Dataset Information

A unified framework for link prediction based on non-negative matrix factorization with coupling multivariate information.

ABSTRACT: Many link prediction methods have been developed to infer unobserved links or predict missing links based on the observed network structure that is always incomplete and subject to interfering noise. Thus, the performance of existing methods is usually limited in that their computation depends only on input graph structures, and they do not consider external information. The effects of social influence and homophily suggest that both network structure and node attribute information should help to resolve the task of link prediction. This work proposes SASNMF, a link prediction unified framework based on non-negative matrix factorization that considers not only graph structure but also the internal and external auxiliary information, which refers to both the node attributes and the structural latent feature information extracted from the network. Furthermore, three different combinations of internal and external information are proposed and input into the framework to solve the link prediction problem. Extensive experimental results on thirteen real networks, five node attribute networks and eight non-attribute networks show that the proposed framework has competitive performance compared with benchmark methods and state-of-the-art methods, indicating the superiority of the presented algorithm.

SUBMITTER: Wang W

PROVIDER: S-EPMC6264521 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

A unified framework for link prediction based on non-negative matrix factorization with coupling multivariate information.

Wang Wenjun W Tang Minghu M Jiao Pengfei P

PloS one 20181129 11

Many link prediction methods have been developed to infer unobserved links or predict missing links based on the observed network structure that is always incomplete and subject to interfering noise. Thus, the performance of existing methods is usually limited in that their computation depends only on input graph structures, and they do not consider external information. The effects of social influence and homophily suggest that both network structure and node attribute information should help t ...[more]

PMID: 30496261

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Project description:The relationship between grey matter volume (GMV) patterns and age can be captured by multivariate pattern analysis, allowing prediction of individuals' age based on structural imaging. Raw data, voxel-wise GMV and non-sparse factorization (with Principal Component Analysis, PCA) show good performance but do not promote relatively localized brain components for post-hoc examinations. Here we evaluated a non-negative matrix factorization (NNMF) approach to provide a reduced, but also interpretable representation of GMV data in age prediction frameworks in healthy and clinical populations. This examination was performed using three datasets: a multi-site cohort of life-span healthy adults, a single site cohort of older adults and clinical samples from the ADNI dataset with healthy subjects, participants with Mild Cognitive Impairment and patients with Alzheimer's disease (AD) subsamples. T1-weighted images were preprocessed with VBM8 standard settings to compute GMV values after normalization, segmentation and modulation for non-linear transformations only. Non-negative matrix factorization was computed on the GM voxel-wise values for a range of granularities (50-690 components) and LASSO (Least Absolute Shrinkage and Selection Operator) regression were used for age prediction. First, we compared the performance of our data compression procedure (i.e., NNMF) to various other approaches (i.e., uncompressed VBM data, PCA-based factorization and parcellation-based compression). We then investigated the impact of the granularity on the accuracy of age prediction, as well as the transferability of the factorization and model generalization across datasets. We finally validated our framework by examining age prediction in ADNI samples. Our results showed that our framework favorably compares with other approaches. They also demonstrated that the NNMF based factorization derived from one dataset could be efficiently applied to compress VBM data of another dataset and that granularities between 300 and 500 components give an optimal representation for age prediction. In addition to the good performance in healthy subjects our framework provided relatively localized brain regions as the features contributing to the prediction, thereby offering further insights into structural changes due to brain aging. Finally, our validation in clinical populations showed that our framework is sensitive to deviance from normal structural variations in pathological aging.

Project description:Background:Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression co-clustering, patient stratification, and gene-disease 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 tri-factorization, a popular method that is not limited by the assumption of standard matrix factorization about data residing in one latent space. Matrix tri-factorization 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 block-wise approach for latent factor learning in matrix tri-factorization. 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 tri-factorization. In a study on large biomedical datasets we show that our approach scales well on multi-processor and multi-GPU architectures. On a four-GPU system we demonstrate that our approach can be more than 100-times faster than its single-processor counterpart. Conclusions:A general approach for scaling non-negative matrix tri-factorization is proposed. The approach is especially useful parallel matrix factorization implemented in a multi-GPU 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.

Dataset Information

A unified framework for link prediction based on non-negative matrix factorization with coupling multivariate information.

Publications

A unified framework for link prediction based on non-negative matrix factorization with coupling multivariate information.

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