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From photorealistic sketches to schematic diagrams, drawing provides a versatile medium for communicating about the visual world. How do images spanning such a broad range of appearances reliably convey meaning? Do viewers understand…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent success of graph neural networks for learning molecular…
Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…
Deep learning models have become fundamental tools in drug design. In particular, large language models trained on biochemical sequences learn feature vectors that guide drug discovery through virtual screening. However, such models do not…
The complexity of molecular and cellular processes forces experimental studies to focus on subsystems. To study the functioning of biological systems across levels of structural and functional organisation, we require tools to compose and…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
Aesthetics, among other criteria, can be statistically examined in terms of the complexity required for creating and decrypting a work of art. We propose three laws of aesthetic complexity. According to the first law of aesthetic…
Rule sets are often used in Machine Learning (ML) as a way to communicate the model logic in settings where transparency and intelligibility are necessary. Rule sets are typically presented as a text-based list of logical statements…
Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
Diagrams are common tools for representing complex concepts, relationships and events, often when it would be difficult to portray the same information with natural images. Understanding natural images has been extensively studied in…
Biological research spans scales and methodologies, generating complex data visualizations such as images, text, numbers, networks, and maps. With increasingly large and multimodal datasets, effective visualization is essential for…
The ability to represent scientific data and concepts visually is becoming increasingly important due to the unprecedented exponential growth of computational power during the present digital age. The data sets and simulations scientists in…
Procedural models (i.e. symbolic programs that output visual data) are a historically-popular method for representing graphics content: vegetation, buildings, textures, etc. They offer many advantages: interpretable design parameters,…
Biomedical knowledge graphs (KGs) are widely used across research and translational settings, yet their design decisions and implementation are often opaque. Unlike ontologies that more frequently adhere to established creation principles,…
RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an intuitive plain-text, or string,…