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Research Output

2020

Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks

Xu, Z., Chou, J., Zhang, X. S., Luo, Y., Isakova, T., Adekkanattu, P., Ancker, J. S., Jiang, G., Kiefer, R. C., Pacheco, J. A., Rasmussen, L. V., Pathak, J. & Wang, F., Feb 2020, In : Journal of Biomedical Informatics. 102, 103361.

Research output: Contribution to journalArticle

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

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 2019, In : Journal of Biomedical Informatics. 96, 103247.

Research output: Contribution to journalArticle

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

5 Scopus citations
Open Access
6 Scopus citations

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

1 Scopus citations

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

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
2 Scopus citations
4 Scopus citations

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

2 Scopus citations

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

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

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

1 Scopus citations

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

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

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

Mixture-based Multiple Imputation Model for Clinical Data with a Temporal Dimension

Xue, Y., Klabjan, D. & Luo, Y., Dec 2019, Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019. Baru, C., Huan, J., Khan, L., Hu, X. T., Ak, R., Tian, Y., Barga, R., Zaniolo, C., Lee, K. & Ye, Y. F. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 245-252 8 p. 9005672. (Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019).

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

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

6 Scopus citations

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

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

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

1 Scopus citations

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

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

2018

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

24 Scopus citations

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

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

29 Scopus citations

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

5 Scopus citations

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

2 Scopus citations

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

2 Scopus citations

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

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

6 Scopus citations

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

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

17 Scopus citations

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

2 Scopus citations

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

6 Scopus citations
2017

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

19 Scopus citations

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

4 Scopus citations
1 Scopus citations

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

33 Scopus citations

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

36 Scopus citations
12 Scopus citations

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

18 Scopus citations
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

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

23 Scopus citations

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

24 Scopus citations
2015

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

22 Scopus citations
2014

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

1 Scopus citations