Karin M. Verspoor

According to our database1, Karin M. Verspoor authored at least 132 papers between 1998 and 2019.

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Bibliography

2019
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.
Journal of Computational Biology, 2019

From POS tagging to dependency parsing for biomedical event extraction.
BMC Bioinformatics, 2019

Automated assessment of biological database assertions using the scientific literature.
BMC Bioinformatics, 2019

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

A Bag-of-concepts Model Improves Relation Extraction in a Narrow Knowledge Domain with Limited Data.
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2019

End-to-End Neural Relation Extraction Using Deep Biaffine Attention.
Proceedings of the Advances in Information Retrieval, 2019

Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings.
Proceedings of the 18th BioNLP Workshop and Shared Task, 2019

2018
The Dagstuhl Perspectives Workshop on Performance Modeling and Prediction.
SIGIR Forum, 2018

The randomized information coefficient: assessing dependencies in noisy data.
Machine Learning, 2018

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases.
J. Data and Information Quality, 2018

CommViz: Visualization of semantic patterns in large social communication networks.
Information Visualization, 2018

Web Forum Retrieval and Text Analytics: A Survey.
Foundations and Trends in Information Retrieval, 2018

From Evaluating to Forecasting Performance: How to Turn Information Retrieval, Natural Language Processing and Recommender Systems into Predictive Sciences (Dagstuhl Perspectives Workshop 17442).
Dagstuhl Manifestos, 2018

A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration.
BMC Bioinformatics, 2018

Exploiting graph kernels for high performance biomedical relation extraction.
J. Biomedical Semantics, 2018

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.
Database, 2018

Findings of the WMT 2018 Biomedical Translation Shared Task: Evaluation on Medline test sets.
Proceedings of the Third Conference on Machine Translation: Shared Task Papers, 2018

Privacy-Preserving Access Control in Electronic Health Record Linkage.
Proceedings of the 17th IEEE International Conference On Trust, 2018

Semantic-Based Policy Composition for Privacy-Demanding Data Linkage.
Proceedings of the 17th IEEE International Conference On Trust, 2018

Parallel Corpora for the Biomedical Domain.
Proceedings of the Eleventh International Conference on Language Resources and Evaluation, 2018

Detecting Misflagged Duplicate Questions in Community Question-Answering Archives.
Proceedings of the Twelfth International Conference on Web and Social Media, 2018

An Improved Neural Network Model for Joint POS Tagging and Dependency Parsing.
Proceedings of the CoNLL 2018 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies, Brussels, Belgium, October 31, 2018

Convolutional neural networks for chemical-disease relation extraction are improved with character-based word embeddings.
Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018, 2018

DrKnow: A Diagnostic Learning Tool with Feedback from Automated Clinical Decision Support.
Proceedings of the AMIA 2018, 2018

Comparing CNN and LSTM character-level embeddings in BiLSTM-CRF models for chemical and disease named entity recognition.
Proceedings of the Ninth International Workshop on Health Text Mining and Information Analysis, 2018

2017
Automated detection of records in biological sequence databases that are inconsistent with the literature.
Journal of Biomedical Informatics, 2017

Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes.
BMC Bioinformatics, 2017

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

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.
Database, 2017

Literature consistency of bioinformatics sequence databases is effective for assessing record quality.
Database, 2017

Multi-field query expansion is effective for biomedical dataset retrieval.
Database, 2017

Findings of the WMT 2017 Biomedical Translation Shared Task.
Proceedings of the Second Conference on Machine Translation, 2017

SemEval-2017 Task 3: Community Question Answering.
Proceedings of the 11th International Workshop on Semantic Evaluation, 2017

Characterising the Scope of Exposome Research: A Generalisable Approach.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

Diagnostic Machine Learning Models for Acute Abdominal Pain: Towards an e-Learning Tool for Medical Students.
Proceedings of the MEDINFO 2017: Precision Healthcare through Informatics, 2017

A Semantic-Based K-Anonymity Scheme for Health Record Linkage.
Proceedings of the Integrating and Connecting Care, 2017

Understanding Health Professionals' Informal Learning in Online Social Networks: A Cross-Sectional Survey.
Proceedings of the Integrating and Connecting Care, 2017

Learning Biological Sequence Types Using the Literature.
Proceedings of the 2017 ACM on Conference on Information and Knowledge Management, 2017

Textual Emotion Classification: An Interoperability Study on Cross-Genre Data Sets.
Proceedings of the AI 2017: Advances in Artificial Intelligence, 2017

Automatic Negation and Speculation Detection in Veterinary Clinical Text.
Proceedings of the Australasian Language Technology Association Workshop, 2017

2016
Establishing a baseline for literature mining human genetic variants and their relationships to disease cohorts.
BMC Med. Inf. & Decision Making, 2016

Adjusting for Chance Clustering Comparison Measures.
J. Mach. Learn. Res., 2016

Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources.
Journal of Biomedical Informatics, 2016

A categorical analysis of coreference resolution errors in biomedical texts.
Journal of Biomedical Informatics, 2016

A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning.
BMC Systems Biology, 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.
J. Biomedical Semantics, 2016

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

Coreference resolution improves extraction of Biological Expression Language statements from texts.
Database, 2016


Exploiting Tree Kernels for High Performance Chemical Induced Disease Relation Extraction.
Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, 2016

Rev at SemEval-2016 Task 2: Aligning Chunks by Lexical, Part of Speech and Semantic Equivalence.
Proceedings of the 10th International Workshop on Semantic Evaluation, 2016

A Framework to Adjust Dependency Measure Estimates for Chance.
Proceedings of the 2016 SIAM International Conference on Data Mining, 2016

Towards Early Discovery of Salient Health Threats: A Social Media Emotion Classification Technique.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Innovation in Designing Health Information Websites: Results from a Quantitative Study.
Proceedings of the 20th Pacific Asia Conference on Information Systems, 2016

What are health website visitors doing: insights from visualisations towards exploratory search.
Proceedings of the 28th Australian Conference on Computer-Human Interaction, 2016

Finding and Exploring Health Information with a Slider-Based User Interface.
Proceedings of the Digital Health Innovation for Consumers, Clinicians, Connectivity and Community, 2016

Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study.
Proceedings of the Digital Health Innovation for Consumers, Clinicians, Connectivity and Community, 2016

SeeDev Binary Event Extraction using SVMs and a Rich Feature Set.
Proceedings of the 4th BioNLP Shared Task Workshop, BioNLP 2016, 2016

Evaluation of CD-HIT for constructing non-redundant databases.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

ASM Kernel: Graph Kernel using Approximate Subgraph Matching for Relation Extraction.
Proceedings of the Australasian Language Technology Association Workshop 2016, Melbourne, Australia, December 5, 2016

Syndromic Surveillance through Measuring Lexical Shift in Emergency Department Chief Complaint Texts.
Proceedings of the Australasian Language Technology Association Workshop 2016, Melbourne, Australia, December 5, 2016

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

Special issue on bio-ontologies and phenotypes.
J. Biomedical Semantics, 2015

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.
J. Biomedical Semantics, 2015

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.
Bioinformatics, 2015

Better Health Explorer: Designing for Health Information Seekers.
Proceedings of the Annual Meeting of the Australian Special Interest Group for Computer Human Interaction, 2015

Extraction of Fine-grained Semantic Relations for the Human Variome.
Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics, 2015

DTMBIO 2015: International Workshop on Data and Text Mining in Biomedical Informatics.
Proceedings of the 24th ACM International Conference on Information and Knowledge Management, 2015

Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases.
Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics, 2015

Drawing on millions of biomedical journal publications to do predictive biology.
Proceedings of the 2015 International Conference on Big Data and Smart Computing, 2015

CQADupStack: A Benchmark Data Set for Community Question-Answering Research.
Proceedings of the 20th Australasian Document Computing Symposium, 2015

Structural Alignment as the Basis to Improve Significant Change Detection in Versioned Sentences.
Proceedings of the Australasian Language Technology Association Workshop, 2015

Domain Adaption of Named Entity Recognition to Support Credit Risk Assessment.
Proceedings of the Australasian Language Technology Association Workshop, 2015

2014
Biomedical Text Mining: State-of-the-Art, Open Problems and Future Challenges.
Proceedings of the Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database.
Source Code for Biology and Medicine, 2014

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

Literature mining of genetic variants for curation: quantifying the importance of supplementary material.
Database, 2014

BioC interoperability track overview.
Database, 2014

Practice-based Evidence in Medicine: Where Information Retrieval Meets Data Mining.
Proceedings of the Medical Information Retrieval Workshop at SIGIR co-located with the 37th annual international ACM SIGIR conference (ACM SIGIR 2014), 2014

Designing for Health Exploratory Seeking Behaviour.
Proceedings of the Medical Information Retrieval Workshop at SIGIR co-located with the 37th annual international ACM SIGIR conference (ACM SIGIR 2014), 2014

Evaluation of Coreference Resolution for Biomedical Text.
Proceedings of the Medical Information Retrieval Workshop at SIGIR co-located with the 37th annual international ACM SIGIR conference (ACM SIGIR 2014), 2014

Online Health Information seeking Behaviour: Understanding Different Search Approaches.
Proceedings of the 18th Pacific Asia Conference on Information Systems, 2014

Two platforms for research in Human Communication Science: The AusTalk corpus and the Alveo Virtual Laboratory.
Proceedings of the 2014 17th Oriental Chapter of the International Committee for the Co-ordination and Standardization of Speech Databases and Assessment Techniques (COCOSDA), 2014

Standardized Mutual Information for Clustering Comparisons: One Step Further in Adjustment for Chance.
Proceedings of the 31th International Conference on Machine Learning, 2014

Mapping Biomedical Vocabularies: A Semi-Automated Term Matching Approach.
Proceedings of the Integrating Information Technology and Management for Quality of Care [ICIMTH 2014, 2014

What Can We Get From 1000 Tokens? A Case Study of Multilingual POS Tagging For Resource-Poor Languages.
Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing, 2014

Integrating UIMA with Alveo, a human communication science virtual laboratory.
Proceedings of the Workshop on Open Infrastructures and Analysis Frameworks for HLT, 2014

Exploring Temporal Patterns in Emergency Department Triage Notes with Topic Models.
Proceedings of the Australasian Language Technology Association Workshop, 2014

Automated Generation of Test Suites for Error Analysis of Concept Recognition Systems.
Proceedings of the Australasian Language Technology Association Workshop, 2014

Analysis of Coreference Relations in the Biomedical Literature.
Proceedings of the Australasian Language Technology Association Workshop, 2014

2013
Acquisition and evaluation of verb subcategorization resources for biomedicine.
Journal of Biomedical Informatics, 2013

Approaches to verb subcategorization for biomedicine.
Journal of Biomedical Informatics, 2013

Combining heterogeneous data sources for accurate functional annotation of proteins.
BMC Bioinformatics, 2013

Representing annotation compositionality and provenance for the Semantic Web.
J. Biomedical Semantics, 2013

Annotating the biomedical literature for the human variome.
Database, 2013

BioC: a minimalist approach to interoperability for biomedical text processing.
Database, 2013

Detection of Protein Catalytic Sites in the Biomedical Literature.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing.
Proceedings of the 2013 Workshop on Biomedical Natural Language Processing, 2013

Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data.
Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, 2013

Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics.
Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, 2013

e-Learning with Kaggle in Class: Adapting the ALTA Shared Task 2013 to a Class Project.
Proceedings of the Australasian Language Technology Association Workshop, 2013

Impact of Corpus Diversity and Complexity on NER Performance.
Proceedings of the Australasian Language Technology Association Workshop, 2013

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 Bioinformatics, 2012

Concept annotation in the CRAFT corpus.
BMC Bioinformatics, 2012

Literature mining of protein-residue associations with graph rules learned through distant supervision.
J. Biomedical Semantics, 2012

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.
J. Biomedical Semantics, 2012

Simple Similarity-based Question Answering Strategies for Biomedical Text.
Proceedings of the CLEF 2012 Evaluation Labs and Workshop, 2012

Extracting structured information from free-text medication prescriptions using dependencies.
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics, 2012

Towards Adaptation of Linguistic Annotations to Scholarly Annotation Formalisms on the Semantic Web.
Proceedings of the Sixth Linguistic Annotation Workshop, 2012

Subgraph Matching-Based Literature Mining for Biomedical Relations and Events.
Proceedings of the Information Retrieval and Knowledge Discovery in Biomedical Text, 2012

2011
High-Precision Biological Event Extraction: Effects of System and of Data.
Computational Intelligence, 2011

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

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

Pattern Learning through Distant Supervision for Extraction of Protein-Residue Associations in the Biomedical Literature.
Proceedings of the 10th International Conference on Machine Learning and Applications and Workshops, 2011

From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text.
Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon, USA, June 24, 2011, 2011

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

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

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

A UIMA wrapper for the NCBO annotator.
Bioinformatics, 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

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

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

Ontology quality assurance through analysis of term transformations.
Bioinformatics, 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
Exploiting Term Relations for Semantic Hierarchy Construction.
Proceedings of the 2th IEEE International Conference on Semantic Computing (ICSC 2008), 2008

A Semantics-Enhanced Language Model for Unsupervised Word Sense Disambiguation.
Proceedings of the Computational Linguistics and Intelligent Text Processing, 2008

2007
Knowledge Integration in OpenWorlds: Utilizing the Mathematics of Hierarchical Structure.
Proceedings of the First IEEE International Conference on Semantic Computing (ICSC 2007), 2007

2006
Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families.
Proceedings of the Biocomputing 2006, 2006

2005
Protein annotation as term categorization in the gene ontology using word proximity networks.
BMC Bioinformatics, 2005

1998
Dynamic Document Delivery: Generating Natural Language Texts on Demand.
Proceedings of the Ninth International Workshop on Database and Expert Systems Applications, 1998

Automatic English-Chinese Name Transliteration for Development of Multilingual Resources.
Proceedings of the 36th Annual Meeting of the Association for Computational Linguistics and 17th International Conference on Computational Linguistics, 1998


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