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Scalable nonnegative matrix trifactorization
BioData Mining volume 10, Article number: 41 (2017)
Abstract
Background
Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression coclustering, patient stratification, and genedisease association mining. Matrix factorization learns a latent data model that takes a data matrix and transforms it into a latent feature space enabling generalization, noise removal and feature discovery. However, factorization algorithms are numerically intensive, and hence there is a pressing challenge to scale current algorithms to work with large datasets. Our focus in this paper is matrix trifactorization, a popular method that is not limited by the assumption of standard matrix factorization about data residing in one latent space. Matrix trifactorization solves this by inferring a separate latent space for each dimension in a data matrix, and a latent mapping of interactions between the inferred spaces, making the approach particularly suitable for biomedical data mining.
Results
We developed a blockwise approach for latent factor learning in matrix trifactorization. The approach partitions a data matrix into disjoint submatrices that are treated independently and fed into a parallel factorization system. An appealing property of the proposed approach is its mathematical equivalence with serial matrix trifactorization. In a study on large biomedical datasets we show that our approach scales well on multiprocessor and multiGPU architectures. On a fourGPU system we demonstrate that our approach can be more than 100times faster than its singleprocessor counterpart.
Conclusions
A general approach for scaling nonnegative matrix trifactorization is proposed. The approach is especially useful parallel matrix factorization implemented in a multiGPU environment. We expect the new approach will be useful in emerging procedures for latent factor analysis, notably for data integration, where many large data matrices need to be collectively factorized.
Background
Biomedical data are becoming increasingly challenging to analyze due to their sheer volume and complexity. Dimensionality reduction approaches address challenges in modern biomedical data analytics by learning useful projections of data into a smaller, compact and patternrich latent space. An especially popular dimensionality reduction approach uses matrix factorization [1]. Numerous nonnegative matrix factorization methods have successfully been used for gene expression analysis [2–4], patient stratification [5], drugtarget interaction discovery [6], gene phenotyping [7], and magnetic resonance image analysis [8–10].
Nonnegative (twofactor) matrix factorization considers as input a data matrix X and learns two latent factors, U and V, such that their product U V approximates X, X≈U V, under some criterion of approximation error. One class of nonnegative matrix factorization approaches is nonnegative matrix trifactorization, which extends a twofactor model by introducing a third latent factor S, such that X≈U S V ^{T} [11]. This representation is more appropriate for nonsquare data because it explicitly models data interactions through a latent factor S [12]. Several optimization techniques for parallel nonnegative (twofactor) matrix factorization have recently been proposed [13–15]. These techniques first partition matrix X into blocks and then exploit the blockmatrix multiplication when learning U and V. However, such a straightforward approach does not apply to matrix trifactorization because, as we show in the Methods section, the learning of any block of U and V depends on factor S.
In this paper, we develop a principled mathematical approach and an algorithmic solution to latent factor learning for nonnegative matrix trifactorization. While there exists an initial solution to speed up the latent factor learning procedure using accelerated matrix operations on a MapReduce cluster [16], this approach is not optimal because it requires a specialized architecture [17]. Even more importantly, in the case of twofactor nonnegative matrix factorization, it was shown that the MapReducebased approach was outperformed by blockwise approaches by two orders of magnitude [18]. Blockwise approaches also provide the means for load balancing. These related studies thus encourage the development of a blockwise approach for matrix trifactorization.
The paper makes the following contributions. We develop a blockwise approach for matrix trifactorization. The new approach enables fast factorization on concurrent systems, such as multiprocessor and multiGPU architectures. We report on two variants of the approach: one variant for orthogonal matrix factorization [11] and the other for nonorthogonal matrix factorization [19]. We provide implementation of the new approach for both multiprocessor and multiGPU architectures. We evaluate the proposed approach with respect to dataset shape and size, parallelization degree, factorization rank, and data sparsity. In experiments on several biomedical datasets, we demonstrate that the new approach provides substantial speedups. The speedup is most pronounced on multiGPU architectures, where matrix trifactorization can be more than 100times faster than its serial counterpart.
Methods
We start by describing the notation, factorization model, and matrix trifactorization algorithm. The algorithm starts by initializing the latent factors, which are then iteratively revised until convergence. We then introduce a block data representation and provide an algorithm for partitioning data matrices into blocks. Finally, we develop the blockwise latent factor update rules and present the blockwise matrix trifactorization algorithm.
Preliminaries: nonnegative matrix trifactorization
Consider a nonnegative data matrix \({\mathbf {X}} \in \mathbb {R}^{n \times m}_{+}\), where n rows typically describe data instances and m columns provide their features. Nonnegative matrix trifactorization (NMTF) learns a decomposition of X into three latent factors \(\mathbf {U} \in \mathbb {R}_{+}^{n \times k_{1}}\), \(\mathbf {S} \in \mathbb {R}_{+}^{k_{1} \times k_{2}}\), and \(\mathbf {V} \in \mathbb {R}_{+}^{m \times k_{2}}\) by minimizing the reconstruction error \(F({\mathbf U},{\mathbf S},{\mathbf V})=\left \{\mathbf X}{\mathbf U}{\mathbf S}{\mathbf V}^{T}\right \_{Fro}^{2}\) [20, 21]. Columns in factors U and V are latent vectors and provide the basis of the vector space into which the data (columns and rows of X, respectively) are projected. Factorization ranks k _{1},k _{2}≪ min(m,n) are model parameters that specify the number of latent vectors.
Reconstruction error is typically minimized using the multiplicative update rules [1]. The rules are derived by computing the gradient of the reconstruction error F with respect to model parameters U, S, and V and by solving the gradient equations for the model parameters. This procedure results in the following set of update rules [19]:
where ∘ represents the elementwise product and the division is performed elementwise. The matrix trifactorization algorithm starts by initializing latent factors using small random values and then iteratively applies the update rules in Eqs. (1–3) until convergence [1].
An oftendesired variant [11] of matrix trifactorization imposes orthogonality constraints on the latent vectors. Orthogonality helps in data interpretation because latent vectors are independent of each other and can thus be associated with a particular combination of input features (for U) or input data instances (for V) [22, 23]. The objective function of orthogonal matrix trifactorization is \(F({\mathbf U},{\mathbf S},{\mathbf V})=\left \{\mathbf X}{\mathbf U}{\mathbf S}{\mathbf V}^{T}\right \_{Fro}^{2}\), under the constraint that U ^{T} U=I and V ^{T} V=I, where I is an identity matrix. Following a similar procedure of gradient computation as described above, we arrive at the following update rules for orthogonal matrix trifactorization [11]:
Blockwise multiplicative update rules
We present a blockwise formulation of multiplicative update rules for NMTF. We partition the input data X into N×M blocks, X ^{(i,j)}, where i∈{0,1,…,N−1} and j∈{0,1,…,M−1}. Conversely, latent factor U is rowpartitioned into N blocks, and V is columnpartitioned into M blocks. Figure 1 shows an example where matrix X is rowpartitioned into N=3 blocks and columnpartitioned into M=2 blocks.
Using this blockwise data representation we reformulate the multiplicative update rules from Eqs. (1–3) as follows:
where i and j denote ith row and jth column matrix block, respectively. Notice that our block partitioning scheme and update rules in Eqs. (7–9) preserve all properties of factorizing a nonpartitioned matrix X. That is, the result of blockwise matrix trifactorization is identical to the result returned by nonpartitioned matrix trifactorization as proposed by Long et al. [19]. For example, consider an update for factor U in Eq. (1) and its blockwise variant in Eq. (7). To show that these two update rules are equivalent, we need to check that the values in U ^{(i)} are identical to the values of U at corresponding positions. Notice that division in both updates is elementwise; hence, we can independently check equivalency of numerator and denominator. For example, the numerator in Eq. (1) is expressed as X V S ^{T}. An ith row of this expression can be written in a blockwise manner as \(\sum _{j}{\mathbf X^{(i,j)}}{\mathbf V^{(j)}}{\mathbf S}^{T}\), which is exactly the corresponding numerator in Eq. (7). The equivalency of other terms of nonpartitioned and blockwise updated rules are further shown in the proof of equivalence of blockwise and nonblockwise formulation of NMTF (Additional file 1: Section 1).
Next, we propose update rules for blockwise orthogonal matrix trifactorization:
The formulation is identical to the nonblockwise formulation originally proposed in Ding et al. [11] and shown in Eqs. (4–6). As before, this property is important because it indicates the proposed blockwise update rules yield latent factors that are identical to the nonblockwise update rules in Ding et al. [11].
Matrix partitioning
To effectively partition data matrix X and latent factors U, V and S into blocks, we distinguish between sparse and dense data matrices. In general, most elements of sparse data matrices are zero, whereas most elements of dense matrices are nonzero [24]. In the case of dense matrix X, our matrix partitioning procedure splits X into contiguous blocks of approximately equal size. In the case of sparse matrix X, we adapt the block size such that each block contains approximately equal number of nonzero elements. Such partitioning leads to workload balancing when factorization is carried out in parallel.
The details of matrix partitioning are provided in Algorithm 1. The algorithm takes as input a data matrix X and a desired blockwise configuration and returns an appropriate partitioning of X. Additional parameters are the number of row blocks N and column blocks M. Partitioning of latent factors U, V and S is determined by the partitioning of matrix X (for example, see Fig. 2).
Overview of blockwise matrix trifactorization
A complete algorithm for matrix trifactorization is given as Algorithm 2. The algorithm starts with matrix partitioning, followed by initialization of latent factors. Initial latent factors are then iteratively refined until convergence using the proposed blockwise multiplicative update rules. While not the subject of this paper, convergence is heuristically determined by observing the value of the objective function or the quality of latent factors and corresponding reconstruction error [11, 19].
Data and experimental setup
To test the benefits of the blockwise trifactorization approach, we implemented the approach on multiprocessor and multiGPU architecture. We then tested the implementation on several biomedical datasets. Here, we describe the datasets, evaluation approach and implementation details.
Data
We considered the following six datasets (Table 1):

TCGABRCA is an RNASeq gene expression dataset from the GDC databases [25]. The dataset contains expression measurements [26] of genes and gene variants from almost 1,300 human samples.

ETABM185 is a microarray gene expression dataset [27] available at ArrayExpress database with accession number ETABM185 [28]. It contains gene expression measurements from almost 6,000 human samples representing different cell and tissue types.

Fetus denotes the fetusspecific functional interaction network from the GIANT database [29]. This is a network on human genes where two genes are connected if they are specifically coexpressed in fetal tissue. The fetusspecific gene interaction network [30] has 30 million interactions and is the sparsest network dataset in the GIANT database.

Retina denotes the retinaspecific functional interaction network from the GIANT database [29]. This is a network on human genes where two genes are connected if they are specifically coexpressed in retinal tissue. The retinaspecific gene interaction network [31] has 147 million interactions.

Cochlea denotes the cochleaspecific functional interaction network from the GIANT database [29]. This is a network on human genes where two genes are connected if they are specifically coexpressed in cochlear tissue. The cochleaspecific gene interaction network [32] has 280 million interactions and is the densest network dataset in the GIANT database.

TCGAMethyl is a DNA methylation dataset from the GDC database [25], which contains 10,181 samples from Illumina Human Methylation 450 platform [33]. Each sample contains methylation beta values for over 485,577 CpG sites.
Experimental setup
We factorized each dataset on multiprocessor and on multiGPU architectures. To asses the runtime statistics for a single iteration of factorization, factorization was run for 100 iterations, and measurements were averaged across ten runs. To test relationship between scalability and factorization rank, we varied parameter k, such that k∈{10,20,…,100}. For a given dataset and a given value of factorization rank, factor matrices were initialized to the same values across different platforms.
We considered the following runtime metrics:

Speedup was expressed as the ratio between processing time t _{ A } for single iteration on observed architecture A, and processing time t _{ C P U−1} on a singleCPU: \(s_{\mathrm A} = \frac {t_{A}}{t_{CPU1}}\).

Efficiency was expressed as a fraction of linear speedup, a speedup that assumes that p processing units would reduce the runtime by a factor of p. For an system A _{ p } with p processing units, we compute efficiency relative to performance of a singleunit system A _{1} on the same architecture. The formula is: \(E_{A_{p}} = \frac {T_{A_{1}}}{p T_{A_{p}}}\). Efficiency of \(E_{A_{p}}=1\) indicates a linear speedup. Communication cost pushes efficiency below this optimal value.
Implementation
We implemented the blockwise matrix factorization in a Python module. To support multiGPU architecture we use PyCUDA [34]. Communication between processing units uses OpenMPI [35] with Mpi4py Python interface [36]. Matrix operations are accelerated with OpenBLAS [37] on multiprocessor architectures and CuBLAS [38] on GPUs. On multiprocessor architectures we use NumPy for dense matrices and SciPy for operations on sparse matrices. On GPUs we use Scikitcuda [39] for dense matrix operations and CuSPARSE [40] with Pythoncudacffi [41] for operations on sparse matrices. Our implementation is available online [42].
All experiments were run on a computational server with Intel Xeon E51650 processor and on four NVIDIA Titan X (Maxwell) GPUs, each with 12 GB of memory. Given p processing units, we split input data matrix X into p blocks, testing various block configurations. Each block was passed to a processing unit that communicated the block with other units when data for next computational steps were required. Figure 3 shows an example of this computational and data transfer workflow for one update of matrix U on a 2×2block configuration. Notice this workflow applies to both 4GPU and 4processor architecture.
Results
We here present results for nonorthogonal blockwise matrix trifactorization. Results for orthogonal blockwise matrix trifactorization are qualitatively the same and are provided in the Additional file 1.
Figures 4 and 5 show speedups achieved on multiprocessing and multiGPU architectures, respectively, for each of six considered biomedical datasets. Runtime performance was tested on architectures with one, two or four processing units. Data matrices were partitioned according to block configurations in Table 2.
Efficiency of parallel implementation depends on dataset shape and on chosen block configuration. Measurements illustrating this dependency are shown in Fig. 6 for multiprocessor architectures and in Fig. 7 for multiGPU architectures.
One bottleneck of GPUbased architectures is communication overhead that occurs when copying data between GPU boards. This overhead was also observed in our experiments. For example, up to 50% of time needed to factorize TCGABRCA dataset in a 4GPU environment was spent for communication. On larger datasets, however, this overhead was less pronounced. A detailed analysis is provided in Additional file 1: Figures S6 and S8. The communication overhead on multiprocessor architectures is negligible as shown in the Additional file 1: Figures S5 and S7.
We also studied algorithm scalability with respect to factorization rank. Figure 9 shows runtime of one iteration as a function of factorization rank value on a fourGPU architecture using a 2×2block configuration. Figure 8 shows the results on a fourprocessor architecture.
Using matrix partitioning approach presented in Algorithm 1, we can increase speedup on sparse datasets that have imbalanced distribution of nonzero elements. The approach adapts matrix block size based on the number of nonzero elements. In Additional file 1: Figure S11 we show factorization speedup attributed to the adaptive nature of Algorithm 1, and compared to nonadaptive partitioning of data matrix into equally sized blocks. We observe a speedup of up to 1.4times on multiprocessor architecture, and up to 1.2times on multiGPU architecture.
Discussion
Speedup
Speedup on GPUarchitectures is substantial, and pronounced with the dataset size and number of GPUs. For example, factorization on a retina dataset was 150times faster than that on a single processor. Datasets in Fig. 5 are ordered by their number of nonzero elements, and we can observe a steady increase in speedup. Similar trends can also be observed on multiprocessor architectures (Fig. 4), but the speedups are substantially lower than those on the GPUs.
For TCGAMethyl dataset, the complete data matrix occupies about 19 GBytes of GPU’s memory (Additional file 1: Table S1). With a 12 GBytes of total memory on each GPU, and considering the overhead of libraries and temporary data matrices for interGPU communication, the data does not fit to the working memory in 1×1 and 1×2 block configurations. Running the factorization with 1×4 block configurations on 1GPU or 2GPU is feasible, but due to insufficient memory to store all necessary blocks in a single GPU requires a transfer of data between main memory and GPUs which severely impacts the runtime and prohibits any speedup. On this large dataset, a configuration with 4GPUs has sufficient memory and provides for excellent speedup (Fig. 5). This case also demonstrates that for large datasets the proposed approach requires setups with the adequate number of GPUs that can keep all the data in working GPU memory.
Efficiency effects of block configuration
Block configuration plays a significant role in minimizing the impact of data transfers and balancing the load across devices (Figs. 6 and 7). Tall datasets (ETABM185) favor rowwise partitioning (e.g., 2×1 and 4×1). Wide datasets (TCGABRCA, TCGAMethyl) favor columnwise partitioning (1×2 and 1×4). The two mentioned datasets, ETABM185 and TCGABRCA, are also those where the effect of the block configuration on efficiency was most pronounced. This observation highlights that suitable block configuration is data dependent, and also indicates that the selection of block configuration can be automated.
The drop in efficiency under a particular choice of block configuration can be explained by increased communication overhead (Additional file 1: Figures S5 and S6). As we increase the number of devices that run in parallel, we need to perform additional data transfers that are not needed on setups with one matrix block. For example, in the case of tall dataset EMTAB185 and columnwise partitioning (1×4), over 40% of factorization runtime was spent for transferring data between GPUs. On the other hand, in the case of wide TCGABRCA dataset, the lowest efficiency was measured when rowwise partitioning (4×1) was used, because communication cost was the highest.
Factorization rank
Next, we evaluate the performance of our approach when varying the value of the matrix factorization rank. Factorization rank is a vital parameter of all matrix factorization methods because it determines the number of latent vectors. A larger factorization rank means the inferred latent model has a larger degree of freedom and can thus better approximate the input data matrix [43]. However, increasing factorization rank demands more computational resources and can result in poorer generalization performance [44]. Instead of determining the optimal factorization rank for a given dataset, our goal here is to investigate how the scalability of the proposed blockwise matrix factorization algorithm depends on the value of the factorization rank and on the sparsity of the input data matrix.
Figure 8 shows the iteration time of NMTF as a function of factorization rank on a 4processor architecture. We can observe that by increasing the factorization rank, the time of iteration increases linearly. For this analysis, both parameters k _{1} and k _{2}, were set with equal values and shown as a single factorization rank parameter. Partitioning was done according to Table 2. When using a single process, the iteration time is proportionally slower according to the speedup shown in Fig. 4.
Figure 9 shows results that correspond to iteration time on 4GPU architecture. We can see stepwise increases in iteration time, which is a result of the way the multiplication kernel utilizes the physical resources of the GPU [45]. The multiplication on the GPU is done on tiles of data which are processed by several threads in parallel. If the matrix shape is not aligned to the tile size, the border tiles will not make full use of the resources [46].
When comparing the factorization time of a sparse dataset (Fetus) and dense datasets (Retina, Cochlea) of similar size, the benefits of using sparse data structure are substantial. On a GPU, the factorization time on a sparse dataset (Fetus) is slower than on comparable dense datasets (Retina, Cochlea). This is because multiplication with sparse structures requires slower nonsequential memory access [47].
Interpretation of factorization results
Matrix factorization methods can be used to gain a better understanding of the data and their relationships as the methods identify cluster structures and detect potential new associations. The latent factors learned by NMTF reveal clusters in each of the two dimensions of the input data (matrices U and V) and encode cluster interactions (matrix S). The analysis of the latent factors can then lead to data interpretation, cluster discovery, and to prediction of new interactions.
We here demonstrate that trifactorization can lead to the reconstruction of biologically meaningful interactions. We have used a DNA methylation dataset (TCGAMethyl, Table 1) consisting of 10,181 tissue samples from 33 cancer types. Tissue samples are profiled using methylation beta values for 485,577 CpG sites of the DNA. From these, we have considered only the sites that are related to 567 genes with known cancer interactions as listed in the Sanger cancer catalog [48]. Of those, 491 genes were included in our dataset and altogether involved 14,299 methylation sites. The resulting matrix had 10,181 rows and 14,299 columns. We factorized the matrix using factorization ranks k _{1}=25, k _{2}=30, which yielded an optimal data compression with respect to the accuracy evaluated on a validation dataset (see Additional file 1: Figure S15).
Additional file 1: Table S2 lists five resulting cluster pairs that relate clusters of genes (from matrix V) and clusters of cancer types (from matrix U) with highest interaction scores in matrix S. First, we note that factorization revealed related cancer types, with, for example, colon, stomach and rectum adenocarcinoma (Additional file 1: Table S2, first row) forming its own group. Also, we found several common Gene Ontology annotations for the clustered genes (Additional file 1: Table S3). Most importantly, we found evidence in published literature for a majority of interactions between genes and cancer types inferred through matrix trifactorization. For example, GATA2 was suggested as a prospective indicator for poor prognosis in patients with colorectal cancer [49], and FAT4 functions as a tumor suppressor for stomach cancer [50]. Other supporting publications are listed in Additional file 1: Table S2.
Transcriptional silencing by DNA methylation plays an important role in the onset of cancer [51, 52]. It is thus encouraging that some of the critical interactions between methylated genes and diseases can be inferred, as demonstrated by this analysis, by nonnegative matrix factorization of methylation cancer data alone.
Conclusion
Nonnegative matrix trifactorization is a successful modeling approach that can reveal hidden patterns in biomedical datasets. Current serial factorization approaches take substantial runtime, particularly for larger datasets. We proposed a blockwise approach to speed up matrix trifactorization through parallel execution. Experiments show the approach easily scales to very large datasets, and can achieve speedups of up to two orders of magnitude on current GPUbased architectures. We anticipate the proposed approach will be important for data integration, where matrix trifactorization on large collections of data matrices [53] has already been proven superior and where execution times run into days.
Abbreviations
 CPU:

Central processing unit
 GPU:

Graphics processing unit
 MPI:

Message passing interface
 NMTF:

Nonnegative matrix trifactorization
 PU:

Processing unit
 RNA:

Ribonucleic acid
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Acknowledgements
This work was supported by Slovenian Research Agency grant P20209 and by a grant HealthF52010242038 from European Union FP7 programme.
Availability of data and materials
A Python library implementing the proposed blockwise matrix trifactorization is available at the GitHub repository https://github.com/acopar/crow.
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AC and Mž developed the method; AC implemented the method and performed the experiments; and AC, Mž and BZ wrote the manuscript. BZ coordinated the project. All authors read and approved the final manuscript.
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Document with mathematical proofs, results for impact of communication, impact of balancing sparse datasets and results for orthogonal NMTF. (PDF 317 kb)
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Čopar, A., žitnik, M. & Zupan, B. Scalable nonnegative matrix trifactorization. BioData Mining 10, 41 (2017). https://doi.org/10.1186/s1304001701606
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DOI: https://doi.org/10.1186/s1304001701606