Solving y=f(x) in healthcare with AI

Selected Publications

For full publication, please see my Google Scholar page.

* indicates corresponding/senior author, † indicates co-first author

2022

  • J Yu, J Pacheco, A Ghosh, Y Luo, …, L Rasmussen. Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8) 2022 22(23) 1-9

  • C Mao, L Yao, Y Luo*. MedGCN: Medication Recommendation and Lab Test Imputation via Graph Convolutional Networks. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3) 2022 doi.org/10.1016/j.jbi.2022.104000

  • C Mao, L Yao, Y Luo*. ImageGCN: Multi-Relational Image Graph Convolutional Networks for Disease Identification with Chest X-rays. IEEE Transactions on Medical Imaging (TMI, a top medical imaging journal, IF 10.048) 2022 doi.org/10.1109/TMI.2022.3153322

  • Y Luo*, D Lloyd-Jones, R Wunderink. Proactive vs Reactive Machine Learning in Health Care. JAMA (a top medical journal IF 56.3): 2021 doi:10.1001/jama.2021.24935

  • Hophan SL, Odnokoz O, Liu H, Luo Y, Khan S, Gradishar W, Zhou Z, Badve S, Torres MA, Wan Y. Ductal carcinoma in situ of breast: from molecular etiology to therapeutic management. Endocrinology (IF 4.7) 2022 https://doi.org/10.1210/endocr/bqac027

  • Z Zeng†, Y Li†, Y Li†, Y Luo*. Statistical and machine learning methods for spatially resolved transcriptomics data analysis. Genome Biology (a top genomics journal IF 13.6): 2022 (2022) 23:83 1-23

  • Y Li, X Wu, P Yang, G Jiang, Luo Y, Machine Learning for Lung Cancer Diagnosis, Treatment and Prognosis, GPB (under review) [pdf]

2021

  • Luo Y, Evaluating the state-of-the-art in missing data imputation for clinical data, Briefings in Bioinformatics (a top bioinformatics journal IF 11.6) 2021 https://doi.org/10.1093/bib/bbab489

  • J Zhu, I Wolf, C Dulberger, H Won, J Kester, J Judd, S Wirth, R Clark, Y Li, Y Luo, T Gray, J Wade, K Derbyshire, S Fortune, E Rubin. Spatiotemporal localization of proteins in mycobacteria. Cell Reports (IF 9.4) 2021 (to appear)

  • L El-Shennawy†, A Hoffmann†, N Dashzeveg†, K McAndrews†, …, Y Luo, …, R Kalluri*, D Fang*, H Liu*. Circulating ACE2-expressing Extracellular Vesicles as an Innate Antiviral Response and A Decoy Therapy to Block Broad Strains of SARS-CoV-2, Nature Communications (IF 14.9) 2021 (to appear)

  • Zhao Y, Luo Y*. Unsupervised Learning to Subphenotype Delirium Patients from Electronic Health Records, IEEE International Conference on Bioinformatics and Biomedicine 2021 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%)

  • Shin J, Li Y, Luo Y*. Early Prediction of Mortality in Critical Care Setting in Sepsis Patients Using Structured Features and Unstructured Clinical Notes, IEEE International Conference on Bioinformatics and Biomedicine 2021 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%)

  • Li Y, Shah S, Arnett D, Irvin R, Luo Y*. SNPs Filtered by Allele Frequency Improve the Prediction of Hypertension Subtypes, IEEE International Conference on Bioinformatics and Biomedicine 2021 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%)

  • Zhao Y, Ison M, Luo Y*. COVID Vaccine and Cardiovascular Risks: A Natural Language Analysis of Vaccine Adverse Event Reports, IEEE International Conference on Bioinformatics and Biomedicine 2021 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%)

  • Li Y, Liu Q, Zeng Z, Luo Y*. Unsupervised clustering analysis reveals global population structure of SARS-CoV-2, IEEE International Conference on Bioinformatics and Biomedicine 2021 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%)

  • Tang M, Shin HJ, Metcalf-Doetsch W, Luo Y, Lindholm PF, Kwaan H, Naidech AM. Antiplatelet Medications and Biomarkers of Hemostasis May Explain the Association of Hematoma Appearance and Subsequent Hematoma Expansion After Intracerebral Hemorrhage. Neurocritical Care. 2021 Oct 27:1-6.

  • Z Zeng, C Mao, A Vo, X Li, J Nugent, S Khan, S Clare, Y Luo*. Deep learning for cancer type classification and driver gene identification. BMC Bioinformatics (a major bioinformatics journal IF 3.1) 22, 491 (2021). https://doi.org/10.1186/s12859-021-04400-4

  • Li, Y., Luo, Y*. Optimizing the evaluation of gene-targeted panels for tumor mutational burden estimation. Sci Rep (IF 4.3) 11, 21072 (2021). https://doi.org/10.1038/s41598-021-00626-7

  • Na J, Zong N, Wang C, Midthun DE, Luo Y, Yang P, Jiang G. Characterizing phenotypic abnormalities associated with high-risk individuals developing lung cancer using electronic health records from the All of Us researcher workbench. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5). 2021 28(11) 2313–2324.

  • Murphy J, Shin HJ, Wang H, Luo Y, Jahromi B, Bleck TP, Cella D, Naidech AM. Clusters Across Multiple Domains of Health-Related Quality of Life Reveal Complex Patient Outcomes After Subarachnoid Hemorrhage. Critical care explorations. 2021 Sep;3(9).

  • GM Weber, HG Zhang, …, Luo Y, …, Brat, G. International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study, Journal of Medical Internet Research 23 (10), e31400

  • Bhavani SV†, Luo Y†, Miller WD, Sanchez-Pinto LN, Han X, Mao C, Sandikci B, Peek ME, Coopersmith CM, Michelson KN, Parker WF. Simulation of Ventilator Allocation in Critically Ill Patients with COVID-19. Am J Respir Crit Care Med (AJRCCM, a top journal on pulmonary and critical care, IF 21.4). 2021 Sep 9. doi: 10.1164/rccm.202106-1453LE. PMID: 34499587.

  • Na J, Zong N, Wang C, Midthun DE, Luo Y, Yang P, Jiang G. Characterizing phenotypic abnormalities associated with high-risk individuals developing lung cancer using electronic health records from the All of Us researcher workbench. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5). 2021. https://10.1093/jamia/ocab174. PMID: 34505903.

  • Hutch MR, Liu M, Avillach P, Luo Y*, Bourgeois FT*. National Trends in Disease Activity for COVID-19 among Children in the US. Frontiers in Pediatrics. 2021:646.

  • EH Weissler, T Naumann, T Andersson, R Ranganath, O Elemento, Y Luo, ... The role of machine learning in clinical research: transforming the future of evidence generation. Trials (IF 2.0) 22 (1), 1-15, 2021

  • Bourgeois FT, … Luo Y, … Avillach P. International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA Open (a top biomedical sciences journal by JAMA, IF 8.5) 2021;4(6):e2112596. doi:10.1001/jamanetworkopen.2021.12596

  • Walunas TL, … Luo Y, Kho A, Rosalind R. Evaluation of structured data from electronic health records to identify clinical classification criteria attributes for systemic lupus erythematosus. Lupus Science & Medicine 2021;8:e000488. doi: 10.1136/lupus-2021-000488

  • Liu G, … Luo Y, … Feng Q. A Mendelian randomization approach utilizing HMG-coenzyme-A reductase gene variation to evaluate the association of statin-induced LDL cholesterol lowering with non-cardiovascular disease phenotypes. JAMA Open (a top biomedical sciences journal by JAMA, IF 8.5) 2020 accepted.

  • Ding M, Luo Y*. Unsupervised phenotyping of sepsis using nonnegative matrix factorization of temporal trends from a multivariate panel of physiological measurements. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8). 2021 Apr;21(5):1-5.

  • Wen A, Rasmussen LV, Stone D, Liu S, Kiefer R, Adekkanattu P, Brandt PS, Pacheco JA, Luo Y, Wang F, Pathak J, Liu H, Jiang G. CQL4NLP: Development and Integration of FHIR NLP Extensions in Clinical Quality Language for EHR-driven Phenotyping. AMIA Annual Symposium Proceedings (a top medical informatics conference) 2021 Full paper, 624-633.

  • S Liu, Y Luo, D Stone, N Zong, A Wen, Y Yu, L Rasmussen, F Wang, J Pathak, H Liu, G Jiang. Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets. AMIA Informatics Summit (a top medical informatics conference) 2021 Full paper, Distinguished Paper Award.

  • Klann JG, … Luo Y, … Murphy SN. Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5). 2021 https://doi.org/10.1093/jamia/ocab018.

  • Wang H, Li Y, Hutch M, Naidech A, Luo Y*. Using Tweets to Understand How COVID-19–Related Health Beliefs Are Affected in the Age of Social Media: Twitter Data Analysis Study. Journal of medical Internet research (a top medical informatics journal IF 5.4). 2021 Feb;23(2).

  • A Cao, Y Luo*, D Klabjan*. Open-Set Recognition with Gaussian Mixture Variational Autoencoders. Proceedings of AAAI Conference on Artificial Intelligence (a top AI conference, acceptance rate 21%) 2021 Full paper.

  • Y Luo*, C Mao. PANTHER: Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning. Proceedings of AAAI Conference on Artificial Intelligence (a top AI conference, acceptance rate 21%) 2021 Full paper, 371-380.

  • Kohane IS, …, Luo Y, …, Cai T. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. Journal of medical Internet research (a top medical informatics journal IF 5.4). 2021 Jan 10;23(3):e22219.

  • Kou W, Carlson DA, Baumann AJ, Donnan E, Luo Y, Pandolfino JE, Etemadi M. A deep-learning-based unsupervised model on esophageal manometry using variational autoencoder. Artificial Intelligence in Medicine (AIIM, a top medical informatics journal IF 5.3). 2021 Feb 1;112:102006.

2020

  • Li Y, Luo Y*. Performance-weighted-voting model: an ensemble machine learning method for cancer type classification using whole-exome sequencing mutation. Quantitative Biology. 2020 Dec;8(4):347-58.

  • Dennis SR, Simuni T, Luo Y*. A Predictive Model for Parkinson’s Disease Reveals Candidate Gene Sets for Progression Subtype. In2020 IEEE International Conference on Bioinformatics and Biomedicine (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%) 2020 Dec 16 (pp. 417-420).

  • Li Y, Wang H, Luo Y*. A comparison of pre-trained vision-and-language models for multimodal representation learning across medical images and reports. In2020 IEEE International Conference on Bioinformatics and Biomedicine (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%) 2020 Dec 16 (pp. 1999-2004).

  • Yeh, P., Pan, Y., Sanchez-Pinto, L. N., Luo, Y*. Hyperchloremia in critically ill patients: association with outcomes and prediction using electronic health record data. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8), 20(14), 1-10 (2020).

  • Ye, J., Yao, L., Shen, J., Janarthanam, R., Luo, Y*. Predicting mortality in critically ill patients with diabetes using machine learning and clinical notes. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8), 20:11, 1-7 (2020).

  • Li, Y., Luo, Y*. Performance-weighted-voting model: an ensemble machine learning method for cancer type classification using whole-exome sequencing mutation. Quant Biol 8, 347–358 (2020). https://doi.org/10.1007/s40484-020-0226-1

  • H Wang, Y Li, SA Khan, Y Luo*. Prediction of Breast Cancer Distant Recurrence Using Natural Language Processing and Knowledge-guided Convolutional Neural Network. Artificial Intelligence in Medicine (AIIM, a top medical informatics journal IF 5.3) 110, p.101977.

  • Y Ma, H Jiang, S Shah, D Arnett, M Irvin, Y Luo*. Genetic-Based Hypertension Subtype Identification Using Informative SNPs. Genes (IF 2.984) 11(11):1265 PMID: 33121163.

  • Z Zeng, A Amin, A Roy, NE Pulliam, LC Karavites, S Espino, I Helenowski, X Li, Y Luo*, SA Khan*. Preoperative magnetic resonance imaging use and oncologic outcomes in premenopausal breast cancer patients. npj Breast Cancer (a top breast cancer journal, IF 6.9) 6, 49 (2020)

  • Y Luo, C Mao. ScanMap: Supervised Confounding Aware Non-negative Matrix Factorization for Polygenic Risk Modeling. Machine Learning for Healthcare Conference 2020 (a top machine learning conference), 27-45

  • Xu Z, Wang F, Adekkanattu P, Bose B, Vekaria V, Brandt P, Jiang G, Kiefer RC, Luo Y, Pacheco JA, Rasmussen LV. Subphenotyping depression using machine learning and electronic health records. Learning health systems. 2020 Oct;4(4):e10241

  • J Xu, F Wang, Z Xu, P Adekkanattu, P Brandt, G Jiang, RC Kiefer, Y Luo, C Mao, JA Pacheco, LV Rasmussen, Y Zhang, R Isaacson, J Pathak. Data-driven discovery of probable Alzheimer's disease and related dementia subphenotypes using electronic health records. Learning Health Systems 2020 doi:10.1002/lrh2.10246

  • G Eickelberg, L N Sanchez-Pinto, Y Luo*. Predictive modeling of bacterial infections and antibiotic therapy needs in critically ill adults. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3) 2020

  • Y Luo†, A Eran†, N P. Palmer, P Avillach, A Levy-Moonshine, P Szolovits, I S. Kohane. A Multidimensional Precision Medicine Approach Identifies an Autism Subtype Characterized by Dyslipidemia. Nature Medicine (a top medical journal, IF 53.4) 26, 1375–1379, 2020 https://doi.org/10.1038/s41591-020-1007-0.

  • N Sanchez-Pinto, E Stroup, T Pendergrast, N Pinto, Y Luo*. Derivation and Validation of Novel Phenotypes of Multiple Organ Dysfunction Syndrome in Critically Ill Children. JAMA Open (a top biomedical sciences journal by JAMA, IF 8.5) 2020;3(8):e209271. doi:10.1001/jamanetworkopen.2020.9271.

  • Z Zeng, A Vo, X Li, A Shidfar, P Saldana, L Blanco, X Xuei, Y Luo*, S.A. Khan*, S.E. Clare*. Somatic Genetic Aberrations in Benign Breast Disease and the Risk of Subsequent Breast Cancer. npj Breast Cancer (a top breast cancer journal, IF 6.9) 2020 6(1), 1-11.

  • PS Brandt, RC Kiefer​​, JA Pacheco​​, P Adekkanattu, ET Sholle, FS Ahmad, J Xu, Z Xu, JS Ancker, F Wang​​, ​Y Luo, ​G Jiang, J Pathak, LV Rasmussen. Towards Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language. Learning Health Systems 2020 doi.org/10.1002/lrh2.10233

  • Rasmussen LV, Hoell C, Smith ME, Chisholm R, Starren J, Aufox S, Luo Y, Rasmussen-Torvik LJ. Solutions for Unexpected Challenges Encountered when Integrating Research Genomics Results into the EHR. ACI Open. 2020 Jul;4(02):e132-5.

  • Y Ma, Y Luo, H Jiang. A Novel Normalization and Differential Abundance Test Framework for Microbiome Data. Bioinformatics (a top bioinformatics journal, IF 6.9) 2020 doi.org/10.1093/bioinformatics/btaa255.

  • Z Xu, J Chou, X Zhang, Y Luo, T Isakova, P Adekkanattu, JS Ancker, G Jiang, RC Kiefer, JA Pacheco, LV Rasmussen. Identifying Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3) 2020 Jan 3:103361.

  • Y Xue, D Klabjan, Y Luo*. Mixture-based Multiple Imputation Model for Clinical Data with a Temporal Dimension. Proceedings of IEEE International Conference on Big Data (a top research conference in big data, acceptance rate 19%) 2019, full paper

  • S Chowdhury, C Zhang, P Yu, Y Luo*. Med2Meta: Learning Representations for Medical Concepts with Meta-Embeddings. Proceedings of 13th International Conference on Health Informatics (a top health informatics conference) 2020, full paper.

2019

  • P Yeh, Y Pan, L. Sanchez-Pinto, Y Luo*. Using Machine Learning to Predict Hyperchloremia in Critically Ill Patients. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (a top research conference in bioinformatics and biomedicine, acceptance rate 19%) 2019, full paper.

  • E Stroup, Y Luo, L Sanchez-Pinto. Phenotyping Multiple Organ Dysfunction Syndrome Using Temporal Trends in Critically Ill Children. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (a top research conference in bioinformatics and biomedicine, acceptance rate 19%) 2019, full paper.

  • N Shang, C Liu, LV Rasmussen, CN Ta, ... Y Luo … WQ Wei. (2019). Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3). 2019 99, 103293. PMID: 31542521

  • Hong N, Wen A, Stone DJ, Tsuji S, Kingsbury PR, Rasmussen LV, Pacheco JA, Adekkanattu P, Wang F, Luo Y, Pathak J. Developing a FHIR-based EHR Phenotyping Framework: A Case Study for Identification of Patients with Obesity and Multiple Comorbidities from Discharge Summaries. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3). 2019 Oct 14:103310. PMID: 31622801

  • L Yao, Z Jin, C Mao, Y Zhang, Y Luo*. Traditional Chinese Medicine Clinical Records Classification with BERT and Domain Specific Corpora​. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2019 doi: 10.1093/jamia/ocz164 PMID: 31550356

  • LV Rasmussen, PS Brandt, G Jiang, RC Kiefer, JA Pacheco, P Adekkanattu, JS Ancker, F Wang, Z Xu, J Pathak, Y Luo*. Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms. Proceedings of AMIA Annual Symposium (a top medical informatics conference) 2019, full paper.

  • P Adekkanattu, G Jiang, Y Luo, PR Kingsbury, Z Xu, LV Rasmussen, JA Pacheco, RC Kiefer, DJ Stone, PS Brandt, L Yao, Y Zhong, Y Deng, F Wang, JS Ancker, TR Campion, J Pathak. Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. Proceedings of AMIA Annual Symposium (a top medical informatics conference) 2019, full paper.

  • Z. Zeng, A. H. Vo, C. Mao, S. E. Clare*, S. A. Khan*, Y. Luo*. Cancer classification and pathway discovery using non-negative matrix factorization. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3), vol. 96, p. 103247, 2019. PMID: 31271844

  • Z Zeng, L Yao, A Roy, X Li, S Espino, S Clare, S Khan, Y Luo*. Identifying Breast Cancer Distant Recurrences from Electronic Health Records Using Machine Learning. Journal of Healthcare Informatics Research 2019 doi: 10.1007/s41666-019-00046-3.

  • L Zimmerman, P Reyfman, A Smith, Z Zeng, N Sanchez-Pinto, A Kho, Y Luo*. Early Prediction of Acute Kidney Injury Following ICU Admission. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8) vol. 19, no. S1, pp. 5-16, 2019. PMID: 30700291; PMCID: PMC6354330.

  • L Yao, C Mao, Y Luo*. Graph Convolutional Networks for Text Classification. Proceedings of AAAI Conference on Artificial Intelligence (a top AI conference, acceptance rate 16%) 2019 Full paper.

  • Z Xu, Y Feng, Y Li, A Srivastava, P Adekkanattu, J Ancker, G Jiang, R Kiefer, K Lee, J Pacheco, L Rasmussen, J Pathak, Y Luo*, F Wang*. Predictive Modeling of the Risk of Acute Kidney Injury in Critical Care: A Systematic Investigation of the Class Imbalance Problem. AMIA Informatics Summit (a top medical informatics conference) 2019 Full paper. PMID: 31259038; PMCID: PMC6568062.

  • Z Zeng, Y Zhao, M Sun, AH Vo, J Starren, Y Luo*. Rich Text Formatted EHR Narratives – A Hidden and Ignored Trove. MedInfo (a top medical informatics conference) 2019 Full paper. PMID: 31437968

  • Z Xu, Y Luo, P Adekkanattu, J Ancker, G Jiang, R Kiefer, J Pacheco, L Rasmussen, J Pathak, F Wang. Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care. MedInfo (a top medical informatics conference) 2019 Full paper. PMID: 31437966

  • M Sun, J Baron, A Dighe, P Szolovits, R Wunderink, T Isakova, Y Luo*. Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes and Structured Multivariate Physiological Measurements. MedInfo (a top medical informatics conference) 2019 Full paper. PMID: 31437947

  • H Wang, Y Li, H Ning, J Wilkins, D Lloyd-Jones, Y Luo*. Using Machine Learning to Integrate Sociobehavioral Factors in Predicting Cardiovascular-Related Mortality Risk. MedInfo (a top medical informatics conference) 2019 Full paper. PMID: 31437960

  • H Sun, R Jin, Y Luo. Supervised Subgraph Augmented Non-Negative Matrix Factorization for Interpretable Manufacturing Time Series Data Analytics. IISE Transactions (a top industrial engineering journal, IF 1.8) 2019:1-21.

  • C Mao, A Eran, Y Luo*. Efficient Genomic Interval Queries Using Augmented Range Trees. Scientific Reports (IF 4.3) 2019: 9:5059 10.1038/s41598-019-41451-3 PMID: 30911095

  • H Sharma, C Mao, Y Zhang, H Vatani, L Yao, Y Zhong, L Rasmussen, G Jiang, J Pathak, Y Luo*. Developing a Portable Natural Language Processing Based Phenotyping System. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8): Vol 19, Suppl 3, 2019. PMID: 30943974

  • L Yao, C Mao, Y Luo*. Clinical Text Classification with Rule-based Features and Knowledge-guided Convolutional Neural Networks. BMC Medical Informatics and Decision Making (a major medical informatics journal IF 2.8): Vol 19, Suppl 3, 2019. PMID: 30943960

  • Y Luo*, C Mao, Y Yang, F Wang, FS Ahmad, D Arnett, MR Irvin, SJ Shah. Integrating Hypertension Phenotype and Genotype with Hybrid Non-negative Matrix Factorization. Bioinformatics (a top bioinformatics journal, IF 6.9): vol. 35, no. 8, pp. 1395-1403, 2019. PMID: 30239588; PMCID: PMC6477985.

2018

  • Y Li, R Jin, Y Luo*. Classifying relations in clinical narratives using Segment Graph Convolutional and Recurrent Neural Networks (Seg-GCRNs). Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2018 26 (3), 262-268 PMID: 30590613, PMID: 30590613; PMCID: PMC6351971.

  • Z Zeng, X Li, S Espino, A Roy, K Kitsch, S Clare, S Khan, X Jiang, R Neapolitan, Y Luo*. Using natural language processing and machine learning to identify breast cancer local recurrence. BMC Bioinformatics (a major bioinformatics journal IF 3.1) 2018 19 (s17): 65-74. PMID: 30591037; PMCID: PMC6309052.

  • G Chao, C Mao, F Wang, Y Zhao, Y Luo*. Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2018 (top research conference in bioinformatics and biomedicine, acceptance rate 19.6%), 1189-1194.

  • C Mao, Y Pan, Z Zeng, L Yao, Y Luo*. Deep Generative Classifiers for Thoracic Disease Diagnosis with Chest X-ray Images. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2018 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%), 1209-1214.

  • Y Zhong, Y Deng L Rasmussen, J Pacheco, M Smith, J Starren, W Wei, P Speltz, J Denny, N Walton, G Hripcsak, C Chute, Y Luo*. Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2018 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%), 1143-1146.

  • Y Li, L Yao, C Mao, A Srivastava, X Jiang, Y Luo*. Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2018 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%), 683-686.

  • Y Luo*, P Szolovits. Implementing a Portable Clinical NLP System with a Common Data Model – a LISP Perspective. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2018 (a top research conference in bioinformatics and biomedicine, acceptance rate 19.6%), 461-466.

  • Z Zeng, X Li, S Espino, A Roy, K Kitsch, S Clare, S Khan, Y Luo*. Using Clinical Narratives and Structured Data To Identify Distant Recurrences in Breast Cancer. Proceedings of IEEE International Conference on Healthcare Informatics (ICHI) 2018, Vol 1 (pp. 44-52), doi: 10.1109/ICHI.2018.00013.

  • X Zhang, L He, K Chen, Y Luo, J Zhou, F Wang. Multi-View Graph Convolutional Network and Its Applications on Neuroimage Analysis for Parkinson's Disease. Proceedings of AMIA Annual Symposium (a top medical informatics conference) 2018, full paper.

  • Y Luo*, Y Cheng, O Uzuner, P Szolovits, J Starren. Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2018 25(1) 93-98, doi: 10.1093/jamia/ocx090 PMID: 29025149, PMCID: PMC6381760.

  • Y Luo, P Szolovits, A Dighe, J Baron. 3D-MICE: Integration of Cross-Sectional and Longitudinal Imputation for Multi-Analyte Longitudinal Clinical Data. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2018 25(6) 645-653: doi: 10.1093/jamia/ocx133. PMID: 29202205

  • Z Zeng, X Jiang, X Li, A Wells, Y Luo, R Neapolitan. Conjugated equine estrogen and medroxyprogesterone acetate are associated with decreased risk of breast cancer relative to bioidentical hormone therapy and controls. PLOS One (IF 2.8) 2018 13.5 e0197064 PMID: 29768475.

  • R Garg, S Prabhakaran, J Holl, Y Luo, R Faigle, K Kording, A Naidech*. Improving the Accuracy of Scores to Predict Gastrostomy after Intracerebral Hemorrhage with Machine Learning. Journal of Stroke and Cerebrovascular Diseases (IF 1.6) 2018 pii: S1052-3057(18)30468-3: PMID: 30201458.

  • C Mao, Y Zhao, M Sun, Y Luo*, Are My EHRs Private Enough? - Event-level Privacy Protection. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB, a major bioinformatics journal IF 3.7) 2018 doi: 10.1109/TCBB.2018.2850037 PMID: 29994487.

  • Y Xue, D Klabjan, Y Luo*, Predicting ICU readmission using grouped physiological and medication trends. Artificial Intelligence in Medicine (AIIM, a top medical informatics journal, IF 5.3) 2018 doi: 10.1016/j.artmed.2018.08.004 PMID: 30213670; PMCID: PMC6474661.

  • Z Zeng, Y Deng, X Li, T Naumann, Y Luo*. Natural Language Processing for EHR-Based Computational Phenotyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB, a major bioinformatics journal IF 3.7) 2018 doi: 10.1109/TCBB.2018.2849968 PMID: 29994486, PMCID: PMC6309052.

  • N Sanchez-Pinto, Y Luo, M Churpek*. Big Data and Data Science in Critical Care. CHEST (a top critical care journal IF 9.4): 2018 May 9. pii: S0012-3692(18)30725-6, doi: 10.1016/j.chest.2018.04.037. PMID: 29752973

2017

  • Z Zeng, X Li, S Espino, A Roy, K Kitsch, S Clare, S Khan, Y Luo*. Contralateral Breast Cancer Event Detection Using Natural Language Processing. Proceedings of AMIA Annual Symposium (a top medical informatics conference) 2017, PMID: 29854260.

  • Y Luo*. Recurrent Neural Networks for Classifying Relations in Clinical Notes. Journal of Biomedical Informatics (JBI, a top medical informatics journal, IF 6.3) 2017 72 85-95 PMID : 28694119

  • Y Luo*, F Ahmed, S Shah. Tensor Factorization for Precision Medicine in Heart Failure with Preserved Ejection Fraction, J. of Cardiovasc. Trans. Res. (IF 4.1) 2017, doi: 10.1007/s12265-016-9727-8 PMCID: 5515683

  • Y Luo*, WK Thompson, TM Herr, Z Zeng, MA Berendsen, SR Jonnalagadda, MB Carson, J Starren. Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review. Drug Safety (a top journal on pharmacoepidemiology and pharmacovigilance IF 5.6) 2017 40 (11) 1075–1089 doi: 10.1007/s40264-017-0558-6. PMID: 28643174

2016

  • Y Luo*, Y Xin, R Joshi, L Celi, P Szolovits. Predicting ICU Mortality Risk by Grouping Temporal Trends from a Multivariate Panel of Physiologic Measurements. Proceedings of AAAI Conference on Artificial Intelligence (a top AI conference, acceptance rate 26%) 2016 (pp. 42-50).

  • Y Luo*, P Szolovits. Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records. Biomedical Informatics Insights 2016:8 29-38, doi: 10.4137/BII.S38916. PMCID: 4954589

  • Y Luo, P Szolovits, A Dighe, J Baron. Using Machine Learning to Predict Laboratory Test Results. American Journal of Clinical Pathology (AJCP, a top clinical pathology journal IF 2.5) 2016 145:778-788 doi: 10.1093/ajcp/aqw064. PMID: 27329638

  • Y Luo*, Ö Uzuner, P Szolovits. Bridging Semantics and Syntax with Graph Algorithms - State-of-the-Art of Extracting Biomedical Relations. Briefings in Bioinformatics (a top bioinformatics journal IF 11.6) 2016 18 (1), 160-178 doi: 10.1093/bib/bbw001. PMCID: 5221425

  • Y Luo*, F Wang, P Szolovits. Tensor Factorization towards Precision Medicine. Briefings in Bioinformatics (a top bioinformatics journal IF 11.6) 2016 18 (3), 511-514 doi: 10.1093/bib/bbw026. PMID: 26994614

2015 and before

  • Y Luo*, Y Xin, E Hochberg, R Joshi, O Uzuner, P Szolovits. Subgraph Augmented Non-Negative Tensor Factorization (SANTF) for Modeling Clinical Text. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2015 22(5) 1009-1019 doi: 10.1093/jamia/ocv016. PMCID: 4986663

  • Y Luo, AR Sohani, Hochberg E, P Szolovits. Automatic Lymphoma Classification with Sentence Subgraph Mining from Pathology Reports. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2014 21(5):824-832. PMCID: 4147603

  • Y Luo, G Riedlinger, P Szolovits. Text Mining in Cancer Gene and Pathway Prioritization. Cancer Informatics 2014 13(S1): 69-79. PMCID: 4216063

  • Y Luo, Ö Uzuner. Semi-Supervised Learning to Identify UMLS Semantic Relations. Proceedings of AMIA Joint Summits (a top medical informatics conference) 2014. PMCID: 4419772

  • Y Luo, T Boucher, T Oral, D Osofsky, S Weber. A Study on Crowdsourcing Enterprise Question Collection and Annotation. Proceedings of Language Resources and Evaluation Conference (LREC, a major natural language processing conference) 2014 (pp. 181-188).

  • Ö Uzuner, T Sibanda, Y Luo, P Szolovits. A De-Identifier for Medical Discharge Summaries. Artificial Intelligence in Medicine (AIIM, a top medical informatics journal IF 5.3) 2008 42(1): 13-35 PMID: 18053696.

  • Ö Uzuner, I Goldstein, Y Luo, I Kohane. Identifying Patient Smoking Status from Medical Discharge Records. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2008 15(1): 14-24. PMCID: 2274873

  • Ö Uzuner, Y Luo, P Szolovits. Evaluating the State-of-the-Art in Automatic De-identification. Journal of the American Medical Informatics Association (JAMIA, a top medical informatics journal, IF 4.5) 2007 14(5): 550-563. PMCID: 1975792