% Use this file for citations not found in the ACL Anthology (contained in "anthology.bib").


@article{Xu2015,
  author    = {Xu, Dongkuan and Tian, Yingjie},
  title     = {A Comprehensive Survey of Clustering Algorithms},
  journal   = {Annals of Data Science},
  volume    = {2},
  number    = {2},
  pages     = {165--193},
  year      = {2015},
  month     = jun,
  doi       = {10.1007/s40745-015-0040-1},
  url       = {https://doi.org/10.1007/s40745-015-0040-1},
  issn      = {2198-5812}
}

@article{CHIARAMELLO201622,
title = {Use of “off-the-shelf” information extraction algorithms in clinical informatics: A feasibility study of {MetaMap} annotation of {Italian} medical notes},
journal = {Journal of Biomedical Informatics},
volume = {63},
pages = {22-32},
year = {2016},
issn = {1532-0464},
doi = {https://doi.org/10.1016/j.jbi.2016.07.017},
url = {https://www.sciencedirect.com/science/article/pii/S1532046416300715},
author = {Emma Chiaramello and Francesco Pinciroli and Alberico Bonalumi and Angelo Caroli and Gabriella Tognola},
keywords = {Information extraction, Unstructured clinical notes, Italian language, MetaMap, Failure analysis, EHR data reuse},
}

@misc{lee2024nvembed,
    title={{NV-Embed}: Improved Techniques for Training {LLMs} as Generalist Embedding Models},
    author={Chankyu Lee and Rajarshi Roy and Mengyao Xu and Jonathan Raiman and Mohammad Shoeybi and Bryan Catanzaro and Wei Ping},
    year={2024},
    eprint={2405.17428},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}

@Inbook{Magnini2023,
author="Magnini, Bernardo
and Altuna, Bego{\~{n}}a
and Lavelli, Alberto
and Minard, Anne-Lyse
and Speranza, Manuela
and Zanoli, Roberto",
editor="Rehm, Georg",
title="European Clinical Case Corpus",
bookTitle="European Language Grid: A Language Technology Platform for Multilingual Europe",
year="2023",
publisher="Springer International Publishing",
address="Cham",
pages="283--288",
isbn="978-3-031-17258-8",
doi="10.1007/978-3-031-17258-8_17",
url="https://doi.org/10.1007/978-3-031-17258-8_17"
}

@article{Meidt2025,
  author    = {Meidt, Alexandra and Walter, Carolin and Lehmann, Christoph U and Dugas, Martin},
  title     = {Medical researchers' perception of sharing of metadata from case report forms},
  journal   = {Learning Health Systems},
  volume    = {9},
  number    = {1},
  pages     = {e10456},
  year      = {2025},
  month     = jan,
  doi       = {10.1002/lrh2.10456},
  pmid      = {39822926},
  pmc       = {PMC11733469},
  issn      = {2379-6146},
  language  = {English},
  affiliation = {Institute of Medical Informatics, University of Münster, Münster, Germany; University of Texas Southwestern Medical Center, Dallas, Texas, USA; Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany},
  keywords  = {case report forms, clinical research, cross-sectional survey, interoperability, metadata classification, metadata repository, metadata standards, metadata trends, sharing of metadata, translational research},
  note      = {The authors declare that they have no conflicts of interest.}
}

@article{Nahm2011,
  author    = {Nahm, Monique and Shepherd, John and Buzenberg, Anna and Rostami, Ramin and Corcoran, Andrew and McCall, Jennifer and Pietrobon, Roberto},
  title     = {Design and implementation of an institutional case report form library},
  journal   = {Clinical Trials},
  volume    = {8},
  number    = {1},
  pages     = {94--102},
  year      = {2011},
  month     = feb,
  doi       = {10.1177/1740774510391916},
  pmid      = {21163853},
  pmc       = {PMC3494996},
  language  = {English},
  note      = {Epub 2010 Dec 16},
}

@article{Gutierrez-Sacristan2024,
  author    = {Gutiérrez-Sacristán, Alba and Makwana, Simran and Dionne, Audrey and Mahanta, Simran and Dyer, Karla J. and Serrano, Faridis and Watrin, Carmen and Pages, Pierre and Mousavi, Sajad and Degala, Anil and Lyons, Jessica and Pillion, Danielle and Zachariasse, Joany M. and Shekerdemian, Lara S. and Truong, Dongngan T. and Newburger, Jane W. and Avillach, Paul},
  title     = {Development and validation of an open-source pipeline for automatic population of case report forms from electronic health records: a pediatric multi-center prospective study},
  journal   = {eBioMedicine},
  volume    = {108},
  year      = {2024},
  month     = oct,
  doi       = {10.1016/j.ebiom.2024.105337},
  url       = {https://doi.org/10.1016/j.ebiom.2024.105337},
  publisher = {Elsevier},
  issn      = {2352-3964},
  note      = {doi: 10.1016/j.ebiom.2024.105337}
}

@article{Cheng2022,
  author    = {Cheng, A. C. and Banasiewicz, M. K. and Johnson, J. D. and Sulieman, L. and Kennedy, N. and Delacqua, F. and Lewis, A. A. and Joly, M. M. and Bistran-Hall, A. J. and Collins, S. and Self, W. H. and Shotwell, M. S. and Lindsell, C. J. and Harris, P. A.},
  title     = {Evaluating automated electronic case report form data entry from electronic health records},
  journal   = {Journal of Clinical and Translational Science},
  volume    = {7},
  number    = {1},
  pages     = {e29},
  year      = {2022},
  month     = dec,
  doi       = {10.1017/cts.2022.514},
  pmid      = {36845316},
  pmc       = {PMC9947602}
}

@article{MacKenzie2016,
  author    = {Mac Kenzie, W. R. and Davidson, A. J. and Wiesenthal, A. and Engel, J. P. and Turner, K. and Conn, L. and Becker, S. J. and Moffatt, S. and Groseclose, S. L. and Jellison, J. and Stinn, J. and Garrett, N. Y. and Helmus, L. and Harmon, B. and Richards, C. L. and Lumpkin, J. R. and Iademarco, M. F.},
  title     = {The Promise of Electronic Case Reporting},
  journal   = {Public Health Reports},
  volume    = {131},
  number    = {6},
  pages     = {742--746},
  year      = {2016},
  month     = nov,
  doi       = {10.1177/0033354916670871},
  pmid      = {28123218},
  pmc       = {PMC5230835},
  note      = {Epub 2016 Oct 13}
}

@article{Knicely2024,
  author    = {Knicely, K. and Loonsk, J. W. and Hamilton, J. J. and Fine, A. and Conn, L. A.},
  title     = {Electronic Case Reporting Development, Implementation, and Expansion in the United States},
  journal   = {Public Health Reports},
  volume    = {139},
  number    = {4},
  pages     = {432--442},
  year      = {2024},
  month     = jul,
  doi       = {10.1177/00333549241227160},
  pmid      = {38411134},
  pmc       = {PMC11284980},
  note      = {Epub 2024 Feb 27}
}


@misc{lee2025nvembedimprovedtechniquestraining,
      title={NV-Embed: Improved Techniques for Training LLMs as Generalist Embedding Models}, 
      author={Chankyu Lee and Rajarshi Roy and Mengyao Xu and Jonathan Raiman and Mohammad Shoeybi and Bryan Catanzaro and Wei Ping},
      year={2025},
      eprint={2405.17428},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2405.17428}, 
}

@article{DeSouza29102009,
author = {Cynthia M. DeSouza, Anna T. R. Legedza and Abdul J. Sankoh},
title = {An Overview of Practical Approaches for Handling Missing Data in Clinical Trials},
journal = {Journal of Biopharmaceutical Statistics},
volume = {19},
number = {6},
pages = {1055--1073},
year = {2009},
publisher = {Taylor \& Francis},
doi = {10.1080/10543400903242795},
note ={PMID: 20183464},
URL = {https://doi.org/10.1080/10543400903242795},
eprint = {https://doi.org/10.1080/10543400903242795}
}

@article{Bellary2014,
  author    = {Bellary, Shantala and Krishnankutty, Binny and Latha, M. S.},
  title     = {Basics of case report form designing in clinical research},
  journal   = {Perspectives in Clinical Research},
  volume    = {5},
  number    = {4},
  pages     = {159--166},
  year      = {2014},
  month     = oct,
  doi       = {10.4103/2229-3485.140555}
}


@misc{UMLS2024,
  author       = {{National Library of Medicine (US)}},
  title        = {{UMLS} Knowledge Sources [dataset on the Internet]. Release 2024AA},
  year         = {2024},
  month        = may,
  publisher    = {National Library of Medicine},
  address      = {Bethesda, MD},
  note         = {Cited 2025 March},
  url          = {http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html}
}

@misc{openai2024gpt4technicalreport,
      title={GPT-4 Technical Report}, 
      author={OpenAI and Josh Achiam et al},
      year={2024},
      eprint={2303.08774},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2303.08774}, 
}

@misc{zhang2025jasperstelladistillationsota,
      title={Jasper and {Stella}: distillation of {SOTA} embedding models}, 
      author={Dun Zhang and Jiacheng Li and Ziyang Zeng and Fulong Wang},
      year={2025},
      eprint={2412.19048},
      archivePrefix={arXiv},
      primaryClass={cs.IR},
      url={https://arxiv.org/abs/2412.19048}, 
}
@misc{Ghosh2025,
  author       = {Ghosh, Soumitra and Altuna, Begona and Farzi, Saeed and Ferrazzi, Pietro and Lavelli, Alberto and Mezzanotte, Giulia and Speranza, Manuela and Magnini, Bernardo},
  title        = {Low-resource Information Extraction with the {European Clinical Case Corpus}},
  year         = {2025},
  month        = mar,
  archivePrefix = {arXiv},
  note         = {arXiv preprint}
}

@article{LU201519,
title = {Parallel heuristics for scalable community detection},
journal = {Parallel Computing},
volume = {47},
pages = {19-37},
year = {2015},
issn = {0167-8191},
doi = {https://doi.org/10.1016/j.parco.2015.03.003},
url = {https://www.sciencedirect.com/science/article/pii/S0167819115000472},
author = {Hao Lu and Mahantesh Halappanavar and Ananth Kalyanaraman},
keywords = {Community detection, Parallel graph heuristics, Graph coloring, Graph clustering}
}


@misc{grattafiori2024llama3herdmodels,
      title={The {Llama} 3 Herd of Models}, 
      author={Aaron Grattafiori et al.},
      year={2024},
      eprint={2407.21783},
      archivePrefix={arXiv},
      primaryClass={cs.AI},
      url={https://arxiv.org/abs/2407.21783}, 
}

@misc{qwen2025qwen25technicalreport,
      title={Qwen2.5 Technical Report}, 
      author={Qwen and An Yang et al.},
      year={2025},
      eprint={2412.15115},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2412.15115}, 
}

@inproceedings{kwon2023efficient,
  title={Efficient Memory Management for Large Language Model Serving with {PagedAttention}},
  author={Woosuk Kwon and Zhuohan Li and Siyuan Zhuang and Ying Sheng and Lianmin Zheng and Cody Hao Yu and Joseph E. Gonzalez and Hao Zhang and Ion Stoica},
  booktitle={Proceedings of the ACM SIGOPS 29th Symposium on Operating Systems Principles},
  year={2023}
}

@article{Bellary2014,
  author    = {Bellary, Shantala and Krishnankutty, Binny and Latha, M. S.},
  title     = {Basics of case report form designing in clinical research},
  journal   = {Perspectives in Clinical Research},
  volume    = {5},
  number    = {4},
  pages     = {159--166},
  year      = {2014},
  month     = oct,
  doi       = {10.4103/2229-3485.140555},
  pmid      = {25276625},
  pmc       = {PMC4170533}
}

@article{Rinaldi2025,
  author    = {Rinaldi, Eugenia and Stellmach, Caroline and Thun, Sylvia},
  title     = {How to Design Electronic Case Report Form (eCRF) Questions to Maximize Semantic Interoperability in Clinical Research},
  journal   = {Interactive Journal of Medical Research},
  volume    = {14},
  pages     = {e51598},
  year      = {2025},
  doi       = {10.2196/51598},
  url       = {https://www.i-jmr.org/2025/1/e51598}
}


@article{Petavy2019,
  author    = {Pétavy, Frank and others},
  title     = {Global standardization of clinical research data},
  journal   = {Applied Clinical Trials},
  volume    = {28},
  number    = {4},
  pages     = {20--23},
  year      = {2019},
  url       = {https://www.appliedclinicaltrialsonline.com/view/global-standardization-clinical-research-data}
}

@article{Richesson2011,
  author    = {Richesson, Rachel L. and Nadkarni, Prakash},
  title     = {Data standards for clinical research data collection forms: current status and challenges},
  journal   = {Journal of the American Medical Informatics Association},
  volume    = {18},
  number    = {3},
  pages     = {341--346},
  year      = {2011},
  month     = may,
  doi       = {10.1136/amiajnl-2011-000107},
  pmid      = {21486890},
  pmc       = {PMC3078665}
}

@article{LIN201549,
title = {A multi-technique approach to bridge electronic case report form design and data standard adoption},
journal = {Journal of Biomedical Informatics},
volume = {53},
pages = {49-57},
year = {2015},
issn = {1532-0464},
doi = {https://doi.org/10.1016/j.jbi.2014.08.013},
url = {https://www.sciencedirect.com/science/article/pii/S1532046414001944},
author = {Ching-Heng Lin and Nai-Yuan Wu and Der-Ming Liou},
}

@article{Fleischmann2017,
  author    = {Fleischmann, Robert and Decker, Anne-Marie and Kraft, Antje and Mai, Knut and Schmidt, Sein},
  title     = {Mobile electronic versus paper case report forms in clinical trials: a randomized controlled trial},
  journal   = {BMC Medical Research Methodology},
  volume    = {17},
  number    = {1},
  pages     = {153},
  year      = {2017},
  month     = dec,
  doi       = {10.1186/s12874-017-0429-y},
  url       = {https://doi.org/10.1186/s12874-017-0429-y},
  issn      = {1471-2288}
}


@article{Xu2015clustering,
  author    = {Xu, Dongkuan and Tian, Yingjie},
  title     = {A Comprehensive Survey of Clustering Algorithms},
  journal   = {Annals of Data Science},
  year      = {2015},
  %volume    = {2},
  %number    = {2},
  %pages     = {165--193},
  %month     = jun,
  %doi       = {10.1007/s40745-015-0040-1},
  %url       = {https://doi.org/10.1007/s40745-015-0040-1},
  %issn      = {2198-5812}
}