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2020 – today
- 2025
[j42]Xubing Hao, Xiaojin Li, Yan Huang, Jay Shi, Rashmie Abeysinghe, Cui Tao, Kirk Roberts, Guo-Qiang Zhang, Licong Cui
:
Quantitatively assessing the impact of the quality of SNOMED CT subtype hierarchy on cohort queries. J. Am. Medical Informatics Assoc. 32(1): 89-96 (2025)- 2024
- [j41]Ekin Soysal, Kirk Roberts:
PheNormGPT: a framework for extraction and normalization of key medical findings. Database J. Biol. Databases Curation 2024 (2024) - [j40]Yan Hu, Qingyu Chen, Jingcheng Du, Xueqing Peng, Vipina Kuttichi Keloth, Xu Zuo, Yujia Zhou, Zehan Li, Xiaoqian Jiang, Zhiyong Lu, Kirk Roberts, Hua Xu:
Improving large language models for clinical named entity recognition via prompt engineering. J. Am. Medical Informatics Assoc. 31(9): 1812-1820 (2024) - [j39]Zhao Li, Qiang Wei, Liang-Chin Huang, Jianfu Li, Yan Hu, Yao-Shun Chuang, Jianping He, Avisha Das, Vipina Kuttichi Keloth, Yuntao Yang, Chiamaka S. Diala, Kirk E. Roberts, Cui Tao, Xiaoqian Jiang, W. Jim Zheng, Hua Xu:
Ensemble pretrained language models to extract biomedical knowledge from literature. J. Am. Medical Informatics Assoc. 31(9): 1904-1911 (2024) - [j38]Sonish Sivarajkumar, Haneef Ahamed Mohammad, David Oniani, Kirk Roberts, William R. Hersh, Hongfang Liu, Daqing He, Shyam Visweswaran, Yanshan Wang:
Clinical Information Retrieval: A Literature Review. J. Heal. Informatics Res. 8(2): 313-352 (2024) - [c79]Xubing Hao, Licong Cui, Cui Tao, Kirk Roberts, Muhammad Amith:
Analyzing Llama 3-based Approach for Axiom Translation from Ontologies. KBC-LM/LM-KBC@ISWC 2024 - [p1]William R. Hersh, Kirk Roberts:
IR in Biomedicine. Information Retrieval: Advanced Topics and Techniques 2024: 577-610 - [e5]Tristan Naumann, Asma Ben Abacha, Steven Bethard, Kirk Roberts, Danielle S. Bitterman:
Proceedings of the 6th Clinical Natural Language Processing Workshop, ClinicalNLP@NAACL 2024, Mexico City, Mexico, June 21, 2024. Association for Computational Linguistics 2024, ISBN 979-8-89176-109-4 [contents] - [e4]Dina Demner-Fushman, Sophia Ananiadou, Makoto Miwa, Kirk Roberts, Junichi Tsujii:
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2024, Bangkok, Thailand, August 16, 2024. Association for Computational Linguistics 2024, ISBN 979-8-89176-130-8 [contents] - [i30]Yumeng Yang, Ashley Gilliam, Ethan B. Ludmir, Kirk Roberts:
Exploring the Generalization of Cancer Clinical Trial Eligibility Classifiers Across Diseases. CoRR abs/2403.17135 (2024) - [i29]Enshuo Hsu, Kirk Roberts:
Leveraging Large Language Models for Knowledge-free Weak Supervision in Clinical Natural Language Processing. CoRR abs/2406.06723 (2024) - [i28]Yumeng Yang, Peter Krusche, Kristyn Pantoja, Cheng Shi, Ethan B. Ludmir, Kirk Roberts, Gen Zhu:
Using Large Language Models to Generate Clinical Trial Tables and Figures. CoRR abs/2409.12046 (2024) - [i27]Yiming Li, Fang Li, Kirk Roberts, Licong Cui, Cui Tao, Hua Xu:
A Comparative Study of Recent Large Language Models on Generating Hospital Discharge Summaries for Lung Cancer Patients. CoRR abs/2411.03805 (2024) - [i26]Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina Kuttichi Keloth, Vincent J. Zhang, Ruey-Ling Weng, Qingyu Chen, Xiaoqian Jiang, Kirk E. Roberts, Hua Xu:
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models? CoRR abs/2411.10020 (2024) - [i25]Enshuo Hsu, Kirk Roberts:
LLM-IE: A Python Package for Generative Information Extraction with Large Language Models. CoRR abs/2411.11779 (2024) - [i24]Deepak Gupta, Dina Demner-Fushman, William R. Hersh, Steven Bedrick, Kirk Roberts:
Overview of TREC 2024 Biomedical Generative Retrieval (BioGen) Track. CoRR abs/2411.18069 (2024) - 2023
- [j37]Sarvesh Soni, Surabhi Datta, Kirk Roberts:
quEHRy: a question answering system to query electronic health records. J. Am. Medical Informatics Assoc. 30(6): 1091-1102 (2023) - [j36]Tavleen Singh, Kirk Roberts, Trevor Cohen, Nathan K. Cobb, Amy Franklin, Sahiti Myneni:
Discerning conversational context in online health communities for personalized digital behavior change solutions using Pragmatics to Reveal Intent in Social Media (PRISM) framework. J. Biomed. Informatics 140: 104324 (2023) - [j35]Zitong Zhang, Braja Gopal Patra, Ashraf Yaseen, Jie Zhu, Rachit Sabharwal, Kirk Roberts, Tru Cao, Hulin Wu:
Scholarly recommendation systems: a literature survey. Knowl. Inf. Syst. 65(11): 4433-4478 (2023) - [j34]Xubing Hao, Rashmie Abeysinghe, Kirk Roberts, Licong Cui:
Logical definition-based identification of potential missing concepts in SNOMED CT. BMC Medical Informatics Decis. Mak. 23(1): 87 (2023) - [j33]Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu:
The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Medicine 6 (2023) - [c78]Samiksha Pachade, Surabhi Datta, Y. Dong, Sergio Salazar Marioni, Rania Abdelkhaleq, A. Niktabe, Kirk Roberts, Sunil A. Sheth, Luca Giancardo:
Self-Supervised Learning with Radiology Reports, A Comparative Analysis of Strategies for Large Vessel Occlusion and Brain CTA Images. ISBI 2023: 1-5 - [c77]Muhammad Amith, Licong Cui, Kirk Roberts, Cui Tao:
Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research. WWW (Companion Volume) 2023: 820-825 - [e3]Tristan Naumann, Asma Ben Abacha, Steven Bethard, Kirk Roberts, Anna Rumshisky:
Proceedings of the 5th Clinical Natural Language Processing Workshop, ClinicalNLP@ACL 2023, Toronto, Canada, July 14, 2023. Association for Computational Linguistics 2023, ISBN 978-1-959429-88-3 [contents] - [i23]Muhammad Amith, Licong Cui, Kirk Roberts, Cui Tao:
Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research. CoRR abs/2303.11991 (2023) - [i22]Surabhi Datta, Tasneem Kaochar, Hio Cheng Lam, Nelly Nwosu, Luca Giancardo, Alice Z. Chuang, Robert M. Feldman, Kirk Roberts:
Eye-SpatialNet: Spatial Information Extraction from Ophthalmology Notes. CoRR abs/2305.11948 (2023) - [i21]Alaleh Hamidi, Kirk Roberts:
Evaluation of AI Chatbots for Patient-Specific EHR Questions. CoRR abs/2306.02549 (2023) - [i20]Yumeng Yang, Soumya Jayaraj, Ethan B. Ludmir, Kirk Roberts:
Text Classification of Cancer Clinical Trial Eligibility Criteria. CoRR abs/2309.07812 (2023) - [i19]Jayetri Bardhan, Kirk Roberts, Daisy Zhe Wang:
Question Answering for Electronic Health Records: A Scoping Review of datasets and models. CoRR abs/2310.08759 (2023) - 2022
- [j32]Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao:
Toward a standard formal semantic representation of the model card report. BMC Bioinform. 23(1): 281 (2022) - [j31]Surabhi Datta, Kirk Roberts:
Fine-grained spatial information extraction in radiology as two-turn question answering. Int. J. Medical Informatics 158(February): 104628 (2022) - [j30]Akshat Kumar, Heath Goodrum, Ashley Kim, Carly Stender, Kirk Roberts, Elmer V. Bernstam:
Closing the loop: automatically identifying abnormal imaging results in scanned documents. J. Am. Medical Informatics Assoc. 29(5): 831-840 (2022) - [c76]Surabhi Datta, Tasneem Kaochar, Hio Cheng Lam, Nelly Nwosu, Alice Z. Chuang, Robert M. Feldman, Kirk Roberts:
Eye-SpatialNet: Spatial Information Extraction from Ophthalmology Notes. AMIA 2022 - [c75]Sarvesh Soni, Kirk Roberts:
Toward a Neural Semantic Parsing System for EHR Question Answering. AMIA 2022 - [c74]Jayetri Bardhan, Anthony M. Colas, Kirk Roberts, Daisy Zhe Wang:
DrugEHRQA: A Question Answering Dataset on Structured and Unstructured Electronic Health Records For Medicine Related Queries. LREC 2022: 1083-1097 - [c73]Surabhi Datta, Hio Cheng Lam, Atieh Pajouhi, Sunitha Mogalla, Kirk Roberts:
A Cross-document Coreference Dataset for Longitudinal Tracking across Radiology Reports. LREC 2022: 3686-3695 - [c72]Sarvesh Soni, Meghana Gudala, Atieh Pajouhi, Kirk Roberts:
RadQA: A Question Answering Dataset to Improve Comprehension of Radiology Reports. LREC 2022: 6250-6259 - [c71]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, Steven Bedrick, William R. Hersh:
Overview of the TREC 2022 Clinical Trials Track. TREC 2022 - [i18]Jayetri Bardhan, Anthony M. Colas, Kirk Roberts, Daisy Zhe Wang:
DrugEHRQA: A Question Answering Dataset on Structured and Unstructured Electronic Health Records For Medicine Related Queries. CoRR abs/2205.01290 (2022) - [i17]Sarvesh Soni, Kirk Roberts:
Toward a Neural Semantic Parsing System for EHR Question Answering. CoRR abs/2211.04569 (2022) - 2021
- [j29]Sarvesh Soni, Kirk Roberts:
An evaluation of two commercial deep learning-based information retrieval systems for COVID-19 literature. J. Am. Medical Informatics Assoc. 28(1): 132-137 (2021) - [j28]Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts:
Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review. J. Biomed. Informatics 115: 103671 (2021) - [j27]Yuqi Si, Elmer V. Bernstam, Kirk Roberts:
Generalized and transferable patient language representation for phenotyping with limited data. J. Biomed. Informatics 116: 103726 (2021) - [j26]Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen M. Voorhees, Lucy Lu Wang, William R. Hersh:
Searching for scientific evidence in a pandemic: An overview of TREC-COVID. J. Biomed. Informatics 121: 103865 (2021) - [c70]Patricia Ngantcha, Muhammad Tuan Amith, Kirk Roberts, John A. Valenza, Muhammad F. Walji, Cui Tao:
Dental EHR-infused Persona Ontologies to Enrich Dental Dialogue Interaction of Agents. BIBM 2021: 1818-1825 - [c69]Patricia Ngantcha, Muhammad Amith, Cui Tao, Kirk Roberts:
Patient-Provider Communication Training Models for Interactive Speech Devices. HCI (16) 2021: 250-268 - [c68]Ellen M. Voorhees, Kirk Roberts:
On the Quality of the TREC-COVID IR Test Collections. SIGIR 2021: 2422-2428 - [i16]Yuqi Si, Elmer V. Bernstam, Kirk Roberts:
Generalized and Transferable Patient Language Representation for Phenotyping with Limited Data. CoRR abs/2103.00482 (2021) - [i15]Yuqi Si, Kirk Roberts:
Hierarchical Transformer Networks for Longitudinal Clinical Document Classification. CoRR abs/2104.08444 (2021) - [i14]Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen M. Voorhees, Lucy Lu Wang, William R. Hersh:
Searching for Scientific Evidence in a Pandemic: An Overview of TREC-COVID. CoRR abs/2104.09632 (2021) - [i13]Enshuo Hsu, Ioannis Malagaris, Yong-Fang Kuo, Rizwana Sultana, Kirk Roberts:
Deep learning-based NLP Data Pipeline for EHR Scanned Document Information Extraction. CoRR abs/2110.11864 (2021) - 2020
- [j25]Braja Gopal Patra, Kirk Roberts, Hulin Wu:
A content-based dataset recommendation system for researchers - a case study on Gene Expression Omnibus (GEO) repository. Database J. Biol. Databases Curation 2020 (2020) - [j24]Braja Gopal Patra, Babak Soltanalizadeh, Nan Deng, Leqing Wu, Vahed Maroufy, Canglin Wu, W. Jim Zheng, Kirk Roberts, Hulin Wu, Ashraf Yaseen:
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries. Database J. Biol. Databases Curation 2020 (2020) - [j23]Heath Goodrum, Kirk Roberts, Elmer V. Bernstam:
Automatic classification of scanned electronic health record documents. Int. J. Medical Informatics 144: 104302 (2020) - [j22]Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu:
Deep learning in clinical natural language processing: a methodical review. J. Am. Medical Informatics Assoc. 27(3): 457-470 (2020) - [j21]Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen M. Voorhees, Lucy Lu Wang, William R. Hersh:
TREC-COVID: rationale and structure of an information retrieval shared task for COVID-19. J. Am. Medical Informatics Assoc. 27(9): 1431-1436 (2020) - [j20]Braja Gopal Patra, Vahed Maroufy, Babak Soltanalizadeh, Nan Deng, W. Jim Zheng, Kirk Roberts, Hulin Wu:
A content-based literature recommendation system for datasets to improve data reusability - A case study on Gene Expression Omnibus (GEO) datasets. J. Biomed. Informatics 104: 103399 (2020) - [j19]Surabhi Datta, Yuqi Si, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman, Kirk Roberts:
Understanding spatial language in radiology: Representation framework, annotation, and spatial relation extraction from chest X-ray reports using deep learning. J. Biomed. Informatics 108: 103473 (2020) - [j18]Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. BMC Medical Informatics Decis. Mak. 20-S(4): 259 (2020) - [j17]Ellen M. Voorhees, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, William R. Hersh, Kyle Lo, Kirk Roberts, Ian Soboroff, Lucy Lu Wang:
TREC-COVID: constructing a pandemic information retrieval test collection. SIGIR Forum 54(1): 1:1-1:12 (2020) - [c67]Surabhi Datta, Jordan Godfrey-Stovall, Kirk Roberts:
RadLex Normalization in Radiology Reports. AMIA 2020 - [c66]Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts:
Deep Representation Learning of Patient Data from Electronic Health Records: A Systematic Review. AMIA 2020 - [c65]Sarvesh Soni, Kirk Roberts:
Patient Cohort Retrieval using Transformer Language Models. AMIA 2020 - [c64]Muhammad Amith, Jing Wang, Grace Xiong, Kirk Roberts, Cui Tao:
A health consumer ontology of fast food information. BIBM 2020: 1714-1719 - [c63]Jordan Sanders, Meghana Gudala, Kathleen E. Hamilton, Nishtha Prasad, Jordan Godfrey-Stovall, Eduardo Blanco, Jane Elizabeth Hamilton, Kirk Roberts:
Extracting Adherence Information from Electronic Health Records. COLING 2020: 680-695 - [c62]Surabhi Datta, Morgan Ulinski, Jordan Godfrey-Stovall, Shekhar Khanpara, Roy Riascos-Castaneda, Kirk Roberts:
Rad-SpatialNet: A Frame-based Resource for Fine-Grained Spatial Relations in Radiology Reports. LREC 2020: 2251-2260 - [c61]Sarvesh Soni, Kirk Roberts:
Evaluation of Dataset Selection for Pre-Training and Fine-Tuning Transformer Language Models for Clinical Question Answering. LREC 2020: 5532-5538 - [c60]Kate Fultz Hollis, Kirk Roberts, Steven Bedrick, William R. Hersh:
Addressing the Search Challenges of Precision Medicine with Information Retrieval Systems and Physician Readers. MIE 2020: 813-817 - [c59]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, Steven Bedrick, William R. Hersh:
Overview of the TREC 2020 Precision Medicine Track. TREC 2020 - [e2]Anna Rumshisky, Kirk Roberts, Steven Bethard, Tristan Naumann:
Proceedings of the 3rd Clinical Natural Language Processing Workshop, ClinicalNLP@EMNLP 2020, Online, November 19, 2020. Association for Computational Linguistics 2020, ISBN 978-1-952148-74-3 [contents] - [i12]Ellen M. Voorhees, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, William R. Hersh, Kyle Lo, Kirk Roberts, Ian Soboroff, Lucy Lu Wang:
TREC-COVID: Constructing a Pandemic Information Retrieval Test Collection. CoRR abs/2005.04474 (2020) - [i11]Sarvesh Soni, Kirk Roberts:
An Evaluation of Two Commercial Deep Learning-Based Information Retrieval Systems for COVID-19 Literature. CoRR abs/2007.03106 (2020) - [i10]Sarvesh Soni, Kirk Roberts:
Patient Cohort Retrieval using Transformer Language Models. CoRR abs/2009.05121 (2020) - [i9]Surabhi Datta, Jordan Godfrey-Stovall, Kirk Roberts:
RadLex Normalization in Radiology Reports. CoRR abs/2009.05128 (2020) - [i8]Nicholas Greenspan, Yuqi Si, Kirk Roberts:
Extracting Concepts for Precision Oncology from the Biomedical Literature. CoRR abs/2010.00074 (2020) - [i7]Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy A. Miller, Fei Wang, W. Jim Zheng, Kirk Roberts:
Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review. CoRR abs/2010.02809 (2020) - [i6]Surabhi Datta, Shekhar Khanpara, Roy F. Riascos, Kirk Roberts:
Leveraging Spatial Information in Radiology Reports for Ischemic Stroke Phenotyping. CoRR abs/2010.05096 (2020)
2010 – 2019
- 2019
- [j16]Muhammad Amith, Kirk Roberts, Cui Tao:
Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management. BMC Bioinform. 20-S(21): 706 (2019) - [j15]Yuqi Si, Jingqi Wang, Hua Xu, Kirk E. Roberts:
Enhancing clinical concept extraction with contextual embeddings. J. Am. Medical Informatics Assoc. 26(11): 1297-1304 (2019) - [j14]Ziyi Li, Kirk Roberts, Xiaoqian Jiang, Qi Long:
Distributed learning from multiple EHR databases: Contextual embedding models for medical events. J. Biomed. Informatics 92 (2019) - [j13]Surabhi Datta, Elmer V. Bernstam, Kirk Roberts:
A frame semantic overview of NLP-based information extraction for cancer-related EHR notes. J. Biomed. Informatics 100 (2019) - [c58]Surabhi Datta, Elmer V. Bernstam, Kirk Roberts:
A frame semantic overview of NLP-based information extraction for cancer-related EHR notes: a scoping review. AMIA 2019 - [c57]Braja Gopal Patra, Kirk Roberts, Hulin Wu:
A Dataset Recommendation System for Researchers based on Publications. AMIA 2019 - [c56]Sarvesh Soni, Meghana Gudala, Daisy Zhe Wang, Kirk Roberts:
Using FHIR to Construct a Corpus of Clinical Questions Annotated with Logical Forms and Answers. AMIA 2019 - [c55]Qiang Wei, Zongcheng Ji, Yuqi Si, Jingcheng Du, Jingqi Wang, Firat Tiryaki, Stephen Wu, Cui Tao, Kirk Roberts, Hua Xu:
Relation Extraction from Clinical Narratives Using Pre-trained Language Models. AMIA 2019 - [c54]Muhammad Amith, Licong Cui, Kirk Roberts, Hua Xu, Cui Tao:
Ontology of Consumer Health Vocabulary: providing a formal and interoperable semantic resource for linking lay language and medical terminology. BIBM 2019: 1177-1178 - [c53]Sarvesh Soni, Kirk Roberts:
A Paraphrase Generation System for EHR Question Answering. BioNLP@ACL 2019: 20-29 - [c52]Heath Goodrum, Meghana Gudala, Ankita Misra, Kirk Roberts:
Extraction of Lactation Frames from Drug Labels and LactMed. BioNLP@ACL 2019: 191-200 - [c51]Muhammad Amith, Anna Zhu, Rachel Cunningham, Rebecca Lin, Lara S. Savas, Laura Shay, Yong Chen, Yang Gong, Julie Boom, Kirk Roberts, Cui Tao:
Early Usability Assessment of a Conversational Agent for HPV Vaccination. ITCH 2019: 17-23 - [c50]Tavleen Singh, Carlos A. Perez, Kirk Roberts, Nathan K. Cobb, Amy Franklin, Sahiti Myneni:
Characterization of Behavioral Transitions Through Social Media Analysis: A Mixed-Methods Approach. MedInfo 2019: 1228-1232 - [c49]Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines. SEPDA@ISWC 2019: 24-30 - [c48]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar, Shubham Pant, Funda Meric-Bernstam:
Overview of the TREC 2019 Precision Medicine Track. TREC 2019 - [i5]Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts:
Enhancing Clinical Concept Extraction with Contextual Embedding. CoRR abs/1902.08691 (2019) - [i4]Surabhi Datta, Elmer V. Bernstam, Kirk Roberts:
A frame semantic overview of NLP-based information extraction for cancer-related EHR notes. CoRR abs/1904.01655 (2019) - [i3]Surabhi Datta, Yuqi Si, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman, Kirk Roberts:
Understanding Spatial Language in Radiology: Representation Framework, Annotation, and Spatial Relation Extraction from Chest X-ray Reports using Deep Learning. CoRR abs/1908.04485 (2019) - 2018
- [c47]Dina Demner-Fushman, Joseph M. Tonning, Kin Wah Fung, Phong Do, Richard D. Boyce, Kirk Roberts:
Adverse Reactions and Drug-Drug Interaction Extraction tracks at the Text Analysis Conference (TAC). AMIA 2018 - [c46]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar, Shubham Pant:
Benchmarking Information Retrieval for Precision Oncology: the TREC Precision Medicine Track. AMIA 2018 - [c45]Yuqi Si, Kirk E. Roberts:
A Frame-Based NLP System for Cancer-Related Information Extraction. AMIA 2018 - [c44]Kirk Roberts, Yuqi Si, Anshul Gandhi, Elmer V. Bernstam:
A FrameNet for Cancer Information in Clinical Narratives: Schema and Annotation. LREC 2018 - [c43]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar:
Overview of the TREC 2018 Precision Medicine Track. TREC 2018 - 2017
- [j12]Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu:
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database J. Biol. Databases Curation 2017: bax061 (2017) - [j11]Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Trevor Cohen, Hua Xu:
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database J. Biol. Databases Curation 2017: bax068 (2017) - [j10]Kirk Roberts, Mary Regina Boland, Lisiane Pruinelli, Jina J. Dcruz, Andrew B. L. Berry, Mattias Georgsson, Rebecca Hazen, Raymond Francis Sarmiento, Uba Backonja, Kun-Hsing Yu, Yun Jiang, Patricia Flatley Brennan:
Biomedical informatics advancing the national health agenda: the AMIA 2015 year-in-review in clinical and consumer informatics. J. Am. Medical Informatics Assoc. 24(e1): e185-e190 (2017) - [j9]Ariel Deardorff, Kate Masterton, Kirk Roberts, Halil Kilicoglu, Dina Demner-Fushman:
A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. J. Assoc. Inf. Sci. Technol. 68(7): 1724-1736 (2017) - [c42]Hee-Jin Lee, Yaoyun Zhang, Kirk Roberts, Hua Xu:
Leveraging existing corpora for de-identification of psychiatric notes using domain adaptation. AMIA 2017 - [c41]Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, Trevor Cohen, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu:
Information Retrieval for Biomedical Datasets: The 2016 bioCADDIE Challenge. AMIA 2017 - [c40]Kirk Roberts, Braja Gopal Patra:
A Semantic Parsing Method for Mapping Clinical Questions to Logical Forms. AMIA 2017 - [c39]Parisa Kordjamshidi, Taher Rahgooy, Marie-Francine Moens, James Pustejovsky, Umar Manzoor, Kirk Roberts:
CLEF 2017: Multimodal Spatial Role Labeling Task Working Notes. CLEF (Working Notes) 2017 - [c38]Parisa Kordjamshidi, Taher Rahgooy, Marie-Francine Moens, James Pustejovsky, Umar Manzoor, Kirk Roberts:
CLEF 2017: Multimodal Spatial Role Labeling (mSpRL) Task Overview. CLEF 2017: 367-376 - [c37]Olivia R. Zhang, Yaoyun Zhang, Jun Xu, Kirk Roberts, Xiang Y. Zhang, Hua Xu:
Interweaving Domain Knowledge and Unsupervised Learning for Psychiatric Stressor Extraction from Clinical Notes. IEA/AIE (2) 2017: 396-406 - [c36]Luca Giancardo, Kirk Roberts, Zhongming Zhao:
Representation Learning for Retinal Vasculature Embeddings. FIFI/OMIA@MICCAI 2017: 243-250 - [c35]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh, Steven Bedrick, Alexander J. Lazar, Shubham Pant:
Overview of the TREC 2017 Precision Medicine Track. TREC 2017 - [i2]Kirk Roberts, Dina Demner-Fushman, Joseph M. Tonning:
Overview of the TAC 2017 Adverse Reaction Extraction from Drug Labels Track. TAC 2017 - 2016
- [j8]Kirk Roberts, Matthew S. Simpson, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh:
State-of-the-art in biomedical literature retrieval for clinical cases: a survey of the TREC 2014 CDS track. Inf. Retr. J. 19(1-2): 113-148 (2016) - [j7]Kirk Roberts, Dina Demner-Fushman:
Interactive use of online health resources: a comparison of consumer and professional questions. J. Am. Medical Informatics Assoc. 23(4): 802-811 (2016) - [c34]Kirk Roberts:
Assessing the Corpus Size vs. Similarity Trade-off for Word Embeddings in Clinical NLP. ClinicalNLP@COLING 2016 2016: 54-63 - [c33]Yassine Mrabet, Halil Kilicoglu, Kirk Roberts, Dina Demner-Fushman:
Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA 2016 - [c32]Kirk Roberts, Laritza M. Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman:
Resource Classification for Medical Questions. AMIA 2016 - [c31]Hoo-Chang Shin, Kirk Roberts, Le Lu, Dina Demner-Fushman, Jianhua Yao, Ronald M. Summers:
Learning to Read Chest X-Rays: Recurrent Neural Cascade Model for Automated Image Annotation. CVPR 2016: 2497-2506 - [c30]Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman:
Annotating Named Entities in Consumer Health Questions. LREC 2016 - [c29]Kirk Roberts, Dina Demner-Fushman:
Annotating Logical Forms for EHR Questions. LREC 2016 - [c28]Kirk Roberts, Dina Demner-Fushman, Ellen M. Voorhees, William R. Hersh:
Overview of the TREC 2016 Clinical Decision Support Track. TREC 2016 - [e1]Anna Rumshisky, Kirk Roberts, Steven Bethard, Tristan Naumann:
Proceedings of the Clinical Natural Language Processing Workshop, ClinicalNLP@COLING 2016, Osaka, Japan, December 11, 2016. The COLING 2016 Organizing Committee 2016, ISBN 978-4-87974-710-5 [contents] - [i1]Hoo-Chang Shin, Kirk Roberts, Le Lu, Dina Demner-Fushman, Jianhua Yao, Ronald M. Summers:
Learning to Read Chest X-Rays: Recurrent Neural Cascade Model for Automated Image Annotation. CoRR abs/1603.08486 (2016) - 2015
- [j6]Kirk Roberts, Sonya E. Shooshan, Laritza Rodriguez, Swapna Abhyankar, Halil Kilicoglu, Dina Demner-Fushman:
The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs. J. Biomed. Informatics 58: S111-S119 (2015) - [c27]Halil Kilicoglu, Marcelo Fiszman, Kirk Roberts, Dina Demner-Fushman:
An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA 2015 - [c26]Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman:
Automatic Extraction and Post-coordination of Spatial Relations in Consumer Language. AMIA 2015 - [c25]Kirk Roberts, Matthew S. Simpson, Ellen M. Voorhees, William R. Hersh:
Overview of the TREC 2015 Clinical Decision Support Track. TREC 2015 - 2014
- [c24]Kirk Roberts, Amos Cahan, Dina Demner-Fushman:
Error Propagation in EHRs via Copy/Paste: An Analysis of Relative Dates. AMIA 2014 - [c23]Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman:
Automatically Classifying Question Types for Consumer Health Questions. AMIA 2014 - [c22]Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman:
Decomposing Consumer Health Questions. BioNLP@ACL 2014: 29-37 - [c21]Kirk Roberts, Sanda M. Harabagiu, Michael A. Skinner:
Structuring Operative Notes using Active Learning. BioNLP@ACL 2014: 68-76 - [c20]Kirk Roberts, Kate Masterton, Marcelo Fiszman, Halil Kilicoglu, Dina Demner-Fushman:
Annotating Question Decomposition on Complex Medical Questions. LREC 2014: 2598-2602 - 2013
- [j5]Kirk Roberts, Bryan Rink, Sanda M. Harabagiu:
A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. J. Am. Medical Informatics Assoc. 20(5): 867-875 (2013) - [c19]Kirk Roberts, Michael A. Skinner, Sanda M. Harabagiu:
Recognizing Spatial Containment Relations between Event Mentions. IWCS 2013: 216-227 - 2012
- [j4]Bryan Rink, Kirk Roberts, Sanda M. Harabagiu:
A supervised framework for resolving coreference in clinical records. J. Am. Medical Informatics Assoc. 19(5): 875-882 (2012) - [c18]Kirk Roberts, Bryan Rink, Sanda M. Harabagiu, Richard H. Scheuermann, Seth M. Toomay, Travis Browning, Teresa Bosler, Ronald M. Peshock:
A Machine Learning Approach for Identifying Anatomical Locations of Actionable Findings in Radiology Reports. AMIA 2012 - [c17]Kirk Roberts, Sanda M. Harabagiu:
Locational relativity and domain constraints in spatial questions. SIGSPATIAL/GIS 2012: 219-228 - [c16]Kirk Roberts, Travis R. Goodwin, Sanda M. Harabagiu:
Annotating Spatial Containment Relations Between Events. LREC 2012: 3052-3059 - [c15]Kirk Roberts, Michael A. Roach, Joseph Johnson, Josh Guthrie, Sanda M. Harabagiu:
EmpaTweet: Annotating and Detecting Emotions on Twitter. LREC 2012: 3806-3813 - [c14]Kirk Roberts, Sanda M. Harabagiu:
UTD-SpRL: A Joint Approach to Spatial Role Labeling. SemEval@NAACL-HLT 2012: 419-424 - [c13]Travis R. Goodwin, Bryan Rink, Kirk Roberts, Sanda M. Harabagiu:
UTDHLT: COPACETIC System for Choosing Plausible Alternatives. SemEval@NAACL-HLT 2012: 461-466 - [c12]Travis R. Goodwin, Kirk Roberts, Bryan Rink, Sanda M. Harabagiu:
Cohort Sherpherd II: Verifying Cohort Constraints from Hospital Visits. TREC 2012 - 2011
- [j3]Kirk Roberts, Sanda M. Harabagiu:
Detecting New and Emerging Events in Streaming News Documents. Int. J. Semantic Comput. 5(4): 407-431 (2011) - [j2]Kirk Roberts, Sanda M. Harabagiu:
A flexible framework for deriving assertions from electronic medical records. J. Am. Medical Informatics Assoc. 18(5): 568-573 (2011) - [j1]Bryan Rink, Sanda M. Harabagiu, Kirk Roberts:
Automatic extraction of relations between medical concepts in clinical texts. J. Am. Medical Informatics Assoc. 18(5): 594-600 (2011) - [c11]Kirk Roberts, Sanda M. Harabagiu:
Unsupervised Learning of Selectional Restrictions and Detection of Argument Coercions. EMNLP 2011: 980-990 - [c10]Kirk Roberts, Sanda M. Harabagiu:
Detecting New and Emerging Events from Textual Sources. ICSC 2011: 67-74 - [c9]Travis R. Goodwin, Bryan Rink, Kirk Roberts, Sanda M. Harabagiu:
Cohort Shepherd: Discoving Cohort Traits from Hospital Visits. TREC 2011 - 2010
- [c8]Kirk Roberts, Cosmin Adrian Bejan, Sanda M. Harabagiu:
Toponym Disambiguation Using Events. FLAIRS 2010 - [c7]Cristina Nicolae, Gabriel Nicolae, Kirk Roberts:
C-3: Coherence and Coreference Corpus. LREC 2010 - [c6]Kirk Roberts, Srikanth Gullapalli, Cosmin Adrian Bejan, Sanda M. Harabagiu:
A Linguistic Resource for Semantic Parsing of Motion Events. LREC 2010 - [c5]Kirk Roberts, Sanda M. Harabagiu:
UTDMet: Combining WordNet and Corpus Data for Argument Coercion Detection. SemEval@ACL 2010: 252-255
2000 – 2009
- 2009
- [c4]Kirk Roberts:
Building an Annotated Textual Inference Corpus for Motion and Space. TextInfer@ACL 2009: 48-51 - 2008
- [c3]Kirk Roberts, Andrew Hickl:
Scaling Answer Type Detection to Large Hierarchies. LREC 2008 - 2007
- [c2]Andrew Hickl, Kirk Roberts, Bryan Rink, Jeremy Bensley, Tobias Jungen, Ying Shi, John Williams:
Question Answering with LCC's CHAUCER-2 at TREC 2007. TREC 2007 - 2006
- [c1]Andrew Hickl, John Williams, Jeremy Bensley, Kirk Roberts, Ying Shi, Bryan Rink:
Question Answering with LCC's CHAUCER at TREC 2006. TREC 2006
Coauthor Index
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