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Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful…
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are…
Research into the processes of photoionised nebulae plays a significant part in our understanding of stellar evolution. It is extremely difficult to visually represent or model ionised nebula, requiring astronomers to employ sophisticated…
The growth of large, programatically accessible bibliometrics databases presents new opportunities for complex analyses of publication metadata. In addition to providing a wealth of information about authors and institutions, databases such…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
Imaging of biological cells and tissues often relies on fluorescent labels, which offer high contrast with molecular specificity. The use of exogenous labeling agents, however, may alter the normal physiology of the bio-specimens.…
Denoising diffusion models have emerged as powerful tools for image manipulation, yet interactive, localized editing workflows remain underdeveloped. We introduce Layered Diffusion Brushes (LDB), a novel training-free framework that enables…
We describe a set of tools for analyzing, visualizing, and assessing architectural/construction progress with unordered photo collections and 3D building models. With our interface, a user guides the registration of the model in one of the…
Due to the availability of increasingly large amounts of visual data, there is a growing need for tools that can help users find relevant images. While existing tools can perform image retrieval based on similarity or metadata, they fall…
In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…
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…
PGMax is an open-source Python package for (a) easily specifying discrete Probabilistic Graphical Models (PGMs) as factor graphs; and (b) automatically running efficient and scalable loopy belief propagation (LBP) in JAX. PGMax supports…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
In this work, we pose the question of whether, by considering qualitative information such as a sample target image as input, one can produce a rendered image of scientific data that is similar to the target. The algorithm resulting from…
Recognizing the layout of unstructured digital documents is an important step when parsing the documents into structured machine-readable format for downstream applications. Deep neural networks that are developed for computer vision have…
Diagrams are essential tools for problem-solving and communication as they externalize conceptual structures using spatial relationships. But when picking a diagramming framework, users are faced with a dilemma. They can either use a highly…
Multiplex Imaging (MI) enables the simultaneous visualization of multiple biological markers in separate imaging channels at subcellular resolution, providing valuable insights into cell-type heterogeneity and spatial organization. However,…
Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…
scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented…
Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking…