Truncated Cauchy Non-Negative Matrix Factorization.

Non-negative matrix factorization (NMF) minimizes the euclidean distance between the data matrix and its low rank approximation, and it fails when applied to corrupted data because the loss function is sensitive to outliers. In this paper, we propose a Truncated CauchyNMF loss that handle outliers by truncating large errors, and develop a Truncated CauchyNMF to robustly learn the subspace on noisy datasets contaminated by outliers. We theoretically analyze the robustness of Truncated CauchyNMF comparing with the competing models and theoretically prove that Truncated CauchyNMF has a generalization bound which converges at a rate of order , where is the sample size.

Systematic Identification and Assessment of Therapeutic Targets for Breast Cancer Based on Genome-Wide RNA Interference Transcriptomes.

With accumulating public omics data, great efforts have been made to characterize the genetic heterogeneity of breast cancer. However, identifying novel targets and selecting the best from the sizeable lists of candidate targets is still a key challenge for targeted therapy, largely owing to the lack of economical, efficient and systematic discovery and assessment to prioritize potential therapeutic targets. Here, we describe an approach that combines the computational evaluation and objective, multifaceted assessment to systematically identify and prioritize targets for biological validation and therapeutic exploration.

Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.

Background: Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although improvement in the sensitivity of computational drug repositioning methods has identified numerous credible repositioning opportunities, few have been progressed. Arguably the "black box" nature of drug action in a new indication is one of the main blocks to progression, highlighting the need for methods that inform on the broader target mechanism in the disease context.

Semi-Supervised Projective Non-Negative Matrix Factorization for Cancer Classification.

Advances in DNA microarray technologies have made gene expression profiles a significant candidate in identifying different types of cancers. Traditional learning-based cancer identification methods utilize labeled samples to train a classifier, but they are inconvenient for practical application because labels are quite expensive in the clinical cancer research community. This paper proposes a semi-supervised projective non-negative matrix factorization method (Semi-PNMF) to learn an effective classifier from both labeled and unlabeled samples, thus boosting subsequent cancer classification performance.

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. This paper proposes an accurate and sensitive gene ranking method that implements discriminant non-negative matrix factorization (DNMF) for RNA-seq data. To the best of our knowledge, this is the first work to explore the utility of DNMF for gene ranking.

Online multi-modal robust non-negative dictionary learning for visual tracking.

Dictionary learning is a method of acquiring a collection of atoms for subsequent signal representation. Due to its excellent representation ability, dictionary learning has been widely applied in multimedia and computer vision. However, conventional dictionary learning algorithms fail to deal with multi-modal datasets.

Discriminant projective non-negative matrix factorization.

Projective non-negative matrix factorization (PNMF) projects high-dimensional non-negative examples X onto a lower-dimensional subspace spanned by a non-negative basis W and considers W(T) X as their coefficients, i.e., X≈WW(T) X.

Limited-memory fast gradient descent method for graph regularized nonnegative matrix factorization.

Graph regularized nonnegative matrix factorization (GNMF) decomposes a nonnegative data matrix X[Symbol:see text]R(m x n) to the product of two lower-rank nonnegative factor matrices, i.e.,W[Symbol:see text]R(m x r) and H[Symbol:see text]R(r x n) (r < min {m,n}) and aims to preserve the local geometric structure of the dataset by minimizing squared Euclidean distance or Kullback-Leibler (KL) divergence between X and WH.

Online nonnegative matrix factorization with robust stochastic approximation.

Nonnegative matrix factorization (NMF) has become a popular dimension-reduction method and has been widely applied to image processing and pattern recognition problems. However, conventional NMF learning methods require the entire dataset to reside in the memory and thus cannot be applied to large-scale or streaming datasets. In this paper, we propose an efficient online RSA-NMF algorithm (OR-NMF) that learns NMF in an incremental fashion and thus solves this problem.

Non-negative patch alignment framework.

In this paper, we present a non-negative patch alignment framework (NPAF) to unify popular non-negative matrix factorization (NMF) related dimension reduction algorithms. It offers a new viewpoint to better understand the common property of different NMF algorithms. Although multiplicative update rule (MUR) can solve NPAF and is easy to implement, it converges slowly.

Manifold regularized discriminative nonnegative matrix factorization with fast gradient descent.

Nonnegative matrix factorization (NMF) has become a popular data-representation method and has been widely used in image processing and pattern-recognition problems. This is because the learned bases can be interpreted as a natural parts-based representation of data and this interpretation is consistent with the psychological intuition of combining parts to form a whole. For practical classification tasks, however, NMF ignores both the local geometry of data and the discriminative information of different classes.

[An iterative method for prediction of RNA secondary structures including pseudoknots based on minimum of free energy and covariance].

Most functional RNA molecules have characteristic, highly conserved structures, such as pseudoknots. But the prediction of RNA pseudoknots has largely remained a difficult problem, and many existing algorithms for prediction of RNA secondary structures do not have the ability to predict pseudoknots. Here we present a new method for predicting RNA secondary structures including pseudoknots through iteration.