dNTF)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)
To decompose a binary tensor (\(\mathcal{X}\)), non-negative CP decomposition (a.k.a. non-negative tensor factorization; NTF (Cichocki 2007; CICHOCK 2009)) can be applied. NTF appoximates \(\mathcal{X}\) (\(N \times M \times L\)) as the mode-product of a core tensor \(S\) (\(J \times J \times J\)) and factor matrices \(A_1\) (\(J \times N\)), \(A_2\) (\(J \times M\)), and \(A_3\) (\(J \times L\)).
\[ \mathcal{X} \approx \mathcal{S} \times_{1} A_1 \times_{2} A_2 \times_{3} A_3\ \mathrm{s.t.}\ \mathcal{S} \geq 0, A_{k} \geq 0\ (k=1 \ldots 3) \]
Note that _{k} is the mode-\(k\)
product (CICHOCK 2009) and the core tensor
\(S\) has non-negative values only in
the diagonal element. For the details, see NTF function of
nnTensor
package.
In BTF, a rank parameter \(J\)
(\(\leq \min(N, M)\)) is 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. BTF is achieved by
specifying the binary regularization parameter as a large value like the
below:
set.seed(123456)
out_dNTF <- dNTF(X, Bin_A=c(1e+2, 1e+2, 1e+2), algorithm="KL", rank=4)
str(out_dNTF, 2)## List of 6
## $ S : num [1:4] 2.24 2.23 2.24 2.24
## $ A :List of 3
## ..$ : num [1:4, 1:30] 9.99e-01 2.22e-16 2.22e-16 1.00 9.99e-01 ...
## ..$ : num [1:4, 1:30] 1.00 2.22e-16 2.22e-16 2.22e-16 1.00 ...
## ..$ : num [1:4, 1:30] 4.47e-01 9.94e-17 9.93e-17 9.93e-17 4.47e-01 ...
## $ RecError : Named num [1:28] 1.00e-09 2.67e+01 2.45e+01 2.36e+01 2.27e+01 ...
## ..- attr(*, "names")= chr [1:28] "offset" "1" "2" "3" ...
## $ TrainRecError: Named num [1:28] 1.00e-09 2.67e+01 2.45e+01 2.36e+01 2.27e+01 ...
## ..- attr(*, "names")= chr [1:28] "offset" "1" "2" "3" ...
## $ TestRecError : Named num [1:28] 1e-09 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00 ...
## ..- attr(*, "names")= chr [1:28] "offset" "1" "2" "3" ...
## $ RelChange : Named num [1:28] 1.00e-09 2.56e-02 8.80e-02 4.16e-02 3.89e-02 ...
## ..- attr(*, "names")= chr [1:28] "offset" "1" "2" "3" ...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_dNTF$RecError[-1]), type="b", main="Reconstruction Error")
plot(log10(out_dNTF$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 dNTF.
recX <- recTensor(out_dNTF$S, out_dNTF$A)
layout(t(1:2))
plotTensor3D(X)
plotTensor3D(recX, thr=0)
The histograms of \(A_{k}\)s show that all the factor matrices \(A_{k}\) looks binary.
layout(t(1:3))
hist(out_dNTF$A[[1]], main="A1", breaks=100)
hist(out_dNTF$A[[2]], main="A2", breaks=100)
hist(out_dNTF$A[[3]], main="A3", breaks=100)
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)
In SBTF, a rank parameter \(J\)
(\(\leq \min(N, M)\)) is 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_dNTF2 <- dNTF(X2, Bin_A=c(1e+5, 1e+5, 1e-10), algorithm="KL", rank=4)
str(out_dNTF2, 2)## List of 6
## $ S : num [1:4] 13.1 31.7 112.1 1474.1
## $ A :List of 3
## ..$ : num [1:4, 1:30] 0.00704 0.00175 0.47548 0.00303 0.00653 ...
## ..$ : num [1:4, 1:30] 0.00905 0.00602 0.10119 0.00226 0.0092 ...
## ..$ : num [1:4, 1:30] 0.1385 0.2206 0.0447 0.0048 0.1523 ...
## $ RecError : Named num [1:101] 1.00e-09 2.46e+04 3.90e+03 2.96e+03 6.38e+03 ...
## ..- attr(*, "names")= chr [1:101] "offset" "1" "2" "3" ...
## $ TrainRecError: Named num [1:101] 1.00e-09 2.46e+04 3.90e+03 2.96e+03 6.38e+03 ...
## ..- 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 8.23e-01 5.30 3.19e-01 5.36e-01 ...
## ..- 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_dNTF2$RecError[-1]), type="b", main="Reconstruction Error")
plot(log10(out_dNTF2$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 dNTF.
recX <- recTensor(out_dNTF2$S, out_dNTF2$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_dNTF2$A[[1]], main="A1", breaks=100)
hist(out_dNTF2$A[[2]], main="A2", breaks=100)
hist(out_dNTF2$A[[3]], main="A3", breaks=100)
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-conda-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /home/koki/miniconda3/lib/libopenblasp-r0.3.17.so
##
## 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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] nnTensor_1.1.12 fields_13.3 viridis_0.6.2 viridisLite_0.4.0
## [5] spam_2.8-0 dcTensor_1.0.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.8 highr_0.9 RColorBrewer_1.1-2 rTensor_1.4.8
## [5] bslib_0.3.1 compiler_3.6.3 pillar_1.7.0 jquerylib_0.1.4
## [9] tools_3.6.3 dotCall64_1.0-1 digest_0.6.29 jsonlite_1.8.0
## [13] evaluate_0.15 lifecycle_1.0.1 tibble_3.1.2 gtable_0.3.0
## [17] pkgconfig_2.0.3 rlang_0.4.11 DBI_1.1.2 yaml_2.3.5
## [21] xfun_0.29 fastmap_1.1.0 gridExtra_2.3 stringr_1.4.0
## [25] dplyr_1.0.6 knitr_1.37 generics_0.1.2 sass_0.4.0
## [29] vctrs_0.3.8 maps_3.4.0 plot3D_1.4 tidyselect_1.1.1
## [33] grid_3.6.3 glue_1.4.2 R6_2.5.1 fansi_1.0.2
## [37] tcltk_3.6.3 rmarkdown_2.11 purrr_0.3.4 ggplot2_3.3.5
## [41] magrittr_2.0.2 scales_1.1.1 htmltools_0.5.2 ellipsis_0.3.2
## [45] MASS_7.3-55 tagcloud_0.6 misc3d_0.9-1 assertthat_0.2.1
## [49] colorspace_2.0-3 utf8_1.2.2 stringi_1.7.6 munsell_0.5.0
## [53] crayon_1.5.0