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We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in…
One of the central goals in precision health is the understanding and interpretation of high-dimensional biological data to identify genes and markers associated with disease initiation, development, and outcomes. Though significant effort…
Semi-Nonnegative Matrix Factorization (semi-NMF) extends classical Nonnegative Matrix Factorization (NMF) by allowing the basis matrix to contain both positive and negative entries, making it suitable for decomposing data with mixed signs.…
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…
Matrix factorization techniques, especially Nonnegative Matrix Factorization (NMF), have been widely used for dimensionality reduction and interpretable data representation. However, existing NMF-based methods are inherently single-scale…
By combining related objects, unsupervised machine learning techniques aim to reveal the underlying patterns in a data set. Non-negative Matrix Factorization (NMF) is a data mining technique that splits data matrices by imposing…
We introduce a new method based on nonnegative matrix factorization, Neural NMF, for detecting latent hierarchical structure in data. Datasets with hierarchical structure arise in a wide variety of fields, such as document classification,…
Denoising diffusion probabilistic models (DDPMs) have pioneered new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided…
Molecular emission from the galactic and extragalactic interstellar medium (ISM) is often used to determine the physical conditions of the dense gas. However, even from spatially resolved regions, the observed molecules are not necessarily…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
Dimensionality reduction and matrix factorization techniques are important and useful machine-learning techniques in many fields. Nonnegative matrix factorization (NMF) is particularly useful for spectral analysis and image processing in…
Nonnegative Matrix Factorization (NMF) is a widely used technique for data representation. Inspired by the expressive power of deep learning, several NMF variants equipped with deep architectures have been proposed. However, these methods…
We propose an efficient distributed out-of-memory implementation of the Non-negative Matrix Factorization (NMF) algorithm for heterogeneous high-performance-computing (HPC) systems. The proposed implementation is based on prior work on…
Nonnegative Matrix Factorization (NMF) is an important unsupervised learning method to extract meaningful features from data. To address the NMF problem within a polynomial time framework, researchers have introduced a separability…
Non-negative matrix factorization (NMF) and non-negative tensor factorization (NTF) decompose non-negative high-dimensional data into non-negative low-rank components. NMF and NTF methods are popular for their intrinsic interpretability and…
We propose a new method to enforce priors on the solution of the nonnegative matrix factorization (NMF). The proposed algorithm can be used for denoising or single-channel source separation (SCSS) applications. The NMF solution is guided to…
In this paper, we incorporate a graph filter deconvolution step into the classical geometric convolutional neural network pipeline. More precisely, under the assumption that the graph domain plays a role in the generation of the observed…
Background: Mining gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. In this work, we explore the plausibility of detecting gene modules by…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
Nonnegative matrix factorization (NMF) is a powerful technique for dimension reduction, extracting latent factors and learning part-based representation. For large datasets, NMF performance depends on some major issues: fast algorithms,…