Package 'DelayedTensor'

Title: R package for sparse and out-of-core arithmetic and decomposition of Tensor
Description: DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.
Authors: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <[email protected]>
License: Artistic-2.0
Version: 1.13.0
Built: 2024-11-29 05:26:55 UTC
Source: https://github.com/bioc/DelayedTensor

Help Index

R package for sparse and out-of-core arithmetic and decomposition of Tensor

Description

DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.

Details

The DESCRIPTION file:

Package: DelayedTensor
Type: Package
Title: R package for sparse and out-of-core arithmetic and decomposition of Tensor
Version: 1.13.0
Authors@R: c(person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "[email protected]"))
Depends: R (>= 4.1.0)
Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum,
Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate
Description: DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.
License: Artistic-2.0
biocViews: Software, Infrastructure, DataRepresentation, DimensionReduction
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
BugReports: https://github.com/rikenbit/DelayedTensor/issues
Repository: https://bioc.r-universe.dev
RemoteUrl: https://github.com/bioc/DelayedTensor
RemoteRef: HEAD
RemoteSha: 35f745ff4ac57c3f7acba76b2d2deecebdd13c5f
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <[email protected]>

Index of help topics: 

DelayedDiagonalArray    Diagonal DelayedArray
DelayedTensor-package   R package for sparse and out-of-core arithmetic
                        and decomposition of Tensor
cbind_list              Mode-binding against list
cp-methods              Canonical Polyadic Decomposition
cs_fold-methods         Column Space Folding of 2D DelayedArray
cs_unfold-methods       Tensor Column Space Unfolding of DelayedArray
diag-methods            DelayedArray Diagonals
einsum                  Einstein Summation of DelayedArray
fnorm-methods           Tensor Frobenius Norm of DelayedArray
fold-methods            Tensor folding of 2D DelayedArray
getSparse               Getter of the intermediate/output DelayedArray
                        object in DelayedTensor
getVerbose              Getter function to control the verbose messages
                        from DelayedTensor
hadamard-methods        Hadamard Product of DelayedArray
hadamard_list           Hadamard Product against list
hosvd-methods           (Truncated-)Higher-order SVD
human_mid_brain         Matrix object of human mid brain data
innerProd-methods       Tensors Inner Product of DelayedArray
k_fold-methods          k-mode Folding of 2D DelayedArray
k_unfold-methods        Tensor k-mode Unfolding of DelayedArray
khatri_rao-methods      Khatri-Rao Product of DelayedArray
khatri_rao_list         Khatri-Rao Product against list
kronecker-methods       Kronecker Product of DelayedArray
kronecker_list          Kronecker Product against list
list_rep                Replicate of arbitrary object
matvec-methods          Tensor Matvec Unfolding of DelayedArray
modeMean-methods        Tensor Mean Across Single Mode of DelayedArray
modeSum-methods         Tensor Sum Across Single Mode of DelayedArray
modebind_list           Mode-binding against list
mouse_mid_brain         Matrix object of mouse mid brain data
mpca-methods            Multilinear Principal Components Analysis
outerProd-methods       Tensors Outer Product of DelayedArray
pvd-methods             Population Value Decomposition
rbind_list              Mode-binding against list
rs_fold-methods         Row Space Folding of 2D DelayedArray
rs_unfold-methods       Tensor Row Space Unfolding of DelayedArray
setSparse               Setter to set the intermediate DelayedArray
                        object in DelayedTensor
setVerbose              Setter to set the verbose mode of DelayedTensor
ttl                     DelayedArray Times List
ttm-methods             Tensor Times Matrix (m-Mode Product)
tucker-methods          Tucker Decomposition
unfold-methods          Tensor Unfolding of 2D DelayedArray
unmatvec-methods        Unmatvec Folding of 2D DelayedArray
vec-methods             Tensor Vectorization of DelayedArray

Author(s)

Koki Tsuyuzaki [aut, cre]

Maintainer: Koki Tsuyuzaki <[email protected]>

See Also

# Unfold operations unfold, k_unfold, matvec, rs_unfold, cs_unfold, ttl # Fold operations fold, k_fold, unmatvec, rs_fold, cs_fold, ttm # Vectorization vec # Norm operations fnorm, innerProd # Diagonal operations / Diagonal Tensor diag, DelayedDiagonalArray # Mode-wise operations modeSum, modeMean # Tensor product operations hadamard, hadamard_list, kronecker, kronecker_list, khatri_rao, khatri_rao_list # Utilities list_rep, modebind_list, rbind_list, cbind_list # Decomposition operations hosvd, cp, tucker, mpca, pvd # Einsum operation einsum

Examples

ls("package:DelayedTensor")

Mode-binding against list

Description

Returns the binded DelayedArray in column space.

Usage

cbind_list(L)

Arguments

L

list of 2D DelayedArray

Details

This is a wrapper function to modebind_list, when the DelayedArrays are 2D.

Value

2D DelayedArray object

Note

The dimensions of column in each DelayedArray must match.

See Also

modebind_list

Examples

library("DelayedRandomArray")
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,3)),
    'darr2' = RandomUnifArray(c(2,3)))
cbind_list(dlizt)

Canonical Polyadic Decomposition

Description

Canonical Polyadic (CP) decomposition of a tensor, aka CANDECOMP/PARAFRAC. Approximate a K-Tensor using a sum of num_components rank-1 K-Tensors. A rank-1 K-Tensor can be written as an outer product of K vectors. There are a total of num_compoents *darr@num_modes vectors in the output, stored in darr@num_modes matrices, each with num_components columns. This is an iterative algorithm, with two possible stopping conditions: either relative error in Frobenius norm has gotten below tol, or the max_iter number of iterations has been reached. For more details on CP decomposition, consult Kolda and Bader (2009).

Usage

cp(darr, num_components=NULL, max_iter=25, tol=1e-05)

## S4 method for signature 'DelayedArray'
cp(darr, num_components, max_iter, tol)

Arguments

darr

Tensor with K modes
num_components

the number of rank-1 K-Tensors to use in approximation
max_iter

maximum number of iterations if error stays above tol
tol

relative Frobenius norm error tolerance

Details

This function is an extension of the cp by DelayedArray.

Uses the Alternating Least Squares (ALS) estimation procedure. A progress bar is included to help monitor operations on large tensors.

Value

a list containing the following

lambdas

a vector of normalizing constants, one for each component

U

a list of matrices - one for each mode - each matrix with num_components columns

conv

whether or not resid < tol by the last iteration

norm_percent

the percent of Frobenius norm explained by the approximation

est

estimate of darr after compression

fnorm_resid

the Frobenius norm of the error fnorm(est-darr)

all_resids

vector containing the Frobenius norm of error for all the iterations

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

tucker

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(3,4,5))
cp(darr, num_components=2)

Column Space Folding of 2D DelayedArray

Description

The inverse operation to cs_unfold.

Usage

cs_fold(mat, m = NULL, modes = NULL)

## S4 method for signature 'DelayedArray'
cs_fold(mat, m, modes)

Arguments

mat

DelayedArray object (only 2D)
m

the mode corresponding to cs_unfold
modes

the original modes of the DelayedArray

Details

This function is an extension of the cs_fold by DelayedArray.

This is a wrapper function to fold.

Value

DelayedArray (higher than 2D)

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

fold, cs_unfold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT3 <- DelayedTensor::cs_unfold(darr, m=3)
identical(
    as.array(DelayedTensor::cs_fold(matT3, m=3, modes=c(2,3,4))),
    as.array(darr))

Tensor Column Space Unfolding of DelayedArray

Description

Please see matvec and unfold.

Usage

cs_unfold(darr, m)

## S4 method for signature 'DelayedArray'
cs_unfold(darr, m)

Arguments

darr

DelayedArray object
m

mode to be unfolded on

Details

This function is an extension of the cs_unfold by DelayedArray.

This is a wrapper function to unfold.

Value

DelayedArray (2D)

See Also

unfold, cs_fold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
DelayedTensor::cs_unfold(darr, m=3)

Diagonal DelayedArray

Description

Constructor of the diagonal of a DelayedArray.

Usage

DelayedDiagonalArray(shape, value)

Arguments

shape

Shape of DelayedArray (mode of Tensor)
value

either a single value or a vector. This argument is optional. If nothing is specified, 1s are filled with each diagonal element.

Details

See also diag or diag.

Value

DelayedArray object

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

diag, diag

Examples

darr <- DelayedDiagonalArray(2:4, 5)
DelayedTensor::diag(darr)

DelayedArray Diagonals

Description

Extract or replace the diagonal of a DelayedArray, or substitute the elements to the diagonal DelayedArray.

Usage

diag(darr)
diag(darr) <- value

## S4 method for signature 'DelayedArray'
diag(darr)
## S4 replacement method for signature 'DelayedArray'
diag(darr) <- value

Arguments

darr

DelayedArray object
value

either a single value or a vector of length equal to that of the current diagonal. Should be of a mode which can be coerced to that of darr.

Details

See also DelayedDiagonalArray or diag.

Value

1D DelayedArray (vector) with length min(dim(darr))

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

DelayedDiagonalArray

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
DelayedTensor::diag(darr)
DelayedTensor::diag(darr)[1] <- 11111
DelayedTensor::diag(darr)[2] <- 22222
DelayedTensor::diag(darr)

Einstein Summation of DelayedArray

Description

Einstein summation is a convenient and concise notation for operations on n-dimensional arrays.

NOTE: Sparse mode of einsum is not available for now.

Usage

einsum(subscripts, ...)

Arguments

subscripts

a string in Einstein notation where arrays are separated by ',' and the result is separated by '->'. For example "ij,jk->ik" corresponds to a standard matrix multiplication. Whitespace inside the subscripts is ignored. Unlike the equivalent functions in Python, einsum only supports the explicit mode. This means that the subscripts must contain '->'.
...

the DelayedArrays that are combined.

Details

This function is an extension of the einsum by DelayedArray.

Value

The einsum function returns an array with one dimension for each index in the result of the subscripts. For example "ij,jk->ik" produces a 2-dimensional array, "abc,cd,de->abe" produces a 3-dimensional array.

Examples

library("DelayedArray")
library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(4,8))
darr2 <- RandomUnifArray(c(8,3))

# Matrix Multiply
darr1 %*% darr2
DelayedTensor::einsum("ij,jk -> ik", darr1, darr2)

# Diag
mat_sq <- RandomUnifArray(c(4,4))
DelayedTensor::diag(mat_sq)
einsum("ii->i", mat_sq)

# Trace
sum(DelayedTensor::diag(mat_sq))
einsum("ii->", mat_sq)

# Scalar product
darr3 <- RandomUnifArray(c(4,8))
darr3 * darr1
einsum("ij,ij->ij", darr3, darr1)

# Transpose
t(darr1)
einsum("ij->ji", darr1)

# Batched L2 norm
arr1 <- as.array(darr1)
arr3 <- as.array(darr3)
darr4 <- DelayedArray(array(c(arr1, arr3), dim = c(dim(arr1), 2)))

c(sum(darr1^2), sum(darr3^2))
einsum("ijb,ijb->b", darr4, darr4)

Tensor Frobenius Norm of DelayedArray

Description

Returns the Frobenius norm of the Tensor instance.

Usage

fnorm(darr)

## S4 method for signature 'DelayedArray'
fnorm(darr)

Arguments

darr

DelayedArray object

Details

This function is an extension of the fnorm by DelayedArray.

Value

numeric Frobenius norm of darr

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
fnorm(darr)

Tensor folding of 2D DelayedArray

Description

General folding of a 2D DelayedArray into a higher-order DelayedArray(Tensor). This is designed to be the inverse function to unfold, with the same ordering of the indices. This amounts to following: if we were to unfold a Tensor using a set of row_idx and col_idx, then we can fold the resulting matrix back into the original Tensor using the same row_idx and col_idx.

Usage

fold(mat, row_idx = NULL, col_idx = NULL, modes = NULL)

## S4 method for signature 'DelayedArray'
fold(mat, row_idx, col_idx, modes)

Arguments

mat

DelayedArray object (only 2D)
row_idx

the indices of the modes that are mapped onto the row space
col_idx

the indices of the modes that are mapped onto the column space
modes

the modes of the output DelayedArray

Details

This function is an extension of the fold by DelayedArray.

Value

DelayedArray object with modes given by modes

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

unfold, k_fold, unmatvec, rs_fold, cs_fold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT3 <- DelayedTensor::unfold(darr, row_idx=2, col_idx=c(3,1))
identical(
    as.array(DelayedTensor::fold(matT3, row_idx=2,col_idx=c(3,1),
        modes=c(2,3,4))),
    as.array(darr))

Getter of the intermediate/output DelayedArray object in DelayedTensor

Description

Whether the intermediate and output DelayedArray used in DelayedTensor is used as sparse tensor or not.

NOTE: Sparse mode is experimental! Whether it contributes to higher speed and lower memory is quite dependent on the sparsity of the DelayedArray, and the current implementation does not recognize the block size, which may cause Out-of-Memory errors.

Usage

getSparse()

Value

TRUE or FALSE (Default: FALSE)

Examples

getSparse()

Getter function to control the verbose messages from DelayedTensor

Description

Returns the verbose setting of DelayedTensor functions.

Usage

getVerbose()

Value

TRUE or FALSE (Default: FALSE)

Examples

getVerbose()

Hadamard Product against list

Description

Returns the hadamard (element-wise) product from a list of matrices or vectors. Commonly used for n-mode products and various Tensor decompositions.

Usage

hadamard_list(L)

Arguments

L

list of DelayedArray

Details

This function is an extension of the hadamard_list by DelayedArray.

Value

matrix that is the Hadamard product

Note

The modes/dimensions of each element in the list must match.

See Also

khatri_rao, khatri_rao_list, kronecker, kronecker_list, hadamard

Examples

library("DelayedRandomArray")
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,3,4)),
    'darr2' = RandomUnifArray(c(2,3,4)))
hadamard_list(dlizt)

Hadamard Product of DelayedArray

Description

Returns the Hadamard product of two Tensors. Commonly used for n-mode products and various Tensor decompositions.

Usage

hadamard(darr1, darr2)

## S4 method for signature 'DelayedArray,DelayedArray'
hadamard(darr1, darr2)

Arguments

darr1

first DelayedArray object
darr2

second DelayedArray object

Value

matrix that is the Hadamard product

Note

The modes/dimensions of each element of two Tensors must match.

See Also

khatri_rao, khatri_rao_list, kronecker, kronecker_list, hadamard_list

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,4))
darr2 <- RandomUnifArray(c(2,4))
hadamard(darr1, darr1)

(Truncated-)Higher-order SVD

Description

Higher-order SVD of a K-Tensor. Write the K-Tensor as a (m-mode) product of a core Tensor (possibly smaller modes) and K orthogonal factor matrices. Truncations can be specified via ranks (making them smaller than the original modes of the K-Tensor will result in a truncation). For the mathematical details on HOSVD, consult Lathauwer et. al. (2000).

Usage

hosvd(darr, ranks=NULL)

## S4 method for signature 'DelayedArray'
hosvd(darr, ranks)

Arguments

darr

Tensor with K modes
ranks

a vector of desired modes in the output core tensor, default is darr@modes

Details

This function is an extension of the hosvd by DelayedArray.

A progress bar is included to help monitor operations on large tensors.

Value

a list containing the following:

Z

core tensor with modes speficied by ranks

U

a list of orthogonal matrices, one for each mode

est

estimate of darr after compression

fnorm_resid

the Frobenius norm of the error fnorm(est-darr) - if there was no truncation, then this is on the order of mach_eps * fnorm.

Note

The length of ranks must match darr@num_modes.

References

L. Lathauwer, B.Moor, J. Vanderwalle "A multilinear singular value decomposition". Journal of Matrix Analysis and Applications 2000.

See Also

tucker

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(3,4,5))
hosvd(darr, ranks=c(2,1,3))

Matrix object of human mid brain data

Description

A matrix with 500 rows (genes) * 1977 columns (cells).

Usage

data(human_mid_brain)

Details

The data matrix is downloaded from GEO Series GSE76381 (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE76381&format=file). For the details, see inst/script/make-data.R.

References

Y-h. Taguchi and T. Turki (2019) Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. Frontiers in Genetics, 10(864): 10:3389/fgene.2019.00864

See Also

mouse_mid_brain

Examples

data(human_mid_brain)

Tensors Inner Product of DelayedArray

Description

Returns the inner product between two Tensors

Usage

innerProd(darr1, darr2)

## S4 method for signature 'DelayedArray,DelayedArray'
innerProd(darr1, darr2)

Arguments

darr1

first DelayedArray object
darr2

second DelayedArray object

Details

This function is an extension of the innerProd by DelayedArray.

Value

inner product between darr1 and darr2

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,3,4))
darr2 <- RandomUnifArray(c(2,3,4))
innerProd(darr1, darr2)

k-mode Folding of 2D DelayedArray

Description

k-mode folding of a matrix into a Tensor. This is the inverse funtion to k_unfold in the m mode. In particular, k_fold(k_unfold(darr, m), m, dim(darr)) will result in the original Tensor.

Usage

k_fold(mat, m = NULL, modes = NULL)

## S4 method for signature 'DelayedArray'
k_fold(mat, m, modes)

Arguments

mat

DelayedArray object (only 2D)
m

the index of the mode that is mapped onto the row indices
modes

the modes of the output DelayedArray

Details

This function is an extension of the k_fold by DelayedArray.

This is a wrapper function to fold.

Value

DelayedArray object with modes given by modes

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

fold, k_unfold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT2 <- k_unfold(darr, m=2)
identical(
    as.array(k_fold(matT2, m=2, modes=c(2,3,4))),
    as.array(darr))

Tensor k-mode Unfolding of DelayedArray

Description

Unfolding of a tensor by mapping the kth mode (specified through parameter m), and all other modes onto the column space. This the most common type of unfolding operation for Tucker decompositions and its variants. Also known as k-mode matricization.

Usage

k_unfold(darr, m)

## S4 method for signature 'DelayedArray'
k_unfold(darr, m)

Arguments

darr

DelayedArray object
m

the index of the mode to unfold on

Details

This function is an extension of the k_unfold by DelayedArray.

This is a wrapper function to unfold.

See also k_unfold(darr, m=NULL)

Value

matrix with dim(darr)[m] rows and prod(dim(darr)[-m]) columns

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

unfold, k_fold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
rs_unfold(darr, m=2)

Khatri-Rao Product against list

Description

Returns the Khatri-Rao product from a list of matrices or vectors. Commonly used for n-mode products and various Tensor decompositions.

Usage

khatri_rao_list(L, reverse = FALSE)

Arguments

L

list of DelayedArray
reverse

whether or not to reverse the order

Details

This function is an extension of the khatri_rao_list by DelayedArray.

Value

matrix that is the Khatri-Rao product

Note

The number of columns must match in every element of the input list.

See Also

hadamard, hadamard_list, kronecker, kronecker_list, khatri_rao

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,3))
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,4)),
    'darr2' = RandomUnifArray(c(3,4)))
khatri_rao_list(dlizt)

Khatri-Rao Product of DelayedArray

Description

Returns the Khatri-Rao (column-wise Kronecker) product of two matrices. If the inputs are vectors then this is the same as the Kronecker product.

Usage

khatri_rao(darr1, darr2)

## S4 method for signature 'DelayedArray,DelayedArray'
khatri_rao(darr1, darr2)

Arguments

darr1

first DelayedArray object
darr2

second DelayedArray object

Details

This function is an extension of the khatri_rao by DelayedArray.

Value

matrix that is the Khatri-Rao product

Note

The number of columns must match in the two inputs.

See Also

hadamard, hadamard_list, kronecker, kronecker_list, khatri_rao_list

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,4))
darr2 <- RandomUnifArray(c(3,4))
khatri_rao(darr1, darr2)

Kronecker Product against list

Description

Returns the Kronecker product from a list of matrices or vectors. Commonly used for n-mode products and various Tensor decompositions.

Usage

kronecker_list(L)

Arguments

L

list of DelayedArray

Details

This function is an extension of the kronecker_list by DelayedArray.

Value

matrix that is the Kronecker product

See Also

khatri_rao, khatri_rao_list, hadamard, hadamard_list, kronecker

Examples

library("DelayedRandomArray")
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,3,4)),
    'darr2' = RandomUnifArray(c(2,3,4)))
kronecker_list(dlizt)

Kronecker Product of DelayedArray

Description

Returns the Kronecker product of two Tensors. Commonly used for n-mode products and various Tensor decompositions.

Usage

kronecker(darr1, darr2)

## S4 method for signature 'DelayedArray,DelayedArray'
kronecker(darr1, darr2)

Arguments

darr1

first DelayedArray object
darr2

second DelayedArray object

Value

matrix that is the Kronecker product

See Also

khatri_rao, khatri_rao_list, hadamard, hadamard_list, kronecker_list

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,3))
darr2 <- RandomUnifArray(c(4,5))
kronecker(darr1, darr2)

Replicate of arbitrary object

Description

Returns the replicates of base obejct x.

Usage

list_rep(x, n=NULL)

Arguments

x

Any object
n

Number of replicate

Value

List

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
list_rep(darr, 3)

Tensor Matvec Unfolding of DelayedArray

Description

For 3-tensors only. Stacks the slices along the third mode.

Usage

matvec(darr)

## S4 method for signature 'DelayedArray'
matvec(darr)

Arguments

darr

DelayedArray object

Details

This function is an extension of the matvec by DelayedArray.

This is a wrapper function to unfold.

Value

matrix with prod(dim(darr)[-m]) rows and dim(darr)[m] columns

References

M. Kilmer, K. Braman, N. Hao, and R. Hoover, "Third-order tensors as operators on matrices: a theoretical and computational framework with applications in imaging". SIAM Journal on Matrix Analysis and Applications 2013.

See Also

unfold, unmatvec

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matvec(darr)

Mode-binding against list

Description

Returns the binded DelayedArray in mode-m.

Usage

modebind_list(L, m=NULL)

Arguments

L

list of DelayedArray
m

list of DelayedArray

Value

DelayedArray object

Note

The dimensions of mode m must match.

See Also

rbind_list, cbind_list

Examples

library("DelayedRandomArray")
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,3,4)),
    'darr2' = RandomUnifArray(c(2,3,4)))
modebind_list(dlizt, m=1)
modebind_list(dlizt, m=2)
modebind_list(dlizt, m=3)

Tensor Mean Across Single Mode of DelayedArray

Description

Given a mode for a K-tensor, this returns the K-1 tensor resulting from taking the mean across that particular mode.

Usage

modeMean(darr, m = NULL, drop = FALSE)

## S4 method for signature 'DelayedArray'
modeMean(darr, m, drop)

Arguments

darr

DelayedArray object
m

the index of the mode to average across
drop

whether or not mode m should be dropped

Details

This function is an extension of the modeMean by DelayedArray.

NOTE: Sparse mode of modeMean is not available for now.

modeMean(darr, m=NULL, drop=FALSE)

Value

K-1 or K Tensor, where K = length(dim(darr))

See Also

modeSum

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(1,2,3))
modeMean(darr, 1, drop=FALSE)
modeMean(darr, 1, drop=TRUE)
modeMean(darr, 2)
modeMean(darr, 3)

Tensor Sum Across Single Mode of DelayedArray

Description

Given a mode for a K-tensor, this returns the K-1 tensor resulting from summing across that particular mode.

Usage

modeSum(darr, m = NULL, drop = FALSE)

## S4 method for signature 'DelayedArray'
modeSum(darr, m, drop)

Arguments

darr

DelayedArray object
m

the index of the mode to sum across
drop

whether or not mode m should be dropped

Details

This function is an extension of the modeSum by DelayedArray.

NOTE: Sparse mode of modeSum is not available for now.

modeSum(darr, m=NULL, drop=FALSE)

Value

K-1 or K tensor, where K = length(dim(darr))

See Also

modeMean

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(1,2,3))
modeSum(darr, 1, drop=FALSE)
modeSum(darr, 1, drop=TRUE)
modeSum(darr, 2)
modeSum(darr, 3)

Matrix object of mouse mid brain data

Description

A matrix with 500 rows (genes) * 1907 columns (cells).

Usage

data(mouse_mid_brain)

Details

The data matrix is downloaded from GEO Series GSE76381 (https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE76381&format=file). For the details, see inst/script/make-data.R.

References

Y-h. Taguchi and T. Turki (2019) Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. Frontiers in Genetics, 10(864): 10:3389/fgene.2019.00864

See Also

mouse_mid_brain

Examples

data(mouse_mid_brain)

Multilinear Principal Components Analysis

Description

This is basically the Tucker decomposition of a K-Tensor, tucker, with one of the modes uncompressed. If K = 3, then this is also known as the Generalized Low Rank Approximation of Matrices (GLRAM). This implementation assumes that the last mode is the measurement mode and hence uncompressed. This is an iterative algorithm, with two possible stopping conditions: either relative error in Frobenius norm has gotten below tol, or the max_iter number of iterations has been reached. For more details on the MPCA of tensors, consult Lu et al. (2008).

Usage

mpca(darr, ranks=NULL, max_iter=25, tol=1e-05)

## S4 method for signature 'DelayedArray'
mpca(darr, ranks, max_iter, tol)

Arguments

darr

Tensor with K modes
ranks

a vector of the compressed modes of the output core Tensor, this has length K-1
max_iter

maximum number of iterations if error stays above tol
tol

relative Frobenius norm error tolerance

Details

This function is an extension of the mpca by DelayedArray.

Uses the Alternating Least Squares (ALS) estimation procedure. A progress bar is included to help monitor operations on large tensors.

Value

a list containing the following:

Z_ext

the extended core tensor, with the first K-1 modes given by ranks

U

a list of K-1 orthgonal factor matrices - one for each compressed mode, with the number of columns of the matrices given by ranks

conv

whether or not resid < tol by the last iteration

est

estimate of darr after compression

norm_percent

the percent of Frobenius norm explained by the approximation

fnorm_resid

the Frobenius norm of the error fnorm(est-darr)

all_resids

vector containing the Frobenius norm of error for all the iterations

Note

The length of ranks must match darr@num_modes-1.

References

H. Lu, K. Plataniotis, A. Venetsanopoulos, "Mpca: Multilinear principal component analysis of tensor objects". IEEE Trans. Neural networks, 2008.

See Also

tucker, hosvd

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(3,4,5))
mpca(darr, ranks=c(1,2))

Tensors Outer Product of DelayedArray

Description

Returns the outer product between two Tensors

Usage

outerProd(darr1, darr2)

## S4 method for signature 'DelayedArray,DelayedArray'
outerProd(darr1, darr2)

Arguments

darr1

first DelayedArray object
darr2

second DelayedArray object

Details

NOTE: Sparse mode of outerProd is not available for now.

Value

outer product between darr1 and darr2

Examples

library("DelayedRandomArray")
darr1 <- RandomUnifArray(c(2,3))
darr2 <- RandomUnifArray(c(4,5))
outerProd(darr1, darr2)

Population Value Decomposition

Description

The default Population Value Decomposition (PVD) of a series of 2D images. Constructs population-level matrices P, V, and D to account for variances within as well as across the images. Structurally similar to Tucker (tucker) and GLRAM (mpca), but retains crucial differences. Requires 2*n3 + 2 parameters to specified the final ranks of P, V, and D, where n3 is the third mode (how many images are in the set). Consult Crainiceanu et al. (2013) for the construction and rationale behind the PVD model.

Usage

pvd(darr, uranks=NULL, wranks=NULL, a=NULL, b=NULL)

## S4 method for signature 'DelayedArray'
pvd(darr, uranks, wranks, a, b)

Arguments

darr

3D DelayedArray (Tensor) with the third mode being the measurement mode
uranks

ranks of the U matrices
wranks

ranks of the W matrices
a

rank of P = U%*%t(U)
b

rank of D = W%*%t(W)

Details

This function is an extension of the pvd by DelayedArray.

The PVD is not an iterative method, but instead relies on n3 + 2 separate PCA decompositions. The third mode is for how many images are in the set.

Value

a list containing the following:

P

population-level matrix P = U%*%t(U), where U is constructed by stacking the truncated left eigenvectors of slicewise PCA along the third mode

V

a list of image-level core matrices

D

population-leve matrix D = W%*%t(W), where W is constructed by stacking the truncated right eigenvectors of slicewise PCA along the third mode

est

estimate of darr after compression

norm_percent

the percent of Frobenius norm explained by the approximation

fnorm_resid

the Frobenius norm of the error fnorm(est-darr)

References

C. Crainiceanu, B. Caffo, S. Luo, V. Zipunnikov, N. Punjabi, "Population value decomposition: a framework for the analysis of image populations". Journal of the American Statistical Association, 2013.

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(3,4,5))
pvd(darr, uranks=rep(2,5), wranks=rep(3,5), a=2, b=3)

Mode-binding against list

Description

Returns the binded DelayedArray in row space.

Usage

rbind_list(L)

Arguments

L

list of 2D DelayedArray

Details

This is a wrapper function to modebind_list, when the DelayedArrays are 2D.

Value

2D DelayedArray object

Note

The dimensions of row in each DelayedArray must match.

See Also

modebind_list

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
dlizt <- list(
    'darr1' = RandomUnifArray(c(2,3)),
    'darr2' = RandomUnifArray(c(2,3)))
rbind_list(dlizt)

Row Space Folding of 2D DelayedArray

Description

The inverse operation to rs_unfold.

Usage

rs_fold(mat, m = NULL, modes = NULL)

## S4 method for signature 'DelayedArray'
rs_fold(mat, m, modes)

Arguments

mat

DelayedArray object (only 2D)
m

the mode corresponding to rs_unfold
modes

the original modes of the DelayedArray

Details

This function is an extension of the rs_fold by DelayedArray.

This is a wrapper function to fold.

Value

DelayedArray (higher than 2D)

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

fold, rs_unfold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT2 <- rs_unfold(darr, m=2)
identical(
    as.array(rs_fold(matT2, m=2, modes=c(2,3,4))),
    as.array(darr))

Tensor Row Space Unfolding of DelayedArray

Description

Please see k_unfold and unfold.

Usage

rs_unfold(darr, m)

## S4 method for signature 'DelayedArray'
rs_unfold(darr, m)

Arguments

darr

DelayedArray object
m

mode to be unfolded on

Details

This function is an extension of the rs_unfold by DelayedArray.

This is a wrapper function to unfold.

See also rs_unfold(darr, m=NULL)

Value

DelayedArray (2D)

See Also

unfold, rs_fold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT2 <- rs_unfold(darr, m=2)

Setter to set the intermediate DelayedArray object in DelayedTensor

Description

Set whether the intermediate and output DelayedArray used in DelayedTensor is used as sparse tensor or not.

NOTE: Sparse mode is experimental! Whether it contributes to higher speed and lower memory is quite dependent on the sparsity of the DelayedArray, and the current implementation does not recognize the block size, which may cause Out-of-Memory errors.

Usage

setSparse(as.sparse=FALSE)

Arguments

as.sparse

TRUE or FALSE (Default: FALSE)

Value

Nothing

Examples

setSparse(TRUE)
setSparse(FALSE)

Setter to set the verbose mode of DelayedTensor

Description

Set the verbose message to monitor the block-processing procedure.

Usage

setVerbose(as.verbose=FALSE)

Arguments

as.verbose

TRUE or FALSE (Default: FALSE)

Value

Nothing

Examples

setVerbose(TRUE)
setVerbose(FALSE)

DelayedArray Times List

Description

Contracted (m-Mode) product between a Tensor of arbitrary number of modes and a list of matrices. The result is folded back into Tensor.

Usage

ttl(darr, list_mat, ms=NULL)

Arguments

darr

DelayedArray object with K modes
list_mat

a list of 2D DelayedArray objects
ms

a vector of modes to contract on (order should match the order of list_mat)

Details

This function is an extension of the ttl by DelayedArray.

This is a wrapper function to unfold.

Performs ttm repeated for a single Tensor and a list of matrices on multiple modes. For instance, suppose we want to do multiply a Tensor object darr with three matrices mat1, mat2, mat3 on modes 1, 2, and 3. We could do ttm(ttm(ttm(darr,mat1,1),mat2,2),3), or we could do ttl(darr,list(mat1,mat2,mat3),c(1,2,3)). The order of the matrices in the list should obviously match the order of the modes. This is a common operation for various Tensor decompositions such as CP and Tucker. For the math on the m-Mode Product, see Kolda and Bader (2009).

Value

DelayedArray object with K modes (Tensor)

Note

The returned Tensor does not drop any modes equal to 1.

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

ttm

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(3,4,5))
dlizt <- list(
    'darr1' = RandomUnifArray(c(10,3)),
    'darr2' = RandomUnifArray(c(10,4)))
ttl(darr, dlizt, ms=c(1,2))

Tensor Times Matrix (m-Mode Product)

Description

Contracted (m-Mode) product between a DelayedArray (Tensor) of arbitrary number of modes and a matrix. The result is folded back into Tensor.

Usage

ttm(darr, mat, m = NULL)

## S4 method for signature 'DelayedArray,DelayedArray'
ttm(darr, mat, m)

Arguments

darr

DelayedArray object
mat

input 2D DelayedArray with same number columns as the mth mode of darr
m

the mode to contract on

Details

This function is an extension of the ttm by DelayedArray.

By definition, rs_unfold(ttm(darr, mat), m) = mat%*%rs_unfold(darr, m), so the number of columns in mat must match the mth mode of darr. For the math on the m-Mode Product, see Kolda and Bader (2009).

Value

a DelayedArray object with K modes

Note

The mth mode of darr must match the number of columns in mat. By default, the returned Tensor does not drop any modes equal to 1.

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

rs_unfold, ttl

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
mat <- RandomUnifArray(c(10,4))
ttm(darr, mat, m=3)

Tucker Decomposition

Description

The Tucker decomposition of a tensor. Approximates a K-Tensor using a n-mode product of a core tensor (with modes specified by ranks) with orthogonal factor matrices. If there is no truncation in one of the modes, then this is the same as the MPCA, mpca. If there is no truncation in all the modes (i.e. ranks = darr@modes), then this is the same as the HOSVD, hosvd. This is an iterative algorithm, with two possible stopping conditions: either relative error in Frobenius norm has gotten below tol, or the max_iter number of iterations has been reached. For more details on the Tucker decomposition, consult Kolda and Bader (2009).

Usage

tucker(darr, ranks=NULL, max_iter=25, tol=1e-05)

## S4 method for signature 'DelayedArray'
tucker(darr, ranks, max_iter, tol)

Arguments

darr

Tensor with K modes
ranks

a vector of the modes of the output core Tensor
max_iter

maximum number of iterations if error stays above tol
tol

relative Frobenius norm error tolerance

Details

This function is an extension of the tucker by DelayedArray.

Uses the Alternating Least Squares (ALS) estimation procedure also known as Higher-Order Orthogonal Iteration (HOOI). Intialized using a (Truncated-)HOSVD. A progress bar is included to help monitor operations on large tensors.

Value

a list containing the following:

Z

the core tensor, with modes specified by ranks

U

a list of orthgonal factor matrices - one for each mode, with the number of columns of the matrices given by ranks

conv

whether or not resid < tol by the last iteration

est

estimate of darr after compression

norm_percent

the percent of Frobenius norm explained by the approximation

fnorm_resid

the Frobenius norm of the error fnorm(est-darr)

all_resids

vector containing the Frobenius norm of error for all the iterations

Note

The length of ranks must match darr@num_modes.

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

hosvd, mpca

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
tucker(darr, ranks=c(1,2,3))

Tensor Unfolding of 2D DelayedArray

Description

Unfolds the tensor into a matrix, with the modes in rs onto the rows and modes in cs onto the columns. Note that c(rs,cs) must have the same elements (order doesn't matter) as dim(darr). Within the rows and columns, the order of the unfolding is determined by the order of the modes. This convention is consistent with Kolda and Bader (2009).

Usage

unfold(darr, row_idx, col_idx)

## S4 method for signature 'DelayedArray'
unfold(darr, row_idx, col_idx)

Arguments

darr

DelayedArray object
row_idx

the indices of the modes to map onto the row space
col_idx

the indices of the modes to map onto the column space

Details

This function is an extension of the unfold by DelayedArray.

For Row Space Unfolding or m-mode Unfolding, see rs_unfold. For Column Space Unfolding or matvec, see cs_unfold.

vec returns the vectorization of the tensor.

Value

2D DelayedArray with prod(row_idx) rows and prod(col_idx) columns

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

k_unfold, matvec, rs_unfold, cs_unfold

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
unfold(darr, row_idx=2, col_idx=c(3,1))

Unmatvec Folding of 2D DelayedArray

Description

The inverse operation to matvec-methods, turning a matrix into a Tensor. For a full account of matrix folding/unfolding operations, consult Kolda and Bader (2009).

Usage

unmatvec(mat, modes = NULL)

## S4 method for signature 'DelayedArray'
unmatvec(mat, modes)

Arguments

mat

DelayedArray object (only 2D)
modes

the modes of the output DelayedArray

Details

This function is an extension of the unmatvec by DelayedArray.

This is a wrapper function to fold.

Value

DelayedArray object with modes given by modes

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

See Also

fold, matvec

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
matT1 <- matvec(darr)
identical(
    as.array(unmatvec(matT1, modes=c(2,3,4))),
    as.array(darr))

Tensor Vectorization of DelayedArray

Description

Change the dimension of DelayedArray from multi-dimension (e.g. array) to single-dimension (e.g. vector).

Usage

vec(darr)

## S4 method for signature 'DelayedArray'
vec(darr)

Arguments

darr

DelayedArray object

Details

This function is an extension of the vec by DelayedArray.

Value

1D DelayedArray (vector) with length prod(dim(darr))

References

T. Kolda, B. Bader, "Tensor decomposition and applications". SIAM Applied Mathematics and Applications 2009.

Examples

library("DelayedRandomArray")
darr <- RandomUnifArray(c(2,3,4))
vec(darr)