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List of works by Hongfang Liu

A Bibliometric Analysis on Cancer Population Science with Topic Modeling

scientific article published on 25 March 2015

A Comparison of Word Embeddings for the Biomedical Natural Language Processing

scientific article published on 12 September 2018

A Corpus-Driven Standardization Framework for Encoding Clinical Problems with HL7 FHIR

scientific article published on 16 August 2020

A Frequency-based Strategy of Obtaining Sentences from Clinical Data Repository for Crowdsourcing

scientific article published on January 2015

A Part-Of-Speech term weighting scheme for biomedical information retrieval

scientific article

A Text-Mining Framework for Supporting Systematic Reviews

scholarly article published 31 August 2016

A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text

scientific article published on January 2016

A common type system for clinical natural language processing

scientific article published on 3 January 2013

A comparison study of biomedical short form definition detection algorithms

A comparison study on algorithms of detecting long forms for short forms in biomedical text

scientific article

A hybrid approach to sentiment sentence classification in suicide notes.

scientific article

A study of transportability of an existing smoking status detection module across institutions.

scientific article published on 3 November 2012

Achievability to Extract Specific Date Information for Cancer Research

scientific article published on 01 January 2019

An Infinite Mixture Model for Coreference Resolution in Clinical Notes

scientific article published on 22 July 2016

An author topic analysis of tobacco regulation investigators

scientific article published on 7 April 2014

An automated approach for ranking journals to help in clinician decision support

scientific article published on 14 November 2014

An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics

scientific article published on 4 December 2010

An exploratory study of news article clustering for web-based bio-surveillance

An information extraction framework for cohort identification using electronic health records

scientific article published on 18 March 2013

Analysis of Clinical Variations in Asthma Care Documented in Electronic Health Records Between Staff and Resident Physicians.

scientific article

Analysis of cross-institutional medication description patterns in clinical narratives

scientific article published on 24 June 2013

Application of a Natural Language Processing Algorithm to Asthma Ascertainment. An Automated Chart Review

scientific article published on 4 April 2017

Artificial Intelligence and Data Science for Healthcare: Bridging Data-Centric AI and People-Centric Healthcare

scientific article published on 25 August 2024

Artificial intelligence approaches using natural language processing to advance EHR-based clinical research

scientific article published on 26 December 2019

Ascertainment of Asthma Prognosis Using Natural Language Processing from Electronic Medical Records

scientific article published on 10 February 2018

Assessing Unmet Information Needs of Breast Cancer Survivors: Exploratory Study of Online Health Forums Using Text Classification and Retrieval.

scientific article published on 15 May 2018

Assessing the Need of Discourse-Level Analysis in Identifying Evidence of Drug-Disease Relations in Scientific Literature.

scientific article published on January 2015

Assessment of the impact of EHR heterogeneity for clinical research through a case study of silent brain infarction

scientific article published on 30 March 2020

Association of Ankle-Brachial Indices With Limb Revascularization or Amputation in Patients With Peripheral Artery Disease

scholarly article published 7 December 2018

Automated chart review for asthma cohort identification using natural language processing: an exploratory study

scientific article published on 12 August 2013

Automated chart review utilizing natural language processing algorithm for asthma predictive index

scientific article published on 13 February 2018

Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing

scientific article published on 13 May 2019

Automated recommendation for cervical cancer screening and surveillance

scientific article

Automatic extraction and assessment of lifestyle exposures for Alzheimer's disease using natural language processing

scientific article published on 06 August 2019

Automating the Transformation of Free-Text Clinical Problems into SNOMED CT Expressions

scientific article published on 30 May 2020

BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences

scientific article

BELTracker: evidence sentence retrieval for BEL statements

scientific article published on 12 May 2016

BioTagger-GM: a gene/protein name recognition system.

scientific article published on 11 December 2008

BioThesaurus: a web-based thesaurus of protein and gene names

scientific article published on 02 November 2005

Burden of hospitalization in clinically diagnosed peripheral artery disease: A community-based study

scientific article

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

scientific article published on 24 November 2017

COVID-19 TestNorm - A tool to normalize COVID-19 testing names to LOINC codes

scientific article published on 22 June 2020

Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval

Classifying protein complexes from candidate subgraphs using fuzzy machine learning model

scholarly article published October 2012

Clinical Concept Extraction: a Methodology Review

scientific article published on 05 August 2020

Clinical Decision Support for Colonoscopy Surveillance Using Natural Language Processing

Clinical Information Extraction Applications: A Literature Review

scientific article published on 18 November 2017

Clinical decision support with automated text processing for cervical cancer screening ⬇️

scientific article published on April 29, 2012

Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions

scientific article published on 30 November 2017

Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol)

scientific article published on 01 February 2020

Comparison of Three Information Sources for Smoking Information in Electronic Health Records

scientific article published on 08 December 2016

Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification

scientific article published on 04 April 2013

Constructing Co-occurrence Network Embeddings to Assist Association Extraction for COVID-19 and Other Coronavirus Infectious Diseases

scientific article published on 27 May 2020

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.

scientific article

Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose

scientific article

Coverage Evaluation of CTCAE for Capturing the Immune-related Adverse Events Leveraging Text Mining Technologies

scientific article published on 06 May 2019

DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx

scientific article published on 16 March 2015

Data-driven Sublanguage Analysis for Cancer Genomics Knowledge Modeling: Applications in Mining Oncological Genetics Information from Patients' Genetic Reports

scientific article published on 30 May 2020

Deep Denoising of Raw Biomedical Knowledge Graph From COVID-19 Literature, LitCovid, and Pubtator: Framework Development and Validation

scientific article published on 03 June 2022

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes

scientific article published on 28 June 2018

Detecting Lifestyle Risk Factors for Chronic Kidney Disease With Comorbidities: Association Rule Mining Analysis of Web-Based Survey Data

scientific article published on 10 December 2019

Detecting Pharmacovigilance Signals Combining Electronic Medical Records With Spontaneous Reports: A Case Study of Conventional Disease-Modifying Antirheumatic Drugs for Rheumatoid Arthritis

scholarly article by Liwei Wang et al published 2018 in Frontiers in Pharmacology

Detecting and Filtering Immune-Related Adverse Events Signal Based on Text Mining and Observational Health Data Sciences and Informatics Common Data Model: Framework Development Study

scientific article published on 12 June 2020

Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?

scientific article published on 17 January 2014

Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes

scientific article published on 06 November 2018

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP

scientific article published on 01 August 2019

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

scientific article published on 14 October 2019

Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data

scientific article published on 18 October 2019

Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records

scientific article published on 01 March 2020

Development of dbOGAP: A bioinformatics resource of O-GlcNAcylated proteins and site prediction

article

Discovering adverse drug events combining spontaneous reports with electronic medical records: a case study of conventional DMARDs and biologics for rheumatoid arthritis

scientific article

Discovering associations between problem list and practice setting

Discovery of Noncancer Drug Effects on Survival in Electronic Health Records of Patients With Cancer: A New Paradigm for Drug Repurposing

scientific article published on 01 May 2019

Distinction between medical and non-medical usages of short forms in clinical narratives.

scientific article

Document Classification for Mining Host Pathogen Protein-Protein Interactions

Document classification for mining host pathogen protein-protein interactions

scientific article published on 15 May 2010

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

scientific article

Early Identification of Childhood Asthma: The Role of Informatics in an Era of Electronic Health Records

article

Early genetic aberrations in patients with sporadic colorectal cancer

scientific article published on 19 September 2017

Ease of adoption of clinical natural language processing software: An evaluation of five systems

scientific article

Effect of a Novel Clinical Decision Support Tool on the Efficiency and Accuracy of Treatment Recommendations for Cholesterol Management

scientific article published on 08 February 2017

Enhancing acronym/abbreviation knowledge bases with semantic information.

scientific article published on 11 October 2007

Ensembles of natural language processing systems for portable phenotyping solutions

scientific article published on 23 October 2019

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

scientific article published on 13 April 2016

Evaluating the Impact of Dictionary Updates on Automatic Annotations Based on Clinical NLP Systems

scientific article published on 06 May 2019

Evaluation of the effect of decision support on the efficiency of primary care providers in the outpatient practice

scientific article

Exploring Gaps of Family History Documentation in EHR for Precision Medicine -A Case Study of Familial Hypercholesterolemia Ascertainment

scientific article published on 20 July 2016

Extracting chemical-protein relations using attention-based neural networks

scientific article published on 01 January 2018

Family History Extraction From Synthetic Clinical Narratives Using Natural Language Processing: Overview and Evaluation of a Challenge Data Set and Solutions for the 2019 National NLP Clinical Challenges (n2c2)/Open Health Natural Language Processin

scientific article published in 2021

Feasibility of pooling annotated corpora for clinical concept extraction

scientific article published on 19 March 2012

Formative evaluation of the accuracy of a clinical decision support system for cervical cancer screening.

scientific article published on 05 April 2013

Framework for a protein ontology

Framework for a protein ontology

scientific article

Generality and reuse in a common type system for clinical natural language processing

article published in 2011

Granular Quality Reporting for Cervical Cytology Testing

scientific article published on 25 March 2015

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology

scientific article published on 27 June 2019

Headwords and Suffixes in Biomedical Names

Human gene/protein synonym dictionary from WikiLinks

article

Identification of Patients with Family History of Pancreatic Cancer--Investigation of an NLP System Portability.

scientific article published on January 2015

Identifying Abdominal Aortic Aneurysm Cases and Controls using Natural Language Processing of Radiology Reports

scientific article published on 18 March 2013

Identifying Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes

scientific article published on 01 February 2016

Identifying protein complexes with fuzzy machine learning model

scientific article

Impact of Diverse Data Sources on Computational Phenotyping

scientific article published on 03 June 2020

Impact of Patient Reminders on Papanicolaou Test Completion for High-Risk Patients Identified by a Clinical Decision Support System

scientific article

Implementation of a Cohort Retrieval System for Clinical Data Repositories Using the Observational Medical Outcomes Partnership Common Data Model: Proof-of-Concept System Validation

scientific article published on 06 October 2020

Improving the Accuracy of a Clinical Decision Support System for Cervical Cancer Screening and Surveillance

scientific article

Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases

Information Extraction for Populating Lung Cancer Clinical Research Data

scientific article published on 01 June 2019

Integrating information retrieval with distant supervision for gene ontology annotation

scientific article

Investigating the impact of disease and health record duration on the eMERGE algorithm for rheumatoid arthritis

scientific article published on 01 April 2020

Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development

scientific article published on 20 July 2016

Learning Semantic Tags from Big Data for Clinical Text Representation.

scientific article

Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature

Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis.

scientific article published in January 2017

Leveraging the Electronic Health Record to Create an Automated Real-Time Prognostic Tool for Peripheral Arterial Disease

scientific article published on 01 December 2018

Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts

scientific article published on 01 January 2017

MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks

scientific article published on 04 October 2023

Mapping Gene/Protein Names in Free Text to Biomedical Databases

article

MedXN: an open source medication extraction and normalization tool for clinical text

scientific article

Mining peripheral arterial disease cases from narrative clinical notes using natural language processing

scientific article published on 8 February 2017

Modeling asynchronous event sequences with RNNs

scientific article published on 05 June 2018

Natural Language Processing for Asthma Ascertainment in Different Practice Settings

scientific article published on 17 June 2017

Natural Language Processing for the Evaluation of Methodological Standards and Best Practices of EHR-based Clinical Research

scientific article published on 30 May 2020

Natural Language Processing for the Identification of Silent Brain Infarcts From Neuroimaging Reports

scientific article published on 21 April 2019

Natural language processing for populating lung cancer clinical research data

scientific article published on 05 December 2019

Natural language processing of radiology reports for identification of skeletal site-specific fractures

Need of informatics in designing interoperable clinical registries.

scientific article published on 10 October 2017

Open Source Clinical NLP - More than Any Single System

scientific article published on 7 April 2014

Operationalizing Semantic Medline for meeting the information needs at point of care

scientific article published on 25 March 2015

Overview of BioCreative II gene mention recognition

scientific article published on September 2008

Overview of BioCreative II gene normalization

scientific article published on September 2008

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Overview of the gene ontology task at BioCreative IV

scientific article

Patient-level temporal aggregation for text-based asthma status ascertainment

scientific article

Peripheral Neutrophil to Lymphocyte Ratio Improves Prognostication in Colon Cancer

scientific article published on 25 January 2017

Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology

Pooling annotated corpora for clinical concept extraction

scientific article published on 8 January 2013

Populating Physician Biographical Pages Based on EMR Data

scientific article

Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery

scientific article published on May 2016

Preliminary exploration of survival analysis using the OHDSI common data model: a case study of intrahepatic cholangiocarcinoma

Privacy-Preserving Predictive Modeling: Harmonization of Contextual Embeddings From Different Sources.

scientific article published on 16 May 2018

Provider Survey on Automated Clinical Decision Support System for Cardiovascular Risk Assessment.

scientific article published on 6 May 2019

Provider Survey on Automated Clinical Decision Support for Cardiovascular Risk Assessment

scholarly article published March 2019

Rapid identification of familial hypercholesterolemia from electronic health records: The SEARCH study

scientific article published on 6 August 2016

Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches.

scientific article published on 16 October 2017

Relationship Between Very Cold Outside Weather and Surgical Outcome: Integrating Shallow and Deep Artificial Neural Nets

scientific article published on 01 August 2019

Selected articles from the BioCreative/OHNLP challenge 2018

scientific article published on 27 December 2019

Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature ⬇️

scientific article published on October 22, 2011

Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP

scientific article published on 05 December 2018

Support vector machine-based mucin-type o-linked glycosylation site prediction using enhanced sequence feature encoding.

scientific article published on 14 November 2009

Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes

scientific article

Systematic Analysis of Adverse Event Reports for Sex Differences in Adverse Drug Events

scientific article published on 22 April 2016

Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes

Systematic Analysis of Free-Text Family History in Electronic Health Record

scientific article

Systematic identification of latent disease-gene associations from PubMed articles

scientific article

TGF-beta signaling proteins and the Protein Ontology

scientific article

Test collections for electronic health record-based clinical information retrieval

scientific article published on 04 June 2019

The 2019 n2c2/OHNLP Track on Clinical Semantic Textual Similarity: Overview

scientific article published on 27 November 2020

The CHEMDNER corpus of chemicals and drugs and its annotation principles

scientific article

The Sublanguage of Clinical Problem Lists: A Corpus Analysis

scientific article published on 05 December 2018

The gene normalization task in BioCreative III

scientific article (publication date: 3 October 2011)

Time Lapse to Colorectal Cancer: Telomere Dynamics Define the Malignant Potential of Polyps

scientific article published on 01 September 2016

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events

scientific article published on 06 July 2020

Toward a Learning Health-care System - Knowledge Delivery at the Point of Care Empowered by Big Data and NLP.

scientific article

Towards Transforming Expert-based Content to Evidence-based Content

scientific article published on 7 April 2014

Towards a semantic lexicon for clinical natural language processing ⬇️

scientific article published on November 3, 2012

Towards pathway curation through literature mining--a case study using PharmGKB.

scientific article published on January 2014

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis

scientific article

Unsupervised machine learning for the discovery of latent disease clusters and patient subgroups using electronic health records

scientific article published on 28 December 2019

Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes

Using SNOMED-CT to encode summary level data - a corpus analysis ⬇️

scientific article published on March 19, 2012

Using Social Media Data to Identify Potential Candidates for Drug Repurposing: A Feasibility Study

scientific article

Using empirically constructed lexical resources for named entity recognition

scientific article published on 24 June 2013

Using large clinical corpora for query expansion in text-based cohort identification

scientific article (publication date: June 2014)

Using machine learning for concept extraction on clinical documents from multiple data sources

scientific article

Utilization of Electronic Medical Records and Biomedical Literature to Support the Diagnosis of Rare Diseases Using Data Fusion and Collaborative Filtering Approaches

scientific article

Workflow-based Data Reconciliation for Clinical Decision Support: Case of Colorectal Cancer Screening and Surveillance

scientific article

dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.

scientific article

iProLINK: an integrated protein resource for literature mining

scientific article published on December 2004

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