Clinical trial cohort selection based on multi-level rule-based natural language processing system. - Long Chen; Yu Gu 017; Xin Ji; Chao Lou; Zhiyong Sun; Haodan Li; Yuan Gao; Yang Huang (J. Am. Medical Informatics Assoc., 2019)

Clinical concept normalization with a hybrid natural language processing system combining multilevel matching and machine learning ranking. - Long Chen; Wenbo Fu; Yu Gu 017; Zhiyong Sun; Haodan Li; Enyu Li; Li Jiang; Yuan Gao; Yang Huang (J. Am. Medical Informatics Assoc., 2020)

Extracting medications and associated adverse drug events using a natural language processing system combining knowledge base and deep learning. - Long Chen; Yu Gu 017; Xin Ji; Zhiyong Sun; Haodan Li; Yuan Gao; Yang Huang (J. Am. Medical Informatics Assoc., 2020)

Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing. - Yu Gu 017; Robert Tinn; Hao Cheng 002; Michael Lucas; Naoto Usuyama; Xiaodong Liu 003; Tristan Naumann; Jianfeng Gao 001; Hoifung Poon (ACM Trans. Comput. Heal., 2022)

Interactive Span Recommendation for Biomedical Text. - Louis Blankemeier; Theodore Zhao; Robert Tinn; Sid Kiblawi; Yu Gu 017; Akshay Chaudhari; Hoifung Poon; Sheng Zhang 012; Mu Wei; Joseph Preston (ClinicalNLP@ACL, 2023)

Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology. - Cliff Wong; Sheng Zhang 012; Yu Gu 017; Christine Moung; Jacob Abel; Naoto Usuyama; Roshanthi Weerasinghe; Brian Piening; Tristan Naumann; Carlo Bifulco; Hoifung Poon (MLHC, 2023)

Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events. - Yu Gu 017; Sheng Zhang 012; Naoto Usuyama; Yonas Woldesenbet; Cliff Wong; Praneeth Sanapathi; Mu Wei; Naveen Valluri; Erika Strandberg; Tristan Naumann; Hoifung Poon (CoRR, 2023)

BiomedJourney: Counterfactual Biomedical Image Generation by Instruction-Learning from Multimodal Patient Journeys. - Yu Gu 017; Jianwei Yang; Naoto Usuyama; Chunyuan Li; Sheng Zhang 012; Matthew P. Lungren; Jianfeng Gao 001; Hoifung Poon (CoRR, 2023)

Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision. - Sam Preston; Mu Wei; Rajesh Rao; Robert Tinn; Naoto Usuyama; Michael Lucas; Yu Gu 017; Roshanthi Weerasinghe; Soohee Lee; Brian Piening; Paul Tittel; Naveen Valluri; et al. (Patterns, 2023)

Fine-tuning large neural language models for biomedical natural language processing. - Robert Tinn; Hao Cheng 002; Yu Gu 017; Naoto Usuyama; Xiaodong Liu 003; Tristan Naumann; Jianfeng Gao 001; Hoifung Poon (Patterns, 2023)

UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition. - Wenxuan Zhou; Sheng Zhang 012; Yu Gu 017; Muhao Chen 001; Hoifung Poon (ICLR, 2024)

Foundation Models for Biomedical Image Segmentation: A Survey. - Ho Hin Lee; Yu Gu 017; Theodore Zhao; Yanbo Xu; Jianwei Yang; Naoto Usuyama; Cliff Wong; Mu Wei; Bennett A. Landman; Yuankai Huo; Alberto Santamaría-Pang; Hoifung Poon (CoRR, 2024)

Training Small Multimodal Models to Bridge Biomedical Competency Gap: A Case Study in Radiology Imaging. - Juan Manuel Zambrano Chaves; Shih-Cheng Huang; Yanbo Xu; Hanwen Xu; Naoto Usuyama; Sheng Zhang 012; Fei Wang 060; Yujia Xie; Mahmoud Khademi; Ziyi Yang; Hany Hassan Awadalla; Julia Gong; et al. (CoRR, 2024)

BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once. - Theodore Zhao; Yu Gu 017; Jianwei Yang; Naoto Usuyama; Ho Hin Lee; Tristan Naumann; Jianfeng Gao 001; Angela Crabtree; Jacob Abel; Christine Moung; Brian Piening; Carlo Bifulco; et al. (CoRR, 2024)

Magma: A Foundation Model for Multimodal AI Agents. - Jianwei Yang; Reuben Tan; Qianhui Wu; Ruijie Zheng; Baolin Peng; Yongyuan Liang; Yu Gu 017; Mu Cai; Seonghyeon Ye; Joel Jang; Yuquan Deng; Jianfeng Gao 001 (CVPR, 2025)

Universal Abstraction: Harnessing Frontier Models to Structure Real-World Data at Scale. - Cliff Wong; Sam Preston; Qianchu Liu; Zelalem Gero; Jass Bagga; Sheng Zhang 012; Shrey Jain; Theodore Zhao; Yu Gu 017; Yanbo Xu; Sid Kiblawi; Roshanthi Weerasinghe; et al. (CoRR, 2025)

Magma: A Foundation Model for Multimodal AI Agents. - Jianwei Yang; Reuben Tan; Qianhui Wu; Ruijie Zheng; Baolin Peng; Yongyuan Liang; Yu Gu 017; Mu Cai; Seonghyeon Ye; Joel Jang; Yuquan Deng; Lars Liden; et al. (CoRR, 2025)

X-Reasoner: Towards Generalizable Reasoning Across Modalities and Domains. - Qianchu Liu; Sheng Zhang 012; Guanghui Qin; Timothy Ossowski; Yu Gu 017; Ying Jin; Sid Kiblawi; Sam Preston; Mu Wei; Paul Vozila; Tristan Naumann; Hoifung Poon (CoRR, 2025)