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Register a new userPANTHER: Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning
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Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.
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This paper is concerned with improving the empirical convergence speed of block-coordinate descent algorithms for approximate nonnegative tensor factorization (NTF). We propose an extrapolation strategy in-between block updates, referred to as heuristic extrapolation with restarts (HER). HER significantly accelerates the empirical convergence speed of most existing block-coordinate algorithms for dense NTF, in particular for challenging computational scenarios, while requiring a negligible additional computational budget.
Low rank tensor learning, such as tensor completion and multilinear multitask learning, has received much attention in recent years. In this paper, we propose higher order matching pursuit for low rank tensor learning problems with a convex or a nonconvex cost function, which is a generalization of the matching pursuit type methods. At each iteration, the main cost of the proposed methods is only to compute a rank-one tensor, which can be done efficiently, making the proposed methods scalable to large scale problems. Moreover, storing the resulting rank-one tensors is of low storage requirement, which can help to break the curse of dimensionality. The linear convergence rate of the proposed methods is established in various circumstances. Along with the main methods, we also provide a method of low computational complexity for approximately computing the rank-one tensors, with provable approximation ratio, which helps to improve the efficiency of the main methods and to analyze the convergence rate. Experimental results on synthetic as well as real datasets verify the efficiency and effectiveness of the proposed methods.
Most methods for dimensionality reduction are based on either tensor representation or local geometry learning. However, the tensor-based methods severely rely on the assumption of global and multilinear structures in high-dimensional data; and the manifold learning methods suffer from the out-of-sample problem. In this paper, bridging the tensor decomposition and manifold learning, we propose a novel method, called Hypergraph Regularized Nonnegative Tensor Factorization (HyperNTF). HyperNTF can preserve nonnegativity in tensor factorization, and uncover the higher-order relationship among the nearest neighborhoods. Clustering analysis with HyperNTF has low computation and storage costs. The experiments on four synthetic data show a desirable property of hypergraph in uncovering the high-order correlation to unfold the curved manifolds. Moreover, the numerical experiments on six real datasets suggest that HyperNTF robustly outperforms state-of-the-art algorithms in clustering analysis.
Various factorization-based methods have been proposed to leverage second-order, or higher-order cross features for boosting the performance of predictive models. They generally enumerate all the cross features under a predefined maximum order, and then identify useful feature interactions through model training, which suffer from two drawbacks. First, they have to make a trade-off between the expressiveness of higher-order cross features and the computational cost, resulting in suboptimal predictions. Second, enumerating all the cross features, including irrelevant ones, may introduce noisy feature combinations that degrade model performance. In this work, we propose the Adaptive Factorization Network (AFN), a new model that learns arbitrary-order cross features adaptively from data. The core of AFN is a logarithmic transformation layer to convert the power of each feature in a feature combination into the coefficient to be learned. The experimental results on four real datasets demonstrate the superior predictive performance of AFN against the start-of-the-arts.
Non-negative matrix factorization (NMF) has become a popular method for representing meaningful data by extracting a non-negative basis feature from an observed non-negative data matrix. Some of the unique features of this method in identifying hidden data put this method amongst the powerful methods in the machine learning area. The NMF is a known non-convex optimization problem and the initial point has a significant effect on finding an efficient local solution. In this paper, we investigate the most popular initialization procedures proposed for NMF so far. We describe each method and present some of their advantages and disadvantages. Finally, some numerical results to illustrate the performance of each algorithm are presented.
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