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2020 – today
- 2023
[j133]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)- [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) - [c97]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 - [c96]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 - [c95]Qiao Jin, Andrew Shin, Zhiyong Lu:
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. SIGIR 2023: 2092-2097 - [i63]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) - [i62]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) - [i61]Qiao Jin, Andrew Shin, Zhiyong Lu:
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search. CoRR abs/2304.04590 (2023) - [i60]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) - [i59]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) - [i58]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) - [i57]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) - [i56]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) - [i55]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) - [i54]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) - [i53]Qiao Jin, Robert Leaman, Zhiyong Lu:
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. CoRR abs/2307.09683 (2023) - [i52]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) - [i51]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) - [i50]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) - 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 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) - [c94]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 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 - [c93]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 - [c92]Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu:
BioRED: A Comprehensive Biomedical Relation Extraction Dataset. AMIA 2022 - [c91]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 - [c90]Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng:
Radiology Text Analysis System (RadText): Architecture and Evaluation. ICHI 2022: 288-296 - [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]