PXD044264 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis |
Description | The 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). |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_07:16:27.269.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Erik Hartman |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-08-01 06:55:28 | ID requested | |
1 | 2023-09-05 08:28:39 | announced | |
⏵ 2 | 2023-11-14 07:16:27 | announced | 2023-11-14: 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 affiliation | Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden |
contact email | johan.malmstrom@med.lu.se |
lab head | |
Erik Hartman |
contact affiliation | Lund University |
contact email | erik.hartman@hotmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD044264
- Label: PRIDE project
- Name: Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis