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In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…
Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse,…
This paper introduces a method for learning to generate line drawings from 3D models. Our architecture incorporates a differentiable module operating on geometric features of the 3D model, and an image-based module operating on view-based…
Image captioning applied to biomedical images can assist and accelerate the diagnosis process followed by clinicians. This article is the first survey of biomedical image captioning, discussing datasets, evaluation measures, and state of…
Graphs are common mathematical structures that are visual and intuitive. They constitute a natural and seamless way for system modelling in science, engineering and beyond, including computer science, biology, business process modelling,…
Probabilistic graphical modeling is a branch of machine learning that uses probability distributions to describe the world, make predictions, and support decision-making under uncertainty. Underlying this modeling framework is an elegant…
We present a generator of virtual molecules that selects valid chemistry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated structures. Compared to existing…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The representation of a biochemical network as a graph is the coarsest level of description in cellular biochemistry. By studying the network structure one can draw conclusions on the large scale organisation of the biochemical processes.…
This book collects the lectures about graph theory and its applications which were given to students of mathematical departments of Moscow State University and Peking University. Graph theory is a very wide field with a lot of applications…
Illustrations are an essential transmission instrument. For an historian, the first step in studying their evolution in a corpus of similar manuscripts is to identify which ones correspond to each other. This image collation task is…
Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
The visual representation of concepts or ideas through the use of simple shapes has always been explored in the history of Humanity, and it is believed to be the origin of writing. We focus on computational generation of visual symbols to…