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ORCIDJason Alan Fries
Jason A. Fries
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- affiliation: Stanford University
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2020 – today
- 2024
[j13]Lin Lawrence Guo, Keith E. Morse
, Catherine Aftandilian, Ethan Steinberg, Jason Alan Fries, José D. Posada, Scott Lanyon Fleming, Joshua Lemmon, Karim Jessa, Nigam Shah, Lillian Sung:
Characterizing the limitations of using diagnosis codes in the context of machine learning for healthcare. BMC Medical Informatics Decis. Mak. 24(1): 51 (2024)- [j12]Lin Lawrence Guo, Jason Alan Fries, Ethan Steinberg, Scott Lanyon Fleming, Keith E. Morse, Catherine Aftandilian, José D. Posada, Nigam Shah, Lillian Sung:
A multi-center study on the adaptability of a shared foundation model for electronic health records. npj Digit. Medicine 7(1) (2024) - [j11]Wui Ip, Maria Xenochristou, Elaine Sui, Elyse Ruan, Ryan Ribeira, Debadutta Dash, Malathi Srinivasan, Maja Artandi, Jesutofunmi A. Omiye, Nicholas Scoulios, Hayden L. Hofmann, Ali Mottaghi, Zhenzhen Weng, Abhinav Kumar, Ananya Ganesh, Jason A. Fries, Serena Yeung-Levy, Lawrence V. Hofmann:
Hospitalization prediction from the emergency department using computer vision AI with short patient video clips. npj Digit. Medicine 7(1) (2024) - [c15]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:
MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records. AAAI 2024: 22021-22030 - [c14]Ethan Steinberg, Jason Alan Fries, Yizhe Xu, Nigam Shah:
MOTOR: A Time-to-Event Foundation Model For Structured Medical Records. ICLR 2024 - [i26]Hyewon Jeong, Sarah Jabbour, Yuzhe Yang, Rahul Thapa, Hussein Mozannar, William Jongwon Han, Nikita Mehandru, Michael Wornow, Vladislav Lialin, Xin Liu, Alejandro Lozano, Jiacheng Zhu, Rafal Dariusz Kocielnik, Keith Harrigian, Haoran Zhang, Edward Lee, Milos Vukadinovic, Aparna Balagopalan, Vincent Jeanselme, Katherine Matton, Ilker Demirel, Jason A. Fries, Parisa Rashidi, Brett K. Beaulieu-Jones, Xuhai Orson Xu, Matthew B. A. McDermott, Tristan Naumann, Monica Agrawal, Marinka Zitnik, Berk Ustun, Edward Choi, Kristen Yeom, Gamze Gürsoy, Marzyeh Ghassemi, Emma Pierson, George H. Chen, Sanjat Kanjilal, Michael Oberst, Linying Zhang, Harvineet Singh, Tom Hartvigsen, Helen Zhou, Chinasa T. Okolo:
Recent Advances, Applications, and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2023 Symposium. CoRR abs/2403.01628 (2024) - [i25]Louis Blankemeier, Joseph Paul Cohen, Ashwin Kumar, Dave Van Veen, Syed Jamal Safdar Gardezi, Magdalini Paschali, Zhihong Chen, Jean-Benoit Delbrouck, Eduardo Pontes Reis, Cesar Truyts, Christian Bluethgen, Malte Engmann Kjeldskov Jensen, Sophie Ostmeier, Maya Varma, Jeya Maria Jose Valanarasu, Zhongnan Fang, Zepeng Huo, Zaid Nabulsi, Diego Ardila, Wei-Hung Weng, Edson Amaro Júnior, Neera Ahuja, Jason Alan Fries, Nigam H. Shah, Andrew Johnston, Robert D. Boutin, Andrew Wentland, Curtis P. Langlotz, Jason Hom, Sergios Gatidis, Akshay S. Chaudhari:
Merlin: A Vision Language Foundation Model for 3D Computed Tomography. CoRR abs/2406.06512 (2024) - [i24]Ethan Steinberg, Michael Wornow, Suhana Bedi, Jason Alan Fries, Matthew B. A. McDermott, Nigam H. Shah:
meds_reader: A fast and efficient EHR processing library. CoRR abs/2409.09095 (2024) - [i23]Zepeng Huo, Jason Alan Fries, Alejandro Lozano, Jeya Maria Jose Valanarasu, Ethan Steinberg, Louis Blankemeier, Akshay S. Chaudhari, Curtis P. Langlotz, Nigam H. Shah:
Time-to-Event Pretraining for 3D Medical Imaging. CoRR abs/2411.09361 (2024) - [i22]Monica Munnangi, Akshay Swaminathan, Jason Alan Fries, Jenelle A. Jindal, Sanjana Narayanan, Iván López, Lucia Tu, Philip Chung, Jesutofunmi A. Omiye, Mehr Kashyap, Nigam Shah:
Assessing the Limitations of Large Language Models in Clinical Fact Decomposition. CoRR abs/2412.12422 (2024) - [i21]Michael Wornow, Suhana Bedi, Miguel Angel Fuentes Hernandez, Ethan Steinberg, Jason Alan Fries, Christopher Ré, Sanmi Koyejo, Nigam H. Shah:
Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHRs. CoRR abs/2412.16178 (2024) - 2023
- [j10]Joshua Lemmon, Lin Lawrence Guo, Ethan Steinberg, Keith E. Morse, Scott Lanyon Fleming, Catherine Aftandilian, Stephen R. Pfohl, José D. Posada, Nigam Shah, Jason Alan Fries, Lillian Sung:
Self-supervised machine learning using adult inpatient data produces effective models for pediatric clinical prediction tasks. J. Am. Medical Informatics Assoc. 30(12): 2004-2011 (2023) - [j9]Michael Wornow, Yizhe Xu, Rahul Thapa, Birju S. Patel, Ethan Steinberg, Scott L. Fleming, Michael A. Pfeffer, Jason Alan Fries, Nigam H. Shah:
The shaky foundations of large language models and foundation models for electronic health records. npj Digit. Medicine 6 (2023) - [c13]Louis Blankemeier, Jason A. Fries, Robert Tinn, Joseph Preston, Nigam Shah, Akshay Chaudhari:
Efficient Diagnosis Assignment Using Unstructured Clinical Notes. ACL (2) 2023: 485-494 - [c12]Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg, Chia-Chun Chiang, Curtis P. Langlotz, Matthew P. Lungren, Serena Yeung, Nigam Shah, Jason Alan Fries:
INSPECT: A Multimodal Dataset for Patient Outcome Prediction of Pulmonary Embolisms. NeurIPS 2023 - [c11]Michael Wornow, Rahul Thapa, Ethan Steinberg, Jason A. Fries, Nigam Shah:
EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models. NeurIPS 2023 - [i20]Ethan Steinberg, Yizhe Xu, Jason A. Fries, Nigam Shah:
Self-Supervised Time-to-Event Modeling with Structured Medical Records. CoRR abs/2301.03150 (2023) - [i19]Michael Wornow, Yizhe Xu, Rahul Thapa, Birju S. Patel, Ethan Steinberg, Scott L. Fleming, Michael A. Pfeffer, Jason A. Fries, Nigam H. Shah:
The Shaky Foundations of Clinical Foundation Models: A Survey of Large Language Models and Foundation Models for EMRs. CoRR abs/2303.12961 (2023) - [i18]Michael Wornow, Rahul Thapa, Ethan Steinberg, Jason A. Fries, Nigam Shah:
EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models. CoRR abs/2307.02028 (2023) - [i17]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:
MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records. CoRR abs/2308.14089 (2023) - [i16]Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg, Chia-Chun Chiang, Matthew P. Lungren, Curtis P. Langlotz, Serena Yeung, Nigam H. Shah, Jason A. Fries:
INSPECT: A Multimodal Dataset for Pulmonary Embolism Diagnosis and Prognosis. CoRR abs/2311.10798 (2023) - [i15]Lin Lawrence Guo, Jason A. Fries, Ethan Steinberg, Scott Lanyon Fleming, Keith E. Morse, Catherine Aftandilian, José D. Posada, Nigam Shah, Lillian Sung:
A Multi-Center Study on the Adaptability of a Shared Foundation Model for Electronic Health Records. CoRR abs/2311.11483 (2023) - 2022
- [c10]Stephen H. Bach, Victor Sanh, Zheng Xin Yong, Albert Webson, Colin Raffel, Nihal V. Nayak, Abheesht Sharma, Taewoon Kim, M. Saiful Bari, Thibault Févry, Zaid Alyafeai, Manan Dey, Andrea Santilli, Zhiqing Sun, Srulik Ben-David, Canwen Xu, Gunjan Chhablani, Han Wang, Jason Alan Fries, Maged Saeed AlShaibani, Shanya Sharma, Urmish Thakker, Khalid Almubarak, Xiangru Tang, Dragomir R. Radev, Mike Tian-Jian Jiang, Alexander M. Rush:
PromptSource: An Integrated Development Environment and Repository for Natural Language Prompts. ACL (demo) 2022: 93-104 - [c9]Victor Sanh, Albert Webson, Colin Raffel, Stephen H. Bach, Lintang Sutawika, Zaid Alyafeai, Antoine Chaffin, Arnaud Stiegler, Arun Raja, Manan Dey, M Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal V. Nayak, Debajyoti Datta, Jonathan Chang, Mike Tian-Jian Jiang, Han Wang, Matteo Manica, Sheng Shen, Zheng Xin Yong, Harshit Pandey, Rachel Bawden, Thomas Wang, Trishala Neeraj, Jos Rozen, Abheesht Sharma, Andrea Santilli, Thibault Févry, Jason Alan Fries, Ryan Teehan, Teven Le Scao, Stella Biderman, Leo Gao, Thomas Wolf, Alexander M. Rush:
Multitask Prompted Training Enables Zero-Shot Task Generalization. ICLR 2022 - [c8]Jason A. Fries, Leon Weber, Natasha Seelam, Gabriel Altay, Debajyoti Datta, Samuele Garda, Sunny Kang, Rosaline Su, Wojciech Kusa, Samuel Cahyawijaya, Fabio Barth, Simon Ott, Matthias Samwald, Stephen H. Bach, Stella Biderman, Mario Sänger, Bo Wang, Alison Callahan, Daniel León Periñán, Théo Gigant, Patrick Haller, Jenny Chim, José D. Posada, John M. Giorgi, Karthik Rangasai Sivaraman, Marc Pàmies, Marianna Nezhurina, Robert Martin, Michael Cullan, Moritz Freidank, Nathan Dahlberg, Shubhanshu Mishra, Shamik Bose, Nicholas Broad, Yanis Labrak, Shlok Deshmukh, Sid Kiblawi, Ayush Singh, Minh Chien Vu, Trishala Neeraj, Jonas Golde, Albert Villanova del Moral, Benjamin Beilharz:
BigBio: A Framework for Data-Centric Biomedical Natural Language Processing. NeurIPS 2022 - [i14]Stephen H. Bach, Victor Sanh, Zheng Xin Yong, Albert Webson, Colin Raffel, Nihal V. Nayak, Abheesht Sharma, Taewoon Kim, M. Saiful Bari, Thibault Févry, Zaid Alyafeai, Manan Dey, Andrea Santilli, Zhiqing Sun, Srulik Ben-David, Canwen Xu, Gunjan Chhablani, Han Wang, Jason Alan Fries, Maged Saeed AlShaibani, Shanya Sharma, Urmish Thakker, Khalid Almubarak, Xiangru Tang, Mike Tian-Jian Jiang, Alexander M. Rush:
PromptSource: An Integrated Development Environment and Repository for Natural Language Prompts. CoRR abs/2202.01279 (2022) - [i13]Ryan Smith, Jason A. Fries, Braden Hancock, Stephen H. Bach:
Language Models in the Loop: Incorporating Prompting into Weak Supervision. CoRR abs/2205.02318 (2022) - [i12]Jason Alan Fries, Leon Weber, Natasha Seelam, Gabriel Altay, Debajyoti Datta, Samuele Garda, Myungsun Kang, Ruisi Su, Wojciech Kusa, Samuel Cahyawijaya, Fabio Barth, Simon Ott, Matthias Samwald, Stephen H. Bach, Stella Biderman, Mario Sänger, Bo Wang, Alison Callahan, Daniel León Periñán, Théo Gigant, Patrick Haller, Jenny Chim, José David Posada, John Michael Giorgi, Karthik Rangasai Sivaraman, Marc Pàmies, Marianna Nezhurina, Robert Martin, Michael Cullan, Moritz Freidank, Nathan Dahlberg, Shubhanshu Mishra, Shamik Bose, Nicholas Michio Broad, Yanis Labrak, Shlok S. Deshmukh, Sid Kiblawi, Ayush Singh, Minh Chien Vu, Trishala Neeraj, Jonas Golde, Albert Villanova del Moral, Benjamin Beilharz:
BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing. CoRR abs/2206.15076 (2022) - 2021
- [j8]Lin Lawrence Guo, Stephen R. Pfohl, Jason Alan Fries, José D. Posada, Scott L. Fleming, Catherine Aftandilian, Nigam Shah, Lillian Sung:
Systematic Review of Approaches to Preserve Machine Learning Performance in the Presence of Temporal Dataset Shift in Clinical Medicine. Appl. Clin. Inform. 12(4): 808-815 (2021) - [j7]Ethan Steinberg, Kenneth Jung, Jason A. Fries, Conor K. Corbin, Stephen R. Pfohl, Nigam H. Shah:
Language models are an effective representation learning technique for electronic health record data. J. Biomed. Informatics 113: 103637 (2021) - [i11]Victor Sanh, Albert Webson, Colin Raffel, Stephen H. Bach, Lintang Sutawika, Zaid Alyafeai, Antoine Chaffin, Arnaud Stiegler, Teven Le Scao, Arun Raja, Manan Dey, M. Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal V. Nayak, Debajyoti Datta, Jonathan Chang, Mike Tian-Jian Jiang, Han Wang, Matteo Manica, Sheng Shen, Zheng Xin Yong, Harshit Pandey, Rachel Bawden, Thomas Wang, Trishala Neeraj, Jos Rozen, Abheesht Sharma, Andrea Santilli, Thibault Févry, Jason Alan Fries, Ryan Teehan, Stella Biderman, Leo Gao, Tali Bers, Thomas Wolf, Alexander M. Rush:
Multitask Prompted Training Enables Zero-Shot Task Generalization. CoRR abs/2110.08207 (2021) - [i10]Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries, Alaa Youssef, Timothy J. Amrhein, Marcello Chang, Imon Banerjee, Daniel L. Rubin, Lei Xing, Nigam Shah, Matthew P. Lungren:
RadFusion: Benchmarking Performance and Fairness for Multimodal Pulmonary Embolism Detection from CT and EHR. CoRR abs/2111.11665 (2021) - 2020
- [j6]Sehj Kashyap, Saurabh Gombar, Steve Yadlowsky, Alison Callahan, Jason A. Fries, Benjamin A. Pinsky, Nigam H. Shah:
Measure what matters: Counts of hospitalized patients are a better metric for health system capacity planning for a reopening. J. Am. Medical Informatics Assoc. 27(7): 1026-1131 (2020) - [j5]Alison Callahan, Ethan Steinberg, Jason A. Fries, Saurabh Gombar, Birju S. Patel, Conor K. Corbin, Nigam H. Shah:
Estimating the efficacy of symptom-based screening for COVID-19. npj Digit. Medicine 3 (2020) - [j4]Adam S. Miner, Albert Haque, Jason A. Fries, Scott L. Fleming, Denise E. Wilfley, G. Terence Wilson, Arnold Milstein, Dan Jurafsky, Bruce A. Arnow, W. Stewart Agras, Li Fei-Fei, Nigam H. Shah:
Assessing the accuracy of automatic speech recognition for psychotherapy. npj Digit. Medicine 3 (2020) - [j3]Alexander Ratner, Stephen H. Bach, Henry R. Ehrenberg, Jason A. Fries, Sen Wu, Christopher Ré:
Snorkel: rapid training data creation with weak supervision. VLDB J. 29(2-3): 709-730 (2020) - [i9]Ethan Steinberg, Kenneth Jung, Jason A. Fries, Conor K. Corbin, Stephen R. Pfohl, Nigam H. Shah:
Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data. CoRR abs/2001.05295 (2020) - [i8]Jason A. Fries, Ethan Steinberg, Saelig Khattar, Scott L. Fleming, José D. Posada, Alison Callahan, Nigam H. Shah:
Trove: Ontology-driven weak supervision for medical entity classification. CoRR abs/2008.01972 (2020)
2010 – 2019
- 2019
- [j2]Alison Callahan, Jason A. Fries, Christopher Ré, James I Huddleston III, Nicholas J. Giori, Scott L. Delp, Nigam H. Shah:
Medical device surveillance with electronic health records. npj Digit. Medicine 2 (2019) - [c7]Paroma Varma, Frederic Sala, Shiori Sagawa, Jason Alan Fries, Daniel Y. Fu, Saelig Khattar, Ashwini Ramamoorthy, Ke Xiao, Kayvon Fatahalian, James Priest, Christopher Ré:
Multi-Resolution Weak Supervision for Sequential Data. NeurIPS 2019: 192-203 - [i7]Alison Callahan, Jason A. Fries, Christopher Ré, James I Huddleston III, Nicholas J. Giori, Scott L. Delp, Nigam H. Shah:
Medical device surveillance with electronic health records. CoRR abs/1904.07640 (2019) - [i6]Frederic Sala, Paroma Varma, Jason A. Fries, Daniel Y. Fu, Shiori Sagawa, Saelig Khattar, Ashwini Ramamoorthy, Ke Xiao, Kayvon Fatahalian, James Priest, Christopher Ré:
Multi-Resolution Weak Supervision for Sequential Data. CoRR abs/1910.09505 (2019) - [i5]Anitha Kannan, Jason Alan Fries, Eric Kramer, Jen Jen Chen, Nigam Shah, Xavier Amatriain:
The accuracy vs. coverage trade-off in patient-facing diagnosis models. CoRR abs/1912.08041 (2019) - 2018
- [i4]Natalia Antropova, Andrew L. Beam, Brett K. Beaulieu-Jones, Irene Chen, Corey Chivers, Adrian V. Dalca, Samuel G. Finlayson, Madalina Fiterau, Jason Alan Fries, Marzyeh Ghassemi, Mike Hughes, Bruno Jedynak, Jasvinder S. Kandola, Matthew B. A. McDermott, Tristan Naumann, Peter Schulam, Farah Shamout, Alexandre Yahi:
Machine Learning for Health (ML4H) Workshop at NeurIPS 2018. CoRR abs/1811.07216 (2018) - 2017
- [j1]Alexander Ratner, Stephen H. Bach, Henry R. Ehrenberg, Jason Alan Fries, Sen Wu, Christopher Ré:
Snorkel: Rapid Training Data Creation with Weak Supervision. Proc. VLDB Endow. 11(3): 269-282 (2017) - [c6]Alexander Ratner, Stephen H. Bach, Henry R. Ehrenberg, Jason Alan Fries, Sen Wu, Christopher Ré:
Snorkel: A System for Lightweight Extraction. CIDR 2017 - [c5]Madalina Fiterau, Suvrat Bhooshan, Jason A. Fries, Charles Bournhonesque, Jennifer L. Hicks, Eni Halilaj, Christopher Ré, Scott L. Delp:
ShortFuse: Biomedical Time Series Representations in the Presence of Structured Information. MLHC 2017: 59-74 - [i3]Jason A. Fries, Sen Wu, Alexander Ratner, Christopher Ré:
SwellShark: A Generative Model for Biomedical Named Entity Recognition without Labeled Data. CoRR abs/1704.06360 (2017) - [i2]Alexander Ratner, Stephen H. Bach, Henry R. Ehrenberg, Jason Alan Fries, Sen Wu, Christopher Ré:
Snorkel: Rapid Training Data Creation with Weak Supervision. CoRR abs/1711.10160 (2017) - 2016
- [c4]Jason Alan Fries:
Brundlefly at SemEval-2016 Task 12: Recurrent Neural Networks vs. Joint Inference for Clinical Temporal Information Extraction. SemEval@NAACL-HLT 2016: 1274-1279 - [c3]Henry R. Ehrenberg, Jaeho Shin, Alexander J. Ratner, Jason A. Fries, Christopher Ré:
Data programming with DDLite: putting humans in a different part of the loop. HILDA@SIGMOD 2016: 13 - [i1]Jason Alan Fries:
Brundlefly at SemEval-2016 Task 12: Recurrent Neural Networks vs. Joint Inference for Clinical Temporal Information Extraction. CoRR abs/1606.01433 (2016) - 2014
- [c2]Jason A. Fries, Philip M. Polgreen, Alberto M. Segre:
Mining the Demographics of Craigslist Casual Sex Ads to Inform Public Health Policy. ICHI 2014: 61-70 - 2012
- [c1]Jason A. Fries, Alberto M. Segre, Philip Polgreen:
Using Online Classified Ads to Identify the Geographic Footprints of Anonymous, Casual Sex-Seeking Individuals. SocialCom/PASSAT 2012: 402-410
Coauthor Index
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