• 4450 Citations
  • 36 Scopus h-Index
19992019

Research output per year

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Research Output

2019
4 Scopus citations

Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility

Zhao, Y., Wang, Y., Wang, H., Yan, B., Shen, F., Peterson, K. J., Rocca, W. A., St. Sauver, J. & Liu, H. D., 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. 1310-1317 8 p. 8621269. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

A privacy-preserving distributed filtering framework for NLP artifacts

Sadat, M. N., Aziz, M. M. A., Mohammed, N., Pakhomov, S., Liu, H. D. & Jiang, X., Sep 7 2019, In : BMC Medical Informatics and Decision Making. 19, 1, 183.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing

Moon, S., Liu, S., Scott, C. G., Samudrala, S., Abidian, M. M., Geske, J. B., Noseworthy, P., Shellum, J. L., Chaudhry, R., Ommen, S. R., Nishimura, R. A., Liu, H. D. & Arruda-Olson, A. M., Aug 1 2019, In : International Journal of Medical Informatics. 128, p. 32-38 7 p.

Research output: Contribution to journalArticle

Open Access
2 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 customizable cancer information extraction modules for pathology reports using clamp

Soysal, E., Warner, J. L., Wang, J., Jiang, M., Harvey, K., Jain, S. K., Dong, X., Song, H. Y., Siddhanamatha, H., Wang, L., Dai, Q., Chen, Q., Du, X., Tao, C., Yang, P., Denny, J. C., Liu, H. D. & Xu, H., 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. 1041-1045 5 p. (Studies in Health Technology and Informatics; vol. 264).

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

Discovering associations between problem list and practice setting

Wang, L., Wang, Y., Shen, F., Rastegar-Mojarad, M. & Liu, H. D., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 69.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Early identification of childhood asthma: The role of informatics in an era of electronic health records

Seol, H. Y., Sohn, S., Liu, H. D., Wi, C. I., Ryu, E., Park, M. & Juhn, Y. J., Jan 1 2019, In : Frontiers in Pediatrics. 7, APR, 113.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

Ensembles of natural language processing systems for portable phenotyping solutions

Liu, C., Ta, C. N., Rogers, J. R., Li, Z., Lee, J., Butler, A. M., Shang, N., Kury, F. S. P., Wang, L., Shen, F., Liu, H., Ena, L., Friedman, C. & Weng, C., Dec 2019, In : Journal of Biomedical Informatics. 100, 103318.

Research output: Contribution to journalArticle

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology

Shen, F., Peng, S., Fan, Y., Wen, A., Liu, S., Wang, Y., Wang, L. & Liu, H., Aug 2019, In : Journal of Biomedical Informatics. 96, 103246.

Research output: Contribution to journalArticle

1 Scopus citations

Integrating word embedding neural networks with pubmed abstracts to extract keyword proximity of chronic diseases

Tafti, A. P., Wang, Y., Shen, F., Sagheb, E., Kingsbury, P. & Liu, H., May 2019, 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 8834626. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).

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

Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome

Peng, S., Fan, Y., Wang, L., Wen, A., Liu, X., Liu, H. D. & Shen, F., 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. 1302-1309 8 p. 8621226. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

2 Scopus citations

Natural language processing for the identification of silent brain infarcts from neuroimaging reports

Fu, S., Leung, L. Y., Wang, Y., Raulli, A. O., Kallmes, D. F., Kinsman, K. A., Nelson, K. B., Clark, M. S., Luetmer, P. H., Kingsbury, P. R., Kent, D. M. & Liu, H. D., May 1 2019, In : Journal of medical Internet research. 21, 5, e12109.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Natural language processing of radiology reports for identification of skeletal site-specific fractures

Wang, Y., Mehrabi, S., Sohn, S., Atkinson, E. J., Amin, S. & Liu, H. D., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 73.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Overview of the BioCreative VI Precision Medicine Track: Mining protein interactions and mutations for precision medicine

Islamaj Doǧan, R., Kim, S., Chatr-Aryamontri, A., Wei, C. H., Comeau, D. C., Antunes, R., Matos, S., Chen, Q., Elangovan, A., Panyam, N. C., Verspoor, K., Liu, H. D., Wang, Y., Liu, Z., Altlnel, B., Hüsünbeyi, Z. M., Özgür, A., Fergadis, A., Wang, C. K., Dai, H. J. & 7 others, Tran, T., Kavuluru, R., Luo, L., Steppi, A., Zhang, J., Qu, J. & Lu, Z., Jan 28 2019, In : Database. 2019

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine

Gonzalez-Hernandez, G., Lu, Z., Leaman, R., Weissenbacher, D., Boland, M. R., Chen, Y., Du, J., Fluck, J., Greene, C. S., Holmes, J., Kashyap, A., Nielsen, R. L., Ouyang, Z., Schaaf, S., Taroni, J. N., Tao, C., Zhang, Y. & Liu, H. D., Jan 1 2019, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 24, p. 449-454 6 p.

Research output: Contribution to journalArticle

Rare disease knowledge enrichment through a data-driven approach

Shen, F., Zhao, Y., Wang, L., Mojarad, M. R., Wang, Y., Liu, S. & Liu, H. D., Feb 14 2019, In : BMC Medical Informatics and Decision Making. 19, 1, 752.

Research output: Contribution to journalArticle

4 Scopus citations

Relationship between very cold outside weather and surgical outcome: Integrating shallow and deep artificial neural nets

Tafti, A. P., Dong, Y., Habermann, E. B., Liu, H. D. & Herasevich, V. D., 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. 1783-1784 2 p. (Studies in Health Technology and Informatics; vol. 264).

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

A Comparison of Lifestyle Interventions for Alzheimer's Disease Extracted from Clinical Notes and Literature

Zhou, X., Liu, H. D. & Wang, Y., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 74-75 2 p. 8411812

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

A comparison of word embeddings for the biomedical natural language processing

Wang, Y., Liu, S., Afzal, N., Rastegar-Mojarad, M., Wang, L., Shen, F., Kingsbury, P. & Liu, H. D., Nov 1 2018, In : Journal of Biomedical Informatics. 87, p. 12-20 9 p.

Research output: Contribution to journalArticle

41 Scopus citations

Advances in text mining and visualization for precision medicine

Gonzalez-Hernandez, G., Sarker, A., O’Connor, K., Greene, C. & Liu, H. D., Jan 1 2018, PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018. 212669 ed. World Scientific Publishing Co. Pte Ltd, p. 559-565 7 p.

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

1 Scopus citations

Ascertainment of asthma prognosis using natural language processing from electronic medical records

Sohn, S., Wi, C. I., Wu, S. T., Liu, H. D., Ryu, E., Krusemark, E., Seabright, A., Voge, G. A. & Juhn, Y. J., Jan 1 2018, (Accepted/In press) In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticle

5 Scopus citations
3 Scopus citations

Association of Ankle-Brachial Indices With Limb Revascularization or Amputation in Patients With Peripheral Artery Disease

Moussa Pacha, H., Mallipeddi, V. P., Afzal, N., Moon, S., Kaggal, V. C., Kalra, M., Oderich, G., Wennberg, P. W., Rooke, T. W., Scott, C. G., Kullo, I. J., McBane, R. D., Nishimura, R. A., Chaudhry, R., Liu, H. D. & Arruda-Olson, A. M., Dec 7 2018, In : JAMA Network Open. 1, 8, p. e185547

Research output: Contribution to journalArticle

Open Access

Automated chart review utilizing natural language processing algorithm for asthma predictive index

Kaur, H., Sohn, S., Wi, C. I., Ryu, E., Park, M., Bachman, K., Kita, H., Croghan, I. T., Castro-Rodriguez, J. A., Voge, G. A., Liu, H. D. & Juhn, Y. J., Feb 13 2018, In : BMC Pulmonary Medicine. 18, 1, 34.

Research output: Contribution to journalArticle

9 Scopus citations

Automatic Extraction of Major Osteoporotic Fractures from Radiology Reports using Natural Language Processing

Wang, Y., Mehrabi, S., Sohn, S., Atkinson, E., Amin, S. & Liu, H. D., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 64-65 2 p. 8411807

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

BioCreative/OHNLP Challenge 2018

Rastegar-Mojarad, M., Liu, S., Wang, Y., Afzal, N., Wang, L., Shen, F., Fu, S. & Liu, H. D., Aug 15 2018, ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 1 p.

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

1 Scopus citations

Burden of hospitalization in clinically diagnosed peripheral artery disease: A community-based study

Arruda-Olson, A. M., Moussa Pacha, H., Afzal, N., Abram, S., Lewis, B. R., Isseh, I., Haddad, R., Scott, C. G., Bailey, K. R., Liu, H. D., Rooke, T. W. & Kullo, I. J., Feb 1 2018, In : Vascular Medicine (United Kingdom). 23, 1, p. 23-31 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines

Soysal, E., Wang, J., Jiang, M., Wu, Y., Pakhomov, S., Liu, H. D. & Xu, H., Mar 1 2018, In : Journal of the American Medical Informatics Association. 25, 3, p. 331-336 6 p.

Research output: Contribution to journalArticle

23 Scopus citations

Clinical documentation variations and NLP system portability: A case study in asthma birth cohorts across institutions

Sohn, S., Wang, Y., Wi, C. I., Krusemark, E. A., Ryu, E., Ali, M. H., Juhn, Y. J. & Liu, H. D., Mar 1 2018, In : Journal of the American Medical Informatics Association. 25, 3, p. 353-359 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

Clinical information extraction applications: A literature review

Wang, Y., Wang, L., Rastegar-Mojarad, M., Moon, S., Shen, F., Afzal, N., Liu, S., Zeng, Y., Mehrabi, S., Sohn, S. & Liu, H. D., Jan 1 2018, In : Journal of Biomedical Informatics. 77, p. 34-49 16 p.

Research output: Contribution to journalReview article

81 Scopus citations

Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement

Shen, F., Liu, S., Wang, Y., Wang, L., Wen, A., Limper, A. H. & Liu, H. D., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 29-33 5 p. 8411677

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

3 Scopus citations

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes

Son, J. H., Xie, G., Yuan, C., Ena, L., Li, Z., Goldstein, A., Huang, L., Wang, L., Shen, F., Liu, H. D., Mehl, K., Groopman, E. E., Marasa, M., Kiryluk, K., Gharavi, A. G., Chung, W. K., Hripcsak, G., Friedman, C., Weng, C. & Wang, K., Jul 5 2018, In : American Journal of Human Genetics. 103, 1, p. 58-73 16 p.

Research output: Contribution to journalArticle

19 Scopus citations

Detecting pharmacovigilance signals combining electronic medical records with spontaneous reports: A case study of conventional disease-modifying antirheumatic drugs for rheumatoid arthritis

Wang, L., Rastegar-Mojarad, M., Ji, Z., Liu, S., Liu, K., Moon, S., Shen, F., Wang, Y., Yao, L., Davis, J. M. III. & Liu, H. D., Aug 7 2018, In : Frontiers in Pharmacology. 9, AUG, 875.

Research output: Contribution to journalArticle

2 Scopus citations

Electronic Health Record Phenotypes for Precision Medicine: Perspectives and Caveats From Treatment of Breast Cancer at a Single Institution

Breitenstein, M. K., Liu, H. D., Maxwell, K. N., Pathak, J. & Zhang, R., Jan 1 2018, In : Clinical and Translational Science. 11, 1, p. 85-92 8 p.

Research output: Contribution to journalArticle

5 Scopus citations

Extracting chemical-protein relations using attention-based neural networks

Liu, S., Shen, F., Komandur Elayavilli, R., Wang, Y., Rastegar-Mojarad, M., Chaudhary, V. & Liu, H. D., Jan 1 2018, In : Database : the journal of biological databases and curation. 2018

Research output: Contribution to journalArticle

3 Scopus citations

Identification of Genetic Causality Statements in Medline Abstracts Leveraging Distant Supervision

Wang, L., Rastegar-Mojarad, M., Komandur Elayavilli, R. K. E., Wang, Y. & Liu, H. D., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 1-8 8 p. 8411674

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

Impact of Patient Reminders on Papanicolaou Test Completion for High-Risk Patients Identified by a Clinical Decision Support System

Mac Laughlin, K., Kessler, M. E., Komandur Elayavilli, R., Hickey, B. C., Scheitel, M. R., Wagholikar, K. B., Liu, H. D., Kremers, W. K. & Chaudhry, R., May 1 2018, In : Journal of Women's Health. 27, 5, p. 569-574 6 p.

Research output: Contribution to journalArticle

2 Scopus citations

Improving the Accuracy of a Clinical Decision Support System for Cervical Cancer Screening and Surveillance

Ravikumar, K. E., Mac Laughlin, K., Scheitel, M. R., Kessler, M., Wagholikar, K. B., Liu, H. D. & Chaudhry, R., Jan 1 2018, In : Applied Clinical Informatics. 9, 1, p. 62-71 10 p.

Research output: Contribution to journalArticle

1 Scopus citations
1 Scopus citations

Leveraging the electronic health record to create an automated real-time prognostic tool for peripheral arterial disease

Arruda-Olson, A. M., Afzal, N., Mallipeddi, V. P., Said, A., Pacha, H. M., Moon, S., Chaudhry, A. P., Scott, C. G., Bailey, K. R., Rooke, T. W., Wennberg, P. W., Kaggal, V. C., Oderich, G., Kullo, I. J., Nishimura, R. A., Chaudhry, R. & Liu, H. D., Dec 1 2018, In : Journal of the American Heart Association. 7, 23, e009680.

Research output: Contribution to journalArticle

2 Scopus citations

MedSTS: a resource for clinical semantic textual similarity

Wang, Y., Afzal, N., Fu, S., Wang, L., Shen, F., Rastegar-Mojarad, M. & Liu, H. D., Jan 1 2018, (Accepted/In press) In : Language Resources and Evaluation.

Research output: Contribution to journalArticle

2 Scopus citations

Modeling asynchronous event sequences with RNNs

Wu, S., Liu, S., Sohn, S., Moon, S., Wi, C. I., Juhn, Y. J. & Liu, H. D., Jul 1 2018, In : Journal of Biomedical Informatics. 83, p. 167-177 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Natural language processing of clinical notes for identification of critical limb ischemia

Afzal, N., Mallipeddi, V. P., Sohn, S., Liu, H. D., Chaudhry, R., Scott, C. G., Kullo, I. J. & Arruda-Olson, A. M., Mar 1 2018, In : International Journal of Medical Informatics. 111, p. 83-89 7 p.

Research output: Contribution to journalArticle

14 Scopus citations

Postoperative bleeding risk prediction for patients undergoing colorectal surgery

Chen, D., Afzal, N., Sohn, S., Habermann, E. B., Naessens, J. M., Larson, D. & Liu, H. D., Jan 1 2018, (Accepted/In press) In : Surgery (United States).

Research output: Contribution to journalArticle

Predicting Practice Setting Using Topic Modeling

Wang, L., Wang, Y., Shen, F., Rastegar-Mojarad, M. & Liu, H. D., Jul 16 2018, Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. Institute of Electrical and Electronics Engineers Inc., p. 62-63 2 p. 8411806

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

Preliminary exploration of survival analysis using the OHDSI common data model: A case study of intrahepatic cholangiocarcinoma

Hong, N., Zhang, N., Wu, H., Lu, S., Yu, Y., Hou, L., Lu, Y., Liu, H. D. & Jiang, G. D., Dec 7 2018, In : BMC Medical Informatics and Decision Making. 18, 116.

Research output: Contribution to journalArticle

1 Scopus citations
1 Scopus citations