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Research Output 2006 2020

2020

Supervised subgraph augmented non-negative matrix factorization for interpretable manufacturing time series data analytics

Sun, H., Jin, R. & Luo, Y., Jan 2 2020, In : IISE Transactions. 52, 1, p. 120-131 12 p.

Research output: Contribution to journalArticle

Factorization
Time series
Splines
Defects
2019

Cancer classification and pathway discovery using non-negative matrix factorization

Zeng, Z., Vo, A. H., Mao, C., Clare, S. E., Khan, S. A. & Luo, Y., Aug 1 2019, In : Journal of Biomedical Informatics. 96, 103247.

Research output: Contribution to journalArticle

Factorization
Mutation
Neoplasms
Classifiers
Support vector machines

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

Zhong, Y., Rasmussen, L., Deng, Y., Pacheco, J., Smith, M. E., Starren, J. B., Wei, W. Q., Speltz, P., Denny, J., Walton, N., Hripcsak, G., Chute, C. G. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1143-1146 4 p. 8621240. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phenotype
Electronic Health Records
Proxy
Macros
Learning systems
4 Citations (Scopus)
Learning
Dependency (Psychology)
Datasets
4 Citations (Scopus)
Open Access
Learning
Neural Networks (Computer)
Unified Medical Language System
Natural Language Processing
Informatics
1 Citation (Scopus)

Deep Generative Classifiers for Thoracic Disease Diagnosis with Chest X-ray Images

Mao, C., Yao, L., Pan, Y., Luo, Y. & Zeng, Z., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1209-1214 6 p. 8621107. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Thoracic Diseases
Classifiers
Thorax
X-Rays
X rays

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

Hong, N., Wen, A., Stone, D. J., Tsuji, S., Kingsbury, P. R., Rasmussen, L. V., Pacheco, J. A., Adekkanattu, P., Wang, F., Luo, Y., Pathak, J., Liu, H. & Jiang, G., Nov 2019, In : Journal of Biomedical Informatics. 99, 103310.

Research output: Contribution to journalArticle

Interoperability
Comorbidity
Obesity
Delivery of Health Care
Learning systems
2 Citations (Scopus)

Developing a portable natural language processing based phenotyping system

Sharma, H., Mao, C., Zhang, Y., Vatani, H., Yao, L., Zhong, Y., Rasmussen, L., Jiang, G., Pathak, J. & Luo, Y., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 78.

Research output: Contribution to journalArticle

Open Access
Natural Language Processing
Information Systems
Patient Discharge Summaries
Obesity
Unified Medical Language System
2 Citations (Scopus)
Acute Kidney Injury
Intensive Care Units
Critical Care
Creatinine
Logistic Models
2 Citations (Scopus)

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes

Li, Y., Yao, L., Mao, C., Srivastava, A., Jiang, X. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 683-686 4 p. 8621574. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Critical Care
Acute Kidney Injury
Intensive care units
Critical Illness
Supervised learning

Early prediction of acute kidney injury in critical care setting using clinical notes and structured multivariate physiological measurements

Sun, M., Baron, J., Dighe, A., Szolovits, P., Wunderink, R. G., Isakova, T. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 368-372 5 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Intensive care units
Critical Care
Acute Kidney Injury
Supervised learning
Learning systems

Efficient Genomic Interval Queries Using Augmented Range Trees

Mao, C., Eran, A. & Luo, Y., Dec 1 2019, In : Scientific reports. 9, 1, 5059.

Research output: Contribution to journalArticle

Open Access
Genome
Precision Medicine
Population
Datasets
1 Citation (Scopus)

Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective

Luo, Y. & Szolovits, P., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 461-466 6 p. 8621521. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Unified Medical Language System
Search Engine
Semantics
Information Systems
Data structures

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization

Luo, Y., Mao, C., Yang, Y., Wang, F., Ahmad, F. S., Arnett, D., Irvin, M. R. & Shah, S. J., Aug 15 2019, In : Bioinformatics (Oxford, England). 35, 16, 1 p.

Research output: Contribution to journalArticle

Open Access
Non-negative Matrix Factorization
Hypertension
Genotype
Factorization
Phenotype
Non-negative Matrix Factorization
Hypertension
Genotype
Factorization
Phenotype

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization

Luo, Y., Mao, C., Yang, Y., Wang, F., Ahmad, F. S., Arnett, D., Irvin, M. R. & Shah, S. J., Jan 1 2019, In : Bioinformatics. 35, 8, p. 1395-1403 9 p.

Research output: Contribution to journalArticle

Non-negative Matrix Factorization
Hypertension
Genotype
Factorization
Phenotype

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network

Shang, N., Liu, C., Rasmussen, L. V., Ta, C. N., Caroll, R. J., Benoit, B., Lingren, T., Dikilitas, O., Mentch, F. D., Carrell, D. S., Wei, W. Q., Luo, Y., Gainer, V. S., Kullo, I. J., Pacheco, J. A., Hakonarson, H., Walunas, T. L., Denny, J. C., Wiley, K., Murphy, S. N. & 2 others, Hripcsak, G. & Weng, C., Nov 2019, In : Journal of Biomedical Informatics. 99, 103293.

Research output: Contribution to journalArticle

Electronic medical equipment
Electronic Health Records
Genomics
Phenotype
Engineers
4 Citations (Scopus)

Predicting ICU readmission using grouped physiological and medication trends

Xue, Y., Klabjan, D. & Luo, Y., Apr 1 2019, In : Artificial Intelligence In Medicine. 95, p. 27-37 11 p.

Research output: Contribution to journalArticle

Intensive care units
Intensive Care Units
Logistic Models
Statistics
Aptitude

Rich text formatted EHR narratives: A hidden and ignored trove

Zeng, Z., Zhao, Y., Sun, M., Vo, A. H., Starren, J. B. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 472-476 5 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Electronic Health Records
Health
Management Information Systems
Data warehouses
Community Hospital

Stratified mortality prediction of patients with acute kidney injury in critical care

Xu, Z., Luo, Y., Adekkanattu, P., Ancker, J. S., Jiang, G., Kiefer, R. C., Pacheco, J. A., Rasmussen, L. V., Pathak, J. & Wang, F., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 462-466 5 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Critical Care
Acute Kidney Injury
Mortality
Learning systems
Critical Illness
1 Citation (Scopus)

Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk

Chao, G., Mao, C., Wang, F., Zhao, Y. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1189-1194 6 p. 8621403. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Intensive care units
Factorization
Mortality
Logistics
Time series

Traditional Chinese medicine clinical records classification with BERT and domain specific corpora

Yao, L., Jin, Z., Mao, C., Zhang, Y. & Luo, Y., Nov 15 2019, In : Journal of the American Medical Informatics Association. 26, 12, p. 1632-1636 5 p.

Research output: Contribution to journalArticle

Chinese Traditional Medicine
Learning
Benchmarking
Language
Delivery of Health Care

Using machine learning to integrate socio-behavioral factors in predicting cardiovascular-related mortality risk

Wang, H., Li, Y., Ning, H., Wilkins, J. T., Lloyd-Jones, D. M. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 433-437 5 p. (Studies in Health Technology and Informatics; vol. 264).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Learning systems
Mortality
Learning algorithms
Cardiovascular Diseases
Early Diagnosis
2018
23 Citations (Scopus)

3D-MICE: Integration of cross-sectional and longitudinal imputation for multi-analyte longitudinal clinical data

Luo, Y., Szolovits, P., Dighe, A. S. & Baron, J. M., Jun 1 2018, In : Journal of the American Medical Informatics Association. 25, 6, p. 645-653 9 p.

Research output: Contribution to journalArticle

Clinical Decision Support Systems
Data Mining
Datasets
Machine Learning

Are My EHRs Private Enough? - Event-level Privacy Protection

Mao, C., Zhao, Y., Sun, M. & Luo, Y., 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. p. 2850037 1 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Big Data and Data Science in Critical Care

Sanchez-Pinto, L. N., Luo, Y. & Churpek, M. M., Nov 2018, In : CHEST. 154, 5, p. 1239-1248 10 p.

Research output: Contribution to journalReview article

Critical Care
Growth
Information Systems
Critical Illness
Publications
4 Citations (Scopus)

Clinical Text Classification with Rule-based Features and Knowledge-guided Convolutional Neural Networks

Yao, L., Mao, C. & Luo, Y., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 70-71 2 p. 8411810. (Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Learning
Natural Language Processing
Informatics
Obesity
Neural networks
2 Citations (Scopus)

Conjugated equine estrogen and medroxyprogesterone acetate are associated with decreased risk of breast cancer relative to bioidentical hormone therapy and controls

Zeng, Z., Jiang, X., Li, X., Wells, A., Luo, Y. & Neapolitan, R. E., May 2018, In : PloS one. 13, 5, e0197064.

Research output: Contribution to journalArticle

medroxyprogesterone
Conjugated (USP) Estrogens
Medroxyprogesterone Acetate
risk reduction
breast neoplasms
2 Citations (Scopus)

Improving the Accuracy of Scores to Predict Gastrostomy after Intracerebral Hemorrhage with Machine Learning

Garg, R., Prabhakaran, S., Holl, J. L., Luo, Y., Faigle, R., Kording, K. & Naidech, A. M., Dec 2018, In : Journal of Stroke and Cerebrovascular Diseases. 27, 12, p. 3570-3574 5 p.

Research output: Contribution to journalArticle

Gastrostomy
Cerebral Hemorrhage
Area Under Curve
Logistic Models
Glasgow Coma Scale

Local Breast Recurrence Detection Using Nature Language Processing

Zeng, Z., Li, X., Espino, S., Roy, A., Kitsch, K., Clare, S., Khan, S., Jiang, X., Neapolitan, R. & Luo, Y., 2018, In : BMC Bioinformatics.

Research output: Contribution to journalArticle

Multi-View Graph Convolutional Network and Its Applications on Neuroimage Analysis for Parkinson's Disease

Zhang, X., He, L., Chen, K., Luo, Y., Zhou, J. & Wang, F., Jan 1 2018, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2018, p. 1147-1156 10 p.

Research output: Contribution to journalArticle

Parkinson Disease
Neurodegenerative Diseases
Area Under Curve
Passive Cutaneous Anaphylaxis
Neuroimaging
5 Citations (Scopus)

Natural Language Processing for EHR-Based Computational Phenotyping

Zeng, Z., Deng, Y., Li, X., Naumann, T. & Luo, Y., 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. p. 2849968 1 p.

Research output: Contribution to journalArticle

Portable Phenotyping System: A Portable Machine-Learning Approach to i2b2 Obesity Challenge

Sharma, H., Mao, C., Zhang, Y., Vatani, H., Yao, L., Zhong, Y., Rasmussen, L., Jiang, G., Pathak, J. & Luo, Y., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 86-87 2 p. 8411818. (Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Patient Discharge Summaries
Obesity
Unified Medical Language System
Information Systems
Comorbidity
16 Citations (Scopus)

Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes

Luo, Y., Cheng, Y., Uzuner, Ö., Szolovits, P. & Starren, J. B., Jan 1 2018, In : Journal of the American Medical Informatics Association. 25, 1, p. 93-98 6 p., ocx090.

Research output: Contribution to journalArticle

Learning
Datasets
2 Citations (Scopus)

Using clinical narratives and structured data to identify distant recurrences in breast cancer

Zexian, Z., Ankita, R., Xiaoyu, L., Sasa, E., Clare, S. E., Khan, S. A. & Luo, Y., Jul 24 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics, ICHI 2018. Institute of Electrical and Electronics Engineers Inc., p. 44-52 9 p. 8419346. (Proceedings - 2018 IEEE International Conference on Healthcare Informatics, ICHI 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Breast Neoplasms
Electronic Health Records
Recurrence
Health
Area Under Curve
6 Citations (Scopus)

Using natural language processing and machine learning to identify breast cancer local recurrence

Zeng, Z., Espino, S., Roy, A., Li, X., Khan, S. A., Clare, S. E., Jiang, X., Neapolitan, R. & Luo, Y., Dec 28 2018, In : BMC bioinformatics. 19, 498.

Research output: Contribution to journalArticle

Natural Language Processing
Breast Cancer
Recurrence
Natural Language
Learning systems
2017
18 Citations (Scopus)

Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations

Luo, Y., Uzuner, Ö. & Szolovits, P., Jan 1 2017, In : Briefings in Bioinformatics. 18, 1, p. 160-178 19 p.

Research output: Contribution to journalArticle

Semantics
Bridge approaches
Research
Medical Informatics
Pharmacogenetics
4 Citations (Scopus)

Contralateral Breast Cancer Event Detection Using Nature Language Processing

Zeng, Z., Li, X., Espino, S., Roy, A., Kitsch, K., Clare, S. E., Khan, S. A. & Luo, Y., Jan 1 2017, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2017, p. 1885-1892 8 p.

Research output: Contribution to journalArticle

Language
Breast Neoplasms
Pathology
Area Under Curve
Cohort Studies
1 Citation (Scopus)
Bioinformatics
Computational Biology
Semantics
28 Citations (Scopus)

Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review

Luo, Y., Thompson, W. K., Herr, T. M., Zeng, Z., Berendsen, M. A., Jonnalagadda, S. R., Carson, M. B. & Starren, J. B., Nov 1 2017, In : Drug Safety. 40, 11, p. 1075-1089 15 p.

Research output: Contribution to journalReview article

Natural Language Processing
Pharmacovigilance
Electronic Health Records
Drug-Related Side Effects and Adverse Reactions
Health
35 Citations (Scopus)

Recurrent neural networks for classifying relations in clinical notes

Luo, Y., Aug 2017, In : Journal of Biomedical Informatics. 72, p. 85-95 11 p.

Research output: Contribution to journalArticle

Recurrent neural networks
Medical problems
Long-Term Memory
Short-Term Memory
12 Citations (Scopus)
Precision Medicine
Heart Failure
State Medicine
Uncertainty
Therapeutics
18 Citations (Scopus)

Tensor factorization toward precision medicine

Luo, Y., Wang, F. & Szolovits, P., May 1 2017, In : Briefings in Bioinformatics. 18, 3, p. 511-514 4 p.

Research output: Contribution to journalComment/debate

Precision Medicine
Factorization
Medicine
Tensors
Scalability
2016

Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records

Luo, Y. & Szolovits, P., 2016, In : Biomedical Informatics Insights. 8, p. 29-38 10 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Predicting ICU mortality risk by grouping temporal trends from a multivariate panel of physiologic measurements

Luo, Y., Xin, Y., Joshi, R., Celi, L. & Szolovits, P., Jan 1 2016, 30th AAAI Conference on Artificial Intelligence, AAAI 2016. AAAI press, p. 42-50 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Intensive care units
Factorization
Learning systems
Time series
Logistics
22 Citations (Scopus)

Using machine learning to predict laboratory test results

Luo, Y., Szolovits, P., Dighe, A. S. & Baron, J. M., Jun 1 2016, In : American Journal of Clinical Pathology. 145, 6, p. 778-788 11 p.

Research output: Contribution to journalArticle

Ferritins
Clinical Decision Support Systems
Clinical Laboratory Techniques
Area Under Curve
Machine Learning
2015
22 Citations (Scopus)

Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text

Luo, Y., Xin, Y., Hochberg, E., Joshi, R., Uzuner, O. & Szolovits, P., Jan 1 2015, In : Journal of the American Medical Informatics Association. 22, 5, p. 1009-1019 11 p.

Research output: Contribution to journalArticle

Cluster Analysis
Medical Electronics
Selection Bias
Electronic Health Records
Learning
2014
1 Citation (Scopus)

A study on expert sourcing enterprise question collection and classification

Luo, Y., Boucher, T., Oral, T., Osofsky, D. & Weber, S., Jan 1 2014, Proceedings of the 9th International Conference on Language Resources and Evaluation, LREC 2014. Calzolari, N., Choukri, K., Goggi, S., Declerck, T., Mariani, J., Maegaard, B., Moreno, A., Odijk, J., Mazo, H., Piperidis, S. & Loftsson, H. (eds.). European Language Resources Association (ELRA), p. 181-188 8 p. (Proceedings of the 9th International Conference on Language Resources and Evaluation, LREC 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

expert
sales
ability
Enterprise
Sourcing
31 Citations (Scopus)

Automatic lymphoma classification with sentence subgraph mining from pathology reports

Luo, Y., Sohani, A. R., Hochberg, E. P. & Szolovits, P., Jan 1 2014, In : Journal of the American Medical Informatics Association. 21, 5, p. 824-832 9 p.

Research output: Contribution to journalArticle

Lymphoma
Pathology
Unified Medical Language System
Follicular Lymphoma
Burkitt Lymphoma