PXD044264-2

PXD044264 is an original dataset announced via ProteomeXchange.

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

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.

Dataset with its publication pending

submitter keyword: machine learning, sepsis, neural networks, dia, proteome,aki

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/09/PXD044264

PRIDE project URI

• PRIDE
  1. PXD044264
     1. Label: PRIDE project
     2. Name: Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis