Related papers: Parallel multi-objective algorithms for the molecu…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
The coupling of models for the different components of the Soil-Vegetation-Atmosphere-System is required to investigate component interactions and feedback processes. However, the component models for atmosphere, land-surface and subsurface…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The viability of a new drug molecule is a time and resource intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibitor…
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…
The aim of the inverse chemical design is to develop new molecules with given optimized molecular properties or objectives. Recently, generative deep learning (DL) networks are considered as the state-of-the-art in inverse chemical design…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property, where design of novel drugs is an important topic in bioinformatics and chemo-informatics. The…
Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…
We present a novel formulation of the multiple object tracking problem which integrates low and mid-level features. In particular, we formulate the tracking problem as a quadratic program coupling detections and dense point trajectories.…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
In this paper we propose an optimization-based framework to multiple object matching. The framework takes maps computed between pairs of objects as input, and outputs maps that are consistent among all pairs of objects. The central idea of…
In drug discovery, molecular docking aims at characterizing the binding of a drug-like molecule to a macromolecule. AutoDock-GPU, a state-of-the-art docking software, estimates the geometrical conformation of a docked ligand-protein complex…
Particle accelerators are invaluable tools for research in the basic and applied sciences, in fields such as materials science, chemistry, the biosciences, particle physics, nuclear physics and medicine. The design, commissioning, and…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Molecular optimization is a key challenge in drug discovery and material science domain, involving the design of molecules with desired properties. Existing methods focus predominantly on single-property optimization, necessitating…
Data-driven modeling plays an increasingly important role in different areas of engineering. For most of existing methods, such as genetic programming (GP), the convergence speed might be too slow for large scale problems with a large…
Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen…
A rational design of new therapeutic drugs aims to find a molecular structure with desired biological functionality, e.g., an ability to activate or suppress a specific protein via binding to it. Molecular docking is a common technique for…
In recent years, with the development of microarray technique, discovery of useful knowledge from microarray data has become very important. Biclustering is a very useful data mining technique for discovering genes which have similar…
Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative…