Hua Xu

Orcid: 0000-0002-5274-4672

Affiliations:
  • University of Texas Health Science Center at Houston, School of Biomedical Informatics, TX, USA
  • Vanderbilt University, School of Medicine, Department of Biomedical Informatics, Nashville, TN, USA (former)


According to our database1, Hua Xu authored at least 300 papers between 2003 and 2024.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Dataset
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2024
Identifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models.
J. Heal. Informatics Res., June, 2024

Prompt Tuning in Biomedical Relation Extraction.
J. Heal. Informatics Res., June, 2024

Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition.
J. Am. Medical Informatics Assoc., January, 2024

Artificial intelligence-powered pharmacovigilance: A review of machine and deep learning in clinical text-based adverse drug event detection for benchmark datasets.
J. Biomed. Informatics, 2024

Developing deep learning-based strategies to predict the risk of hepatocellular carcinoma among patients with nonalcoholic fatty liver disease from electronic health records.
J. Biomed. Informatics, 2024

A scoping review of fair machine learning techniques when using real-world data.
J. Biomed. Informatics, 2024

FedFSA: Hybrid and federated framework for functional status ascertainment across institutions.
J. Biomed. Informatics, 2024

A span-based model for extracting overlapping PICO entities from randomized controlled trial publications.
J. Am. Medical Informatics Assoc., 2024

Confidence score: a data-driven measure for inclusive systematic reviews considering unpublished preprints.
J. Am. Medical Informatics Assoc., 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.
CoRR, 2024

Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
CoRR, 2024

Augmenting Biomedical Named Entity Recognition with General-domain Resources.
CoRR, 2024

CancerLLM: A Large Language Model in Cancer Domain.
CoRR, 2024

Unsupervised Multimodal Clustering for Semantics Discovery in Multimodal Utterances.
CoRR, 2024

BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine.
CoRR, 2024

Relation Extraction Using Large Language Models: A Case Study on Acupuncture Point Locations.
CoRR, 2024

Me LLaMA: Foundation Large Language Models for Medical Applications.
CoRR, 2024

2023
Towards More Generalizable and Accurate Sentence Classification in Medical Abstracts with Less Data.
J. Heal. Informatics Res., December, 2023

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C).
J. Am. Medical Informatics Assoc., November, 2023

Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach.
Bioinform., September, 2023

Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO).
J. Am. Medical Informatics Assoc., August, 2023

Representing and utilizing clinical textual data for real world studies: An OHDSI approach.
J. Biomed. Informatics, June, 2023

A hierarchical strategy to minimize privacy risk when linking "De-identified" data in biomedical research consortia.
J. Biomed. Informatics, March, 2023

Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions.
J. Am. Medical Informatics Assoc., 2023

Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias.
Int. J. Medical Informatics, 2023

MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing.
CoRR, 2023

Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations.
CoRR, 2023

Zero-shot Clinical Entity Recognition using ChatGPT.
CoRR, 2023

Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers.
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023

Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature.
Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

Development of a Natural Language Processing Tool to Extract Acupuncture Point Location Terms.
Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

Suicide Tendency Prediction from Psychiatric Notes Using Transformer Models.
Proceedings of the 11th IEEE International Conference on Healthcare Informatics, 2023

FinFax: Fast Interpretation of Fax with NLP.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022
The <i>All of Us</i> Research Program: Data quality, utility, and diversity.
Patterns, 2022

A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora.
BMC Medical Informatics Decis. Mak., 2022

GAR-Net: A Graph Attention Reasoning Network for conversation understanding.
Knowl. Based Syst., 2022

Novel informatics approaches to COVID-19 Research: From methods to applications.
J. Biomed. Informatics, 2022

Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature.
J. Biomed. Informatics, 2022

Combining human and machine intelligence for clinical trial eligibility querying.
J. Am. Medical Informatics Assoc., 2022

Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO).
CoRR, 2022

Make Acoustic and Visual Cues Matter: CH-SIMS v2.0 Dataset and AV-Mixup Consistent Module.
CoRR, 2022

Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing.
Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements.
Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

Improving Sentence Classification in Abstracts of Randomized Controlled Trial using Prompt Learning.
Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning.
Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues.
Proceedings of the 21st Workshop on Biomedical Language Processing, 2022

ClinicalLayoutLM: A Pre-trained Multi-modal Model for Understanding Scanned Document in Electronic Health Records.
Proceedings of the IEEE International Conference on Big Data, 2022

Automated Identification of Missing IS-A Relations in the Human Phenotype Ontology.
Proceedings of the AMIA 2022, 2022

Fast Textual Corpus Retrieval from Electronic Health Records using PDF Parser and TxtSplit Tools.
Proceedings of the AMIA 2022, 2022

Existing and emerging privacy challenges and solutions for federated data coordination.
Proceedings of the AMIA 2022, 2022

2021
Representation iterative fusion based on heterogeneous graph neural network for joint entity and relation extraction.
Knowl. Based Syst., 2021

COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model.
J. Am. Medical Informatics Assoc., 2021

Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition.
J. Am. Medical Informatics Assoc., 2021

Privacy-protecting, reliable response data discovery using COVID-19 patient observations.
J. Am. Medical Informatics Assoc., 2021

Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning.
J. Am. Medical Informatics Assoc., 2021

The application of artificial intelligence and data integration in COVID-19 studies: a scoping review.
J. Am. Medical Informatics Assoc., 2021

From Tokenization to Self-Supervision: Building a High-Performance Information Extraction System for Chemical Reactions in Patents.
Frontiers Res. Metrics Anal., 2021

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C).
CoRR, 2021

Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data.
CoRR, 2021

An Empirical Study of UMLS Concept Extraction from Clinical Notes using Boolean Combination Ensembles.
CoRR, 2021

Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature.
CoRR, 2021

How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles.
Briefings Bioinform., 2021

Study of Pre-trained Language Models for Named Entity Recognition in Clinical Trial Eligibility Criteria from Multiple Corpora.
Proceedings of the 9th IEEE International Conference on Healthcare Informatics, 2021

Robustly Pre-Trained Neural Model for Direct Temporal Relation Extraction.
Proceedings of the 9th IEEE International Conference on Healthcare Informatics, 2021

CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

TEXTOIR: An Integrated and Visualized Platform for Text Open Intent Recognition.
Proceedings of the Joint Conference of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing, 2021

2020
Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents.
BMC Medical Informatics Decis. Mak., 2020

A study of entity-linking methods for normalizing Chinese diagnosis and procedure terms to ICD codes.
J. Biomed. Informatics, 2020

Deep learning in clinical natural language processing: a methodical review.
J. Am. Medical Informatics Assoc., 2020

A study of deep learning approaches for medication and adverse drug event extraction from clinical text.
J. Am. Medical Informatics Assoc., 2020

Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies.
J. Am. Medical Informatics Assoc., 2020

SCOR: A secure international informatics infrastructure to investigate COVID-19.
J. Am. Medical Informatics Assoc., 2020

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.
J. Am. Medical Informatics Assoc., 2020

Learning from local to global: An efficient distributed algorithm for modeling time-to-event data.
J. Am. Medical Informatics Assoc., 2020

Learning from electronic health records across multiple sites: A communication-efficient and privacy-preserving distributed algorithm.
J. Am. Medical Informatics Assoc., 2020

COVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes.
J. Am. Medical Informatics Assoc., 2020

Recognizing software names in biomedical literature using machine learning.
Health Informatics J., 2020

Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics.
Health Informatics J., 2020

Ontological representation-oriented term normalization and standardization of the Research Domain Criteria.
Health Informatics J., 2020

Named Entity Recognition from Table Headers in Randomized Controlled Trial Articles.
Proceedings of the 8th IEEE International Conference on Healthcare Informatics, 2020

A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives.
Proceedings of the 8th IEEE International Conference on Healthcare Informatics, 2020

Opioid2FHIR: A system for extracting FHIR-compatible opioid prescriptions from clinical text.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study.
Proceedings of the AMIA 2020, 2020

LANN: An integrated online annotation tool for information extraction.
Proceedings of the AMIA 2020, 2020

The Open Health Natural Language Processing Collaboratory.
Proceedings of the AMIA 2020, 2020

2019
Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison.
BMC Medical Informatics Decis. Mak., 2019

Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text.
BMC Medical Informatics Decis. Mak., 2019

A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text.
BMC Medical Informatics Decis. Mak., 2019

Time-sensitive clinical concept embeddings learned from large electronic health records.
BMC Medical Informatics Decis. Mak., 2019

Editorial: The second international workshop on health natural language processing (HealthNLP 2019).
BMC Medical Informatics Decis. Mak., 2019

Special issue of BMC medical informatics and decision making on health natural language processing.
BMC Medical Informatics Decis. Mak., 2019

Temporal indexing of medical entity in Chinese clinical notes.
BMC Medical Informatics Decis. Mak., 2019

Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text.
BMC Medical Informatics Decis. Mak., 2019

Cost-aware active learning for named entity recognition in clinical text.
J. Am. Medical Informatics Assoc., 2019

Enhancing clinical concept extraction with contextual embeddings.
J. Am. Medical Informatics Assoc., 2019

Extracting entities with attributes in clinical text via joint deep learning.
J. Am. Medical Informatics Assoc., 2019

Psychiatric stressor recognition from clinical notes to reveal association with suicide.
Health Informatics J., 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

The Strength of the Weakest Supervision: Topic Classification Using Class Labels.
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2019

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP.
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

Detect Attributes of Medical Concepts via Sequence Labeling.
Proceedings of the 2019 IEEE International Conference on Healthcare Informatics, 2019

Ontology of Consumer Health Vocabulary: providing a formal and interoperable semantic resource for linking lay language and medical terminology.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Relation Extraction from Clinical Narratives Using Pre-trained Language Models.
Proceedings of the AMIA 2019, 2019

CLAMP-ATR: A deep learning pipeline for attribute recognition of clinical concepts.
Proceedings of the AMIA 2019, 2019

Achievability to Extract Specific Date Information for Cancer Research.
Proceedings of the AMIA 2019, 2019

2018
Identifying direct temporal relations between time and events from clinical notes.
BMC Medical Informatics Decis. Mak., 2018

Extracting psychiatric stressors for suicide from social media using deep learning.
BMC Medical Informatics Decis. Mak., 2018

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

Predict effective drug combination by deep belief network and ontology fingerprints.
J. Biomed. Informatics, 2018

Interactive medical word sense disambiguation through informed learning.
J. Am. Medical Informatics Assoc., 2018

Toward a normalized clinical drug knowledge base in China - applying the RxNorm model to Chinese clinical drugs.
J. Am. Medical Informatics Assoc., 2018

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.
J. Am. Medical Informatics Assoc., 2018

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

User needs analysis and usability assessment of DataMed - a biomedical data discovery index.
J. Am. Medical Informatics Assoc., 2018

DataMed - an open source discovery index for finding biomedical datasets.
J. Am. Medical Informatics Assoc., 2018

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

Parsing Clinical Text: How Good are the state-of-the-art Deep Learning Based Parsers?
Proceedings of the IEEE International Conference on Healthcare Informatics Workshops, 2018

Exploring Temporal Patterns of Suicidal Behavior on Twitter.
Proceedings of the IEEE International Conference on Healthcare Informatics Workshops, 2018

Term Standardization and Normalization for Research Domain Criteria (RDoC).
Proceedings of the IEEE International Conference on Healthcare Informatics Workshops, 2018

Guideline-driven data quality assessment- A case study of warfarin management.
Proceedings of the AMIA 2018, 2018

CLAMP-PA: A machine learning based pre-annotation pipeline for corpus construction of clinical concepts.
Proceedings of the AMIA 2018, 2018

Detecting Anatomical Entities in Clinical Text.
Proceedings of the AMIA 2018, 2018

Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition.
Proceedings of the AMIA 2018, 2018

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

Building a Biomedical Bilingual Parallel Corpus between Chinese and English from PubMed.
Proceedings of the AMIA 2018, 2018

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

Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data.
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 Medical Informatics Decis. Mak., 2017

Entity recognition from clinical texts via recurrent neural network.
BMC Medical Informatics Decis. Mak., 2017

An active learning-enabled annotation system for clinical named entity recognition.
BMC Medical Informatics Decis. Mak., 2017

Lightweight predicate extraction for patient-level cancer information and ontology development.
BMC Medical Informatics Decis. Mak., 2017

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

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

A systematic analysis of FDA-approved anticancer drugs.
BMC Syst. Biol., 2017

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

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

Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge.
Database J. Biol. Databases Curation, 2017

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

Identification of adverse drug-drug interactions through causal association rule discovery from spontaneous adverse event reports.
Artif. Intell. 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

Meeting User Needs for a Data Discovery Index of Biomedical Big Data.
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).
J. Am. Medical Informatics Assoc., 2016

Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov.
J. Am. Medical Informatics Assoc., 2016

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

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

Extracting drug-enzyme relation from literature as evidence for drug drug interaction.
J. Biomed. Semant., 2016

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

CD-REST: a system for extracting chemical-induced disease relation in literature.
Database J. Biol. Databases Curation, 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 Comput. Biol., 2015

Parsing clinical text: how good are the state-of-the-art parsers?
BMC Medical Informatics Decis. Mak., 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.
J. Biomed. Informatics, 2015

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

Domain adaptation for semantic role labeling of clinical text.
J. Am. Medical Informatics Assoc., 2015

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
J. Am. Medical Informatics Assoc., 2015

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

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

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

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.
Database J. Biol. Databases Curation, 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.
J. Biomed. Informatics, 2014

Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning.
J. Am. Medical Informatics Assoc., 2014

Research and applications: A comprehensive study of named entity recognition in Chinese clinical text.
J. Am. Medical Informatics Assoc., 2014

Research and applications: Assisted annotation of medical free text using RapTAT.
J. Am. Medical Informatics Assoc., 2014

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.
J. Am. Medical Informatics Assoc., 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

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

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 Medical Informatics Decis. Mak., 2013

Research and applications: ICD-9 tobacco use codes are effective identifiers of smoking status.
J. Am. Medical Informatics Assoc., 2013

Development and evaluation of an ensemble resource linking medications to their indications.
J. Am. Medical Informatics Assoc., 2013

A hybrid system for temporal information extraction from clinical text.
J. Am. Medical Informatics Assoc., 2013

Research and applications: Machine learning for predicting the response of breast cancer to neoadjuvant chemotherapy.
J. Am. Medical Informatics Assoc., 2013

Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records.
J. Am. Medical Informatics Assoc., 2013

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
J. Am. Medical Informatics Assoc., 2013

Applying active learning to supervised word sense disambiguation in MEDLINE.
J. Am. Medical Informatics Assoc., 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 Explor., 2012

Recognition of medication information from discharge summaries using ensembles of classifiers.
BMC Medical Informatics Decis. Mak., 2012

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

Applying active learning to assertion classification of concepts in clinical text.
J. Biomed. Informatics, 2012

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs.
J. Am. Medical Informatics Assoc., 2012

Portability of an algorithm to identify rheumatoid arthritis in electronic health records.
J. Am. Medical Informatics Assoc., 2012

Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches.
Int. J. Data Min. Bioinform., 2012

Advances in systems biology: computational algorithms and applications.
BMC Syst. Biol., 2012

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

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

Clinical entity recognition using structural support vector machines with rich features.
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical 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.
J. Biomed. Informatics, 2011

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
J. Am. Medical Informatics Assoc., 2011

Data from clinical notes: a perspective on the tension between structure and flexible documentation.
J. Am. Medical Informatics Assoc., 2011

A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.
J. Am. Medical Informatics Assoc., 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.
J. Am. Medical Informatics Assoc., 2010

Integrating existing natural language processing tools for medication extraction from discharge summaries.
J. Am. Medical Informatics Assoc., 2010

Extracting timing and status descriptors for colonoscopy testing from electronic medical records.
J. Am. Medical Informatics Assoc., 2010

Identifying potential drugs that induce QT prolongation using electronic medical records.
BMC Bioinform., 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.
J. Am. Medical Informatics Assoc., 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.
J. Am. Medical Informatics Assoc., 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.
J. Biomed. Informatics, 2007

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

Gene symbol disambiguation using knowledge-based profiles.
Bioinform., 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 Bioinform., 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


  Loading...