Automatically Extracting Ontologically Specified Data from HTML Tables of Unknown Structure. - David W. Embley; Cui Tao; Stephen W. Liddle (ER, 2002)

Speaker-independent speech recognition based on fast neural network. - Cui Tao; Taiyi Zhang (Int. J. Artif. Intell. Tools, 2003)

Automating the extraction of data from HTML tables with unknown structure. - David W. Embley; Cui Tao; Stephen W. Liddle (Data Knowl. Eng., 2005)

Automatic Creation of Web Services from Extraction Ontologies. - Cui Tao; Yihong Ding; Deryle W. Lonsdale (ER (Workshops), 2006)

Toward Making Online Biological Data Machine Understandable. - Cui Tao (ISWC, 2006)

Automatic Hidden-Web Table Interpretation by Sibling Page Comparison. - Cui Tao; David W. Embley (ER, 2007)

Seed-Based Generation of Personalized Bio-ontologies for Information Extraction. - Cui Tao; David W. Embley (ER Workshops, 2007)

A Web of Knowledge: A Conceptual-Modeling Perspective. - David W. Embley; Stephen W. Liddle; Cui Tao (The Evolution of Conceptual Modeling, 2008)

A Conceptual-Model-Based Computational Alembic for a Web of Knowledge. - David W. Embley; Stephen W. Liddle; Deryle W. Lonsdale; George Nagy; Yuri A. Tijerino; Robert Clawson; Jordan Crabtree; Yihong Ding; Piyushee Jha; Zonghui Lian; Stephen Lynn; Raghav K. Padmanabhan; et al. (ER, 2008)

FOCIH: Form-Based Ontology Creation and Information Harvesting. - Cui Tao; David W. Embley; Stephen W. Liddle (ER, 2009)

Automatic hidden-web table interpretation, conceptualization, and semantic annotation. - Cui Tao; David W. Embley (Data Knowl. Eng., 2009)

KBB: A Knowledge-Bundle Builder for Research Studies. - David W. Embley; Stephen W. Liddle; Deryle W. Lonsdale; Aaron P. Stewart; Cui Tao (ER Workshops, 2010)

Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. - Cui Tao; Harold R. Solbrig; Deepak K. Sharma; Wei-Qi Wei; Guergana K. Savova; Christopher G. Chute (ISWC (2), 2010)

Proposed SKOS Extensions for BioPortal Terminology Services. - Cui Tao; Natalya Fridman Noy; Harold R. Solbrig; Nigam H. Shah; Mark A. Musen; Christopher G. Chute (JIST, 2011)

Wireless extensions of CANBUS in industrial applications. - Wen Chen 017; Lei Kong; Yun Wu 002; Xiaohui Liao; Cui Tao (BMEI, 2011)

Managing interoperability and complexity inhealth systems: MIXHS'11 workshop summary. - Matt-Mouley Bouamrane; Cui Tao (CIKM, 2011)

Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based Approaches. - Cui Tao; Guoqian Jiang; Kimberly Clark; Deepak K. Sharma; Christopher G. Chute (ICBO, 2011)

Common Terminology Services 2 (CTS2) for Biomedical Community. - Cui Tao; Harold R. Solbrig; Pradip Kanjamala; Kevin J. Peterson; Craig Stancle; Christopher G. Chute (AMIA, 2012)

Ontology-Based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data. - Dingcheng Li; Cui Tao; Hongfang Liu; Christopher G. Chute (CGC, 2012)

An overview of electronic health information management systems quality assessment. - Matt-Mouley Bouamrane; Frances S. Mair; Cui Tao (MIX-HS, 2012)

Modeling UIMA type system using web ontology language: towards interoperability among UIMA-based NLP tools. - Hongfang Liu; Stephen T. Wu; Cui Tao; Christopher G. Chute (MIX-HS, 2012)

Managing interoperability and compleXity in health systems - MIXHS'12. - Cui Tao; Matt-Mouley Bouamrane (CIKM, 2012)

Optimizing semantic MEDLINE for translational science studies using semantic web technologies. - Cui Tao; Yuji Zhang 001; Guoqian Jiang; Matt-Mouley Bouamrane; Christopher G. Chute (MIX-HS, 2012)

A Semantic-Web Oriented Representation of Clinical Element Model for Secondary Use of Electronic Healthcare Data. - Cui Tao; Guoqian Jiang; Thomas A. Oniki; Robert R. Freimuth; Jyotishman Pathak; Qian Zhu 003; Deepak K. Sharma; Stanley M. Huff; Christopher G. Chute (HISB, 2012)

Towards event sequence representation, reasoning and visualization for EHR data. - Cui Tao; Krist Wongsuphasawat; Kimberly Clark; Catherine Plaisant; Ben Shneiderman; Christopher G. Chute (IHI, 2012)

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). - Yongqun He; Luca Toldo; Gully Burns; Cui Tao; Darrell R. Abernethy (J. Biomed. Semant., 2012)

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. - Cui Tao; Yongqun He; Hannah Yang; Gregory A. Poland; Christopher G. Chute (J. Biomed. Semant., 2012)

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. - Stephen T. Wu; Hongfang Liu; Dingcheng Li; Cui Tao; Mark A. Musen; Christopher G. Chute; Nigam H. Shah (J. Am. Medical Informatics Assoc., 2012)

Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project. - 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 (J. Biomed. Informatics, 2012)

Combining Infobuttons and Semantic Web Rules for Identifying Patterns and Delivering Highly-Personalized Education Materials. - Nathan C. Hulse; Jie Long; Cui Tao (AMIA, 2013)

Coreference Resolution from Medical Corpus with Topic Modeling. - Dingcheng Li; Liwei Wang 010; Cui Tao; Christopher G. Chute; Hongfang Liu (AMIA, 2013)

Adding Search Engine Functionality to Infobutton Manager Platform. - Jie Long; Nathan C. Hulse; Cui Tao; Guilherme Del Fiol (AMIA, 2013)

Introduction and Implementation of Common Terminology Services 2 (CTS2). - Cui Tao; Harold R. Solbrig; Craig Stancl; Kevin J. Peterson; Cory M. Endle; Scott Bauer; Deepak K. Sharma; Christopher G. Chute (AMIA, 2013)

An integrative computational approach to identify disease-specific networks from PubMed literature information. - Yuji Zhang 001; Dingcheng Li; Cui Tao; Feichen Shen; Hongfang Liu (BIBM, 2013)

Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (VDOS+DO@ICBO, 2013)

Phenotyping on EHR Data Using OWL and Semantic Web Technologies. - Cui Tao; Dingcheng Li; Feichen Shen; Zonghui Lian; Jyotishman Pathak; Hongfang Liu; Christopher G. Chute (ICSH, 2013)

Isosemantic Rendering of Clinical Information Using Formal Ontologies and RDF. - Catalina Martínez-Costa; Diego Boscá; María Del Carmen Legaz-García; Cui Tao; Jesualdo Tomás Fernández-Breis; Stefan Schulz 001; Christopher G. Chute (MedInfo, 2013)

Ontology-based Temporal Analysis for Medical Device Adverse Event - A Use Case Study on Late Stent Thrombosis. - Kimberly Clark; Deepak K. Sharma; Rui Qin; Christopher G. Chute; Cui Tao (SWAT4LS, 2013)

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (J. Biomed. Semant., 2013)

Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. - Sunghwan Sohn; Kavishwar B. Wagholikar; Dingcheng Li; Siddhartha Jonnalagadda; Cui Tao; Ravikumar Komandur Elayavilli; Hongfang Liu (J. Am. Medical Informatics Assoc., 2013)

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. - Cui Tao; Guoqian Jiang; Thomas A. Oniki; Robert R. Freimuth; Qian Zhu 003; Deepak K. Sharma; Jyotishman Pathak; Stanley M. Huff; Christopher G. Chute (J. Am. Medical Informatics Assoc., 2013)

Terminology representation guidelines for biomedical ontologies in the semantic web notations. - Cui Tao; Jyotishman Pathak; Harold R. Solbrig; Wei-Qi Wei; Christopher G. Chute (J. Biomed. Informatics, 2013)

Semantator: Semantic annotator for converting biomedical text to linked data. - Cui Tao; Dezhao Song; Deepak K. Sharma; Christopher G. Chute (J. Biomed. Informatics, 2013)

Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study. - Qian Zhu 003; Robert R. Freimuth; Zonghui Lian; Scott Bauer; Jyotishman Pathak; Cui Tao; Matthew J. Durski; Christopher G. Chute (J. Biomed. Informatics, 2013)

Enhancing the TURF Framework with a Workflow Ontology. - Craig Harrington; Cui Tao; Keith A. Butler; Jiajie Zhang (AMIA, 2014)

Enabling Locally-Developed Content For Access Through the Infobutton By Means of Automated Concept Annotation. - Nathan C. Hulse; Jie Long; Xiaomin Xu; Cui Tao (AMIA, 2014)

An Integrative Framework for Drug Target Prediction and Repurposing. - Jingchun Sun; Cui Tao; Kevin W. Zhu; W. Jim Zheng; Junjie Chen; Hua Xu 001 (AMIA, 2014)

Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. - Feichen Shen; Dingcheng Li; Hongfang Liu; Yugyung Lee; Jyotishman Pathak; Christopher G. Chute; Cui Tao (BHI, 2014)

An Initial Framework for an Ontology-based Mobile Application for Vaccine Information Retrieval and Education. - Muhammad Amith; Cui Tao (ICBO, 2014)

Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature. - Guocai Chen; Jieyi Zhao; Trevor Cohen; Cui Tao; Jingchun Sun; Hua Xu 001; Elmer V. Bernstam; Jia Zeng; Amber M. Johnson; Vijaykumar Holla; Ann Balley; Funda Meric-Bernstam; et al. (ICBO, 2014)

Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches. - Cui Tao; Jingchun Sun; W. Jim Zheng; Junjie Chen; Hua Xu 001 (ICBO, 2014)

Ontology-based Normalization for Disease-Lab test Relation Extraction. - Yaoyun Zhang; Jingqi Wang; Cui Tao; Hua Xu 001 (ICBO, 2014)

Pharmacological Class Data Representation in the Web Ontology Language (OWL). - Qian Zhu 003; Cui Tao (ICBO, 2014)

A Prototype Mobile Virtual Assistant for Semantic-Based Vaccine Information Retrieval. - Muhammad Amith; Cui Tao (ICSH, 2014)

Linked Vaccine Adverse Event Data Representation from VAERS for Biomedical Informatics Research. - Cui Tao; Puqiang Wu; Yuji Zhang 001 (PAKDD Workshops, 2014)

Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics Approaches. - Qian Zhu 003; Cui Tao; Feichen Shen; Christopher G. Chute (Pacific Symposium on Biocomputing, 2014)

A Work Domain Ontology for Modeling Emergency Department Workflow. - Cui Tao; Nnaemeka Okafor; Amit M. Mehta; Charles L. Maddow; David J. Robinson; Brent King; Jiajie Zhang; Amy Franklin (SWAT4LS, 2014)

GSO: A Semantic Web Ontology to Capture 3D Genome Structure. - W. Jim Zheng; Jingcheng Du; Jijun Tang; Cui Tao (SWAT4LS, 2014)

Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies. - Cui Tao; Puqiang Wu; Yi Luo; Yuji Zhang 001 (BioData Min., 2014)

A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis. - Kimberly Clark; Deepak K. Sharma; Rui Qin; Christopher G. Chute; Cui Tao (J. Biomed. Semant., 2014)

OAE: The Ontology of Adverse Events. - Yongqun He; Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Abra Guo; Shelley Zhang 002; Desikan Jagannathan; Luca Toldo; Cui Tao; Barry Smith 001 (J. Biomed. Semant., 2014)

A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). - Cui Tao; Yongqun He; Sivaram Arabandi (J. Biomed. Semant., 2014)

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. - Yuji Zhang 001; Cui Tao; Guoqian Jiang; Asha A. Nair; Jian Su; Christopher G. Chute; Hongfang Liu (J. Biomed. Semant., 2014)

Model Checking for Verification of Interactive Health IT Systems. - Keith A. Butler; Eric Mercer; Ali Bahrami; Cui Tao (AMIA, 2015)

Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach. - Guoqian Jiang; Harold R. Solbrig; Eric Prud'hommeaux; Cui Tao; Chunhua Weng; Christopher G. Chute (AMIA, 2015)

Analysis of empty responses from electronic resources in infobutton managers. - Jie Long; Nathan C. Hulse; Cui Tao (AMIA, 2015)

Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing. - Chen Liang 005; Jingchun Sun; Cui Tao (MedInfo, 2015)

Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living. - Sahiti Myneni; Muhammad Amith; Yimin Geng; Cui Tao (MedInfo, 2015)

Trivalent Influenza Vaccine Adverse Event Analysis Based On MedDRA System Organ Classes Using VAERS Data. - Cui Tao; Jingcheng Du; Yi Cai; Yong Chen 016 (MedInfo, 2015)

A Web Application Towards Semiotic-based Evaluation of Biomedical Ontologies. - Muhammad Amith; Cui Tao (BDM2I@ISWC, 2015)

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. - Guocai Chen; Jieyi Zhao; Trevor Cohen; Cui Tao; Jingchun Sun; Hua Xu 001; Elmer V. Bernstam; Andrew Lawson; Jia Zeng; Amber M. Johnson; Vijaykumar Holla; Ann M. Bailey; et al. (Database J. Biol. Databases Curation, 2015)

Colorectal cancer drug target prediction using ontology-based inference and network analysis. - Cui Tao; Jingchun Sun; W. Jim Zheng; Junjie Chen; Hua Xu 001 (Database J. Biol. Databases Curation, 2015)

Developing VISO: Vaccine Information Statement Ontology for patient education. - Muhammad Amith; Yang Gong; Rachel Cunningham; Julie Boom; Cui Tao (J. Biomed. Semant., 2015)

Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS. - Yuji Zhang 001; Puqiang Wu; Yi Luo; Cui Tao (J. Biomed. Semant., 2015)

Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes. - María Del Carmen Legaz-García; Marcos Menárguez Tortosa; Jesualdo Tomás Fernández-Breis; Christopher G. Chute; Cui Tao (J. Am. Medical Informatics Assoc., 2015)

A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. - Jeffrey S. Grethe; Ibrahim Burak Özyurt; Hua Xu 001; Xiaoling Chen; Ruiling Liu; Ergin Soysal; Anupama E. Gururaj; Hyeon-Eui Kim; Trevor Cohen; Todd R. Johnson; Mandana Salimi; Saeid Pournejati; et al. (AMIA, 2016)

Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. - Hua Xu 001; Jeffrey S. Grethe; Xiaoling Chen; Ruiling Liu; Ergin Soysal; Anupama E. Gururaj; Yueling Li; Ibrahim Burak Özyurt; Hyeon-Eui Kim; Trevor Cohen; Todd R. Johnson; Mandana Salimi; et al. (AMIA, 2016)

A representational analysis of a temporal indeterminancy display in clinical events. - Mohcine Madkour; Hsing-yi Song; Jingcheng Du; Cui Tao (BIBM, 2016)

Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing. - Chen Liang; Jingchun Sun; Cui Tao (CRI, 2016)

Towards a HPV Vaccine Knowledgebase for Patient Education Content. - Dennis Wang; Rachel Cunningham; Julie Boom; Muhammad Amith; Cui Tao (Nursing Informatics, 2016)

Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011. - Jingcheng Du; Yi Cai; Yong Chen 016; Cui Tao (J. Biomed. Semant., 2016)

Vaccine and Drug Ontology Studies (VDOS 2014). - Cui Tao; Yongqun He; Sivaram Arabandi (J. Biomed. Semant., 2016)

Extracting drug-enzyme relation from literature as evidence for drug drug interaction. - Yaoyun Zhang; Heng-Yi Wu; Jingcheng Du; Jun Xu 007; Jingqi Wang; Cui Tao; Lang Li 001; Hua Xu 001 (J. Biomed. Semant., 2016)

Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction. - Yaoyun Zhang; Heng-Yi Wu; Jingcheng Du; Jun Xu 007; Jingqi Wang; Cui Tao; Lang Li 001; Hua Xu 001 (J. Biomed. Semant., 2016)

Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain. - Mohcine Madkour; Driss Benhaddou; Cui Tao (Comput. Methods Programs Biomed., 2016)

From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. - Marcelline R. Harris; Frank J. Manion; Hsing-yi Song; Yongqun He; Muhamamd F. Amith; Cui Tao (AMIA, 2017)

Big Data to Knowledge (BD2K) and the Application of Metadata. - Guoqian Jiang; Walter S. Campbell; Timothy Clark; Cui Tao; Mark A. Musen (AMIA, 2017)

A Twitter Study of the Relationship between the Geographic Variations of HPV Vaccination Rates and Online Information in the United States. - Hansi Zhang; Yunpeng Zhao; Christopher Wheldon; Xinsong Du; Terrell Brown; Yi Guo 005; Stephanie Staras; Jingcheng Du; Cui Tao; Jiang Bian 001 (AMIA, 2017)

A pilot study of mining association between psychiatric stressors and symptoms in tweets. - Jingcheng Du; Yaoyun Zhang; Cui Tao; Hua Xu 001 (BIBM, 2017)

Towards practical temporal relation extraction from clinical notes: An analysis of direct temporal relations. - Hee-Jin Lee; Yaoyun Zhang; Jun Xu 007; Cui Tao; Hua Xu 001; Min Jiang 007 (BIBM, 2017)

Designing an ontology for emotion-driven visual representations. - Rebecca Lin; Muhammad Tuan Amith; Chen Liang 005; Cui Tao (BIBM, 2017)

Computer-aided diagnosis of four common cutaneous diseases using deep learning algorithm. - Xinyuan Zhang 006; Shiqi Wang 008; Jie Liu; Cui Tao (BIBM, 2017)

Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. - Sijia Liu 002; Liwei Wang 010; Donna M. Ihrke; Vipin Chaudhary; Cui Tao; Chunhua Weng; Hongfang Liu (CRI, 2017)

Leveraging Machine Learning Based Approaches to Assess Human Papillomavirus Vaccination Sentiment Trends with Twitter. - Jingcheng Du; Jun Xu 007; Hsing-yi Song; Cui Tao (CRI, 2017)

Post-marketing Drug Safety Evaluation Using Data Mining Based on FAERS. - Rui Duan 004; Xinyuan Zhang 003; Jingcheng Du; Jing Huang 021; Cui Tao; Yong Chen 016 (DMBD, 2017)

Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification. - Muhammad Amith; Yaoyun Zhang; Hua Xu 001; Cui Tao (IEA/AIE (2), 2017)

Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. - Muhammad Amith; Frank J. Manion; Marcelline R. Harris; Yaoyun Zhang; Hua Xu 001; Cui Tao (MedInfo, 2017)

Comparing the Human Papillomavirus Vaccination Opinions Trends from Different Twitter User Groups with a Machine Learning Based System and Semiparametric Nonlinear Regression. - Jingcheng Du; Jing Huang 021; Rui Duan 004; Yong Chen 016; Cui Tao (MedInfo, 2017)

Comparing Different Adverse Effects Among Multiple Drugs Using FAERS Data. - Jing Huang 021; Xinyuan Zhang 003; Jingcheng Du; Rui Duan 004; Liu Yang; Jason H. Moore; Yong Chen 016; Cui Tao (MedInfo, 2017)

Modulated evaluation metrics for drug-based ontologies. - Muhammad Amith; Cui Tao (J. Biomed. Semant., 2017)

Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets. - Jingcheng Du; Jun Xu 007; Hsing-yi Song; Xiangyu Liu; Cui Tao (J. Biomed. Semant., 2017)

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. - Deepak K. Sharma; Harold R. Solbrig; Cui Tao; Chunhua Weng; Christopher G. Chute; Guoqian Jiang (J. Biomed. Semant., 2017)

Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content. - Muhammad Amith; Rachel Cunningham; Lara S. Savas; Julie Boom; Roger W. Schvaneveldt; Cui Tao; Trevor Cohen (J. Biomed. Informatics, 2017)

Lightweight predicate extraction for patient-level cancer information and ontology development. - Muhammad Amith; Hsing-yi Song; Yaoyun Zhang; Hua Xu 001; Cui Tao (BMC Medical Informatics Decis. Mak., 2017)

A signal detection method for temporal variation of adverse effect with vaccine adverse event reporting system data. - Yi Cai; Jingcheng Du; Jing Huang 021; Susan S. Ellenberg; Sean Hennessy; Cui Tao; Yong Chen 016 (BMC Medical Informatics Decis. Mak., 2017)

Leveraging machine learning-based approaches to assess human papillomavirus vaccination sentiment trends with Twitter data. - Jingcheng Du; Jun Xu 007; Hsing-yi Song; Cui Tao (BMC Medical Informatics Decis. Mak., 2017)

Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. - Cui Tao; Yang Gong; Hua Xu 001; Zhongming Zhao (BMC Medical Informatics Decis. Mak., 2017)

Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. - Jing An; Mandana Salimi; Anupama E. Gururaj; Cui Tao; Degui Zhi; Hua Xu 001 (AMIA, 2018)

Mining Human Papillomavirus Vaccination Health Beliefs from Twitter Using Attentive Recurrent Neural Network. - Jingcheng Du; Fang Li 011; Yuxi Jia; Yang Xiang 003; Lu Tang; Sahiti Myneni; Cui Tao (AMIA, 2018)

Construction of Drug Repurposing-oriented Alzheimer's Disease Ontology. - Fang Li 011; Jingcheng Du; Guozheng Rao; Cui Tao (AMIA, 2018)

Development and Validation of an Ontological Representation of the US Common Rule. - Frank J. Manion; Marcelline R. Harris; Muhamamd F. Amith; Cui Tao (AMIA, 2018)

Identification of Rare Adverse Events with Year-varying Reporting Rates for FLU4 Vaccine in VAERS. - Jiayi Tong; Jing Huang 021; Jingcheng Du; Yi Cai; Cui Tao; Yong Chen 016 (AMIA, 2018)

Asthma Onset Prediction Using Structured EMR Data. - Yang Xiang 003; Jun Xu 007; Jingcheng Du; Degui Zhi; Cui Tao (AMIA, 2018)

Computer Aided Diagnosis of Chest X-rays using by Combining Deep Convolutional Neural Networks. - Xinyuan Zhang 006; Sicheng Zhou; Luca Giancardo; Cui Tao (AMIA, 2018)

OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BIBM, 2018)

X-A-BiLSTM: a Deep Learning Approach for Depression Detection in Imbalanced Data. - Qing Cong; Zhiyong Feng 002; Fang Li 011; Yang Xiang 003; Guozheng Rao; Cui Tao (BIBM, 2018)

Constructing Biomedical Knowledge Graph Based on SemMedDB and Linked Open Data. - Qing Cong; Zhiyong Feng 002; Fang Li 011; Li Zhang 059; Guozheng Rao; Cui Tao (BIBM, 2018)

Comparing adverse effects of Hepatitis C drugs using FAERS data. - Jing Huang 021; Xinyuan Zhang 003; Jiayi Tong; Jingcheng Du; Rui Duan 004; Liu Yang; Jason H. Moore; Yong Chen 016; Cui Tao (BIBM, 2018)

VEO-Engine: Interfacing and Reasoning with an Emotion Ontology for Device Visual Expression. - Muhammad Amith; Rebecca Lin; Chen Liang 005; Yang Gong; Cui Tao (HCI (29), 2018)

Coordinated Evolution of Ontologies of Informed Consent. - J. Neil Otte; Cooper Stansbury; Jonathan Vajda; Frank J. Manion; Elizabeth Umberfield; Yongqun He; Marcelline R. Harris; Jihad S. Obeid; Mathias Brochhausen; William D. Duncan; Cui Tao (ICBO, 2018)

Term Standardization and Normalization for Research Domain Criteria (RDoC). - Fang Li 011; Guozheng Rao; Jingcheng Du; Yang Xiang 003; Yaoyun Zhang; Salih Selek; Jane Elizabeth Hamilton; Hua Xu 001; Cui Tao (ICHI Workshops, 2018)

Exploring Temporal Patterns of Suicidal Behavior on Twitter. - Jianhong Luo; Jingcheng Du; Cui Tao; Hua Xu 001; Yaoyun Zhang (ICHI Workshops, 2018)

Comparing Pharmacovigilance Outcomes Between FAERS and EMR Data for Acute Mania Patients. - Xinyuan Zhang 003; Rui Duan 004; Jingcheng Du; Jing Huang 021; Yong Chen 016; Cui Tao (ICHI Workshops, 2018)

Representing vaccine misinformation using ontologies. - Muhammad Amith; Cui Tao (J. Biomed. Semant., 2018)

Toward a normalized clinical drug knowledge base in China - applying the RxNorm model to Chinese clinical drugs. - Li Wang 077; Yaoyun Zhang; Min Jiang 007; Jingqi Wang; Jiancheng Dong; Yun Liu 020; Cui Tao; Guoqian Jiang; Yi Zhou 005; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2018)

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. - Muhammad Amith; Zhe He 001; Jiang Bian 001; Juan Antonio Lossio-Ventura; Cui Tao (J. Biomed. Informatics, 2018)

Extracting psychiatric stressors for suicide from social media using deep learning. - Jingcheng Du; Yaoyun Zhang; Jianhong Luo; Yuxi Jia; Qiang Wei 002; Cui Tao; Hua Xu 001 (BMC Medical Informatics Decis. Mak., 2018)

Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). - Zhe He 001; Cui Tao; Jiang Bian 001; Rui Zhang 028; Jingshan Huang (BMC Medical Informatics Decis. Mak., 2018)

Identifying direct temporal relations between time and events from clinical notes. - Hee-Jin Lee; Yaoyun Zhang; Min Jiang 007; Jun Xu 007; Cui Tao; Hua Xu 001 (BMC Medical Informatics Decis. Mak., 2018)

Visualized Emotion Ontology: a model for representing visual cues of emotions. - Rebecca Lin; Muhammad Amith; Chen Liang 005; Rui Duan 004; Yong Chen 016; Cui Tao (BMC Medical Informatics Decis. Mak., 2018)

Towards improving diagnosis of skin diseases by combining deep neural network and human knowledge. - Xinyuan Zhang 006; Shiqi Wang 008; Jie Liu; Cui Tao (BMC Medical Informatics Decis. Mak., 2018)

A Scoping Review to Identify Biobank Classification and Permissions to Share Metadata. - Marcelline R. Harris; Frank J. Manion; Madhuri Sankaranarayanapillai; Hsing-yi Song; Marisa Conte; Cui Tao (AMIA, 2019)

Refactoring and Expanding the Informed Consent Ontology (ICO). - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Marcelline R. Harris; Frank J. Manion; Cui Tao (AMIA, 2019)

Expanding the Representation of Permissions and Deontic Roles in the Informed Consent Ontology (ICO). - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Marcelline R. Harris; Elizabeth Umberfield; Frank J. Manion; Cui Tao (AMIA, 2019)

Relation Extraction from Clinical Narratives Using Pre-trained Language Models. - Qiang Wei 002; Zongcheng Ji; Yuqi Si; Jingcheng Du; Jingqi Wang; Firat Tiryaki; Stephen Wu 004; Cui Tao; Kirk Roberts; Hua Xu 001 (AMIA, 2019)

Ontology of Consumer Health Vocabulary: providing a formal and interoperable semantic resource for linking lay language and medical terminology. - Muhammad Amith; Licong Cui; Kirk Roberts; Hua Xu 001; Cui Tao (BIBM, 2019)

NET-EXPO: A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs. - Muhammad Tuan Amith; Kayo Fujimoto; Cui Tao (HCI (35), 2019)

Alexa, What Should I Eat? : A Personalized Virtual Nutrition Coach for Native American Diabetes Patients Using Amazon's Smart Speaker Technology. - Bikesh Maharjan; Juan Li 004; Jun Kong; Cui Tao (HealthCom, 2019)

Using Stases to Enrich Queries for When and Where Regulations Are in Force. - Jonathan M. Vajda; J. Neil Otte; Cooper Stansbury; Frank J. Manion; Marcelline R. Harris; Cui Tao (ICBO, 2019)

Systematic Design of Drug Repurposing-Oriented Alzheimer's Disease Ontology. - Fang Li 011; Mingqiang Wang; Huy Anh Pham; Yang Xiang 003; Muhammad Tuan Amith; Cui Tao; Jingcheng Du; Guozheng Rao (ICHI, 2019)

Early Usability Assessment of a Conversational Agent for HPV Vaccination. - Muhammad Amith; Anna Zhu; Rachel Cunningham; Rebecca Lin; Lara S. Savas; Laura Shay; Yong Chen 016; Yang Gong; Julie Boom; Kirk Roberts; Cui Tao (ITCH, 2019)

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. - Ergin Soysal; Jeremy L. Warner; Jingqi Wang; Min Jiang 007; Krysten Harvey; Sandeep Kumar Jain; Xiao Dong; Hsing-yi Song; Harish Siddhanamatha; Liwei Wang 010; Qi Dai; Qingxia Chen; et al. (MedInfo, 2019)

Text Mining and Machine Learning for Precision Medicine. - Graciela Gonzalez 001; Zhiyong Lu; Robert Leaman; Davy Weissenbacher; Mary Regina Boland; Yong Chen 016; Jingcheng Du; Juliane Fluck; Casey S. Greene; John H. Holmes; Aditya Kashyap; Rikke Linnemann Nielsen; et al. (PSB, 2019)

An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines. - Muhammad Amith; Rebecca Lin; Licong Cui; Dennis Wang; Anna Zhu; Grace Xiong; Hua Xu 001; Kirk Roberts; Cui Tao (SEPDA@ISWC, 2019)

A Multi-Source Linked Open Data Fusion Method for Gene Disorder Drug Relationship Querying. - Guozheng Rao; Li Zhang 059; Xiaowang Zhang; Wenwen Li; Fang Li 011; Cui Tao (SEPDA@ISWC, 2019)

Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management. - Muhammad Amith; Kirk Roberts; Cui Tao (BMC Bioinform., 2019)

A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). - Junguk Hur; Cui Tao; Yongqun He (BMC Bioinform., 2019)

Exploring difference in public perceptions on HPV vaccine between gender groups from Twitter using deep learning. - Jingcheng Du; Chongliang Luo; Qiang Wei; Yong Chen 016; Cui Tao (CoRR, 2019)

Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. - Hansi Zhang; Christopher Wheldon; Adam G. Dunn; Cui Tao; Jinhai Huo; Rui Zhang 028; Mattia Prosperi; Yi Guo 005; Jiang Bian 001 (CoRR, 2019)

ML-Net: multi-label classification of biomedical texts with deep neural networks. - Jingcheng Du; Qingyu Chen 001; Yifan Peng 002; Yang Xiang 003; Cui Tao; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2019)

Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men. - Yang Xiang 003; Kayo Fujimoto; John A. Schneider; Yuxi Jia; Degui Zhi; Cui Tao (J. Am. Medical Informatics Assoc., 2019)

Architecture and usability of OntoKeeper, an ontology evaluation tool. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BMC Medical Informatics Decis. Mak., 2019)

Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. - Guocai Chen; Yuxi Jia; Lisha Zhu; Ping Li; Lin Zhang; Cui Tao; W. Jim Zheng (BMC Medical Informatics Decis. Mak., 2019)

Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). - Zhe He 001; Jiang Bian 001; Cui Tao; Rui Zhang 028 (BMC Medical Informatics Decis. Mak., 2019)

Comparing drug safety of hepatitis C therapies using post-market data. - Jing Huang 021; Xinyuan Zhang 003; Jiayi Tong; Jingcheng Du; Rui Duan 004; Liu Yang; Jason H. Moore; Cui Tao; Yong Chen 016 (BMC Medical Informatics Decis. Mak., 2019)

Time-sensitive clinical concept embeddings learned from large electronic health records. - Yang Xiang 003; Jun Xu 007; Yuqi Si; Zhiheng Li 004; Laila Rasmy; Yujia Zhou 003; Firat Tiryaki; Fang Li 011; Yaoyun Zhang; Yonghui Wu; Xiaoqian Jiang; W. Jim Zheng; et al. (BMC Medical Informatics Decis. Mak., 2019)

The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018). - Yaoyun Zhang; Cui Tao; Yang Gong; Kai Wang 063; Zhongming Zhao (BMC Medical Informatics Decis. Mak., 2019)

Leveraging deep learning to understand health beliefs about the Human Papillomavirus Vaccine from social media. - Jingcheng Du; Rachel Cunningham; Yang Xiang 001; Fang Li 011; Yuxi Jia; Julie A. Boom; Sahiti Myneni; Jiang Bian 001; Chongliang Luo; Yong Chen 016; Cui Tao (npj Digit. Medicine, 2019)

Leverage Real-World Longitudinal Data in Large Clinical Research Networks for Alzheimer's Disease and Related Dementia (ADRD). - Rui Duan 004; Zhaoyi Chen; Jiayi Tong; Chongliang Luo; Tianchen Lyu; Cui Tao; Demetrius Maraganore; Jiang Bian 001; Yong Chen 016 (AMIA, 2020)

Identifying Clinical Risk Factors for Opioid Use Disorder using a Distributed Algorithm to Combine Real-World Data from a Large Clinical Data Research Network. - Jiayi Tong; Zhaoyi Chen; Rui Duan 004; Wei-Hsuan Lo-Ciganic; Tianchen Lyu; Cui Tao; Peter A. Merkel; Henry R. Kranzler; Jiang Bian 001; Yong Chen 016 (AMIA, 2020)

A health consumer ontology of fast food information. - Muhammad Amith; Jing Wang; Grace Xiong; Kirk Roberts; Cui Tao (BIBM, 2020)

An Interactive Game for Changing Youth Behavior Regarding E-cigarettes. - Angela Xu; Muhammad Amith; Jianfu Li; Lu Tang 005; Cui Tao (HCI (38), 2020)

Development and Evaluation of ADCareOnto - an Ontology for Personalized Home Care for Persons with Alzheimer's Disease. - Juan Li 004; Rasha Hendawi; Vikram Pandey; Rafa Alenezi; Xin Wang; Bo Xie 001; Cui Tao (HealthCom, 2020)

Named Entity Recognition from Table Headers in Randomized Controlled Trial Articles. - Qiang Wei 002; Yujia Zhou 003; Bo Zhao 001; Xinyue Hu 002; Qiaozhu Mei; Cui Tao; Hua Xu 001 (ICHI, 2020)

Examining Potential Usability and Health Beliefs Among Young Adults Using a Conversational Agent for HPV Vaccine Counseling. - Muhammad Amith; Rebecca Lin; Rachel Cunningham; Qiwei Luna Wu; Lara S. Savas; Yang Gong; Julie A. Boom; Lu Tang 005; Cui Tao (CoRR, 2020)

Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction. - Laila Rasmy; Yang Xiang 003; Ziqian Xie; Cui Tao; Degui Zhi (CoRR, 2020)

Semantic based model of Conceptual Work Products for formal verification of complex interactive systems. - Mohcine Madkour; Keith A. Butler; Eric Mercer; Ali Bahrami; Cui Tao (CoRR, 2020)

Exploring the semantics in mental health research. - Jiang Bian 001; Yaoyun Zhang; Cui Tao (Health Informatics J., 2020)

On the evidence consistency of pharmacovigilance outcomes between Food and Drug Administration Adverse Event Reporting System and electronic medical record data for acute mania patients. - Rui Duan 004; Xinyuan Zhang 003; Jingcheng Du; Jing Huang 021; Cui Tao; Yong Chen 016 (Health Informatics J., 2020)

Ontological representation-oriented term normalization and standardization of the Research Domain Criteria. - Fang Li 011; Guozheng Rao; Jingcheng Du; Yang Xiang 003; Yaoyun Zhang; Salih Selek; Jane Elizabeth Hamilton; Hua Xu 001; Cui Tao (Health Informatics J., 2020)

Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics. - Jianhong Luo; Jingcheng Du; Cui Tao; Hua Xu 001; Yaoyun Zhang (Health Informatics J., 2020)

Recognizing software names in biomedical literature using machine learning. - Qiang Wei 002; Yaoyun Zhang; Muhammad Amith; Rebecca Lin; Jenay Lapeyrolerie; Cui Tao; Hua Xu 001 (Health Informatics J., 2020)

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. - Fang Li 011; Jingcheng Du; Yongqun He; Hsing-yi Song; Mohcine Madkour; Guozheng Rao; Yang Xiang 003; Yi Luo; Henry W. Chen; Sijia Liu 002; Liwei Wang 010; Hongfang Liu; et al. (J. Am. Medical Informatics Assoc., 2020)

Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. - Laila Rasmy; Firat Tiryaki; Yujia Zhou 003; Yang Xiang 003; Cui Tao; Hua Xu 001; Degui Zhi (J. Am. Medical Informatics Assoc., 2020)

iDISK: the integrated DIetary Supplements Knowledge base. - Rubina F. Rizvi; Jake Vasilakes; Terrence J. Adam; Genevieve B. Melton; Jeffrey R. Bishop; Jiang Bian 001; Cui Tao; Rui Zhang 028 (J. Am. Medical Informatics Assoc., 2020)

A study of deep learning approaches for medication and adverse drug event extraction from clinical text. - Qiang Wei 002; Zongcheng Ji; Zhiheng Li 004; Jingcheng Du; Jingqi Wang; Jun Xu 007; Yang Xiang 003; Firat Tiryaki; Stephen Wu 004; Yaoyun Zhang; Cui Tao; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2020)

Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. - Hansi Zhang; Christopher Wheldon; Adam G. Dunn; Cui Tao; Jinhai Huo; Rui Zhang 028; Mattia Prosperi; Yi Guo 005; Jiang Bian 001 (J. Am. Medical Informatics Assoc., 2020)

Friend of a Friend with Benefits ontology (FOAF+): extending a social network ontology for public health. - Muhammad Amith; Kayo Fujimoto; Rebecca Mauldin; Cui Tao (BMC Medical Informatics Decis. Mak., 2020)

Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. - Muhammad Amith; Rebecca Lin; Licong Cui; Dennis Wang; Anna Zhu; Grace Xiong; Hua Xu 001; Kirk Roberts; Cui Tao (BMC Medical Informatics Decis. Mak., 2020)

Selected articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). - Zhe He 001; Cui Tao; Jiang Bian 001; Rui Zhang 028 (BMC Medical Informatics Decis. Mak., 2020)

A semantic relationship mining method among disorders, genes, and drugs from different biomedical datasets. - Li Zhang 059; Jiamei Hu; Qianzhi Xu; Fang Li 011; Guozheng Rao; Cui Tao (BMC Medical Informatics Decis. Mak., 2020)

Expressing and Executing Informed Consent Permissions using SWRL: The All of Us Use Case. - Muhammad Amith; Marcelline R. Harris; Cooper Stansbury; Kathleen Ford; Frank J. Manion; Cui Tao (AMIA, 2021)

FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. - Daniel J. Stone; Sijia Liu 002; Yuan Luo 001; Andrew Wen; Nansu Zong; Luke V. Rasmussen; Prakash Adekkanattu; Pascal S. Brandt; Jennifer A. Pacheco; Fei Wang 001; Cui Tao; Jyotishman Pathak; et al. (AMIA, 2021)

Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. - Yunpeng Zhao; Pengfei Yin; Yongqiu Li; Xing He 003; Jingcheng Du; Cui Tao; Yi Guo 005; Mattia Prosperi; Pierangelo Veltri; Xi Yang 015; Yonghui Wu; Jiang Bian 001 (AMIA, 2021)

Developing Ontologies to Standardize Descriptions of Visual and Dermoscopic Elements. - Rebecca Z. Lin; Muhammad Tuan Amith; Xinyuan Zhang 003; Cynthia Wang; Jeremy Light; John Strickley; Cui Tao (BIBM, 2021)

Dental EHR-infused Persona Ontologies to Enrich Dental Dialogue Interaction of Agents. - Patricia Ngantcha; Muhammad Tuan Amith; Kirk Roberts; John A. Valenza; Muhammad F. Walji; Cui Tao (BIBM, 2021)

Patient-Provider Communication Training Models for Interactive Speech Devices. - Patricia Ngantcha; Muhammad Amith; Cui Tao; Kirk Roberts (HCI (16), 2021)

Experimenting with a Prototype Interactive Narrative Game to Improve Knowledge and Beliefs for the HPV Vaccine. - Anna Zhu; Muhammad Amith; Lu Tang 005; Rachel Cunningham; Angela Xu; Julie A. Boom; Cui Tao (HCI (43), 2021)

Understanding Public Perceptions of Measles from Twitter Using Multi-Task Convolutional Neural Networks. - Samuel Wang; Jingcheng Du; Lu Tang 005; Cui Tao (MedInfo, 2021)

Knowledge Graph-based Neurodegenerative Diseases and Diet Relationship Discovery. - Yi Nian; Jingcheng Du; Larry Bu; Fang Li 011; Xinyue Hu 002; Yuji Zhang 001; Cui Tao (CoRR, 2021)

Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning. - Jingcheng Du; Yang Xiang 003; Madhuri Sankaranarayanapillai; Meng Zhang; Jingqi Wang; Yuqi Si; Huy Anh Pham; Hua Xu 001; Yong Chen 016; Cui Tao (J. Am. Medical Informatics Assoc., 2021)

COVID-19 trial graph: a linked graph for COVID-19 clinical trials. - Jingcheng Du; Qing Wang; Jingqi Wang; Prerana Ramesh; Yang Xiang 003; Xiaoqian Jiang; Cui Tao (J. Am. Medical Informatics Assoc., 2021)

The ontology of fast food facts: conceptualization of nutritional fast food data for consumers and semantic web applications. - Muhammad Amith; Chidinma Onye; Tracey Ledoux; Grace Xiong; Cui Tao (BMC Medical Informatics Decis. Mak., 2021)

Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. - Laila Rasmy; Yang Xiang 003; Ziqian Xie; Cui Tao; Degui Zhi (npj Digit. Medicine, 2021)

Ontologies in the Behavioral Sciences: Accelerating Research and the Accessibility and Use of Knowledge. - Mark A. Musen; Jiang Bian 001; Bruce Chorpita; Vimla L. Patel; Cui Tao (AMIA, 2022)

Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. - Evan Yu; Cui Tao; Jingcheng Du; Degui Zhi; Yang Xiang 003; Kayo Fujimoto; Xi Luo; John A. Schneider (AMIA, 2022)

Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. - Jianping He 002; Fang Li 011; Xinyue Hu 002; Jianfu Li; Yi Nian; Jingqi Wang; Yang Xiang 003; Qiang Wei 002; Hua Xu 001; Cui Tao (ICHI, 2022)

Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. - Warren Manuel; Rashmie Abeysinghe; Yongqun He; Cui Tao; Licong Cui (J. Biomed. Semant., 2022)

Toward a standard formal semantic representation of the model card report. - Muhammad Tuan Amith; Licong Cui; Degui Zhi; Kirk Roberts; Xiaoqian Jiang; Fang Li 011; Evan Yu; Cui Tao (BMC Bioinform., 2022)

Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. - Yi Nian; Xinyue Hu 002; Rui Zhang 028; Jingna Feng; Jingcheng Du; Fang Li 011; Larry Bu; Yuji Zhang 001; Yong Chen 016; Cui Tao (BMC Bioinform., 2022)

Mining On Alzheimer's Diseases Related Knowledge Graph to Identity Potential AD-related Semantic Triples for Drug Repurposing. - Yi Nian; Xinyue Hu 002; Rui Zhang 028; Jingna Feng; Jingcheng Du; Fang Li 011; Yong Chen 016; Cui Tao (CoRR, 2022)

Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO). - Yifang Dang; Fang Li 011; Xinyue Hu 002; Vipina Kuttichi Keloth; Meng Zhang; Sunyang Fu; Jingcheng Du; J. Wilfred Fan; Muhammad F. Amith; Evan Yu; Hongfang Liu; Xiaoqian Jiang; et al. (CoRR, 2022)

Replay with Stochastic Neural Transformation for Online Continual EEG Classification. - Tiehang Duan; Zhenyi Wang 001; Gianfranco Doretto; Fang Li 011; Cui Tao; Donald A. Adjeroh (BIBM, 2023)

Distributionally Robust Cross Subject EEG Decoding. - Tiehang Duan; Zhenyi Wang 001; Gianfranco Doretto; Fang Li 011; Cui Tao; Donald A. Adjeroh (ECAI, 2023)

Evaluating Domain-Independent Small Talk Conversations to Improve Clinical Communication Interaction for Human and Machine. - Chloe Aguilar; Muhammad Amith; Lu Tang 005; Jane Hamilton; Lara S. Savas; Daniel Rhee; Tazrin Khan; Cui Tao (HCI (18), 2023)

Empowering Personalized Health Data Queries with Knowledge Graph and GPT-Enhanced Voice Assistant. - Xin Wang; Wordh Ul Hasan; Juan Li 004; Rasha Hendawi; Yang Du; Bo Xie 001; Cui Tao (HPCC/DSS/SmartCity/DependSys, 2023)

Suicide Tendency Prediction from Psychiatric Notes Using Transformer Models. - Zehan Li; Iqra Ameer; Yan Hu; Ahmed Abdelhameed; Cui Tao; Salih Selek; Hua Xu 001 (ICHI, 2023)

Development of a Natural Language Processing Tool to Extract Acupuncture Point Location Terms. - Yiming Li; Xueqing Peng; Jianfu Li; Suyuan Peng; Donghong Pei; Cui Tao; Hua Xu 001; Na Hong (ICHI, 2023)

Named Entity Recognition and Normalization for Alzheimer's Disease Eligibility Criteria. - Zenan Sun; Cui Tao (ICHI, 2023)

Honoring Heritage, Managing Health: A Mobile Diabetes Self-Management App for Native Americans with Cultural Sensitivity and Local Factors. - Wordh Ul Hasan; Juan Li 004; Shadi Alian; Tianyi Liang; Vikram Pandey; Kimia Tuz Zaman; Jun Kong; Cui Tao (ISCC, 2023)

Empowering Caregivers of Alzheimer's Disease and Related Dementias (ADRD) with a GPT-Powered Voice Assistant: Leveraging Peer Insights from Social Media. - Kimia Tuz Zaman; Wordh Ul Hasan; Juan Li 004; Cui Tao (ISCC, 2023)

Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research. - Muhammad Amith; Licong Cui; Kirk Roberts; Cui Tao (WWW (Companion Volume), 2023)

Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions. - Fang Li 011; Yi Nian; Zenan Sun; Cui Tao (CoRR, 2023)

Explainable Graph Neural Network for Alzheimer's Disease And Related Dementias Risk Prediction. - Xinyue Hu 002; Zenan Sun; Yi Nian; Yifang Dang; Fang Li 011; Jingna Feng; Evan Yu; Cui Tao (CoRR, 2023)

AE-GPT: Using Large Language Models to Extract Adverse Events from Surveillance Reports-A Use Case with Influenza Vaccine Adverse Events. - Yiming Li; Jianfu Li; Jianping He 002; Cui Tao (CoRR, 2023)

An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. - Song Wang 026; Yifang Dang; Zhaoyi Sun; Ying Ding 001; Jyotishman Pathak; Cui Tao; Yunyu Xiao; Yifan Peng 002 (J. Am. Medical Informatics Assoc., 2023)

Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). - Yifang Dang; Fang Li 011; Xinyue Hu 002; Vipina Kuttichi Keloth; Meng Zhang; Sunyang Fu; Muhammad F. Amith; J. Wilfred Fan; Jingcheng Du; Evan Yu; Hongfang Liu; Xiaoqian Jiang; et al. (J. Am. Medical Informatics Assoc., 2023)

Machine learning-based donor permission extraction from informed consent documents. - Meng Zhang; Madhuri Sankaranarayanapillai; Jingcheng Du; Yang Xiang 003; Frank J. Manion; Marcelline R. Harris; Cooper Stansbury; Huy Anh Pham; Cui Tao (BMC Bioinform., 2023)

An ontology-based approach for harmonization and cross-cohort query of Alzheimer's disease data resources. - Xubing Hao; Xiaojin Li; Guo-Qiang Zhang 001; Cui Tao; Paul E. Schulz; Licong Cui (BMC Medical Informatics Decis. Mak., 2023)

DEVO: an ontology to assist with dermoscopic feature standardization. - Xinyuan Zhang 003; Rebecca Z. Lin; Muhammad Tuan Amith; Cynthia Wang; Jeremy Light; John Strickley; Cui Tao (BMC Medical Informatics Decis. Mak., 2023)

Translating motivational interviewing for the HPV vaccine into a computable ontology model for automated AI conversational interaction. - Nicole Moore; Muhammad Amith; Ana Neumann; Jane Hamilton; Lu Tang 005; Lara S. Savas; Cui Tao (CHI Extended Abstracts, 2024)

Developing a Computational Representation of Human Physical Activity and Exercise Using Open Ontology-Based Approach: A Tai Chi Use Case. - Eloisa Nguyen; Rebecca Z. Lin; Yang Gong; Cui Tao; Muhammad Tuan Amith (ICHI, 2024)

Analyzing Llama 3-based Approach for Axiom Translation from Ontologies. - Xubing Hao; Licong Cui; Cui Tao; Kirk Roberts; Muhammad Amith (KBC-LM/LM-KBC@ISWC, 2024)

CareCompanion: A Personalized Virtual Assistant for Enhancing Support and Independence in ADRD Patients and Older Adults. - Wordh Ul Hasan; Kimia Tuz Zaman; Mohammed Shalan; Xin Wang; Juan Li 004; Bo Xie 001; Cui Tao (SmartNets, 2024)

Design and optimization of a high-speed maize seed guiding device based on DEM-CFD coupling method. - Hongsheng Li 001; Li Yang 013; Dongxing Zhang; Cui Tao; Xiantao He; Chunji Xie; Chuan Li; Zhaohui Du; Tianpu Xiao; Zhimin Li; Haoyu Wang (Comput. Electron. Agric., 2024)

Uncovering Misattributed Suicide Causes through Annotation Inconsistency Detection in Death Investigation Notes. - Song Wang 026; Yiliang Zhou; Ziqiang Han; Cui Tao; Yunyu Xiao; Ying Ding 001; Joydeep Ghosh; Yifan Peng 002 (CoRR, 2024)

Improving Entity Recognition Using Ensembles of Deep Learning and Fine-tuned Large Language Models: A Case Study on Adverse Event Extraction from Multiple Sources. - Yiming Li; Deepthi Viswaroopan; William He; Jianfu Li; Xu Zuo; Hua Xu 001; Cui Tao (CoRR, 2024)

A Comparative Study of Recent Large Language Models on Generating Hospital Discharge Summaries for Lung Cancer Patients. - Yiming Li; Fang Li 011; Kirk Roberts; Licong Cui; Cui Tao; Hua Xu 001 (CoRR, 2024)

Prompting Large Language Models for Clinical Temporal Relation Extraction. - Jianping He 002; Laila Rasmy; Haifang Li; Jianfu Li; Zenan Sun; Evan Yu; Degui Zhi; Cui Tao (CoRR, 2024)

Relation extraction using large language models: a case study on acupuncture point locations. - Yiming Li; Xueqing Peng; Jianfu Li; Xu Zuo; Suyuan Peng; Donghong Pei; Cui Tao; Hua Xu 001; Na Hong (J. Am. Medical Informatics Assoc., 2024)

Ensemble pretrained language models to extract biomedical knowledge from literature. - Zhao Li; Qiang Wei 002; Liang-Chin Huang; Jianfu Li; Yan Hu; Yao-Shun Chuang; Jianping He 002; Avisha Das; Vipina Kuttichi Keloth; Yuntao Yang; Chiamaka S. Diala; Kirk E. Roberts; et al. (J. Am. Medical Informatics Assoc., 2024)

RefAI: a GPT-powered retrieval-augmented generative tool for biomedical literature recommendation and summarization. - Yiming Li; Jeff Zhao; Manqi Li; Yifang Dang; Evan Yu; Jianfu Li; Zenan Sun; Usama Hussein; Jianguo Wen; Ahmed M. Abdelhameed; Junhua Mai; Shenduo Li; et al. (J. Am. Medical Informatics Assoc., 2024)

FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. - Sunyang Fu; Heling Jia; Maria Vassilaki; Vipina Kuttichi Keloth; Yifang Dang; Yujia Zhou 003; Muskan Garg; Ronald C. Petersen; Jennifer St Sauver; Sungrim Moon; Liwei Wang 010; Andrew Wen; et al. (J. Biomed. Informatics, 2024)

Artificial intelligence-powered pharmacovigilance: A review of machine and deep learning in clinical text-based adverse drug event detection for benchmark datasets. - Yiming Li; Wei Tao; Zehan Li; Zenan Sun; Fang Li 011; Susan H. Fenton; Hua Xu 001; Cui Tao (J. Biomed. Informatics, 2024)

Improving tabular data extraction in scanned laboratory reports using deep learning models. - Yiming Li; Qiang Wei 002; Xinghan Chen; Jianfu Li; Cui Tao; Hua Xu 001 (J. Biomed. Informatics, 2024)

Online continual decoding of streaming EEG signal with a balanced and informative memory buffer. - Tiehang Duan; Zhenyi Wang 001; Fang Li 011; Gianfranco Doretto; Donald A. Adjeroh; Yiyi Yin; Cui Tao (Neural Networks, 2024)

Lessons learned from annotation of VAERS reports on adverse events following influenza vaccination and related to Guillain-Barré syndrome. - Madhuri Sankaranarayanapillai; Su Wang; Hangyu Ji; Hsing-yi Song; Cui Tao (BMC Medical Informatics Decis. Mak., 2024)

Evaluating MedDRA-to-ICD terminology mappings. - Xinyuan Zhang 003; Yixue Feng 001; Fang Li 011; Jin Ding; Danyal Tahseen; Ezekiel Hinojosa; Yong Chen 016; Cui Tao (BMC Medical Informatics Decis. Mak., 2024)

Prompt Tuning in Biomedical Relation Extraction. - Jianping He 002; Fang Li 011; Jianfu Li; Xinyue Hu 002; Yi Nian; Yang Xiang 003; Jingqi Wang; Qiang Wei 002; Yiming Li; Hua Xu 001; Cui Tao (J. Heal. Informatics Res., 2024)

Retain and Adapt: Online Sequential EEG Classification With Subject Shift. - Tiehang Duan; Zhenyi Wang 001; Li Shen 008; Gianfranco Doretto; Donald A. Adjeroh; Fang Li 011; Cui Tao (IEEE Trans. Artif. Intell., 2024)

Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models. - Jianfu Li; Yiming Li; Yuanyi Pan; Jinjing Guo; Zenan Sun; Fang Li 011; Yongqun He; Cui Tao (J. Biomed. Semant., 2024)

Constructing A Conversation-First Dialogue Model for Comprehensive, Evidence-Based Counseling for HPV Vaccination for Young Adults. - Lu Tang 005; Chenying Weng; Serena Hou; Lara S. Savas; Ana Neumann; Nicole Moore; Jane Hamilton; Daniel Rhee; Cui Tao; Licong Cui; Muhammad Amith (HCI (26), 2025)

Developing a High-Performing Network Computation of Big Bipartite Network Data Toward Alcohol Use Disorder Treatment Referrals. - Muhammad; Sharon Andrews; Angela Heads; Bruno Kluwe-Schiavon; Atchyutha Veni Choday; Ramya Poonam; Sai Venkat Ballem; Cui Tao; Jane Hamilton (ICSC, 2025)

Quantitatively assessing the impact of the quality of SNOMED CT subtype hierarchy on cohort queries. - Xubing Hao; Xiaojin Li; Yan Huang 034; Jay Shi; Rashmie Abeysinghe; Cui Tao; Kirk Roberts; Guo-Qiang Zhang 001; Licong Cui (J. Am. Medical Informatics Assoc., 2025)

A comparative study of recent large language models on generating hospital discharge summaries for lung cancer patients. - Yiming Li; Fang Li 011; Na Hong; Manqi Li; Kirk Roberts; Licong Cui; Cui Tao; Hua Xu 001 (J. Biomed. Informatics, 2025)

Improving entity recognition using ensembles of deep learning and fine-tuned large language models: A case study on adverse event extraction from VAERS and social media. - Yiming Li; Deepthi Viswaroopan; William He; Jianfu Li; Xu Zuo; Hua Xu 001; Cui Tao (J. Biomed. Informatics, 2025)

Social determinants of health extraction from clinical notes across institutions using large language models. - Vipina Kuttichi Keloth; Salih Selek; Qingyu Chen 001; Christopher Gilman; Sunyang Fu; Yifang Dang; Xinghan Chen; Xinyue Hu 002; Yujia Zhou 003; Huan He; Jungwei W. Fan 001; Karen Wang; et al. (npj Digit. Medicine, 2025)

Advancing Pancreatic Cancer Prediction with a Next Visit Token Prediction Head on top of Med-BERT. - Jianping He 002; Laila Rasmy; Degui Zhi; Cui Tao (CoRR, 2025)

LLM-Match: An Open-Sourced Patient Matching Model Based on Large Language Models and Retrieval-Augmented Generation. - Xiaodi Li; Shaika Chowdhury; Chung-Il Wi; Maria Vassilaki; Xiaoke Liu; Terence T. Sio; Owen Garrick; Young J. Juhn; James R. Cerhan; Cui Tao; Nansu Zong (CoRR, 2025)

Launching Insights: A Pilot Study on Leveraging Real-World Observational Data from the Mayo Clinic Platform to Advance Clinical Research. - Yue Yu; Xinyue Hu; Sivaraman Rajaganapathy; Jingna Feng; Ahmed Abdelhameed; Xiaodi Li; Jianfu Li; Ken Liu; Liu Yang; Nilufer Taner; Phil Fiero; Soulmaz Boroumand; et al. (CoRR, 2025)

ETT-CKGE: Efficient Task-driven Tokens for Continual Knowledge Graph Embedding. - Lijing Zhu; Qizhen Lan; Qing Tian; Wenbo Sun; Li Yang; Lu Xia; Yixin Xie; Xi Xiao; Tiehang Duan; Cui Tao; Shuteng Niu (CoRR, 2025)