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Unstructured data(e.g., images, videos, PDF files, etc.) contain semantic information, for example, the facial feature of a person and the plate number of a vehicle. There could be semantic relationships between data items which are not…
The amount of medical images stored in hospitals is increasing faster than ever; however, utilizing the accumulated medical images has been limited. This is because existing content-based medical image retrieval (CBMIR) systems usually…
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of complex biological behaviors. To promote model sharing and…
Rapid advancements in imaging techniques and analytical methods over the past decade have revolutionized our ability to comprehensively probe the biological world at multiple scales, pinpointing the type, quantity, location, and even…
VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics…
Denoising diffusion probabilistic models (DDPMs) have achieved unprecedented success in computer vision. However, they remain underutilized in medical imaging, a field crucial for disease diagnosis and treatment planning. This is primarily…
phyloDB is a modular and extensible framework for large-scale phylogenetic analyses, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an…
polyDB is a database for discrete geometric objects. The database is accessible via web and an interface from the software package polymake. It contains various datasets from the area of lattice polytopes, combinatorial polytopes, matroids…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur…
Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and…
BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified…
Like many scientific fields, new chemistry literature has grown at a staggering pace, with thousands of papers released every month. A large portion of chemistry literature focuses on new molecules and reactions between molecules. Most…
Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular…
Self-supervised learning (SSL) has emerged as a promising paradigm for medical image analysis by harnessing unannotated data. Despite their potential, the existing SSL approaches overlook the high anatomical similarity inherent in medical…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
Brain Imaging Data Structure (BIDS) allows the user to organise brain imaging data into a clear and easy standard directory structure. BIDS is widely supported by the scientific community and is considered a powerful standard for…
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…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…