Zhiyong Lu

Orcid: 0000-0001-9998-916X

According to our database1, Zhiyong Lu authored at least 287 papers between 2003 and 2024.

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Bibliography

2024
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.
Bioinform., February, 2024

Universal detection and segmentation of lymph nodes in multi-parametric MRI.
Int. J. Comput. Assist. Radiol. Surg., January, 2024

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.
Medical Image Anal., 2024

Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness.
J. Biomed. Informatics, 2024

A survey of recent methods for addressing AI fairness and bias in biomedicine.
J. Biomed. Informatics, 2024

Adversarial Attacks on Large Language Models in Medicine.
CoRR, 2024

MedCalc-Bench: Evaluating Large Language Models for Medical Calculations.
CoRR, 2024

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

GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases.
CoRR, 2024

Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.
CoRR, 2024

EnzChemRED, a rich enzyme chemistry relation extraction dataset.
CoRR, 2024

Decomposing Vision-based LLM Predictions for Auto-Evaluation with GPT-4.
CoRR, 2024

Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark.
CoRR, 2024

AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning.
CoRR, 2024

Benchmarking Retrieval-Augmented Generation for Medicine.
CoRR, 2024

Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science.
CoRR, 2024

Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles.
CoRR, 2024

Quality of Answers of Generative Large Language Models vs Peer Patients for Interpreting Lab Test Results for Lay Patients: Evaluation Study.
CoRR, 2024

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports.
CoRR, 2024

Unmasking and Quantifying Racial Bias of Large Language Models in Medical Report Generation.
CoRR, 2024

PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge.
CoRR, 2024

Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine.
CoRR, 2024

Detection of abdominopelvic lymph nodes in multi-parametric MRI.
Comput. Medical Imaging Graph., 2024

2023
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.
Bioinform., December, 2023

Trigonometric projection statistics histograms for 3D local feature representation and shape description.
Pattern Recognit., November, 2023

A scoping review on multimodal deep learning in biomedical images and texts.
J. Biomed. Informatics, October, 2023

BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets.
J. Biomed. Informatics, October, 2023

GNorm2: an improved gene name recognition and normalization system.
Bioinform., October, 2023

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.
Bioinform., October, 2023

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.
Bioinform., May, 2023

Universal lymph node detection in T2 MRI using neural networks.
Int. J. Comput. Assist. Radiol. Surg., February, 2023

Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns, January, 2023

Database resources of the National Center for Biotechnology Information in 2023.
Nucleic Acids Res., January, 2023

LitCovid in 2022: an information resource for the COVID-19 literature.
Nucleic Acids Res., January, 2023

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

Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness.
CoRR, 2023

Matching Patients to Clinical Trials with Large Language Models.
CoRR, 2023

PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search.
CoRR, 2023

BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval.
CoRR, 2023

Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR, 2023

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

Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning.
CoRR, 2023

Bioformer: an efficient transformer language model for biomedical text mining.
CoRR, 2023

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII.
Database J. Biol. Databases Curation, 2023

LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search.
Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2023

Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans.
Proceedings of the Medical Imaging 2023: Image Processing, 2023

Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

Universal lymph node detection in multiparametric MRI with selective augmentation.
Proceedings of the Medical Imaging 2023: Computer-Aided Diagnosis, 2023

Multi-stage Literature Retrieval System Trained by PubMed Search Logs for Biomedical Question Answering.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), 2023

2022
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Robust convolutional neural networks against adversarial attacks on medical images.
Pattern Recognit., 2022

Predicting myocardial infarction through retinal scans and minimal personal information.
Nat. Mach. Intell., 2022

Database resources of the national center for biotechnology information.
Nucleic Acids Res., 2022

Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images.
Medical Image Anal., 2022

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology.
J. Biomed. Informatics, 2022

Towards a unified search: Improving PubMed retrieval with full text.
J. Biomed. Informatics, 2022

Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR, 2022

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR, 2022

A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis.
CoRR, 2022

tmVar 3.0: an improved variant concept recognition and normalization tool.
Bioinform., 2022

A sequence labeling framework for extracting drug-protein relations from biomedical literature.
Database J. Biol. Databases Curation, 2022

NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.
Database J. Biol. Databases Curation, 2022

A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation, 2022

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
Database J. Biol. Databases Curation, 2022

Assigning species information to corresponding genes by a sequence labeling framework.
Database J. Biol. Databases Curation, 2022

BioRED: a rich biomedical relation extraction dataset.
Briefings Bioinform., 2022

Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.
Proceedings of the Machine Learning in Medical Imaging - 13th International Workshop, 2022

Lymph node detection in T2 MRI with transformers.
Proceedings of the Medical Imaging 2022: Computer-Aided Diagnosis, 2022

Radiology Text Analysis System (RadText): Architecture and Evaluation.
Proceedings of the 10th IEEE International Conference on Healthcare Informatics, 2022

PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles.
Proceedings of the AMIA 2022, 2022

BioRED: A Comprehensive Biomedical Relation Extraction Dataset.
Proceedings of the AMIA 2022, 2022

Deep learning automated diagnosis and quantitative classification of cataract type and severity: quantifying the effectiveness and usability of deep learning-assisted disease diagnosis models with 14 ophthalmologists and multi-center validations.
Proceedings of the AMIA 2022, 2022


2021
Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training.
IEEE Trans. Medical Imaging, 2021

Loss-Based Attention for Interpreting Image-Level Prediction of Convolutional Neural Networks.
IEEE Trans. Image Process., 2021

COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature.
IEEE Trans. Big Data, 2021

Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2021

LitSuggest: a web-based system for literature recommendation and curation using machine learning.
Nucleic Acids Res., 2021

LitCovid: an open database of COVID-19 literature.
Nucleic Acids Res., 2021

NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.
J. Biomed. Informatics, 2021

Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration.
J. Am. Medical Informatics Assoc., 2021

Perceiving and Modeling Density is All You Need for Image Dehazing.
CoRR, 2021

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology.
Bioinform., 2021

BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer.
Bioinform., 2021

Recent advances in biomedical literature mining.
Briefings Bioinform., 2021

Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.
Briefings Bioinform., 2021

Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI.
Proceedings of the Machine Learning in Medical Imaging - 12th International Workshop, 2021

Detection of Lymph Nodes in T2 MRI Using Neural Network Ensembles.
Proceedings of the Machine Learning in Medical Imaging - 12th International Workshop, 2021

Learning Few-Shot Chest X-Ray Diagnosis Using Images From The Published Scientific Literature.
Proceedings of the 18th IEEE International Symposium on Biomedical Imaging, 2021

Research on Deep Neural Network Model Compression Based on Quantification Pruning and Huffmann Encoding.
Proceedings of the Intelligent Computing Theories and Application, 2021

SDWNet: A Straight Dilated Network with Wavelet Transformation for image Deblurring.
Proceedings of the IEEE/CVF International Conference on Computer Vision Workshops, 2021

Measuring the relative importance of full text sections for information retrieval from scientific literature.
Proceedings of the 20th Workshop on Biomedical Language Processing, 2021

Improving PubMed Retrieval by Integrating Abstract and Full Text Search.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Informatics-izing the National Institutes of Health.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Deep learning detection of reticular pseudodrusen using multi-modal, multi-task, and multi-attention mechanisms: towards automated and accessible classification of age-related macular degeneration.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
BMC Medical Informatics Decis. Mak., April, 2020

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

Automated abnormality classification of chest radiographs using deep convolutional neural networks.
npj Digit. Medicine, 2020

Predicting risk of late age-related macular degeneration using deep learning.
npj Digit. Medicine, 2020

Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res., 2020

TeamTat: a collaborative text annotation tool.
Nucleic Acids Res., 2020

Better synonyms for enriching biomedical search.
J. Am. Medical Informatics Assoc., 2020

Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration.
CoRR, 2020

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR, 2020

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

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.
Bioinform., 2020

DTF: Deep Tensor Factorization for predicting anticancer drug synergy.
Bioinform., 2020

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

COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs.
Proceedings of the Interpretable and Annotation-Efficient Learning for Medical Image Computing, 2020

A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2.
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 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

Detection of reticular pseudodrusen using deep learning.
Proceedings of the AMIA 2020, 2020

Automatic recognition of abdominal lymph nodes from clinical text.
Proceedings of the 3rd Clinical Natural Language Processing Workshop, 2020

2019
PubTator central: automated concept annotation for biomedical full text articles.
Nucleic Acids Res., 2019

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

LitSense: making sense of biomedical literature at sentence level.
Nucleic Acids Res., 2019

ML-Net: multi-label classification of biomedical texts with deep neural networks.
J. Am. Medical Informatics Assoc., 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
Mining Related Articles for Automatic Journal Cataloging.
J. Data Inf. Sci., 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

An Integrative Approach for Discovery of New Uses of Existing Drugs.
Data Sci. J., 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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