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Mass spectrometry is a widespread approach to work out what are the constituents of a material. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based…
We introduce the ParClusterers Benchmark Suite (PCBS) -- a collection of highly scalable parallel graph clustering algorithms and benchmarking tools that streamline comparing different graph clustering algorithms and implementations. The…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
Spectral molecular imaging is a new imaging technique able to discriminate and quantify different components of tissue simultaneously at high spatial and high energy resolution. Our MARS scanner is an x-ray based small animal CT system…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
The emergence of quantum computers as a new computational paradigm has been accompanied by speculation concerning the scope and timeline of their anticipated revolutionary changes. While quantum computing is still in its infancy, the…
We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical $N$-body simulations.…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
In this paper, we present MCBench, a benchmark suite designed to assess the quality of Monte Carlo (MC) samples. The benchmark suite enables quantitative comparisons of samples by applying different metrics, including basic statistical…
As Large Language Models (LLMs) demonstrate exceptional performance across various domains, deploying LLMs on edge devices has emerged as a new trend. Quantization techniques, which reduce the size and memory requirements of LLMs, are…
Mass spectrometry based clinical proteomics has emerged as a powerful tool for highthroughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in…
Mass cytometry technology enables the simultaneous measurement of over 40 proteins on single cells. This has helped immunologists to increase their understanding of heterogeneity, complexity, and lineage relationships of white blood cells.…
Traditional post-training quantization (PTQ) is considered an effective approach to reduce model size and accelerate inference of large-scale language models (LLMs). However, existing low-rank PTQ methods require costly fine-tuning to…
Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same…
This work describes a domain embedding technique between two non-matching meshes used for generating realizations of spatially correlated random fields with applications to large-scale sampling-based uncertainty quantification. The goal is…
Computed tomography (CT) is routinely used in clinical practice to evaluate a wide variety of medical conditions. While CT scans provide diagnoses, they also offer the ability to extract quantitative body composition metrics to analyze…
Recent advances in machine learning (ML) have accelerated progress in calibrating and operating quantum dot (QD) devices. However, most ML approaches rely on access to large, representative datasets designed to capture the full spectrum of…
We present DASPack, a high-performance, open-source compression tool specifically designed for distributed acoustic sensing (DAS) data. As DAS becomes a key technology for real-time, high-density, and long-range monitoring in fields such as…