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Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of…

Mixture - modeling of mass spectra is an approach with many potential applications including peak detection and quantification, smoothing, de-noising, feature extraction and spectral signal compression. However, existing algorithms do not…

The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…

MALDI mass spectrometry imaging (MALDI MSI) is a spatially resolved analytical tool for biological tissue analysis by measuring mass-to-charge ratios of ionized molecules. With increasing spatial and mass resolution of MALDI MSI data,…

Medical image segmentation is vital for clinical diagnosis, yet current deep learning methods often demand extensive expert effort, i.e., either through annotating large training datasets or providing prompts at inference time for each new…

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…

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…

The optimization of the electrodes manufacturing process constitutes one of the most critical steps to ensure high-quality Lithium-Ion Battery (LIB) cells, in particular for automotive applications. Because LIB electrode manufacturing is a…

We present a new pipeline utilizing machine learning for classifying short-duration features in raw time-ordered data (TOD) of cosmic microwave background survey observations. The pipeline, specifically designed for the Atacama Cosmology…

Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…

Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…

While machine learning (ML) includes a valuable array of tools for analyzing biomedical data, significant time and expertise is required to assemble effective, rigorous, and unbiased pipelines. Automated ML (AutoML) tools seek to facilitate…

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline…

In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…

In order to achieve state-of-the-art performance, modern machine learning techniques require careful data pre-processing and hyperparameter tuning. Moreover, given the ever increasing number of machine learning models being developed, model…

Mammography is the primary imaging modality used for early detection and diagnosis of breast cancer. X-ray mammogram analysis mainly refers to the localization of suspicious regions of interest followed by segmentation, towards further…

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…

Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of…

This study proposes a framework for the automated hyperparameter optimization of a bearing fault detection pipeline for permanent magnet synchronous motors (PMSMs) without the need of external sensors. A automated machine learning (AutoML)…

Functional Magnetic Resonance Imaging (fMRI) relies on multi-step data processing pipelines to accurately determine brain activity; among them, the crucial step of spatial smoothing. These pipelines are commonly suboptimal, given the local…