Hua Xu

According to our database1, Hua Xu authored at least 191 papers between 2003 and 2019.

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Bibliography

2019
Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison.
BMC Med. Inf. & Decision Making, 2019

A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text.
BMC Med. Inf. & Decision Making, 2019

Special issue of BMC medical informatics and decision making on health natural language processing.
BMC Med. Inf. & Decision Making, 2019

Temporal indexing of medical entity in Chinese clinical notes.
BMC Med. Inf. & Decision Making, 2019

Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text.
BMC Med. Inf. & Decision Making, 2019

BERT-based Ranking for Biomedical Entity Normalization.
CoRR, 2019

Enhancing Clinical Concept Extraction with Contextual Embedding.
CoRR, 2019

An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines.
Proceedings of the 4th International Workshop on Semantics-Powered Data Mining and Analytics co-located with the 18th International Semantic Web Conference (ISWC 2019), 2019

2018
Identifying direct temporal relations between time and events from clinical notes.
BMC Med. Inf. & Decision Making, 2018

Extracting psychiatric stressors for suicide from social media using deep learning.
BMC Med. Inf. & Decision Making, 2018

Analysis of treatment pathways for three chronic diseases using OMOP CDM.
J. Medical Systems, 2018

A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set.
Journal of Biomedical Informatics, 2018

Predict effective drug combination by deep belief network and ontology fingerprints.
Journal of Biomedical Informatics, 2018

Interactive medical word sense disambiguation through informed learning.
JAMIA, 2018

Toward a normalized clinical drug knowledge base in China - applying the RxNorm model to Chinese clinical drugs.
JAMIA, 2018

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.
JAMIA, 2018

PIE: A prior knowledge guided integrated likelihood estimation method for bias reduction in association studies using electronic health records data.
JAMIA, 2018

User needs analysis and usability assessment of DataMed - a biomedical data discovery index.
JAMIA, 2018

DataMed - an open source discovery index for finding biomedical datasets.
JAMIA, 2018

Extraction of BI-RADS findings from breast ultrasound reports in Chinese using deep learning approaches.
I. J. Medical Informatics, 2018

Clinical text annotation - what factors are associated with the cost of time?
Proceedings of the AMIA 2018, 2018

Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research.
Proceedings of the AMIA 2018, 2018

2017
Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data.
BMC Med. Inf. & Decision Making, 2017

Entity recognition from clinical texts via recurrent neural network.
BMC Med. Inf. & Decision Making, 2017

An active learning-enabled annotation system for clinical named entity recognition.
BMC Med. Inf. & Decision Making, 2017

Lightweight predicate extraction for patient-level cancer information and ontology development.
BMC Med. Inf. & Decision Making, 2017

A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
JAMIA, 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.
BMC Systems Biology, 2017

A systematic analysis of FDA-approved anticancer drugs.
BMC Systems Biology, 2017

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
BMC Bioinformatics, 2017

CNN-based ranking for biomedical entity normalization.
BMC Bioinformatics, 2017

Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge.
Database, 2017

A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge.
Database, 2017

Identification of adverse drug-drug interactions through causal association rule discovery from spontaneous adverse event reports.
Artificial Intelligence in Medicine, 2017

UTH_CCB System for Adverse Drug Reaction Extraction from Drug Labels at TAC-ADR 2017.
Proceedings of the 2017 Text Analysis Conference, 2017

Comparing Cancer Information Needs for Consumers in the US and China.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Expressing Biomedical Ontologies in Natural Language for Expert Evaluation.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Interweaving Domain Knowledge and Unsupervised Learning for Psychiatric Stressor Extraction from Clinical Notes.
Proceedings of the Advances in Artificial Intelligence: From Theory to Practice, 2017

Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification.
Proceedings of the Advances in Artificial Intelligence: From Theory to Practice, 2017

Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients.
Proceedings of the Summit on Clinical Research Informatics, 2017

A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records.
Proceedings of the Summit on Clinical Research Informatics, 2017

Using ensembles of NLP engines without a common type system to improve abbreviation disambiguation.
Proceedings of the Summit on Clinical Research Informatics, 2017

Towards practical temporal relation extraction from clinical notes: An analysis of direct temporal relations.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

A pilot study of mining association between psychiatric stressors and symptoms in tweets.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Evaluating Word Embeddings from Multiple Domains for Symptom Recognition in Psychiatric Notes.
Proceedings of the AMIA 2017, 2017

Detecting Body Location Modifiers of Disorders in Clinical Texts via Sequence Labeling.
Proceedings of the AMIA 2017, 2017

Detecting Contradictory and Consistent Citations in Biomedical Literature.
Proceedings of the AMIA 2017, 2017

CLAMP - A User-Centric Clinical Natural Language Processing Toolkit.
Proceedings of the AMIA 2017, 2017

Clinical Named Entity Recognition Using Deep Learning Models.
Proceedings of the AMIA 2017, 2017

Matching Consumer Health Vocabulary with Professional Medical Terms Through Concept Embedding.
Proceedings of the AMIA 2017, 2017

Interactive Medical Word Sense Disambiguation with Instance and Feature Labeling.
Proceedings of the AMIA 2017, 2017

Identifying Disease Hierarchical Relation with Concept Embeddings and Distant Supervision.
Proceedings of the AMIA 2017, 2017

Information Retrieval for Biomedical Datasets: The 2016 bioCADDIE Challenge.
Proceedings of the AMIA 2017, 2017

Clinical Natural Language Processing in Languages Other Than English.
Proceedings of the AMIA 2017, 2017

Leveraging existing corpora for de-identification of psychiatric notes using domain adaptation.
Proceedings of the AMIA 2017, 2017

AMICUS: A Metasystem for Interoperation and Combination of UIMA Systems.
Proceedings of the AMIA 2017, 2017

A Natural Language Processing System for Biomedical Dataset Retrieval.
Proceedings of the AMIA 2017, 2017

2016
Automated identification of molecular effects of drugs (AIMED).
JAMIA, 2016

Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov.
JAMIA, 2016

Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature.
BMC Systems Biology, 2016

Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction.
J. Biomedical Semantics, 2016

Extracting drug-enzyme relation from literature as evidence for drug drug interaction.
J. Biomedical Semantics, 2016

Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.
Database, 2016

CD-REST: a system for extracting chemical-induced disease relation in literature.
Database, 2016

UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes.
Proceedings of the 10th International Workshop on Semantic Evaluation, 2016

Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network.
Proceedings of the Summit on Clinical Research Informatics, 2016

Using synthetic clinical data to train an HMM-based POS tagger.
Proceedings of the 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics, 2016

Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features.
Proceedings of the AMIA 2016, 2016


What Can Neural Networks Learn from Unlabeled Clinical Narratives?
Proceedings of the AMIA 2016, 2016

A Study of Active Learning for Document Selection in Clinical Named Entity Recognition.
Proceedings of the AMIA 2016, 2016

Clinical Word Sense Disambiguation with Interactive Search and Classification.
Proceedings of the AMIA 2016, 2016

Semantic Relatedness and Similarity between Biomedical Concepts.
Proceedings of the AMIA 2016, 2016

Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time.
Proceedings of the AMIA 2016, 2016

Natural Language Processing Working Group Pre-Symposium: Graduate Student Consortium and 'Hackathon'.
Proceedings of the AMIA 2016, 2016

Literature-Based Discovery of Confounding in Observational Clinical Data.
Proceedings of the AMIA 2016, 2016

Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations.
Proceedings of the AMIA 2016, 2016


An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies.
Proceedings of the AMIA 2016, 2016

GWAS Finder: Search Engine for GWAS Datasets in Biomedical Literature.
Proceedings of the AMIA 2016, 2016

2015
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
PLoS Computational Biology, 2015

Parsing clinical text: how good are the state-of-the-art parsers?
BMC Med. Inf. & Decision Making, 2015

A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature.
J. Cheminformatics, 2015

The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics, 2015

Ease of adoption of clinical natural language processing software: An evaluation of five systems.
Journal of Biomedical Informatics, 2015

A study of active learning methods for named entity recognition in clinical text.
Journal of Biomedical Informatics, 2015

Domain adaptation for semantic role labeling of clinical text.
JAMIA, 2015

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
JAMIA, 2015

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.
BMC Systems Biology, 2015

A comparative study of disease genes and drug targets in the human protein interactome.
BMC Bioinformatics, 2015

Colorectal cancer drug target prediction using ontology-based inference and network analysis.
Database, 2015

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.
Database, 2015

UTH-CCB: The Participation of the SemEval 2015 Challenge - Task 14.
Proceedings of the 9th International Workshop on Semantic Evaluation, 2015

Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

Clinical Abbreviation Disambiguation Using Neural Word Embeddings.
Proceedings of the Workshop on Biomedical Natural Language Processing, BioNLP@IJCNLP 2015, 2015

A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text.
Proceedings of the AMIA 2015, 2015

Recognizing Disjoint Clinical Concepts in Clinical Text Using Machine Learning-based Methods.
Proceedings of the AMIA 2015, 2015

Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP) - a user-centric NLP system.
Proceedings of the AMIA 2015, 2015

Real Time Active Learning Study for Clinical Named Entity Recognition.
Proceedings of the AMIA 2015, 2015

Citation Sentiment Analysis in Clinical Trial Papers.
Proceedings of the AMIA 2015, 2015

2014
Identifying plausible adverse drug reactions using knowledge extracted from the literature.
Journal of Biomedical Informatics, 2014

Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning.
JAMIA, 2014

Research and applications: A comprehensive study of named entity recognition in Chinese clinical text.
JAMIA, 2014

Research and applications: Assisted annotation of medical free text using RapTAT.
JAMIA, 2014

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.
JAMIA, 2014

UTH_CCB: A report for SemEval 2014 - Task 7 Analysis of Clinical Text.
Proceedings of the 8th International Workshop on Semantic Evaluation, 2014

Ontology-based Normalization for Disease-Lab test Relation Extraction.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Quality of Care Metric Reporting from Clinical Narratives: Assessing Ontology Components.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Parsing Clinical Text: How Good are the State-of-the-Art Parsers?
Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, 2014

DTMBIO 2014: International Workshop on Data and Text Mining in Biomedical Informatics.
Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management, 2014

Domain Adaptation for Semantic Role Labeling of Clinical Text.
Proceedings of the AMIA 2014, 2014

Mining electronic health record data to detect drug-repurposing signals for cancers.
Proceedings of the AMIA 2014, 2014

Development of a Unified Computable Problem-Medication Knowledge base.
Proceedings of the AMIA 2014, 2014

An Integrative Framework for Drug Target Prediction and Repurposing.
Proceedings of the AMIA 2014, 2014

Identifying Metastases from Pathology Reports in Lung Cancer Patients.
Proceedings of the AMIA 2014, 2014

Identifying Plausible Adverse Drug Reactions Using Knowledge Extracted from the Literature.
Proceedings of the AMIA 2014, 2014

A study of synonym extraction from clinical texts using semantic vector models.
Proceedings of the AMIA 2014, 2014

Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting.
Proceedings of the AMIA 2014, 2014

Building a Treebank of hospital discharge summaries.
Proceedings of the AMIA 2014, 2014

A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions.
Proceedings of the AMIA 2014, 2014

Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies.
Proceedings of the AMIA 2014, 2014

2013
Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features.
BMC Med. Inf. & Decision Making, 2013

Research and applications: ICD-9 tobacco use codes are effective identifiers of smoking status.
JAMIA, 2013

Development and evaluation of an ensemble resource linking medications to their indications.
JAMIA, 2013

A hybrid system for temporal information extraction from clinical text.
JAMIA, 2013

Research and applications: Machine learning for predicting the response of breast cancer to neoadjuvant chemotherapy.
JAMIA, 2013

Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records.
JAMIA, 2013

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
JAMIA, 2013

Applying active learning to supervised word sense disambiguation in MEDLINE.
JAMIA, 2013

Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages.
Proceedings of the MEDINFO 2013, 2013

Evaluation of Vector Space Models for Medical Disorders Information Retrieval.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

Clinical Acronym/Abbreviation Normalization using a Hybrid Approach.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

A prototype application for real-time recognition and disambiguation of clinical abbreviations.
Proceedings of the Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, 2013

DTMBIO 2013: international workshop on data and text mining in biomedical informatics.
Proceedings of the 22nd ACM International Conference on Information and Knowledge Management, 2013

Messaging to your doctors: understanding patient-provider communications via a portal system.
Proceedings of the 2013 ACM SIGCHI Conference on Human Factors in Computing Systems, 2013

Correlating adverse drug reactions with biological pathways in humans.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Understanding Consumers' Information Needs about Breast Cancer by Analyzing Online Questions.
Proceedings of the AMIA 2013, 2013

Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries.
Proceedings of the AMIA 2013, 2013

Word Sense Disambiguation of Clinical Abbreviations with Hyperdimensional Computing.
Proceedings of the AMIA 2013, 2013

Ontology-Based Entity Extraction of Quality Metrics from Narrative Texts.
Proceedings of the AMIA 2013, 2013

A Study of Active Learning Methods for Clinical Entities Recognition.
Proceedings of the AMIA 2013, 2013

Informatics Infrastructure for Routine Personalized Medicine.
Proceedings of the AMIA 2013, 2013

2012
Data mining methodologies for pharmacovigilance.
SIGKDD Explorations, 2012

Recognition of medication information from discharge summaries using ensembles of classifiers.
BMC Med. Inf. & Decision Making, 2012

A new clustering method for detecting rare senses of abbreviations in clinical notes.
Journal of Biomedical Informatics, 2012

Applying active learning to assertion classification of concepts in clinical text.
Journal of Biomedical Informatics, 2012

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs.
JAMIA, 2012

Portability of an algorithm to identify rheumatoid arthritis in electronic health records.
JAMIA, 2012

Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches.
IJDMB, 2012

Advances in systems biology: computational algorithms and applications.
BMC Systems Biology, 2012

Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks.
BMC Systems Biology, 2012

DTome: a web-based tool for drug-target interactome construction.
BMC Bioinformatics, 2012

Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

DTMBIO 2012: international workshop on data and text mining in biomedical informatics.
Proceedings of the 21st ACM International Conference on Information and Knowledge Management, 2012

Understanding patient-provider communication entered via a patient portal system.
Proceedings of the Information, Interaction, Innovation: Celebrating the Past, Constructing the Present and Creating the Future, 2012

Combining Corpus-derived Sense Profiles with Estimated Frequency Information to Disambiguate Clinical Abbreviations.
Proceedings of the AMIA 2012, 2012

Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies.
Proceedings of the AMIA 2012, 2012

A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries.
Proceedings of the AMIA 2012, 2012

Clinical Entity Recognition Using Structural Support Vector Machines.
Proceedings of the AMIA 2012, 2012

Understanding Patient-Provider Communication via a Patient Portal.
Proceedings of the AMIA 2012, 2012

MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text.
Proceedings of the AMIA 2012, 2012

A Study of Transportability of an Existing Smoking Status Detection Module across Institutions.
Proceedings of the AMIA 2012, 2012

Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method.
Proceedings of the AMIA 2012, 2012

2011
Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences.
Journal of Biomedical Informatics, 2011

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
JAMIA, 2011

Data from clinical notes: a perspective on the tension between structure and flexible documentation.
JAMIA, 2011

A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.
JAMIA, 2011

An initial study of full parsing of clinical text using the Stanford Parser.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010
Application of information technology: MedEx: a medication information extraction system for clinical narratives.
JAMIA, 2010

Integrating existing natural language processing tools for medication extraction from discharge summaries.
JAMIA, 2010

Extracting timing and status descriptors for colonoscopy testing from electronic medical records.
JAMIA, 2010

Identifying potential drugs that induce QT prolongation using electronic medical records.
BMC Bioinformatics, 2010

Recognizing Medication related Entities in Hospital Discharge Summaries using Support Vector Machine.
Proceedings of the COLING 2010, 2010

2009
Research Paper: Methods for Building Sense Inventories of Abbreviations in Clinical Notes.
JAMIA, 2009

Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records.
Proceedings of the AMIA 2009, 2009

2008
Research Paper: Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents: An Initial Study.
JAMIA, 2008

Methods for Building Sense Inventories of Abbreviations in Clinical Notes.
Proceedings of the AMIA 2008, 2008

2007
Natural language processing and visualization in the molecular imaging domain.
Journal of Biomedical Informatics, 2007

Using contextual and lexical features to restructure and validate the classification of biomedical concepts.
BMC Bioinformatics, 2007

Gene symbol disambiguation using knowledge-based profiles.
Bioinformatics, 2007

Using Distributional Analysis to Semantically Classify UMLS Concepts.
Proceedings of the MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics, 2007

Combining multiple evidence for gene symbol disambiguation.
Proceedings of the Biological, translational, and clinical language processing, 2007

A Study of Abbreviations in Clinical Notes.
Proceedings of the AMIA 2007, 2007

2006
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues.
BMC Bioinformatics, 2006

A Natural Language Processing (NLP) Tool to Assist in the Curation Of the Laboratory Mouse Tumor Biology Database.
Proceedings of the AMIA 2006, 2006

2004
Facilitating Cancer Research using Natural Language Processing of Pathology Reports.
Proceedings of the MEDINFO 2004, 2004

2003
Facilitating Research in Pathology using Natural Language Processing.
Proceedings of the AMIA 2003, 2003


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