Related papers: Graph Regularized Probabilistic Matrix Factorizati…
Concomitant administration of drugs can cause drug-drug interactions (DDIs). Some drug combinations are beneficial, but other ones may cause negative effects which are previously unrecorded. Previous works on DDI prediction usually rely on…
Drug repurposing has historically been an economically infeasible process for identifying novel uses for abandoned drugs. Modern machine learning has enabled the identification of complex biochemical intricacies in candidate drugs; however,…
In recent years, there has been a growing interest in mathematical models leading to the minimization, in a symmetric matrix space, of a Bregman divergence coupled with a regularization term. We address problems of this type within a…
Dyadic Data Prediction (DDP) is an important problem in many research areas. This paper develops a novel fully Bayesian nonparametric framework which integrates two popular and complementary approaches, discrete mixed membership modeling…
Predicting unknown drug-drug interactions (DDIs) is crucial for improving medication safety. Previous efforts in DDI prediction have typically focused on binary classification or predicting DDI categories, with the absence of explanatory…
Examining Drug-Drug Interactions (DDIs) is a pivotal element in the process of drug development. DDIs occur when one drug's properties are affected by the inclusion of other drugs. Detecting favorable DDIs has the potential to pave the way…
Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…
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…
We observe an undirected graph $G$ without multiple edges and self-loops, which is to represent a protein-protein interaction (PPI) network. We assume that $G$ evolved under the duplication-mutation with complementarity (DMC) model from a…
The use of multiple drugs accounts for almost 30% of all hospital admission and is the 5th leading cause of death in America. Since over 30% of all adverse drug events (ADEs) are thought to be caused by drug-drug interactions (DDI), better…
With the development of blockchain technology, the cryptocurrency based on blockchain technology is becoming more and more popular. This gave birth to a huge cryptocurrency transaction network has received widespread attention. Link…
Non-negative matrix factorization (NMF) is one of the most popular decomposition techniques for multivariate data. NMF is a core method for many machine-learning related computational problems, such as data compression, feature extraction,…
Aggregating pharmaceutical data in the drug-target interaction (DTI) domain has the potential to deliver life-saving breakthroughs. It is, however, notoriously difficult due to regulatory constraints and commercial interests. This work…
Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
In the non-negative matrix factorization (NMF) problem, the input is an $m\times n$ matrix $M$ with non-negative entries and the goal is to factorize it as $M\approx AW$. The $m\times k$ matrix $A$ and the $k\times n$ matrix $W$ are both…
Probabilistic graphical models provide a powerful tool to describe complex statistical structure, with many real-world applications in science and engineering from controlling robotic arms to understanding neuronal computations. A major…
The discovery of drug-target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from…
Non-Negative Matrix Factorization (NMF) is an unsupervised learning method offering low-rank representations across various domains such as audio processing, biomedical signal analysis, and image recognition. The incorporation of…
We propose a unified framework to speed up the existing stochastic matrix factorization (SMF) algorithms via variance reduction. Our framework is general and it subsumes several well-known SMF formulations in the literature. We perform a…