Zhiyong Lu

According to our database1, Zhiyong Lu authored at least 174 papers between 2003 and 2020.

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Bibliography

2020
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
PLoS Comput. Biol., 2020

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology.
CoRR, 2020

Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR, 2020

Predicting risk of late age-related macular degeneration using deep learning.
CoRR, 2020

COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from biomedical literature.
CoRR, 2020

TeamTat: a collaborative text annotation tool.
CoRR, 2020

FullMeSH: improving large-scale MeSH indexing with full text.
Bioinform., 2020

An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining.
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 2020

2019
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2019

ML-Net: multi-label classification of biomedical texts with deep neural networks.
J. Am. Medical Informatics Assoc., 2019

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
CoRR, 2019

A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
CoRR, 2019

Exploring Semi-supervised Variational Autoencoders for Biomedical Relation Extraction.
CoRR, 2019

PMC text mining subset in BioC: about three million full-text articles and growing.
Bioinform., 2019

Using deep learning to identify translational research in genomic medicine beyond bench to bedside.
Database J. Biol. Databases Curation, 2019

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database.
Database J. Biol. Databases Curation, 2019

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation, 2019


MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2019, 2019

Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports.
Proceedings of the 16th IEEE International Symposium on Biomedical Imaging, 2019

A self-attention based deep learning method for lesion attribute detection from CT reports.
Proceedings of the 2019 IEEE International Conference on Healthcare Informatics, 2019

BioSentVec: creating sentence embeddings for biomedical texts.
Proceedings of the 2019 IEEE International Conference on Healthcare Informatics, 2019

Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology.
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2019

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets.
Proceedings of the 18th BioNLP Workshop and Shared Task, 2019

Biomedical Mention Disambiguation using a Deep Learning Approach.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

A Text-Mining System for Concept Annotation in Biomedical Full Text Articles.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

Evaluation of Five Sentence Similarity Models on Electronic Medical Records.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs.
Proceedings of the AMIA 2019, 2019

Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs.
Proceedings of the Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, 2019

ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases.
Proceedings of the Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, 2019

2018
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
PLoS Comput. Biol., 2018

ezTag: tagging biomedical concepts via interactive learning.
Nucleic Acids Res., 2018

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.
Nucleic Acids Res., 2018

A multi-task deep learning model for the classification of Age-related Macular Degeneration.
CoRR, 2018

DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs.
CoRR, 2018

PubMed Labs: An experimental platform for improving biomedical literature search.
CoRR, 2018

PMC text mining subset in BioC: 2.3 million full text articles and growing.
CoRR, 2018

Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models.
CoRR, 2018

tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine.
Bioinform., 2018

Generalizing biomedical relation classification with neural adversarial domain adaptation.
Bioinform., 2018

A Field Sensor: computing the composition and intent of PubMed queries.
Database J. Biol. Databases Curation, 2018

Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Database J. Biol. Databases Curation, 2018

Assisting document triage for human kinome curation via machine learning.
Database J. Biol. Databases Curation, 2018

Overview of the BioCreative VI text-mining services for Kinome Curation Track.
Database J. Biol. Databases Curation, 2018

PubMed Labs: an experimental system for improving biomedical literature search.
Database J. Biol. Databases Curation, 2018

A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval.
Proceedings of the 2018 World Wide Web Conference on World Wide Web, 2018

Personalized neural language models for real-world query auto completion.
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2018

TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays.
Proceedings of the 2018 IEEE Conference on Computer Vision and Pattern Recognition, 2018

SingleCite: Towards an improved Single Citation Search in PubMed.
Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018, 2018

MeSH-based dataset for measuring the relevance of text retrieval.
Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018, 2018

Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Experimenting new search and user interface in PubMed Labs.
Proceedings of the AMIA 2018, 2018

Online evaluation of PubMed's new relevance search algorithm.
Proceedings of the AMIA 2018, 2018

2017
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents.
J. Biomed. Informatics, 2017

NegBio: a high-performance tool for negation and uncertainty detection in radiology reports.
CoRR, 2017

DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks.
BMC Syst. Biol., 2017

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.
J. Biomed. Semant., 2017

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Bioinform., 2017

Exploiting Virtual Metadata Servers to Provide Multi-Level Consistency for Key-Value Object-Based Data Store.
Proceedings of the 2017 International Conference on Networking, Architecture, and Storage, 2017

ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases.
Proceedings of the 2017 IEEE Conference on Computer Vision and Pattern Recognition, 2017

Deep learning for extracting protein-protein interactions from biomedical literature.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

Text Mining Radiology Reports for Deep Learning Radiology Images.
Proceedings of the AMIA 2017, 2017

New Relevance Search Algorithm for PubMed.
Proceedings of the AMIA 2017, 2017

2016
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.
PLoS Comput. Biol., 2016

Improving chemical disease relation extraction with rich features and weakly labeled data.
J. Cheminformatics, 2016

Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature.
J. Am. Medical Informatics Assoc., 2016

Bridging the Gap: a Semantic Similarity Measure between Queries and Documents.
CoRR, 2016

Beyond accuracy: creating interoperable and scalable text-mining web services.
Bioinform., 2016

TaggerOne: joint named entity recognition and normalization with semi-Markov Models.
Bioinform., 2016

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.
Database J. Biol. Databases Curation, 2016

Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation, 2016

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Database J. Biol. Databases Curation, 2016

BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
Database J. Biol. Databases Curation, 2016

Mining chemical patents with an ensemble of open systems.
Database J. Biol. Databases Curation, 2016

Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.
Database J. Biol. Databases Curation, 2016

A survey of current trends in computational drug repositioning.
Briefings Bioinform., 2016

Crowdsourcing in biomedicine: challenges and opportunities.
Briefings Bioinform., 2016

Community challenges in biomedical text mining over 10 years: success, failure and the future.
Briefings Bioinform., 2016

Large-scale Semantic Indexing with Biomedical Ontologies.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

BioCconvert: A Conversion Tool Between BioC and PubAnnotation.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

PubTermVariants: biomedical term variants and their use for PubMed search.
Proceedings of the 15th Workshop on Biomedical Natural Language Processing, 2016

Exploring Query Expansion for Entity Searches in PubMed.
Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis, 2016

2015
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text.
IEEE J. Biomed. Health Informatics, 2015

tmChem: a high performance approach for chemical named entity recognition and normalization.
J. Cheminformatics, 2015

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

Challenges in clinical natural language processing for automated disorder normalization.
J. Biomed. Informatics, 2015

Identifying named entities from PubMed®; for enriching semantic categories.
BMC Bioinform., 2015

Scaling drug indication curation through crowdsourcing.
Database J. Biol. Databases Curation, 2015

Session Introduction.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

NCBI at the 2015 BioASQ Challenge Task: Baseline Results from MeSH Now.
Proceedings of the Working Notes of CLEF 2015, 2015

2014
LabeledIn: Cataloging labeled indications for human drugs.
J. Biomed. Informatics, 2014

NCBI disease corpus: A resource for disease name recognition and concept normalization.
J. Biomed. Informatics, 2014

Author name disambiguation for PubMed.
J. Assoc. Inf. Sci. Technol., 2014

Overview of the gene ontology task at BioCreative IV.
Database J. Biol. Databases Curation, 2014

<i>tmBioC</i>: improving interoperability of text-mining tools with BioC.
Database J. Biol. Databases Curation, 2014

BioC interoperability track overview.
Database J. Biol. Databases Curation, 2014

Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing.
Database J. Biol. Databases Curation, 2014

BC4GO: a full-text corpus for the BioCreative IV GO task.
Database J. Biol. Databases Curation, 2014

BioCreative-IV virtual issue.
Database J. Biol. Databases Curation, 2014

Session Introduction.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering.
Proceedings of the Working Notes for CLEF 2014 Conference, 2014

Automated Disease Normalization with Low Rank Approximations.
Proceedings of BioNLP, Baltimore, Maryland, USA, 2014

SimConcept: a hybrid approach for simplifying composite named entities in biomedicine.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

Text mining tools for assisting literature curation.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

Disease named entity recognition and normalization with DNorm.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

Automatic Extraction of Drug Indications from FDA Drug Labels.
Proceedings of the AMIA 2014, 2014

2013
PubTator: a web-based text mining tool for assisting biocuration.
Nucleic Acids Res., 2013

Pathway-based drug repositioning using causal inference.
BMC Bioinform., 2013

tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Bioinform., 2013

DNorm: disease name normalization with pairwise learning to rank.
Bioinform., 2013

BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation, 2013

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation, 2013

Session Introduction.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Toward Creating a Gold Standard of Drug Indications from FDA Drug Labels.
Proceedings of the IEEE International Conference on Healthcare Informatics, 2013

NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

A systematic comparison of current sources of disease knowledge.
Proceedings of the AMIA 2013, 2013

Predicting clicks of PubMed articles.
Proceedings of the AMIA 2013, 2013

DNorm: A New Method and Online Tool for Disease Name Normalization.
Proceedings of the AMIA 2013, 2013

NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization.
Proceedings of the AMIA 2013, 2013

2012
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2012

Automatic identification and normalization of dosage forms in drug monographs.
BMC Medical Informatics Decis. Mak., 2012

Systematic identification of pharmacogenomics information from clinical trials.
J. Biomed. Informatics, 2012

BioCreative-2012 Virtual Issue.
Database J. Biol. Databases Curation, 2012

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.
Database J. Biol. Databases Curation, 2012

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
Database J. Biol. Databases Curation, 2012

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.
Database J. Biol. Databases Curation, 2012

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
Database J. Biol. Databases Curation, 2012

Linking multiple disease-related resources through UMLS.
Proceedings of the ACM International Health Informatics Symposium, 2012

A Network Approach for Computational Drug Repositioning.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

Improving Online Access to Drug-Related Information.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012

An improved corpus of disease mentions in PubMed citations.
Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, 2012

A new method for computational drug repositioning using drug pairwise similarity.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

An Inference Method for Disease Name Normalization.
Proceedings of the Information Retrieval and Knowledge Discovery in Biomedical Text, 2012

2011
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2011

Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction.
J. Biomed. Informatics, 2011

Recommending MeSH terms for annotating biomedical articles.
J. Am. Medical Informatics Assoc., 2011

The gene normalization task in BioCreative III.
BMC Bioinform., 2011

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform., 2011

A context-blocks model for identifying clinical relationships in patient records.
BMC Bioinform., 2011

BioCreative III interactive task: an overview.
BMC Bioinform., 2011

Overview of the BioCreative III Workshop.
BMC Bioinform., 2011

Extraction of data deposition statements from the literature: a method for automatically tracking research results.
Bioinform., 2011

PubMed and beyond: a survey of web tools for searching biomedical literature.
Database J. Biol. Databases Curation, 2011

Automatic extraction of data deposition statements: where do the research results go?
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011

2010
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2010

Extracting Rx information from clinical narrative.
J. Am. Medical Informatics Assoc., 2010

Click-words: learning to predict document keywords from a user perspective.
Bioinform., 2010

Automatic integration of drug indications from multiple health resources.
Proceedings of the ACM International Health Informatics Symposium, 2010

A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records.
Proceedings of the Ninth International Conference on Machine Learning and Applications, 2010

Learning to Annotate Scientific Publications.
Proceedings of the COLING 2010, 2010

2009
Improving accuracy for identifying related PubMed queries by an integrated approach.
J. Biomed. Informatics, 2009

Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
J. Am. Medical Informatics Assoc., 2009

Evaluation of query expansion using MeSH in PubMed.
Inf. Retr., 2009

Identifying related journals through log analysis.
Bioinform., 2009

Understanding PubMed<sup>®</sup> user search behavior through log analysis.
Database J. Biol. Databases Curation, 2009

Summarizing Documents by Measuring the Importance of a Subset of Vertices within a Graph.
Proceedings of the 2009 IEEE/WIC/ACM International Conference on Web Intelligence, 2009

Users' adjustments to unsuccessful queries in biomedical search.
Proceedings of the 2009 Joint International Conference on Digital Libraries, 2009

Exploring Two Biomedical Text Genres for Disease Recognition.
Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, 2009

Towards Automatic Generation of Gene Summary.
Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, 2009

Finding Query Suggestions for PubMed.
Proceedings of the AMIA 2009, 2009

2008
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.
BMC Bioinform., 2008

Semantic role labeling for protein transport predicates.
BMC Bioinform., 2008

Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
Proceedings of the AMIA 2008, 2008

2007
Association Rules in the Relational Calculus
CoRR, 2007

Generif Quality Assurance as Summary Revision.
Proceedings of the Biocomputing 2007, 2007

2006
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.
Proceedings of the Fifteenth Text REtrieval Conference, 2006

Finding GeneRIFs via Gene Ontology Annotations.
Proceedings of the Biocomputing 2006, 2006

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.
Proceedings of the Biocomputing 2006, 2006

2005
GO Molecular Function Terms Are Predictive of Subcellular Localization.
Proceedings of the Biocomputing 2005, 2005

2004
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations.
Nucleic Acids Res., 2004

Predicting subcellular localization of proteins using machine-learned classifiers.
Bioinform., 2004

2003
Automatic Extraction of Clusters from Hierarchical Clustering Representations.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2003


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