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8. Discretized Non-negative Tucker Decomposition (`dNTD`)

#### Koki Tsuyuzaki

#### 2025-08-25

# Introduction

In this vignette, we consider approximating a non-negative tensor as a product of binary or non-negative low-rank matrices (a.k.a., factor matrices).

Test data is available from `toyModel`.

    library("dcTensor")
    X <- dcTensor::toyModel("dNTF")

You will see that there are four blocks in the data tensor as follows.

    suppressMessages(library("nnTensor"))
    plotTensor3D(X)

# Binary Tensor Factorization (BTF)

Here, we introduce a non-negative tensor decomposition method, non-negative Tucker decomposition (NTD (Kim 2007; CICHOCK 2009)). The difference with the NTF is that different ranks can be specified for factor matrices such as \(A_1\) (\(J1 \times N\)), \(A_2\) (\(J2 \times M\)), and \(A_3\) (\(J3 \times L\)) and that the core tensor can have non-negative values in the non-diagonal elements. This degree of freedom will show that NTD fits the second set of data well. For the details, see `NTD` function of nnTensor package.

## Basic Usage

In BTF by NTD, rank parameters are needed to be set in advance. Other settings such as the number of iterations (`num.iter`) or factorization algorithm (`algorithm`) are also available. For the details of arguments of dNTD, see `?dNTD`. After the calculation, various objects are returned by `dNTD`. BTF is achieved by specifying the binary regularization parameter as a large value like the below:

    set.seed(123456)
    out_dNTD <- dNTD(X, Bin_A=c(1e+6, 1e+6, 1e+6), thr=1e-20, rank=c(4,4,4))
    str(out_dNTD, 2)

    ## List of 6
    ##  $ S            :Formal class 'Tensor' [package "rTensor"] with 3 slots
    ##  $ A            :List of 3
    ##   ..$ A1: num [1:4, 1:30] 0 0 0.000353 0 0 ...
    ##   ..$ A2: num [1:4, 1:30] 0 1 0 0 0 ...
    ##   ..$ A3: num [1:4, 1:30] 0 1 0 0 0 ...
    ##  $ RecError     : Named num [1:101] 1.00e-19 3.11e-14 3.12e-14 3.13e-14 3.07e-14 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ TrainRecError: Named num [1:101] 1.00e-19 3.11e-14 3.12e-14 3.13e-14 3.07e-14 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ TestRecError : Named num [1:101] 1e-19 0e+00 0e+00 0e+00 0e+00 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ RelChange    : Named num [1:101] 1.00e-19 8.93e+16 4.76e-03 3.15e-03 2.11e-02 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...

After the calculation, various objects are returned by `dNTD`.

The reconstruction error (`RecError`) and relative error (`RelChange`, the amount of change from the reconstruction error in the previous step) can be used to diagnose whether the calculation is converged or not.

    layout(t(1:2))
    plot(log10(out_dNTD$RecError[-1]), type="b", main="Reconstruction Error")
    plot(log10(out_dNTD$RelChange[-1]), type="b", main="Relative Change")

The product of core tensor \(S\) and factor matrices \(A_{k}\) shows whether the original data is well-recovered by `dNTD`.

    recX <- recTensor(out_dNTD$S, out_dNTD$A)
    layout(t(1:2))
    plotTensor3D(X)
    plotTensor3D(recX, thr=0)

The histograms of \(A_{k}\)s show that \(A_{k}\) looks binary.

    layout(t(1:3))
    hist(out_dNTD$A[[1]], main="A1", breaks=100)
    hist(out_dNTD$A[[2]], main="A2", breaks=100)
    hist(out_dNTD$A[[3]], main="A3", breaks=100)

# Semi-Binary Tensor Factorization (SBTF)

Here, we define this formalization as semi-binary tensor factorization (SBTF). SBTF can capture discrete patterns from non-negative matrices.

To demonstrate SBMF, next we use a non-negative tensor from the `nnTensor` package. You will see that there are four blocks in the data tensor as follows.

    X2 <- nnTensor::toyModel("CP")
    plotTensor3D(X2)

## Basic Usage

In SBTF by NTD, rank parameters are needed to be set in advance. Other settings such as the number of iterations (`num.iter`) or factorization algorithm (`algorithm`) are also available. For the details of arguments of dNTF, see `?dNTF`. After the calculation, various objects are returned by `dNTF`. SBTF is achieved by specifying the binary regularization parameter as a large value like the below:

    set.seed(123456)
    out_dNTD2 <- dNTD(X2, Bin_A=c(1e-10, 1e-10, 1e+5), rank=c(4,4,4))
    str(out_dNTD2, 2)

    ## List of 6
    ##  $ S            :Formal class 'Tensor' [package "rTensor"] with 3 slots
    ##  $ A            :List of 3
    ##   ..$ A1: num [1:4, 1:30] 1.29e-08 1.22e-08 6.94e-06 1.04e-08 2.54e-08 ...
    ##   ..$ A2: num [1:4, 1:30] 7.89e-02 1.05e+01 1.73e-16 3.85e-02 3.94e-02 ...
    ##   ..$ A3: num [1:4, 1:30] 0.001979 1.019649 0.001033 0.002067 0.000236 ...
    ##  $ RecError     : Named num [1:101] 1.00e-09 2.92e+02 2.92e+02 2.92e+02 2.92e+02 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ TrainRecError: Named num [1:101] 1.00e-09 2.92e+02 2.92e+02 2.92e+02 2.92e+02 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ TestRecError : Named num [1:101] 1e-09 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
    ##  $ RelChange    : Named num [1:101] 1.00e-09 1.12e+07 1.09e-03 9.36e-04 7.81e-04 ...
    ##   ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...

`RecError` and `RelChange` can be used to diagnose whether the calculation is converged or not.

    layout(t(1:2))
    plot(log10(out_dNTD2$RecError[-1]), type="b", main="Reconstruction Error")
    plot(log10(out_dNTD2$RelChange[-1]), type="b", main="Relative Change")

The product of core tensor \(S\) and factor matrices \(A_{k}\) shows whether the original data is well-recovered by `dNTD`.

    recX <- recTensor(out_dNTD2$S, out_dNTD2$A)
    layout(t(1:2))
    plotTensor3D(X2)
    plotTensor3D(recX, thr=0)

The histograms of \(A_{k}\)s show that \(A_{k}\) looks binary.

    layout(t(1:3))
    hist(out_dNTD2$A[[1]], main="A1", breaks=100)
    hist(out_dNTD2$A[[2]], main="A2", breaks=100)
    hist(out_dNTD2$A[[3]], main="A3", breaks=100)

# Session Information

    ## R version 4.4.3 (2025-02-28)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Rocky Linux 9.5 (Blue Onyx)
    ##
    ## Matrix products: default
    ## BLAS:   /opt/R/4.4.3/lib64/R/lib/libRblas.so
    ## LAPACK: /opt/R/4.4.3/lib64/R/lib/libRlapack.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: Asia/Tokyo
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] nnTensor_1.3.0    fields_16.3.1     viridisLite_0.4.2 spam_2.11-1
    ## [5] dcTensor_1.3.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] gtable_0.3.6       jsonlite_1.8.9     dplyr_1.1.4        compiler_4.4.3
    ##  [5] maps_3.4.3         tidyselect_1.2.1   Rcpp_1.1.0         plot3D_1.4.2
    ##  [9] tagcloud_0.7.0     jquerylib_0.1.4    scales_1.3.0       yaml_2.3.10
    ## [13] fastmap_1.2.0      ggplot2_3.5.1      R6_2.6.1           generics_0.1.3
    ## [17] tcltk_4.4.3        knitr_1.50         MASS_7.3-65        dotCall64_1.1-1
    ## [21] misc3d_0.9-1       tibble_3.3.0       munsell_0.5.1      pillar_1.10.1
    ## [25] bslib_0.9.0        RColorBrewer_1.1-3 rlang_1.1.6        cachem_1.1.0
    ## [29] xfun_0.53          sass_0.4.10        cli_3.6.5          magrittr_2.0.3
    ## [33] digest_0.6.37      grid_4.4.3         rTensor_1.4.9      lifecycle_1.0.4
    ## [37] vctrs_0.6.5        evaluate_1.0.3     glue_1.8.0         colorspace_2.1-1
    ## [41] rmarkdown_2.29     pkgconfig_2.0.3    tools_4.4.3        htmltools_0.5.8.1

# References

CICHOCK, A. et al. 2009. Nonnegative Matrix and Tensor Factorizations. Wiley.

Kim, Y.-D. et al. 2007. “Nonnegative Tucker Decomposition.” IEEE CVPR, 1–8.