Related papers: GAN-TAT: A Novel Framework Using Protein Interacti…

One of the attractive characteristics of deep neural networks is their ability to transfer knowledge obtained in one domain to other related domains. As a result, high-quality networks can be trained in domains with relatively little…

As a necessary process in drug development, finding a drug compound that can selectively bind to a specific protein is highly challenging and costly. Drug-target affinity (DTA), which represents the strength of drug-target interaction…

Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network…

Motivation: Drug combination is a sensible strategy for disease treatment by improving the efficacy and reducing concomitant side effects. Due to the large number of possible combinations among candidate compounds, exhaustive screening is…

Generative Adversarial Networks (GANs) have proven to be a powerful tool for generating realistic synthetic data. However, traditional GANs often struggle to capture complex relationships between features which results in generation of…

The drug discovery and development process is a long and expensive one, costing over 1 billion USD on average per drug and taking 10-15 years. To reduce the high levels of attrition throughout the process, there has been a growing interest…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

Drug-target relationships may now be predicted computationally using bioinformatics data, which is a valuable tool for understanding pharmacological effects, enhancing drug development efficiency, and advancing related research. A number of…

I present IGAN (Inferent Generative Adversarial Networks), a neural architecture that learns both a generative and an inference model on a complex high dimensional data distribution, i.e. a bidirectional mapping between data samples and a…

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…

As a new approach to train generative models, \emph{generative adversarial networks} (GANs) have achieved considerable success in image generation. This framework has also recently been applied to data with graph structures. We propose…

Gene-based testing is a commonly employed strategy in many genetic association studies. Gene-trait associations can be complex due to underlying population heterogeneity, gene-environment interactions, and various other reasons. Existing…

Predicting medications is a crucial task in many intelligent healthcare systems. It can assist doctors in making informed medication decisions for patients according to electronic medical records (EMRs). However, medication prediction is a…

Gene essentiality, the necessity of a specific gene for the survival of an organism, is crucial to our understanding of cellular processes and identifying drug targets. Experimental determination of gene essentiality requires large growth…

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to…

Accurate prediction of the binding affinity between drugs and target proteins is a core task in computer-aided drug design. Existing deep learning methods tend to ignore the information of internal sub-structural features of drug molecules…

The application of machine learning methods to analyze changes in gene expression patterns has recently emerged as a powerful approach in cancer research, enhancing our understanding of the molecular mechanisms underpinning cancer…

Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique…

We investigate molecular mechanisms of resistant or sensitive response of cancer drug combination therapies in an inductive and interpretable manner. Though deep learning algorithms are widely used in the drug synergy prediction problem, it…

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the…