Jonathan H. Chen

According to our database, Jonathan H. Chen authored at least 66 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Diagnostic reasoning prompts reveal the potential for large language model interpretability in medicine.

Thomas Savage, Ashwin Nayak, Robert Gallo, Ekanath Rangan, Jonathan H. Chen

npj Digit. Medicine, 2024

Fine Tuning Large Language Models for Medicine: The Role and Importance of Direct Preference Optimization.

Thomas Savage, Stephen Ma, Abdessalem Boukil, Vishwesh Patel, Ekanath Rangan, Ivan Rodriguez, Jonathan H. Chen

CoRR, 2024

Quantization-free Lossy Image Compression Using Integer Matrix Factorization.

Pooya Ashtari, Pourya Behmandpoor, Fateme Nateghi Haredasht, Jonathan H. Chen, Panagiotis Patrinos, Sabine Van Huffel

CoRR, 2024

Many-Shot In-Context Learning in Multimodal Foundation Models.

Yixing Jiang, Jeremy Irvin, Ji Hun Wang, Muhammad Ahmed Chaudhry, Jonathan H. Chen, Andrew Y. Ng

CoRR, 2024

Standing on FURM ground - A framework for evaluating Fair, Useful, and Reliable AI Models in healthcare systems.

Alison Callahan, Duncan C. McElfresh, Juan M. Banda, Gabrielle Bunney, Danton Char, Jonathan H. Chen, Conor K. Corbin, Debadutta Dash, Norman L. Downing, Sneha S. Jain, Nikesh Kotecha, Jonathan Masterson, Michelle M. Mello, Keith E. Morse, Srikar Nallan, Abby Pandya, Anurang Revri, Aditya Sharma, Christopher D. Sharp, Rahul Thapa, Michael Wornow, Alaa Youssef, Michael A. Pfeffer, Nigam H. Shah

CoRR, 2024

MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records.

Scott L. Fleming, Alejandro Lozano, William J. Haberkorn, Jenelle A. Jindal, Eduardo Pontes Reis, Rahul Thapa, Louis Blankemeier, Julian Z. Genkins, Ethan Steinberg, Ashwin Nayak, Birju S. Patel, Chia-Chun Chiang, Alison Callahan, Zepeng Huo, Sergios Gatidis, Scott J. Adams, Oluseyi Fayanju, Shreya J. Shah, Thomas Savage, Ethan Goh, Akshay S. Chaudhari, Nima Aghaeepour, Christopher D. Sharp, Michael A. Pfeffer, Percy Liang, Jonathan H. Chen, Keith E. Morse, Emma P. Brunskill, Jason A. Fries, Nigam H. Shah

Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024

2023

Selective prediction for extracting unstructured clinical data.

Akshay Swaminathan, Iván López, William Wang, Ujwal Srivastava, Edward Tran, Aarohi Bhargava-Shah, Janet Y. Wu, Alexander L. Ren, Kaitlin Caoili, Brandon Bui, Layth Alkhani, Susan Lee, Nathan Mohit, Noel Seo, Nicholas Macedo, Winson Cheng, Charles Liu, Reena Thomas, Jonathan H. Chen, Olivier Gevaert

J. Am. Medical Informatics Assoc., December, 2023

Clinical outcome prediction using observational supervision with electronic health records and audit logs.

Nandita Bhaskhar, Wui Ip, Jonathan H. Chen, Daniel L. Rubin

J. Biomed. Informatics, November, 2023

DEPLOYR: a technical framework for deploying custom real-time machine learning models into the electronic medical record.

Conor K. Corbin, Rob Maclay, Aakash Acharya, Sreedevi Mony, Soumya Punnathanam, Rahul Thapa, Nikesh Kotecha, Nigam H. Shah, Jonathan H. Chen

J. Am. Medical Informatics Assoc., August, 2023

Natural language processing system for rapid detection and intervention of mental health crisis chat messages.

Akshay Swaminathan, Iván López, Rafael Antonio Garcia Mar, Tyler Heist, Tom McClintock, Kaitlin Caoili, Madeline Grace, Matthew Rubashkin, Michael N. Boggs, Jonathan H. Chen, Olivier Gevaert, David Mou, Matthew K. Nock

npj Digit. Medicine, 2023

Graph-based clinical recommender: Predicting specialists procedure orders using graph representation learning.

Sajjad Fouladvand, Federico Reyes Gomez, Hamed Nilforoshan, Matthew Schwede, Morteza Noshad, Olivia Jee, Jiaxuan You, Rok Sosic, Jure Leskovec, Jonathan H. Chen

J. Biomed. Informatics, 2023

Evaluation of GPT-3.5 and GPT-4 for supporting real-world information needs in healthcare delivery.

Debadutta Dash, Rahul Thapa, Juan M. Banda, Akshay Swaminathan, Morgan Cheatham, Mehr Kashyap, Nikesh Kotecha, Jonathan H. Chen, Saurabh Gombar, Lance Downing, Rachel Pedreira, Ethan Goh, Angel Arnaout, Garret Kenn Morris, Honor Magon, Matthew P. Lungren, Eric Horvitz, Nigam H. Shah

CoRR, 2023

2022

Signal from the noise: A mixed graphical and quantitative process mining approach to evaluate care pathways applied to emergency stroke care.

Morteza Noshad, Christian Rose, Jonathan H. Chen

J. Biomed. Informatics, 2022

Team is brain: leveraging EHR audit log data for new insights into acute care processes.

Christian Rose, Robert Thombley, Morteza Noshad, Yun Lu, Heather A Clancy, David Schlessinger, Ron C. Li, Vincent X. Liu, Jonathan H. Chen, Julia Adler-Milstein

J. Am. Medical Informatics Assoc., 2022

Interruptive Electronic Alerts for Choosing Wisely Recommendations: A Cluster Randomized Controlled Trial.

Vy T. Ho, Rachael C. Aikens, Geoffrey J. Tso, Paul A. Heidenreich, Christopher D. Sharp, Steven M. Asch, Jonathan H. Chen, Neil K. Shah

J. Am. Medical Informatics Assoc., 2022

Avoiding Biased Clinical Machine Learning Model Performance Estimates in the Presence of Label Selection.

Conor K. Corbin, Michael Baiocchi, Jonathan H. Chen

CoRR, 2022

Electrocardiographic Deep Learning for Predicting Post-Procedural Mortality.

David Ouyang, John Theurer, Nathan R. Stein, J. Weston Hughes, Pierre Elias, Bryan He, Neal Yuan, Grant Duffy, Roopinder K. Sandhu, Joseph Ebinger, Patrick Botting, Melvin Jujjavarapu, Brian Claggett, James E. Tooley, Tim Poterucha, Jonathan H. Chen, Michael Nurok, Marco V. Perez, Adler J. Perotte, James Y. Zou, Nancy R. Cook, Sumeet S. Chugh, Susan Cheng, Christine M. Albert

CoRR, 2022

Leveraging EHR Audit Log Data to Unlock New Insights into Care Processes and Outcomes.

Christian Rose, Robert Thombley, Morteza Noshad, Ron Li, Wendy Lu, Heather A Clancy, David Schlessinger, Vincent X. Liu, Jonathan H. Chen, Julia Adler-Milstein

Proceedings of the AMIA 2022, 2022

Gaps in Nephrology Referral Care Utilization in Patients at High-Risk of Progression to Kidney Failure.

Samson Peter, Maggie Wang, Chi D. Chu, Delphine S. Tuot, Arhana Chattopadhyay, Jonathan H. Chen

Proceedings of the AMIA 2022, 2022

Modifiable Inpatient Cost Variability at a Large Academic Medical Center.

Kush Gupta, Jason Hom, Ted Ross, Jonathan Masterson, Alexander Chin, Arnold Milstein, Jonathan H. Chen

Proceedings of the AMIA 2022, 2022

How to Avoid Incorrect Clinical Machine Learning Model Performance Estimates When Class Labels Are Only Partially Observed.

Conor K. Corbin, Michael Baiocchi, Jonathan H. Chen

Proceedings of the AMIA 2022, 2022

2021

stratamatch: Prognostic Score Stratification Using a Pilot Design.

Rachael C. Aikens, Joseph Rigdon, Justin Lee, Michael T. M. Baiocchi, Andrew B. Goldstone, Peter Chiu, Y. Joseph Woo, Jonathan H. Chen

R J., 2021

Machine learning for initial insulin estimation in hospitalized patients.

Minh Nguyen, Ivana Jankovic, Laurynas Kalesinskas, Michael T. M. Baiocchi, Jonathan H. Chen

J. Am. Medical Informatics Assoc., 2021

Developing machine learning models to personalize care levels among emergency room patients for hospital admission.

Minh Nguyen, Conor K. Corbin, Tiffany Eulalio, Nicolai P. Ostberg, Gautam Machiraju, Ben J. Marafino, Michael Baiocchi, Christian Rose, Jonathan H. Chen

J. Am. Medical Informatics Assoc., 2021

Engaging Housestaff as Informatics Collaborators: Educational and Operational Opportunities.

Jared A. Shenson, Ivana Jankovic, Hyo Jung Hong, Benjamin Weia, Lee White, Jonathan H. Chen, Matthew Eisenberg

Appl. Clin. Inform., 2021

Computational Challenges and Artificial Intelligence in Precision Medicine.

Olga Afanasiev, Joanne Berghout, Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jonathan H. Chen, Roxana Daneshjou, Lukasz Kidzinski

Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

Signal from the Noise: Quantitative Measures of Conformity and Variability From Process Mining Maps.

Christian Rose, Morteza Noshad, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Predicting Level of Care for Emergency Hospital Admissions to Optimize Triage.

Minh Nguyen, Nicolai P. Ostberg, Conor K. Corbin, Tiffany Eulalio, Gautam Machiraju, Ben J. Marafino, Michael Baiocchi, Christian Rose, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Randomized user testing of recommender system clinical decision support.

Andre Kumar, Rachael C. Aikens, Jason Horn, Lisa Shieh, Mark A. Musen, Michael Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Machine Learning Predictability of Clinical Next Generation Sequencing for Hematologic Malignancies to Guide High-Value Precision Medicine.

Grace Y. E. Kim, Morteza Noshad, Henning Stehr, Rebecca Rojansky, Dita Gratzinger, Jean Oak, Rondeep Brar, David Iberri, Christina Kong, James L. Zehnder, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

A Data-Driven Algorithm to Recommend Initial Clinical Workup for Outpatient Specialty Referral.

Wui Ip, Priya Prahalad, Jonathan Palma, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

A Retrospective Analysis of Machine Learning Driven Antibiotic Selection in the Emergency Department.

Conor K. Corbin, Arhana Chattopadhyah, Lillian Sung, Amy Chang, Stan Deresinski, Jonathan H. Chen

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Deep learning interpretation of echocardiograms.

Amirata Ghorbani, David Ouyang, Abubakar Abid, Bryan He, Jonathan H. Chen, Robert A. Harrington, David H. Liang, Euan A. Ashley, James Y. Zou

npj Digit. Medicine, 2020

Explainable artificial intelligence models using real-world electronic health record data: a systematic scoping review.

Seyedeh Neelufar Payrovnaziri, Zhaoyi Chen, Pablo Rengifo-Moreno, Tim Miller, Jiang Bian, Jonathan H. Chen, Xiuwen Liu, Zhe He

J. Am. Medical Informatics Assoc., 2020

OrderRex clinical user testing: a randomized trial of recommender system decision support on simulated cases.

Andre Kumar, Rachael C. Aikens, Jason Hom, Lisa Shieh, Jonathan Chiang, David Morales, Divya Saini, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen

J. Am. Medical Informatics Assoc., 2020

Clinical Recommender System: Predicting Medical Specialty Diagnostic Choices with Neural Network Ensembles.

Morteza Noshad, Ivana Jankovic, Jonathan H. Chen

CoRR, 2020

Session Introduction.

Roxana Daneshjou, Lukasz Kidzinski, Olga Afanasiev, Jonathan H. Chen

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Data-Driven Clinical Decision Support for Computerized Physician Order Entry: Development, Evaluation, and Implementation.

Yiye Zhang, Jonathan H. Chen, Adam Wright, Jessica S. Ancker, Marc Tobias

Proceedings of the AMIA 2020, 2020

Context is Key: Using the Audit Log to Capture Contextual Factors Affecting Stroke Care Processes.

Morteza Noshad, Christian Rose, Robert Thombley, Jonathan Chiang, Conor K. Corbin, Minh Nguyen, Vincent X. Liu, Julia Adler-Milstein, Jonathan H. Chen

Proceedings of the AMIA 2020, 2020

It's not just a last mile problem: Partnering with process improvement and human factors to integrate machine learning into healthcare delivery.

Ron C. Li, Naveen Muthu, Margaret Smith, Swaminathan Kandaswamy, Jonathan H. Chen

Proceedings of the AMIA 2020, 2020

2019

Assessing clinical heterogeneity in sepsis through treatment patterns and machine learning.

Alison E. Fohner, John D. Greene, Brian L. Lawson, Jonathan H. Chen, Patricia Kipnis, Gabriel J. Escobar, Vincent X. Liu

J. Am. Medical Informatics Assoc., 2019

Prevalence and Predictability of Low Yield Inpatient Laboratory Diagnostic Tests.

Song Xu, Jason Horn, Santhosh Balasubramanian, Lee F. Schroeder, Nader Najafi, Shivaal Roy, Jonathan H. Chen

Proceedings of the AMIA 2019, 2019

Detecting unanticipated actions downstream from clinical decision support: a data mining approach.

Ron C. Li, Imon Banerjee, Daniel L. Rubin, Jonathan H. Chen

Proceedings of the AMIA 2019, 2019

2018

An evaluation of clinical order patterns machine-learned from clinician cohorts stratified by patient mortality outcomes.

Jason K. Wang, Jason Hom, Santhosh Balasubramanian, Alejandro Schuler, Nigam H. Shah, Mary K. Goldstein, Michael T. M. Baiocchi, Jonathan H. Chen

J. Biomed. Informatics, 2018

Impact of problem-based charting on the utilization and accuracy of the electronic problem list.

Ron C. Li, Trit Garg, Tony Cun, Lisa Shieh, Gomathi Krishnan, Daniel Z. Fang, Jonathan H. Chen

J. Am. Medical Informatics Assoc., 2018

A "bottom up" data driven approach to curating electronic order sets.

Ron C. Li, Jason K. Wang, Christopher D. Sharp, Jonathan H. Chen

Proceedings of the AMIA 2018, 2018

Machine Learning Predictable Inpatient Lab Results for High-Value Care.

Santhosh Balasubramanian, Jason Hom, Shivaal Roy, Jonathan H. Chen

Proceedings of the AMIA 2018, 2018

2017

Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets.

Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Lester W. Mackey, Russ B. Altman

J. Am. Medical Informatics Assoc., 2017

Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets.

Jonathan H. Chen, Muthuraman Alagappan, Mary K. Goldstein, Steven M. Asch, Russ B. Altman

Int. J. Medical Informatics, 2017

The Training of Next Generation Data Scientists in Biomedicine.

Lana X. Garmire, Stephen V. Gliske, Quynh C. Nguyen, Jonathan H. Chen, Shamim Nemati, John D. Van Horn, Jason H. Moore, Carol Shreffler, Michelle Dunn

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

The New HIT: Human Health Information Technology.

Tiffany I. Leung, Mary K. Goldstein, Mark A. Musen, Ruth Cronkite, Jonathan H. Chen, Assaf Gottlieb, Eran Leitersdorf

Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Problem based charting: a method for improving problem list utilization and completeness.

Ron C. Li, Lisa Shieh, Gomathi Krishnan, Daniel Z. Fang, Jonathan H. Chen

Proceedings of the Summit on Clinical Research Informatics, 2017

Decaying Relevance of Clinical Data when Predicting Future Decisions.

Muthuraman Alagappan, Mary K. Goldstein, Steven M. Asch, Russ B. Altman, Jonathan H. Chen

Proceedings of the Summit on Clinical Research Informatics, 2017

Impact of Clinician Experience on Machine Learned Clinical Order Patterns.

Jason K. Wang, Alejandro Schuler, Nigam Shah, Jonathan H. Chen

Proceedings of the AMIA 2017, 2017

2016

OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records.

Jonathan H. Chen, Tanya Podchiyska, Russ B. Altman

J. Am. Medical Informatics Assoc., 2016

Dynamically Evolving Clinical Practices and Implications for Predicting Medical Decisions.

Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Automated Organization of Electronic Health Record Data by Probabilistic Topic Modeling to Inform Clinical Decision Making.

Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Lester W. Mackey, Russ B. Altman

Proceedings of the Summit on Clinical Research Informatics, 2016

Usability of an Automated Recommender System for Clinical Order Entry.

Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman

Proceedings of the AMIA 2016, 2016

2014

"Doctors who ordered this also ordered..." Automated physician order recommendations and outcome predictions by data-mining electronic medical records.

Jonathan H. Chen, Russ B. Altman

Proceedings of the AMIA 2014, 2014

2011

Learning to Predict Chemical Reactions.

Matthew A. Kayala, Chloé-Agathe Azencott, Jonathan H. Chen, Pierre Baldi

J. Chem. Inf. Model., 2011

2009

No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms.

Jonathan H. Chen, Pierre Baldi

J. Chem. Inf. Model., 2009

2007

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.

Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi

J. Chem. Inf. Model., 2007

ChemDB update - full-text search and virtual chemical space.

Jonathan H. Chen, Erik Linstead, Sanjay Joshua Swamidass, Dennis Wang, Pierre Baldi

Bioinform., 2007

2006

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.

Samuel A. Danziger, Sanjay Joshua Swamidass, Jue Zeng, Lawrence R. Dearth, Qiang Lu, Jonathan H. Chen, Jianlin Cheng, Vinh P. Hoang, Hiroto Saigo, Ray Luo, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

2005

ChemDB: a public database of small molecules and related chemoinformatics resources.

Jonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi

Bioinform., 2005

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.

Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005