John R. Caskey

dblp:330/7743 · DBLP profile ↗
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5ranked-venue papers
1as first author
5since 2021 · last 2026
0000-0001-5665-524XORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 5 · 1 first-author · 5 since 2021
YearPublicationVenuePosition
2026 Explainable multimodal deep learning models for variable-length sequences in critically ill patients
Jennifer Martin, Majid Afshar, Askar Safipour Afshar, John R. Caskey, Dmitriy Dligach, Yanjun Gao, Jifan Gao, Guanhua Chen 0002, Anoop M. Mayampurath, Matthew M. Churpek
J. Biomed. Informatics4
2024 Automated stratification of trauma injury severity across multiple body regions using multi-modal, multi-class machine learning models
abstract
OBJECTIVE: The timely stratification of trauma injury severity can enhance the quality of trauma care but it requires intense manual annotation from certified trauma coders. The objective of this study is to develop machine learning models for the stratification of trauma injury severity across various body regions using clinical text and structured electronic health records (EHRs) data. MATERIALS AND METHODS: Our study utilized clinical documents and structured EHR variables linked with the trauma registry data to create 2 machine learning models with different approaches to representing text. The first one fuses concept unique identifiers (CUIs) extracted from free text with structured EHR variables, while the second one integrates free text with structured EHR variables. Temporal validation was undertaken to ensure the models' temporal generalizability. Additionally, analyses to assess the variable importance were conducted. RESULTS: Both models demonstrated impressive performance in categorizing leg injuries, achieving high accuracy with macro-F1 scores of over 0.8. Additionally, they showed considerable accuracy, with macro-F1 scores exceeding or near 0.7, in assessing injuries in the areas of the chest and head. We showed in our variable importance analysis that the most important features in the model have strong face validity in determining clinically relevant trauma injuries. DISCUSSION: The CUI-based model achieves comparable performance, if not higher, compared to the free-text-based model, with reduced complexity. Furthermore, integrating structured EHR data improves performance, particularly when the text modalities are insufficiently indicative. CONCLUSIONS: Our multi-modal, multiclass models can provide accurate stratification of trauma injury severity and clinically relevant interpretations.
Jifan Gao, Guanhua Chen 0002, Ann P. O'Rourke, John R. Caskey, Kyle A. Carey, Madeline Oguss, Anne Stey, Dmitriy Dligach, Timothy A. Miller, Anoop M. Mayampurath, Matthew M. Churpek, Majid Afshar
J. Am. Medical Informatics Assoc.4
2023 DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing
Yanjun Gao, Dmitriy Dligach, Timothy A. Miller, John R. Caskey, Brihat Sharma, Matthew M. Churpek, Majid Afshar
J. Biomed. Informatics4
2022 Identifying infected patients using semi-supervised and transfer learning
abstract
OBJECTIVES: Early identification of infection improves outcomes, but developing models for early identification requires determining infection status with manual chart review, limiting sample size. Therefore, we aimed to compare semi-supervised and transfer learning algorithms with algorithms based solely on manual chart review for identifying infection in hospitalized patients. MATERIALS AND METHODS: This multicenter retrospective study of admissions to 6 hospitals included "gold-standard" labels of infection from manual chart review and "silver-standard" labels from nonchart-reviewed patients using the Sepsis-3 infection criteria based on antibiotic and culture orders. "Gold-standard" labeled admissions were randomly allocated to training (70%) and testing (30%) datasets. Using patient characteristics, vital signs, and laboratory data from the first 24 hours of admission, we derived deep learning and non-deep learning models using transfer learning and semi-supervised methods. Performance was compared in the gold-standard test set using discrimination and calibration metrics. RESULTS: The study comprised 432 965 admissions, of which 2724 underwent chart review. In the test set, deep learning and non-deep learning approaches had similar discrimination (area under the receiver operating characteristic curve of 0.82). Semi-supervised and transfer learning approaches did not improve discrimination over models fit using only silver- or gold-standard data. Transfer learning had the best calibration (unreliability index P value: .997, Brier score: 0.173), followed by self-learning gradient boosted machine (P value: .67, Brier score: 0.170). DISCUSSION: Deep learning and non-deep learning models performed similarly for identifying infection, as did models developed using Sepsis-3 and manual chart review labels. CONCLUSION: In a multicenter study of almost 3000 chart-reviewed patients, semi-supervised and transfer learning models showed similar performance for model discrimination as baseline XGBoost, while transfer learning improved calibration.
Fereshteh S. Bashiri, John R. Caskey, Anoop M. Mayampurath, Nicole Dussault, Jay Dumanian, Sivasubramanium Bhavani, Kyle A. Carey, Emily R. Gilbert, Christopher J. Winslow, Nirav Shah 0004, Dana P. Edelson, Majid Afshar, Matthew M. Churpek
J. Am. Medical Informatics Assoc.2
2021 Sepsis Prediction Using Semi-Supervised and Transfer Learning
John R. Caskey, Fereshteh S. Bashiri, Anoop M. Mayampurath, Nicole Dussault, Jay Dumanian, Sivasubramanium Bhavani, Kyle A. Carey, Emily R. Gilbert, Christopher J. Winslow, Nirav Shah 0004, Dana P. Edelson, Majid Afshar, Matthew M. Churpek
AMIA1