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Quantitative proteomics plays a central role in uncovering regulatory mechanisms, identifying disease biomarkers, and guiding the development of precision therapies. These insights are often obtained through complex Bayesian models, whose…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells.…
Machine learning-based classifiers are commonly evaluated by metrics like accuracy, but deeper analysis is required to understand their strengths and weaknesses. MLMC is a visual exploration tool that tackles the challenge of multi-label…
Uncertainty quantification in automated image analysis is highly desired in many applications. Typically, machine learning models in classification or segmentation are only developed to provide binary answers; however, quantifying the…
It is critical to deploy complicated neural network models on hardware with limited resources. This paper proposes a novel model quantization method, named the Low-Cost Proxy-Based Adaptive Mixed-Precision Model Quantization (LCPAQ), which…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Atom probe tomography (APT) is a valuable near-atomic scale imaging technique, which yields mass spectrographic data. Experimental correctness can often pivot on the identification of peaks within a dataset, this is a manual process where…
Recent advances in large language model (LLM) pretraining have led to high-quality LLMs with impressive abilities. By compressing such LLMs via quantization to 3-4 bits per parameter, they can fit into memory-limited devices such as laptops…
Due to its specificity, fluorescence microscopy (FM) has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit FM's utility. Recently, it has been shown that…
SpectraMatcher is a cross-platform desktop application for interactive comparison of experimental and computed vibronic spectra, designed to assist in the recognition and assignment of spectral patterns. It provides an intuitive graphical…
Objective: Quantitative real-time PCR is widely used for gene expression analysis, yet inconsistencies in data storage and reporting limit reproducibility. While MIQE guidelines define the minimal information required for publication, they…
We sought to develop a quantitative tool to quickly determine relative differences in MRI volumes both within and between large MR imaging cohorts (such as available in The Cancer Imaging Archive (TCIA)), in order to help determine the…
As large language models (LLMs) continue to advance, the need for up-to-date and well-organized benchmarks becomes increasingly critical. However, many existing datasets are scattered, difficult to manage, and make it challenging to perform…
A spectral decomposition method has been implemented to identify and quantify isotopic source terms in high-resolution gamma-ray spectroscopy in static geometry and shielding scenarios. Monte-Carlo simulations were used to build the…
Creating scalable, reliable, and well-motivated benchmarks for quantum computers is challenging: straightforward approaches to benchmarking suffer from exponential scaling, are insensitive to important errors, or use poorly-motivated…
This manuscript describes the software package SCOUT, which analyzes, characterizes, and corrects one-dimensional signals. Specifically, it allows to check and correct for stationarity, detect spurious samples, check for normality, check…
Targeting at the realization of scalable photonic quantum technologies, the generation of many photons, their propagation in large optical networks, and a subsequent detection and analysis of sophisticated quantum correlations are essential…
We describe in this paper a new, public software for accurate "PSF-matched" multiband photometry for images of different resolution and depth, that we have named ConvPhot, of which we analyse performances and limitations. It is designed to…
Post-training quantization (PTQ) with computational invariance for Large Language Models~(LLMs) have demonstrated remarkable advances, however, their application to Multimodal Large Language Models~(MLLMs) presents substantial challenges.…