Related papers: SketchBio: A Scientist's 3D Interface for Molecula…

This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function, as…

Life and physical sciences have always been quick to adopt the latest advances in machine learning to accelerate scientific discovery. Examples of this are cell segmentation or cancer detection. Nevertheless, these exceptional results are…

We introduce the concept of code shaping, an interaction paradigm for editing code using free-form sketch annotations directly on top of the code and console output. To evaluate this concept, we conducted a three-stage design study with 18…

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…

Large language models (LLMs) represented by GPT family have achieved remarkable success. The characteristics of LLMs lie in their ability to accommodate a wide range of tasks through a generative approach. However, the flexibility of their…

Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…

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…

With exquisite precision and reproducibility, cells orchestrate the cooperative action of thousands of nanometer-sized molecular motors to carry out mechanical tasks at much larger length scales, such as cell motility, division and…

3D modeling based on point clouds is an efficient way to reconstruct and create detailed 3D content. However, the geometric procedure may lose accuracy due to high redundancy and the absence of an explicit structure. In this work, we…

We propose a novel image-to-pencil translation method that could not only generate high-quality pencil sketches but also offer the drawing process. Existing pencil sketch algorithms are based on texture rendering rather than the direct…

This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…

Background: The construction, evolution and usage of complex artificial intelligence (AI) models demand expensive computational resources. While currently available high-performance computing environments support well this complexity, the…

Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…

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…

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

This work aims to investigate the problem of 3D modeling using single free-hand sketches, which is one of the most natural ways we humans express ideas. Although sketch-based 3D modeling can drastically make the 3D modeling process more…

Creative sketching or doodling is an expressive activity, where imaginative and previously unseen depictions of everyday visual objects are drawn. Creative sketch image generation is a challenging vision problem, where the task is to…

The production of high-quality 2D animation is highly labor-intensive process, as animators are currently required to draw and color a large number of frames by hand. We present SketchColour, the first sketch-to-colour pipeline for 2D…

Natural organisms utilize distributed actuation through their musculoskeletal systems to adapt their gait for traversing diverse terrains or to morph their bodies for varied tasks. A longstanding challenge in robotics is to emulate this…

There is an increasing need in our society to achieve faster advances in Science to tackle urgent problems, such as climate changes, environmental hazards, sustainable energy systems, pandemics, among others. In certain domains like…