arXiv subjects

Jarrod Mosier

Publications and source records attributed to Jarrod Mosier.

4 recordsLinked to original sources

arXiv2026

DINIRS: Digital Twin for Individualized Treatment Effects of Non-Invasive Respiratory Support Strategies

Objective: Choosing between noninvasive respiratory support (NIRS) and invasive mechanical ventilation (IMV) for patients with acute respiratory failure is a complex, time-sensitive decision with heterogeneous treatment effects across patient subgroups. Although clinical trials and guidelines provide population-level guidance, it remains unclear which patients benefit more from NIRS than IMV. We developed and validated a censoring-aware Digital Twin framework for Individualized Treatment Effects of Non-Invasive Respiratory Support (DINIRS) to estimate individualized treatment effects (ITEs) that capture mortality and ventilation duration. Materials and Methods: We trained DINIRS on 23 baseline clinical variables from the first 24 ICU hours in 5,336 MIMIC-IV patients with acute respiratory failure. We used a transformer encoder with a survival attention gate to decompose 28-day ventilator-free days (VFD-28) into survival probability and conditional ventilation duration. A cross-fitted, doubly robust learner estimated ITEs. We externally validated DINIRS in 2,540 patients from the multi-site eICU-CRD dataset. Results: The DINIRS policy achieved a mean benefit of 2.07 ventilator-free days per patient (207 per 100 patients) compared with the observed practice. Predicted NIRS benefit was higher among patients with less organ dysfunction (88.4% versus 49.0%) and persisted across hypoxemia severity. External validation reproduced this pattern without retraining. Discussion: Our analysis revealed that the NIRS benefit stemmed from shorter ventilation among survivors rather than from reduced mortality, indicating that avoiding intubation-associated complications was the primary mechanism. Conclusion: This study demonstrated individualized estimation of NIRS benefit using ICU data, though prospective validation is needed before these estimates inform treatment decisions.

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arXiv2025

Development and Evaluation of an Ontology for Non-Invasive Respiratory Support in Acute Care

Managing patients with respiratory failure increasingly involves noninvasive respiratory support (NIRS) strategies to support respiration, often preventing the need for invasive mechanical ventilation. However, despite the rapidly expanding use of NIRS, there remains a significant challenge to its optimal use across all medical circumstances. It lacks a unified ontological structure, complicating guidance on NIRS modalities across healthcare systems. This study introduced NIRS ontology to support knowledge representation in acute care settings by providing a unified framework that enhances data clarity and interoperability, laying the groundwork for future clinical decision-making. We developed NIRS ontology using the Web Ontology Language (OWL) and Protege to organize clinical concepts and relationships. To enable rule-based clinical reasoning beyond hierarchical structures, we added Semantic Web Rule Language (SWRL) rules. We evaluated logical reasoning by adding a sample of 6 patient scenarios and used SPARQL queries to retrieve and test targeted inferences. The ontology has 145 classes, 11 object properties, and 18 data properties across 949 axioms that establish concept relationships. To standardize clinical concepts, we added 392 annotations, including descriptive definitions based on controlled vocabularies. SPARQL query evaluations across clinical scenarios confirmed the ontology ability to support rule based reasoning and therapy recommendations, providing a foundation for consistent documentation practices, integration into clinical data models, and advanced analysis of NIRS outcomes. In conclusion, we unified NIRS concepts into an ontological framework and demonstrated its applicability through the evaluation of patient scenarios and alignment with standardized vocabularies.

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arXiv2025

SHREC: A Framework for Advancing Next-Generation Computational Phenotyping with Large Language Models

Computational phenotyping is a central informatics activity with resulting cohorts supporting a wide variety of applications. However, it is time-intensive because of manual data review and limited automation. Since LLMs have demonstrated promising capabilities for text classification, comprehension, and generation, we posit they will perform well at repetitive manual review tasks traditionally performed by human experts. To support next-generation computational phenotyping, we developed SHREC, a framework for integrating LLMs into end-to-end phenotyping pipelines. We applied and tested three lightweight LLMs (Gemma2 27 billion, Mistral Small 24 billion, and Phi-4 14 billion) to classify concepts and phenotype patients using phenotypes for ARF respiratory support therapies. All models performed well on concept classification, with the best (Mistral) achieving an AUROC of 0.896. For phenotyping, models demonstrated near-perfect specificity for all phenotypes with the top-performing model (Mistral) achieving an average AUROC of 0.853 for single-therapy phenotypes. In conclusion, lightweight LLMs can assist researchers with resource-intensive phenotyping tasks. Several advantages of LLMs included their ability to adapt to new tasks with prompt engineering alone and their ability to incorporate raw EHR data. Future steps include determining optimal strategies for integrating biomedical data and understanding reasoning errors

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arXiv2023

Computable Phenotypes for Post-acute sequelae of SARS-CoV-2: A National COVID Cohort Collaborative Analysis

Post-acute sequelae of SARS-CoV-2 (PASC) is an increasingly recognized yet incompletely understood public health concern. Several studies have examined various ways to phenotype PASC to better characterize this heterogeneous condition. However, many gaps in PASC phenotyping research exist, including a lack of the following: 1) standardized definitions for PASC based on symptomatology; 2) generalizable and reproducible phenotyping heuristics and meta-heuristics; and 3) phenotypes based on both COVID-19 severity and symptom duration. In this study, we defined computable phenotypes (or heuristics) and meta-heuristics for PASC phenotypes based on COVID-19 severity and symptom duration. We also developed a symptom profile for PASC based on a common data standard. We identified four phenotypes based on COVID-19 severity (mild vs. moderate/severe) and duration of PASC symptoms (subacute vs. chronic). The symptoms groups with the highest frequency among phenotypes were cardiovascular and neuropsychiatric with each phenotype characterized by a different set of symptoms.

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