List of works by Zhiyong Lu

A Deep Learning Approach for Automated Detection of Geographic Atrophy from Color Fundus Photographs

scientific article published on 11 June 2019

A Deep Phenotype Association Study Reveals Specific Phenotype Associations with Genetic Variants in Age-related Macular Degeneration: Age-Related Eye Disease Study 2 (AREDS2) Report No. 14.

scientific article published on 30 October 2017

A Field Sensor: computing the composition and intent of PubMed queries

scientific article published on 01 January 2018

A context-blocks model for identifying clinical relationships in patient records

scientific article

A multi-task deep learning model for the classification of Age-related Macular Degeneration

scientific article published on 06 May 2019

A survey of current trends in computational drug repositioning

scientific article

A textual representation scheme for identifying clinical relationships in patient records

scientific article published on 01 February 2011

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

scientific article

Accessing biomedical literature in the current information landscape

scientific article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

scientific article published on 17 January 2013

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

scientific article

Assisting document triage for human kinome curation via machine learning

scholarly article by Yi-Yu Hsu et al published 1 January 2018 in Database

Author keywords in biomedical journal articles

scientific article

Author name disambiguation for PubMed

scientific article

Automated abnormality classification of chest radiographs using deep convolutional neural networks

scientific article published on 14 May 2020

Automatic extraction of drug indications from FDA drug labels

scientific article

Automatic identification and normalization of dosage forms in drug monographs

scientific article

BC4GO: a full-text corpus for the BioCreative IV GO task

scientific article

Best Match: New relevance search for PubMed

Better synonyms for enriching biomedical search

scientific article published on 21 October 2020

Beyond accuracy: creating interoperable and scalable text-mining web services

scientific article (publication date: 16 February 2016)

BioC interoperability track overview

scientific article

BioC: a minimalist approach to interoperability for biomedical text processing

scientific article

BioCreative III interactive task: an overview

scientific article

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

scientific article

BioCreative-2012 virtual issue

scientific article published on 5 December 2012

BioCreative-IV virtual issue

scientific article published on 22 May 2014

BioWordVec, improving biomedical word embeddings with subword information and MeSH

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

scientific article (publication date: 2012)

Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents

scientific article published on 3 October 2017

Challenges in clinical natural language processing for automated disorder normalization

scientific article published on 14 July 2015

Click-words: learning to predict document keywords from a user perspective ⬇️

scientific article published on November 1, 2010

Concept recognition for extracting protein interaction relations from biomedical text

scientific article published on September 2008

Crowdsourcing and mining crowd data

scientific article

Crowdsourcing in biomedicine: challenges and opportunities

scientific article published in January 2016

DNorm: disease name normalization with pairwise learning to rank

scientific article published on 21 August 2013

Database resources of the National Center for Biotechnology Information

scientific article (published 2012-01-01)

Database resources of the National Center for Biotechnology Information

scientific article

Database resources of the National Center for Biotechnology Information

scientific article (published 2010-01-01)

Database resources of the National Center for Biotechnology Information

scientific article published on 01 January 2019

Database resources of the National Center for Biotechnology Information

scientific article published on 01 January 2020

Database resources of the National Center for Biotechnology Information

scientific article published on 23 October 2020

Deep learning automated detection of reticular pseudodrusen from fundus autofluorescence images or color fundus photographs in AREDS2

scientific article published on 21 May 2020

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

scientific article published on 30 April 2020

DeepSeeNet: A Deep Learning Model for Automated Classification of Patient-based Age-related Macular Degeneration Severity from Color Fundus Photographs

scientific article published on 22 November 2018

Editor's introduction to the special issue of the 6th Biomedical Linked Annotation Hackathon (BLAH6)

scientific article published on 24 June 2020

Evaluating relevance ranking strategies for MEDLINE retrieval

scientific article

Evaluating relevance ranking strategies for MEDLINE retrieval

scientific article published on 24 October 2008

Evaluation of Query Expansion Using MeSH in PubMed

scientific article

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

scientific article

Extracting Rx information from clinical narrative ⬇️

scientific article published on September 1, 2010

Extracting chemical-protein relations with ensembles of SVM and deep learning models

scientific article published on 01 January 2018

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

scientific article

Finding GeneRIFs via gene ontology annotations.

scientific article

Finding query suggestions for PubMed

scientific article

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

scientific article

GeneRIF quality assurance as summary revision

scientific article

Generalizing biomedical relation classification with neural adversarial domain adaptation

scientific article published on 01 September 2018

How user intelligence is improving PubMed

scientific article published on 01 October 2018

Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing

scientific article

Identifying named entities from PubMed for enriching semantic categories

scientific article

Identifying related journals through log analysis

scientific article

Improving accuracy for identifying related PubMed queries by an integrated approach

scientific article

Improving chemical disease relation extraction with rich features and weakly labeled data

scientific article (publication date: 7 October 2016)

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

scientific article

Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining

scientific article published on 27 June 2019

Keep up with the latest coronavirus research

scientific article published on 01 March 2020

LabeledIn: cataloging labeled indications for human drugs

scientific article

Large-scale event extraction from literature with multi-level gene normalization

scientific article

LitCovid: an open database of COVID-19 literature

scientific article published on 09 November 2020

LitSense: making sense of biomedical literature at sentence level

scientific article published on 01 July 2019

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

scientific article published in July 2018

ML-Net: multi-label classification of biomedical texts with deep neural networks

scientific article published on 01 November 2019

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank

scientific article

Mining chemical patents with an ensemble of open systems

scientific article (publication date: 2016)

NCBI disease corpus: a resource for disease name recognition and concept normalization

scientific article (publication date: February 2014)

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

scientific article

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study ⬇️

scientific article published on 13 July 2017

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

scientific article published on 14 December 2016

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

scientific article

Opportunities And Obstacles For Deep Learning In Biology And Medicine

scholarly article published 28 May 2017

Overview of BioCreative II gene normalization

scientific article published on September 2008

Overview of the BioCreative III Workshop

scientific article

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

Overview of the BioCreative VI text-mining services for Kinome Curation Track

scientific article published on 01 January 2018

Overview of the gene ontology task at BioCreative IV

scientific article

Overview of the interactive task in BioCreative V

scientific article (publication date: 2016)

PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed

scientific article published on 30 May 2020

PMC text mining subset in BioC: about three million full-text articles and growing

scientific article published on 01 September 2019

Pathway-based drug repositioning using causal inference

scientific article

Predicting clicks of PubMed articles

scientific article

Predicting risk of late age-related macular degeneration using deep learning

scientific article published on 27 August 2020

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

scientific article

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

scientific article

PubMed Labs: an experimental system for improving biomedical literature search

PubMed Phrases, an open set of coherent phrases for searching biomedical literature.

scientific article

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

scientific article published on 01 January 2019

PubTator central: automated concept annotation for biomedical full text articles

scientific article published on 01 July 2019

PubTator: a web-based text mining tool for assisting biocuration

scientific article (publication date: July 2013)

Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature

scientific article published on 07 August 2020

Recommending MeSH terms for annotating biomedical articles

scientific article

SR4GN: a species recognition software tool for gene normalization

scientific article (publication date: 2012)

Scaling drug indication curation through crowdsourcing

scientific article

Semantic role labeling for protein transport predicates

scientific article

Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction ⬇️

scientific article published on November 20, 2010

SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine

scientific article published on 01 January 2014

SimConcept: a hybrid approach for simplifying composite named entities in biomedical text

scientific article

Systematic identification of pharmacogenomics information from clinical trials

scientific article

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

scientific article

TeamTat: a collaborative text annotation tool

scientific article published on 08 May 2020

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

scientific article

Text Mining for Drug Discovery

scientific article published on 01 January 2019

Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health

scientific article

Text Mining for Translational Bioinformatics

scientific article published on 25 August 2015

Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature

scientific article

The CHEMDNER corpus of chemicals and drugs and its annotation principles

scientific article

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

scientific article

The gene normalization task in BioCreative III

scientific article (publication date: 3 October 2011)

Tracking human genes along the translational continuum

scientific article published on 16 October 2019

Understanding PubMed user search behavior through log analysis

scientific article (publication date: 2009)

Using deep learning to identify translational research in genomic medicine beyond bench to bedside

scholarly article by Yi-Yu Hsu et al published 1 January 2019 in Database

ezTag: tagging biomedical concepts via interactive learning.

scientific article published in July 2018

tmBioC: improving interoperability of text-mining tools with BioC.

scientific article

tmChem: a high performance approach for chemical named entity recognition and normalization

scientific article

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

scientific article published in September 2017

tmVar: a text mining approach for extracting sequence variants in biomedical literature

scientific article

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