2024

Hopper JL, Li S, MacInnis RJ, Dowty JG, Nguyen TL, Bui M, Dite GS, Esser VFC, Ye Z, Makalic E, Schmidt DF, Goudey B, Alpen K, Kapuscinski M, Win AK, Dugué P, Milne RL, Jayasekara H, Brooks JD, Malta S, Ferreira L, Campbell AC, Young JT, Tu N, Sung J, Giles GG, Buchanan D, Winship I, Terry MB, Southey MC, Jenkins MA. Breast and bowel cancers diagnosed in people ‘too young to have cancer’: A blueprint for research using family and twin studies, Genet Epidemiol, 2024.

Mu J, Liu S, Burkitt AN, Grayden DB. Multi-frequency steady-state visual evoked potential dataset, Scientific Data 11 (26): 1-15, 2024.

Ye Z, Dite, GS, Nguyen TL, MacInnis RJ, Schmidt DF, Makalic E, Al-Qershi OM, Nguyen-Dumont T, Goudey B, Stone J. Genetic and environmental causes of variation in an automated breast cancer risk factor based on mammographic textures, Cancer Epidemiol Biomarkers Prev. 33 (2): 306 - 313, 2024.

2023

Chorev, M, Haderlein, J, Chandra, S., Menon, G., Burton, B.J.L., Pearce, I., McKibbin, M., Thottarath, S., Karatsai, E., Chandak, S., et al. A Multi-Modal AI-Driven Cohort Selection Tool to Predict Suboptimal Non-Responders to Aflibercept Loading-Phase for Neovascular Age-Related Macular Degeneration: PRECISE Study Report 1. J. Clin. Med., 12, 3013. 2023.

Eskikand PZ, Soto-Breceda A, Cook MJ, Burkitt AN, Grayden DB. Inhibitory stabilized network behaviour in a balanced neural mass model of a cortical column, Neural Networks, Vol 166, pp. 296-312, 2023.

Haderlein JF, Peterson ADH, Burkitt AN, Mareels IMY, Grayden DB. Autoregressive models for biomedical signal processing, 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 24-28 July 2023.

Kokorin K, Mu J, John SE, Grayden DB. Predictive shared control of robotic arms using simulated brain-computer interface inputs, 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 24-28 July 2023.

Ma C, Shen A, Yoshikawa H, Iwakura T, Beck D, Baldwin, T. On the Effectiveness of Images in Multi-modal Text Classification: An Annotation Study, ACM Transactions on Asian and Low-Resource Language Information Processing, Vol.22(3), pp. 1-19, 2023.

Mahendra R, Spina D, Verspoor K. (2023) ITTC at SemEval 2023-Task 7: Document Retrieval and Sentence Similarity for Evidence Retrieval in Clinical Trial Data. In Proceedings of the 17th International Workshop on Semantic Evaluation, Toronto, Canada. Association for Computational Linguistics. https://aclanthology.org/2023.semeval-1.316/

Pu Y, Beck D, Verspoor K. Graph embedding-based link prediction for literature-based discovery in Alzheimer’s Disease. Journal of Biomedical Informatics. DOI: 10.1016/j.jbi.2023.104464. 2023.

Rasheed S, Bennett J, Yoo P, Opie N, Burkitt AN, Grayden DB (2023) Removing Cardiac Artifacts from Endovascular Interface Data, ICNS NeuroEng Workshop, 2023.

Rasheed S., Bennett J, Yoo P, Opie N, Burkitt AN, Grayden DB. (2023) Decoding Eye Movements from Brain Signals, 45th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2023

Šuster S, Baldwin T, Lau J, Jimeno Yepes A, Martinez Iraola D, Otmakhova Y, Verspoor K. Automating Quality Assessment of Medical Evidence in Systematic Reviews: Model Development and Validation Study. J Med, Vol. 25. 2023.

Suster S, Baldwin T, Verspoor K. Analysis of predictive performance and reliability of classifiers for quality assessment of medical evidence revealed important variation by medical area. Journal of Clinical Epidemiology. DOI: 10.1016/j.jclinepi.2023.04.006. 2023.

Šuster S, Baldwin T, Verspoor K. Promoting Fairness in Classification of Quality of Medical Evidence. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 413–426, Toronto, Canada. Association for Computational Linguistics. https://aclanthology.org/2023.bionlp-1.39/. 2023.

Truong HT, Baldwin T, Verspoor K, Cohn T. Language models are not naysayers: an analysis of language models on negation benchmarks. In Proceedings of the 12th Joint Conference on Lexical and Computational Semantics (*SEM 2023), pages 101–114, Toronto, Canada. Association for Computational Linguistics. https://aclanthology.org/2023.starsem-1.10/ Best Paper Award. 2023.

Wenzel M, Huberfeld G, Grayden DB, de Curtis, M, Trevelyan AJ. A debate on the neuronal origin of focal seizures, Epilepsia 64, S37 - S48, 2023.

West, J, Bozorgi ZD, Herron J, Chizeck HJ, Chambers JD, Li L. Machine learning seizure prediction: one problematic but accepted practice. Journal of Neural Engineering, Vol 20(1), 2023.

Zarei Eskikand P, Soto-Breceda A, Cook MJ, Burkitt AN, Grayden DB. Inhibitory stabilized network behaviour in a balanced neural mass model of a cortical column, Neural Networks 166, pp. 296-312, 2023.

Zehra RS, Mu J, Syiem BV, Burkitt AN, Grayden DB. Evaluation of optimal stimuli for SSVEP-based augmented reality brain-computer interfaces, IEEE Access 11, pp. 87305-87315, 2023.

Zehra S, Mu J, Burkitt AN, Grayden DB. Effect of alpha range activity on SSVEP decoding in brain-computer interfaces, 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 24-28 July 2023.

2022

Sarwar T, Seifollahi S, Chan J, Zhang X, Aksakalli V, Hudson I, Verspoor K, Cavedon L. The Secondary Use of Electronic Health Records for Data Mining: Data Characteristics and Challenges, ACM Computing Surveys, Vol. 55(2), pp. 1-40, 2022.

Wang Y, Beck D, Baldwin T, Verspoor K. Uncertainty Estimation and Reduction of Pre-trained Models for Text Regression. Transactions of the Association for Computational Linguistics, Vol. 10, pp. 680–696, 2022.

Blades F, Chambers JD, Aumann TD, Nguyen CTO, Wong VHY, Aprico A, NHwoke EC, Bui BC, Grayden, DB, Kilpatrick TJ, Binder MD. White matter tract conductivity is resistant to wide variations in paranodal structure and myelin thickness accompanying the loss of Tyro3: an experimental and simulated analysis. Brain Structure and Function, Vol. 227, pp. 2035–2048, 2022.

Wang S, Šuster S, Baldwin T, Verspoor K. Predicting Publication of Clinical Trials Using Structured and Unstructured Data: Model Development and Validation Study. J Med Internet Res, Vol 24(12), 2022.

Goudey B, Geard N, Verspoor K, Zobel J. Propagation, detection and correction of errors using the sequence database network, Briefings in Bioinformatics. Vol 23(6), 2022.

Song Y, Lee S, Bell D, Goudey B, Zhou R. Binding Affinity Calculations of Gluten Peptides to HLA Risk Modifiers: DQ2.5 versus DQ7.5. J Phys Chem B. Vol 126(28), pp. 5151-5160, 2022.

Chen J, Goudey B, Zobel J, Geard N, Verspoor K, Exploring automatic inconsistency detection for literature-based gene ontology annotation, Bioinformatics, Vol 38(1), pp. i273 - i281, 2022.

2021

Bennett JD, John SW, Grayden DB, Burkitt AN. (2021) A neurophysiological approach to spatial filter selection for adaptive brain-computer interfaces, Journal of Neural Engineering, vol. 8 (2).

Bhatia S, Lau JH, Baldwin T. (2021) Automatic Classification of Neutralization Techniques in the Narrative of Climate Change Scepticism, In Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics – Human Language Technologies (NAACL HLT 2021).

Breen J, Baldwin T, Bond F. (2021) Identification of Neologisms in Japanese Corpora using Synthesis, In Proceedings of the XiX EURALEX International Congress (EURALEX 2021).

Chen Z, Maturana MI, Burkitt AN, Cook MJ, Grayden DB (2021) High-frequency oscillations in epilepsy: What have we learned and what needs to be addressed, Neurology, 96 (9): 439-448.

Cohen KB, Ripple A, Ben Abacha A, Bodenreider O, Hargraves O, Verspoor K, Zweigenbaum P, Demner-Fushman D. (2021) Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. In Proceedings of AMIA 2021.

Fivez P, Šuster S, Daelemans W. (2021) Conceptual Grounding Constraints for Truly Robust Biomedical Name Representations, EACL.

Fivez P, Šuster S, Daelemans W. (2021) Integrating Higher-Level Semantics into Robust Biomedical Name Representations. Workshop on Health Text Mining and Information Analysis (LOUHI), EACL.

Haderlein JF, Mareels IMY, Peterson ADH, Eskikand PZ, Burkitt AN, Grayden DB. (2021). On the benefit of overparameterization in state reconstruction, 2021 60th IEEE Conference on Decision and Control (CDC), 2021, pp. 1580-1585.

Jiang F, Cohn T. (2021). Incorporating Syntax and Semantics in Coreference Resolution with Heterogeneous Graph Attention Network. In NAACL 2021.

Koto F, Lau JH, Baldwin T. (2021) Discourse Probing of Pretrained Language Models, In Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics – Human Language Technologies (NAACL HLT 2021).

Koto F, Lau JH, Baldwin T. (2021) Evaluating the Efficacy of Summarization Evaluation across Languages, Findings of ACL, pp. 801—812.

Koto F, Lau JH, Baldwin T. (2021) IndoBERTweet: A Pretrained Language Model for Indonesian Twitter with Effective Domain-Specific Vocabulary Initialization, In Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP 2021), Online and Punta Cana, Dominican Republic, pp. 10660—10668.

Koto F, Lau JH, Baldwin T. (2021) Top-down Discourse Parsing via Sequence Labelling, In Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2021), virtual, pp. 715-726.

Li M, Cai W, Liu R, Weng Y, Zhao X, Wang C, Chen X, Liu Z, Pan C, Li M, Zheng Y, Liu Y, Salim FD, Verspoor K, Liang X, Chang X. (2021) FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark. In Proceedings of NeurIPS 2021.

Li H, Gong Y, Jiao J, Zhang R, Baldwin T, Duan N. (2021) KFCNet: Knowledge Filtering and Contrastive Learning for Generative Commonsense Reasoning , In Findings of EMNLP, Online and Punta Cana, Dominican Republic, pp. 2918—2928.

Ma C, Shen A, Yoshikawa H, Iwakura T, Beck D, Baldwin T. (2021) On the (In)Effectiveness of Images for Text Classification, In Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2021), virtual, pp. 42—48.

Mistica M, Lau JH, Merrifield B, Fazio K, Baldwin T. (2021) Semi-automatic Triage of Requests for Free Legal Assistance, In Proceedings of the Natural Legal Language Processing Workshop 2021, online, Online and Punta Cana, Dominican Republic, pp. 217—227.

Reddy S, Bhaskar R, Padmanabhan S, Verspoor K, Mamillapalli C, Lahoti R, Makinen VP, Pradhan S, Kushwah P, Sinha S. Use and validation of text mining and cluster algorithms to derive insights from Corona Virus Disease-2019 (COVID19) medical literature, Computer Methods and Programs in Biomedicine Update, Vol 1, no. 100010, 2021.

Schultz BG, Tarigoppula VSA (Adi), Noffs G, Azocar SR, van der Walt A, Grayden DB, Vogel AP, Automatic speech recognition in neurodegenerative disease, International Journal of Speech Technology, 2021.

Shen A, Mistica M, Salehi B, Li H, Baldwin T, Qi J. Evaluating Document Coherence Modeling. Transactions of the Association for Computational Linguistics, Vol. 9, pp. 621–640, 2021.

Verspoor K. The Evolution of Clinical Knowledge During COVID-19: Towards a Global Learning Health System. Yearbook of Medical Informatics. Vol. 30(01), pp. 176-184, 2021.

2020

Chen Z, Grayden DB, Burkitt AN, Seneviratne U, D’Souza WJ, French C, Karoly PJ, Dell K, Leyde K, Cook MJ, Maturana MI (2020) Spatiotemporal patterns of high-frequency activity (80-170 Hz) in long-term intracranial EEG, Neurology 10.1212

Kitayama, Kotaro, Shivashankar Subramanian and Timothy Baldwin (2020) Popularity Prediction of Online Petitions using a Multimodal Deep Regression Model, In Proceedings of the 2020 Australasian Language Technology Workshop (ALTW 2020), virtual, pp. 110—104.

Koto, Fajri, Afshin Rahimi, Jey Han Lau and Timothy Baldwin (2020) IndoLEM and IndoBERT: A Benchmark Dataset and Pre-trained Language Model for Indonesian NLP, In Proceedings of the 28th International Conference on Computational Linguistics (COLING 2020), virtual, pp. 757—770.

Koto, Fajri, Jey Han Lau and Timothy Baldwin (2020) Liputan6: A Large-scale Indonesian Dataset for Text Summarisation, In Proceedings of the 1st Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics and the 10th International Joint Conference on Natural Language Processing (AACL-IJCNLP 2020), virtual, pp. 598—608.

Leins, Kobi, Jey Han Lau and Timothy Baldwin (2020) Give Me Convenience and Give Her Death: Who Should Decide What Uses of NLP are Appropriate, and on What Basis?, In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics (ACL 2020), pp. 2908—2913.

Mathur, Nitika, Timothy Baldwin and Trevor Cohn (2020) Tangled up in BLEU: Reevaluating the Evaluation of Automatic Machine Translation Evaluation Metrics, In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics (ACL 2020), pp. 4984—4997.

Maturana M, Meisel C, Dell K, Karoly P, D’Souza W, Grayden DB, Burkitt AN, Jiruska P, Kudlacek J, Hlinka J, Cook MJ, Kuhlmann L, Freestone DR (2020) Critical slowing down as a biomarker for seizure susceptibility, Nature Communications 11, 1-12.

Otmakhova Y, Verspoor K, Baldwin T, Suster S. (2020) Improved Topic Representations of Medical Documents to Assist COVID-19 Literature Exploration. NLP COVID-19 Workshop at EMNLP 2020.

Pederson M, Verspoor K, Jenkinson M, Law M, Abbott DF, Jackson GD (2020). Artificial Intelligence for clinical decision support in neurology. Brain Communications, 2 (2).

Rahimi A, Baldwin T, Verspoor K. (2020) WikiUMLS: Aligning UMLS to Wikipedia via Cross-lingual Neural Ranking. COLING 2020: 5957-5962.

Shen, Aili, Bahar Salehi, Jianzhong Qi and Timothy Baldwin (2020) A Multimodal Approach to Assessing Document Quality, Journal of Artificial Intelligence Research Vol 68, pp. 607—632.

Sushil M, Šuster S, Daelamans W. Distilling neural networks into skipgram-level decision lists. arXiv preprint arXiv:2005.07111. 2020.

Verspoor K, Cohen KB, Conway M, de Bruijn B, Dredze M, Mihalcea R, Wallace B, editors (2020) Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020. Association of Computational Linguistics.

Verspoor K, Cohen KB, Dredze M, Ferrara E, May J, Munro R, Paris C, Wallace B, editors (2020) Proceedings of the 1st Workshop on NLP for COVID-19 at ACL 2020. Association of Computational Linguistics.

Verspoor K, Suster S, Otmakhova Y, Mendis S, Zhai Z, Fang B, Lau JH, Baldwin T, Jimeno Yepes A, Martinez D. (2020) COVID-SEE: Scientific Evidence Explorer for COVID-19 Related Research. arXiv preprint arXiv:2008.07880, 2020.

Wang, Yuxia, Fei Liu, Karin Verspoor and Timothy Baldwin (2020) Evaluating the Utility of Model Configurations and Data Augmentation on Clinical Semantic Textual Similarity, In Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing (BioNLP 2020), pp. 105—111.

Wang, Yuxia, Karin Verspoor and Timothy Baldwin (2020) Learning from Unlabelled Data for Clinical Semantic Textual Similarity, In Proceedings of the 3rd Clinical Natural Language Processing Workshop.

Zarei Eskikand P, Kameneva T, Burkitt AN, Grayden DB, Ibbotson MR (2020) Adaptive surround modulation of MT neurons: A computational model, Frontiers in Neural Circuits 14, 529345.

2019

Petri, M., Moffat, A., Mackenzie, J., Culpepper, J.S. and Beck, D., 2019, July. Accelerated query processing via similarity score prediction. In Proceedings of the 42nd International ACM SIGIR Conference on Research and Development in Information Retrieval (pp. 485-494).

McCaughey, Tristan, David M. Budden, Paul G. Sanfilippo, George EC Gooden, Li Fan, Eva Fenwick, Gwyneth Rees, Casimir MacGregor, Lei Si, Christine Chen, Helena Hai Liang, Alice Pébay, Timothy Baldwin and Alex W Hewitt (2019) A need for better understanding is the major determinant for public perceptions of human gene editing, Human Gene Therapy 30(1), pp. 36—43.

Shen, Aili, Bahar Salehi, Timothy Baldwin and Jianzhong Qi (2019) A Joint Model for Multimodal Document Quality Assessment, In Proceedings of the 2019 Joint Conference on Digital Libraries (JCDL 2019), Urbana-Champaign, USA.

Brian Hur, Laura Y. Hardefeldt, Karin Verspoor, Timothy Baldwin and James R Gilkerson (2019) Using Natural Language Processing and VetCompass to understand antimicrobial usage patterns in Australia, Australian Veterinary Journal 97(8), pp. 298—300.

Li, Yitong, Timothy Baldwin and Trevor Cohn (2019) Semi-supervised Stochastic Domain Adaptation using Variational Inference, In Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics (ACL 2019), Florence, Italy, pp. 1923—1934.

Aili Shen, Daniel Beck, Bahar Salehi, Jianzhong Qi and Timothy Baldwin (2019) Modelling Uncertainty in Collaborative Document Quality Assessment, In Proceedings of the 5th Workshop on Noisy User-generated Text (W-NUT 2019), Hong Kong, pp. 191—201.

Shen, Aili, Bahar Salehi, Jianzhong Qi and Timothy Baldwin (2019) Feature-guided Neural Model Training for Supervised Document Representation Learning, In Proceedings of the 2019 Australasian Language Technology Workshop (ALTW 2019), Sydney, Australia, pp. 47—51.

Koto, Fajri, Jey Han Lau and Timothy Baldwin (2019) Improved Document Modelling with a Neural Discourse Parser, In Proceedings of the 2019 Australasian Language Technology Workshop (ALTW 2019), Sydney, Australia, pp. 67—76.

Arora, Gaurav, Afshin Rahimi and Timothy Baldwin (2019) Does an LSTM forget more than a CNN?, In Proceedings of the 2019 Australasian Language Technology Workshop (ALTW 2019), Sydney, Australia, pp. 77—86.

Burnham, S.C., Loi, S.M., Doecke, J., Fedyashov, V., Dore, V., Villemagne, V.L. and Masters, C.L., 2019. The dawn of robust individualised risk models for dementia. The Lancet Neurology, 18(11), pp.985-987.

Hassanzadeh H, Nguyen A, Verspoor K*. (2019) Quantifying Semantic Similarity of Clinical Evidence in the Biomedical Literature to Facilitate Related Evidence Synthesis. Journal of Biomedical Informatics. Volume 100, 103321. doi: 10.1016/j.jbi.2019.103321 [Q1/SJR 1.02]

Islamaj Doğan R, Kim S, Chatr-aryamontri A, Wei CH, Comeau DC, Antunes R, Matos S, Chen Q, Elangovan A, Panyam NC, Verspoor K, Liu H, Wang Y, Liu Z, Altınel B, Hüsünbeyi ZM, Özgür A, Fergadis A, Wang CK, Dai HJ, Tran T, Kavuluru R, Luo L, Steppi A, Zhang J, Qu J, Lu Z. (2019) Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine, Database: The Journal of Biological Databases and Curation, Volume 2019, 1 January 2019, bay147, doi:10.1093/database/bay147 [PMID: 30689846] [Q1/SJR 2.2]

Lopez-Campos G, Kiossoglou P, Borda A, Hawthorne C, Gray K, Verspoor K*. (2019) Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis. MedInfo 2019. Stud Health Technol Inform. 264:1530-1531. doi: 10.3233/SHTI190519. [PMID: 31438216]

Bawden R, Cohen KB, Grozea C, Jimeno Yepes A, Kittner A, Krallinger M, Mah N, Névéol A, Neves M, Soares F, Siu A, Uceda M, Verspoor K, Vicente Navarro M. (2019) Automatic translation of biomedical texts: the biomedical task at the Workshop for Machine Translation. AMIA Natural Language Processing Working Group Pre-Symposium at the American Medical Informatics Association meeting AMIA2019, Washington DC.

Bawden R, Cohen KB, Grozea C, Jimeno Yepes A, Kittner M, Krallinger M, Mah N, Neveol A, Neves M, Soares F, Siu A, Verspoor K, Vicente Navarro M. (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 (WMT), Volume 3: Shared Task Papers (Day 2) pages 29–53.

Chen J, Verspoor K*, Zhai Z. (2019) A bag-of-concepts model improves relation extraction in a narrow knowledge domain with limited data. Proceedings of the Student Research Workshop (SRW) at NAACL 2019. https://arxiv.org/abs/1904.10743