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Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns.
Learning a similarity metric discriminatively, with application to face verification
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Sharing and community curation of mass spectrometry data with global natural products social molecular networking
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Identification of small molecules using accurate mass ms/ms search
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Integrated probabilistic annotation: a bayesian-based annotation method for metabolomic profiles integrating biochemical connections, isotope patterns, and adduct relationships
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Sirius 4: a rapid tool for turning tandem mass spectra into metabolite structure information
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Supervised contrastive learning
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A comprehensive survey on regularization strategies in machine learning
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Emergence of molecular structures from repository-scale self-supervised learning on tandem mass spectra
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ipapy2: Integrated probabilistic annotation (ipa) 2.0—an improved bayesian-based method for the annotation of lc–ms/ms untargeted metabolomics data
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Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Goldman, S., Wohlwend, J., Stražar, M., Haroush, G., Xavier, R. J., and Coley, C. W. (2023) · 2023
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NIST (2020) · 2020
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Contrastive multiview coding
Tian, Y., Krishnan, D., and Isola, P. (2020) · 2020
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
Dührkop, K., Nothias, L.-F., Fleischauer, M., Reher, R., Ludwig, M., Hoffmann, M. A., Petras, D., Gerwick, W. H., Rousu, J., Dorrestein, P. C., et al · 2021
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Spec2vec: Improved mass spectral similarity scoring through learning of structural relationships
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Learning transferable visual models from natural language supervision
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Cfm-id 4.0: more accurate esi-ms/ms spectral prediction and compound identification
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Massformer: Tandem mass spectrum prediction for small molecules using graph transformers
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An end-to-end deep learning framework for translating mass spectra to de-novo molecules
Litsa, E. E., Chenthamarakshan, V., Das, P., and Kavraki, L. E. (2023) · 2023
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Cmssp: A contrastive mass spectra-structure pretraining model for metabolite identification
Chen, L., Xia, B., Wang, Y., Huang, X., Gu, Y., Wu, W., and Zhou, Y. (2024) · 2024
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An ensemble spectral prediction (ESP) model for metabolite annotation
Li, X., Zhou Chen, Y., Kalia, A., Zhu, H., Liu, L.-p., and Hassoun, S. (2024) · 2024
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Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking
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MassBank of North America
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Msbert: Embedding tandem mass spectra into chemically rational space by mask learning and contrastive learning
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Chemembed: A deep learning framework for metabolite identification using enhanced ms/ms data and multidimensional molecular embeddings
Faizan-Khan, M., Giné, R., Badia, J. M., Pérez-Ribera, M., Junza, A., Vinaixa, M., Sales-Pardo, M., Guimerà, R., and Yanes, O. (2025) · 2025
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