Related papers: pyssam -- a Python library for statistical modelli…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
We present an overview of Sherpa, an open source Python project, and discuss its development history, broad design concepts and capabilities. Sherpa contains powerful tools for combining parametric models into complex expressions that can…
Biologically inspired model (BIM) for image recognition is a robust computational architecture, which has attracted widespread attention. BIM can be described as a four-layer structure based on the mechanisms of the visual cortex. Although…
Medical image segmentation and video object segmentation are essential for diagnosing and analyzing diseases by identifying and measuring biological structures. Recent advances in natural domain have been driven by foundation models like…
1. Natural sounds have been recorded for millions of hours over the previous decades using passive acoustic monitoring. Improvements in deep learning models have vastly accelerated the analysis of large portions of this data. While new…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
The present paper proposes a novel method of quantification of the variation in biofilm architecture, in correlation with the alteration of growth conditions that include, variations of substrate and conditioning layer. The polymeric…
This study investigates the potential of eye-tracking technology and the Segment Anything Model (SAM) to design a collaborative human-computer interaction system that automates medical image segmentation. We present the \textbf{GazeSAM}…
Open-source 3D data processing libraries originally developed for computer vision and pattern recognition are used to align and compare molecular shapes and sub-shapes. Here, a shape is represented by a set of points distributed on the van…
Loss landscapes are a powerful tool for understanding neural network optimization and generalization, yet traditional low-dimensional analyses often miss complex topological features. We present Landscaper, an open-source Python package for…
The Structural Similarity (SSIM) Index is a very widely used image/video quality model that continues to play an important role in the perceptual evaluation of compression algorithms, encoding recipes and numerous other image/video…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
Accurate simulation of astronomical observations is a critical element for any modern analyses, be it to measure event rates, analyses population properties, validate or train pipelines, account for selection effects, or correct biases. We…
Wavelength calibration is a routine and critical part of any spectral work-flow, but many astronomers still resort to matching detected peaks and emission lines by hand. We present RASCAL (RANSAC Assisted Spectral CALibration), a python…
There have been growing discussions on estimating and subsequently reducing the operational carbon footprint of enterprise data centers. The design and intelligent control for data centers have an important impact on data center carbon…
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…
As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark…
In response to a concerning trend of selectively emphasizing metrics in medical image segmentation (MIS) studies, we introduce \texttt{seg-metrics}, an open-source Python package for standardized MIS model evaluation. Unlike existing…
We present GLEAM (Galaxy Line Emission & Absorption Modeling), a Python tool for fitting Gaussian models to emission and absorption lines in large samples of 1D extragalactic spectra. GLEAM is tailored to work well in batch mode without…