Karin Verspoor

Orcid: 0000-0002-8661-1544

Affiliations:
  • University of Melbourne, School of Computing and Information Systems, Australia
  • National ICT, Victoria, Australia (former)


According to our database1, Karin Verspoor authored at least 228 papers between 1998 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Focused Contrastive Loss for Classification With Pre-Trained Language Models.
IEEE Trans. Knowl. Data Eng., July, 2024

The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII.
Database J. Biol. Databases Curation, January, 2024

Graph Transformers: A Survey.
CoRR, 2024

Revisiting subword tokenization: A case study on affixal negation in large language models.
CoRR, 2024

EMBRE: Entity-aware Masking for Biomedical Relation Extraction.
CoRR, 2024

Effectiveness of Cross-linguistic Extraction of Genetic Information using Generative Large Language Models.
Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2024) co-located with the Conference of the Spanish Society for Natural Language Processing (SEPLN 2024), 2024

Revisiting subword tokenization: A case study on affixal negation in large language models.
Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), 2024

Principles from Clinical Research for NLP Model Generalization.
Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), 2024

Intervention extraction in preclinical animal studies of Alzheimer's Disease: Enhancing regex performance with language model-based filtering.
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, 2024

Do Numbers Matter? Types and Prevalence of Numbers in Clinical Texts.
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, 2024

Towards Explainable Deep Learning for Non-melanoma Skin Cancer Diagnosis.
Proceedings of the AI 2024: Advances in Artificial Intelligence, 2024

2023
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing.
J. Biomed. Semant., December, 2023

Graph embedding-based link prediction for literature-based discovery in Alzheimer's Disease.
J. Biomed. Informatics, September, 2023

Attention-based multimodal fusion with contrast for robust clinical prediction in the face of missing modalities.
J. Biomed. Informatics, September, 2023

An evaluation of existing text de-identification tools for use with patient progress notes from Australian general practice.
Int. J. Medical Informatics, May, 2023

Detecting evidence of invasive fungal infections in cytology and histopathology reports enriched with concept-level annotations.
J. Biomed. Informatics, March, 2023

Collective Human Opinions in Semantic Textual Similarity.
Trans. Assoc. Comput. Linguistics, 2023

The Secondary Use of Electronic Health Records for Data Mining: Data Characteristics and Challenges.
ACM Comput. Surv., 2023

Improving Text-based Early Prediction by Distillation from Privileged Time-Series Text.
CoRR, 2023

Language models are not naysayers: an analysis of language models on negation benchmarks.
Proceedings of the The 12th Joint Conference on Lexical and Computational Semantics, 2023

ITTC at SemEval 2023-Task 7: Document Retrieval and Sentence Similarity for Evidence Retrieval in Clinical Trial Data.
Proceedings of the The 17th International Workshop on Semantic Evaluation, 2023

Understanding Clinician EHR Data Quality for Reuse in Predictive Modelling.
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023

Uncovering Variations in Clinical Notes for NLP Modeling.
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023

Designing a Digital Health Solution: A Platform for Automated Surveillance of Fungal Infection.
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023

Deep Outdated Fact Detection in Knowledge Graphs.
Proceedings of the IEEE International Conference on Data Mining, 2023

Effects of Human Adversarial and Affable Samples on BERT Generalizability.
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2023, 2023

Promoting Fairness in Classification of Quality of Medical Evidence.
Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, 2023

CRF-based recognition of invasive fungal infection concepts in CHIFIR clinical reports.
Proceedings of the 21st Annual Workshop of the Australasian Language Technology Association, 2023

2022
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk.
Bioinform., November, 2022

Identification of focus versus background entities in scientific literature.
Dataset, January, 2022

Uncertainty Estimation and Reduction of Pre-trained Models for Text Regression.
Trans. Assoc. Comput. Linguistics, 2022

"Note Bloat" impacts deep learning-based NLP models for clinical prediction tasks.
J. Biomed. Informatics, 2022

Detection of self-harm and suicidal ideation in emergency department triage notes.
J. Am. Medical Informatics Assoc., 2022

Tasks as needs: reframing the paradigm of clinical natural language processing research for real-world decision support.
J. Am. Medical Informatics Assoc., 2022

Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT.
BMC Bioinform., 2022

Propagation, detection and correction of errors using the sequence database network.
Briefings Bioinform., 2022

Why Bother Enabling Biomedical Literature Analysis with Semantics?
Proceedings of the Companion of The Web Conference 2022, Virtual Event / Lyon, France, April 25, 2022

The READ-BioMed Team in LivingNER Task 1 (2022): Adaptation of an English Annotation System to Spanish.
Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2022) co-located with the Conference of the Spanish Society for Natural Language Processing (SEPLN 2022), 2022

Improving negation detection with negation-focused pre-training.
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2022

Not another Negation Benchmark: The NaN-NLI Test Suite for Sub-clausal Negation.
Proceedings of the 2nd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics and the 12th International Joint Conference on Natural Language Processing, 2022

M3: Multi-level dataset for Multi-document summarisation of Medical studies.
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2022, 2022

The ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.
Proceedings of the Advances in Information Retrieval, 2022

Cross-modal Clinical Graph Transformer for Ophthalmic Report Generation.
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022

Noisy Label Regularisation for Textual Regression.
Proceedings of the 29th International Conference on Computational Linguistics, 2022

READ-BioMed@SocialDisNER: Adaptation of an Annotation System to Spanish Tweets.
Proceedings of The Seventh Workshop on Social Media Mining for Health Applications, 2022

LED down the rabbit hole: exploring the potential of global attention for biomedical multi-document summarisation.
Proceedings of the Third Workshop on Scholarly Document Processing, 2022

Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.
Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2022

Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents.
Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022

What does it take to bake a cake? The RecipeRef corpus and anaphora resolution in procedural text.
Proceedings of the Findings of the Association for Computational Linguistics: ACL 2022, 2022

The patient is more dead than alive: exploring the current state of the multi-document summarisation of the biomedical literature.
Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 2022

Distinguishing between focus and background entities in biomedical corpora using discourse structure and transformers.
Proceedings of the 13th International Workshop on Health Text Mining and Information Analysis, 2022

2021
Early prediction of diagnostic-related groups and estimation of hospital cost by processing clinical notes.
npj Digit. Medicine, 2021

ChemTables: a dataset for semantic classification on tables in chemical patents.
J. Cheminformatics, 2021

ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents.
Frontiers Res. Metrics Anal., 2021

Impact of detecting clinical trial elements in exploration of COVID-19 literature.
CoRR, 2021

Machine learning with a reduced dimensionality representation of comprehensive Pentacam tomography parameters to identify subclinical keratoconus.
Comput. Biol. Medicine, 2021

Automatic consistency assurance for literature-based gene ontology annotation.
BMC Bioinform., 2021

PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data.
Bioinform., 2021

Evaluation of consensus strategies for haplotype phasing.
Briefings Bioinform., 2021

ITTC @ TREC 2021 Clinical Trials Track.
Proceedings of the Thirtieth Text REtrieval Conference, 2021

Advanced Methods for Big Data Analytics in Women's Health.
Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark.
Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks 1, 2021

Impact of detecting clinical trial elements in exploration of COVID-19 literature.
Proceedings of the 9th IEEE International Conference on Healthcare Informatics, 2021

Brief Description of COVID-SEE: The Scientific Evidence Explorer for COVID-19 Related Research.
Proceedings of the Advances in Information Retrieval, 2021

ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.
Proceedings of the Advances in Information Retrieval, 2021

ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical Domain.
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume, 2021

Memorization vs. Generalization : Quantifying Data Leakage in NLP Performance Evaluation.
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume, 2021

Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.
Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2021

Extended Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents.
Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum, Bucharest, Romania, September 21st - to, 2021

Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases.
Genom. Proteom. Bioinform., 2020

Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts.
CoRR, 2020

COVID-SEE: Scientific Evidence Explorer for COVID-19 Related Research.
CoRR, 2020

Testing Contextualized Word Embeddings to Improve NER in Spanish Clinical Case Narratives.
IEEE Access, 2020

Improved Topic Representations of Medical Documents to Assist COVID-19 Literature Exploration.
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 2020

ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents.
Proceedings of the Advances in Information Retrieval, 2020

WikiUMLS: Aligning UMLS to Wikipedia via Cross-lingual Neural Ranking.
Proceedings of the 28th International Conference on Computational Linguistics, 2020


Overview of ChEMU 2020: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents.
Proceedings of the Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2020

Evaluating the Utility of Model Configurations and Data Augmentation on Clinical Semantic Textual Similarity.
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 2020

Domain Adaptation and Instance Selection for Disease Syndrome Classification over Veterinary Clinical Notes.
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 2020

Learning from Unlabelled Data for Clinical Semantic Textual Similarity.
Proceedings of the 3rd Clinical Natural Language Processing Workshop, 2020

2019
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.
J. Comput. Biol., 2019

Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.
J. Biomed. Informatics, 2019

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
F1000Research, 2019

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

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

Exploring effective approaches for haplotype block phasing.
BMC Bioinform., 2019

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

Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies.
Proceedings of the Fourth Conference on Machine Translation, 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

Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis.
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 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

Detecting Chemical Reactions in Patents.
Proceedings of the The 17th Annual Workshop of the Australasian Language Technology Association, 2019

2018
Literature consistency of bioinformatics sequence databases is effective for assessing record quality.
Dataset, May, 2018

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

The randomized information coefficient: assessing dependencies in noisy data.
Mach. Learn., 2018

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases.
ACM J. Data Inf. Qual., 2018

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

Web Forum Retrieval and Text Analytics: A Survey.
Found. Trends Inf. Retr., 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 Bioinform., 2018

Exploiting graph kernels for high performance biomedical relation extraction.
J. Biomed. Semant., 2018

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.
Database J. Biol. Databases Curation, 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.
J. Biomed. Informatics, 2017

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

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

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

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

Multi-field query expansion is effective for biomedical dataset retrieval.
Database J. Biol. Databases Curation, 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

Sequence Clustering Methods and Completeness of Biological Database Search.
Proceedings of the Workshop on Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap co-located with 26th International Joint Conference on Artificial Intelligence (IJCAI 2017), 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 Medical Informatics Decis. Mak., 2016

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

Towards a Methodology for Nursing-Specific Clinical Decision Support Systems (CDSS).
J. Decis. Syst., 2016

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

A categorical analysis of coreference resolution errors in biomedical texts.
J. Biomed. Informatics, 2016

Analysing health professionals' learning interactions in online social networks: A social network analysis approach.
CoRR, 2016

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

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

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

Coreference resolution improves extraction of Biological Expression Language statements from texts.
Database J. Biol. Databases Curation, 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
Optimizing graph-based patterns to extract biomedical events from the literature.
BMC Bioinform., December, 2015

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

Special issue on bio-ontologies and phenotypes.
J. Biomed. Semant., 2015

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

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.
Bioinform., 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 Biol. Medicine, 2014

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature.
F1000Research, 2014

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

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

BioC interoperability track overview.
Database J. Biol. Databases Curation, 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.
J. Biomed. Informatics, 2013

Approaches to verb subcategorization for biomedicine.
J. Biomed. Informatics, 2013

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

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

Annotating the biomedical literature for the human variome.
Database J. Biol. Databases Curation, 2013

BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation, 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 Bioinform., 2012

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

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

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.
J. Biomed. Semant., 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.
Comput. Intell., 2011

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

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

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 Bioinform., 2009

Ontology quality assurance through analysis of term transformations.
Bioinform., 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
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks
CoRR, 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 Bioinform., 2005

1998
Predictivity vs. Stipulativity in the Lexicon.
Proceedings of the 12th Pacific Asia Conference on Language, Information and Computation, 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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