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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
(2021)
Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm-Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.
Pädagogischer Umgang mit Körpererkundungsspielen in der Arbeit mit Kindern von 0 bis 6 Jahren
(2021)
Musik im Strafvollzug
(2021)
Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are generally considered to be characteristic signatures of the chemical compound they originate from, yet the chemical structure itself usually cannot be easily deduced from the spectrum. Often, spectral similarity measures are used as a proxy for structural similarity but this approach is strongly limited by a generally poor correlation between both metrics. Here, we propose MS2DeepScore: a novel Siamese neural network to predict the structural similarity between two chemical structures solely based on their MS/MS fragmentation spectra. Using a cleaned dataset of > 100,000 mass spectra of about 15,000 unique known compounds, we trained MS2DeepScore to predict structural similarity scores for spectrum pairs with high accuracy. In addition, sampling different model varieties through Monte-Carlo Dropout is used to further improve the predictions and assess the model's prediction uncertainty. On 3600 spectra of 500 unseen compounds, MS2DeepScore is able to identify highly-reliable structural matches and to predict Tanimoto scores for pairs of molecules based on their fragment spectra with a root mean squared error of about 0.15. Furthermore, the prediction uncertainty estimate can be used to select a subset of predictions with a root mean squared error of about 0.1. Furthermore, we demonstrate that MS2DeepScore outperforms classical spectral similarity measures in retrieving chemically related compound pairs from large mass spectral datasets, thereby illustrating its potential for spectral library matching. Finally, MS2DeepScore can also be used to create chemically meaningful mass spectral embeddings that could be used to cluster large numbers of spectra. Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity measures have great potential for a range of metabolomics data processing pipelines.
This paper investigates the implementation of a human body model for the simulation of a jumping motion in Simulink. It contains details to get an insight into modern biomechanics without previous experience. In the simulation, a Hill-Type muscle is used to generate joint momentum with a phenomenologically realistic relationship between muscle length and force. The simulation published with this article is one of many solutions to design a humanoid simulation. The paper guides through the implemented build and explains its range of application.
Homeoffice und Führung
(2021)
Gender in the making: An empirical approach to understand gender relations in the maker movement
(2021)
Community Music
(2021)
Aufgrund der §§ 2 Abs. 4 S. 1, 26 Abs. 3 S. 2 des Gesetzes über die Hochschulen des Landes Nord-rhein-Westfalen (Hochschulgesetz - HG) vom 16.09.2014 (GV.NRW. S. 547) in der aktuell gültigen Fassung und der Grundordnung der Hochschule Düsseldorf vom 08.10.2015 (Verkündungsblatt der Hochschule Düsseldorf, Amtliche Mitteilung Nr. 414) in der aktuell gültigen Fassung hat der Fachbereichsrat des Fachbereichs Design der Hochschule Düsseldorf die folgende Ordnung als Satzung erlassen.
Aufgrund des § 82a Absatz 1 Satz 1 des Gesetzes über die Hochschulen des Landes Nordrhein-Westfalen (Hochschulgesetz - HG) vom 16.09.2014 (GV. NRW. S. 547) in der aktuell gültigen Fassung in Verbindung mit der Verordnung zur Bewältigung der durch die Coronavirus SARS-CoV-2- Epidemie an den Hochschulbetrieb gestellten Herausforderungen (Corona-Epidemie-Hochschulverordnung) vom 01.12.2021 (GV. NRW. S. 81) in der aktuell gültigen Fassung hat das Präsidium der Hochschule Düsseldorf die folgende Ordnung als Satzung erlassen.