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2020 – today
- 2024
[j152]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)- [j151]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) - [j150]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) - [j149]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) - [j148]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) - [j147]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) - [j146]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) - [j145]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) - [j144]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) - [j143]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. J. Biomed. Informatics 159: 104731 (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 - [i91]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) - [i90]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) - [i89]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) - [i88]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) - [i87]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) - [i86]Ashley Shin, Qiao Jin, James T. Anibal, Zhiyong Lu:
Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles. CoRR abs/2402.03484 (2024) - [i85]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) - [i84]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) - [i83]Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang:
Benchmarking Retrieval-Augmented Generation for Medicine. CoRR abs/2402.13178 (2024) - [i82]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) - [i81]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) - [i80]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) - [i79]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) - [i78]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) - [i77]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) - [i76]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) - [i75]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) - [i74]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) - [i73]Yifan Yang, Qiao Jin, Furong Huang, Zhiyong Lu:
Adversarial Attacks on Large Language Models in Medicine. CoRR abs/2406.12259 (2024) - [i72]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) - [i71]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) - [i70]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) - [i69]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) - [i68]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) - [i67]Betina Idnay, Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos, Douglas S. Bell, Cody Bumgardner, Thomas R. Campion Jr., Victor M. Castro, James J. Cimino, I. Glenn Cohen, David A. Dorr, Peter L. Elkin, Jungwei W. Fan, Todd Ferris, David J. Foran, David A. Hanauer, Mike Hogarth, Kun Huang, Jayashree Kalpathy-Cramer, Manoj Kandpal, Niranjan S. Karnik, Avnish Katoch, Albert M. Lai, Christophe G. Lambert, Lang Li, Christopher Lindsell, Jinze Liu, Zhiyong Lu, Yuan Luo, Peter McGarvey, Eneida A. Mendonça, Parsa Mirhaji, Shawn N. Murphy, John D. Osborne, Ioannis Ch. Paschalidis, Paul A. Harris, Fred W. Prior, Nicholas J. Shaheen, Nawar Shara, Ida Sim, Umberto Tachinardi, Lemuel R. Waitman, Rosalind J. Wright, Adrian H. Zai, Kai Zheng, Sandra Soo-Jin Lee, Bradley A. Malin, Karthik Natarajan, W. Nicholson Price, Rui Zhang, Yiye Zhang, Hua Xu, Jiang Bian, Chunhua Weng, Yifan Peng:
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. CoRR abs/2410.12793 (2024) - [i66]Yifan Yang, Qiao Jin, Qingqing Zhu, Zhizheng Wang, Francisco Erramuspe Álvarez, Nicholas Wan, Benjamin Hou, Zhiyong Lu:
Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing Large Language Models in Healthcare. CoRR abs/2410.18460 (2024) - [i65]Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M. Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu:
Demystifying Large Language Models for Medicine: A Primer. CoRR abs/2410.18856 (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. 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. 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. 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]Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers:
Universal Lymph Node Detection in T2 MRI using Neural Networks. CoRR abs/2204.00622 (2022) - [i47]Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. CoRR abs/2204.03637 (2022) - [i46]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. CoRR abs/2204.04263 (2022) - [i45]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. CoRR abs/2204.08649 (2022) - [i44]Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng:
Radiology Text Analysis System (RadText): Architecture and Evaluation. CoRR abs/2204.09599 (2022) - [i43]Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, 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, 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, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. CoRR abs/2204.09781 (2022) - [i42]Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu:
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework. CoRR abs/2205.03853 (2022) - [i41]Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR abs/2209.08124 (2022) - [i40]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. CoRR abs/2209.13428 (2022) - [i39]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. CoRR abs/2211.16944 (2022) - 2021
- [j111]Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu:
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. Briefings Bioinform. 22(3) (2021) - [j110]Sendong Zhao, Chang Su, Zhiyong Lu, Fei Wang:
Recent advances in biomedical literature mining. Briefings Bioinform. 22(3) (2021) - [j109]Po-Ting Lai, Zhiyong Lu:
BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer. Bioinform. 36(24): 5678-5685 (2021) - [j108]Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. Bioinform. 37(13): 1884-1890 (2021) - [j107]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration. J. Am. Medical Informatics Assoc. 28(6): 1135-1148 (2021) - [j106]Rezarta Islamaj Dogan, Chih-Hsuan Wei, David Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov, Keiko Sekiya, Janice Ward, Zhiyong Lu:
NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J. Biomed. Informatics 118: 103779 (2021) - [j105]Eric W. Sayers, Jeffrey Beck, Evan Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Nuala A. O'Leary, Lon Phan, Sanjida H. Rangwala, Valerie A. Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 49(Database-Issue): D10-D17 (2021) - [j104]Qingyu Chen, Alexis Allot, Zhiyong Lu:
LitCovid: an open database of COVID-19 literature. Nucleic Acids Res. 49(Database-Issue): D1534-D1540 (2021) - [j103]Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu:
LitSuggest: a web-based system for literature recommendation and curation using machine learning. Nucleic Acids Res. 49(Webserver-Issue): 352-358 (2021) - [j102]Yifan Peng, Yuxing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu:
COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature. IEEE Trans. Big Data 7(1): 3-12 (2021) - [j101]Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Pingjun Chen, Yun Liang, Zhiyong Lu, Zhenhua Guo:
Loss-Based Attention for Interpreting Image-Level Prediction of Convolutional Neural Networks. IEEE Trans. Image Process. 30: 1662-1675 (2021) - [j100]Angshuman Paul, Thomas C. Shen, Sungwon Lee, Niranjan Balachandar, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training. IEEE Trans. Medical Imaging 40(10): 2642-2655 (2021) - [c88]Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu:
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation. AMIA 2021 - [c87]Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu:
Deep learning detection of reticular pseudodrusen using multi-modal, multi-task, and multi-attention mechanisms: towards automated and accessible classification of age-related macular degeneration. AMIA 2021 - [c86]Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang:
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS. AMIA 2021 - [c85]Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora. AMIA 2021 - [c84]Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu:
NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature. AMIA 2021 - [c83]Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu:
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. AMIA 2021 - [c82]Clement J. McDonald, Patricia Flatley Brennan, Michael F. Chiang, Joshua Denny, Zhiyong Lu:
Informatics-izing the National Institutes of Health. AMIA 2021 - [c81]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Improving PubMed Retrieval by Integrating Abstract and Full Text Search. AMIA 2021 - [c80]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Measuring the relative importance of full text sections for information retrieval from scientific literature. BioNLP@NAACL-HLT 2021: 247-256 - [c79]Wenbin Zou, Mingchao Jiang, Yunchen Zhang, Liang Chen, Zhiyong Lu, Yi Wu:
SDWNet: A Straight Dilated Network with Wavelet Transformation for image Deblurring. ICCVW 2021: 1895-1904 - [c78]Cong Wei, Zhiyong Lu, Zhiyong Lin, Chong Zhong:
Research on Deep Neural Network Model Compression Based on Quantification Pruning and Huffmann Encoding. ICIC (2) 2021: 522-531 - [c77]Angshuman Paul, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Learning Few-Shot Chest X-Ray Diagnosis Using Images From The Published Scientific Literature. ISBI 2021: 344-348 - [c76]Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers:
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI. MLMI@MICCAI 2021: 101-109 - [c75]Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Detection of Lymph Nodes in T2 MRI Using Neural Network Ensembles. MLMI@MICCAI 2021: 682-691 - [i38]Po-Ting Lai, Zhiyong Lu:
BERT-GT: Cross-sentence n-ary relation extraction with BERT and Graph Transformer. CoRR abs/2101.04158 (2021) - [i37]Wenbin Zou, Mingchao Jiang, Yunchen Zhang, Liang Chen, Zhiyong Lu, Yi Wu:
SDWNet: A Straight Dilated Network with Wavelet Transformation for Image Deblurring. CoRR abs/2110.05803 (2021) - [i36]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. CoRR abs/2111.04885 (2021) - [i35]Tian Ye, Mingchao Jiang, Yunchen Zhang, Liang Chen, ErKang Chen, Pen Chen, Zhiyong Lu:
Perceiving and Modeling Density is All You Need for Image Dehazing. CoRR abs/2111.09733 (2021) - 2020
- [j99]Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
FullMeSH: improving large-scale MeSH indexing with full text. Bioinform. 36(5): 1533-1541 (2020) - [j98]Xiaoqiong Wei, Chengxin Zhang, Peter L. Freddolino, Yang Zhang, Zhiyong Lu:
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinform. 36(16): 4383-4388 (2020) - [j97]Zexuan Sun, Shujun Huang, Peiran Jiang, Pingzhao Hu, Zhiyong Lu:
DTF: Deep Tensor Factorization for predicting anticancer drug synergy. Bioinform. 36(16): 4483-4489 (2020) - [j96]Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu:
Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. 27(12): 1894-1902 (2020) - [j95]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. BMC Medical Informatics Decis. Mak. 20-S(1): 73 (2020) - [j94]Eric W. Sayers, Jeffrey Beck, J. Rodney Brister, Evan Bolton, Kathi Canese, Donald C. Comeau, Kathryn Funk, Anne Ketter, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Anatoliy Kuznetsov, Stacy Lathrop, Zhiyong Lu, Kelly M. McGarvey, Thomas L. Madden, Terence D. Murphy, Nuala A. O'Leary, Lon Phan, Valerie A. Schneider, Françoise Thibaud-Nissen, Barton W. Trawick, Kim D. Pruitt, James Ostell:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 48(Database-Issue): D9-D16 (2020) - [j93]Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: a collaborative text annotation tool. Nucleic Acids Res. 48(Webserver-Issue): W5-W11 (2020) - [j92]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. npj Digit. Medicine 3 (2020) - [j91]Yuxing Tang, Youbao Tang, Yifan Peng, Ke Yan, Mohammadhadi Bagheri, Bernadette A. Redd, Catherine J. Brandon, Zhiyong Lu, Mei Han, Jing Xiao, Ronald M. Summers:
Automated abnormality classification of chest radiographs using deep convolutional neural networks. npj Digit. Medicine 3 (2020) - [j90]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16(4) (2020) - [c74]Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald M. Summers, Zhiyong Lu:
Automatic recognition of abdominal lymph nodes from clinical text. ClinicalNLP@EMNLP 2020: 101-110 - [c73]Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrón, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Detection of reticular pseudodrusen using deep learning. AMIA 2020 - [c72]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. BioNLP 2020: 205-214 - [c71]Robert Leaman, Zhiyong Lu:
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. NLP4COVID@EMNLP 2020 - [c70]Angshuman Paul, Thomas C. Shen, Niranjan Balachandar, Yuxing Tang, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs. iMIMIC/MIL3ID/LABELS@MICCAI 2020: 103-111 - [i34]Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: a collaborative text annotation tool. CoRR abs/2004.11894 (2020) - [i33]Yifan Peng, Qingyu Chen, Zhiyong Lu:
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining. CoRR abs/2005.02799 (2020) - [i32]Yifan Peng, Yuxing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu:
COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from biomedical literature. CoRR abs/2006.06177 (2020) - [i31]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
Predicting risk of late age-related macular degeneration using deep learning. CoRR abs/2007.09550 (2020) - [i30]Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu:
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR abs/2008.03397 (2020) - [i29]Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. CoRR abs/2009.08478 (2020) - [i28]Robert Leaman, Zhiyong Lu:
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. CoRR abs/2010.14588 (2020) - [i27]Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu:
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR abs/2010.16413 (2020) - [i26]Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu:
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration. CoRR abs/2011.05142 (2020)
2010 – 2019
- 2019
- [j89]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j88]Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J. Khoury, Zhiyong Lu:
Using deep learning to identify translational research in genomic medicine beyond bench to bedside. Database J. Biol. Databases Curation 2019: baz010 (2019) - [j87]Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu:
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. Database J. Biol. Databases Curation 2019: baz064 (2019) - [j86]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: about three million full-text articles and growing. Bioinform. 35(18): 3533-3535 (2019) - [j85]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. J. Am. Medical Informatics Assoc. 26(11): 1279-1285 (2019) - [j84]Eric W. Sayers, Richa Agarwala, Evan Bolton, J. Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J. Bradley Holmes, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Aron Marchler-Bauer, Lon Phan, Valerie A. Schneider, Conrad L. Schoch, Kim D. Pruitt, James Ostell:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 47(Database-Issue): D23-D28 (2019) - [j83]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res. 47(Webserver-Issue): W587-W593 (2019) - [j82]Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. 47(Webserver-Issue): W594-W599 (2019) - [c69]Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs. AMIA 2019 - [c68]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. BCB 2019: 307-313 - [c67]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB 2019: 533 - [c66]Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. BCB 2019: 540 - [c65]Yifan Peng, Shankai Yan, Zhiyong Lu:
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. BioNLP@ACL 2019: 58-65 - [c64]Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers:
Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology. CVPR 2019: 8523-8532 - [c63]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. ICHI 2019: 1-5 - [c62]Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu:
A self-attention based deep learning method for lesion attribute detection from CT reports. ICHI 2019: 1-5 - [c61]Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports. ISBI 2019: 285-288 - [c60]Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers:
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. MICCAI (6) 2019: 194-202 - [c59]Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu:
Text Mining and Machine Learning for Precision Medicine. PSB 2019: 449-454 - [p2]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers:
ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on Weakly Supervised Classification and Localization of Common Thorax Diseases. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics 2019: 369-392 - [p1]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers:
Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs. Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics 2019: 393-412 - [i25]Yijia Zhang, Zhiyong Lu:
Exploring Semi-supervised Variational Autoencoders for Biomedical Relation Extraction. CoRR abs/1901.06103 (2019) - [i24]Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers:
Fine-grained lesion annotation in CT images with knowledge mined from radiology reports. CoRR abs/1903.01505 (2019) - [i23]Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers:
Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning from Radiology Reports and Label Ontology. CoRR abs/1904.04661 (2019) - [i22]Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu:
A self-attention based deep learning method for lesion attribute detection from CT reports. CoRR abs/1904.13018 (2019) - [i21]Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew:
A deep learning approach for automated detection of geographic atrophy from color fundus photographs. CoRR abs/1906.03153 (2019) - [i20]Yifan Peng, Shankai Yan, Zhiyong Lu:
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. CoRR abs/1906.05474 (2019) - [i19]Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers:
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation. CoRR abs/1908.04373 (2019) - [i18]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR abs/1909.03044 (2019) - [i17]Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu:
Biomedical Mention Disambiguation using a Deep Learning Approach. CoRR abs/1909.10416 (2019) - [i16]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR abs/1912.10846 (2019) - 2018
- [j81]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
A Field Sensor: computing the composition and intent of PubMed queries. Database J. Biol. Databases Curation 2018: bay052 (2018) - [j80]Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu:
Extracting chemical-protein relations with ensembles of SVM and deep learning models. Database J. Biol. Databases Curation 2018: bay073 (2018) - [j79]Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu:
Assisting document triage for human kinome curation via machine learning. Database J. Biol. Databases Curation 2018: bay091 (2018) - [j78]Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu:
PubMed Labs: an experimental system for improving biomedical literature search. Database J. Biol. Databases Curation 2018: bay094 (2018) - [j77]Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch:
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation 2018: bay104 (2018) - [j76]Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu:
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. Bioinform. 34(1): 80-87 (2018) - [j75]Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu:
Generalizing biomedical relation classification with neural adversarial domain adaptation. Bioinform. 34(17): 2973-2981 (2018) - [j74]Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
ezTag: tagging biomedical concepts via interactive learning. Nucleic Acids Res. 46(Webserver-Issue): W523-W529 (2018) - [j73]Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu:
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Nucleic Acids Res. 46(Webserver-Issue): W530-W536 (2018) - [j72]Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline A. L. MacArthur, Sylvain Poux, Lionel Breuza, Alan J. Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu:
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PLoS Comput. Biol. 14(8) (2018) - [c58]Nicolas Fiorini, Zhiyong Lu:
Online evaluation of PubMed's new relevance search algorithm. AMIA 2018 - [c57]Zhiyong Lu, Nicolas Fiorini:
Experimenting new search and user interface in PubMed Labs. AMIA 2018 - [c56]Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu:
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB 2018: 531-532 - [c55]Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu:
SingleCite: Towards an improved Single Citation Search in PubMed. BioNLP 2018: 151-155 - [c54]Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
MeSH-based dataset for measuring the relevance of text retrieval. BioNLP 2018: 161-165 - [c53]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers:
TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays. CVPR 2018: 9049-9058 - [c52]Nicolas Fiorini, Zhiyong Lu:
Personalized neural language models for real-world query auto completion. NAACL-HLT (3) 2018: 208-215 - [c51]Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu:
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. WWW 2018: 77-86 - [i15]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers:
TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-rays. CoRR abs/1801.04334 (2018) - [i14]Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu:
Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models. CoRR abs/1802.01255 (2018) - [i13]Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu:
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval. CoRR abs/1802.10078 (2018) - [i12]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: 2.3 million full text articles and growing. CoRR abs/1804.05957 (2018) - [i11]Nicolas Fiorini, Zhiyong Lu:
Personalized neural language models for real-world query auto completion. CoRR abs/1804.06439 (2018) - [i10]Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu:
PubMed Labs: An experimental platform for improving biomedical literature search. CoRR abs/1806.04004 (2018) - [i9]Qingyu Chen, Yifan Peng, Zhiyong Lu:
BioSentVec: creating sentence embeddings for biomedical texts. CoRR abs/1810.09302 (2018) - [i8]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. CoRR abs/1811.05475 (2018) - [i7]Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs. CoRR abs/1811.07492 (2018) - [i6]Qingyu Chen, Yifan Peng, Tiarnan D. Keenan, Shazia Dharssi, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu:
A multi-task deep learning model for the classification of Age-related Macular Degeneration. CoRR abs/1812.00422 (2018) - 2017
- [j71]Sylvain Poux, Cecilia N. Arighi, Michele Magrane, Alex Bateman, Chih-Hsuan Wei, Zhiyong Lu, Emmanuel Boutet, Hema Bye-A-Jee, Maria Livia Famiglietti, Bernd Roechert, The UniProt Consortium:
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinform. 33(21): 3454-3460 (2017) - [j70]Yuqing Mao, Zhiyong Lu:
MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank. J. Biomed. Semant. 8(1): 15:1-15:9 (2017) - [j69]Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu:
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. BMC Syst. Biol. 11(3): 23:1-23:11 (2017) - [j68]Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu:
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. J. Biomed. Informatics 75: 122-127 (2017) - [j67]Yuqing Mao, Zhiyong Lu:
Mining Related Articles for Automatic Journal Cataloging. J. Data Inf. Sci. 1(2): 45-59 (2017) - [c50]Nicolas Fiorini, Zhiyong Lu:
New Relevance Search Algorithm for PubMed. AMIA 2017 - [c49]Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald M. Summers, Zhiyong Lu:
Text Mining Radiology Reports for Deep Learning Radiology Images. AMIA 2017 - [c48]Yifan Peng, Zhiyong Lu:
Deep learning for extracting protein-protein interactions from biomedical literature. BioNLP 2017: 29-38 - [c47]Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu:
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017: 171-175 - [c46]Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu:
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs. BioNLP 2017: 222-231 - [c45]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers:
ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. CVPR 2017: 3462-3471 - [c44]Xiaozhao Zhuang, Xiaoyang Qu, Zhiyong Lu, Jiguang Wan, Changsheng Xie:
Exploiting Virtual Metadata Servers to Provide Multi-Level Consistency for Key-Value Object-Based Data Store. NAS 2017: 1-6 - [i5]Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers:
ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases. CoRR abs/1705.02315 (2017) - [i4]Yifan Peng, Zhiyong Lu:
Deep learning for extracting protein-protein interactions from biomedical literature. CoRR abs/1706.01556 (2017) - [i3]Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald M. Summers, Zhiyong Lu:
NegBio: a high-performance tool for negation and uncertainty detection in radiology reports. CoRR abs/1712.05898 (2017) - 2016
- [j66]Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu:
A survey of current trends in computational drug repositioning. Briefings Bioinform. 17(1): 2-12 (2016) - [j65]Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu:
Crowdsourcing in biomedicine: challenges and opportunities. Briefings Bioinform. 17(1): 23-32 (2016) - [j64]Chung-Chi Huang, Zhiyong Lu:
Community challenges in biomedical text mining over 10 years: success, failure and the future. Briefings Bioinform. 17(1): 132-144 (2016) - [j63]Chung-Chi Huang, Zhiyong Lu:
Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation. Database J. Biol. Databases Curation 2016 (2016) - [j62]Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu:
Mining chemical patents with an ensemble of open systems. Database J. Biol. Databases Curation 2016 (2016) - [j61]Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, Zhiyong Lu:
BioCreative V CDR task corpus: a resource for chemical disease relation extraction. Database J. Biol. Databases Curation 2016 (2016) - [j60]Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre, Shawn W. Polson, Ioannis Xenarios, Cecilia N. Arighi, Zhiyong Lu:
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database J. Biol. Databases Curation 2016 (2016) - [j59]Qinghua Wang, Shabbir Syed-Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos, Afroza Khanam Irin, Lars Juhl Jensen, Silvia Jimenez, Toni Rose Jue, Ingrid M. Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M. Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre, Sandra E. Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu, Lynette Hirschman, Cecilia N. Arighi:
Overview of the interactive task in BioCreative V. Database J. Biol. Databases Curation 2016 (2016) - [j58]Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu:
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database J. Biol. Databases Curation 2016 (2016) - [j57]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Beyond accuracy: creating interoperable and scalable text-mining web services. Bioinform. 32(12): 1907-1910 (2016) - [j56]Robert Leaman, Zhiyong Lu:
TaggerOne: joint named entity recognition and normalization with semi-Markov Models. Bioinform. 32(18): 2839-2846 (2016) - [j55]Ayush Singhal, Michael Simmons, Zhiyong Lu:
Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature. J. Am. Medical Informatics Assoc. 23(4): 766-772 (2016) - [j54]Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu:
Improving chemical disease relation extraction with rich features and weakly labeled data. J. Cheminformatics 8(1): 53:1-53:12 (2016) - [j53]Ayush Singhal, Michael Simmons, Zhiyong Lu:
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine. PLoS Comput. Biol. 12(11) (2016) - [c43]Chung-Chi Huang, Zhiyong Lu:
Exploring Query Expansion for Entity Searches in PubMed. Louhi@EMNLP 2016: 106-112 - [c42]Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu:
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. BCB 2016: 527 - [c41]Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur:
PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL 2016: 141-145 - [c40]Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu:
BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative 2016 - [c39]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Large-scale Semantic Indexing with Biomedical Ontologies. ICBO/BioCreative 2016 - [i2]Sun Kim, W. John Wilbur, Zhiyong Lu:
Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. CoRR abs/1608.01972 (2016) - 2015
- [j52]Ritu Khare, John D. Burger, John S. Aberdeen, David Tresner-Kirsch, Theodore J. Corrales, Lynette Hirschman, Zhiyong Lu:
Scaling drug indication curation through crowdsourcing. Database J. Biol. Databases Curation 2015 (2015) - [j51]Sun Kim, Zhiyong Lu, W. John Wilbur:
Identifying named entities from PubMed®; for enriching semantic categories. BMC Bioinform. 16: 57:1-57:10 (2015) - [j50]Jiao Li, Zhiyong Lu:
An Integrative Approach for Discovery of New Uses of Existing Drugs. Data Sci. J. 14: 9 (2015) - [j49]Robert Leaman, Ritu Khare, Zhiyong Lu:
Challenges in clinical natural language processing for automated disorder normalization. J. Biomed. Informatics 57: 28-37 (2015) - [j48]Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia:
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7(S-1): S2 (2015) - [j47]Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu:
tmChem: a high performance approach for chemical named entity recognition and normalization. J. Cheminformatics 7(S-1): S3 (2015) - [j46]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text. IEEE J. Biomed. Health Informatics 19(4): 1385-1391 (2015) - [c38]Yuqing Mao, Zhiyong Lu:
NCBI at the 2015 BioASQ Challenge Task: Baseline Results from MeSH Now. CLEF (Working Notes) 2015 - [c37]Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu:
Session Introduction. Pacific Symposium on Biocomputing 2015: 267-269 - 2014
- [j45]Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014) - [j44]Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu:
BC4GO: a full-text corpus for the BioCreative IV GO task. Database J. Biol. Databases Curation 2014 (2014) - [j43]John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John S. Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman:
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing. Database J. Biol. Databases Curation 2014 (2014) - [j42]Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Dogan, Antonio Jimeno-Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana L. Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC interoperability track overview. Database J. Biol. Databases Curation 2014 (2014) - [j41]Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu:
tmBioC: improving interoperability of text-mining tools with BioC. Database J. Biol. Databases Curation 2014 (2014) - [j40]Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu:
Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation 2014 (2014) - [j39]Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur:
Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. 65(4): 765-781 (2014) - [j38]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI disease corpus: A resource for disease name recognition and concept normalization. J. Biomed. Informatics 47: 1-10 (2014) - [j37]Ritu Khare, Jiao Li, Zhiyong Lu:
LabeledIn: Cataloging labeled indications for human drugs. J. Biomed. Informatics 52: 448-456 (2014) - [c36]Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu:
Automatic Extraction of Drug Indications from FDA Drug Labels. AMIA 2014 - [c35]Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. BCB 2014: 138-146 - [c34]Robert Leaman, Zhiyong Lu:
Disease named entity recognition and normalization with DNorm. BCB 2014: 587 - [c33]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
Text mining tools for assisting literature curation. BCB 2014: 590-591 - [c32]Robert Leaman, Zhiyong Lu:
Automated Disease Normalization with Low Rank Approximations. BioNLP@ACL 2014: 24-28 - [c31]Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu:
NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering. CLEF (Working Notes) 2014: 1319-1327 - [c30]S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte:
Session Introduction. Pacific Symposium on Biocomputing 2014: 110-113 - 2013
- [j36]Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013) - [j35]Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [j34]Chih-Hsuan Wei, Bethany R. Harris, Hung-Yu Kao, Zhiyong Lu:
tmVar: a text mining approach for extracting sequence variants in biomedical literature. Bioinform. 29(11): 1433-1439 (2013) - [j33]Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu:
DNorm: disease name normalization with pairwise learning to rank. Bioinform. 29(22): 2909-2917 (2013) - [j32]Jiao Li, Zhiyong Lu:
Pathway-based drug repositioning using causal inference. BMC Bioinform. 14(S-16): S3 (2013) - [j31]Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 41(Webserver-Issue): 518-522 (2013) - [c29]Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu:
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. AMIA 2013 - [c28]Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu:
DNorm: A New Method and Online Tool for Disease Name Normalization. AMIA 2013 - [c27]Yuqing Mao, Zhiyong Lu:
Predicting clicks of PubMed articles. AMIA 2013 - [c26]Aurélie Névéol, Bastien Rance, Zhiyong Lu:
A systematic comparison of current sources of disease knowledge. AMIA 2013 - [c25]Robert Leaman, Ritu Khare, Zhiyong Lu:
NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm. CLEF (Working Notes) 2013 - [c24]Ritu Khare, Jiao Li, Zhiyong Lu:
Toward Creating a Gold Standard of Drug Indications from FDA Drug Labels. ICHI 2013: 30-35 - [c23]Zhiyong Lu, Pankaj Agarwal, Atul J. Butte:
Session Introduction. Pacific Symposium on Biocomputing 2013: 1-4 - 2012
- [j30]Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur:
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database J. Biol. Databases Curation 2012 (2012) - [j29]Zhiyong Lu, Lynette Hirschman:
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. Database J. Biol. Databases Curation 2012 (2012) - [j28]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database J. Biol. Databases Curation 2012 (2012) - [j27]Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu:
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database J. Biol. Databases Curation 2012 (2012) - [j26]Cathy H. Wu, Cecilia N. Arighi, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn J. Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur:
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012) - [j25]Jiao Li, Zhiyong Lu:
Systematic identification of pharmacogenomics information from clinical trials. J. Biomed. Informatics 45(5): 870-878 (2012) - [j24]Jiao Li, Zhiyong Lu:
Automatic identification and normalization of dosage forms in drug monographs. BMC Medical Informatics Decis. Mak. 12: 9 (2012) - [j23]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40(Database-Issue): 13-25 (2012) - [c22]Rezarta Islamaj Dogan, Zhiyong Lu:
An Inference Method for Disease Name Normalization. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text 2012 - [c21]Jiao Li, Zhiyong Lu:
A new method for computational drug repositioning using drug pairwise similarity. BIBM 2012: 1-4 - [c20]Rezarta Islamaj Dogan, Zhiyong Lu:
An improved corpus of disease mentions in PubMed citations. BioNLP@HLT-NAACL 2012: 91-99 - [c19]Jiao Li, Zhiyong Lu:
A Network Approach for Computational Drug Repositioning. HISB 2012: 83 - [c18]Jiao Li, Ritu Khare, Zhiyong Lu:
Improving Online Access to Drug-Related Information. HISB 2012: 148 - [c17]Aurélie Névéol, Jiao Li, Zhiyong Lu:
Linking multiple disease-related resources through UMLS. IHI 2012: 767-772 - 2011
- [j22]Zhiyong Lu:
PubMed and beyond: a survey of web tools for searching biomedical literature. Database J. Biol. Databases Curation 2011 (2011) - [j21]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinform. 27(23): 3306-3312 (2011) - [j20]Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu:
A context-blocks model for identifying clinical relationships in patient records. BMC Bioinform. 12(S-3): S3 (2011) - [j19]Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu:
Overview of the BioCreative III Workshop. BMC Bioinform. 12(S-8): S1 (2011) - [j18]Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur:
The gene normalization task in BioCreative III. BMC Bioinform. 12(S-8): S2 (2011) - [j17]Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu:
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12(S-8): S3 (2011) - [j16]Cecilia N. Arighi, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle G. Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman, Cathy H. Wu:
BioCreative III interactive task: an overview. BMC Bioinform. 12(S-8): S4 (2011) - [j15]Minlie Huang, Aurélie Névéol, Zhiyong Lu:
Recommending MeSH terms for annotating biomedical articles. J. Am. Medical Informatics Assoc. 18(5): 660-667 (2011) - [j14]Aurélie Névéol, Rezarta Islamaj Dogan, Zhiyong Lu:
Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction. J. Biomed. Informatics 44(2): 310-318 (2011) - [j13]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39(Database-Issue): 38-51 (2011) - [c16]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Automatic extraction of data deposition statements: where do the research results go? BioNLP@ACL 2011: 103-104 - 2010
- [j12]Rezarta Islamaj Dogan, Zhiyong Lu:
Click-words: learning to predict document keywords from a user perspective. Bioinform. 26(21): 2767-2775 (2010) - [j11]James G. Mork, Olivier Bodenreider, Dina Demner-Fushman, Rezarta Islamaj Dogan, François-Michel Lang, Zhiyong Lu, Aurélie Névéol, Lee B. Peters, Sonya E. Shooshan, Alan R. Aronson:
Extracting Rx information from clinical narrative. J. Am. Medical Informatics Assoc. 17(5): 536-539 (2010) - [j10]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 38(Database-Issue): 5-16 (2010) - [c15]Minlie Huang, Zhiyong Lu:
Learning to Annotate Scientific Publications. COLING (Posters) 2010: 463-471 - [c14]Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu:
A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records. ICMLA 2010: 995-998 - [c13]Aurélie Névéol, Zhiyong Lu:
Automatic integration of drug indications from multiple health resources. IHI 2010: 666-673
2000 – 2009
- 2009
- [j9]Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu:
Understanding PubMed® user search behavior through log analysis. Database J. Biol. Databases Curation 2009 (2009) - [j8]Zhiyong Lu, Natalie Xie, W. John Wilbur:
Identifying related journals through log analysis. Bioinform. 25(22): 3038-3039 (2009) - [j7]Zhiyong Lu, Won Kim, W. John Wilbur:
Evaluation of query expansion using MeSH in PubMed. Inf. Retr. 12(1): 69-80 (2009) - [j6]Zhiyong Lu, Won Kim, W. John Wilbur:
Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. J. Am. Medical Informatics Assoc. 16(1): 32-36 (2009) - [j5]Zhiyong Lu, W. John Wilbur:
Improving accuracy for identifying related PubMed queries by an integrated approach. J. Biomed. Informatics 42(5): 831-838 (2009) - [c12]Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi:
Finding Query Suggestions for PubMed. AMIA 2009 - [c11]Feng Jin, Minlie Huang, Zhiyong Lu, Xiaoyan Zhu:
Towards Automatic Generation of Gene Summary. BioNLP@HLT-NAACL 2009: 97-105 - [c10]Aurélie Névéol, Won Kim, W. John Wilbur, Zhiyong Lu:
Exploring Two Biomedical Text Genres for Disease Recognition. BioNLP@HLT-NAACL 2009: 144-152 - [c9]G. Craig Murray, Jimmy Lin, W. John Wilbur, Zhiyong Lu:
Users' adjustments to unsuccessful queries in biomedical search. JCDL 2009: 433-434 - [c8]Shouyuan Chen, Minlie Huang, Zhiyong Lu:
Summarizing Documents by Measuring the Importance of a Subset of Vertices within a Graph. Web Intelligence 2009: 269-272 - 2008
- [j4]Steven Bethard, Zhiyong Lu, James H. Martin, Lawrence Hunter:
Semantic role labeling for protein transport predicates. BMC Bioinform. 9 (2008) - [j3]Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen:
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinform. 9 (2008) - [c7]Zhiyong Lu, Won Kim, W. John Wilbur:
Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. AMIA 2008 - 2007
- [c6]Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
Generif Quality Assurance as Summary Revision. Pacific Symposium on Biocomputing 2007: 269-280 - [i1]Oliver Schulte, Flavia Moser, Martin Ester, Zhiyong Lu:
Association Rules in the Relational Calculus. CoRR abs/0710.2083 (2007) - 2006
- [c5]Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter:
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Pacific Symposium on Biocomputing 2006: 28-39 - [c4]Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter:
Finding GeneRIFs via Gene Ontology Annotations. Pacific Symposium on Biocomputing 2006: 52-63 - [c3]J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter:
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. TREC 2006 - 2005
- [c2]Zhiyong Lu, Lawrence Hunter:
GO Molecular Function Terms Are Predictive of Subcellular Localization. Pacific Symposium on Biocomputing 2005 - 2004
- [j2]Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner:
Predicting subcellular localization of proteins using machine-learned classifiers. Bioinform. 20(4): 547-556 (2004) - [j1]Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, David Meeuwis:
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res. 32(Web-Server-Issue): 365-371 (2004) - 2003
- [c1]Jörg Sander, Xuejie Qin, Zhiyong Lu, Nan Niu, Alex Kovarsky:
Automatic Extraction of Clusters from Hierarchical Clustering Representations. PAKDD 2003: 75-87
Coauthor Index
[j150] [j146] [j143] [i90] [i82] [i75] [i74] [i69] [i68] [i65] [j136] [j135] [j130] [j128] [j127] [c97] [i64] [i63] [i61] [i60] [i58] [i57] [i56] [i50] [j124] [j123] [j114] [j113] [j112] [c95] [c94] [c89] [i49] [i45] [i43] [i42] [i41] [i40] [i39] [j107] [j104] [j103] [c88] [c87] [c86] [c83] [c76] [j96] [j95] [j92] [j90] [c74] [c73] [c72] [i33] [i31] [i30] [i27] [i26] [j89] [j85] [j82] [c69] [c67] [c63] [i21] [i18] [i16] [c56] [i9] [i8] [i7] [i6]
Rezarta Islamaj Dogan
aka: Rezarta Islamaj
aka: Rezarta Islamaj
Tiarnan D. Keenan
aka: Tiarnan D. L. Keenan
aka: Tiarnan D. L. Keenan
[j147] [j145] [j144] [j142] [j141] [j140] [j139] [j138] [i91] [i84] [i78] [i71] [i67] [i65] [j131] [c98] [i59] [i55] [i52] [i51] [j116] [j113] [c91] [c90] [c89] [i44] [j107] [j102] [j100] [c86] [c77] [c75] [i36] [j92] [j91] [c74] [c73] [c72] [c70] [i33] [i32] [i31] [i30] [i26] [j85] [c69] [c65] [c64] [c63] [c62] [c61] [c60] [p2] [p1] [i24] [i23] [i22] [i21] [i20] [i19] [j80] [j73] [c53] [i15] [i14] [i9] [i8] [i7] [i6] [c49] [c48] [c47] [c45] [i5] [i4] [i3] [j58] [j54] [j42] [j35]
[j152] [j151] [j143] [i90] [i79] [i77] [i75] [j136] [j134] [j130] [j128] [i64] [i57] [j125] [j124] [j120] [j119] [c93] [c92] [i47] [i46] [i42] [i40] [i39] [j111] [j106] [j90] [i30] [i27] [j89] [j88] [j86] [j83] [c68] [c66] [i17] [i16] [j79] [j77] [j76] [j74] [j73] [j72] [i12] [j71] [c47] [j62] [j61] [j58] [j57] [j54] [c40] [c39] [j47] [j46] [j44] [j43] [j41] [c36] [c35] [c33] [c31] [j36] [j34] [j31] [c28] [j30] [j27] [j18]
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