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With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The…
Designing synthetic routes for novel molecules is pivotal in various fields like medicine and chemistry. In this process, researchers need to explore a set of synthetic reactions to transform starting molecules into intermediates step by…
Optical flow computation is essential in the early stages of the video processing pipeline. This paper focuses on a less explored problem in this area, the 360$^\circ$ optical flow estimation using deep neural networks to support…
Morphing is a long-standing problem in vision and computer graphics, requiring a time-dependent warping for feature alignment and a blending for smooth interpolation. Recently, multilayer perceptrons (MLPs) have been explored as implicit…
The recent development of Large Language Models (LLMs) with strong reasoning ability has driven research in various domains such as mathematics, coding, and scientific discovery. Meanwhile, 3D visual grounding, as a fundamental task in 3D…
There is no settled universal 3D representation for geometry with many alternatives such as point clouds, meshes, implicit functions, and voxels to name a few. In this work, we present a new, compelling alternative for representing shapes…
Exploratory search starts with ill-defined goals and involves browsing, learning, and formulating new targets for search. To fluidly support such dynamic search behaviours, we focus on devising interactive visual facets (IVF), visualising…
While protein language models (PLMs) are one of the most promising avenues of research for future de novo protein design, the way in which they transform sequences to hidden representations, as well as the information encoded in such…
Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Researchers got success in mining the Web usage data effectively and efficiently. But representation of the mined patterns is often not in a form suitable for direct human consumption. Hence mechanisms and tools that can represent mined…
Interaction is critical for data analysis and sensemaking. However, designing interactive physicalizations is challenging as it requires cross-disciplinary knowledge in visualization, fabrication, and electronics. Interactive…
Multivariate networks are commonly found in real-world data-driven applications. Uncovering and understanding the relations of interest in multivariate networks is not a trivial task. This paper presents a visual analytics workflow for…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
In the face of complex decisions, people often engage in a three-stage process that spans from (1) exploring and analyzing pertinent information (intelligence); (2) generating and exploring alternative options (design); and ultimately…