Development and validation of an electronic medical record-based alert score for detection of inpatient deterioration outside the ICU. - Patricia Kipnis; Benjamin J. Turk; David A. Wulf; Juan Carlos LaGuardia; Vincent X. Liu; Matthew M. Churpek; Santiago Romero-Brufau; Gabriel J. Escobar (J. Biomed. Informatics, 2016)

A Deeper Exploration of Contagious Risk and the Neighborhood Effect. - Anoop M. Mayampurath; Dana P. Edelson; Michael D. Howell; Matthew M. Churpek; Samuel L. Volchenboum (CRI, 2017)

A Computable Phenotype for Acute Respiratory Distress Syndrome Using Natural Language Processing and Machine Learning. - Majid Afshar; Cara Joyce; Anthony Oakey; Perry Formanek; Philip Yang; Matthew M. Churpek; Richard S. Cooper; Ron Price; Susan J. Zelisko; Dmitriy Dligach (AMIA, 2018)

Comparison of variable selection methods for clinical predictive modeling. - L. Nelson Sanchez-Pinto; Laura Ruth Venable; John Fahrenbach; Matthew M. Churpek (Int. J. Medical Informatics, 2018)

Bias Assessment and Correction in Machine Learning Algorithms: A Use-Case in a Natural Language Processing Algorithm to Identify Hospitalized Patients with Unhealthy Alcohol Use. - Marissa Borgese; Cara Joyce; Emily E. Anderson; Matthew M. Churpek; Majid Afshar (AMIA, 2021)

Sepsis Prediction Using Semi-Supervised and Transfer Learning. - John R. Caskey; Fereshteh S. Bashiri; Anoop M. Mayampurath; Nicole Dussault; Jay Dumanian; Sivasubramanium V. Bhavani; Kyle A. Carey; Emily R. Gilbert; Christopher J. Winslow; Nirav S. Shah; Dana P. Edelson; Majid Afshar; et al. (AMIA, 2021)

A multi-label classifier to screen different types of substance misuse in hospitalized patients. - Brihat Sharma; Dmitriy Dligach; Hale Thomson; Matthew M. Churpek; Niranjan S. Karnik; Majid Afshar (AMIA, 2021)

The Addition of United States Census-Tract Data Does Not Improve the Prediction of Substance Misuse. - Daniel To; Cara Joyce; Sujay Kulshrestha; Brihat Sharma; Dmitriy Dligach; Matthew M. Churpek; Majid Afshar (AMIA, 2021)

Bias and fairness assessment of a natural language processing opioid misuse classifier: detection and mitigation of electronic health record data disadvantages across racial subgroups. - Hale M. Thompson; Brihat Sharma; Sameer Bhalla; Randy Boley; Connor McCluskey; Dmitriy Dligach; Matthew M. Churpek; Niranjan S. Karnik; Majid Afshar (J. Am. Medical Informatics Assoc., 2021)

Explaining Alerts from a Pediatric Deterioration Prediction Model Using Clinical Text. - Anoop M. Mayampurath; Kyle A. Carey; Priti Jani; Majid Afshar; Matthew M. Churpek; Dmitriy Dligach (AMIA, 2022)

Summarizing Patients' Problems from Hospital Progress Notes Using Pre-trained Sequence-to-Sequence Models. - Yanjun Gao; Dmitriy Dligach; Timothy Miller 002; Dongfang Xu; Matthew M. Churpek; Majid Afshar (COLING, 2022)

Hierarchical Annotation for Building A Suite of Clinical Natural Language Processing Tasks: Progress Note Understanding. - Yanjun Gao; Dmitriy Dligach; Timothy Miller 002; Samuel Tesch; Ryan Laffin; Matthew M. Churpek; Majid Afshar (LREC, 2022)

Identifying infected patients using semi-supervised and transfer learning. - Fereshteh S. Bashiri; John R. Caskey; Anoop M. Mayampurath; Nicole Dussault; Jay Dumanian; Sivasubramanium V. Bhavani; Kyle A. Carey; Emily R. Gilbert; Christopher J. Winslow; Nirav S. Shah; Dana P. Edelson; Majid Afshar; et al. (J. Am. Medical Informatics Assoc., 2022)

A scoping review of publicly available language tasks in clinical natural language processing. - Yanjun Gao; Dmitriy Dligach; Leslie Christensen; Samuel Tesch; Ryan Laffin; Dongfang Xu; Timothy Miller 002; Özlem Uzuner; Matthew M. Churpek; Majid Afshar (J. Am. Medical Informatics Assoc., 2022)

Multi-Task Training with In-Domain Language Models for Diagnostic Reasoning. - Brihat Sharma; Yanjun Gao; Timothy Miller 002; Matthew M. Churpek; Majid Afshar; Dmitriy Dligach (ClinicalNLP@ACL, 2023)

Overview of the Problem List Summarization (ProbSum) 2023 Shared Task on Summarizing Patients' Active Diagnoses and Problems from Electronic Health Record Progress Notes. - Yanjun Gao; Dmitriy Dligach; Timothy Miller 002; Matthew M. Churpek; Majid Afshar (CoRR, 2023)

Leveraging A Medical Knowledge Graph into Large Language Models for Diagnosis Prediction. - Yanjun Gao; Ruizhe Li 001; John R. Caskey; Dmitriy Dligach; Timothy Miller 002; Matthew M. Churpek; Majid Afshar (CoRR, 2023)

Comparison of time series clustering methods for identifying novel subphenotypes of patients with infection. - Sivasubramanium V. Bhavani; Li Xiong 001; Abish Pius; Matthew W. Semler; Edward T. Qian; Philip A. Verhoef; Chad Robichaux; Craig M. Coopersmith; Matthew M. Churpek (J. Am. Medical Informatics Assoc., 2023)

DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing. - Yanjun Gao; Dmitriy Dligach; Timothy Miller 002; John R. Caskey; Brihat Sharma; Matthew M. Churpek; Majid Afshar (J. Biomed. Informatics, 2023)

Progress Note Understanding - Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task. - Yanjun Gao; Dmitriy Dligach; Timothy Miller 002; Matthew M. Churpek; Özlem Uzuner; Majid Afshar (J. Biomed. Informatics, 2023)

When Raw Data Prevails: Are Large Language Model Embeddings Effective in Numerical Data Representation for Medical Machine Learning Applications? - Yanjun Gao; Skatje Myers; Shan Chen 004; Dmitriy Dligach; Timothy A. Miller; Danielle S. Bitterman; Matthew M. Churpek; Majid Afshar (EMNLP (Findings), 2024)

Position Paper On Diagnostic Uncertainty Estimation from Large Language Models: Next-Word Probability Is Not Pre-test Probability. - Yanjun Gao; Skatje Myers; Shan Chen 004; Dmitriy Dligach; Timothy A. Miller; Danielle S. Bitterman; Guanhua Chen; Anoop M. Mayampurath; Matthew M. Churpek; Majid Afshar (CoRR, 2024)

Development and external validation of deep learning clinical prediction models using variable-length time series data. - Fereshteh S. Bashiri; Kyle A. Carey; Jennie Martin; Jay L. Koyner; Dana P. Edelson; Emily R. Gilbert; Anoop M. Mayampurath; Majid Afshar; Matthew M. Churpek (J. Am. Medical Informatics Assoc., 2024)

Automated stratification of trauma injury severity across multiple body regions using multi-modal, multi-class machine learning models. - Jifan Gao; Guanhua Chen; Ann P. O'Rourke; John R. Caskey; Kyle A. Carey; Madeline Oguss; Anne Stey; Dmitriy Dligach; Timothy Miller 002; Anoop M. Mayampurath; Matthew M. Churpek; Majid Afshar (J. Am. Medical Informatics Assoc., 2024)

Lessons learned on information retrieval in electronic health records: a comparison of embedding models and pooling strategies. - Skatje Myers; Timothy A. Miller; Yanjun Gao; Matthew M. Churpek; Anoop M. Mayampurath; Dmitriy Dligach; Majid Afshar (J. Am. Medical Informatics Assoc., 2025)