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2020 – today
- 2024
- [j151]Rezarta Islamaj, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Melo Almeida, Richard A. A. Jonker, Sofia I R. Conceição, Diana F. Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee, Yi-Yu Hsu, Mingjie Li, Karin Verspoor, Zhiyong Lu:
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database J. Biol. Databases Curation 2024 (2024) - [j150]Rezarta Islamaj, Chih-Hsuan Wei, Po-Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar, Nicholas Miliaras, Oleg Rodionov, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Zhiyong Lu:
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. Database J. Biol. Databases Curation 2024 (2024) - [j149]Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. Bioinform. 40(2) (2024) - [j148]Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers:
Universal detection and segmentation of lymph nodes in multi-parametric MRI. Int. J. Comput. Assist. Radiol. Surg. 19(1): 163-170 (2024) - [j147]Tejas Sudharshan Mathai, Thomas C. Shen, Daniel C. Elton, Sungwon Lee, Zhiyong Lu, Ronald M. Summers:
Detection of abdominopelvic lymph nodes in multi-parametric MRI. Comput. Medical Imaging Graph. 114: 102363 (2024) - [j146]Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian:
Large language models in biomedicine and health: current research landscape and future directions. J. Am. Medical Informatics Assoc. 31(9): 1801-1811 (2024) - [j145]Yan Hu, Qingyu Chen, Jingcheng Du, Xueqing Peng, Vipina Kuttichi Keloth, Xu Zuo, Yujia Zhou, Zehan Li, Xiaoqian Jiang, Zhiyong Lu, Kirk Roberts, Hua Xu:
Improving large language models for clinical named entity recognition via prompt engineering. J. Am. Medical Informatics Assoc. 31(9): 1812-1820 (2024) - [j144]Gongbo Zhang, Qiao Jin, Denis Jered McInerney, Yong Chen, Fei Wang, Curtis L. Cole, Qian Yang, Yanshan Wang, Bradley A. Malin, Mor Peleg, Byron C. Wallace, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. J. Biomed. Informatics 153: 104640 (2024) - [j143]Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu:
A survey of recent methods for addressing AI fairness and bias in biomedicine. J. Biomed. Informatics 154: 104646 (2024) - [j142]Gregory Holste, Yiliang Zhou, Song Wang, Ajay Jaiswal, Mingquan Lin, Sherry Zhuge, Yuzhe Yang, Dongkyun Kim, Trong-Hieu Nguyen Mau, Minh-Triet Tran, Jaehyup Jeong, Wongi Park, Jongbin Ryu, Feng Hong, Arsh Verma, Yosuke Yamagishi, Changhyun Kim, Hyeryeong Seo, Myungjoo Kang, Leo Anthony Celi, Zhiyong Lu, Ronald M. Summers, George Shih, Zhangyang Wang, Yifan Peng:
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. Medical Image Anal. 97: 103224 (2024) - [j141]Gregory Holste, Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah Van Tassel, Kyle Kovacs, Emily Y. Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng:
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. npj Digit. Medicine 7(1) (2024) - [j140]Gregory Holste, Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah Van Tassel, Kyle Kovacs, Emily Y. Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng:
Author Correction: Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. npj Digit. Medicine 7(1) (2024) - [j139]Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M. Cheung, Robert Chen, Ronald M. Summers, Justin F. Rousseau, Peiyun Ni, Marc J. Landsman, Sally L. Baxter, Subhi J. Al'Aref, Yijia Li, Alexander Chen, Josef A. Brejt, Michael F. Chiang, Yifan Peng, Zhiyong Lu:
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. npj Digit. Medicine 7(1) (2024) - [j138]Gongbo Zhang, Qiao Jin, Yiliang Zhou, Song Wang, Betina Idnay, Yiming Luo, Elizabeth Park, Jordan G. Nestor, Matthew E. Spotnitz, Ali Soroush, Thomas Campion, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Closing the gap between open source and commercial large language models for medical evidence summarization. npj Digit. Medicine 7(1) (2024) - [c102]Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang:
Benchmarking Retrieval-Augmented Generation for Medicine. ACL (Findings) 2024: 6233-6251 - [c101]Qingqing Zhu, Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xin Gao, Ronald M. Summers, Zhiyong Lu:
Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for AI-generated Radiology Reports. ICHI 2024: 402-411 - [i88]Qiao Jin, Fangyuan Chen, Yiliang Zhou, Ziyang Xu, Justin M. Cheung, Robert Chen, Ronald M. Summers, Justin F. Rousseau, Peiyun Ni, Marc J. Landsman, Sally L. Baxter, Subhi J. Al'Aref, Yijia Li, Michael F. Chiang, Yifan Peng, Zhiyong Lu:
Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine. CoRR abs/2401.08396 (2024) - [i87]Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu:
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. CoRR abs/2401.11048 (2024) - [i86]Yifan Yang, Xiaoyu Liu, Qiao Jin, Furong Huang, Zhiyong Lu:
Unmasking and Quantifying Racial Bias of Large Language Models in Medical Report Generation. CoRR abs/2401.13867 (2024) - [i85]Qingqing Zhu, Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xin Gao, Ronald M. Summers, Zhiyong Lu:
Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports. CoRR abs/2401.16578 (2024) - [i84]Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Y. Garcia Arguello, Patrick Murray, Zhiyong Lu:
Quality of Answers of Generative Large Language Models vs Peer Patients for Interpreting Lab Test Results for Lay Patients: Evaluation Study. CoRR abs/2402.01693 (2024) - [i83]Ashley Shin, Qiao Jin, James Anibal, Zhiyong Lu:
Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles. CoRR abs/2402.03484 (2024) - [i82]Xiangru Tang, Qiao Jin, Kunlun Zhu, Tongxin Yuan, Yichi Zhang, Wangchunshu Zhou, Meng Qu, Yilun Zhao, Jian Tang, Zhuosheng Zhang, Arman Cohan, Zhiyong Lu, Mark Gerstein:
Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science. CoRR abs/2402.04247 (2024) - [i81]Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu:
A survey of recent methods for addressing AI fairness and bias in biomedicine. CoRR abs/2402.08250 (2024) - [i80]Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang:
Benchmarking Retrieval-Augmented Generation for Medicine. CoRR abs/2402.13178 (2024) - [i79]Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu:
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning. CoRR abs/2402.13225 (2024) - [i78]Xiuying Chen, Tairan Wang, Qingqing Zhu, Taicheng Guo, Shen Gao, Zhiyong Lu, Xin Gao, Xiangliang Zhang:
Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark. CoRR abs/2402.14359 (2024) - [i77]Qingqing Zhu, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Qiao Jin, Xiuying Chen, Zhizheng Wang, Ruida Cheng, Ronald M. Summers, Zhiyong Lu:
Decomposing Vision-based LLM Predictions for Auto-Evaluation with GPT-4. CoRR abs/2403.05680 (2024) - [i76]Po-Ting Lai, Elisabeth Coudert, Lucila Aimo, Kristian B. Axelsen, Lionel Breuza, Edouard De Castro, Marc Feuermann, Anne Morgat, Lucille Pourcel, Ivo Pedruzzi, Sylvain Poux, Nicole Redaschi, Catherine Rivoire, Anastasia Sveshnikova, Chih-Hsuan Wei, Robert Leaman, Ling Luo, Zhiyong Lu, Alan J. Bridge:
EnzChemRED, a rich enzyme chemistry relation extraction dataset. CoRR abs/2404.14209 (2024) - [i75]Gregory Holste, Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah Van Tassel, Kyle Kovacs, Emily Y. Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng:
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling. CoRR abs/2405.08780 (2024) - [i74]Zhizheng Wang, Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po-Ting Lai, Qingqing Zhu, Chi-Ping Day, Christina Ross, Zhiyong Lu:
GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases. CoRR abs/2405.16205 (2024) - [i73]Benjamin Hou, Qingqing Zhu, Tejas Sudarshan Mathai, Qiao Jin, Zhiyong Lu, Ronald M. Summers:
Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification. CoRR abs/2406.03688 (2024) - [i72]Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen:
Augmenting Biomedical Named Entity Recognition with General-domain Resources. CoRR abs/2406.10671 (2024) - [i71]Nikhil Khandekar, Qiao Jin, Guangzhi Xiong, Soren Dunn, Serina S. Applebaum, Zain Anwar, Maame Sarfo-Gyamfi, Conrad W. Safranek, Abid A Anwar, Andrew Zhang, Aidan Gilson, Maxwell B. Singer, Amisha D. Dave, Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu:
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations. CoRR abs/2406.12036 (2024) - [i70]Yifan Yang, Qiao Jin, Furong Huang, Zhiyong Lu:
Adversarial Attacks on Large Language Models in Medicine. CoRR abs/2406.12259 (2024) - [i69]Zifeng Wang, Lang Cao, Benjamin P. Danek, Yichi Zhang, Qiao Jin, Zhiyong Lu, Jimeng Sun:
Accelerating Clinical Evidence Synthesis with Large Language Models. CoRR abs/2406.17755 (2024) - [i68]Gongbo Zhang, Qiao Jin, Yiliang Zhou, Song Wang, Betina Ross S. Idnay, Yiming Luo, Elizabeth Park, Jordan G. Nestor, Matthew E. Spotnitz, Ali Soroush, Thomas Campion, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Closing the gap between open-source and commercial large language models for medical evidence summarization. CoRR abs/2408.00588 (2024) - [i67]Guangzhi Xiong, Qiao Jin, Xiao Wang, Minjia Zhang, Zhiyong Lu, Aidong Zhang:
Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions. CoRR abs/2408.00727 (2024) - [i66]Aidan Gilson, Xuguang Ai, Thilaka Arunachalam, Ziyou Chen, Ki Xiong Cheong, Amisha D. Dave, Cameron Duic, Mercy Kibe, Annette Kaminaka, Minali Prasad, Fares Siddig, Maxwell B. Singer, Wendy Wong, Qiao Jin, Tiarnan D. L. Keenan, Xia Hu, Emily Y. Chew, Zhiyong Lu, Hua Xu, Ron A. Adelman, Yih-Chung Tham, Qingyu Chen:
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology. CoRR abs/2409.13902 (2024) - [i65]Qingyu Chen, Tiarnan D. L. Keenan, Elvira Agrón, Alexis Allot, Emily Guan, Bryant Duong, Amr S. Elsawy, Benjamin Hou, Cancan Xue, Sanjeeb Bhandari, Geoff Broadhead, Chantal Cousineau-Krieger, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Luis Haddock, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Dimosthenis Mantopoulos, Mitul C. Mehta, Ayman G. Nahri, Mutaz AL-Nawaflh, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Stiefel, Alisa T. Thavikulwat, Keith Wroblewski, Tham Yih Chung, Chui Ming Gemmy Cheung, Ching-Yu Cheng, Emily Y. Chew, Michelle R. Hribar, Michael F. Chiang, Zhiyong Lu:
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning. CoRR abs/2409.15087 (2024) - 2023
- [j137]Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E. Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu:
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database J. Biol. Databases Curation 2023 (2023) - [j136]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinform. 39(5) (2023) - [j135]Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. Bioinform. 39(10) (2023) - [j134]Chih-Hsuan Wei, Ling Luo, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu:
GNorm2: an improved gene name recognition and normalization system. Bioinform. 39(10) (2023) - [j133]Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo, Zhiyong Lu, Peter N. Robinson:
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts. Bioinform. 39(12) (2023) - [j132]Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers:
Universal lymph node detection in T2 MRI using neural networks. Int. J. Comput. Assist. Radiol. Surg. 18(2): 313-318 (2023) - [j131]Zhaoyi Sun, Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng:
A scoping review on multimodal deep learning in biomedical images and texts. J. Biomed. Informatics 146: 104482 (2023) - [j130]Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu:
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. J. Biomed. Informatics 146: 104487 (2023) - [j129]Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Catherine M. Farrell, Michael Feldgarden, Anna M. Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Adriana J. Malheiro, Aron Marchler-Bauer, Terence D. Murphy, Lon Phan, Shashikant Pujar, Sanjida H. Rangwala, Valerie A. Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 51(D1): 29-38 (2023) - [j128]Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
LitCovid in 2022: an information resource for the COVID-19 literature. Nucleic Acids Res. 51(D1): 1512-1518 (2023) - [j127]Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4(1): 100659 (2023) - [j126]Xingsheng Liu, Anhu Li, Jianfeng Sun, Zhiyong Lu:
Trigonometric projection statistics histograms for 3D local feature representation and shape description. Pattern Recognit. 143: 109727 (2023) - [c100]Ashley Shin, Qiao Jin, Zhiyong Lu:
Multi-stage Literature Retrieval System Trained by PubMed Search Logs for Biomedical Question Answering. CLEF (Working Notes) 2023: 178-189 - [c99]Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers:
Universal lymph node detection in multiparametric MRI with selective augmentation. Medical Imaging: Computer-Aided Diagnosis 2023 - [c98]Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu:
Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports. MICCAI (5) 2023: 189-198 - [c97]Amr S. Elsawy, Tiarnan D. Kenan, Qingyu Chen, Xiaoshuang Shi, Emily Y. Chew, Zhiyong Lu:
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans. Medical Imaging: Image Processing 2023 - [c96]Qiao Jin, Andrew Shin, Zhiyong Lu:
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. SIGIR 2023: 2092-2097 - [i64]Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang:
Bioformer: an efficient transformer language model for biomedical text mining. CoRR abs/2302.01588 (2023) - [i63]Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu:
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning. CoRR abs/2302.09636 (2023) - [i62]Qiao Jin, Andrew Shin, Zhiyong Lu:
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. CoRR abs/2304.04590 (2023) - [i61]Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information. CoRR abs/2304.09667 (2023) - [i60]Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu:
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. CoRR abs/2305.16326 (2023) - [i59]Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu:
Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports. CoRR abs/2306.08749 (2023) - [i58]Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C. Comeau, Rezarta Islamaj, Aadit Kapoor, Xin Gao, Zhiyong Lu:
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health. CoRR abs/2306.10070 (2023) - [i57]Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu:
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets. CoRR abs/2306.11189 (2023) - [i56]Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval. CoRR abs/2307.00589 (2023) - [i55]Zhaoyi Sun, Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng:
A scoping review on multimodal deep learning in biomedical images and texts. CoRR abs/2307.07362 (2023) - [i54]Qiao Jin, Robert Leaman, Zhiyong Lu:
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. CoRR abs/2307.09683 (2023) - [i53]Qiao Jin, Zifeng Wang, Charalampos S. Floudas, Jimeng Sun, Zhiyong Lu:
Matching Patients to Clinical Trials with Large Language Models. CoRR abs/2307.15051 (2023) - [i52]Gregory Holste, Yiliang Zhou, Song Wang, Ajay Jaiswal, Mingquan Lin, Sherry Zhuge, Yuzhe Yang, Dongkyun Kim, Trong-Hieu Nguyen Mau, Minh-Triet Tran, Jaehyup Jeong, Wongi Park, Jongbin Ryu, Feng Hong, Arsh Verma, Yosuke Yamagishi, Changhyun Kim, Hyeryeong Seo, Myungjoo Kang, Leo Anthony Celi, Zhiyong Lu, Ronald M. Summers, George Shih, Zhangyang Wang, Yifan Peng:
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge. CoRR abs/2310.16112 (2023) - [i51]Gongbo Zhang, Qiao Jin, Denis Jered McInerney, Yong Chen, Fei Wang, Curtis L. Cole, Qian Yang, Yanshan Wang, Bradley A. Malin, Mor Peleg, Byron C. Wallace, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness. CoRR abs/2311.11211 (2023) - [i50]Rui Yang, Qingcheng Zeng, Keen You, Yujie Qiao, Lucas Huang, Chiachun Hsieh, Benjamin Rosand, Jeremy Goldwasser, Amisha D. Dave, Tiarnan D. L. Keenan, Emily Y. Chew, Dragomir Radev, Zhiyong Lu, Hua Xu, Qingyu Chen, Irene Li:
MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing. CoRR abs/2311.16588 (2023) - 2022
- [j125]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: a rich biomedical relation extraction dataset. Briefings Bioinform. 23(5) (2022) - [j124]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu:
Assigning species information to corresponding genes by a sequence labeling framework. Database J. Biol. Databases Curation 2022(2022) (2022) - [j123]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database J. Biol. Databases Curation 2022(2022) (2022) - [j122]Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j121]Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu:
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. Database J. Biol. Databases Curation 2022(2022) (2022) - [j120]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu:
A sequence labeling framework for extracting drug-protein relations from biomedical literature. Database J. Biol. Databases Curation 2022(2022) (2022) - [j119]Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. Bioinform. 38(18): 4449-4451 (2022) - [j118]Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J. Biomed. Informatics 129: 104059 (2022) - [j117]Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Towards a unified search: Improving PubMed retrieval with full text. J. Biomed. Informatics 134: 104211 (2022) - [j116]Shuai Wang, Yingying Zhu, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Youbao Tang, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images. Medical Image Anal. 77: 102345 (2022) - [j115]Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Ryan Connor, Kathryn Funk, Chris Kelly, Sunghwan Kim, Tom Madej, Aron Marchler-Bauer, Christopher J. Lanczycki, Stacy Lathrop, Zhiyong Lu, Françoise Thibaud-Nissen, Terence D. Murphy, Lon Phan, Yuri Skripchenko, Tony Tse, Jiyao Wang, Rebecca Williams, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the national center for biotechnology information. Nucleic Acids Res. 50(D1): 20-26 (2022) - [j114]Andres Diaz-Pinto, Nishant Ravikumar, Rahman Attar, Avan Suinesiaputra, Yitian Zhao, Eylem Levelt, Erica Dall' Armellina, Marco Lorenzi, Qingyu Chen, Tiarnan D. L. Keenan, Elvira Agrón, Emily Y. Chew, Zhiyong Lu, Chris P. Gale, Richard P. Gale, Sven Plein, Alejandro F. Frangi:
Predicting myocardial infarction through retinal scans and minimal personal information. Nat. Mach. Intell. 4(1): 55-61 (2022) - [j113]Xiaoshuang Shi, Yifan Peng, Qingyu Chen, Tiarnan D. Keenan, Alisa T. Thavikulwat, Sungwon Lee, Yuxing Tang, Emily Y. Chew, Ronald M. Summers, Zhiyong Lu:
Robust convolutional neural networks against adversarial attacks on medical images. Pattern Recognit. 132: 108923 (2022) - [j112]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2584-2595 (2022) - [c95]Qingyu Chen, Tiarnan D. Keenan, Alexis Allot, Sanjeeb Bhandari, Geoff Broadhead, Chantal Cousineau-Krieger, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Steifel, Alisa T. Thavikulwat, Keith Wroblewski, Sirisha Koirala, Tom Murickan, Michael F. Chiang, Michelle R. Hribar, Emily Y. Chew, Zhiyong Lu:
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows. AMIA 2022 - [c94]Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu:
Deep learning automated diagnosis and quantitative classification of cataract type and severity: quantifying the effectiveness and usability of deep learning-assisted disease diagnosis models with 14 ophthalmologists and multi-center validations. AMIA 2022 - [c93]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. AMIA 2022 - [c92]Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu:
PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA 2022 - [c91]Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng:
Radiology Text Analysis System (RadText): Architecture and Evaluation. ICHI 2022: 288-296 - [c90]Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Lymph node detection in T2 MRI with transformers. Medical Imaging: Computer-Aided Diagnosis 2022 - [c89]Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng:
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning. MLMI@MICCAI 2022: 11-20 - [i49]Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu:
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis. CoRR abs/2201.07317 (2022) - [i48]