publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2025

  1. magma.png
    Magma: A Foundation Model for Multimodal AI Agents
    Jianwei Yang, Reuben Tan, Qianhui Wu, and 10 more authors
    2025
  2. QuantRad: Advancing Quantitative Reliability in Radiology Report Generation with Cascaded Decoders
    Ying Jin, Noel C Codella, Yanbo Xu, and 4 more authors
    arXiv preprint arXiv:x, 2025
  3. LLaVA-Rad MIMIC-CXR Annotations
    Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, and 8 more authors
    arXiv preprint arXiv:x, 2025
  4. Universal Abstraction: Harnessing Frontier Models to Structure Real-World Data at Scale
    Cliff Wong, Sam Preston, Qianchu Liu, and 8 more authors
    arXiv preprint arXiv:2502.00943, 2025

2024

  1. universalner.svg
    Universalner: Targeted distillation from large language models for open named entity recognition
    Wenxuan Zhou, Sheng Zhang, Yu Gu, and 2 more authors
    In ICLR, 2024
  2. biomedjourney.png
    Biomedjourney: Counterfactual biomedical image generation by instruction-learning from multimodal patient journeys
    Yu Gu, Jianwei Yang, Naoto Usuyama, and 5 more authors
    arXiv preprint arXiv:2310.10765, 2024
  3. Foundation Models for Biomedical Image Segmentation: A Survey
    Ho Hin* Lee, Yu* Gu, Theodore Zhao, and 8 more authors
    arXiv preprint arXiv:2401.07654, 2024
  4. Training small multimodal models to bridge biomedical competency gap: A case study in radiology imaging
    Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, and 8 more authors
    CoRR, 2024
  5. BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once
    Theodore Zhao, Yu Gu, Jianwei Yang, and 8 more authors
    arXiv preprint arXiv:2405.12971, 2024
  6. gigapath.webp
    A whole-slide foundation model for digital pathology from real-world data
    Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, and 8 more authors
    Nature, 2024
  7. Medimageinsight: An open-source embedding model for general domain medical imaging
    Noel CF Codella, Ying Jin, Shrey Jain, and 8 more authors
    arXiv preprint arXiv:2410.06542, 2024
  8. biomedparse.png
    A foundation model for joint segmentation, detection and recognition of biomedical objects across nine modalities
    Theodore* Zhao, Yu* Gu, Jianwei Yang, and 8 more authors
    Nature methods, 2024

2023

  1. Fine-tuning large neural language models for biomedical natural language processing
    Robert Tinn, Hao Cheng, Yu Gu, and 5 more authors
    Cell Press Patterns, 2023
  2. Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
    Sam Preston, Mu Wei, Rajesh Rao, and 8 more authors
    Patterns, 2023
  3. Distilling large language models for biomedical knowledge extraction: A case study on adverse drug events
    Yu Gu, Sheng Zhang, Naoto Usuyama, and 8 more authors
    arXiv preprint arXiv:2307.06439, 2023
  4. Interactive Span Recommendation for Biomedical Text
    Louis Blankemeier, Theodore Zhao, Robert Tinn, and 7 more authors
    In ACL - Proceedings of the 5th Clinical Natural Language Processing Workshop, 2023
  5. Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision
    Sam Preston, Mu Wei, Rajesh Rao, and 8 more authors
    Cell Press Patterns, 2023
  6. Scaling clinical trial matching using large language models: a case study in oncology
    Cliff Wong, Sheng Zhang, Yu Gu, and 8 more authors
    In Machine Learning for Healthcare Conference, 2023
  7. Kola: Carefully benchmarking world knowledge of large language models
    Jifan Yu, Xiaozhi Wang, Shangqing Tu, and 8 more authors
    arXiv preprint arXiv:2306.09296, 2023

2022

  1. pubmedbert.png
    Domain-specific language model pretraining for biomedical natural language processing
    Yu Gu, Robert Tinn, Hao Cheng, and 6 more authors
    ACM, 2022
    Awarded

2021

  1. Domain-specific language model pretraining for biomedical natural language processing
    Yu Gu, Robert Tinn, Hao Cheng, and 6 more authors
    ACM Transactions on Computing for Healthcare (HEALTH), 2021

2020

  1. Extracting medications and associated adverse drug events using a natural language processing system combining knowledge base and deep learning
    Long Chen*, Yu Gu*, Xin Ji, and 4 more authors
    Journal of the American Medical Informatics Association, 2020
  2. Clinical concept normalization with a hybrid natural language processing system combining multilevel matching and machine learning ranking
    Long Chen, Wenbo Fu, Yu Gu, and 6 more authors
    Journal of the American Medical Informatics Association, 2020
  3. Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing 2020
    Y Gu, R Tinn, H Cheng, and 6 more authors
    arXiv preprint arXiv:2007.15779, 2020
  4. Domain-specific language model pretraining for biomedical natural language processing. arXiv
    Yu Gu, Robert Tinn, Hao Cheng, and 6 more authors
    preprint, 2020

2019

  1. Clinical trial cohort selection based on multi-level rule-based natural language processing system
    Long Chen*, Yu Gu*, Xin Ji, and 5 more authors
    Journal of the American Medical Informatics Association, 2019

2017

  1. Symptom severity classification with gradient tree boosting
    Yang Liu, Yu Gu, John Chu Nguyen, and 4 more authors
    Journal of biomedical informatics, 2017