Karin Verspoor
Orcid: 0000-0002-8661-1544Affiliations:
- University of Melbourne, School of Computing and Information Systems, Australia
- National ICT, Victoria, Australia (former)
According to our database1,
Karin Verspoor
authored at least 218 papers
between 1998 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
Legend:
Book In proceedings Article PhD thesis Dataset OtherLinks
Online presence:
-
on twitter.com
-
on orkg.org
-
on orcid.org
-
on dl.acm.org
On csauthors.net:
Bibliography
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
The Secondary Use of Electronic Health Records for Data Mining: Data Characteristics and Challenges.
ACM Comput. Surv., 2023
CoRR, 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
Proceedings of the MEDINFO 2023 - The Future Is Accessible, 2023
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
Proceedings of the IEEE International Conference on Data Mining, 2023
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2023, 2023
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
Trans. Assoc. Comput. Linguistics, 2022
J. Biomed. Informatics, 2022
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
Briefings Bioinform., 2022
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
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2022
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
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2022, 2022
Proceedings of the Advances in Information Retrieval, 2022
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2022
Proceedings of the 29th International Conference on Computational Linguistics, 2022
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
J. Cheminformatics, 2021
ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents.
Frontiers Res. Metrics Anal., 2021
CoRR, 2021
Machine learning with a reduced dimensionality representation of comprehensive Pentacam tomography parameters to identify subclinical keratoconus.
Comput. Biol. Medicine, 2021
BMC Bioinform., 2021
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data.
Bioinform., 2021
Proceedings of the Thirtieth Text REtrieval Conference, 2021
Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021
Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks 1, 2021
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
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
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
Proceedings of the 28th International Conference on Computational Linguistics, 2020
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents.
Proceedings of the Working Notes of CLEF 2020, 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
Proceedings of the 3rd Clinical Natural Language Processing Workshop, 2020
2019
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
BMC Bioinform., 2019
Automated assessment of biological database assertions using the scientific literature.
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
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
Proceedings of the The 17th Annual Workshop of the Australasian Language Technology Association, 2019
2018
SIGIR Forum, 2018
Mach. Learn., 2018
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases.
ACM J. Data Inf. Qual., 2018
Inf. Vis., 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
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
Proceedings of the 17th IEEE International Conference On Trust, 2018
Proceedings of the 17th IEEE International Conference On Trust, 2018
Proceedings of the Eleventh International Conference on Language Resources and Evaluation, 2018
Proceedings of the Twelfth International Conference on Web and Social Media, 2018
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
Database J. Biol. Databases Curation, 2017
Proceedings of the Second Conference on Machine Translation, 2017
Proceedings of the 11th International Workshop on Semantic Evaluation, 2017
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
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
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
Proceedings of the 2017 ACM on Conference on Information and Knowledge Management, 2017
Proceedings of the AI 2017: Advances in Artificial Intelligence, 2017
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
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
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
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
Proceedings of the First Conference on Machine Translation, 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
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
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
Proceedings of the 4th BioNLP Shared Task Workshop, BioNLP 2016, 2016
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
BMC Bioinform., December, 2015
J. Cheminformatics, 2015
Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.
J. Biomed. Semant., 2015
Proceedings of the Annual Meeting of the Australian Special Interest Group for Computer Human Interaction, 2015
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
Proceedings of the 2015 International Conference on Big Data and Smart Computing, 2015
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
Proceedings of the Australasian Language Technology Association Workshop, 2015
2014
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
Proceedings of the Medical Information Retrieval Workshop at SIGIR co-located with the 37th annual international ACM SIGIR conference (ACM SIGIR 2014), 2014
Proceedings of the Medical Information Retrieval Workshop at SIGIR co-located with the 37th annual international ACM SIGIR conference (ACM SIGIR 2014), 2014
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
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
Proceedings of the Workshop on Open Infrastructures and Analysis Frameworks for HLT, 2014
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
Proceedings of the Australasian Language Technology Association Workshop, 2014
2013
J. Biomed. Informatics, 2013
BMC Bioinform., 2013
J. Biomed. Semant., 2013
Database J. Biol. Databases Curation, 2013
Database J. Biol. Databases Curation, 2013
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
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
Literature mining of protein-residue associations with graph rules learned through distant supervision.
J. Biomed. Semant., 2012
J. Biomed. Semant., 2012
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
Proceedings of the Information Retrieval and Knowledge Discovery in Biomedical Text, 2012
2011
Comput. Intell., 2011
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
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011
2010
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
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
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
Bioinform., 2009
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
Proceedings of the 2th IEEE International Conference on Semantic Computing (ICSC 2008), 2008
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
Proceedings of the Biocomputing 2006, 2006
2005
Protein annotation as term categorization in the gene ontology using word proximity networks.
BMC Bioinform., 2005
1998
Proceedings of the 12th Pacific Asia Conference on Language, Information and Computation, 1998
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