not desired, but only testing is, a model can be loaded with the input_model_file (m)
parameter. At the current time, a loaded model cannot be trained further, so specifying both input_model_file (m)
and training_file (t)
is not allowed.
The program is also able to evaluate a model on test data. A test dataset can be specified with the test_file (T)
parameter. Class predictions can be saved with the predictions_file (p)
output parameter. If labels are specified for the test data with the test_labels_file (L)
parameter, then the program will print the accuracy of the predictions on the given test set and its corresponding labels.
For example, to train a softmax regression model on the data 'dataset.csv'
with labels 'labels.csv'
with a maximum of 1000 iterations for training, saving the trained model to 'sr_model.bin'
, the following command can be used:
$ mlpack_softmax_regression training_file dataset.csv labels_file
labels.csv output_model_file sr_model.bin
Then, to use 'sr_model.bin'
to classify the test points in 'test_points.csv'
, saving the output predictions to 'predictions.csv'
, the following command can be used:
$ mlpack_softmax_regression input_model_file sr_model.bin test_file
test_points.csv predictions_file predictions.csv
See also
 mlpack_logistic_regression
 mlpack_random_forest
 Multinomial logistic regression (softmax regression) on Wikipedia
 mlpack::regression::SoftmaxRegression C++ class documentation
mlpack_sparse_coding
Sparse Coding
$ mlpack_sparse_coding [atoms 15] [initial_dictionary_file <string>]
[input_model_file <string>] [lambda1 0] [lambda2 0]
[max_iterations 0] [newton_tolerance 1e06] [normalize]
[objective_tolerance 0.01] [seed 0] [test_file <string>]
[training_file <string>] [codes_file <string>] [dictionary_file
<string>] [output_model_file <string>]
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 (k) 
int 
Number of atoms in the dictionary.  15 
help (h) 
flag 
Default help info. Only exists in CLI binding.  
info 
string 
Print help on a specific option. Only exists in CLI binding.  '' 
initial_dictionary_file (i) 
2d matrix file 
Optional initial dictionary matrix.  '' 
input_model_file (m) 
SparseCoding file 
File containing input sparse coding model.  '' 
lambda1 (l) 
double 
Sparse coding l1norm regularization parameter.  0 
lambda2 (L) 
double 
Sparse coding l2norm regularization parameter.  0 
max_iterations (n) 
int 
Maximum number of iterations for sparse coding (0 indicates no limit).  0 
newton_tolerance (w) 
double 
Tolerance for convergence of Newton method.  1e06 
normalize (N) 
flag 
If set, the input data matrix will be normalized before coding.  
objective_tolerance (o) 
double 
Tolerance for convergence of the objective function.  0.01 
seed (s) 
int 
Random seed. If 0, ‘std::time(NULL)’ is used.  0 
test_file (T) 
2d matrix file 
Optional matrix to be encoded by trained model.  '' 
training_file (t) 
2d matrix file 
Matrix of training data (X).  '' 
verbose (v) 
flag 
Display informational messages and the full list of parameters and timers at the end of execution.  
version (V) 
flag 
Display the version of mlpack. Only exists in CLI binding. 
Output options
name  type  description 

codes_file (c) 
2d matrix file 
Matrix to save the output sparse codes of the test matrix (–test_file) to. 
dictionary_file (d) 
2d matrix file 
Matrix to save the output dictionary to. 
output_model_file (M) 
SparseCoding file 
File to save trained sparse coding model to. 
Detailed documentation
An implementation of Sparse Coding with Dictionary Learning, which achieves sparsity via an l1norm 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 alreadysaved sparse coding model must be specified. An input matrix may be specified with the training_file (t)
option, along with the number of atoms in the dictionary (specified with the atoms (k)
parameter). It is also possible to specify an initial dictionary for the optimization, with the initial_dictionary_file (i)
parameter. An input model may be specified with the input_model_file (m)
parameter.
As an example, to build a sparse coding model on the dataset 'data.csv'
using 200 atoms and an l1regularization parameter of 0.1, saving the model into 'model.bin'
, use
$ mlpack_sparse_coding training_file data.csv atoms 200 lambda1 0.1
output_model_file model.bin
Then, this model could be used to encode a new matrix, 'otherdata.csv'
, and save the output codes to 'codes.csv'
:
$ mlpack_sparse_coding input_model_file model.bin test_file otherdata.csv
codes_file codes.csv
See also
 mlpack_local_coordinate_coding
 Sparse dictionary learning on Wikipedia
 Efficient sparse coding algorithms (pdf)
 Regularization and variable selection via the elastic net
 mlpack::sparse_coding::SparseCoding C++ class documentation
changelog/history
mlpack 3.1.0
20190425

Add DiagonalGaussianDistribution and DiagonalGMM classes to speed up the diagonal covariance computation and deprecate DiagonalConstraint #1666.

Add kernel density estimation (KDE) implementation with bindings to other languages #1301.

Where relevant, all models with a
Train()
method now return adouble
value representing the goodness of fit (i.e. final objective value, error, etc.) #1678. 
Add implementation for linear support vector machine (see
src/mlpack/methods/linear_svm
). 
Change DBSCAN to use PointSelectionPolicy and add OrderedPointSelection #1625.

Residual block support #1594.

Bidirectional RNN #1626.

Dice loss layer (#1674, #1714) and hard sigmoid layer #1776.

output
option changed topredictions
andoutput_probabilities
toprobabilities
for Naive Bayes binding (mlpack_nbc
/nbc()
). Old options are now deprecated and will be preserved until mlpack 4.0.0 #1616. 
Add support for Diagonal GMMs to HMM code (#1658, #1666). This can provide large speedup when a diagonal GMM is acceptable as an emission probability distribution.

Python binding improvements: check parameter type #1717, avoid copying Pandas dataframes #1711, handle Pandas Series objects #1700.
mlpack 3.0.4
20181113

Bump minimum CMake version to 3.3.2.

CMake fixes for Ninja generator by Marc Espie.
mlpack 3.0.3
20180727

Fix Visual Studio compilation issue #1443.

Allow running local_coordinate_coding binding with no initial_dictionary parameter when input_model is not specified #1457.

Make use of OpenMP optional via the CMake ‘USE_OPENMP’ configuration variable #1474.

Accelerate FNN training by 2030% by avoiding redundant calculations #1467.

Fix math::RandomSeed() usage in tests (#1462, #1440).

Generate better Python setup.py with documentation #1460.
mlpack 3.0.2
20180608

Documentation generation fixes for Python bindings #1421.

Fix build error for man pages if commandline bindings are not being built #1424.

Add ‘shuffle’ parameter and Shuffle() method to KFoldCV #1412. This will shuffle the data when the object is constructed, or when Shuffle() is called.

Added neural network layers: AtrousConvolution #1390, Embedding #1401, and LayerNorm (layer normalization) #1389.

Add Pendulum environment for reinforcement learning #1388 and update Mountain Car environment #1394.
mlpack 3.0.1
20180510

Fix intermittently failing tests #1387.

Add bigbatch SGD (BBSGD) optimizer in src/mlpack/core/optimizers/bigbatch_sgd/ #1131.

Fix simple compiler warnings (#1380, #1373).

Simplify NeighborSearch constructor and Train() overloads #1378.

Add warning for OpenMP setting differences (#1358/#1382). When mlpack is compiled with OpenMP but another application is not (or vice versa), a compilation warning will now be issued.

Restructured loss functions in src/mlpack/methods/ann/ #1365.

Add environments for reinforcement learning tests (#1368, #1370, #1329).

Allow single outputs for multiple timestep inputs for recurrent neural networks #1348.

Add He and LeCun normal initializations for neural networks #1342. Neural networks: add He and LeCun normal initializations #1342, add FReLU and SELU activation functions (#1346, #1341), add alphadropout #1349.
mlpack 3.0.0
20180330

Speed and memory improvements for DBSCAN. –single_mode can now be used for situations where previously RAM usage was too high.

Bump minimum required version of Armadillo to 6.500.0.

Add automatically generated Python bindings. These have the same interface as the commandline programs.

Add deep learning infrastructure in src/mlpack/methods/ann/.

Add reinforcement learning infrastructure in src/mlpack/methods/reinforcement_learning/.

Add optimizers: AdaGrad, CMAES, CNE, FrankeWolfe, GradientDescent, GridSearch, IQN, Katyusha, LineSearch, ParallelSGD, SARAH, SCD, SGDR, SMORMS3, SPALeRA, SVRG.

Add hyperparameter tuning infrastructure and crossvalidation infrastructure in src/mlpack/core/cv/ and src/mlpack/core/hpt/.

Fix bug in mean shift.

Add random forests (see src/mlpack/methods/random_forest).

Numerous other bugfixes and testing improvements.

Add randomized Krylov SVD and Block Krylov SVD.
mlpack 2.2.5
20170825
mlpack 2.2.4
20170718

Speed and memory improvements for DBSCAN. –single_mode can now be used for situations where previously RAM usage was too high.

Fix bug in CF causing incorrect recommendations.
mlpack 2.2.3
20170524
 Bug fix for –predictions_file in mlpack_decision_tree program.
mlpack 2.2.2
20170504

Install backwardscompatibility mlpack_allknn and mlpack_allkfn programs; note they are deprecated and will be removed in mlpack 3.0.0 #992.

Fix RStarTree bug that surfaced on OS X only #964.

Small fixes for MiniBatchSGD and SGD and tests.
mlpack 2.2.1
20170413
 Compilation fix for mlpack_nca and mlpack_test on older Armadillo versions #984.
mlpack 2.2.0
20170321

Bugfix for mlpack_knn program #816.

Add decision tree implementation in methods/decision_tree/. This is very similar to a C4.5 tree learner.

Add DBSCAN implementation in methods/dbscan/.

Add support for multidimensional discrete distributions (#810, #830).

Better output for Log::Debug/Log::Info/Log::Warn/Log::Fatal for Armadillo objects (#895, #928).

Refactor categorical CSV loading with boost::spirit for faster loading #681.
mlpack 2.1.1
20161222

HMMs now use random initialization; this should fix some convergence issues #828.

HMMs now initialize emissions according to the distribution of observations #833.

Minor fix for formatted output #814.

Fix DecisionStump to properly work with any input type.
mlpack 2.1.0
20161031

Fixed CoverTree to properly handle singlepoint datasets.

Fixed a bug in CosineTree (and thus QUICSVD) that caused split failures for some datasets #717.

Added mlpack_preprocess_describe program, which can be used to print statistics on a given dataset #742.

Fix prioritized recursion for kfurthestneighbor search (mlpack_kfn and the KFN class), leading to ordersofmagnitude speedups in some cases.

Bump minimum required version of Armadillo to 4.200.0.

Added simple Gradient Descent optimizer, found in src/mlpack/core/optimizers/gradient_descent/ #792.

Added approximate furthest neighbor search algorithms QDAFN and DrusillaSelect in src/mlpack/methods/approx_kfn/, with commandline program mlpack_approx_kfn.
mlpack 2.0.3
20160721

Added multiprobe LSH #691. The parameter ‘T’ to LSHSearch::Search() can now be used to control the number of extra bins that are probed, as can the T (–num_probes) option to mlpack_lsh.

Added the Hilbert R tree to src/mlpack/core/tree/rectangle_tree/ #664. It can be used as the typedef HilbertRTree, and it is now an option in the mlpack_knn, mlpack_kfn, mlpack_range_search, and mlpack_krann commandline programs.

Added the mlpack_preprocess_split and mlpack_preprocess_binarize programs, which can be used for preprocessing code (#650, #666).

Added OpenMP support to LSHSearch and mlpack_lsh #700.
mlpack 2.0.2
20160620

Added the function LSHSearch::Projections(), which returns an arma::cube with each projection table in a slice #663. Instead of Projection(i), you should now use Projections().slice(i).

A new constructor has been added to LSHSearch that creates objects using projection tables provided in an arma::cube #663.

Handle zerovariance dimensions in DET #515.

Add MiniBatchSGD optimizer (src/mlpack/core/optimizers/minibatch_sgd/) and allow its use in mlpack_logistic_regression and mlpack_nca programs.

Add better backtrace support from Grzegorz Krajewski for Log::Fatal messages when compiled with debugging and profiling symbols. This requires libbfd and libdl to be present during compilation.

CosineTree test fix from Mikhail Lozhnikov #358.

Fixed HMM initial state estimation #600.

Changed versioning macros __MLPACK_VERSION_MAJOR, __MLPACK_VERSION_MINOR, and __MLPACK_VERSION_PATCH to MLPACK_VERSION_MAJOR, MLPACK_VERSION_MINOR, and MLPACK_VERSION_PATCH. The old names will remain in place until mlpack 3.0.0.

Renamed mlpack_allknn, mlpack_allkfn, and mlpack_allkrann to mlpack_knn, mlpack_kfn, and mlpack_krann. The mlpack_allknn, mlpack_allkfn, and mlpack_allkrann programs will remain as copies until mlpack 3.0.0.

Add –random_initialization option to mlpack_hmm_train, for use when no labels are provided.

Add –kill_empty_clusters option to mlpack_kmeans and KillEmptyClusters policy for the KMeans class (#595, #596).
mlpack 2.0.1
20160204

Fix CMake to properly detect when MKL is being used with Armadillo.

Minor parameter handling fixes to mlpack_logistic_regression (#504, #505).

Properly install arma_config.hpp.

Memory handling fixes for Hoeffding tree code.

Add functions that allow changing trainingtime parameters to HoeffdingTree class.

Fix infinite loop in sparse coding test.

Documentation spelling fixes #501.

Properly handle covariances for Gaussians with large condition number #496, preventing GMMs from filling with NaNs during training (and also HMMs that use GMMs).

CMake fixes for finding LAPACK and BLAS as Armadillo dependencies when ATLAS is used.

CMake fix for projects using mlpack’s CMake configuration from elsewhere #512.
mlpack 2.0.0
20151224

Removed overclustering support from kmeans because it is not welltested, may be buggy, and is (I think) unused. If this was support you were using, open a bug or get in touch with us; it would not be hard for us to reimplement it.

Refactored KMeans to allow different types of Lloyd iterations.

Added implementations of kmeans: Elkan’s algorithm, Hamerly’s algorithm, PellegMoore’s algorithm, and the DTNN (dualtree nearest neighbor) algorithm.

Significant acceleration of LRSDP via the use of accu(a % b) instead of trace(a * b).

Added MatrixCompletion class (matrix_completion), which performs nuclear norm minimization to fill unknown values of an input matrix.

No more dependence on Boost.Random; now we use C++11 STL random support.

Add softmax regression, contributed by Siddharth Agrawal and QiaoAn Chen.

Changed NeighborSearch, RangeSearch, FastMKS, LSH, and RASearch API; these classes now take the query sets in the Search() method, instead of in the constructor.

Use OpenMP, if available. For now OpenMP support is only available in the DET training code.

Add support for predicting new test point values to LARS and the commandline ‘lars’ program.

Add serialization support for Perceptron and LogisticRegression.

Refactor SoftmaxRegression to predict into an arma::Row
object, and add a softmax_regression program. 
Refactor LSH to allow loading and saving of models.

ToString() is removed entirely #487.

Add –input_model_file and –output_model_file options to appropriate machine learning algorithms.

Rename all executables to start with an “mlpack” prefix #229.

Add HoeffdingTree and mlpack_hoeffding_tree, an implementation of the streaming decision tree methodology from Domingos and Hulten in 2000.
mlpack 1.0.12
20150107
 Switch to 3clause BSD license (from LGPL).
mlpack 1.0.11
20141211

Proper handling of dimension calculation in PCA.

Load parameter vectors properly for LinearRegression models.

Linker fixes for AugLagrangian specializations under Visual Studio.

Add support for observation weights to LinearRegression.

MahalanobisDistance<> now takes the root of the distance by default and therefore satisfies the triangle inequality (TakeRoot now defaults to true).

Better handling of optional Armadillo HDF5 dependency.

Fixes for numerous intermittent test failures.

math::RandomSeed() now sets the random seed for recent (>=3.930) Armadillo versions.

Handle Newton method convergence better for SparseCoding::OptimizeDictionary() and make maximum iterations a parameter.

Known bug: CosineTree construction may fail in some cases on i386 systems #358.
mlpack 1.0.10
20140829

Bugfix for NeighborSearch regression which caused very slow allknn/allkfn. Speeds are now restored to approximately 1.0.8 speeds, with significant improvement for the cover tree #347.

Detect dependencies correctly when ARMA_USE_WRAPPER is not being defined (i.e., libarmadillo.so does not exist).

Bugfix for compilation under Visual Studio #348.
mlpack 1.0.9
20140728

GMM initialization is now safer and provides a working GMM when constructed with only the dimensionality and number of Gaussians #301.

Check for division by 0 in ForwardBackward Algorithm in HMMs #301.

Fix MaxVarianceNewCluster (used when reinitializing clusters for kmeans) #301.

Fixed implementation of Viterbi algorithm in HMM::Predict() #303.

Significant speedups for dualtree algorithms using the cover tree (#235, #314) including a faster implementation of FastMKS.

Fix for LRSDP optimizer so that it compiles and can be used #312.

CF (collaborative filtering) now expects users and items to be zeroindexed, not oneindexed #311.

CF::GetRecommendations() API change: now requires the number of recommendations as the first parameter. The number of users in the local neighborhood should be specified with CF::NumUsersForSimilarity().

Removed incorrect PeriodicHRectBound #58.

Refactor LRSDP into LRSDP class and standalone function to be optimized #305.

Fix for centering in kernel PCA #337.

Added simulated annealing (SA) optimizer, contributed by Zhihao Lou.

HMMs now support initial state probabilities; these can be set in the constructor, trained, or set manually with HMM::Initial() #302.

Added Nyström method for kernel matrix approximation by Marcus Edel.

Kernel PCA now supports using Nyström method for approximation.

Ball trees now work with dualtree algorithms, via the BallBound<> bound structure #307; fixed by Yash Vadalia.

The NMF class is now AMF<>, and supports far more types of factorizations, by Sumedh Ghaisas.

A QUICSVD implementation has returned, written by Siddharth Agrawal and based on older code from Mudit Gupta.

Added perceptron and decision stump by Udit Saxena (these are weak learners for an eventual AdaBoost class).

Sparse autoencoder added by Siddharth Agrawal.
mlpack 1.0.8
20140106

Memory leak in NeighborSearch indexmapping code fixed #298.

GMMs can be trained using the existing model as a starting point by specifying an additional boolean parameter to GMM::Estimate() #296.

Logistic regression implementation added in methods/logistic_regression (see also #293).

LBFGS optimizer now returns its function via Function().

Version information is now obtainable via mlpack::util::GetVersion() or the __MLPACK_VERSION_MAJOR, __MLPACK_VERSION_MINOR, and __MLPACK_VERSION_PATCH macros #297.

Fix typos in allkfn and allkrann output.
mlpack 1.0.7
20131004

Cover tree support for range search (range_search), rankapproximate nearest neighbors (allkrann), minimum spanning tree calculation (emst), and FastMKS (fastmks).

Dualtree FastMKS implementation added and tested.

Added collaborative filtering package (cf) that can provide recommendations when given users and items.

Fix for correctness of Kernel PCA (kernel_pca) #270.

Speedups for PCA and Kernel PCA #198.

Fix for correctness of Neighborhood Components Analysis (NCA) #279.

Minor speedups for dualtree algorithms.

Fix for Naive Bayes Classifier (nbc) #269.

Added a ridge regression option to LinearRegression (linear_regression) #286.

Gaussian Mixture Models (gmm::GMM<>) now support arbitrary covariance matrix constraints #283.

MVU (mvu) removed because it is known to not work #183.

Minor updates and fixes for kernels (in mlpack::kernel).
mlpack 1.0.6
20130613
 Minor bugfix so that FastMKS gets built.
mlpack 1.0.5
20130501

Speedups of cover tree traversers #235.

Addition of rankapproximate nearest neighbors (RANN), found in src/mlpack/methods/rann/.

Addition of fast exact maxkernel search (FastMKS), found in src/mlpack/methods/fastmks/.

Fix for EM covariance estimation; this should improve GMM training time.

More parameters for GMM estimation.

Force GMM and GaussianDistribution covariance matrices to be positive definite, so that training converges much more often.

Add parameter for the tolerance of the BaumWelch algorithm for HMM training.

Fix for compilation with clang compiler.

Fix for kfurthestneighborsearch.
mlpack 1.0.4
20130208

Force minimum Armadillo version to 2.4.2.

Better output of class types to streams; a class with a ToString() method implemented can be sent to a stream with operator«.

Change return type of GMM::Estimate() to double #257.

Style fixes for kmeans and RADICAL.

Handle size_t support correctly with Armadillo 3.6.2 #258.

Add localitysensitive hashing (LSH), found in src/mlpack/methods/lsh/.

Better tests for SGD (stochastic gradient descent) and NCA (neighborhood components analysis).
mlpack 1.0.3
20120916

Remove internal sparse matrix support because Armadillo 3.4.0 now includes it. When using Armadillo versions older than 3.4.0, sparse matrix support is not available.

NCA (neighborhood components analysis) now support an arbitrary optimizer #245, including stochastic gradient descent #249.
mlpack 1.0.2
20120815

Added density estimation trees, found in src/mlpack/methods/det/.

Added nonnegative matrix factorization, found in src/mlpack/methods/nmf/.

Added experimental cover tree implementation, found in src/mlpack/core/tree/cover_tree/ #157.

Better reporting of boost::program_options errors #225.

Fix for timers on Windows (#212, #211).

Fix for allknn and allkfn output #204.

Sparse coding dictionary initialization is now a template parameter #220.
mlpack 1.0.1
20120303

Added kernel principal components analysis (kernel PCA), found in src/mlpack/methods/kernel_pca/ #74.

Fix for LovaszTheta AugLagrangian tests #182.

Fixes for allknn output (#185, #186).

Added range search executable #192.

Adapted citations in documentation to BibTeX; no citations in h output #195.

Stop use of ‘const char*’ and prefer ‘std::string’ #176.

Support seeds for random numbers #177.
mlpack 1.0.0
20111217
 Initial release. See any resolved tickets numbered less than #196 or execute this query: http://www.mlpack.org/trac/query?status=closed&milestone=mlpack+1.0.0