
@article{datta2024autocriteria,
  title="{AutoCriteria}: a generalizable clinical trial eligibility criteria extraction system powered by large language models",
  author={Datta, Surabhi and Lee, Kyeryoung and Paek, Hunki and Manion, Frank J and Ofoegbu, Nneka and Du, Jingcheng and Li, Ying and Huang, Liang-Chin and Wang, Jingqi and Lin, Bin and others},
  journal={Journal of the American Medical Informatics Association},
  volume={31},
  number={2},
  pages={375--385},
  year={2024},
  issn = {1527-974X},
  doi = {10.1093/jamia/ocad218},
  url = {https://doi.org/10.1093/jamia/ocad218},
  eprint = {https://academic.oup.com/jamia/article-pdf/31/2/375/56209472/ocad218.pdf},
  publisher={Oxford University Press}
}

@inproceedings{feng2023chard,
    title = "{CHARD}: Clinical Health-Aware Reasoning Across Dimensions for Text Generation Models",
    author = "Feng, Steven Y.  and
      Khetan, Vivek  and
      Sacaleanu, Bogdan  and
      Gershman, Anatole  and
      Hovy, Eduard",
    editor = "Vlachos, Andreas  and
      Augenstein, Isabelle",
    booktitle = "Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics",
    month = may,
    year = "2023",
    address = "Dubrovnik, Croatia",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.eacl-main.24",
    doi = "10.18653/v1/2023.eacl-main.24",
    pages = "313--327",
}

@inproceedings{jullien-etal-2023-nli4ct,
    title = "{NLI}4{CT}: Multi-Evidence Natural Language Inference for Clinical Trial Reports",
    author = "Jullien, Mael  and
      Valentino, Marco  and
      Frost, Hannah  and
      O{'}Regan, Paul  and
      Landers, D{\'o}nal  and
      Freitas, Andre",
    editor = "Bouamor, Houda  and
      Pino, Juan  and
      Bali, Kalika",
    booktitle = "Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing",
    month = dec,
    year = "2023",
    address = "Singapore",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.emnlp-main.1041",
    doi = "10.18653/v1/2023.emnlp-main.1041",
    pages = "16745--16764",
}

@inproceedings{jullien-etal-2024-semeval,
    title = "{S}em{E}val-2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials",
    author = {Jullien, Ma{\"e}l  and
      Valentino, Marco  and
      Freitas, Andr{\'e}},
    booktitle = "Proceedings of the 18th International Workshop on Semantic Evaluation (SemEval-2024)",
    year = "2024",
    publisher = "Association for Computational Linguistics",
}

@inproceedings{jullien-etal-2023-semeval,
    title = "{S}em{E}val-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data",
    author = {Jullien, Ma{\"e}l  and
      Valentino, Marco  and
      Frost, Hannah  and
      O{'}regan, Paul  and
      Landers, Donal  and
      Freitas, Andr{\'e}},
    editor = {Ojha, Atul Kr.  and
      Do{\u{g}}ru{\"o}z, A. Seza  and
      Da San Martino, Giovanni  and
      Tayyar Madabushi, Harish  and
      Kumar, Ritesh  and
      Sartori, Elisa},
    booktitle = "Proceedings of the 17th International Workshop on Semantic Evaluation (SemEval-2023)",
    month = jul,
    year = "2023",
    address = "Toronto, Canada",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.semeval-1.307",
    doi = "10.18653/v1/2023.semeval-1.307",
    pages = "2216--2226",
}

@misc{kim2023solar,
      title="{SOLAR} 10.7{B}: Scaling Large Language Models with Simple yet Effective Depth Up-Scaling", 
      author={Dahyun Kim and Chanjun Park and Sanghoon Kim and Wonsung Lee and Wonho Song and Yunsu Kim and Hyeonwoo Kim and Yungi Kim and Hyeonju Lee and Jihoo Kim and Changbae Ahn and Seonghoon Yang and Sukyung Lee and Hyunbyung Park and Gyoungjin Gim and Mikyoung Cha and Hwalsuk Lee and Sunghun Kim},
      year={2023},
      eprint={2312.15166},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

@inproceedings{makhervaks2023clinical,
    title = "Clinical Contradiction Detection",
    author = "Makhervaks, Dave  and
      Gillis, Plia  and
      Radinsky, Kira",
    editor = "Bouamor, Houda  and
      Pino, Juan  and
      Bali, Kalika",
    booktitle = "Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing",
    month = dec,
    year = "2023",
    address = "Singapore",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.emnlp-main.80",
    doi = "10.18653/v1/2023.emnlp-main.80",
    pages = "1248--1263",
}

@inproceedings{khetan-etal-2022-mimicause,
    title = "{MIMIC}ause: {R}epresentation and automatic extraction of causal relation types from clinical notes",
    author = "Khetan, Vivek  and
      Rizvi, Md Imbesat  and
      Huber, Jessica  and
      Bartusiak, Paige  and
      Sacaleanu, Bogdan  and
      Fano, Andrew",
    editor = "Muresan, Smaranda  and
      Nakov, Preslav  and
      Villavicencio, Aline",
    booktitle = "Findings of the Association for Computational Linguistics: ACL 2022",
    month = may,
    year = "2022",
    address = "Dublin, Ireland",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.findings-acl.63",
    doi = "10.18653/v1/2022.findings-acl.63",
    pages = "764--773",
}

@inproceedings{pal2023med,
    title = "{M}ed-{HALT}: Medical Domain Hallucination Test for Large Language Models",
    author = "Pal, Ankit  and
      Umapathi, Logesh Kumar  and
      Sankarasubbu, Malaikannan",
    editor = "Jiang, Jing  and
      Reitter, David  and
      Deng, Shumin",
    booktitle = "Proceedings of the 27th Conference on Computational Natural Language Learning (CoNLL)",
    month = dec,
    year = "2023",
    address = "Singapore",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.conll-1.21",
    doi = "10.18653/v1/2023.conll-1.21",
    pages = "314--334",
}

@inproceedings{wang-etal-2023-autotrial,
    title = "{A}uto{T}rial: Prompting Language Models for Clinical Trial Design",
    author = "Wang, Zifeng  and
      Xiao, Cao  and
      Sun, Jimeng",
    editor = "Bouamor, Houda  and
      Pino, Juan  and
      Bali, Kalika",
    booktitle = "Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing",
    month = dec,
    year = "2023",
    address = "Singapore",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.emnlp-main.766",
    doi = "10.18653/v1/2023.emnlp-main.766",
    pages = "12461--12472",
}

@article{Tinn2022,
  author = {Gu, Yu and Tinn, Robert and Cheng, Hao and Lucas, Michael and Usuyama, Naoto and Liu, Xiaodong and Naumann, Tristan and Gao, Jianfeng and Poon, Hoifung},
  year = {2022},
  month = {01},
  pages = {1-23},
  title = {Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing},
  volume = {3},
  journal = {ACM Transactions on Computing for Healthcare},
  doi = {10.1145/3458754}
}

@article{yu2023metamath,
  title={{M}eta{M}ath: Bootstrap Your Own Mathematical Questions for Large Language Models},
  author={Yu, Longhui and Jiang, Weisen and Shi, Han and Yu, Jincheng and Liu, Zhengying and Zhang, Yu and Kwok, James T and Li, Zhenguo and Weller, Adrian and Liu, Weiyang},
  journal={arXiv preprint arXiv:2309.12284},
  eprint = {arXiv:2309.12284},
  year={2023}
}

@inproceedings{pahwa2023bphigh,
    title = "{B}p{H}igh at {S}em{E}val-2023 Task 7: Can Fine-tuned Cross-encoders Outperform {GPT}-3.5 in {NLI} Tasks on Clinical Trial Data?",
    author = "Pahwa, Bhavish  and
      Pahwa, Bhavika",
    editor = {Ojha, Atul Kr.  and
      Do{\u{g}}ru{\"o}z, A. Seza  and
      Da San Martino, Giovanni  and
      Tayyar Madabushi, Harish  and
      Kumar, Ritesh  and
      Sartori, Elisa},
    booktitle = "Proceedings of the 17th International Workshop on Semantic Evaluation (SemEval-2023)",
    month = jul,
    year = "2023",
    address = "Toronto, Canada",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.semeval-1.266",
    doi = "10.18653/v1/2023.semeval-1.266",
    pages = "1936--1944",
}

@inproceedings{deka2022evidence,
  title={Evidence Extraction to Validate Medical Claims in Fake News Detection},
  author={Deka, Pritam and Jurek-Loughrey, Anna and P, Deepak},
  booktitle={International Conference on Health Information Science},
  pages={3--15},
  year={2022},
  url = {https://doi.org/10.1007/978-3-031-20627-6_1},
  doi = {10.1007/978-3-031-20627-6_1},
  organization={Springer}
}

@misc{phan2021scifive,
      title={{S}ci{F}ive: a text-to-text transformer model for biomedical literature}, 
      author={Long N. Phan and James T. Anibal and Hieu Tran and Shaurya Chanana and Erol Bahadroglu and Alec Peltekian and Grégoire Altan-Bonnet},
      year={2021},
      eprint={2106.03598},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

@inproceedings{romanov2018lessons,
    title = {Lessons from Natural Language Inference in the Clinical Domain},
    author = "Romanov, Alexey  and
      Shivade, Chaitanya",
    editor = "Riloff, Ellen  and
      Chiang, David  and
      Hockenmaier, Julia  and
      Tsujii, Jun{'}ichi",
    booktitle = "Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing",
    month = oct # "-" # nov,
    year = "2018",
    address = "Brussels, Belgium",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/D18-1187",
    doi = "10.18653/v1/D18-1187",
    pages = "1586--1596",
}

@article{touvron2023llama,
  title={Llama 2: Open foundation and fine-tuned chat models},
  author={Touvron, Hugo and Martin, Louis and Stone, Kevin and Albert, Peter and Almahairi, Amjad and Babaei, Yasmine and Bashlykov, Nikolay and Batra, Soumya and Bhargava, Prajjwal and Bhosale, Shruti and others},
  journal={arXiv preprint arXiv:2307.09288},
  eprint = {arXiv:2307.09288},
  year={2023}
}

@article{jiang2023mistral,
  title={Mistral 7{B}},
  author={Jiang, Albert Q and Sablayrolles, Alexandre and Mensch, Arthur and Bamford, Chris and Chaplot, Devendra Singh and Casas, Diego de las and Bressand, Florian and Lengyel, Gianna and Lample, Guillaume and Saulnier, Lucile and others},
  journal={arXiv preprint arXiv:2310.06825},
  Eprint = {arXiv:2310.06825},
  year={2023}
}

@article{jahan2023comprehensive,
  title={A comprehensive evaluation of large language models on benchmark biomedical text processing tasks},
  author={Jahan, Israt and Laskar, Md Tahmid Rahman and Peng, Chun and Huang, Jimmy},
  journal={arXiv preprint arXiv:2310.04270},
  Eprint = {arXiv:2310.04270},
  year={2023}
}

@article{kiritchenko2010exact,
  title={{ExaCT}: automatic extraction of clinical trial characteristics from journal publications},
  author={Kiritchenko, Svetlana and De Bruijn, Berry and Carini, Simona and Martin, Joel and Sim, Ida},
  journal={BMC medical informatics and decision making},
  volume={10},
  pages={1--17},
  year={2010},
  url = "https://doi.org/10.1186/1472-6947-10-56",
  doi = "10.1186/1472-6947-10-56",
  publisher={Springer}
}

@book{friedman2015fundamentals,
  title={Fundamentals of clinical trials},
  author={Friedman, Lawrence M and Furberg, Curt D and DeMets, David L and Reboussin, David M and Granger, Christopher B},
  year={2015},
  url = "https://doi.org/10.1007/978-3-319-18539-2",
  doi = "10.1007/978-3-319-18539-2",
  publisher={Springer}
}

@article{gu2021domain,
  title={Domain-specific language model pretraining for biomedical natural language processing},
  author={Gu, Yu and Tinn, Robert and Cheng, Hao and Lucas, Michael and Usuyama, Naoto and Liu, Xiaodong and Naumann, Tristan and Gao, Jianfeng and Poon, Hoifung},
  journal={ACM Transactions on Computing for Healthcare (HEALTH)},
  volume={3},
  number={1},
  pages={1--23},
  year={2021},
  url = "https://doi.org/10.1145/3458754",
  doi = "10.1145/3458754",
  publisher={ACM New York, NY}
}

@inproceedings{conneau2020unsupervised,
    title = "Unsupervised Cross-lingual Representation Learning at Scale",
    author = "Conneau, Alexis  and
      Khandelwal, Kartikay  and
      Goyal, Naman  and
      Chaudhary, Vishrav  and
      Wenzek, Guillaume  and
      Guzm{\'a}n, Francisco  and
      Grave, {\'E}douard  and
      Ott, Myle  and
      Zettlemoyer, Luke  and
      Stoyanov, Veselin",
    editor = "Jurafsky, Dan  and
      Chai, Joyce  and
      Schluter, Natalie  and
      Tetreault, Joel",
    booktitle = "Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics",
    month = jul,
    year = "2020",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2020.acl-main.747",
    doi = "10.18653/v1/2020.acl-main.747",
    pages = "8440--8451",
}

@inproceedings{
  he2021deberta,
  title={{D}E{BERT}A: DECODING-ENHANCED BERT WITH DISENTANGLED ATTENTION},
  author={Pengcheng He and Xiaodong Liu and Jianfeng Gao and Weizhu Chen},
  booktitle={International Conference on Learning Representations},
  year={2021},
  url={https://openreview.net/forum?id=XPZIaotutsD}
}

@misc{Golkar,
  Author = {Siavash Golkar and Mariel Pettee and Michael Eickenberg and Alberto Bietti and Miles Cranmer and Geraud Krawezik and Francois Lanusse and Michael McCabe and Ruben Ohana and Liam Parker and Bruno Régaldo-Saint Blancard and Tiberiu Tesileanu and Kyunghyun Cho and Shirley Ho},
  Title = {x{V}al: A Continuous Number Encoding for Large Language Models},
  Year = {2023},
  Eprint = {arXiv:2310.02989},
}

@misc{sun2020finetune,
      title={How to Fine-Tune BERT for Text Classification?}, 
      author={Chi Sun and Xipeng Qiu and Yige Xu and Xuanjing Huang},
      year={2020},
      eprint={1905.05583},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}