Embedded Files
2025
2025
Ilija Dukovski, Lauren Golden, Jing Zhang, Melisa Osborne, Daniel Segrè, Kirill Korolev. Biophysical metabolic modeling of complex bacterial colony morphology. Cell Systems (2025). https://www.cell.com/cell-systems/abstract/S2405-4712(25)00185-1
Gorjan Radevski, Kiril Gashteovski, Shahbaz Syed, Christopher Malon, Sebastien Nicolas, Chia-Chien Hung, Timo Sztyler, Verena Heußer, Wiem Ben Rim, Masafumi Enomoto, Kunihiro Takeoka, Masafumi Oyamada, Goran Glavas, Carolin Lawrence. On Synthesizing Data for Context Attribution in Question Answering. ACL (1) 2025: 16929-16950
URL: https://aclanthology.org/2025.acl-long.828.pdf
Daniel Philip Rose, Chia-Chien Hung, Marco Lepri, Israa Alqassem, Kiril Gashteovski, Carolin Lawrence. MEDDxAgent: A Unified Modular Agent Framework for Explainable Automatic Differential Diagnosis. ACL (1) 2025: 13803-13826
URL: https://aclanthology.org/2025.acl-long.677/
Seungone Kim, Juyoung Suk, Xiang Yue, Vijay Viswanathan, Seongyun Lee, Yizhong Wang, Kiril Gashteovski, Carolin Lawrence, Sean Welleck, Graham Neubig. Evaluating Language Models as Synthetic Data Generators. ACL (1) 2025: 6385-6403
URL: https://aclanthology.org/2025.acl-long.320/
Karakuzu, A., Blostein, N., Caron, A.V. et al. Rethinking MRI as a measurement device through modular and portable pipelines. Magn Reson Mater Phy (2025). https://doi.org/10.1007/s10334-025-01245-3
2024
2024
Robust Text Classification: Analyzing Prototype-Based Networks
Zhivar Sourati, Darshan Girish Deshpande, Filip Ilievski, Kiril Gashteovski, and Sascha Saralajew.
In Findings of the Association for Computational Linguistics: EMNLP 2024, pages 12736–12757, Miami, Florida, USA.
Association for Computational Linguistics.
https://aclanthology.org/2024.findings-emnlp.745/
Ling-Dong Shi, Maria Florencia Ercoli, Jack Kim, Artur Teixeira de Araujo Jr., Subah Soni, Tracy Satomi Weitz, Alexandra M. Shigenaga, Ilija Dukovski, Rohan Sachdeva, Halbay Turumtay, Katherine B. Louie, Benjamin P. Bowen, Henrik V. Scheller, Daniel Segrè, Trent R. Northen, Pamela C. Ronald, Jillian F. Banfield. Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling bioRxiv 2024.03.13.584915; doi: https://doi.org/10.1101/2024.03.13.584915
Agah Karakuzu, Mathieu Boudreau, Nikola Stikov, Reproducible Research Practices in Magnetic Resonance Neuroimaging: A Review Informed by Advanced Language Models, Magnetic Resonance in Medical Sciences, 10.2463/mrms.rev.2023-0174, (2024). https://doi.org/10.1002/mrm.30111
Agah Karakuzu, Mathieu Boudreau, Nikola Stikov, Reproducible Research Practices in Magnetic Resonance Neuroimaging: A Review Informed by Advanced Language Models, Magnetic Resonance in Medical Sciences, 2024, Volume 23, Issue 3, Pages 252-267. https://doi.org/10.2463/mrms.rev.2023-0174
Luca Gioacchini, Giuseppe Siracusano, Davide Sanvito, Kiril Gashteovski, David Friede, Roberto Bifulco, and Carolin Lawrence. 2024. AgentQuest: A Modular Benchmark Framework to Measure Progress and Improve LLM Agents. In Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 3: System Demonstrations), pages 185–193, Mexico City, Mexico. Association for Computational Linguistics. https://aclanthology.org/2024.naacl-demo.19/
Large Language Models Enable Few-Shot Clustering
Vijay Viswanathan, Kiril Gashteovski, Carolin Lawrence, Tongshuang Wu, Graham Neubig
Transactions of the Association for Computational Linguistics (2024) 12: 321–333.
https://direct.mit.edu/tacl/article/doi/10.1162/tacl_a_00648/120476
doi: https://doi.org/10.1162/tacl_a_00648
David Dukić, Kiril Gashteovski, Goran Glavaš, Jan Snajder.
Leveraging Open Information Extraction for More Robust Domain Transfer of Event Trigger Detection.
Findings of the Association for Computational Linguistics: EACL 2024.
URL: https://aclanthology.org/2024.findings-eacl.80/
Zhao Xu, Wiem Ben Rim, Kiril Gashteovski, Timo Sztyler, Carolin Lawrence.
A Human-Centric Evaluation Platform for Explainable Knowledge Graph Completion.
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations.
URL: https://aclanthology.org/2024.eacl-demo.3/
Ilija Dukovski, Lauren Golden, Jing Zhang, Melisa Osborne, Daniel Segrè, Kirill Korolev.
Biophysical metabolic modeling of complex bacterial colony morphology.
bioRxiv 2024.03.13.584915; doi: https://doi.org/10.1101/2024.03.13.584915
Epilogue: The EU and the Balkans: A Game of Power and Duplicity. In Pathways of Return: Mobility and Transnational Migration in Southeast Europe. Eds. Jasna Čapo, Rozita Dimova and Lumnije Jusufi. Berlin: Peter Lang Academic Publishers. Forthcoming April 2024.
Pathways of Return: Mobility and Transnational Migration in Southeast Europe. Jasna Čapo / Rozita Dimova / Lumnije Jusufi (eds.). Berlin: Peter Lang Academic Publishers. Forthcoming April 2024.
2023
2023
Dimova, Rozita. 2023. Transgressing Realities: Desire and the Border in the Southern Balkans. In: Borders of Desire: Gender and Sexuality at the Eastern Borders of Europe. Eds. Elissa Helms and Tuija Pulkkinen. Manchester: Manchester University Press.
https://manchesteruniversitypress.co.uk/9781526165206/
Radevski, G., Gashteovski, K., Hung, C.C., Lawrence, C. and Glavaš, G., 2023. Linking surface
facts to large-scale knowledge graphs. https://arxiv.org/abs/2310.14909v1
DOI: https://doi.org/10.48550/arXiv.2310.14909
Harding, R. J., Bermudez, P., Bernier, A., Beauvais, M., Bellec, P., Hill, S., ... & Evans, A. C.
(2023). The Canadian Open Neuroscience Platform—An open science framework for the
neuroscience community. PLOS Computational Biology, 19(7), e1011230.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011230
DOI: https://doi.org/10.1371/journal.pcbi.1011230
Boudreau, M., Karakuzu, A., Cohen-Adad, J., Bozkurt, E., Carr, M., Castellaro, M., ... & Stikov,
N. (2023). Results of the ISMRM 2020 joint reproducible research & quantitative MR study
groups reproducibility challenge on phantom and human brain T1 mapping. NeuroLibre
Reproducible Preprints, 10.
https://neurolibre.org/papers/10.55458/neurolibre.00014
DOI: https://doi.org/10.55458/neurolibre.00014
Stikov, N., & Karakuzu, A. (2023). The relaxometry hype cycle. Frontiers in Physiology, 14.
https://www.frontiersin.org/articles/10.3389/fphys.2023.1281147/full
2022
2022
Karakuzu, A., Biswas, L., Cohen‐Adad, J., & Stikov, N. (2022). Vendor‐neutral sequences and fully transparent workflows improve inter‐vendor reproducibility of quantitative MRI. Magnetic Resonance in Medicine, 88(3), 1212-1228.
https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.29292
DOI: https://doi.org/10.1002/mrm.29292
Karakuzu, A., Appelhoff, S., Auer, T., Boudreau, M., Feingold, F., Khan, A. R., ... & De Hollander, G. (2022). qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data. Scientific data, 9(1), 517.
2021
2021
Dimova Rozita. 2021. Border Porosities: Movements of People, Goods and Services in the Southern Balkans. Manchester: Manchester University Press. https://manchesteruniversitypress.co.uk/9781526140630/
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