Question Answering Experiments and Resources. - Boris Katz; Gregory Marton; Sue Felshin; Daniel Loreto; Ben Lu; Federico Mora 001; Özlem Uzuner; Michael McGraw-Herdeg; Natalie Cheung; Alexey Radul; Yuan Kui Shen; Yuan Luo 001; et al. (TREC, 2006)

Viewpoint Paper: Evaluating the State-of-the-Art in Automatic De-identification. - Özlem Uzuner; Yuan Luo 001; Peter Szolovits (J. Am. Medical Informatics Assoc., 2007)

A de-identifier for medical discharge summaries. - Özlem Uzuner; Tawanda C. Sibanda; Yuan Luo 001; Peter Szolovits (Artif. Intell. Medicine, 2008)

Viewpoint Paper: Identifying Patient Smoking Status from Medical Discharge Records. - Özlem Uzuner; Ira Goldstein; Yuan Luo 001; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2008)

Quantifying Information Redundancy in Common Laboratory Tests. - Yuan Luo 001; Jason Baron; Peter Szolovits; Anand Dighe (AMIA, 2014)

Research and applications: Automatic lymphoma classification with sentence subgraph mining from pathology reports. - Yuan Luo 001; Aliyah R. Sohani; Ephraim P. Hochberg; Peter Szolovits (J. Am. Medical Informatics Assoc., 2014)

Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text. - Yuan Luo 001; Yu Xin; Ephraim P. Hochberg; Rohit Joshi; Özlem Uzuner; Peter Szolovits (J. Am. Medical Informatics Assoc., 2015)

Towards unified biomedical modeling with subgraph mining and factorization algorithms. - Yuan Luo 001 (2015)

Predicting ICU Mortality Risk by Grouping Temporal Trends from a Multivariate Panel of Physiologic Measurements. - Yuan Luo 001; Yu Xin; Rohit Joshi; Leo A. Celi; Peter Szolovits (AAAI, 2016)

Computational Phenotyping Methods. - Yuan Luo 001; Jimeng Sun 001; Xiaoqian Jiang; Fei Wang 001 (AMIA, 2016)

Automatic identification and extraction of design patterns of EHR-driven phenotyping algorithms. - Yizhen Zhong; Luke V. Rasmussen; Justin Starren; Yuan Luo 001 (AMIA, 2016)

Contralateral Breast Cancer Event Detection Using Nature Language Processing. - Zexian Zeng; Xiaoyu Li 006; Sasa Espino; Ankita Roy; Kristen Kitsch; Susan E. Clare; Seema A. Khan; Yuan Luo 001 (AMIA, 2017)

Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations. - Yuan Luo 001; Özlem Uzuner; Peter Szolovits (Briefings Bioinform., 2017)

Tensor factorization toward precision medicine. - Yuan Luo 001; Fei Wang 001; Peter Szolovits (Briefings Bioinform., 2017)

Recurrent neural networks for classifying relations in clinical notes. - Yuan Luo 001 (J. Biomed. Informatics, 2017)

Multi-View Graph Convolutional Network and Its Applications on Neuroimage Analysis for Parkinson's Disease. - Xi Zhang; Lifang He 001; Kun Chen 002; Yuan Luo 001; Jiayu Zhou; Fei Wang 001 (AMIA, 2018)

Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk. - Guoqing Chao; Chengsheng Mao; Fei Wang 001; Yuan Zhao; Yuan Luo 001 (BIBM, 2018)

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes. - Yikuan Li; Liang Yao; Chengsheng Mao; Anand Srivastava; Xiaoqian Jiang; Yuan Luo 001 (BIBM, 2018)

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective. - Yuan Luo 001; Peter Szolovits (BIBM, 2018)

Deep Generative Classifiers for Thoracic Disease Diagnosis with Chest X-ray Images. - Chengsheng Mao; Liang Yao; Yiheng Pan; Yuan Luo 001; Zexian Zeng (BIBM, 2018)

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. - Yizhen Zhong; Luke V. Rasmussen; Yu Deng; Jennifer A. Pacheco; Maureen E. Smith; Justin Starren; Wei-Qi Wei; Peter Speltz; Joshua C. Denny; Nephi Walton; George Hripcsak; Christopher G. Chute; et al. (BIBM, 2018)

Portable Phenotyping System: A Portable Machine-Learning Approach to i2b2 Obesity Challenge. - Himanshu Sharma; Chengsheng Mao; Yizhen Zhang 005; Haleh Vatani; Liang Yao; Yizhen Zhong; Luke V. Rasmussen; Guoqian Jiang; Jyotishman Pathak; Yuan Luo 001 (ICHI Workshops, 2018)

Using Clinical Narratives and Structured Data to Identify Distant Recurrences in Breast Cancer. - Zexian Zeng; Ankita Roy; Xiaoyu Li 006; Sasa Espino; Susan E. Clare; Seema A. Khan; Yuan Luo 001 (ICHI, 2018)

Using natural language processing and machine learning to identify breast cancer local recurrence. - Zexian Zeng; Sasa Espino; Ankita Roy; Xiaoyu Li 006; Seema A. Khan; Susan E. Clare; Xia Jiang; Richard E. Neapolitan; Yuan Luo 001 (BMC Bioinform., 2018)

Efficient Genomic Interval Queries Using Augmented Range Trees. - Chengsheng Mao; Alal Eran; Yuan Luo 001 (CoRR, 2018)

Distribution Networks for Open Set Learning. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (CoRR, 2018)

Cancer classification and pathway discovery using non-negative matrix factorization. - Zexian Zeng; Andy H. Vo; Chengsheng Mao; Susan E. Clare; Seema A. Khan; Yuan Luo 001 (CoRR, 2018)

Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes. - Yuan Luo 001; Yu Cheng; Özlem Uzuner; Peter Szolovits; Justin Starren (J. Am. Medical Informatics Assoc., 2018)

3D-MICE: integration of cross-sectional and longitudinal imputation for multi-analyte longitudinal clinical data. - Yuan Luo 001; Peter Szolovits; Anand Dighe; Jason Baron (J. Am. Medical Informatics Assoc., 2018)

Graph Convolutional Networks for Text Classification. - Liang Yao; Chengsheng Mao; Yuan Luo 001 (AAAI, 2019)

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. - Prakash Adekkanattu; Guoqian Jiang; Yuan Luo 001; Paul R. Kingsbury; Zhenxing Xu; Luke V. Rasmussen; Jennifer A. Pacheco; Richard C. Kiefer; Daniel J. Stone; Pascal S. Brandt; Liang Yao; Yizhen Zhong; et al. (AMIA, 2019)

Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms. - Luke V. Rasmussen; Pascal S. Brandt; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Prakash Adekkanattu; Jessica S. Ancker; Fei Wang 001; Zhenxing Xu; Jyotishman Pathak; Yuan Luo 001 (AMIA, 2019)

Phenotyping Multiple Organ Dysfunction Syndrome Using Temporal Trends in Critically Ill Children. - Emily Kunce Stroup; Yuan Luo 001; L. Nelson Sanchez-Pinto (BIBM, 2019)

Using Machine Learning to Predict Hyperchloremia in Critically Ill Patients. - Pete Yeh; Yiheng Pan; L. Nelson Sanchez-Pinto; Yuan Luo 001 (BIBM, 2019)

Mixture-based Multiple Imputation Model for Clinical Data with a Temporal Dimension. - Ye Xue; Diego Klabjan; Yuan Luo 001 (IEEE BigData, 2019)

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes and Structured Multivariate Physiological Measurements. - Mengxin Sun; Jason Baron; Anand Dighe; Peter Szolovits; Richard G. Wunderink; Tamara Isakova; Yuan Luo 001 (MedInfo, 2019)

Using Machine Learning to Integrate Socio-Behavioral Factors in Predicting Cardiovascular-Related Mortality Risk. - Hanyin Wang; Yikuan Li; Hongyan Ning; John Wilkins; Donald Lloyd-Jones; Yuan Luo 001 (MedInfo, 2019)

Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care. - Zhenxing Xu; Yuan Luo 001; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; Fei Wang 001 (MedInfo, 2019)

Rich Text Formatted EHR Narratives: A Hidden and Ignored Trove. - Zexian Zeng; Yuan Zhao; Mengxin Sun; Andy H. Vo; Justin Starren; Yuan Luo 001 (MedInfo, 2019)

Predicting ICU readmission using grouped physiological and medication trends. - Ye Xue; Diego Klabjan; Yuan Luo 001 (Artif. Intell. Medicine, 2019)

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization. - Yuan Luo 001; Chengsheng Mao; Yiben Yang; Fei Wang 001; Faraz S. Ahmad; Donna Arnett; Marguerite R. Irvin; Sanjiv J. Shah (Bioinform., 2019)

MedGCN: Graph Convolutional Networks for Multiple Medical Tasks. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (CoRR, 2019)

Identification of Predictive Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks. - Zhenxing Xu; Jingyuan Chou; Xi Sheryl Zhang; Yuan Luo 001; Tamara Isakova; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; et al. (CoRR, 2019)

KG-BERT: BERT for Knowledge Graph Completion. - Liang Yao; Chengsheng Mao; Yuan Luo 001 (CoRR, 2019)

Mixed Pooling Multi-View Attention Autoencoder for Representation Learning in Healthcare. - Shaika Chowdhury; Chenwei Zhang; Philip S. Yu; Yuan Luo 001 (CoRR, 2019)

Hierarchical Semantic Correspondence Learning for Post-Discharge Patient Mortality Prediction. - Shaika Chowdhury; Chenwei Zhang; Philip S. Yu; Yuan Luo 001 (CoRR, 2019)

Conditional Hierarchical Bayesian Tucker Decomposition. - Adam Sandler; Diego Klabjan; Yuan Luo 001 (CoRR, 2019)

Classifying relations in clinical narratives using segment graph convolutional and recurrent neural networks (Seg-GCRNs). - Yifu Li; Ran Jin; Yuan Luo 001 (J. Am. Medical Informatics Assoc., 2019)

Traditional Chinese medicine clinical records classification with BERT and domain specific corpora. - Liang Yao; Zhe Jin; Chengsheng Mao; Yin Zhang 006; Yuan Luo 001 (J. Am. Medical Informatics Assoc., 2019)

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. - Na Hong; Andrew Wen; Daniel J. Stone; Shintaro Tsuji; Paul R. Kingsbury; Luke V. Rasmussen; Jennifer A. Pacheco; Prakash Adekkanattu; Fei Wang 001; Yuan Luo 001; Jyotishman Pathak; Hongfang Liu; et al. (J. Biomed. Informatics, 2019)

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. - Ning Shang; Cong Liu 020; Luke V. Rasmussen; Casey N. Ta; Robert J. Carroll; Barbara Benoit; Todd Lingren; Ozan Dikilitas; Frank D. Mentch; David S. Carrell; Wei-Qi Wei; Yuan Luo 001; et al. (J. Biomed. Informatics, 2019)

Identifying Breast Cancer Distant Recurrences from Electronic Health Records Using Machine Learning. - Zexian Zeng; Liang Yao; Ankita Roy; Xiaoyu Li 006; Sasa Espino; Susan E. Clare; Seema A. Khan; Yuan Luo 001 (J. Heal. Informatics Res., 2019)

Recent Advances in Supervised Dimension Reduction: A Survey. - Guoqing Chao; Yuan Luo 001; Weiping Ding 001 (Mach. Learn. Knowl. Extr., 2019)

Developing a portable natural language processing based phenotyping system. - Himanshu Sharma; Chengsheng Mao; Yizhen Zhang 005; Haleh Vatani; Liang Yao; Yizhen Zhong; Luke V. Rasmussen; Guoqian Jiang; Jyotishman Pathak; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2019)

Clinical text classification with rule-based features and knowledge-guided convolutional neural networks. - Liang Yao; Chengsheng Mao; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2019)

Early prediction of acute kidney injury following ICU admission using a multivariate panel of physiological measurements. - Lindsay P. Zimmerman; Paul Reyfman; Angela D. R. Smith; Zexian Zeng; Abel N. Kho; L. Nelson Sanchez-Pinto; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2019)

Are My EHRs Private Enough? Event-Level Privacy Protection. - Chengsheng Mao; Yuan Zhao; Mengxin Sun; Yuan Luo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Natural Language Processing for EHR-Based Computational Phenotyping. - Zexian Zeng; Yu Deng; Xiaoyu Li 006; Tristan Naumann; Yuan Luo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Feasibility of Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language. - Pascal S. Brandt; Richard C. Kiefer; Jennifer A. Pacheco; Prakash Adekkanattu; Evan Sholle; Faraz S. Ahmad; Jie Xu 012; Zhenxing Xu; Jessica S. Ancker; Fei Wang 001; Yuan Luo 001; Guoqian Jiang; et al. (AMIA, 2020)

Unsupervised learning for systemic lupus erythematosus subtype identification: electronic health record vs registry data. - Yu Deng; Anika S. Ghosh; Anh H. Chung; Yacob Tedla; Abel N. Kho; Rosalind Ramsey-Goldman; Yuan Luo 001; Theresa L. Walunas (AMIA, 2020)

Identification of Alzheimer's Disease Subtypes from Electronic Health Records Using a Data-Driven Approach. - Jie Xu 012; Fei Wang 001; Zhenxing Xu; Prakash Adekkanattu; Pascal S. Brandt; Guoqian Jiang; Richard C. Kiefer; Yuan Luo 001; Chengsheng Mao; Jennifer A. Pacheco; Luke V. Rasmussen; Yiye Zhang; et al. (AMIA, 2020)

A Predictive Model for Parkinson's Disease Reveals Candidate Gene Sets for Progression Subtype. - Saya R. Dennis; Tanya Simuni; Yuan Luo 001 (BIBM, 2020)

A Comparison of Pre-trained Vision-and-Language Models for Multimodal Representation Learning across Medical Images and Reports. - Yikuan Li; Hanyin Wang; Yuan Luo 001 (BIBM, 2020)

Med2Meta: Learning Representations of Medical Concepts with Meta-embeddings. - Shaika Chowdhury; Chenwei Zhang; Philip S. Yu; Yuan Luo 001 (HEALTHINF, 2020)

A Pre-trained Clinical Language Model for Acute Kidney Injury. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (ICHI, 2020)

ScanMap: Supervised Confounding Aware Non-negative Matrix Factorization for Polygenic Risk Modeling. - Yuan Luo 001; Chengsheng Mao (MLHC, 2020)

Improving Medical NLI Using Context-Aware Domain Knowledge. - Shaika Chowdhury; Philip S. Yu; Yuan Luo 001 (*SEM@COLING, 2020)

Prediction of breast cancer distant recurrence using natural language processing and knowledge-guided convolutional neural network. - Hanyin Wang; Yikuan Li; Seema A. Khan; Yuan Luo 001 (Artif. Intell. Medicine, 2020)

A novel normalization and differential abundance test framework for microbiome data. - Yuanjing Ma; Yuan Luo 001; Hongmei Jiang (Bioinform., 2020)

Towards Expressive Graph Representation. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (CoRR, 2020)

Supervised subgraph augmented non-negative matrix factorization for interpretable manufacturing time series data analytics. - Hongyue Sun; Ran Jin; Yuan Luo 001 (IISE Trans., 2020)

Predictive modeling of bacterial infections and antibiotic therapy needs in critically ill adults. - Garrett Eickelberg; L. Nelson Sanchez-Pinto; Yuan Luo 001 (J. Biomed. Informatics, 2020)

Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks. - Zhenxing Xu; Jingyuan Chou; Xi Sheryl Zhang; Yuan Luo 001; Tamara Isakova; Prakash Adekkanattu; Jessica S. Ancker; Guoqian Jiang; Richard C. Kiefer; Jennifer A. Pacheco; Luke V. Rasmussen; Jyotishman Pathak; et al. (J. Biomed. Informatics, 2020)

Predicting mortality in critically ill patients with diabetes using machine learning and clinical notes. - Jiancheng Ye; Liang Yao; Jiahong Shen; Rethavathi Janarthanam; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2020)

Hyperchloremia in critically ill patients: association with outcomes and prediction using electronic health record data. - Pete Yeh; Yiheng Pan; L. Nelson Sanchez-Pinto; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2020)

Performance-weighted-voting model: an ensemble machine learning method for cancer type classification using whole-exome sequencing mutation. - Yawei Li 002; Yuan Luo 001 (Quant. Biol., 2020)

PANTHER: Pathway Augmented Nonnegative Tensor Factorization for HighER-order Feature Learning. - Yuan Luo 001; Chengsheng Mao (AAAI, 2021)

Open-Set Recognition with Gaussian Mixture Variational Autoencoders. - Alexander Cao; Yuan Luo 001; Diego Klabjan (AAAI, 2021)

Multi-site Evaluation of Longitudinal Changes in Ejection Fraction in Heart Failure Patients Through Data-driven Phenotyping. - Prakash Adekkanattu; Jennifer A. Pacheco; Joseph Kabariti; Daniel J. Stone; Yue Yu; Parag Goyal; Faraz S. Ahmad; Guoqian Jiang; Yuan Luo 001; Luke V. Rasmussen; Pascal S. Brandt; Zhenxing Xu; et al. (AMIA, 2021)

Addressing Bias in the Application of Machine Learning on Real-World Data. - Hossein Estiri; Yuan Luo 001; Hongfang Liu; Suzanne Tamang; Harold P. Lehmann (AMIA, 2021)

Multi-Modal Data Science for Healthcare: State of the Art, Challenges, and Opportunities. - Yuan Luo 001; Fei Wang 001; Benjamin S. Glicksberg; Jessilyn Dunn; Nigam Shah (AMIA, 2021)

Graph Based Machine Learning for Healthcare: State of the Art, Challenges, and Opportunities. - Yuan Luo 001; Fei Wang 001; Marinka Zitnik; Shuiwang Ji (AMIA, 2021)

A Deep Learning Framework Using a Pre-trained BERT Model to Predict the Risk of Progression from Mild Cognitive Impairment to Alzheimer's Disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Jennifer A. Pacheco; Guoqian Jiang; Fei Wang 001; Richard Isaacson; Jyotishman Pathak; Yuan Luo 001 (AMIA, 2021)

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. - Jennifer A. Pacheco; Luke V. Rasmussen; Ken Wiley; Thomas N. Person; David J. Cronkite; Sunghwan Sohn; Shawn N. Murphy; Justin H. Gundelach; Vivian S. Gainer; Victor M. Castro; Cong Liu 020; Todd Lingren; et al. (AMIA, 2021)

FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. - Daniel J. Stone; Sijia Liu 002; Yuan Luo 001; Andrew Wen; Nansu Zong; Luke V. Rasmussen; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Fei Wang 001; Cui Tao; Jyotishman Pathak; et al. (AMIA, 2021)

On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. - Andrew Wen; Luke V. Rasmussen; Daniel J. Stone; Sijia Liu 002; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Yuan Luo 001; Fei Wang 001; Jyotishman Pathak; Hongfang Liu; Guoqian Jiang (AMIA, 2021)

Unsupervised clustering analysis of SARS-Cov-2 population structure reveals six major subtypes at early stage across the world. - Yawei Li 002; Qingyun Liu 009; Zexian Zeng; Yuan Luo 001 (BIBM, 2021)

SNPs Filtered by Allele Frequency Improve the Prediction of Hypertension Subtypes. - Yiming Li; Sanjiv J. Shah; Donna Arnett; Ryan Irvin; Yuan Luo 001 (BIBM, 2021)

Early Prediction of Mortality in Critical Care Setting in Sepsis Patients Using Structured Features and Unstructured Clinical Notes. - Jiyoung Shin; Yikuan Li; Yuan Luo 001 (BIBM, 2021)

COVID Vaccine and Cardiovascular Risks: A Natural Language Analysis of Vaccine Adverse Event Reports. - Yiqing Zhao; Michael G. Ison; Yuan Luo 001 (BIBM, 2021)

Unsupervised Learning to Subphenotype Delirium Patients from Electronic Health Records. - Yiqing Zhao; Yuan Luo 001 (BIBM, 2021)

A deep-learning-based unsupervised model on esophageal manometry using variational autoencoder. - Wenjun Kou; Dustin A. Carlson; Alexandra J. Baumann; Erica Donnan; Yuan Luo 001; John E. Pandolfino; Mozziyar Etemadi (Artif. Intell. Medicine, 2021)

Deep learning for cancer type classification and driver gene identification. - Zexian Zeng; Chengsheng Mao; Andy H. Vo; Xiaoyu Li 006; Janna Ore Nugent; Seema A. Khan; Susan E. Clare; Yuan Luo 001 (BMC Bioinform., 2021)

Non-Convex Optimization with Spectral Radius Regularization. - Adam Sandler; Diego Klabjan; Yuan Luo 001 (CoRR, 2021)

Disparities in Social Determinants among Performances of Mortality Prediction with Machine Learning for Sepsis Patients. - Hanyin Wang; Yikuan Li; Andrew Naidech; Yuan Luo 001 (CoRR, 2021)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chunhua Weng; Cong Liu 020; Adam Cordon; Jingzhi Yu; et al. (CoRR, 2021)

Constrained tensor factorization for computational phenotyping and mortality prediction in patients with cancer. - Francisco Y. Cai; Chengsheng Mao; Yuan Luo 001 (CoRR, 2021)

Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. - Jeffrey G. Klann; Hossein Estiri; Griffin M. Weber; Bertrand Moal; Paul Avillach; Chuan Hong; Amelia L. M. Tan; Brett K. Beaulieu-Jones; Victor M. Castro; Thomas Maulhardt; Alon Geva; Alberto Malovini; et al. (J. Am. Medical Informatics Assoc., 2021)

Characterizing phenotypic abnormalities associated with high-risk individuals developing lung cancer using electronic health records from the All of Us researcher workbench. - Jie Na; Nansu Zong; Chen Wang; David E. Midthun; Yuan Luo 001; Ping Yang; Guoqian Jiang (J. Am. Medical Informatics Assoc., 2021)

Unsupervised phenotyping of sepsis using nonnegative matrix factorization of temporal trends from a multivariate panel of physiological measurements. - Menghan Ding; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2021)

Evaluation of ICU Severity Scores and Mortality Prediction by Race and Ethnicity: A Machine Learning Approach Using MIMIC-IV. - Catherine A. Gao; Plamena Powla; Meghan Hutch; Oluwatosin Akinsola; Yuan Luo 001 (AMIA, 2022)

Aggregation Delayed Federated Learning. - Ye Xue; Diego Klabjan; Yuan Luo 001 (IEEE Big Data, 2022)

PsmPy: A Package for Retrospective Cohort Matching in Python. - Adrienne S. Kline; Yuan Luo 001 (EMBC, 2022)

Improving Graph Representation Learning with Distribution Preserving. - Chengsheng Mao; Yuan Luo 001 (ICDM, 2022)

Evaluating the state of the art in missing data imputation for clinical data. - Yuan Luo 001 (Briefings Bioinform., 2022)

Clinical-Longformer and Clinical-BigBird: Transformers for long clinical sequences. - Yikuan Li; Ramsey M. Wehbe; Faraz S. Ahmad; Hanyin Wang; Yuan Luo 001 (CoRR, 2022)

Distribution Preserving Graph Representation Learning. - Chengsheng Mao; Yuan Luo 001 (CoRR, 2022)

Machine Learning Applications in Lung Cancer Diagnosis, Treatment and Prognosis. - Yawei Li 002; Xin Wu; Ping Yang; Guoqian Jiang; Yuan Luo 001 (CoRR, 2022)

Multimodal Machine Learning in Precision Health. - Adrienne S. Kline; Hanyin Wang; Yikuan Li; Saya R. Dennis; Meghan Hutch; Zhenxing Xu; Fei Wang 001; Feixiong Cheng; Yuan Luo 001 (CoRR, 2022)

AKI-BERT: a Pre-trained Clinical Language Model for Early Prediction of Acute Kidney Injury. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (CoRR, 2022)

Deep Learning Reveals Patterns of Diverse and Changing Sentiments Towards COVID-19 Vaccines Based on 11 Million Tweets. - Hanyin Wang; Meghan R. Hutch; Yikuan Li; Adrienne S. Kline; Sebastian Otero; Leena B. Mithal; Emily S. Miller; Andrew Naidech; Yuan Luo 001 (CoRR, 2022)

AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Yikuan Li; Prakash Adekkanattu; Jennifer A. Pacheco; Borna Bonakdarpour; Robert Vassar; Guoqian Jiang; Fei Wang 001; Jyotishman Pathak; Yuan Luo 001 (CoRR, 2022)

Design and validation of a FHIR-based EHR-driven phenotyping toolbox. - Pascal S. Brandt; Jennifer A. Pacheco; Prakash Adekkanattu; Evan Sholle; Sajjad Abedian; Daniel J. Stone; David Knaack; Jie Xu 012; Zhenxing Xu; Yifan Peng 002; Natalie C. Benda; Fei Wang 001; et al. (J. Am. Medical Informatics Assoc., 2022)

MedGCN: Medication recommendation and lab test imputation via graph convolutional networks. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (J. Biomed. Informatics, 2022)

SurvMaximin: Robust federated approach to transporting survival risk prediction models. - Xuan Wang; Harrison G. Zhang; Xin Xiong; Chuan Hong; Griffin M. Weber; Gabriel A. Brat; Clara-Lea Bonzel; Yuan Luo 001; Rui Duan 004; Nathan P. Palmer; Meghan R. Hutch; Alba Gutiérrez-Sacristán; et al. (J. Biomed. Informatics, 2022)

Comparison between machine learning methods for mortality prediction for sepsis patients with different social determinants. - Hanyin Wang; Yikuan Li; Andrew Naidech; Yuan Luo 001 (BMC Medical Informatics Decis. Mak., 2022)

Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. - Jingzhi Yu; Jennifer A. Pacheco; Anika S. Ghosh; Yuan Luo 001; Chunhua Weng; Ning Shang; Barbara Benoit; David S. Carrell; Robert J. Carroll; Ozan Dikilitas; Robert R. Freimuth; Vivian S. Gainer; et al. (BMC Medical Informatics Decis. Mak., 2022)

Multimodal machine learning in precision health: A scoping review. - Adrienne S. Kline; Hanyin Wang; Yikuan Li; Saya R. Dennis; Meghan Hutch; Zhenxing Xu; Fei Wang 001; Feixiong Cheng; Yuan Luo 001 (npj Digit. Medicine, 2022)

International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. - Harrison G. Zhang; Arianna Dagliati; Zahra Shakeri Hossein Abad; Xin Xiong; Clara-Lea Bonzel; Zongqi Xia; Bryce W. Q. Tan; Paul Avillach; Gabriel A. Brat; Chuan Hong; Michele Morris; Shyam Visweswaran; et al. (npj Digit. Medicine, 2022)

ImageGCN: Multi-Relational Image Graph Convolutional Networks for Disease Identification With Chest X-Rays. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (IEEE Trans. Medical Imaging, 2022)

Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis. - Yawei Li 002; Xin Wu; Ping Yang; Guoqian Jiang; Yuan Luo 001 (Genom. Proteom. Bioinform., 2022)

Natural language processing to identify lupus nephritis phenotype in electronic health records. - Yu Deng; Jennifer A. Pacheco; Anika S. Ghosh; Anh H. Chung; Chengsheng Mao; Joshua C. Smith; Juan Zhao 003; Wei-Qi Wei; April Barnado; Chad Dorn; Chunhua Weng; Cong Liu 020; et al. (BMC Medical Informatics Decis. Mak., 2022)

Pediatric Sepsis Phenotyping Using Vital Sign Trajectories. - Yanyi Jenny Ding; Zhidi Luo; Mindy Szeto; Yuan Luo 001; L. Nelson Sanchez-Pinto (BIBM, 2023)

Deep Reinforcement Learning for Cost-Effective Medical Diagnosis. - Zheng Yu; Yikuan Li; Joseph C. Kim; Kaixuan Huang; Yuan Luo 001; Mengdi Wang (ICLR, 2023)

IRTCI: Item Response Theory for Categorical Imputation. - Adrienne S. Kline; Yuan Luo 001 (CoRR, 2023)

Medical Image Deidentification, Cleaning and Compression Using Pylogik. - Adrienne S. Kline; Vinesh Appadurai; Yuan Luo 001; Sanjiv J. Shah (CoRR, 2023)

Deep Reinforcement Learning for Efficient and Fair Allocation of Health Care Resources. - Yikuan Li; Chengsheng Mao; Kaixuan Huang; Hanyin Wang; Zheng Yu; Mengdi Wang; Yuan Luo 001 (CoRR, 2023)

Enhancing Health Data Interoperability with Large Language Models: A FHIR Study. - Yikuan Li; Hanyin Wang; Halid Ziya Yerebakan; Yoshihisa Shinagawa; Yuan Luo 001 (CoRR, 2023)

Comparing scientific abstracts generated by ChatGPT to real abstracts with detectors and blinded human reviewers. - Catherine A. Gao; Frederick M. Howard; Nikolay S. Markov; Emma C. Dyer; Siddhi Ramesh; Yuan Luo 001; Alexander T. Pearson (npj Digit. Medicine, 2023)

Open-set recognition of breast cancer treatments. - Alexander Cao; Diego Klabjan; Yuan Luo 001 (Artif. Intell. Medicine, 2023)

A comparative study of pretrained language models for long clinical text. - Yikuan Li; Ramsey M. Wehbe; Faraz S. Ahmad; Hanyin Wang; Yuan Luo 001 (J. Am. Medical Informatics Assoc., 2023)

Characterizing variability of electronic health record-driven phenotype definitions. - Pascal S. Brandt; Abel N. Kho; Yuan Luo 001; Jennifer A. Pacheco; Theresa L. Walunas; Hakon Hakonarson; George Hripcsak; Cong Liu 020; Ning Shang; Chunhua Weng; Nephi Walton; David S. Carrell; et al. (J. Am. Medical Informatics Assoc., 2023)

An exploratory survey about using ChatGPT in education, healthcare, and research. - Catherine A. Gao; Mohammad Hosseini 003; David M. Liebovitz; Alexandre Carvalho; Faraz S. Ahmad; Yuan Luo 001; Ngan MacDonald; Kristi L. Holmes; Abel N. Kho (Zenodo, 2023)

Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record? - Amelia L. M. Tan; Emily J. Getzen; Meghan R. Hutch; Zachary H. Strasser; Alba Gutiérrez-Sacristán; Trang T. Le; Arianna Dagliati; Michele Morris; David A. Hanauer; Bertrand Moal; Clara-Lea Bonzel; William Yuan; et al. (J. Biomed. Informatics, 2023)

Patterns of diverse and changing sentiments towards COVID-19 vaccines: a sentiment analysis study integrating 11 million tweets and surveillance data across over 180 countries. - Hanyin Wang; Yikuan Li; Meghan R. Hutch; Adrienne S. Kline; Sebastian Otero; Leena B. Mithal; Emily S. Miller; Andrew Naidech; Yuan Luo 001 (J. Am. Medical Informatics Assoc., 2023)

Special issue on fairness and inclusion in biomedical informatics research: technical and social perspectives. - Shyam Visweswaran; Yuan Luo 001; Mor Peleg (J. Biomed. Informatics, 2023)

AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. - Chengsheng Mao; Jie Xu 012; Luke V. Rasmussen; Yikuan Li; Prakash Adekkanattu; Jennifer A. Pacheco; Borna Bonakdarpour; Robert Vassar; Li Shen; Guoqian Jiang; Fei Wang 001; Jyotishman Pathak; et al. (J. Biomed. Informatics, 2023)

Transportability of bacterial infection prediction models for critically ill patients. - Garrett Eickelberg; Lazaro Nelson Sanchez-Pinto; Adrienne S. Kline; Yuan Luo 001 (J. Am. Medical Informatics Assoc., 2023)

Towards Expressive Graph Representations for Graph Neural Networks. - Chengsheng Mao; Liang Yao; Yuan Luo 001 (ICDM, 2024)

Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. - Betina Idnay; Zihan Xu; William G. Adams; Mohammad Adibuzzaman; Nicholas R. Anderson 001; Neil Bahroos; Douglas S. Bell; Cody Bumgardner; Thomas R. Campion Jr.; Victor M. Castro; James J. Cimino; I. Glenn Cohen; et al. (CoRR, 2024)

Fairness and inclusion methods for biomedical informatics research. - Shyam Visweswaran; Yuan Luo 001; Mor Peleg (J. Biomed. Informatics, 2024)

Deep learning for identifying personal and family history of suicidal thoughts and behaviors from EHRs. - Prakash Adekkanattu; Al'ona Furmanchuk; Yonghui Wu; Aman Pathak; Braja Gopal Patra; Sarah Bost; Destinee Morrow; Grace Hsin-Min Wang; Yuyang Yang; Noah James Forrest; Yuan Luo 001; Theresa L. Walunas; et al. (npj Digit. Medicine, 2024)

Closing the gap: addressing telehealth disparities across specialties in the sustained pandemic era. - Saki Amagai; Edward Vonesh; James Adams; Yuan Luo 001 (npj Digit. Medicine, 2024)

Informing immunotherapy with multi-omics driven machine learning. - Yawei Li 002; Xin Wu; Deyu Fang; Yuan Luo 001 (npj Digit. Medicine, 2024)

Contrasting rule and machine learning based digital self triage systems in the USA. - Bilal A. Naved; Yuan Luo 001 (npj Digit. Medicine, 2024)

Longitudinal clustering of Life's Essential 8 health metrics: application of a novel unsupervised learning method in the CARDIA study. - Peter Graffy; Lindsay P. Zimmerman; Yuan Luo 001; Jingzhi Yu; Yuni Choi; Rachel Zmora; Donald Lloyd-Jones; Norrina B. Allen (J. Am. Medical Informatics Assoc., 2024)

Using machine learning to develop smart reflex testing protocols. - Matthew McDermott; Anand Dighe; Peter Szolovits; Yuan Luo 001; Jason Baron (J. Am. Medical Informatics Assoc., 2024)

Collaborative Resource for Intensive care Translational science, Informatics, Comprehensive Analytics, and Learning (CRITICAL). - Yuan Luo 001; Luke V. Rasmussen; Andrew Williams 005; Jared Houghtaling; Andrew P. Michelson; Philip R. O. Payne; James J. Cimino; John D. Osborne; Prasanth Nannapaneni; Yikuan Li; Saki Amagai; Meghan Hutch; et al. (Zenodo, 2024)

Exploring Large Language Models for Knowledge Graph Completion. - Liang Yao; Jiazhen Peng; Chengsheng Mao; Yuan Luo 001 (ICASSP, 2025)

Leveraging large language models for academic conference organization. - Yuan Luo 001; Yikuan Li; Omolola Ogunyemi; Eileen Koski; Blanca E. Himes (npj Digit. Medicine, 2025)

LLM enabled classification of patient self-reported symptoms and needs in health systems across the USA. - Bilal A. Naved; Shravan Ravishankar; Georges E. Colbert; Andrew Johnston; Quintan M. Slott; Yuan Luo 001 (npj Digit. Medicine, 2025)