相关论文: Open Mass Spectrometry Search Algorithm

Optunity is a free software package dedicated to hyperparameter optimization. It contains various types of solvers, ranging from undirected methods to direct search, particle swarm and evolutionary optimization. The design focuses on ease…

In this article, a software package code named OPSIAL (Optical Plasma Spectral Calculation And Parameters Retrieval) for rigorously calculating optical plasma spectra and for automatically retrieving plasma parameters is presented. OPSIAL…

The Precision Proton Spectrometer (PPS) is a new subdetector of CMS that provides a powerful tool for the advancement of beyond standard model searches. We present recent results obtained with the PPS subdetector illustrating the unique…

Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library…

Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…

In the ordinal Matroid Secretary Problem (MSP), elements from a weighted matroid are presented in random order to an algorithm that must incrementally select a large weight independent set. However, the algorithm can only compare pairs of…

Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of…

We present a new use of Answer Set Programming (ASP) to discover the molecular structure of chemical samples based on the relative abundance of elements and structural fragments, as measured in mass spectrometry. To constrain the…

Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…

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…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

Propensity score matching (PSM) is a pseudo-experimental method that uses statistical techniques to construct an artificial control group by matching each treated unit with one or more untreated units of similar characteristics. To date,…

Overlapping Community Search (OCS) identifies nodes that interact with multiple communities based on a specified query. Existing community search approaches fall into two categories: algorithm-based models and Machine Learning-based (ML)…

Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…

This article introduces an enhanced particle swarm optimizer (PSO), termed Orthogonal PSO with Mutation (OPSO-m). Initially, it proposes an orthogonal array-based learning approach to cultivate an improved initial swarm for PSO,…

Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occupy one of two extremes, either operating (a) by fragmenting…

The development of neuromorphic hardware and modeling of biological neural networks requires algorithms with local learning rules. Artificial neural networks using local learning rules to perform principal subspace analysis (PSA) and…

Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with…

The Constrained Minimal Supersymmetric Standard Model (CMSSM) is one of the simplest and most widely-studied supersymmetric extensions to the standard model of particle physics. Nevertheless, current data do not sufficiently constrain the…