Lawrence Hunter

Orcid: 0000-0003-1455-3370

According to our database1, Lawrence Hunter authored at least 147 papers between 1977 and 2024.

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Bibliography

2024
Desiderata For The Context Use Of Question Answering Systems.
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics, 2024

Comparing Template-based and Template-free Language Model Probing.
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics, 2024

2023
Ontologizing health systems data at scale: making translational discovery a reality.
npj Digit. Medicine, 2023

Creating an ignorance-base: Exploring known unknowns in the scientific literature.
J. Biomed. Informatics, 2023

Who Are All The Stochastic Parrots Imitating? They Should Tell Us!
CoRR, 2023

Emerging Challenges in Personalized Medicine: Assessing Demographic Effects on Biomedical Question Answering Systems.
CoRR, 2023

The Future of Fundamental Science Led by Generative Closed-Loop Artificial Intelligence.
CoRR, 2023

An Open-Source Knowledge Graph Ecosystem for the Life Sciences.
CoRR, 2023

Who Are All The Stochastic Parrots Imitating? They Should Tell Us!
Proceedings of the 13th International Joint Conference on Natural Language Processing and the 3rd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics, 2023

Emerging Challenges in Personalized Medicine: Assessing Demographic Effects on Biomedical Question Answering Systems.
Proceedings of the 13th International Joint Conference on Natural Language Processing and the 3rd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics, 2023

2022
Molecular cartooning with knowledge graphs.
Frontiers Bioinform., 2022

Mind the Knowledge Gap: A Survey of Knowledge-enhanced Dialogue Systems.
CoRR, 2022

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality.
CoRR, 2022

Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome.
CoRR, 2022

BETA: a comprehensive benchmark for computational drug-target prediction.
Briefings Bioinform., 2022

Characterizing Patient Representations for Computational Phenotyping.
Proceedings of the AMIA 2022, 2022

2021
Concept recognition as a machine translation problem.
BMC Bioinform., 2021

Characterization of Anonymous Physician Perspectives on COVID-19 Using Social Media Data.
Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

2020
Hypernetwork Science: From Multidimensional Networks to Computational Topology.
CoRR, 2020

Biocomputing 2021: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2021
, 2020

2019
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery.
npj Digit. Medicine, 2019

Knowledge-based Biomedical Data Science 2019.
CoRR, 2019

P-Hacking Lexical Richness Through Definitions of "Type" and "Token".
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference.
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 2019

2018
OWL-NETS: Transforming OWL representations for improved network inference.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Improving precision in concept normalization.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Three Dimensions of Reproducibility in Natural Language Processing.
Proceedings of the Eleventh International Conference on Language Resources and Evaluation, 2018

2017
Knowledge-based biomedical Data Science.
Data Sci., 2017

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.
BMC Bioinform., 2017

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.
Database J. Biol. Databases Curation, 2017

No-Boundary Thinking in Bioinformatics.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

A semantic knowledge-base approach to drug-drug interaction discovery.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Reproducibility in Biomedical Natural Language Processing.
Proceedings of the AMIA 2017, 2017

2016
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.
J. Biomed. Semant., 2016

Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015
Visual analysis of biological data-knowledge networks.
BMC Bioinform., 2015

KaBOB: ontology-based semantic integration of biomedical databases.
BMC Bioinform., 2015

Reports of the AAAI 2014 Conference Workshops.
AI Mag., 2015

Training the Next Generation of Quantitative Biologists in the Era of Big Data.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

PEAX: Interactive Visual Analysis and Exploration of Complex Clinical Phenotype and Gene Expression Association.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

A Twentieth Anniversary Tribute to PSB.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014
Ontologies in Biological Data Visualization.
IEEE Computer Graphics and Applications, 2014

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.
BMC Bioinform., 2014

Building the Next Generation of Quantitative Biologists.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

Ontology Translation: A Case Study on Translating the Gene Ontology from English to German.
Proceedings of the Natural Language Processing and Information Systems, 2014

2013
Rocky Mountain Conference on Bioinformatics Celebrates 10 Years.
PLoS Comput. Biol., 2013

Chapter 16: Text Mining for Translational Bioinformatics.
PLoS Comput. Biol., 2013

Representing annotation compositionality and provenance for the Semantic Web.
J. Biomed. Semant., 2013

UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features.
Proceedings of the 7th International Workshop on Semantic Evaluation, 2013

Computational Challenges of Mass Phenotyping.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2012
AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline.
J. Am. Medical Informatics Assoc., 2012

Biological Data Visualization (Dagstuhl Seminar 12372).
Dagstuhl Reports, 2012

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.
BMC Bioinform., 2012

Concept annotation in the CRAFT corpus.
BMC Bioinform., 2012

Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It.
Proceedings of the Trustworthy Eternal Systems via Evolving Software, Data and Knowledge, 2012

Invited Talks.
Proceedings of the Discovery Informatics: The Role of AI Research in Innovating Scientific Processes, 2012

2011
Desiderata for ontologies to be used in semantic annotation of biomedical documents.
J. Biomed. Informatics, 2011

U-Compare: A modular NLP workflow construction and evaluation system.
IBM J. Res. Dev., 2011

High-Precision Biological Event Extraction: Effects of System and of Data.
Comput. Intell., 2011

U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC Bioinform., 2011

MetaMap is a Superior Baseline to a Standard Document Retrieval Engine for the Task of Finding Patient Cohorts in Clinical Free Text.
Proceedings of The Twentieth Text REtrieval Conference, 2011

Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles.
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011

Fast and simple semantic class assignment for biomedical text.
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011

A scaleable automated quality assurance technique for semantic representations and proposition banks.
Proceedings of the Fifth Linguistic Annotation Workshop, 2011

2010
Exploring Species-Based Strategies for Gene Normalization.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Current methodologies for translational bioinformatics.
J. Biomed. Informatics, 2010

The structural and content aspects of abstracts versus bodies of full text journal articles are different.
BMC Bioinform., 2010

A UIMA wrapper for the NCBO annotator.
Bioinform., 2010

Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System.
Proceedings of the 4th IEEE International Conference on Semantic Computing (ICSC 2010), 2010

Extraction of Genotype-Phenotype-Drug Relationships from Text: From Entity Recognition to Bioinformatics Application.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Test Suite Design for Biomedical Ontology Concept Recognition Systems.
Proceedings of the International Conference on Language Resources and Evaluation, 2010

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.
Proceedings of the Knowledge-Based and Intelligent Information and Engineering Systems, 2010

An Overview of the CRAFT Concept Annotation Guidelines.
Proceedings of the Fourth Linguistic Annotation Workshop, 2010

2009
Biomedical Discovery Acceleration, with Applications to Craniofacial Development.
PLoS Comput. Biol., 2009

New JBI emphasis on translational bioinformatics.
J. Biomed. Informatics, 2009

The textual characteristics of traditional and Open Access scientific journals are similar.
BMC Bioinform., 2009

Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology.
BMC Bioinform., 2009

Ontology quality assurance through analysis of term transformations.
Bioinform., 2009

U-Compare: share and compare text mining tools with UIMA.
Bioinform., 2009

How interactive visualization can assist investigative analysis: Views and perspectives from domain experts.
Proceedings of the 4th IEEE Symposium on Visual Analytics Science and Technology, 2009

High-precision biological event extraction with a concept recognizer.
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

2008
Getting Started in Text Mining.
PLoS Comput. Biol., 2008

Predicting protein linkages in bacteria: Which method is best depends on task.
BMC Bioinform., 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

Improving protein function prediction methods with integrated literature data.
BMC Bioinform., 2008

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

Identification of OBO nonalignments and its implications for OBO enrichment.
Bioinform., 2008

Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.
Proceedings of the Biocomputing 2008, 2008

A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward Ontology Quality Control.
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.
Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing.
Proceedings of the Software Engineering, 2008

2007
The International Society for Computational Biology 10th Anniversary.
PLoS Comput. Biol., 2007

Enrichment of OBO ontologies.
J. Biomed. Informatics, 2007

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.
J. Bioinform. Comput. Biol., 2007

MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinform., 2007

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

Assessing and Combining Reliability of Protein Interaction Sources.
Proceedings of the Biocomputing 2007, 2007

A Fault Model for Ontology Mapping, Alignment, and Linking Systems.
Proceedings of the Biocomputing 2007, 2007

Manual curation is not sufficient for annotation of genomic databases.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

2006
A critical review of PASBio's argument structures for biomedical verbs.
BMC Bioinform., 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

Refactoring Corpora.
Proceedings of the Workshop on Linking Natural Language and Biology, 2006

2005
BioCreAtIvE Task1A: entity identification with a stochastic tagger.
BMC Bioinform., 2005

Concept Recognition and the TREC Genomics Tasks.
Proceedings of the Fourteenth Text REtrieval Conference, 2005

Implications of Compositionality in the Gene Ontology for Its Curation and Usage .
Proceedings of the Biocomputing 2005, 2005

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

Corpus Design for Biomedical Natural Language Processing.
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, 2005

Empirical data on corpus design and usage in biomedical natural language processing.
Proceedings of the AMIA 2005, 2005

2004
Natural Language Processing and Systems Biology.
Proceedings of the Artificial Intelligence Methods And Tools For Systems Biology, 2004

Life and Its Molecules: A Brief Introduction.
AI Mag., 2004

The Compositional Structure of Gene Ontology Terms.
Proceedings of the Biocomputing 2004, 2004

Integrated Term Weighting, Visualization, and User Interface Development for Bioinformation Retrieval.
Proceedings of the Artificial Intelligence and Simulation, 2004

2003
IBM Research and the University of Colorado - TREC 2003 Genomics Track.
Proceedings of The Twelfth Text REtrieval Conference, 2003

Trajectory Clustering: A Non-Parametric Method for Grouping Gene Expression Time Courses with Applications to Mammary Development.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Special Paper - Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2002
Guest Editors' Introduction-Computer Science and Biology: An Unlikely Pair.
IEEE Intell. Syst., 2002

A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis.
Bioinform., 2002

Preface.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Contrast and variability in gene names.
Proceedings of the ACL 2002 Workshop on Natural Language Processing in the Biomedical Domain, 2002

2001
GEST: a gene expression search tool based on a novel Bayesian similarity metric.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000
Extracting Molecular Binding Relationships from Biomedical Text.
Proceedings of the 6th Applied Natural Language Processing Conference, 2000

1999
Mining molecular binding terminology from biomedical text.
Proceedings of the AMIA 1999, 1999

Comparison of Clustering Metrics and Unsupervised Learning Algorithms on Genome-Wide Gene Expression Level Data.
Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, 1999

1998
Identification of Divergent Functions in Homologous Proteins by Induction over Conserved Modules.
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1997
A Model of Cerebellar Saccadic Motor Learning Using Qualitative Reasoning.
Proceedings of the Biological and Artificial Computation: From Neuroscience to Technology, 1997

Predicting Enzyme Function from Sequence: A Systematic Appraisal.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Identifying Chimerism in Proteins Using Hidden Markov Models of Codon Usage.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1995
Introduction.
Mach. Learn., 1995

1994
The First International Conference on Intelligent Systems for Molecular Biology.
AI Mag., 1994

1993
Computationally Efficient Cluster Representation in Molecular Sequence Megaclassification.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

Finding Relevant Biomolecular Features.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

Grand Challenge AI Applications.
Proceedings of the 13th International Joint Conference on Artificial Intelligence. Chambéry, France, August 28, 1993

1992
Bayesian Classification of Protein Structure.
IEEE Expert, 1992

The use of explicit goals for knowledge to guide inference and learning.
Appl. Intell., 1992

Efficient Classification of Massive, Unsegmented Datastreams.
Proceedings of the Ninth International Workshop on Machine Learning (ML 1992), 1992

Mega-Classification: Discovering Motifs in Massive Datastreams.
Proceedings of the 10th National Conference on Artificial Intelligence, 1992

1991
Artificial Intelligence and Molecular Biology.
AI Mag., 1991

A Goal-Based Approach to Intelligent Information Retrieval.
Proceedings of the Eighth International Workshop (ML91), 1991

1989
Knowledge Acquisition Planning: Results and Prospects.
Proceedings of the Sixth International Workshop on Machine Learning (ML 1989), 1989

1988
Estimating Human Cognitive Capacities: A Response to Landauer.
Cogn. Sci., 1988

1977
Conservation of software science parameters across modularization.
Proceedings of the 1977 annual conference, 1977


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