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ORCIDKarin Verspoor
Karin M. Verspoor – Cornelia Verspoor – Cornelia Maria Verspoor
Person information
- affiliation: University of Melbourne, School of Computing and Information Systems, Australia
- affiliation (former): National ICT, Victoria, Australia
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2020 – today
- 2024
[j83]Rezarta Islamaj
, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Almeida, Richard A. A. Jonker, Sofia I R. Conceição, Diana F. Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin Verspoor, Zhiyong Lu:
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database J. Biol. Databases Curation 2024 (2024)- [j82]Jiayuan He, Yuan Li, Zenan Zhai, Biaoyan Fang, Camilo Thorne, Christian Druckenbrodt, Saber A. Akhondi, Karin Verspoor:
Focused Contrastive Loss for Classification With Pre-Trained Language Models. IEEE Trans. Knowl. Data Eng. 36(7): 3047-3061 (2024) - [c127]Aparna Elangovan, Jiayuan He, Yuan Li, Karin Verspoor:
Principles from Clinical Research for NLP Model Generalization. NAACL-HLT 2024: 2293-2309 - [c126]Thinh Truong, Yulia Otmakhova, Karin Verspoor, Trevor Cohn, Timothy Baldwin:
Revisiting subword tokenization: A case study on affixal negation in large language models. NAACL-HLT 2024: 5082-5095 - [i33]Mingjie Li, Karin Verspoor:
EMBRE: Entity-aware Masking for Biomedical Relation Extraction. CoRR abs/2401.07877 (2024) - [i32]Huiling Tu, Shuo Yu, Vidya Saikrishna, Feng Xia, Karin M. Verspoor:
Deep Outdated Fact Detection in Knowledge Graphs. CoRR abs/2402.03732 (2024) - [i31]Thinh Hung Truong, Yulia Otmakhova, Karin Verspoor, Trevor Cohn, Timothy Baldwin:
Revisiting subword tokenization: A case study on affixal negation in large language models. CoRR abs/2404.02421 (2024) - [i30]Ahsan Shehzad, Feng Xia, Shagufta Abid, Ciyuan Peng, Shuo Yu, Dongyu Zhang, Karin Verspoor:
Graph Transformers: A Survey. CoRR abs/2407.09777 (2024) - 2023
- [j81]Antonio José Jimeno-Yepes, Karin Verspoor:
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing. J. Biomed. Semant. 14(1): 1 (2023) - [j80]Tabinda Sarwar, Sattar Seifollahi, Jeffrey Chan, Xiuzhen Zhang, Vural Aksakalli, Irene Lena Hudson, Karin Verspoor, Lawrence Cavedon:
The Secondary Use of Electronic Health Records for Data Mining: Data Characteristics and Challenges. ACM Comput. Surv. 55(2): 33:1-33:40 (2023) - [j79]Carol El-Hayek, Siamak Barzegar, Noel Faux, Kim Doyle, Priyanka Pillai, Simon J. Mutch, Alaina Vaisey, Roger Ward, Lena Sanci, Adam G. Dunn, Margaret Hellard, Jane S. Hocking, Karin Verspoor, Douglas IR. Boyle:
An evaluation of existing text de-identification tools for use with patient progress notes from Australian general practice. Int. J. Medical Informatics 173: 105021 (2023) - [j78]Vlada Rozova, Anna Khanina, Jasmine C. Teng, Joanne S. K. Teh, Leon J. Worth, Monica A. Slavin, Karin A. Thursky, Karin Verspoor:
Detecting evidence of invasive fungal infections in cytology and histopathology reports enriched with concept-level annotations. J. Biomed. Informatics 139: 104293 (2023) - [j77]Yiyuan Pu, Daniel Beck, Karin Verspoor:
Graph embedding-based link prediction for literature-based discovery in Alzheimer's Disease. J. Biomed. Informatics 145: 104464 (2023) - [j76]Jinghui Liu, Daniel Capurro, Anthony N. Nguyen, Karin Verspoor:
Attention-based multimodal fusion with contrast for robust clinical prediction in the face of missing modalities. J. Biomed. Informatics 145: 104466 (2023) - [j75]Yuxia Wang, Shimin Tao, Ning Xie, Hao Yang, Timothy Baldwin, Karin Verspoor:
Collective Human Opinions in Semantic Textual Similarity. Trans. Assoc. Comput. Linguistics 11: 997-1013 (2023) - [c125]Yang Meng, Vlada Rozova, Karin Verspoor:
CRF-based recognition of invasive fungal infection concepts in CHIFIR clinical reports. ALTA 2023: 130-135 - [c124]Simon Suster, Timothy Baldwin, Karin Verspoor:
Promoting Fairness in Classification of Quality of Medical Evidence. BioNLP@ACL 2023: 413-426 - [c123]Aparna Elangovan, Estrid He, Yuan Li, Karin Verspoor:
Effects of Human Adversarial and Affable Samples on BERT Generalizability. EMNLP (Findings) 2023: 7637-7649 - [c122]Huiling Tu, Shuo Yu, Vidya Saikrishna, Feng Xia, Karin Verspoor:
Deep Outdated Fact Detection in Knowledge Graphs. ICDM (Workshops) 2023: 1443-1452 - [c121]Melinda Wassell, James L. Murray, Chaithra Kumar, Karin Verspoor, Kerryn Butler-Henderson:
Understanding Clinician EHR Data Quality for Reuse in Predictive Modelling. MedInfo 2023: 169-173 - [c120]Anna Khanina, Vlada Rozova, Sri Elkins, Karin Verspoor, Karin A. Thursky:
Designing a Digital Health Solution: A Platform for Automated Surveillance of Fungal Infection. MedInfo 2023: 1454-1455 - [c119]Jinghui Liu, Daniel Capurro, Anthony Nguyen, Karin Verspoor:
Uncovering Variations in Clinical Notes for NLP Modeling. MedInfo 2023: 1460-1461 - [c118]Rahmad Mahendra, Damiano Spina, Karin Verspoor:
ITTC at SemEval 2023-Task 7: Document Retrieval and Sentence Similarity for Evidence Retrieval in Clinical Trial Data. SemEval@ACL 2023: 2338-2342 - [c117]Thinh Hung Truong, Timothy Baldwin, Karin Verspoor, Trevor Cohn:
Language models are not naysayers: an analysis of language models on negation benchmarks. *SEM@ACL 2023: 101-114 - [i29]Jinghui Liu, Daniel Capurro, Anthony N. Nguyen, Karin Verspoor:
Improving Text-based Early Prediction by Distillation from Privileged Time-Series Text. CoRR abs/2301.10887 (2023) - [i28]Thinh Hung Truong, Timothy Baldwin, Karin Verspoor, Trevor Cohn:
Language models are not naysayers: An analysis of language models on negation benchmarks. CoRR abs/2306.08189 (2023) - [i27]Yuxia Wang, Shimin Tao, Ning Xie, Hao Yang, Timothy Baldwin, Karin Verspoor:
Collective Human Opinions in Semantic Textual Similarity. CoRR abs/2308.04114 (2023) - [i26]Aparna Elangovan, Jiayuan He, Yuan Li, Karin Verspoor:
Effects of Human Adversarial and Affable Samples on BERT Generalizability. CoRR abs/2310.08008 (2023) - [i25]Aparna Elangovan, Jiayuan He, Yuan Li, Karin Verspoor:
Principles from Clinical Research for NLP Model Generalization. CoRR abs/2311.03663 (2023) - 2022
- [j74]Benjamin Goudey, Nicholas Geard, Karin Verspoor, Justin Zobel:
Propagation, detection and correction of errors using the sequence database network. Briefings Bioinform. 23(6) (2022) - [j73]Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He:
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk. Bioinform. 38(22): 5026-5032 (2022) - [j72]Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor:
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. BMC Bioinform. 23(1): 4 (2022) - [j71]Vlada Rozova, Katrina Witt, Jo Robinson, Yan Li, Karin Verspoor:
Detection of self-harm and suicidal ideation in emergency department triage notes. J. Am. Medical Informatics Assoc. 29(3): 472-480 (2022) - [j70]Asher Lederman, Reeva Lederman, Karin Verspoor:
Tasks as needs: reframing the paradigm of clinical natural language processing research for real-world decision support. J. Am. Medical Informatics Assoc. 29(10): 1810-1817 (2022) - [j69]Jinghui Liu, Daniel Capurro, Anthony N. Nguyen, Karin Verspoor:
"Note Bloat" impacts deep learning-based NLP models for clinical prediction tasks. J. Biomed. Informatics 133: 104149 (2022) - [j68]Yuxia Wang, Daniel Beck, Karin Verspoor, Timothy Baldwin:
Uncertainty Estimation and Reduction of Pre-trained Models for Text Regression. Trans. Assoc. Comput. Linguistics 10: 680-696 (2022) - [c116]Biaoyan Fang, Timothy Baldwin, Karin Verspoor:
What does it take to bake a cake? The RecipeRef corpus and anaphora resolution in procedural text. ACL (Findings) 2022: 3481-3495 - [c115]Yulia Otmakhova, Karin Verspoor, Timothy Baldwin, Jey Han Lau:
The patient is more dead than alive: exploring the current state of the multi-document summarisation of the biomedical literature. ACL (1) 2022: 5098-5111 - [c114]Antonio Jimeno-Yepes, Karin Verspoor:
Distinguishing between focus and background entities in biomedical corpora using discourse structure and transformers. LOUHI@EMNLP 2022: 35-40 - [c113]Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor:
Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. CLEF 2022: 521-540 - [c112]Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Kojiro Machi, Masaharu Yoshioka, Youngrok Jang, Hosung Song, Junho Lee, Gyeonghun Kim, Yireun Kim, Stanley Jungkyu Choi, Honglak Lee, Kyunghoon Bae, Darshini Mahendran, Christina Tang, Bridget T. McInnes, Timothy Baldwin, Karin Verspoor:
Extended Overview of ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. CLEF (Working Notes) 2022: 758-781 - [c111]Antonio Jimeno-Yepes, Karin Verspoor:
READ-BioMed@SocialDisNER: Adaptation of an Annotation System to Spanish Tweets. SMM4H@COLING 2022: 48-51 - [c110]Yulia Otmakhova, Thinh Hung Truong, Timothy Baldwin, Trevor Cohn, Karin Verspoor, Jey Han Lau:
LED down the rabbit hole: exploring the potential of global attention for biomedical multi-document summarisation. SDP@COLING 2022: 181-187 - [c109]Yuxia Wang, Timothy Baldwin, Karin Verspoor:
Noisy Label Regularisation for Textual Regression. COLING 2022: 4228-4240 - [c108]Mingjie Li, Wenjia Cai, Karin Verspoor, Shirui Pan, Xiaodan Liang, Xiaojun Chang:
Cross-modal Clinical Graph Transformer for Ophthalmic Report Generation. CVPR 2022: 20624-20633 - [c107]Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zenan Zhai, Zubair Afzal, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
The ChEMU 2022 Evaluation Campaign: Information Extraction in Chemical Patents. ECIR (2) 2022: 400-407 - [c106]Yulia Otmakhova, Karin Verspoor, Timothy Baldwin, Antonio Jimeno-Yepes, Jey Han Lau:
M3: Multi-level dataset for Multi-document summarisation of Medical studies. EMNLP (Findings) 2022: 3887-3901 - [c105]Thinh Hung Truong, Yulia Otmakhova, Timothy Baldwin, Trevor Cohn, Jey Han Lau, Karin Verspoor:
Not another Negation Benchmark: The NaN-NLI Test Suite for Sub-clausal Negation. AACL/IJCNLP (1) 2022: 883-894 - [c104]Thinh Hung Truong, Timothy Baldwin, Trevor Cohn, Karin Verspoor:
Improving negation detection with negation-focused pre-training. NAACL-HLT 2022: 4188-4193 - [c103]Antonio Jimeno-Yepes, Karin Verspoor:
The READ-BioMed Team in LivingNER Task 1 (2022): Adaptation of an English Annotation System to Spanish. IberLEF@SEPLN 2022 - [c102]Karin Verspoor:
Why Bother Enabling Biomedical Literature Analysis with Semantics? WWW (Companion Volume) 2022: 822 - [i24]Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor:
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. CoRR abs/2201.02229 (2022) - [i23]Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He:
MPVNN: Mutated Pathway Visible Neural Network Architecture for Interpretable Prediction of Cancer-specific Survival Risk. CoRR abs/2202.00882 (2022) - [i22]Thinh Hung Truong, Yulia Otmakhova, Rahmad Mahendra, Timothy Baldwin, Jey Han Lau, Trevor Cohn, Lawrence Cavedon, Damiano Spina, Karin Verspoor:
ITTC @ TREC 2021 Clinical Trials Track. CoRR abs/2202.07858 (2022) - [i21]Thinh Hung Truong, Timothy Baldwin, Trevor Cohn, Karin Verspoor:
Improving negation detection with negation-focused pre-training. CoRR abs/2205.04012 (2022) - [i20]Mingjie Li, Wenjia Cai, Karin Verspoor, Shirui Pan, Xiaodan Liang, Xiaojun Chang:
Cross-modal Clinical Graph Transformer for Ophthalmic Report Generation. CoRR abs/2206.01988 (2022) - [i19]Yulia Otmakhova, Thinh Hung Truong, Timothy Baldwin, Trevor Cohn, Karin Verspoor, Jey Han Lau:
LED down the rabbit hole: exploring the potential of global attention for biomedical multi-document summarisation. CoRR abs/2209.08698 (2022) - [i18]Thinh Hung Truong, Yulia Otmakhova, Timothy Baldwin, Trevor Cohn, Jey Han Lau, Karin Verspoor:
Not another Negation Benchmark: The NaN-NLI Test Suite for Sub-clausal Negation. CoRR abs/2210.03256 (2022) - 2021
- [j67]Ziad Al Bkhetan, Gursharan Chana, Kotagiri Ramamohanarao, Karin Verspoor, Benjamin Goudey:
Evaluation of consensus strategies for haplotype phasing. Briefings Bioinform. 22(4) (2021) - [j66]Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He:
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data. Bioinform. 36(21): 5187-5193 (2021) - [j65]Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor:
Automatic consistency assurance for literature-based gene ontology annotation. BMC Bioinform. 22(1): 565 (2021) - [j64]Ke Cao, Karin Verspoor, Elsie Chan, Mark Daniell, Srujana Sahebjada, Paul N. Baird:
Machine learning with a reduced dimensionality representation of comprehensive Pentacam tomography parameters to identify subclinical keratoconus. Comput. Biol. Medicine 138: 104884 (2021) - [j63]Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents. Frontiers Res. Metrics Anal. 6: 654438 (2021) - [j62]Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Dat Quoc Nguyen, Trevor Cohn, Karin Verspoor:
ChemTables: a dataset for semantic classification on tables in chemical patents. J. Cheminformatics 13(1): 97 (2021) - [j61]Jinghui Liu, Daniel Capurro, Anthony N. Nguyen, Karin Verspoor:
Early prediction of diagnostic-related groups and estimation of hospital cost by processing clinical notes. npj Digit. Medicine 4 (2021) - [c101]Kevin Bretonnel Cohen, Anna M. Ripple, Asma Ben Abacha, Olivier Bodenreider, Orin Hargraves, Karin Verspoor, Pierre Zweigenbaum, Dina Demner-Fushman:
Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. AMIA 2021 - [c100]Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor:
Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. CLEF 2021: 292-307 - [c99]Yuan Li, Biaoyan Fang, Jiayuan He, Hiyori Yoshikawa, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Timothy Baldwin, Karin Verspoor:
Extended Overview of ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. CLEF (Working Notes) 2021: 693-709 - [c98]Aparna Elangovan, Jiayuan He, Karin Verspoor:
Memorization vs. Generalization : Quantifying Data Leakage in NLP Performance Evaluation. EACL 2021: 1325-1335 - [c97]Biaoyan Fang, Christian Druckenbrodt, Saber A. Akhondi, Jiayuan He, Timothy Baldwin, Karin Verspoor:
ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical Domain. EACL 2021: 1362-1375 - [c96]Karin Verspoor, Simon Suster, Yulia Otmakhova, Shevon Mendis, Zenan Zhai, Biaoyan Fang, Jey Han Lau, Timothy Baldwin, Antonio Jimeno-Yepes, David Martínez:
Brief Description of COVID-SEE: The Scientific Evidence Explorer for COVID-19 Related Research. ECIR (2) 2021: 559-564 - [c95]Jiayuan He, Biaoyan Fang, Hiyori Yoshikawa, Yuan Li, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Zubair Afzal, Zenan Zhai, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
ChEMU 2021: Reaction Reference Resolution and Anaphora Resolution in Chemical Patents. ECIR (2) 2021: 608-615 - [c94]Simon Suster, Karin Verspoor, Timothy Baldwin, Jey Han Lau, Antonio Jimeno-Yepes, David Martinez Iraola, Yulia Otmakhova:
Impact of detecting clinical trial elements in exploration of COVID-19 literature. ICHI 2021: 495-496 - [c93]Mingjie Li, Wenjia Cai, Rui Liu, Yuetian Weng, Xiaoyun Zhao, Cong Wang, Xin Chen, Zhong Liu, Caineng Pan, Mengke Li, Yingfeng Zheng, Yizhi Liu, Flora D. Salim, Karin Verspoor, Xiaodan Liang, Xiaojun Chang:
FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark. NeurIPS Datasets and Benchmarks 2021 - [c92]Mary Regina Boland, Karin Verspoor, Maricel G. Kann, Su Golder, Lisa Levine, Karen O'Conner, Natalia Villanueva-Rosales, Graciela Gonzalez-Hernandez:
Advanced Methods for Big Data Analytics in Women's Health. PSB 2021 - [c91]Hung-Thinh Truong, Yulia Otmakhova, Timothy Baldwin, Jey Han Lau, Trevor Cohn, Karin Verspoor, Rahmad Mahendra, Lawrence Cavedon, Damiano Spina:
ITTC @ TREC 2021 Clinical Trials Track. TREC 2021 - [i17]Aparna Elangovan, Jiayuan He, Karin Verspoor:
Memorization vs. Generalization: Quantifying Data Leakage in NLP Performance Evaluation. CoRR abs/2102.01818 (2021) - [i16]Simon Suster, Karin Verspoor, Timothy Baldwin, Jey Han Lau, Antonio Jimeno-Yepes, David Martínez, Yulia Otmakhova:
Impact of detecting clinical trial elements in exploration of COVID-19 literature. CoRR abs/2105.12261 (2021) - 2020
- [j60]Liliya Akhtyamova, Paloma Martínez, Karin Verspoor, John Cardiff:
Testing Contextualized Word Embeddings to Improve NER in Spanish Clinical Case Narratives. IEEE Access 8: 164717-164726 (2020) - [j59]Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor:
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. 18(2): 91-103 (2020) - [c90]Yuxia Wang, Karin Verspoor, Timothy Baldwin:
Learning from Unlabelled Data for Clinical Semantic Textual Similarity. ClinicalNLP@EMNLP 2020: 227-233 - [c89]Yuxia Wang, Fei Liu, Karin Verspoor, Timothy Baldwin:
Evaluating the Utility of Model Configurations and Data Augmentation on Clinical Semantic Textual Similarity. BioNLP 2020: 105-111 - [c88]Brian Hur, Timothy Baldwin, Karin Verspoor, Laura Hardefeldt, James Gilkerson:
Domain Adaptation and Instance Selection for Disease Syndrome Classification over Veterinary Clinical Notes. BioNLP 2020: 156-166 - [c87]Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
Overview of ChEMU 2020: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents. CLEF 2020: 237-254 - [c86]Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) 2020 - [c85]Afshin Rahimi, Timothy Baldwin, Karin Verspoor:
WikiUMLS: Aligning UMLS to Wikipedia via Cross-lingual Neural Ranking. COLING 2020: 5957-5962 - [c84]Dat Quoc Nguyen, Zenan Zhai, Hiyori Yoshikawa, Biaoyan Fang, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Saber A. Akhondi, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents. ECIR (2) 2020: 572-579 - [c83]Yulia Otmakhova, Karin Verspoor, Timothy Baldwin, Simon Suster:
Improved Topic Representations of Medical Documents to Assist COVID-19 Literature Exploration. NLP4COVID@EMNLP 2020 - [e10]Karin Verspoor, Kevin Bretonnel Cohen, Michael Conway, Berry de Bruijn, Mark Dredze, Rada Mihalcea, Byron C. Wallace:
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020. Association for Computational Linguistics 2020 [contents] - [i15]Afshin Rahimi, Timothy Baldwin, Karin Verspoor:
WikiUMLS: Aligning UMLS to Wikipedia via Cross-lingual Neural Ranking. CoRR abs/2005.01281 (2020) - [i14]Karin Verspoor, Simon Suster, Yulia Otmakhova, Shevon Mendis, Zenan Zhai, Biaoyan Fang, Jey Han Lau, Timothy Baldwin, Antonio Jimeno-Yepes, David Martínez:
COVID-SEE: Scientific Evidence Explorer for COVID-19 Related Research. CoRR abs/2008.07880 (2020) - [i13]Aparna Elangovan, Melissa J. Davis, Karin Verspoor:
Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts. CoRR abs/2008.08727 (2020)
2010 – 2019
- 2019
- [j58]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j57]Dat Quoc Nguyen, Karin Verspoor:
From POS tagging to dependency parsing for biomedical event extraction. BMC Bioinform. 20(1): 72:1-72:13 (2019) - [j56]Mohamed Reda Bouadjenek, Justin Zobel, Karin Verspoor:
Automated assessment of biological database assertions using the scientific literature. BMC Bioinform. 20(1): 216:1-216:22 (2019) - [j55]Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor, Benjamin Goudey:
Exploring effective approaches for haplotype block phasing. BMC Bioinform. 20(1): 540:1-540:14 (2019) - [j54]Hamed Hassanzadeh, Anthony N. Nguyen, Karin Verspoor:
Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis. J. Biomed. Informatics 100 (2019) - [j53]Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor:
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. J. Comput. Biol. 26(6): 605-617 (2019) - [c82]Hiyori Yoshikawa, Dat Quoc Nguyen, Zenan Zhai, Christian Druckenbrodt, Camilo Thorne, Saber A. Akhondi, Timothy Baldwin, Karin Verspoor:
Detecting Chemical Reactions in Patents. ALTA 2019: 100-110 - [c81]Zenan Zhai, Dat Quoc Nguyen, Saber A. Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor:
Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings. BioNLP@ACL 2019: 328-338 - [c80]Dat Quoc Nguyen, Karin Verspoor:
End-to-End Neural Relation Extraction Using Deep Biaffine Attention. ECIR (1) 2019: 729-738 - [c79]Guillermo López-Campos, Philip Kiossoglou, Ann Borda, Christopher Hawthorne, Kathleen Gray, Karin Verspoor:
Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis. MedInfo 2019: 1530-1531 - [c78]Jiyu Chen, Karin Verspoor, Zenan Zhai:
A Bag-of-concepts Model Improves Relation Extraction in a Narrow Knowledge Domain with Limited Data. NAACL-HLT (Student Research Workshop) 2019: 43-52 - [c77]Rachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, Antonio Jimeno-Yepes, Madeleine Kittner, Martin Krallinger, Nancy Mah, Aurélie Névéol, Mariana L. Neves, Felipe Soares, Amy Siu, Karin Verspoor, Maika Vicente Navarro:
Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. WMT (3) 2019: 29-53 - [e9]Ondrej Bojar, Rajen Chatterjee, Christian Federmann, Mark Fishel, Yvette Graham, Barry Haddow, Matthias Huck, Antonio Jimeno-Yepes, Philipp Koehn, André Martins, Christof Monz, Matteo Negri, Aurélie Névéol, Mariana L. Neves, Matt Post, Marco Turchi, Karin Verspoor:
Proceedings of the Fourth Conference on Machine Translation, WMT 2019, Florence, Italy, August 1-2, 2019 - Volume 1: Research Papers. Association for Computational Linguistics 2019, ISBN 978-1-950737-27-7 [contents] - [e8]Ondrej Bojar, Rajen Chatterjee, Christian Federmann, Mark Fishel, Yvette Graham, Barry Haddow, Matthias Huck, Antonio Jimeno-Yepes, Philipp Koehn, André Martins, Christof Monz, Matteo Negri, Aurélie Névéol, Mariana L. Neves, Matt Post, Marco Turchi, Karin Verspoor:
Proceedings of the Fourth Conference on Machine Translation, WMT 2019, Florence, Italy, August 1-2, 2019 - Volume 2: Shared Task Papers, Day 1. Association for Computational Linguistics 2019 [contents] - [e7]Ondrej Bojar, Rajen Chatterjee, Christian Federmann, Mark Fishel, Yvette Graham, Barry Haddow, Matthias Huck, Antonio Jimeno-Yepes, Philipp Koehn, André Martins, Christof Monz, Matteo Negri, Aurélie Névéol, Mariana L. Neves, Matt Post, Marco Turchi, Karin Verspoor:
Proceedings of the Fourth Conference on Machine Translation, WMT 2019, Florence, Italy, August 1-2, 2019 - Volume 3: Shared Task Papers, Day 2. Association for Computational Linguistics 2019 [contents] - [i12]Jiyu Chen, Karin Verspoor, Zenan Zhai:
A bag-of-concepts model improves relation extraction in a narrow knowledge domain with limited data. CoRR abs/1904.10743 (2019) - [i11]Zenan Zhai, Dat Quoc Nguyen, Saber A. Akhondi, Camilo Thorne, Christian Druckenbrodt,