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Journal Articles
- 2025
[j47]Braja Gopal Patra
, Lauren A. Lepow, Praneet Kasi Reddy Jagadeesh Kumar, Veer Vekaria, Mohit Manoj Sharma, Prakash Adekkanattu, Brian Fennessy, Gavin Hynes, Isotta Landi, Jorge A. Sanchez-Ruiz, Euijung Ryu, Joanna M. Biernacka, Girish N. Nadkarni, Ardesheer Talati, Myrna Weissman, Mark Olfson, J. John Mann, Yiye Zhang, Alexander W. Charney, Jyotishman Pathak:
Extracting social support and social isolation information from clinical psychiatry notes: comparing a rule-based natural language processing system and a large language model. J. Am. Medical Informatics Assoc. 32(1): 218-226 (2025)- 2024
- [j46]Pooja M. Desai, Sarah Harkins, Saanjaana Rahman, Shiveen Kumar, Alison Hermann, Rochelle Joly, Yiye Zhang, Jyotishman Pathak, Jessica Kim, Deborah D'angelo, Natalie C. Benda, Meghan Reading Turchioe:
Visualizing machine learning-based predictions of postpartum depression risk for lay audiences. J. Am. Medical Informatics Assoc. 31(2): 289-297 (2024) - [j45]Yifan Liu, Rochelle Joly, Meghan Reading Turchioe, Natalie C. Benda, Alison Hermann, Ashley Beecy, Jyotishman Pathak, Yiye Zhang:
Preparing for the bedside - optimizing a postpartum depression risk prediction model for clinical implementation in a health system. J. Am. Medical Informatics Assoc. 31(6): 1258-1267 (2024) - [j44]Zehao Yu, Cheng Peng, Xi Yang, Chong Dang, Prakash Adekkanattu, Braja Gopal Patra, Yifan Peng, Jyotishman Pathak, Debbie L. Wilson, Ching-Yuan Chang, Wei-Hsuan Lo-Ciganic, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu:
Identifying social determinants of health from clinical narratives: A study of performance, documentation ratio, and potential bias. J. Biomed. Informatics 153: 104642 (2024) - [j43]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, Theresa L. Walunas, Wei-Hsuan Lo-Ciganic, Walid Gelad, Jiang Bian, Yuhua Bao, Mark G. Weiner, David W. Oslin, Jyotishman Pathak:
Deep learning for identifying personal and family history of suicidal thoughts and behaviors from EHRs. npj Digit. Medicine 7(1) (2024) - 2023
- [j42]Pascal S. Brandt, Abel N. Kho, Yuan Luo, Jennifer A. Pacheco, Theresa L. Walunas, Hakon Hakonarson, George Hripcsak, Cong Liu, Ning Shang, Chunhua Weng, Nephi Walton, David S. Carrell, Paul K. Crane, Eric B. Larson, Christopher G. Chute, Iftikhar J. Kullo, Robert J. Carroll, Joshua C. Denny, Andrea H. Ramirez, Wei-Qi Wei, Jyotishman Pathak, Laura K. Wiley, Rachel L. Richesson, Justin B. Starren, Luke V. Rasmussen:
Characterizing variability of electronic health record-driven phenotype definitions. J. Am. Medical Informatics Assoc. 30(3): 427-437 (2023) - [j41]Song Wang, Yifang Dang, Zhaoyi Sun, Ying Ding, Jyotishman Pathak, Cui Tao, Yunyu Xiao, Yifan Peng:
An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. J. Am. Medical Informatics Assoc. 30(8): 1408-1417 (2023) - [j40]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Yikuan Li, Prakash Adekkanattu, Jennifer A. Pacheco, Borna Bonakdarpour, Robert Vassar, Li Shen, Guoqian Jiang, Fei Wang, Jyotishman Pathak, Yuan Luo:
AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. J. Biomed. Informatics 144: 104442 (2023) - 2022
- [j39]Thomas R. Campion Jr., Evan Sholle, Jyotishman Pathak, Stephen B. Johnson, John P. Leonard, Curtis L. Cole:
An architecture for research computing in health to support clinical and translational investigators with electronic patient data. J. Am. Medical Informatics Assoc. 29(4): 677-685 (2022) - [j38]Pascal S. Brandt, Jennifer A. Pacheco, Prakash Adekkanattu, Evan Sholle, Sajjad Abedian, Daniel J. Stone, David Knaack, Jie Xu, Zhenxing Xu, Yifan Peng, Natalie C. Benda, Fei Wang, Yuan Luo, Guoqian Jiang, Jyotishman Pathak, Luke V. Rasmussen:
Design and validation of a FHIR-based EHR-driven phenotyping toolbox. J. Am. Medical Informatics Assoc. 29(9): 1449-1460 (2022) - 2021
- [j37]Yufang Huang, Yifan Liu, Peter A. D. Steel, Kelly M. Axsom, John R. Lee, Sri Lekha Tummalapalli, Fei Wang, Jyotishman Pathak, Lakshminarayanan Subramanian, Yiye Zhang:
Deep significance clustering: a novel approach for identifying risk-stratified and predictive patient subgroups. J. Am. Medical Informatics Assoc. 28(12): 2641-2653 (2021) - [j36]Braja Gopal Patra, Mohit Manoj Sharma, Veer Vekaria, Prakash Adekkanattu, Olga V. Patterson, Benjamin S. Glicksberg, Lauren A. Lepow, Euijung Ryu, Joanna M. Biernacka, Al'ona Furmanchuk, Thomas J. George, William R. Hogan, Yonghui Wu, Xi Yang, Jiang Bian, Myrna Weissman, Priya Wickramaratne, J. John Mann, Mark Olfson, Thomas R. Campion Jr., Mark G. Weiner, Jyotishman Pathak:
Extracting social determinants of health from electronic health records using natural language processing: a systematic review. J. Am. Medical Informatics Assoc. 28(12): 2716-2727 (2021) - 2020
- [j35]Zhenxing Xu, Jingyuan Chou, Xi Sheryl Zhang, Yuan Luo, Tamara Isakova, Prakash Adekkanattu, Jessica S. Ancker, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Luke V. Rasmussen, Jyotishman Pathak, Fei Wang:
Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks. J. Biomed. Informatics 102: 103361 (2020) - 2019
- [j34]Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang:
Drug knowledge bases and their applications in biomedical informatics research. Briefings Bioinform. 20(4): 1308-1321 (2019) - [j33]Evan Sholle, Laura C. Pinheiro, Prakash Adekkanattu, Marcos Davila, Stephen B. Johnson, Jyotishman Pathak, Sanjai Sinha, Cassidie Li, Stasi A Lubansky, Monika M. Safford, Thomas R. Campion Jr.:
Underserved populations with missing race ethnicity data differ significantly from those with structured race/ethnicity documentation. J. Am. Medical Informatics Assoc. 26(8-9): 722-729 (2019) - [j32]Joseph J. DeFerio, Scott Breitinger, Dhruv Khullar, Amit P. Sheth, Jyotishman Pathak:
Social determinants of health in mental health care and research: a case for greater inclusion. J. Am. Medical Informatics Assoc. 26(8-9): 895-899 (2019) - [j31]Na Hong, Andrew Wen, Daniel J. Stone, Shintaro Tsuji, Paul R. Kingsbury, Luke V. Rasmussen, Jennifer A. Pacheco, Prakash Adekkanattu, Fei Wang, Yuan Luo, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J. Biomed. Informatics 99 (2019) - [j30]Himanshu Sharma, Chengsheng Mao, Yizhen Zhang, Haleh Vatani, Liang Yao, Yizhen Zhong, Luke V. Rasmussen, Guoqian Jiang, Jyotishman Pathak, Yuan Luo:
Developing a portable natural language processing based phenotyping system. BMC Medical Informatics Decis. Mak. 19-S(3): 79-87 (2019) - 2018
- [j29]Jessica S. Ancker, Min-hyung Kim, Yiye Zhang, Yongkang Zhang, Jyotishman Pathak:
The potential value of social determinants of health in predicting health outcomes. J. Am. Medical Informatics Assoc. 25(8): 1109-1110 (2018) - [j28]Jennifer A. Pacheco, Luke V. Rasmussen, Richard C. Kiefer, Thomas R. Campion Jr., Peter Speltz, Robert J. Carroll, Sarah C. Stallings, Huan Mo, Monika Ahuja, Guoqian Jiang, Eric R. LaRose, Peggy L. Peissig, Ning Shang, Barbara Benoit, Vivian S. Gainer, Kenneth Borthwick, Kathryn L. Jackson, Ambrish Sharma, Andy Yizhou Wu, Abel N. Kho, Dan M. Roden, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. J. Am. Medical Informatics Assoc. 25(11): 1540-1546 (2018) - [j27]Min-hyung Kim, Samprit Banerjee, Yize Zhao, Fei Wang, Yiye Zhang, Yongjun Zhu, Joseph DeFerio, Lauren Evans, Sang Min Park, Jyotishman Pathak:
Association networks in a matched case-control design - Co-occurrence patterns of preexisting chronic medical conditions in patients with major depression versus their matched controls. J. Biomed. Informatics 87: 88-95 (2018) - 2016
- [j26]Casey L. Overby, John J. Connolly, Christopher G. Chute, Joshua C. Denny, Robert R. Freimuth, Andrea L. Hartzler, Ingrid A. Holm, Shannon F. Manzi, Jyotishman Pathak, Peggy L. Peissig, Maureen E. Smith, Marc S. Williams, Brian H. Shirts, Elena M. Stoffel, Peter Tarczy-Hornoch, Carolyn Rohrer Vitek, Wendy A. Wolf, Justin Starren, Luke V. Rasmussen:
Practical considerations for implementing genomic information resources. Appl. Clin. Inform. 07(03): 870-882 (2016) - [j25]Rachel L. Richesson, Jimeng Sun, Jyotishman Pathak, Abel N. Kho, Joshua C. Denny:
Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. Artif. Intell. Medicine 71: 57-61 (2016) - [j24]Na Hong, Jyotishman Pathak, Christopher G. Chute, Guoqian Jiang:
Developing a modular architecture for creation of rule-based clinical diagnostic criteria. BioData Min. 9: 33 (2016) - [j23]Jacqueline Kirby, Peter Speltz, Luke V. Rasmussen, Melissa A. Basford, Omri Gottesman, Peggy L. Peissig, Jennifer A. Pacheco, Gerard Tromp, Jyotishman Pathak, David S. Carrell, Stephen B. Ellis, Todd Lingren, William K. Thompson, Guergana Savova, Jonathan L. Haines, Dan M. Roden, Paul A. Harris, Joshua C. Denny:
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J. Am. Medical Informatics Assoc. 23(6): 1046-1052 (2016) - [j22]Vahid Taslimitehrani, Guozhu Dong, Naveen L. Pereira, Maryam Panahiazar, Jyotishman Pathak:
Developing EHR-driven heart failure risk prediction models using CPXR(Log) with the probabilistic loss function. J. Biomed. Informatics 60: 260-269 (2016) - [j21]Guoqian Jiang, Richard C. Kiefer, Luke V. Rasmussen, Harold R. Solbrig, Huan Mo, Jennifer A. Pacheco, Jie Xu, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak:
Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J. Biomed. Informatics 62: 232-242 (2016) - 2015
- [j20]Huan Mo, William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Richard C. Kiefer, Qian Zhu, Jie Xu, Enid N. H. Montague, David S. Carrell, Todd Lingren, Frank D. Mentch, Yizhao Ni, Firas H. Wehbe, Peggy L. Peissig, Gerard Tromp, Eric B. Larson, Christopher G. Chute, Jyotishman Pathak, Joshua C. Denny, Peter Speltz, Abel N. Kho, Gail P. Jarvik, Cosmin Adrian Bejan, Marc S. Williams, Kenneth Borthwick, Terrie E. Kitchner, Dan M. Roden, Paul A. Harris:
Desiderata for computable representations of electronic health records-driven phenotype algorithms. J. Am. Medical Informatics Assoc. 22(6): 1220-1230 (2015) - [j19]Jie Xu, Luke V. Rasmussen, Pamela L. Shaw, Guoqian Jiang, Richard C. Kiefer, Huan Mo, Jennifer A. Pacheco, Peter Speltz, Qian Zhu, Joshua C. Denny, Jyotishman Pathak, William K. Thompson, Enid N. H. Montague:
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. J. Am. Medical Informatics Assoc. 22(6): 1251-1260 (2015) - 2014
- [j18]William V. Bobo, Jyotishman Pathak, Hilal Maradit Kremers, Barbara P. Yawn, Scott M. Brue, Cynthia J. Stoppel, Paul E. Croarkin, Jennifer St Sauver, Mark A. Frye, Walter A. Rocca:
Research and applications: An electronic health record driven algorithm to identify incident antidepressant medication users. J. Am. Medical Informatics Assoc. 21(5): 785-791 (2014) - [j17]Luke V. Rasmussen, William K. Thompson, Jennifer A. Pacheco, Abel N. Kho, David Carrell, Jyotishman Pathak, Peggy L. Peissig, Gerard Tromp, Joshua C. Denny, Justin B. Starren:
Design patterns for the development of electronic health record-driven phenotype extraction algorithms. J. Biomed. Informatics 51: 280-286 (2014) - 2013
- [j16]Cui Tao, Guoqian Jiang, Thomas A. Oniki, Robert R. Freimuth, Qian Zhu, Deepak K. Sharma, Jyotishman Pathak, Stanley M. Huff, Christopher G. Chute:
A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J. Am. Medical Informatics Assoc. 20(3): 554-562 (2013) - [j15]Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute:
Terminology representation guidelines for biomedical ontologies in the semantic web notations. J. Biomed. Informatics 46(1): 128-138 (2013) - [j14]Qian Zhu, Robert R. Freimuth, Zonghui Lian, Scott Bauer, Jyotishman Pathak, Cui Tao, Matthew J. Durski, Christopher G. Chute:
Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study. J. Biomed. Informatics 46(2): 286-293 (2013) - [j13]Qian Zhu, Robert R. Freimuth, Jyotishman Pathak, Matthew J. Durski, Christopher G. Chute:
Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. J. Biomed. Informatics 46(4): 690-696 (2013) - 2012
- [j12]Jyotishman Pathak, Richard C. Kiefer, Suzette J. Bielinski, Christopher G. Chute:
Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank. J. Biomed. Semant. 3: 10 (2012) - [j11]Peggy L. Peissig, Luke V. Rasmussen, Richard L. Berg, James G. Linneman, Catherine A. McCarty, Carol Waudby, Lin Chen, Joshua C. Denny, Russell A. Wilke, Jyotishman Pathak, David Carrell, Abel N. Kho, Justin B. Starren:
Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J. Am. Medical Informatics Assoc. 19(2): 225-234 (2012) - [j10]Susan Rea, Jyotishman Pathak, Guergana K. Savova, Thomas A. Oniki, Les Westberg, Calvin E. Beebe, Cui Tao, Craig G. Parker, Peter J. Haug, Stanley M. Huff, Christopher G. Chute:
Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project. J. Biomed. Informatics 45(4): 763-771 (2012) - 2011
- [j9]Jyotishman Pathak, Christopher G. Chute:
Letter: Further revamping VA's NDF-RT drug terminology for clinical research. J. Am. Medical Informatics Assoc. 18(3): 347-348 (2011) - [j8]Jyotishman Pathak, Janey Wang, Sudha Kashyap, Melissa A. Basford, Rongling Li, Daniel R. Masys, Christopher G. Chute:
Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. J. Am. Medical Informatics Assoc. 18(4): 376-386 (2011) - 2010
- [j7]Jyotishman Pathak, Christopher G. Chute:
Analyzing categorical information in two publicly available drug terminologies: RxNorm and NDF-RT. J. Am. Medical Informatics Assoc. 17(4): 432-439 (2010) - [j6]Iftikhar J. Kullo, Jin Fan, Jyotishman Pathak, Guergana K. Savova, Zeenat Ali, Christopher G. Chute:
Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. J. Am. Medical Informatics Assoc. 17(5): 568-574 (2010) - [j5]Jyotishman Pathak, Lee B. Peters, Christopher G. Chute, Olivier Bodenreider:
Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J. Am. Medical Informatics Assoc. 17(6): 714-719 (2010) - 2009
- [j4]Jyotishman Pathak, Thomas M. Johnson, Christopher G. Chute:
Survey of modular ontology techniques and their applications in the biomedical domain. Integr. Comput. Aided Eng. 16(3): 225-242 (2009) - [j3]Jyotishman Pathak, Harold R. Solbrig, James D. Buntrock, Thomas M. Johnson, Christopher G. Chute:
Implementation Brief: LexGrid: A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime. J. Am. Medical Informatics Assoc. 16(3): 305-315 (2009) - [j2]Guoqian Jiang, Jyotishman Pathak, Christopher G. Chute:
Formalizing ICD coding rules using Formal Concept Analysis. J. Biomed. Informatics 42(3): 504-517 (2009) - 2008
- [j1]Jyotishman Pathak, Samik Basu, Robyn R. Lutz, Vasant G. Honavar:
MOSCOE: an Approach for Composing Web Services through Iterative Reformulation of Functional Specifications. Int. J. Artif. Intell. Tools 17(1): 109-138 (2008)
Conference and Workshop Papers
- 2024
- [c129]Richard Li Xu, Song Wang, Zewei Wang, Yuhan Zhang, Yunyu Xiao, Jyotishman Pathak, David Hodge, Yan Leng, S. Craig Watkins, Ying Ding, Yifan Peng:
Analyzing Social Factors to Enhance Suicide Prevention Across Population Groups. ICHI 2024: 189-199 - 2023
- [c128]Reshma Kar, Vijay Kumar Reddy Voddi, Braja Gopal Patra, Jyotishman Pathak:
CoRL: A Cost-Responsive Learning Optimizer for Neural Networks. SMC 2023: 1828-1833 - 2022
- [c127]Meghan Reading Turchioe, Winston Guo, Alexander Volodarskiy, Brittany Taylor, Mollie Hobensack, David Slotwiner, Jyotishman Pathak:
Developing a disease-specific symptom vocabulary for natural language processing. AMIA 2022 - 2021
- [c126]Prakash Adekkanattu, Jennifer A. Pacheco, Joseph Kabariti, Daniel J. Stone, Yue Yu, Parag Goyal, Faraz S. Ahmad, Guoqian Jiang, Yuan Luo, Luke V. Rasmussen, Pascal S. Brandt, Zhenxing Xu, Jie Xu, Fei Wang, Natalie C. Benda, Thomas R. Campion Jr., Jyotishman Pathak:
Multi-site Evaluation of Longitudinal Changes in Ejection Fraction in Heart Failure Patients Through Data-driven Phenotyping. AMIA 2021 - [c125]Natalie C. Benda, Pascal S. Brandt, Jessica S. Ancker, Jennifer A. Pacheco, Prakash Adekkanattu, Guoqian Jiang, Jyotishman Pathak, Luke V. Rasmussen:
Supporting EHR-based Cohort Discovery Through User-centered Design: Results of an Early Formative Usability Study. AMIA 2021 - [c124]Yufang Huang, Yifan Liu, Peter A. D. Steel, Kelly M. Axsom, John R. Lee, Sri Lekha Tummalapalli, Alison Hermann, Rochelle Joly, Fei Wang, Jyotishman Pathak, Lakshminarayanan Subramanian, Yiye Zhang:
Deep Significance Clustering (DICE) a Heterogenous Population. AMIA 2021 - [c123]Lauren A. Lepow, Braja Gopal Patra, Isotta Landi, Prakash Adekkanattu, Jyotishman Pathak, Mark Olfson, J. John Mann, Euijung Ryu, Joanna M. Biernacka, Girish N. Nadkarni, Priya Wickramaratne, Myrna Weissman, Benjamin S. Glicksberg, Alexander Charney:
Extracting Social Isolation Information From Psychiatric Notes in the Electronic Health Records. AMIA 2021 - [c122]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Fei Wang, Richard Isaacson, Jyotishman Pathak, Yuan Luo:
A Deep Learning Framework Using a Pre-trained BERT Model to Predict the Risk of Progression from Mild Cognitive Impairment to Alzheimer's Disease. AMIA 2021 - [c121]Mohit Manoj Sharma, Yonaka Harris, Yiye Zhang, Jyotishman Pathak:
Prescribing Pharmacogenomics Testing: Analyzing the Acceptance of Healthcare Providers through a Survey Study. AMIA 2021 - [c120]Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 2021 - [c119]Andrew Wen, Luke V. Rasmussen, Daniel J. Stone, Sijia Liu, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Yuan Luo, Fei Wang, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA 2021 - [c118]Zehao Yu, Xi Yang, Chong Dang, Songzi Wu, Prakash Adekkanattu, Jyotishman Pathak, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu:
A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models. AMIA 2021 - 2020
- [c117]Pascal S. Brandt, Richard C. Kiefer, Jennifer A. Pacheco, Prakash Adekkanattu, Evan Sholle, Faraz S. Ahmad, Jie Xu, Zhenxing Xu, Jessica S. Ancker, Fei Wang, Yuan Luo, Guoqian Jiang, Jyotishman Pathak, Luke V. Rasmussen:
Feasibility of Cross-Platform EHR-Driven Phenotyping Using Clinical Quality Language. AMIA 2020 - [c116]Marika M. Cusick, Prakash Adekkanattu, Thomas R. Campion Jr., Evan Sholle, Annie C. Myers, George Alexopoulos, Jyotishman Pathak:
Weak Supervision to Classify Unstructured Clinical Text for Current Suicidal Ideation. AMIA 2020 - [c115]Lisa Grossman Liu, Meghan Reading Turchioe, Annie C. Myers, Jyotishman Pathak, David K. Vawdrey, Ruth Masterson Creber:
Visual Rating Scales for Patient-Reported Outcome Measurement: A National Validation Study. AMIA 2020 - [c114]Annie C. Myers, Fariha Ahsan, Rochelle Joly, Alison Hermann, Yiye Zhang, Michael Laskoff, Jyotishman Pathak, Meghan Reading Turchioe:
Provider perspectives on the clinical utility of using a risk prediction tool for postpartum depression. AMIA 2020 - [c113]Annie C. Myers, Lewis Chesebrough, Ruixuan Hu, Meghan Reading Turchioe, Jyotishman Pathak, Ruth Masterson Creber:
Evaluating Commercially Available Mobile Apps for Depression Self-Management. AMIA 2020 - [c112]Wenna Xi, Samprit Banerjee, Robert B. Penfold, Gregory E. Simon, George Alexopoulos, Jyotishman Pathak:
Healthcare Contacts Among Patients with Psychiatric Hospitalization Admitted Through the Emergency Department. AMIA 2020 - [c111]Jie Xu, Fei Wang, Zhenxing Xu, Prakash Adekkanattu, Pascal S. Brandt, Guoqian Jiang, Richard C. Kiefer, Yuan Luo, Chengsheng Mao, Jennifer A. Pacheco, Luke V. Rasmussen, Yiye Zhang, Richard Isaacson, Jyotishman Pathak:
Identification of Alzheimer's Disease Subtypes from Electronic Health Records Using a Data-Driven Approach. AMIA 2020 - 2019
- [c110]Prakash Adekkanattu, Guoqian Jiang, Yuan Luo, Paul R. Kingsbury, Zhenxing Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Richard C. Kiefer, Daniel J. Stone, Pascal S. Brandt, Liang Yao, Yizhen Zhong, Yu Deng, Fei Wang, Jessica S. Ancker, Thomas R. Campion Jr., Jyotishman Pathak:
Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. AMIA 2019 - [c109]Vasa Curcin, Elizabeth Ford, Jyotishman Pathak, Goran Nenadic:
Using Social Media to Study Mental Health Conditions - Challenges and Opportunities. AMIA 2019 - [c108]Joseph J. DeFerio, Annie C. Myers, John M. Meddar, Judith Cukor, Jyotishman Pathak:
Collecting Individual-Level Social Determinants of Health to Inform Patient-Centered Outcomes Research in Mental Health. AMIA 2019 - [c107]Luke V. Rasmussen, Pascal S. Brandt, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Prakash Adekkanattu, Jessica S. Ancker, Fei Wang, Zhenxing Xu, Jyotishman Pathak, Yuan Luo:
Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms. AMIA 2019 - [c106]Evan Sholle, Orrin Belden, Jaclyn Rosenzweig, Jennifer Levine, Joseph Kabariti, Thomas R. Campion Jr., Jyotishman Pathak:
Validation of a Computable Phenotype for Site-Specific Cancer Treatment. AMIA 2019 - [c105]Yiye Zhang, Yonaka Harris, George Alexopoulos, Adam Stracher, Elizabeth Ross, Rainu Kaushal, Jyotishman Pathak:
A Survey of Clinicians' Perception of Pharmacogenomics Testing for Antidepressants. AMIA 2019 - [c104]Zhenxing Xu, Yuan Luo, Prakash Adekkanattu, Jessica S. Ancker, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Luke V. Rasmussen, Jyotishman Pathak, Fei Wang:
Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care. MedInfo 2019: 462-466 - [c103]Shuojia Wang, Jyotishman Pathak, Yiye Zhang:
Using Electronic Health Records and Machine Learning to Predict Postpartum Depression. MedInfo 2019: 888-892 - [c102]Amanuel Alambo, Manas Gaur, Usha Lokala, Ugur Kursuncu, Krishnaprasad Thirunarayan, Amelie Gyrard, Amit P. Sheth, Randon S. Welton, Jyotishman Pathak:
Question Answering for Suicide Risk Assessment Using Reddit. ICSC 2019: 468-473 - [c101]Manas Gaur, Amanuel Alambo, Joy Prakash Sain, Ugur Kursuncu, Krishnaprasad Thirunarayan, Ramakanth Kavuluru, Amit P. Sheth, Randy S. Welton, Jyotishman Pathak:
Knowledge-aware Assessment of Severity of Suicide Risk for Early Intervention. WWW 2019: 514-525 - 2018
- [c100]Prakash Adekkanattu, Evan Sholle, Joseph J. DeFerio, Jyotishman Pathak, Stephen B. Johnson, Thomas R. Campion Jr.:
Ascertaining Depression Severity by Extracting Patient Health Questionnaire-9 (PHQ-9) Scores from Clinical Notes. AMIA 2018 - [c99]Joseph J. DeFerio, Evan Sholle, Kathleen Lee, Jyotishman Pathak:
Methods for Integrating EHRs, Social Determinants of Health, and Built Environment Data for Patient-Centered Research. AMIA 2018 - [c98]Cody M. Phelps, Trisha R. Sanghvi, Ningrui Zhang, Joseph J. DeFerio, Jyotishman Pathak:
Using EHRs to assess gender differences in the utilization of mental health services for patients diagnosed with major depression. AMIA 2018 - [c97]Manas Gaur, Ugur Kursuncu, Amanuel Alambo, Amit P. Sheth, Raminta Daniulaityte, Krishnaprasad Thirunarayan, Jyotishman Pathak:
"Let Me Tell You About Your Mental Health!": Contextualized Classification of Reddit Posts to DSM-5 for Web-based Intervention. CIKM 2018: 753-762 - [c96]Himanshu Sharma, Chengsheng Mao, Yizhen Zhang, Haleh Vatani, Liang Yao, Yizhen Zhong, Luke V. Rasmussen, Guoqian Jiang, Jyotishman Pathak, Yuan Luo:
Portable Phenotyping System: A Portable Machine-Learning Approach to i2b2 Obesity Challenge. ICHI Workshops 2018: 86-87 - [c95]Min-hyung Kim, Yongjun Zhu, Samprit Banerjee, Lauren Evans, Yiye Zhang, Fei Wang, Sang Min Park, Jyotishman Pathak:
Comparing Sex-Specific Association Networks of Chronic Medical Conditions. ICHI 2018: 368-370 - [c94]Amir Hossein Yazdavar, Mohammad Saeid Mahdavinejad, Goonmeet Bajaj, Krishnaprasad Thirunarayan, Jyotishman Pathak, Amit P. Sheth:
Mental Health Analysis Via Social Media Data. ICHI 2018: 459-460 - 2017
- [c93]Richard C. Kiefer, Luke V. Rasmussen, Jennifer A. Pacheco, Peter Speltz, Joshua C. Denny, William K. Thompson, Jyotishman Pathak, Guoqian Jiang:
Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository. AMIA 2017 - [c92]Kathleen Lee, Nicole Gray Weiskopf, Jyotishman Pathak:
A Framework for Data Quality Assessment in Clinical Research Datasets. AMIA 2017 - [c91]Evan Sholle, Joseph Kabariti, Stephen B. Johnson, John P. Leonard, Jyotishman Pathak, Vinay I. Varughese, Curtis L. Cole, Thomas R. Campion Jr.:
Secondary Use of Patients' Electronic Records (SUPER): An Approach for Meeting Specific Data Needs of Clinical and Translational Researchers. AMIA 2017 - [c90]Peter Speltz, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, William K. Thompson, Guoqian Jiang, Jyotishman Pathak, Joshua C. Denny:
The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs. AMIA 2017 - [c89]Amir Hossein Yazdavar, Hussein S. Al-Olimat, Monireh Ebrahimi, Goonmeet Bajaj, Tanvi Banerjee, Krishnaprasad Thirunarayan, Jyotishman Pathak, Amit P. Sheth:
Semi-Supervised Approach to Monitoring Clinical Depressive Symptoms in Social Media. ASONAM 2017: 1191-1198 - [c88]Mingjie Qian, Jyotishman Pathak, Naveen L. Pereira, Chengxiang Zhai:
Temporal reflected logistic regression for probabilistic heart failure survival score prediction. BIBM 2017: 410-416 - [c87]Deepak K. Sharma, Harold R. Solbrig, Eric Prud'hommeaux, Kathleen Lee, Jyotishman Pathak, Guoqian Jiang:
D2Refine: A Platform for Clinical Research Study Data Element Harmonization and Standardization. CRI 2017 - [c86]Che Ngufor, Dennis H. Murphree, Sudhindra Upadhyaya, Jyotishman Pathak, Daryl J. Kor:
Multitask LS-Svm for Predicting Bleeding and Re-operation Due to Bleeding. ICHI 2017: 56-65 - [c85]Ioakeim Perros, Fei Wang, Ping Zhang, Peter B. Walker, Richard W. Vuduc, Jyotishman Pathak, Jimeng Sun:
Polyadic Regression and its Application to Chemogenomics. SDM 2017: 72-80 - 2016
- [c84]Guoqian Jiang, William K. Thompson, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, Huan Mo, Peter Speltz, Joshua C. Denny, Jyotishman Pathak:
An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution. AMIA 2016 - [c83]Min-hyung Kim, Samprit Banerjee, Sang Min Park, Jyotishman Pathak:
Improving risk prediction for depression via Elastic Net regression - Results from Korea National Health Insurance Services Data. AMIA 2016 - [c82]Che Ngufor, Dennis Murphree, Sudhindra Upadhyaya, Nageswar Madde, Jyotishman Pathak, Rickey E. Carter, Daryl J. Kor:
Predicting Prolonged Stay in the ICU Attributable to Bleeding in Patients Offered Plasma Transfusion. AMIA 2016 - [c81]Deepak K. Sharma, Harold R. Solbrig, Eric Prud'hommeaux, Jyotishman Pathak, Guoqian Jiang:
Standardized Representation of Clinical Study Data Dictionaries with CIMI Archetypes. AMIA 2016 - [c80]Huan Mo, Guoqian Jiang, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. CRI 2016 - 2015
- [c79]Che Ngufor, Sudhindra Upadhyaya, Dennis Murphree, Nageswar Madde, Daryl J. Kor, Jyotishman Pathak:
A Heterogeneous Multi-Task Learning for Predicting RBC Transfusion and Perioperative Outcomes. AIME 2015: 287-297 - [c78]Matthew K. Breitenstein, Richard M. Weinshilboum, Jyotishman Pathak, Liewei Wang:
Developing Intermediary Medication Phenotypes via Metabolomics Biotechnology Using an Electronic Health Record-Linked Biobank. AMIA 2015 - [c77]Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Jennifer A. Pacheco, Enid N. H. Montague, Jie Xu, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak:
Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study. AMIA 2015 - [c76]Yoonjung Y. Joo, Jennifer A. Pacheco, Loren L. Armstrong, William K. Thompson, Robert J. Carroll, Joshua C. Denny, Peggy L. Peissig, James G. Linneman, Jyotishman Pathak, Girish N. Nadkarni, Laura Rasmussen-Torvik, M. Geoffrey Hayes, Abel N. Kho:
A Genome- and Phenome- Wide Study of Diverticulosis. AMIA 2015 - [c75]Huan Mo, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME. AMIA 2015 - [c74]Enid N. H. Montague, Jie Xu, Luke V. Rasmussen, Joshua C. Denny, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Peter Speltz, William K. Thompson, Jyotishman Pathak:
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools. AMIA 2015 - [c73]Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy:
(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping. AMIA 2015 - [c72]Jyotishman Pathak, Joshua C. Denny, William K. Thompson, Luke V. Rasmussen:
PhEMA: Phenotype Modeling, Sharing and Execution Architecture. AMIA 2015 - [c71]Che Ngufor, Sudhindra Upadhyaya, Dennis Murphree, Daryl J. Kor, Jyotishman Pathak:
Multi-task learning with selective cross-task transfer for predicting bleeding and other important patient outcomes. DSAA 2015: 1-8 - [c70]Dennis Murphree, Che Ngufor, Sudhindra Upadhyaya, Nageswar Madde, Leanne Clifford, Daryl J. Kor, Jyotishman Pathak:
Ensemble learning approaches to predicting complications of blood transfusion. EMBC 2015: 7222-7225 - [c69]Che Ngufor, Janusz Wojtusiak, Jyotishman Pathak:
A Systematic Prediction of Adverse Drug Reactions Using Pre-clinical Drug Characteristics and Spontaneous Reports. ICHI 2015: 76-81 - [c68]Dennis H. Murphree, Leanne Clifford, Yaxiong Lin, Nagesh Madde, Che Ngufor, Sudhindra Upadhyaya, Jyotishman Pathak, Daryl J. Kor:
Predicting Adverse Reactions to Blood Transfusion. ICHI 2015: 82-89 - [c67]Dennis H. Murphree, Leanne Clifford, Yaxiong Lin, Nagesh Madde, Che Ngufor, Sudhindra Upadhyaya, Jyotishman Pathak, Daryl J. Kor:
A Clinical Decision Support System for Preventing Adverse Reactions to Blood Transfusion. ICHI 2015: 100-104 - [c66]Maryam Panahiazar, Vahid Taslimitehrani, Naveen Pereira, Jyotishman Pathak:
Using EHRs and Machine Learning for Heart Failure Survival Analysis. MedInfo 2015: 40-44 - [c65]Che Ngufor, Dennis Murphree, Sudhindra Upadhyaya, Nageswar Madde, Daryl J. Kor, Jyotishman Pathak:
Effects of Plasma Transfusion on Perioperative Bleeding Complications: A Machine Learning Approach. MedInfo 2015: 721-725 - [c64]Pedro J. Caraballo, Mark A. Parkulo, David Blair, Michelle Elliott, Cloann Schultz, Joseph Sutton, Padma S. Rao, Jamie Bruflat, Robert R. Bleimeyer, John Crooks, Donald B. Gabrielson, Wayne T. Nicholson, Carolyn Rohrer Vitek, Kelly Wix, Suzette J. Bielinski, Jyotishman Pathak, Iftikhar J. Kullo:
Clinical Decision Support to Implement CYP2D6 Drug-Gene Interaction. MedInfo 2015: 946 - [c63]Na Hong, Guoqian Jiang, Jyotishman Pathak, Christopher G. Chute:
A Pilot Study on Modeling of Diagnostic Criteria Using OWL and SWRL. MedInfo 2015: 1093 - [c62]Guoqian Jiang, Harold R. Solbrig, Jyotishman Pathak, Christopher G. Chute:
Developing a Standards-Based Information Model for Representing Computable Diagnostic Criteria: A Feasibility Study of the NQF Quality Data Model. MedInfo 2015: 1097 - [c61]Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak:
A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. MedInfo 2015: 1098 - [c60]Maryam Panahiazar, Vahid Taslimitehrani, Naveen L. Pereira, Jyotishman Pathak:
Using EHRs for Heart Failure Therapy Recommendation Using Multidimensional Patient Similarity Analytics. MIE 2015: 369-373 - [c59]Matthew K. Breitenstein, György J. Simon, Euijung Ryu, Sebastian M. Armasu, Richard M. Weinshilboum, Liewei Wang, Jyotishman Pathak:
Using EHR-Linked Biobank Data to Study Metformin Pharmacogenomics. MIE 2015: 914-918 - [c58]Na Hong, Guoqian Jiang, Jyotishman Pathak, Christopher G. Chute:
Developing a Modular Architecture for Creation of Rule-based Clinical Diagnostic Criteria. BDM2I@ISWC 2015 - 2014
- [c57]Ashutosh Jadhav, Amit P. Sheth, Jyotishman Pathak:
Analysis of Online Information Searching for Cardiovascular Diseases on a Consumer Health Information Portal. AMIA 2014 - [c56]Ashutosh Jadhav, Amit P. Sheth, Jyotishman Pathak:
An Analysis of Mayo Clinic Search Query Logs for Cardiovascular Diseases. AMIA 2014 - [c55]Lara Johnstun, Danielle Groat, Amol Bhalla, Kevin J. Peterson, Jyotishman Pathak, Adela Grando:
Using PhenotypePortal for Checking Clinical Guideline Recommendation Compliance. AMIA 2014 - [c54]Kevin J. Peterson, Jyotishman Pathak:
Scalable and High-Throughput Execution of Clinical Quality Measures from Electronic Health Records using MapReduce and the JBoss(R) Drools Engine. AMIA 2014 - [c53]Luke V. Rasmussen, Jie Xu, Ruijue Liu, Qian Zhu, Jennifer A. Pacheco, Jyotishman Pathak, William K. Thompson, Joshua C. Denny, Huan Mo, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague:
Evaluation of Existing Phenotype Authoring Tools for Clinical Research. AMIA 2014 - [c52]Qian Zhu, Huan Mo, Luke V. Rasmussen, Andrew R. Post, Jennifer A. Pacheco, Jie Xu, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Jyotishman Pathak:
Qualitative evaluation of three phenotype information models to find methotrexate liver injury. AMIA 2014 - [c51]Feichen Shen, Dingcheng Li, Hongfang Liu, Yugyung Lee, Jyotishman Pathak, Christopher G. Chute, Cui Tao:
Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. BHI 2014: 531-534 - [c50]Maryam Panahiazar, Vahid Taslimi, Ashutosh Jadhav, Jyotishman Pathak:
Empowering personalized medicine with big data and semantic web technology: Promises, challenges, and use cases. IEEE BigData 2014: 790-795 - [c49]Aarti Sathyanarayana, Jyotishman Pathak, Rozalina G. McCoy, Santiago Romero-Brufau, Maryam Panaziahar, Jaideep Srivastava:
Clinical Decision Making: A Framework for Predicting Rx Response. ICDM Workshops 2014: 1185-1188 - [c48]Ashutosh Jadhav, Stephen T. Wu, Amit P. Sheth, Jyotishman Pathak:
Online Information Seeking for Cardiovascular Diseases: A Case Study from Mayo Clinic. MIE 2014: 702-706 - [c47]Ashutosh Jadhav, Stephen T. Wu, Amit P. Sheth, Jyotishman Pathak:
What Information about Cardiovascular Diseases do People Search Online? MIE 2014: 1191 - 2013
- [c46]Jyotishman Pathak, Cory M. Endle, Dale Suesse, Kevin J. Peterson, Craig Stancl, Dingcheng Li, Christopher G. Chute:
PhenotypePortal: An Open-Source Library and Platform for Authoring, Executing and Visualization of Electronic Health Records Driven Phenotyping Algorithms. AMIA 2013 - [c45]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
Mining Drug-Drug Interaction Patterns from Linked Clinical Data. AMIA 2013 - [c44]Qian Zhu, Jyotishman Pathak, Robert R. Freimuth, Christopher G. Chute:
Using standardized clinical data modeling and knowledge representation to compute pharmacogenomic data elements. AMIA 2013 - [c43]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
Mining drug-drug interaction patterns from linked data: A case study for Warfarin, Clopidogrel, and Simvastatin. BIBM 2013: 23-30 - [c42]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
Mining Anti-coagulant Drug-Drug Interactions from Electronic Health Records Using Linked Data. DILS 2013: 128-140 - [c41]Cui Tao, Dingcheng Li, Feichen Shen, Zonghui Lian, Jyotishman Pathak, Hongfang Liu, Christopher G. Chute:
Phenotyping on EHR Data Using OWL and Semantic Web Technologies. ICSH 2013: 31-32 - [c40]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
Using Linked Data for Mining Drug-Drug Interactions in Electronic Health Records. MedInfo 2013: 682-686 - 2012
- [c39]Suzette J. Bielinski, Jyotishman Pathak, Hongfang Liu, Sunghwan Sohn, Gail P. Jarvik, David Carrell, Naveen Pereira, Véronique L. Roger:
Using Electronic Health Records to Identify Heart Failure Cohorts with Differentiation for Preserved and Reduced Ejection Fraction. AMIA 2012 - [c38]Robert J. Carroll, Katherine P. Liao, Anne E. Eyler, Lisa Bastarache, Dana C. Crawford, Peggy L. Peissig, Jyotishman Pathak, David Carrell, Abel N. Kho, Rongling Li, Daniel R. Masys, Gail P. Jarvik, Christopher G. Chute, Rex L. Chisholm, Eric B. Larson, Catherine A. McCarty, Iftikhar J. Kullo:
Using PheWAS to Assess Pleiotropy of Genetic Risk Scores for Rheumatoid Arthritis and Coronary Artery Disease in the eMERGE Network. AMIA 2012 - [c37]Cory M. Endle, Sahana Murthy, Dale Suesse, Craig Stancle, Dingcheng Li, Lacey Hart, Christopher G. Chute, Jyotishman Pathak:
Visualization and Reporting of Results for Electronic Health Records Driven Phenotyping using the Open-Source popHealth Platform. AMIA 2012 - [c36]Dingcheng Li, Sahana Murthy, Davide Sottara, Christopher G. Chute, Stanley M. Huff, Jyotishman Pathak, Cory M. Endle, Dale Suesse, Craig Stancle:
Modeling and Executing Electronic Health Records Driven Phenotyping Algorithms using the NQF Quality Data Model and JBoss® Drools Engine. AMIA 2012 - [c35]Jyotishman Pathak, Aref Al-Kali, Jayant Talwalkar, Abel N. Kho, Joshua C. Denny, Sean P. Murphy, Kevin Bruce, Matthew J. Durski, Christopher G. Chute:
Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury. AMIA 2012 - [c34]Jyotishman Pathak, Richard C. Kiefer, Suzette J. Bielinski, Christopher G. Chute:
Mining the Human Phenome using Semantic Web Technologies: A Case Study for Type 2 Diabetes. AMIA 2012 - [c33]Jyotishman Pathak, Richard C. Kiefer, Robert R. Freimuth, Suzette J. Bielinski, Christopher G. Chute:
Mining Genotype-Phenotype Associations from Electronic Health Records and Biorepositories using Semantic Web Technologies. AMIA 2012 - [c32]Joseph Teagno, Richard C. Kiefer, Jyotishman Pathak, G. Q. Zhang, Satya Sanket Sahoo:
A Distributed Semantic Web Approach for Cohort Identification. AMIA 2012 - [c31]William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Peggy L. Peissig, Joshua C. Denny, Abel N. Kho, Aaron W. Miller, Jyotishman Pathak:
An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms. AMIA 2012 - [c30]Cui Tao, Guoqian Jiang, Thomas A. Oniki, Robert R. Freimuth, Jyotishman Pathak, Qian Zhu, Deepak K. Sharma, Stanley M. Huff, Christopher G. Chute:
A Semantic-Web Oriented Representation of Clinical Element Model for Secondary Use of Electronic Healthcare Data. HISB 2012: 133 - [c29]Rachel L. Richesson, Jyotishman Pathak, Wendy McLeod, Ginger Blackmon, Kendra Vehik:
Requirements and Strategy for the Development of a Pediatric Drug Ontology. ICBO 2012 - [c28]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
Applying linked data principles to represent patient's electronic health records at Mayo clinic: a case report. IHI 2012: 455-464 - [c27]Jyotishman Pathak, Laura C. Weiss, Matthew J. Durski, Qian Zhu, Robert R. Freimuth, Christopher G. Chute:
Integrating VA's NDF-RT Drug Terminology with PharmGKB: Preliminary Results. Pacific Symposium on Biocomputing 2012: 400-409 - 2011
- [c26]Guoqian Jiang, Jon D. Duke, Jyotishman Pathak, Christopher G. Chute:
An Ontological Representation of Adverse Drug Events. ICBO 2011 - [c25]Jyotishman Pathak, Shawn P. Murphy, Brian N. Willaert, Hilal M. Kremers, Christopher G. Chute, Barbara P. Yawn, Walter A. Rocca:
Using RxNorm to Extract Medication Data from Electronic Health Records in the Rochester Epidemiology Project. ICBO 2011 - [c24]Jyotishman Pathak, Richard C. Kiefer, Christopher G. Chute:
The linked clinical data project: applying semantic web technologies for clinical and translational research using electronic medical records. SWAT4LS 2011: 94-95 - 2008
- [c23]Jyotishman Pathak, Samik Basu, Vasant G. Honavar:
Composing Web Services through Automatic Reformulation of Service Specifications. IEEE SCC (1) 2008: 361-369 - [c22]Jyotishman Pathak, James D. Buntrock, Christopher G. Chute:
LexSearch: An Approach for Leveraging Semantic Annotations to Searching Ontologies. AAAI Spring Symposium: Semantic Scientific Knowledge Integration 2008: 68-73 - [c21]Jyotishman Pathak, Guoqian Jiang, Sridhar O. Dwarkanath, James D. Buntrock, Christopher G. Chute:
LexValueSets: An Approach for Context-Driven Value Sets Extraction. AMIA 2008 - [c20]Jyotishman Pathak, Thomas M. Johnson, Christopher G. Chute:
Modular ontology techniques and their applications in the biomedical domain. IRI 2008: 351-356 - [c19]Jyotishman Pathak, Guoqian Jiang, Sridhar O. Dwarkanath, James D. Buntrock, Christopher G. Chute:
Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources. ICSC 2008: 460-467 - 2007
- [c18]Nithya Rajamani, Murthy V. Devarakonda, Yu Deng, Wlodek Zadrozny, Jyotishman Pathak:
Business-Activity Driven Search: Addressing the Information Needs of Services Professionals. IEEE SCC 2007: 644-651 - [c17]James D. McCalley, Vasant G. Honavar, Sarah M. Ryan, William Q. Meeker, Daji Qiao, Ronald A. Roberts, Yuan Li, Jyotishman Pathak, Mujing Ye, Yili Hong:
Integrated Decision Algorithms for Auto-steered Electric Transmission System Asset Management. International Conference on Computational Science (1) 2007: 1066-1073 - [c16]Jyotishman Pathak, Samik Basu, Vasant G. Honavar:
On Context-Specific Substitutability of Web Services. ICWS 2007: 192-199 - 2006
- [c15]Doina Caragea, Jun Zhang, Jyotishman Pathak, Vasant G. Honavar:
Learning Classifiers from Distributed, Ontology-Extended Data Sources. DaWaK 2006: 363-373 - [c14]Jyotishman Pathak, Samik Basu, Robyn R. Lutz, Vasant G. Honavar:
Parallel Web Service Composition in MoSCoE: A Choreography-Based Approach. ECOWS 2006: 3-12 - [c13]Jyotishman Pathak, Yong Jiang, Vasant G. Honavar, James D. McCalley:
Condition Data Aggregation with Application to Failure Rate Calculation of Power Transformers. HICSS 2006 - [c12]Jyotishman Pathak, Samik Basu, Robyn R. Lutz, Vasant G. Honavar:
MoSCoE: A Framework for Modeling Web Service Composition and Execution. ICDE Workshops 2006: 143 - [c11]Jyotishman Pathak, Yuan Li, Vasant G. Honavar, James D. McCalley:
A Service-Oriented Architecture for Electric Power Transmission System Asset Management. ICSOC Workshops 2006: 26-37 - [c10]Jyotishman Pathak, Samik Basu, Vasant G. Honavar:
Modeling Web Services by Iterative Reformulation of Functional and Non-functional Requirements. ICSOC 2006: 314-326 - [c9]Jyotishman Pathak, Samik Basu, Robyn R. Lutz, Vasant G. Honavar:
Selecting and Composing Web Services through Iterative Reformulation of Functional Specifications. ICTAI 2006: 445-454 - 2005
- [c8]Doina Caragea, Jun Zhang, Jie Bao, Jyotishman Pathak, Vasant G. Honavar:
Algorithms and Software for Collaborative Discovery from Autonomous, Semantically Heterogeneous, Distributed Information Sources. ALT 2005: 13-44 - [c7]Doina Caragea, Jie Bao, Jyotishman Pathak, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar:
Information Integration from Semantically Heterogeneous Biological Data Sources. DEXA Workshops 2005: 580-584 - [c6]Doina Caragea, Jyotishman Pathak, Jie Bao, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar:
Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. DILS 2005: 175-190 - [c5]Doina Caragea, Jun Zhang, Jie Bao, Jyotishman Pathak, Vasant G. Honavar:
Algorithms and Software for Collaborative Discovery from Autonomous, Semantically Heterogeneous, Distributed Information Sources. Discovery Science 2005: 14 - [c4]Jyotishman Pathak, Neeraj Koul, Doina Caragea, Vasant G. Honavar:
A framework for semantic web services discovery. WIDM 2005: 45-50 - 2004
- [c3]Doina Caragea, Jyotishman Pathak, Vasant G. Honavar:
Learning Classifiers from Semantically Heterogeneous Data. CoopIS/DOA/ODBASE (2) 2004: 963-980 - [c2]Jyotishman Pathak, Doina Caragea, Vasant G. Honavar:
Ontology-Extended Component-Based Workflows : A Framework for Constructing Complex Workflows from Semantically Heterogeneous Software Components. SWDB 2004: 41-56 - 2003
- [c1]Jaime Reinoso, Adrian Silvescu, Doina Caragea, Jyotishman Pathak, Vasant G. Honavar:
Information Extraction and Integration from Heterogeneous, Distributed, Autonomous Information Sources : A Federated Ontology-Driven Query-Centric Approach. IRI 2003: 183-191
Parts in Books or Collections
- 2007
- [p1]Jyotishman Pathak, Samik Basu, Vasant G. Honavar:
Assembling Composite Web Services from Autonomous Components. Emerging Artificial Intelligence Applications in Computer Engineering 2007: 394-405
Editorship
- 2012
- [e1]Alejandro Rodríguez González, Jyotishman Pathak, Mark D. Wilkinson, Nigam Shah, Robert Stevens, Richard D. Boyce, Ángel García-Crespo:
Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine, Boston, USA, November 12, 2012. CEUR Workshop Proceedings 930, CEUR-WS.org 2012 [contents]
Data and Artifacts
- 2021
- [d1]Manas Gaur, Vamsi Aribandi, Amanuel Alambo, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jonanthan Beich, Jyotishman Pathak, Amit P. Sheth:
Characterization of Time-variant and Time-invariant Assessment of Suicidality on Reddit using C-SSRS. Zenodo, 2021
Informal and Other Publications
- 2024
- [i12]Braja Gopal Patra, Lauren A. Lepow, Praneet Kasi Reddy Jagadeesh Kumar, Veer Vekaria, Mohit Manoj Sharma, Prakash Adekkanattu, Brian Fennessy, Gavin Hynes, Isotta Landi, Jorge A. Sanchez-Ruiz, Euijung Ryu, Joanna M. Biernacka, Girish N. Nadkarni, Ardesheer Talati, Myrna Weissman, Mark Olfson, J. John Mann, Alexander W. Charney, Jyotishman Pathak:
Extracting Social Support and Social Isolation Information from Clinical Psychiatry Notes: Comparing a Rule-based NLP System and a Large Language Model. CoRR abs/2403.17199 (2024) - 2022
- [i11]Zehao Yu, Xi Yang, Chong Dang, Prakash Adekkanattu, Braja Gopal Patra, Yifan Peng, Jyotishman Pathak, Debbie L. Wilson, Ching-Yuan Chang, Wei-Hsuan Lo-Ciganic, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu:
SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies. CoRR abs/2212.03000 (2022) - [i10]Chengsheng Mao, Jie Xu, Luke V. Rasmussen, Yikuan Li, Prakash Adekkanattu, Jennifer A. Pacheco, Borna Bonakdarpour, Robert Vassar, Guoqian Jiang, Fei Wang, Jyotishman Pathak, Yuan Luo:
AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease. CoRR abs/2212.06042 (2022) - 2021
- [i9]Manas Gaur, Vamsi Aribandi, Amanuel Alambo, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jonanthan Beich, Jyotishman Pathak, Amit P. Sheth:
Characterization of Time-variant and Time-invariant Assessment of Suicidality on Reddit using C-SSRS. CoRR abs/2104.04140 (2021) - [i8]Zehao Yu, Xi Yang, Chong Dang, Songzi Wu, Prakash Adekkanattu, Jyotishman Pathak, Thomas J. George, William R. Hogan, Yi Guo, Jiang Bian, Yonghui Wu:
A Study of Social and Behavioral Determinants of Health in Lung Cancer Patients Using Transformers-based Natural Language Processing Models. CoRR abs/2108.04949 (2021) - 2020
- [i7]Vaibhav Sourirajan, Anas Belouali, Mary Ann Dutton, Matthew J. Reinhard, Jyotishman Pathak:
A Machine Learning Approach to Detect Suicidal Ideation in US Veterans Based on Acoustic and Linguistic Features of Speech. CoRR abs/2009.09069 (2020) - [i6]Rohith K. Thiruvalluru, Manas Gaur, Krishnaprasad Thirunarayan, Amit P. Sheth, Jyotishman Pathak:
Comparing Suicide Risk Insights derived from Clinical and Social Media data. CoRR abs/2012.11393 (2020) - 2019
- [i5]Amir Hossein Yazdavar, Mohammad Saeid Mahdavinejad, Goonmeet Bajaj, William L. Romine, Amirhassan Monadjemi, Krishnaprasad Thirunarayan, Amit P. Sheth, Jyotishman Pathak:
Fusing Visual, Textual and Connectivity Clues for Studying Mental Health. CoRR abs/1902.06843 (2019) - [i4]Zhenxing Xu, Jingyuan Chou, Xi Sheryl Zhang, Yuan Luo, Tamara Isakova, Prakash Adekkanattu, Jessica S. Ancker, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Luke V. Rasmussen, Jyotishman Pathak, Fei Wang:
Identification of Predictive Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks. CoRR abs/1904.04990 (2019) - [i3]Prakash Adekkanattu, Guoqian Jiang, Yuan Luo, Paul R. Kingsbury, Zhenxing Xu, Luke V. Rasmussen, Jennifer A. Pacheco, Richard C. Kiefer, Daniel J. Stone, Pascal S. Brandt, Liang Yao, Yizhen Zhong, Yu Deng, Fei Wang, Jessica S. Ancker, Thomas R. Campion Jr., Jyotishman Pathak:
Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. CoRR abs/1905.01961 (2019) - 2018
- [i2]Himanshu Sharma, Chengsheng Mao, Yizhen Zhang, Haleh Vatani, Liang Yao, Yizhen Zhong, Luke V. Rasmussen, Guoqian Jiang, Jyotishman Pathak, Yuan Luo:
Developing a Portable Natural Language Processing Based Phenotyping System. CoRR abs/1807.06638 (2018) - 2017
- [i1]Amir Hossein Yazdavar, Hussein S. Al-Olimat, Monireh Ebrahimi, Goonmeet Bajaj, Tanvi Banerjee, Krishnaprasad Thirunarayan, Jyotishman Pathak, Amit P. Sheth:
Semi-Supervised Approach to Monitoring Clinical Depressive Symptoms in Social Media. CoRR abs/1710.05429 (2017)
Coauthor Index
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