Ivan Protsyuk
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View article: Boosting the interpretability of clinical risk scores with intervention predictions
Boosting the interpretability of clinical risk scores with intervention predictions Open
Machine learning systems show significant promise for forecasting patient adverse events via risk scores. However, these risk scores implicitly encode assumptions about future interventions that the patient is likely to receive, based on t…
Multitask prediction of organ dysfunction in the intensive care unit using sequential subnetwork routing Open
Objective Multitask learning (MTL) using electronic health records allows concurrent prediction of multiple endpoints. MTL has shown promise in improving model performance and training efficiency; however, it often suffers from negative tr…
View article: Feature-based Molecular Networking in the GNPS Analysis Environment
Feature-based Molecular Networking in the GNPS Analysis Environment Open
Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds and quantitative interpretation are currently li…
View article: Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis Open
Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially i…
View article: Developing Deep Learning Continuous Risk Models for Early Adverse Event Prediction in Electronic Health Records: an AKI Case Study
Developing Deep Learning Continuous Risk Models for Early Adverse Event Prediction in Electronic Health Records: an AKI Case Study Open
Early detection of patient deterioration is key to unlocking the potential for targeted preventative care and improving patient outcomes. This protocol describes a workflow for developing deep learning continuous risk models for early pred…
View article: The Molecular and Microbial Microenvironments in Chronically Diseased Lungs
The Molecular and Microbial Microenvironments in Chronically Diseased Lungs Open
To visualize the personalized distributions of pathogens, chemical environments including microbial metabolites, pharmaceuticals, and their metabolic products within and between human lungs afflicted with cystic fibrosis, we generated 3D m…
View article: Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation
Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation Open
It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we …
View article: Meta-mass shift chemical profiling of metabolomes from coral reefs
Meta-mass shift chemical profiling of metabolomes from coral reefs Open
Significance Coral reef taxa produce a diverse array of molecules, some of which are important pharmaceuticals. To better understand how molecular diversity is generated on coral reefs, tandem mass spectrometry datasets of coral metabolome…
View article: Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats
Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats Open
The cars we drive, the homes we live in, the restaurants we visit, and the laboratories and offices we work in are all a part of the modern human habitat. Remarkably, little is known about the diversity of chemicals present in these enviro…