Dataset Information

A perturbation-based framework for link prediction via non-negative matrix factorization.

ABSTRACT: Many link prediction methods have been developed to infer unobserved links or predict latent links based on the observed network structure. However, due to network noises and irregular links in real network, the performances of existed methods are usually limited. Considering random noises and irregular links, we propose a perturbation-based framework based on Non-negative Matrix Factorization to predict missing links. We first automatically determine the suitable number of latent features, which is inner rank in NMF, by Colibri method. Then, we perturb training set of a network by perturbation sets many times and get a series of perturbed networks. Finally, the common basis matrix and coefficients matrix of these perturbed networks are obtained via NMF and form similarity matrix of the network for link prediction. Experimental results on fifteen real networks show that the proposed framework has competitive performances compared with state-of-the-art link prediction methods. Correlations between the performances of different methods and the statistics of networks show that those methods with good precisions have similar consistence.

SUBMITTER: Wang W

PROVIDER: S-EPMC5156920 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Publications

A perturbation-based framework for link prediction via non-negative matrix factorization.

Wang Wenjun W Cai Fei F Jiao Pengfei P Pan Lin L

Scientific reports 20161215

Many link prediction methods have been developed to infer unobserved links or predict latent links based on the observed network structure. However, due to network noises and irregular links in real network, the performances of existed methods are usually limited. Considering random noises and irregular links, we propose a perturbation-based framework based on Non-negative Matrix Factorization to predict missing links. We first automatically determine the suitable number of latent features, whic ...[more]

PMID: 27976672

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Project description:BackgroundMatrix 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.ResultsWe 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.ConclusionsA 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.

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:MotivationUnderstanding the underlying mutational processes of cancer patients has been a long-standing goal in the community and promises to provide new insights that could improve cancer diagnoses and treatments. Mutational signatures are summaries of the mutational processes, and improving the derivation of mutational signatures can yield new discoveries previously obscured by technical and biological confounders. Results from existing mutational signature extraction methods depend on the size of available patient cohort and solely focus on the analysis of mutation count data without considering the exploitation of metadata.ResultsHere we present a supervised method that utilizes cancer type as metadata to extract more distinctive signatures. More specifically, we use a negative binomial non-negative matrix factorization and add a support vector machine loss. We show that mutational signatures extracted by our proposed method have a lower reconstruction error and are designed to be more predictive of cancer type than those generated by unsupervised methods. This design reduces the need for elaborate post-processing strategies in order to recover most of the known signatures unlike the existing unsupervised signature extraction methods. Signatures extracted by a supervised model used in conjunction with cancer-type labels are also more robust, especially when using small and potentially cancer-type limited patient cohorts. Finally, we adapted our model such that molecular features can be utilized to derive an according mutational signature. We used APOBEC expression and MUTYH mutation status to demonstrate the possibilities that arise from this ability. We conclude that our method, which exploits available metadata, improves the quality of mutational signatures as well as helps derive more interpretable representations.Availability and implementationhttps://github.com/ratschlab/SNBNMF-mutsig-public.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

A perturbation-based framework for link prediction via non-negative matrix factorization.

Publications

A perturbation-based framework for link prediction via non-negative matrix factorization.

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