Nigam Shah

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 52

Top Topics

Pulmonary Embolism

Machine Learning

Top Venues

J. Am. Medical Informatics Assoc.

Publications

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) (2024)
Ting Fang Tan, Kabilan Elangovan, Jasmine Chiat Ling Ong, Nigam Shah, Joseph Jao-Yiu Sung, Tien Yin Wong, Lan Xue, Nan Liu, Haibo Wang, Chang Fu Kuo, Simon Chesterman, Zee Kin Yeong, Daniel S. W. Ting
A Proposed S.C.O.R.E. Evaluation Framework for Large Language Models : Safety, Consensus, Objectivity, Reproducibility and Explainability. CoRR (2024)
Ethan Steinberg, Jason Alan Fries, Yizhe Xu, Nigam Shah
MOTOR: A Time-to-Event Foundation Model For Structured Medical Records. ICLR (2024)
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)
Alejandro Lozano, Scott L. Fleming, Chia-Chun Chiang, Nigam Shah
Clinfo.ai: An Open-Source Retrieval-Augmented Large Language Model System for Answering Medical Questions using Scientific Literature. CoRR (2023)
Michael Wornow, Rahul Thapa, Ethan Steinberg, Jason A. Fries, Nigam Shah
EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models. NeurIPS (2023)
Louis Blankemeier, Jason A. Fries, Robert Tinn, Joseph Preston, Nigam Shah, Akshay Chaudhari
Efficient Diagnosis Assignment Using Unstructured Clinical Notes. ACL (2) (2023)
Yizhe Xu, Katelyn K. Bechler, Alison Callahan, Nigam Shah
Principled estimation and evaluation of treatment effect heterogeneity: A case study application to dabigatran for patients with atrial fibrillation. J. Biomed. Informatics 143 (2023)
Joshua Lemmon, Lin Lawrence Guo, Ethan Steinberg, Keith E. Morse, Scott Lanyon Fleming, Catherine Aftandilian, Stephen R. Pfohl, Jose 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) (2023)
Diana Cagliero, Natalie Deuitch, Nigam Shah, Chris Feudtner, Danton Char
A framework to identify ethical concerns with ML-guided care workflows: a case study of mortality prediction to guide advance care planning. J. Am. Medical Informatics Assoc. 30 (5) (2023)
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 (2023)
Ethan Steinberg, Yizhe Xu, Jason A. Fries, Nigam Shah
Self-Supervised Time-to-Event Modeling with Structured Medical Records. CoRR (2023)
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)
Michael Wornow, Rahul Thapa, Ethan Steinberg, Jason A. Fries, Nigam Shah
EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models. CoRR (2023)
Katelyn K. Bechler, Nigam Shah
Predicting patients who are likely to develop Lupus Nephritis of those newly diagnosed with Systemic Lupus Erythematosus. AMIA (2022)
Stephen Pfohl, Yizhe Xu, Agata Foryciarz, Nikolaos Ignatiadis, Julian Genkins, Nigam Shah
Net benefit, calibration, threshold selection, and training objectives for algorithmic fairness in healthcare. FAccT (2022)
Tina Hernandez-Boussard, Matthew P. Lungren, Nigam Shah
Corrigendum: Conflicting information from the Food and Drug Administration: Missed opportunity to lead standards for safe and effective medical artificial intelligence solutions. J. Am. Medical Informatics Assoc. 28 (7) (2021)
Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries, Alaa Youssef, Timothy J. Amrhein, Marcello Chang, Imon Banerjee, Daniel Rubin, Lei Xing, Nigam Shah, Matthew P. Lungren
RadFusion: Benchmarking Performance and Fairness for Multimodal Pulmonary Embolism Detection from CT and EHR. CoRR (2021)
Nigam Shah
Summarizing Patients Like Mine via an On-demand Consultation Service. Proc. VLDB Endow. 14 (13) (2021)
Tina Hernandez-Boussard, Matthew P. Lundgren, Nigam Shah
Conflicting information from the Food and Drug Administration: Missed opportunity to lead standards for safe and effective medical artificial intelligence solutions. J. Am. Medical Informatics Assoc. 28 (6) (2021)
Yuan Luo, Fei Wang, Benjamin S. Glicksberg, Jessilyn Dunn, Nigam Shah
Multi-Modal Data Science for Healthcare: State of the Art, Challenges, and Opportunities. AMIA (2021)
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) (2021)
Xu Zuo, Jianfu Li, Bo Zhao, Yujia Zhou, Xiao Dong, Jon D. Duke, Karthik Natarajan, George Hripcsak, Nigam Shah, Juan M. Banda, Ruth M. Reeves, Hua Xu
Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study. AMIA (2020)
Vojtech Huser, Clair Blacketer, Karthik Natarajan, Robert T. Miller, Andrew Williams, Selva Muthu Kumaran Sathappan, José D. Posada, Nigam Shah
Data Quality Assessment of Laboratory Data. AMIA (2020)
Somalee Datta, José D. Posada, Garrick Olson, Wencheng Li, Ciaran O'Reilly, Deepa Balraj, Joseph Mesterhazy, Joseph Pallas, Priyamvada Desai, Nigam Shah
A new paradigm for accelerating clinical data science at Stanford Medicine. CoRR (2020)
Scott L. Fleming, Kuhan Jeyapragasan, Tony Duan, Daisy Yi Ding, Saurabh Gombar, Nigam Shah, Emma Brunskill
Missingness as Stability: Understanding the Structure of Missingness in Longitudinal EHR data and its Impact on Reinforcement Learning in Healthcare. CoRR (2019)
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 (2019)
Martin G. Seneviratne, Juan M. Banda, James D. Brooks, Nigam Shah, Tina Hernandez-Boussard
Identifying cases of metastatic prostate cancer using machine learning on electronic health records. AMIA (2018)
Alejandro Schuler, Nigam Shah
General-purpose validation and model selection when estimating individual treatment effects. CoRR (2018)
Chunhua Weng, Nigam Shah, George Hripcsak
Call for papers: Deep phenotyping for Precision Medicine. J. Biomed. Informatics 87 (2018)
Sarah Poole, Nigam Shah
Addressing vital sign alarm fatigue using personalized alarm thresholds. PSB (2018)
Ruijun Chen, Patrick B. Ryan, Karthik Natarajan, Thomas Falconer, Christian G. Reich, Rohit Vashisht, Nigam Shah, George Hripcsak
Treatment Pathways in Patients with Cancer Using a Large-scale Observational Data Network. AMIA (2018)
Stephen R. Pfohl, Nigam Shah
Transfer learning to adapt predictive models for pediatric patients in the EHR. AMIA (2018)
Juan M. Banda, Yoni Halpern, David A. Sontag, Nigam Shah
Electronic phenotyping with APHRODITE and the Observational Health Sciences and Informatics (OHDSI) data network. CRI (2017)
Jason K. Wang, Alejandro Schuler, Nigam Shah, Jonathan H. Chen
Impact of Clinician Experience on Machine Learned Clinical Order Patterns. AMIA (2017)
Alejandro Schuler, David A. Wulf, Yun Lu, Jennifer M. Baker, Gabriel J. Escobar, Nigam Shah, Vincent X. Liu
A novel propensity modeling approach to estimate the causal impact of acute organ dysfunction on long-term survival in sepsis. CRI (2017)
Vibhu Agarwal, Mathew Smuck, Nigam Shah
Quantifying the relative change in physical activity after Total Knee Arthroplasty using accelerometer based measurements. CRI (2017)
Jon D. Duke, George Hripcsak, Patrick B. Ryan, Nigam Shah
From Large-Scale Network Analytics to Clinical Solutions in OHDSI. AMIA (2017)
Sébastien Dubois, Nathanael Romano, Nigam Shah, Kenneth Jung
Learning Effective Representations from Clinical Notes. CoRR (2017)
Sébastien Dubois, Nathanael Romano, Kenneth Jung, Nigam Shah, David C. Kale
The Effectiveness of Transfer Learning in Electronic Health Records Data. ICLR (Workshop) (2017)
Laura K. Wiley, Peter Tarczy-Hornoch, Joshua C. Denny, Robert R. Freimuth, Casey L. Overby, Nigam Shah, Ross D. Martin, Indra Neil Sarkar
Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J. Am. Medical Informatics Assoc. 23 (2) (2016)
Sarah F. Poole, Shaun J. Grannis, Nigam Shah
Predicting Emergency Department Visits. CRI (2016)
Rohit Vashisht, Kenneth Jung, Nigam Shah
Learning Effective Treatment Pathways for Type-2 Diabetes from a clinical data warehouse. AMIA (2016)
Jon D. Duke, George Hripcsak, Nigam Shah, Patrick B. Ryan, Vojtech Huser
Observational Health Data Sciences and Informatics (OHDSI): A Rapidly Growing International Network for Open Science and Data Analytics in Healthcare. CRI (2016)
Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier
The digital revolution in phenotyping. Briefings Bioinform. 17 (5) (2016)
Vibhu Agarwal, Lichy Han, Isaac Madan, Shaurya Saluja, Aaditya Shidham, Nigam Shah
Predicting hospital visits from geo-tagged Internet search logs. CRI (2016)
Sarah Poole, Lee Frederick Schroeder, Nigam Shah
An unsupervised learning method to identify reference intervals from a clinical database. J. Biomed. Informatics 59 (2016)
Justin Norden, Timothy E. Sweeney, Aleksandra Pavlovic, Euan A. Ashley, Nigam Shah, Cindy Kin, Alexander Morgan
A Pilot Study of the Integration of a Quantified-self Wearable Device with EMR data in the Acute Postoperative Setting. CRI (2016)
Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa N. Soldatova, Michel Dumontier, Nigam Shah
Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. J. Biomed. Semant. 7 (2016)
Kelly Regan, Zachary B. Abrams, Michael Sharpnack, Arunima Srivastava, Kun Huang, Nigam Shah, Philip R. O. Payne
Session Introduction. PSB (2016)
Jon D. Duke, George Hripcsak, Nigam Shah, Patrick B. Ryan
The Value of an Open-Source Observational Research Collaboratory: Results from the OHDSI Initiative. AMIA (2015)
Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang
Recent Advances in Computational Drug Repositioning. AMIA (2015)
Graciela Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey S. Greene, Nigam Shah, Maricel G. Kann, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2014)
Nigam Shah
Medicine in the age of electronic health records. KDD (2014)
Jaewon Yang, Julian J. McAuley, Jure Leskovec, Paea LePendu, Nigam Shah
Finding progression stages in time-evolving event sequences. WWW (2014)
Sandy Huang, Paea LePendu, Srinivasan Iyer, Ming Tai-Seale, David Carrell, Nigam Shah
Predictive Models in Mental Health: From Diagnosis to Treatment. AMIA (2013)
Olivier Curé, Henri Maurer, Nigam Shah, Paea LePendu
Refining Health Outcomes of Interest using Formal Concept Analysis and Semantic Query Expansion. SWAT4LS (2013)
Olivier Curé, Henri Maurer, Nigam Shah, Paea LePendu
Refining health outcomes of interest using formal concept analysis and semantic query expansion. DTMBIO (2013)
Nigam Shah, Paea LePendu, Anna Bauer-Mehren, Srinivasan Iyer, Kenneth Jung, Tyler Cole, Rave Harpaz
Learning Practice-based Evidence from Unstructured Clinical Notes. AMIA (2013)
Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye
Session introduction. Pacific Symposium on Biocomputing (2013)
Haishan Liu, Dejing Dou, Ruoming Jin, Paea LePendu, Nigam Shah
Mining Biomedical Ontologies and Data Using RDF Hypergraphs. ICMLA (1) (2013)
Cameron Neylon, Jan Aerts, C. Titus Brown, Simon J. Coles, Les Hatton, Daniel Lemire, K. Jarrod Millman, Peter Murray-Rust, Fernando Pérez, Neil F. W. Saunders, Nigam Shah, Arfon M. Smith, Gaël Varoquaux, Egon L. Willighagen
Changing computational research. The challenges ahead. Source Code Biol. Medicine 7 (2012)
Byambajargal Byambajav, Tomasz Wiktor Wlodarczyk, Chunming Rong, Paea LePendu, Nigam Shah
Performance of Left Outer Join on Hadoop with Right Side within Single Node Memory Size. AINA Workshops (2012)
Kevin Bretonnel Cohen, Yael Garten, Nigam Shah, Udo Hahn
Session introduction. Pacific Symposium on Biocomputing (2012)
Patricia L. Whetzel, Natasha F. Noy, Nigam Shah, Paul R. Alexander, Michael Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen
Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse. ICBO (2011)
Patricia L. Whetzel, Clément Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah
The NCBO Annotator: Ontology-Based Annotation as a Web Service. ICBO (2011)
Natalya Fridman Noy, Nigam Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen
BioPortal: A Web Repository for Biomedical Ontologies and Data Resources. ISWC (Posters & Demos) (2008)
Nikesh Kotecha, Kyle Bruck, William Lu, Nigam Shah
Pathway knowledge base: An integrated pathway resource using BioPAX. Appl. Ontology 3 (4) (2008)
Clément Jonquet, Mark A. Musen, Nigam Shah
A System for Ontology-Based Annotation of Biomedical Data. DILS (2008)
Wei-Nchih Lee, Nigam Shah, Karanjot Sundlass, Mark A. Musen
Comparison of Ontology-based Semantic-Similarity Measures. AMIA (2008)
Daniel L. Rubin, Nigam Shah, Natalya Fridman Noy
Biomedical ontologies: a functional perspective. Briefings Bioinform. 9 (1) (2008)
Woei-Jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel L. Rubin, Natasha Fridman Noy
Using Annotations from Controlled Vocabularies to Find Meaningful Associations. DILS (2007)
Harith Alani, Natasha Fridman Noy, Nigam Shah, Nigel Shadbolt, Mark A. Musen
Searching ontologies based on content: experiments in the biomedical domain. K-CAP (2007)
Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff
A case study in pathway knowledgebase verification. BMC Bioinform. 7 (2006)
Stephen A. Racunas, Christopher Griffin, Nigam Shah
A Finite Model Theory for Biological Hypotheses. CSB (2004)
Nigam Shah, Jorge Lepre, Yuhai Tu, Gustavo Stolovitzky
Can We Identify Cellular Pathways Implicated in Cancer Using Gene Expression Data? CSB (2003)
Steve Racunas, Nigam Shah, Nina V. Fedoroff
A Contradiction-Based Framework for Testing Gene Regulation Hypotheses. CSB (2003)
Wen-Ben Jone, Nigam Shah, Anita Gleason, Sunil R. Das
PGEN: A Novel Approach to Sequential Circuit Test Generation. VLSI Design 4 (3) (1996)