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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…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…
Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating…
Mathematical understanding is built in many ways. Among these, illustration has been a companion and tool for research for as long as research has taken place. We use the term illustration to encompass any way one might bring a mathematical…
Drawing principles, or aesthetics, are important in graph drawing. They are used as criteria for algorithm design and for quality evaluation. Current aesthetics are described as visual properties that a drawing is required to have to be…
Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks…
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a…
We explore computational approaches for visual guidance to aid in creating aesthetically pleasing art and graphic design. Our work complements and builds on previous work that developed models for how humans look at images. Our approach…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Visual communication, dating back to prehistoric cave paintings, is the use of visual elements to convey ideas and information. In today's visually saturated world, effective design demands an understanding of graphic design principles,…
Authors of biomedical publications often use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a way to concisely communicate such findings,…
Graphics (e.g., figures and charts) are ubiquitous in scientific papers, yet separating graphics from text increases cognitive load in understanding text-graphic connections. Research has found that word-scale graphics, or visual…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…
Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of…
Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…