Related papers: Highly Scalable Tensor Factorization for Predictio…
Joint analysis of data from multiple information repositories facilitates uncovering the underlying structure in heterogeneous datasets. Single and coupled matrix-tensor factorization (CMTF) has been widely used in this context for…
Tensor networks are efficient factorisations of high-dimensional tensors into a network of lower-order tensors. They have been most commonly used to model entanglement in quantum many-body systems and more recently are witnessing increased…
In this paper we address the problem of building a class of robust factorization algorithms that solve for the shape and motion parameters with both affine (weak perspective) and perspective camera models. We introduce a Gaussian/uniform…
High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry…
The contaminated Gaussian distribution represents a simple heavy-tailed elliptical generalization of the Gaussian distribution; unlike the often-considered t-distribution, it also allows for automatic detection of mild outlying or "bad"…
In silico prediction of drug-target interactions (DTI) is significant for drug discovery because it can largely reduce timelines and costs in the drug development process. Specifically, deep learning-based DTI approaches have been shown…
Exploratory cancer drug studies test multiple tumor cell lines against multiple candidate drugs. The goal in each paired (cell line, drug) experiment is to map out the dose-response curve of the cell line as the dose level of the drug…
The vast majority of current machine learning algorithms are designed to predict single responses or a vector of responses, yet many types of response are more naturally organized as matrices or higher-order tensor objects where…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
Low-rank tensor completion has been widely used in computer vision and machine learning. This paper develops a novel multi-modal core tensor factorization (MCTF) method combined with a tensor low-rankness measure and a better nonconvex…
Participation factors (PFs) quantify the interaction between system modes and state variables, and they play a crucial role in various applications such as modal analysis, model reduction, and control design. With increasing system…
Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs)…
The proposed article aims at offering a comprehensive tutorial for the computational aspects of structured matrix and tensor factorization. Unlike existing tutorials that mainly focus on {\it algorithmic procedures} for a small set of…
Dynamic mode decomposition (DMD) has become a powerful data-driven method for analyzing the spatiotemporal dynamics of complex, high-dimensional systems. However, conventional DMD methods are limited to matrix-based formulations, which…
Prediction of new drug-target interactions is extremely important as it can lead the researchers to find new uses for old drugs and to realize the therapeutic profiles or side effects thereof. However, experimental prediction of drug-target…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose a major challenge to medication therapy. Recently, informatics-based approaches are emerging for DDI studies. In this paper, we aim to identify key…
Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with…
Clinical trials are the gold standard for assessing the effectiveness and safety of drugs for treating diseases. Given the vast design space of drug molecules, elevated financial cost, and multi-year timeline of these trials, research on…
Higher-order tensor decompositions have hardly been used in muscle activity analysis despite multichannel electromyography (EMG) datasets naturally occurring as multi-way structures. Here, we seek to demonstrate and discuss the potential of…