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PXD044264

PXD044264 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleInterpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis
DescriptionThe incorporation of machine learning methods into proteomics workflows improves the identification of disease-relevant biomarkers and biological pathways. However, machine learning models, such as deep neural networks, typically suffer from lack of interpretability. Here, we present a deep learning approach to combine biological pathway analysis and biomarker identification to increase the interpretability of proteomics experiments. Our approach integrates a priori knowledge of the relationships between proteins and biological pathways and biological processes into sparse neural networks to create biologically informed neural networks. We employ these networks to differentiate between clinical subphenotypes of septic acute kidney injury and COVID-19, as well as acute respiratory distress syndrome of different aetiologies. To gain biological insight into the complex syndromes, we utilize feature attribution-methods to introspect the networks for the identification of proteins and pathways important for distinguishing between subtypes. The algorithms are implemented in a freely available open source Python-package (https://github.com/InfectionMedicineProteomics/BINN).
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_07:16:27.269.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterErik Hartman
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-08-01 06:55:28ID requested
12023-09-05 08:28:39announced
22023-11-14 07:16:27announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: machine learning, sepsis, neural networks, dia, proteome,aki
Contact List
Johan Malmström
contact affiliationLund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden
contact emailjohan.malmstrom@med.lu.se
lab head
Erik Hartman
contact affiliationLund University
contact emailerik.hartman@hotmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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