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We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of…
Nonnegative matrix factorization (NMF) with group sparsity constraints is formulated as a probabilistic graphical model and, assuming some observed data have been generated by the model, a feasible variational Bayesian algorithm is derived…
In the Nonnegative Matrix Factorization (NMF) problem we are given an $n \times m$ nonnegative matrix $M$ and an integer $r > 0$. Our goal is to express $M$ as $A W$ where $A$ and $W$ are nonnegative matrices of size $n \times r$ and $r…
Lee and Seung (2000) introduced numerical solutions for non-negative matrix factorization (NMF) using iterative multiplicative update algorithms. These algorithms have been actively utilized as dimensionality reduction tools for…
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within cancer research, commonly with Nonnegative Matrix…
Nonnegative matrix factorization (NMF) has been successfully applied in several data mining tasks. Recently, there is an increasing interest in the acceleration of NMF, due to its high cost on large matrices. On the other hand, the privacy…
Machine Learning (ML) alleviates the challenges of high-dimensional data analysis and improves decision making in critical applications like healthcare. Effective cancer type from high-dimensional genetic mutation data can be useful for…
Nonnegative matrix factorization (NMF) has been successfully applied to many areas for classification and clustering. Commonly-used NMF algorithms mainly target on minimizing the $l_2$ distance or Kullback-Leibler (KL) divergence, which may…
Missing link prediction is a method for network analysis, with applications in recommender systems, biology, social sciences, cybersecurity, information retrieval, and Artificial Intelligence (AI) reasoning in Knowledge Graphs. Missing link…
Nonnegative matrix factorization (NMF) has been widely used in machine learning and signal processing because of its non-subtractive, part-based property which enhances interpretability. It is often assumed that the latent dimensionality…
In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes…
In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes…
Given a symmetric nonnegative matrix $A$, symmetric nonnegative matrix factorization (symNMF) is the problem of finding a nonnegative matrix $H$, usually with much fewer columns than $A$, such that $A \approx HH^T$. SymNMF can be used for…
Nonnegative matrix factorization (NMF) is a data analysis technique used in a great variety of applications such as text mining, image processing, hyperspectral data analysis, computational biology, and clustering. In this paper, we…
Non-negative matrix factorization (NMF) is a powerful tool for dimensionality reduction and clustering. Unfortunately, the interpretation of the clustering results from NMF is difficult, especially for the high-dimensional biological data…
Motivated by the reconstruction and the prediction of electricity consumption, we extend Nonnegative Matrix Factorization~(NMF) to take into account side information (column or row features). We consider general linear measurement settings,…
ICU mortality risk prediction is a tough yet important task. On one hand, due to the complex temporal data collected, it is difficult to identify the effective features and interpret them easily; on the other hand, good prediction can help…
A recent theoretical analysis shows the equivalence between non-negative matrix factorization (NMF) and spectral clustering based approach to subspace clustering. As NMF and many of its variants are essentially linear, we introduce a…
Time-frequency representation (TFR) is often used for non-stationary signal analysis. The most intuitive and interpretable TFR is the spectrogram. Recently, a concept of non-negative matrix factorization (NMF) has been successfully applied…
Constrained low-rank matrix approximations have been known for decades as powerful linear dimensionality reduction techniques to be able to extract the information contained in large data sets in a relevant way. However, such low-rank…