Zhiyong Lu

394 papers A* 7B 2C 1Misc 33Journal 284Unranked 65
YearRankTypeTitle / Venue / Authors
2026 J jnl
Anagent For Enhancing Scientific Table & Figure Analysis.
CoRR
Xuehang Guo, Zhiyong Lu, Tom Hope, Qingyun Wang
2026 J jnl
CT-Bench: A Benchmark for Multimodal Lesion Understanding in Computed Tomography.
CoRR
Qingqing Zhu, Qiao Jin, Tejas Sudharshan Mathai, Yin Fang, Zhizheng Wang, Yifan Yang, Maame Sarfo-Gyamfi, Benjamin Hou, Ran Gu, Praveen Thoppey Srinivasan Balamuralikrishna, Kenneth C. Wang, Ronald M. Summers, Zhiyong Lu
2026 J jnl
Condition-Gated Reasoning for Context-Dependent Biomedical Question Answering.
CoRR
Jash Rajesh Parekh, Wonbin Kweon, Joey Chan, Rezarta Islamaj, Robert Leaman, Pengcheng Jiang, Chih-Hsuan Wei, Zhizheng Wang, Zhiyong Lu, Jiawei Han
2026 J jnl
DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research.
CoRR
Zifeng Wang, Zheng Chen, Ziwei Yang, Xuan Wang, Qiao Jin, Yifan Peng, Zhiyong Lu, Jimeng Sun
2026 J jnl
Exploring Anti-Aging Literature via ConvexTopics and Large Language Models.
CoRR
Lana Yeganova, Won Kim, Shubo Tian, Natalie Xie, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2026 J jnl
Med-V1: Small Language Models for Zero-shot and Scalable Biomedical Evidence Attribution.
CoRR
Qiao Jin, Yin Fang, Lauren He, Yifan Yang, Guangzhi Xiong, Zhizheng Wang, Nicholas Wan, Joey Chan, Donald C. Comeau, Robert Leaman, Charalampos S. Floudas, Aidong Zhang, Michael F. Chiang, Yifan Peng, Zhiyong Lu
2026 A* conf
PairSem: LLM-Guided Pairwise Semantic Matching for Scientific Document Retrieval.
WWW
Wonbin Kweon, Runchu Tian, SeongKu Kang, Pengcheng Jiang, Zhiyong Lu, Jiawei Han, Hwanjo Yu
2026 J jnl
VOLMO: Versatile and Open Large Models for Ophthalmology.
CoRR
Zhenyue Qin, Younjoon Chung, Elijah Lee, Wanyue Feng, Xuguang Ai, Serina S. Applebaum, Minjie Zou, Yang Liu, Pan Xiao, Mac Singer, Amisha D. Dave, Aidan Gilson, Tiarnan D. L. Keenan, Emily Y. Chew, Zhiyong Lu, Yih-Chung Tham, Ron Adelman, Luciano V. Del Priore, Qingyu Chen
2025 J jnl
A foundation model for human-AI collaboration in medical literature mining.
CoRR
Zifeng Wang, Lang Cao, Qiao Jin, Joey Chan, Nicholas Wan, Behdad Afzali, Hyunjin Cho, Changin Choi, Mehdi Emamverdi, Manjot K. Gill, Sun-Hyung Kim, Yijia Li, Yi Liu, Hanley Ong, Justin F. Rousseau, Irfan Sheikh, Jenny J. Wei, Ziyang Xu, Christopher M. Zallek, Kyungsang Kim, Yifan Peng, Zhiyong Lu, Jimeng Sun
2025 — conf
AMD-Mamba: A Phenotype-Aware Multi-modal Framework for Robust AMD Prognosis.
MLMI@MICCAI
Puzhen Wu, Mingquan Lin, Qingyu Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Hexin Dong
2025 J jnl
Accelerating clinical evidence synthesis with large language models.
npj Digit. Medicine
Zifeng Wang, Lang Cao, Benjamin P. Danek, Qiao Jin, Zhiyong Lu, Jimeng Sun
2025 J jnl
Benchmarking Retrieval-Augmented Generation for Chemistry.
CoRR
Xianrui Zhong, Bowen Jin, Siru Ouyang, Yanzhen Shen, Qiao Jin, Yin Fang, Zhiyong Lu, Jiawei Han
2025 J jnl
CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray.
CoRR
Mingquan Lin, Gregory Holste, Song Wang, Yiliang Zhou, Yishu Wei, Imon Banerjee, Pengyi Chen, Tianjie Dai, Yuexi Du, Nicha C. Dvornek, Yuyan Ge, Zuowei Guo, Shouhei Hanaoka, Dongkyun Kim, Pablo Messina, Yang Lu, Denis Parra, Donghyun Son, Álvaro Soto, Aisha Urooj, René Vidal, Yosuke Yamagishi, Zefan Yang, Ruichi Zhang, Yang Zhou, Leo Anthony Celi, Ronald M. Summers, Zhiyong Lu, Hao Chen, Adam E. Flanders, George Shih, Zhangyang Wang, Yifan Peng
2025 J jnl
CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray.
Medical Image Anal.
Mingquan Lin, Gregory Holste, Song Wang, Yiliang Zhou, Yishu Wei, Imon Banerjee, Pengyi Chen, Tianjie Dai, Yuexi Du, Nicha C. Dvornek, Yuyan Ge, Zuwei Guo, Shouhei Hanaoka, Dongkyun Kim, Pablo Messina, Yang Lu, Denis Parra, Donghyun Son, Álvaro Soto, Aisha Urooj, René Vidal, Yosuke Yamagishi, Pingkun Yan, Zefan Yang, Ruichi Zhang, Yang Zhou, Leo Anthony Celi, Ronald M. Summers, Zhiyong Lu, Hao Chen, Adam E. Flanders, George Shih, Zhangyang Wang, Yifan Peng
2025 J jnl
Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning.
CoRR
Yin Fang, Qiao Jin, Guangzhi Xiong, Bowen Jin, Xianrui Zhong, Siru Ouyang, Aidong Zhang, Jiawei Han, Zhiyong Lu
2025 J jnl
Efficient 2D CT Foundation Model for Contrast Phase Classification.
CoRR
Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xinya Wang, Ronald M. Summers, Zhiyong Lu
2025 J jnl
Enhancing Biomedical Relation Extraction with Directionality.
CoRR
Po-Ting Lai, Chih-Hsuan Wei, Shubo Tian, Robert Leaman, Zhiyong Lu
2025 J jnl
Enhancing biomedical relation extraction with directionality.
Bioinform.
Po-Ting Lai, Chih-Hsuan Wei, Shubo Tian, Robert Leaman, Zhiyong Lu
2025 J jnl
Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis.
CoRR
Zhizheng Wang, Yifan Yang, Qiao Jin, Zhiyong Lu
2025 J jnl
How well do multimodal LLMs interpret CT scans? An auto-evaluation framework for analyses.
J. Biomed. Informatics
Qingqing Zhu, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Qiao Jin, Xiuying Chen, Zhizheng Wang, Ruida Cheng, Ronald M. Summers, Zhiyong Lu
2025 J jnl
Knowledge-guided Contextual Gene Set Analysis Using Large Language Models.
CoRR
Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei, Qiao Jin, Robert Leaman, Yifan Yang, Shubo Tian, Aodong Qiu, Yin Fang, Qingqing Zhu, Xinghua Lu, Zhiyong Lu
2025 J jnl
LMOD+: A Comprehensive Multimodal Dataset and Benchmark for Developing and Evaluating Multimodal Large Language Models in Ophthalmology.
CoRR
Zhenyue Qin, Yang Liu, Yu Yin, Jinyu Ding, Haoran Zhang, Anran Li, Dylan Campbell, Xuansheng Wu, Ke Zou, Tiarnan D. L. Keenan, Emily Y. Chew, Zhiyong Lu, Yih-Chung Tham, Ninghao Liu, Xiuzhen Zhang, Qingyu Chen
2025 J jnl
Leveraging long context in retrieval augmented language models for medical question answering.
npj Digit. Medicine
Gongbo Zhang, Zihan Xu, Qiao Jin, Fangyi Chen, Yilu Fang, Yi Liu, Justin F. Rousseau, Ziyang Xu, Zhiyong Lu, Chunhua Weng, Yifan Peng
2025 — conf
MedCite: Can Language Models Generate Verifiable Text for Medicine?
ACL (Findings)
Xiao Wang, Mengjue Tan, Qiao Jin, Guangzhi Xiong, Yu Hu, Aidong Zhang, Zhiyong Lu, Minjia Zhang
2025 J jnl
MedCite: Can Language Models Generate Verifiable Text for Medicine?
CoRR
Xiao Wang, Mengjue Tan, Qiao Jin, Guangzhi Xiong, Yu Hu, Aidong Zhang, Zhiyong Lu, Minjia Zhang
2025 J jnl
Memorization in Large Language Models in Medicine: Prevalence, Characteristics, and Implications.
CoRR
Anran Li, Lingfei Qian, Mengmeng Du, Yu Yin, Yan Hu, Zihao Sun, Yihang Fu, Erica Stutz, Xuguang Ai, Qianqian Xie, Rui Zhu, Jimin Huang, Yifan Yang, Siru Liu, Yih-Chung Tham, Lucila Ohno-Machado, Hyunghoon Cho, Zhiyong Lu, Hua Xu, Qingyu Chen
2025 J jnl
New Paradigm for Evaluating Scholar Summaries: A Facet-aware Metric and a Meta-evaluation Benchmark.
ACM Trans. Inf. Syst.
Tairan Wang, Xiuying Chen, Qingqing Zhu, Taicheng Guo, Shen Gao, Zhiyong Lu, Xin Gao, Xiangliang Zhang
2025 J jnl
PairSem: LLM-Guided Pairwise Semantic Matching for Scientific Document Retrieval.
CoRR
Wonbin Kweon, Runchu Tian, SeongKu Kang, Pengcheng Jiang, Zhiyong Lu, Jiawei Han, Hwanjo Yu
2025 J jnl
Preliminary analysis of the impact of lab results on large language model generated differential diagnoses.
npj Digit. Medicine
Balu Bhasuran, Qiao Jin, Yuzhang Xie, Carl Yang, Karim Hanna, Jennifer Costa, Cindy Shavor, Wenshan Han, Zhiyong Lu, Zhe He
2025 J jnl
RAG-Gym: Optimizing Reasoning and Search Agents with Process Supervision.
CoRR
Guangzhi Xiong, Qiao Jin, Xiao Wang, Yin Fang, Haolin Liu, Yifan Yang, Fangyuan Chen, Zhixing Song, Dengyu Wang, Minjia Zhang, Zhiyong Lu, Aidong Zhang
2025 J jnl
Recommending Clinical Trials for Online Patient Cases using Artificial Intelligence.
CoRR
Joey Chan, Qiao Jin, Nicholas Wan, Charalampos S. Floudas, Elisabetta Xue, Zhiyong Lu
2025 — conf
Research on the Design of Community Two-Wheeled Electric Vehicle Parking Facilities Based on Kano-QFD and FBS-TRIZ Models.
HCI (63)
Junnan Ye, Zhiyong Lu
2025 J jnl
Text Embedded Swin-UMamba for DeepLesion Segmentation.
CoRR
Ruida Cheng, Tejas Sudharshan Mathai, Pritam Mukherjee, Benjamin Hou, Qingqing Zhu, Zhiyong Lu, Matthew J. McAuliffe, Ronald M. Summers
2025 J jnl
TrialPanorama: Database and Benchmark for Systematic Review and Design of Clinical Trials.
CoRR
Zifeng Wang, Qiao Jin, Jiacheng Lin, Junyi Gao, Jathurshan Pradeepkumar, Pengcheng Jiang, Benjamin P. Danek, Zhiyong Lu, Jimeng Sun
2025 J jnl
Universal Lymph Node Detection in Multiparametric MRI with Selective Augmentation.
CoRR
Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers
2024 J jnl
A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models.
CoRR
Gongbo Zhang, Zihan Xu, Qiao Jin, Fangyi Chen, Yilu Fang, Yi Liu, Justin F. Rousseau, Ziyang Xu, Zhiyong Lu, Chunhua Weng, Yifan Peng
2024 — conf
A Text-to-Speech Synthesis Method Based on Speaker Transfer.
ICCT
Hongmei Zhang, Zhiyong Lu, Kejia Liu
2024 J jnl
A survey of recent methods for addressing AI fairness and bias in biomedicine.
CoRR
Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu
2024 J jnl
A survey of recent methods for addressing AI fairness and bias in biomedicine.
J. Biomed. Informatics
Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu
2024 J jnl
Accelerating Clinical Evidence Synthesis with Large Language Models.
CoRR
Zifeng Wang, Lang Cao, Benjamin P. Danek, Yichi Zhang, Qiao Jin, Zhiyong Lu, Jimeng Sun
2024 J jnl
Advancing entity recognition in biomedicine via instruction tuning of large language models.
Bioinform.
Vipina Kuttichi Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih-Hsuan Wei, Qiao Jin, Zhiyong Lu, Qingyu Chen, Hua Xu
2024 J jnl
Adversarial Attacks on Large Language Models in Medicine.
CoRR
Yifan Yang, Qiao Jin, Furong Huang, Zhiyong Lu
2024 J jnl
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning.
CoRR
Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu
2024 J jnl
Augmenting Biomedical Named Entity Recognition with General-domain Resources.
CoRR
Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen
2024 J jnl
Augmenting biomedical named entity recognition with general-domain resources.
J. Biomed. Informatics
Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen
2024 J jnl
Author Correction: Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.
npj Digit. Medicine
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
2024 — conf
Benchmarking Retrieval-Augmented Generation for Medicine.
ACL (Findings)
Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang
2024 J jnl
Benchmarking Retrieval-Augmented Generation for Medicine.
CoRR
Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang
2024 J jnl
Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing Large Language Models in Healthcare.
CoRR
Yifan Yang, Qiao Jin, Qingqing Zhu, Zhizheng Wang, Francisco Erramuspe Álvarez, Nicholas Wan, Benjamin Hou, Zhiyong Lu
2024 J jnl
Closing the gap between open source and commercial large language models for medical evidence summarization.
npj Digit. Medicine
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
2024 J jnl
Closing the gap between open-source and commercial large language models for medical evidence summarization.
CoRR
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
2024 J jnl
Decomposing Vision-based LLM Predictions for Auto-Evaluation with GPT-4.
CoRR
Qingqing Zhu, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Qiao Jin, Xiuying Chen, Zhizheng Wang, Ruida Cheng, Ronald M. Summers, Zhiyong Lu
2024 J jnl
Demystifying Large Language Models for Medicine: A Primer.
CoRR
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
2024 J jnl
Detection of abdominopelvic lymph nodes in multi-parametric MRI.
Comput. Medical Imaging Graph.
Tejas Sudharshan Mathai, Thomas C. Shen, Daniel C. Elton, Sungwon Lee, Zhiyong Lu, Ronald M. Summers
2024 J jnl
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology.
CoRR
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
2024 J jnl
Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine.
CoRR
Yifan Yang, Qiao Jin, Robert Leaman, Xiaoyu Liu, Guangzhi Xiong, Maame Sarfo-Gyamfi, Changlin Gong, Santiago Ferrière-Steinert, W. John Wilbur, Xiaojun Li, Jiaxin Yuan, Bang An, Kelvin S. Castro, Francisco Erramuspe Álvarez, Matías Stockle, Aidong Zhang, Furong Huang, Zhiyong Lu
2024 J jnl
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science.
CoRR
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 J. 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
2024 J jnl
EnzChemRED, a rich enzyme chemistry relation extraction dataset.
CoRR
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
2024 J jnl
Evaluating the Impact of Lab Test Results on Large Language Models Generated Differential Diagnoses from Clinical Case Vignettes.
CoRR
Balu Bhasuran, Qiao Jin, Yuzhang Xie, Carl Yang, Karim Hanna, Jennifer Costa, Cindy Shavor, Zhiyong Lu, Zhe He
2024 J jnl
GeneAgent: Self-verification Language Agent for Gene Set Knowledge Discovery using Domain Databases.
CoRR
Zhizheng Wang, Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po-Ting Lai, Qingqing Zhu, Chi-Ping Day, Christina Ross, Zhiyong Lu
2024 J jnl
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.
Bioinform.
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles.
CoRR
Ashley Shin, Qiao Jin, James T. Anibal, Zhiyong Lu
2024 J jnl
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.
CoRR
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
2024 J jnl
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling.
npj Digit. Medicine
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
2024 J jnl
Hidden Flaws Behind Expert-Level Accuracy of GPT-4 Vision in Medicine.
CoRR
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
2024 J jnl
Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine.
npj Digit. Medicine
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
2024 J jnl
Humans Continue to Outperform Large Language Models in Complex Clinical Decision-Making: A Study with Medical Calculators.
CoRR
Nicholas Wan, Qiao Jin, Joey Chan, Guangzhi Xiong, Serina S. Applebaum, Aidan Gilson, Reid McMurry, R. Andrew Taylor, Aidong Zhang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions.
CoRR
Guangzhi Xiong, Qiao Jin, Xiao Wang, Minjia Zhang, Zhiyong Lu, Aidong Zhang
2024 J jnl
Improving large language models for clinical named entity recognition via prompt engineering.
J. Am. Medical Informatics Assoc.
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
2024 J jnl
Large language models in biomedicine and health: current research landscape and future directions.
J. Am. Medical Informatics Assoc.
Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian
2024 — conf
Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for AI-generated Radiology Reports.
ICHI
Qingqing Zhu, Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xin Gao, Ronald M. Summers, Zhiyong Lu
2024 J jnl
Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports.
CoRR
Qingqing Zhu, Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xin Gao, Ronald M. Summers, Zhiyong Lu
2024 J jnl
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness.
J. Biomed. Informatics
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
2024 A* conf
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations.
NeurIPS
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
2024 J jnl
MedCalc-Bench: Evaluating Large Language Models for Medical Calculations.
CoRR
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
2024 J jnl
Opportunities and challenges for ChatGPT and large language models in biomedicine and health.
Briefings Bioinform.
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
2024 J jnl
Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science.
CoRR
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
2024 J jnl
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature.
Bioinform.
Shubo Tian, Qingyu Chen, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2024 J jnl
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge.
CoRR
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Quality of Answers of Generative Large Language Models vs Peer Patients for Interpreting Lab Test Results for Lay Patients: Evaluation Study.
CoRR
Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Y. Garcia Arguello, Patrick Murray, Zhiyong Lu
2024 J jnl
Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'.
Briefings Bioinform.
Shubo Tian, Qiao Jin, Zhiyong Lu
2024 J jnl
Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark.
CoRR
Xiuying Chen, Tairan Wang, Qingqing Zhu, Taicheng Guo, Shen Gao, Zhiyong Lu, Xin Gao, Xiangliang Zhang
2024 J jnl
Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification.
CoRR
Benjamin Hou, Qingqing Zhu, Tejas Sudharshan Mathai, Qiao Jin, Zhiyong Lu, Ronald M. Summers
2024 J jnl
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop.
Database J. Biol. Databases Curation
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
2024 J jnl
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII.
Database J. Biol. Databases Curation
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
2024 J jnl
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning.
CoRR
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
2024 J jnl
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.
Medical Image Anal.
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
2024 J jnl
Universal detection and segmentation of lymph nodes in multi-parametric MRI.
Int. J. Comput. Assist. Radiol. Surg.
Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers
2024 J jnl
Unmasking and Quantifying Racial Bias of Large Language Models in Medical Report Generation.
CoRR
Yifan Yang, Xiaoyu Liu, Qiao Jin, Furong Huang, Zhiyong Lu
2023 J jnl
A scoping review on multimodal deep learning in biomedical images and texts.
CoRR
Zhaoyi Sun, Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng
2023 J jnl
A scoping review on multimodal deep learning in biomedical images and texts.
J. Biomed. Informatics
Zhaoyi Sun, Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng
2023 J jnl
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.
Bioinform.
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2023 B conf
Attention-based 3D convolutional networks for detection of geographic atrophy from optical coherence tomography scans.
Image Processing
Amr S. Elsawy, Tiarnan D. Kenan, Qingyu Chen, Xiaoshuang Shi, Emily Y. Chew, Zhiyong Lu
2023 J jnl
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval.
CoRR
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2023 J jnl
BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets.
CoRR
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
2023 J jnl
BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets.
J. Biomed. Informatics
Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
2023 J jnl
Bioformer: an efficient transformer language model for biomedical text mining.
CoRR
Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang
2023 J jnl
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII.
Database J. Biol. Databases Curation
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
2023 J jnl
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2023 J jnl
Database resources of the National Center for Biotechnology Information in 2023.
Nucleic Acids Res.
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
2023 J jnl
GNorm2: an improved gene name recognition and normalization system.
Bioinform.
Chih-Hsuan Wei, Ling Luo, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu
2023 J jnl
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information.
CoRR
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
2023 J jnl
Interpretable Medical Image Visual Question Answering via Multi-Modal Relationship Graph Learning.
CoRR
Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu
2023 A* conf
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search.
SIGIR
Qiao Jin, Andrew Shin, Zhiyong Lu
2023 J jnl
LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search.
CoRR
Qiao Jin, Andrew Shin, Zhiyong Lu
2023 J jnl
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations.
CoRR
Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu
2023 J jnl
Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness.
CoRR
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
2023 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2023 J jnl
Matching Patients to Clinical Trials with Large Language Models.
CoRR
Qiao Jin, Zifeng Wang, Charalampos S. Floudas, Jimeng Sun, Zhiyong Lu
2023 J jnl
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.
Bioinform.
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2023 J jnl
MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing.
CoRR
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
2023 — conf
Multi-stage Literature Retrieval System Trained by PubMed Search Logs for Biomedical Question Answering.
CLEF (Working Notes)
Ashley Shin, Qiao Jin, Zhiyong Lu
2023 J jnl
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR
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
2023 J jnl
PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search.
CoRR
Qiao Jin, Robert Leaman, Zhiyong Lu
2023 J jnl
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.
Bioinform.
Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo, Zhiyong Lu, Peter N. Robinson
2023 J jnl
Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge.
CoRR
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
2023 J jnl
Trigonometric projection statistics histograms for 3D local feature representation and shape description.
Pattern Recognit.
Xingsheng Liu, Anhu Li, Jianfeng Sun, Zhiyong Lu
2023 J jnl
Universal lymph node detection in T2 MRI using neural networks.
Int. J. Comput. Assist. Radiol. Surg.
Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers
2023 — conf
Universal lymph node detection in multiparametric MRI with selective augmentation.
Computer-Aided Diagnosis
Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers
2023 J jnl
Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports.
CoRR
Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu
2023 — conf
Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology Reports.
MICCAI (5)
Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu
2022 J jnl
A Privacy-Preserving Unsupervised Domain Adaptation Framework for Clinical Text Analysis.
CoRR
Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu
2022 J jnl
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation
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
2022 J jnl
A sequence labeling framework for extracting drug-protein relations from biomedical literature.
Database J. Biol. Databases Curation
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
2022 J jnl
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning.
CoRR
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
2022 J jnl
Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework.
CoRR
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Dogan, Zhiyong Lu
2022 J jnl
Assigning species information to corresponding genes by a sequence labeling framework.
Database J. Biol. Databases Curation
Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
2022 Misc conf
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows.
AMIA
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
2022 Misc conf
BioRED: A Comprehensive Biomedical Relation Extraction Dataset.
AMIA
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
2022 J jnl
BioRED: A Comprehensive Biomedical Relation Extraction Dataset.
CoRR
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
2022 J jnl
BioRED: a rich biomedical relation extraction dataset.
Briefings Bioinform.
Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N. Arighi, Zhiyong Lu
2022 J jnl
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022 J jnl
Database resources of the national center for biotechnology information.
Nucleic Acids Res.
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
2022 Misc conf
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
Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Amr S. Elsawy, Emily Y. Chew, Zhiyong Lu
2022 J jnl
Global-Local attention network with multi-task uncertainty loss for abnormal lymph node detection in MR images.
Medical Image Anal.
Shuai Wang, Yingying Zhu, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Youbao Tang, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2022 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2022 J jnl
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation.
IEEE ACM Trans. Comput. Biol. Bioinform.
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 J jnl
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation.
CoRR
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 — conf
Lymph node detection in T2 MRI with transformers.
Computer-Aided Diagnosis
Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2022 J jnl
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
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
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR
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
2022 J jnl
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.
Database J. Biol. Databases Curation
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
2022 Misc conf
PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles.
AMIA
Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu
2022 J jnl
PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology.
J. Biomed. Informatics
Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2022 — conf
Predicting Age-related Macular Degeneration Progression with Longitudinal Fundus Images Using Deep Learning.
MLMI@MICCAI
Junghwan Lee, Tingyi Wanyan, Qingyu Chen, Tiarnan D. L. Keenan, Benjamin S. Glicksberg, Emily Y. Chew, Zhiyong Lu, Fei Wang, Yifan Peng
2022 J jnl
Predicting myocardial infarction through retinal scans and minimal personal information.
Nat. Mach. Intell.
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
2022 — conf
Radiology Text Analysis System (RadText): Architecture and Evaluation.
ICHI
Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng
2022 J jnl
Radiology Text Analysis System (RadText): Architecture and Evaluation.
CoRR
Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng
2022 J jnl
Robust convolutional neural networks against adversarial attacks on medical images.
Pattern Recognit.
Xiaoshuang Shi, Yifan Peng, Qingyu Chen, Tiarnan D. Keenan, Alisa T. Thavikulwat, Sungwon Lee, Yuxing Tang, Emily Y. Chew, Ronald M. Summers, Zhiyong Lu
2022 J jnl
Towards a unified search: Improving PubMed retrieval with full text.
J. Biomed. Informatics
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2022 J jnl
Universal Lymph Node Detection in T2 MRI using Neural Networks.
CoRR
Tejas Sudharshan Mathai, Sungwon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers
2022 J jnl
tmVar 3.0: an improved variant concept recognition and normalization tool.
Bioinform.
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
2022 J jnl
tmVar 3.0: an improved variant concept recognition and normalization tool.
CoRR
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
2021 Misc conf
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation.
AMIA
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2021 J jnl
BERT-GT: Cross-sentence n-ary relation extraction with BERT and Graph Transformer.
CoRR
Po-Ting Lai, Zhiyong Lu
2021 J jnl
BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer.
Bioinform.
Po-Ting Lai, Zhiyong Lu
2021 J jnl
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
Yifan Peng, Yuxing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu
2021 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2021 Misc conf
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
Qingyu Chen, Tiarnan D. Keenan, Emily Y. Chew, Zhiyong Lu
2021 — conf
Detection of Lymph Nodes in T2 MRI Using Neural Network Ensembles.
MLMI@MICCAI
Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2021 J jnl
Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View Semantic Embedding With Self-Training.
IEEE Trans. Medical Imaging
Angshuman Paul, Thomas C. Shen, Sungwon Lee, Niranjan Balachandar, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2021 Misc conf
Improving PubMed Retrieval by Integrating Abstract and Full Text Search.
AMIA
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2021 Misc conf
Informatics-izing the National Institutes of Health.
AMIA
Clement J. McDonald, Patricia Flatley Brennan, Michael F. Chiang, Joshua C. Denny, Zhiyong Lu
2021 — conf
Learning Few-Shot Chest X-Ray Diagnosis Using Images From The Published Scientific Literature.
ISBI
Angshuman Paul, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2021 — conf
Learning Structure from Visual Semantic Features and Radiology Ontology for Lymph Node Classification on MRI.
MLMI@MICCAI
Yingying Zhu, Shuai Wang, Qingyu Chen, Sungwon Lee, Thomas C. Shen, Daniel C. Elton, Zhiyong Lu, Ronald M. Summers
2021 J jnl
LitCovid: an open database of COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 J jnl
LitSuggest: a web-based system for literature recommendation and curation using machine learning.
Nucleic Acids Res.
Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu
2021 Misc conf
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
AMIA
Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 J jnl
Loss-Based Attention for Interpreting Image-Level Prediction of Convolutional Neural Networks.
IEEE Trans. Image Process.
Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Pingjun Chen, Yun Liang, Zhiyong Lu, Zhenhua Guo
2021 J jnl
Lymph Node Detection in T2 MRI with Transformers.
CoRR
Tejas Sudharshan Mathai, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2021 — conf
Measuring the relative importance of full text sections for information retrieval from scientific literature.
BioNLP@NAACL-HLT
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2021 Misc conf
Multi-task deep learning-based survival analysis on the prognosis of late AMD using the longitudinal data in AREDS.
AMIA
Gregory C. Ghahramani, Matthew Brendel, Mingquan Lin, Qingyu Chen, Tiarnan D. Keenan, Kun Chen, Emily Y. Chew, Zhiyong Lu, Yifan Peng, Fei Wang
2021 J jnl
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.
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
2021 Misc conf
NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature.
AMIA
Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Dorothy Trinh, Deborah Whitman, Keiko Sekiya, Zhiyong Lu
2021 J jnl
NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.
J. Biomed. Informatics
Rezarta Islamaj Dogan, Chih-Hsuan Wei, David Cissel, Nicholas Miliaras, Olga Printseva, Oleg Rodionov, Keiko Sekiya, Janice Ward, Zhiyong Lu
2021 J jnl
Perceiving and Modeling Density is All You Need for Image Dehazing.
CoRR
Tian Ye, Mingchao Jiang, Yunchen Zhang, Liang Chen, Erkang Chen, Pen Chen, Zhiyong Lu
2021 J jnl
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology.
Bioinform.
Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2021 J jnl
Recent advances in biomedical literature mining.
Briefings Bioinform.
Sendong Zhao, Chang Su, Zhiyong Lu, Fei Wang
2021 J jnl
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.
Briefings Bioinform.
Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu
2021 — conf
Research on Deep Neural Network Model Compression Based on Quantification Pruning and Huffmann Encoding.
ICIC (2)
Cong Wei, Zhiyong Lu, Zhiyong Lin, Chong Zhong
2021 J jnl
SDWNet: A Straight Dilated Network with Wavelet Transformation for Image Deblurring.
CoRR
Wenbin Zou, Mingchao Jiang, Yunchen Zhang, Liang Chen, Zhiyong Lu, Yi Wu
2021 — conf
SDWNet: A Straight Dilated Network with Wavelet Transformation for image Deblurring.
ICCVW
Wenbin Zou, Mingchao Jiang, Yunchen Zhang, Liang Chen, Zhiyong Lu, Yi Wu
2021 Misc conf
TeamTat: A Collaborative Text Annotation Tool for Creating Gold-Standard Corpora.
AMIA
Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu
2020 — conf
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2.
NLP4COVID@EMNLP
Robert Leaman, Zhiyong Lu
2020 J jnl
A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2.
CoRR
Robert Leaman, Zhiyong Lu
2020 — conf
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining.
BioNLP
Yifan Peng, Qingyu Chen, Zhiyong Lu
2020 J jnl
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining.
CoRR
Yifan Peng, Qingyu Chen, Zhiyong Lu
2020 J jnl
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2020 J jnl
Automated abnormality classification of chest radiographs using deep convolutional neural networks.
npj Digit. Medicine
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
2020 — conf
Automatic recognition of abdominal lymph nodes from clinical text.
ClinicalNLP@EMNLP
Yifan Peng, Sungwon Lee, Daniel C. Elton, Thomas C. Shen, Yuxing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald M. Summers, Zhiyong Lu
2020 J jnl
Better synonyms for enriching biomedical search.
J. Am. Medical Informatics Assoc.
Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu
2020 J jnl
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.
PLoS Comput. Biol.
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2020 — conf
COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized Zero-Shot Diagnosis of Chest Radiographs.
iMIMIC/MIL3ID/LABELS@MICCAI
Angshuman Paul, Thomas C. Shen, Niranjan Balachandar, Yuxing Tang, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2020 J jnl
COVID-19-CT-CXR: a freely accessible and weakly labeled chest X-ray and CT image collection on COVID-19 from biomedical literature.
CoRR
Yifan Peng, Yuxing Tang, Sungwon Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu
2020 J jnl
DTF: Deep Tensor Factorization for predicting anticancer drug synergy.
Bioinform.
Zexuan Sun, Shujun Huang, Peiran Jiang, Pingzhao Hu, Zhiyong Lu
2020 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2020 J jnl
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.
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2020 J jnl
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.
Bioinform.
Xiaoqiong Wei, Chengxin Zhang, P. L. Freddolino, Yang Zhang, Zhiyong Lu
2020 Misc conf
Detection of reticular pseudodrusen using deep learning.
AMIA
Qingyu Chen, Tiarnan D. Keenan, Yifan Peng, Elvira Agrón, Christopher Hwang, Alisa T. Thavikulwat, Debora Lee, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
FullMeSH: improving large-scale MeSH indexing with full text.
Bioinform.
Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2020 J jnl
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration.
CoRR
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
2020 J jnl
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR
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
2020 J jnl
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology.
CoRR
Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
CoRR
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
npj Digit. Medicine
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
TeamTat: a collaborative text annotation tool.
CoRR
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2020 J jnl
TeamTat: a collaborative text annotation tool.
Nucleic Acids Res.
Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu
2019 — conf
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles.
BCB
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2019 J jnl
A deep learning approach for automated detection of geographic atrophy from color fundus photographs.
CoRR
Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew
2019 Misc conf
A deep learning-based survival model for prediction of progression in late Age-related Macular Degeneration (AMD) from color fundus photographs.
AMIA
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2019 — conf
A self-attention based deep learning method for lesion attribute detection from CT reports.
ICHI
Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu
2019 J jnl
A self-attention based deep learning method for lesion attribute detection from CT reports.
CoRR
Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu
2019 — ch.
Automatic Classification and Reporting of Multiple Common Thorax Diseases Using Chest Radiographs.
Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers
2019 J jnl
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale.
CoRR
Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2019 — conf
BioSentVec: creating sentence embeddings for biomedical texts.
ICHI
Qingyu Chen, Yifan Peng, Zhiyong Lu
2019 — conf
Biomedical Mention Disambiguation using a Deep Learning Approach.
BCB
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
2019 J jnl
Biomedical Mention Disambiguation using a Deep Learning Approach.
CoRR
Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
2019 — ch.
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
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers
2019 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2019 J jnl
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
CoRR
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 — conf
Evaluation of Five Sentence Similarity Models on Electronic Medical Records.
BCB
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 J jnl
Exploring Semi-supervised Variational Autoencoders for Biomedical Relation Extraction.
CoRR
Yijia Zhang, Zhiyong Lu
2019 — conf
Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports.
ISBI
Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2019 J jnl
Fine-grained lesion annotation in CT images with knowledge mined from radiology reports.
CoRR
Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers
2019 A* conf
Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning From Radiology Reports and Label Ontology.
CVPR
Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
2019 J jnl
Holistic and Comprehensive Annotation of Clinically Significant Findings on Diverse CT Images: Learning from Radiology Reports and Label Ontology.
CoRR
Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
2019 J jnl
LitSense: making sense of biomedical literature at sentence level.
Nucleic Acids Res.
Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2019 J jnl
ML-Net: multi-label classification of biomedical texts with deep neural networks.
J. Am. Medical Informatics Assoc.
Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu
2019 — conf
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation.
MICCAI (6)
Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
2019 J jnl
MULAN: Multitask Universal Lesion Analysis Network for Joint Lesion Detection, Tagging, and Segmentation.
CoRR
Ke Yan, Youbao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
2019 J jnl
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation
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
2019 J jnl
PMC text mining subset in BioC: about three million full-text articles and growing.
Bioinform.
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
2019 J jnl
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database.
Database J. Biol. Databases Curation
Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu
2019 J jnl
PubTator central: automated concept annotation for biomedical full text articles.
Nucleic Acids Res.
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2019 Misc conf
Text Mining and Machine Learning for Precision Medicine.
PSB
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
2019 — conf
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets.
BioNLP@ACL
Yifan Peng, Shankai Yan, Zhiyong Lu
2019 J jnl
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets.
CoRR
Yifan Peng, Shankai Yan, Zhiyong Lu
2019 J jnl
Using deep learning to identify translational research in genomic medicine beyond bench to bedside.
Database J. Biol. Databases Curation
Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J. Khoury, Zhiyong Lu
2018 A* conf
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval.
WWW
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2018 J jnl
A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval.
CoRR
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2018 J jnl
A Field Sensor: computing the composition and intent of PubMed queries.
Database J. Biol. Databases Curation
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2018 J jnl
A multi-task deep learning model for the classification of Age-related Macular Degeneration.
CoRR
Qingyu Chen, Yifan Peng, Tiarnan D. Keenan, Shazia Dharssi, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2018 J jnl
Assisting document triage for human kinome curation via machine learning.
Database J. Biol. Databases Curation
Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu
2018 J jnl
BioSentVec: creating sentence embeddings for biomedical texts.
CoRR
Qingyu Chen, Yifan Peng, Zhiyong Lu
2018 J jnl
Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models.
CoRR
Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu
2018 J jnl
DeepSeeNet: A deep learning model for automated classification of patient-based age-related macular degeneration severity from color fundus photographs.
CoRR
Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2018 Misc conf
Experimenting new search and user interface in PubMed Labs.
AMIA
Zhiyong Lu, Nicolas Fiorini
2018 J jnl
Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Database J. Biol. Databases Curation
Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu
2018 J jnl
Generalizing biomedical relation classification with neural adversarial domain adaptation.
Bioinform.
Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu
2018 J jnl
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.
Nucleic Acids Res.
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu
2018 J jnl
ML-Net: multi-label classification of biomedical texts with deep neural networks.
CoRR
Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu
2018 — conf
MeSH-based dataset for measuring the relevance of text retrieval.
BioNLP
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2018 Misc conf
Online evaluation of PubMed's new relevance search algorithm.
AMIA
Nicolas Fiorini, Zhiyong Lu
2018 J jnl
Overview of the BioCreative VI text-mining services for Kinome Curation Track.
Database J. Biol. Databases Curation
Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
2018 J jnl
PMC text mining subset in BioC: 2.3 million full text articles and growing.
CoRR
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
2018 — conf
Personalized neural language models for real-world query auto completion.
NAACL-HLT (3)
Nicolas Fiorini, Zhiyong Lu
2018 J jnl
Personalized neural language models for real-world query auto completion.
CoRR
Nicolas Fiorini, Zhiyong Lu
2018 J jnl
PubMed Labs: An experimental platform for improving biomedical literature search.
CoRR
Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu
2018 J jnl
PubMed Labs: an experimental system for improving biomedical literature search.
Database J. Biol. Databases Curation
Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu
2018 J jnl
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
PLoS Comput. Biol.
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
2018 — conf
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents.
BCB
Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu
2018 — conf
SingleCite: Towards an improved Single Citation Search in PubMed.
BioNLP
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu
2018 A* conf
TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-Rays.
CVPR
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers
2018 J jnl
TieNet: Text-Image Embedding Network for Common Thorax Disease Classification and Reporting in Chest X-rays.
CoRR
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers
2018 J jnl
ezTag: tagging biomedical concepts via interactive learning.
Nucleic Acids Res.
Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2018 J jnl
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine.
Bioinform.
Chih-Hsuan Wei, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu
2017 — conf
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations.
BioNLP
Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu
2017 J jnl
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents.
J. Biomed. Informatics
Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu
2017 A* conf
ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases.
CVPR
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers
2017 J jnl
ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases.
CoRR
Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers
2017 J jnl
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks.
BMC Syst. Biol.
Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu
2017 — conf
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs.
BioNLP
Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
2017 — conf
Deep learning for extracting protein-protein interactions from biomedical literature.
BioNLP
Yifan Peng, Zhiyong Lu
2017 J jnl
Deep learning for extracting protein-protein interactions from biomedical literature.
CoRR
Yifan Peng, Zhiyong Lu
2017 — conf
Exploiting Virtual Metadata Servers to Provide Multi-Level Consistency for Key-Value Object-Based Data Store.
NAS
Xiaozhao Zhuang, Xiaoyang Qu, Zhiyong Lu, Jiguang Wan, Changsheng Xie
2017 J jnl
MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.
J. Biomed. Semant.
Yuqing Mao, Zhiyong Lu
2017 J jnl
Mining Related Articles for Automatic Journal Cataloging.
J. Data Inf. Sci.
Yuqing Mao, Zhiyong Lu
2017 J jnl
NegBio: a high-performance tool for negation and uncertainty detection in radiology reports.
CoRR
Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald M. Summers, Zhiyong Lu
2017 Misc conf
New Relevance Search Algorithm for PubMed.
AMIA
Nicolas Fiorini, Zhiyong Lu
2017 J jnl
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Bioinform.
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, UniProt Consortium
2017 Misc conf
Text Mining Radiology Reports for Deep Learning Radiology Images.
AMIA
Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald M. Summers, Zhiyong Lu
2016 J jnl
A survey of current trends in computational drug repositioning.
Briefings Bioinform.
Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu
2016 J jnl
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
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Jiao Li, Thomas C. Wiegers, Zhiyong Lu
2016 J jnl
Beyond accuracy: creating interoperable and scalable text-mining web services.
Bioinform.
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2016 — conf
BioCconvert: A Conversion Tool Between BioC and PubAnnotation.
ICBO/BioCreative
Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
2016 J jnl
BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
Database J. Biol. Databases Curation
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
2016 J jnl
Bridging the Gap: a Semantic Similarity Measure between Queries and Documents.
CoRR
Sun Kim, W. John Wilbur, Zhiyong Lu
2016 J jnl
Community challenges in biomedical text mining over 10 years: success, failure and the future.
Briefings Bioinform.
Chung-Chi Huang, Zhiyong Lu
2016 J jnl
Crowdsourcing in biomedicine: challenges and opportunities.
Briefings Bioinform.
Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu
2016 — conf
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks.
BCB
Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu
2016 J jnl
Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.
Database J. Biol. Databases Curation
Chung-Chi Huang, Zhiyong Lu
2016 — conf
Exploring Query Expansion for Entity Searches in PubMed.
Louhi@EMNLP
Chung-Chi Huang, Zhiyong Lu
2016 J jnl
Improving chemical disease relation extraction with rich features and weakly labeled data.
J. Cheminformatics
Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu
2016 — conf
Large-scale Semantic Indexing with Biomedical Ontologies.
ICBO/BioCreative
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2016 J jnl
Mining chemical patents with an ensemble of open systems.
Database J. Biol. Databases Curation
Robert Leaman, Chih-Hsuan Wei, Cherry Zou, Zhiyong Lu
2016 J jnl
Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation
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
2016 J jnl
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Database J. Biol. Databases Curation
Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre, Shawn W. Polson, Ioannis Xenarios, Cecilia N. Arighi, Zhiyong Lu
2016 — conf
PubTermVariants: biomedical term variants and their use for PubMed search.
BioNLP@ACL
Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur
2016 J jnl
TaggerOne: joint named entity recognition and normalization with semi-Markov Models.
Bioinform.
Robert Leaman, Zhiyong Lu
2016 J jnl
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.
PLoS Comput. Biol.
Ayush Singhal, Michael Simmons, Zhiyong Lu
2016 J jnl
Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature.
J. Am. Medical Informatics Assoc.
Ayush Singhal, Michael Simmons, Zhiyong Lu
2015 J jnl
An Integrative Approach for Discovery of New Uses of Existing Drugs.
Data Sci. J.
Jiao Li, Zhiyong Lu
2015 J jnl
Challenges in clinical natural language processing for automated disorder normalization.
J. Biomed. Informatics
Robert Leaman, Ritu Khare, Zhiyong Lu
2015 J jnl
Identifying named entities from PubMed®; for enriching semantic categories.
BMC Bioinform.
Sun Kim, Zhiyong Lu, W. John Wilbur
2015 — conf
NCBI at the 2015 BioASQ Challenge Task: Baseline Results from MeSH Now.
CLEF (Working Notes)
Yuqing Mao, Zhiyong Lu
2015 J jnl
Scaling drug indication curation through crowdsourcing.
Database J. Biol. Databases Curation
Ritu Khare, John D. Burger, John S. Aberdeen, David Tresner-Kirsch, Theodore J. Corrales, Lynette Hirschman, Zhiyong Lu
2015 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu
2015 J jnl
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text.
IEEE J. Biomed. Health Informatics
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2015 J jnl
The Application of Semidefinite Integer Programming Model for the Simulation of Complex Networks.
Adv. Complex Syst.
Bo Jiao, Zhiyong Lu, Jianmai Shi
2015 J jnl
The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics
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
2015 J jnl
tmChem: a high performance approach for chemical named entity recognition and normalization.
J. Cheminformatics
Robert Leaman, Chih-Hsuan Wei, Zhiyong Lu
2014 J jnl
Author name disambiguation for PubMed.
J. Assoc. Inf. Sci. Technol.
Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
2014 — conf
Automated Disease Normalization with Low Rank Approximations.
BioNLP@ACL
Robert Leaman, Zhiyong Lu
2014 Misc conf
Automatic Extraction of Drug Indications from FDA Drug Labels.
AMIA
Ritu Khare, Chih-Hsuan Wei, Zhiyong Lu
2014 J jnl
BC4GO: a full-text corpus for the BioCreative IV GO task.
Database J. Biol. Databases Curation
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
2014 J jnl
BioC interoperability track overview.
Database J. Biol. Databases Curation
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
2014 J jnl
BioCreative-IV virtual issue.
Database J. Biol. Databases Curation
Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers
2014 — conf
Disease named entity recognition and normalization with DNorm.
BCB
Robert Leaman, Zhiyong Lu
2014 J jnl
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing.
Database J. Biol. Databases Curation
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
2014 J jnl
LabeledIn: Cataloging labeled indications for human drugs.
J. Biomed. Informatics
Ritu Khare, Jiao Li, Zhiyong Lu
2014 — conf
NCBI at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic Indexing and Question Answering.
CLEF (Working Notes)
Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu
2014 J jnl
NCBI disease corpus: A resource for disease name recognition and concept normalization.
J. Biomed. Informatics
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2014 J jnl
Overview of the gene ontology task at BioCreative IV.
Database J. Biol. Databases Curation
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
2014 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
2014 — conf
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine.
BCB
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
2014 J jnl
Study on the stability of the topology interactive growth mechanism using graph spectra.
IET Commun.
Bo Jiao, Ying Zhou, Jing Du, Chengdong Huang, Zhiyong Lu, Yinglong Liu
2014 — conf
Text mining tools for assisting literature curation.
BCB
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu
2013 Misc conf
A systematic comparison of current sources of disease knowledge.
AMIA
Aurélie Névéol, Bastien Rance, Zhiyong Lu
2013 J jnl
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation
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
2013 J jnl
BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation
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
2013 Misc conf
DNorm: A New Method and Online Tool for Disease Name Normalization.
AMIA
Robert Leaman, Rezarta Islamaj Dogan, Chih-Hsuan Wei, Zhiyong Lu
2013 J jnl
DNorm: disease name normalization with pairwise learning to rank.
Bioinform.
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu
2013 Misc conf
NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization.
AMIA
Rezarta Islamaj Dogan, Robert Leaman, Zhiyong Lu
2013 — conf
NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm.
CLEF (Working Notes)
Robert Leaman, Ritu Khare, Zhiyong Lu
2013 J jnl
Pathway-based drug repositioning using causal inference.
BMC Bioinform.
Jiao Li, Zhiyong Lu
2013 Misc conf
Predicting clicks of PubMed articles.
AMIA
Yuqing Mao, Zhiyong Lu
2013 J jnl
PubTator: a web-based text mining tool for assisting biocuration.
Nucleic Acids Res.
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu
2013 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
2013 — conf
Toward Creating a Gold Standard of Drug Indications from FDA Drug Labels.
ICHI
Ritu Khare, Jiao Li, Zhiyong Lu
2013 J jnl
tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Bioinform.
Chih-Hsuan Wei, Bethany R. Harris, Hung-Yu Kao, Zhiyong Lu
2012 — conf
A Network Approach for Computational Drug Repositioning.
HISB
Jiao Li, Zhiyong Lu
2012 — conf
A new method for computational drug repositioning using drug pairwise similarity.
BIBM
Jiao Li, Zhiyong Lu
2012 J jnl
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.
Database J. Biol. Databases Curation
Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu
2012 — conf
An Inference Method for Disease Name Normalization.
AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text
Rezarta Islamaj Dogan, Zhiyong Lu
2012 — conf
An improved corpus of disease mentions in PubMed citations.
BioNLP@HLT-NAACL
Rezarta Islamaj Dogan, Zhiyong Lu
2012 J jnl
Automatic identification and normalization of dosage forms in drug monographs.
BMC Medical Informatics Decis. Mak.
Jiao Li, Zhiyong Lu
2012 J jnl
BioCreative-2012 Virtual Issue.
Database J. Biol. Databases Curation
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
2012 J jnl
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.
Database J. Biol. Databases Curation
Zhiyong Lu, Lynette Hirschman
2012 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2012 — conf
Improving Online Access to Drug-Related Information.
HISB
Jiao Li, Ritu Khare, Zhiyong Lu
2012 J jnl
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
Database J. Biol. Databases Curation
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2012 — conf
Linking multiple disease-related resources through UMLS.
IHI
Aurélie Névéol, Jiao Li, Zhiyong Lu
2012 J jnl
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
Database J. Biol. Databases Curation
Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
2012 J jnl
Systematic identification of pharmacogenomics information from clinical trials.
J. Biomed. Informatics
Jiao Li, Zhiyong Lu
2011 J jnl
A context-blocks model for identifying clinical relationships in patient records.
BMC Bioinform.
Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
2011 — conf
Automatic extraction of data deposition statements: where do the research results go?
BioNLP@ACL
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2011 J jnl
BioCreative III interactive task: an overview.
BMC Bioinform.
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
2011 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2011 J jnl
Extraction of data deposition statements from the literature: a method for automatically tracking research results.
Bioinform.
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2011 J jnl
Overview of the BioCreative III Workshop.
BMC Bioinform.
Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
2011 J jnl
PubMed and beyond: a survey of web tools for searching biomedical literature.
Database J. Biol. Databases Curation
Zhiyong Lu
2011 J jnl
Recommending MeSH terms for annotating biomedical articles.
J. Am. Medical Informatics Assoc.
Minlie Huang, Aurélie Névéol, Zhiyong Lu
2011 J jnl
Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction.
J. Biomed. Informatics
Aurélie Névéol, Rezarta Islamaj Dogan, Zhiyong Lu
2011 J jnl
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform.
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
2011 J jnl
The gene normalization task in BioCreative III.
BMC Bioinform.
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
2010 C conf
A Textual Representation Scheme for Identifying Clinical Relationships in Patient Records.
ICMLA
Rezarta Islamaj Dogan, Aurélie Névéol, Zhiyong Lu
2010 — conf
Automatic integration of drug indications from multiple health resources.
IHI
Aurélie Névéol, Zhiyong Lu
2010 J jnl
Click-words: learning to predict document keywords from a user perspective.
Bioinform.
Rezarta Islamaj Dogan, Zhiyong Lu
2010 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2010 J jnl
Extracting Rx information from clinical narrative.
J. Am. Medical Informatics Assoc.
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
2010 — conf
Learning to Annotate Scientific Publications.
COLING (Posters)
Minlie Huang, Zhiyong Lu
2009 J jnl
Evaluation of query expansion using MeSH in PubMed.
Inf. Retr.
Zhiyong Lu, Won Kim, W. John Wilbur
2009 — conf
Exploring Two Biomedical Text Genres for Disease Recognition.
BioNLP@HLT-NAACL
Aurélie Névéol, Won Kim, W. John Wilbur, Zhiyong Lu
2009 Misc conf
Finding Query Suggestions for PubMed.
AMIA
Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi
2009 J jnl
Identifying related journals through log analysis.
Bioinform.
Zhiyong Lu, Natalie Xie, W. John Wilbur
2009 J jnl
Improving accuracy for identifying related PubMed queries by an integrated approach.
J. Biomed. Informatics
Zhiyong Lu, W. John Wilbur
2009 — conf
Summarizing Documents by Measuring the Importance of a Subset of Vertices within a Graph.
Web Intelligence
Shouyuan Chen, Minlie Huang, Zhiyong Lu
2009 — conf
Towards Automatic Generation of Gene Summary.
BioNLP@HLT-NAACL
Feng Jin, Minlie Huang, Zhiyong Lu, Xiaoyan Zhu
2009 J jnl
Understanding PubMed
Database J. Biol. Databases Curation
Rezarta Islamaj Dogan, G. Craig Murray, Aurélie Névéol, Zhiyong Lu
2009 — conf
Users' adjustments to unsuccessful queries in biomedical search.
JCDL
G. Craig Murray, Jimmy Lin, W. John Wilbur, Zhiyong Lu
2009 J jnl
Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
J. Am. Medical Informatics Assoc.
Zhiyong Lu, Won Kim, W. John Wilbur
2008 Misc conf
Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
AMIA
Zhiyong Lu, Won Kim, W. John Wilbur
2008 J jnl
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.
Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen
2008 J jnl
Semantic role labeling for protein transport predicates.
BMC Bioinform.
Steven Bethard, Zhiyong Lu, James H. Martin, Lawrence Hunter
2007 J jnl
Association Rules in the Relational Calculus
CoRR
Oliver Schulte, Flavia Moser, Martin Ester, Zhiyong Lu
2007 Misc conf
Generif Quality Assurance as Summary Revision.
Pacific Symposium on Biocomputing
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
2006 — conf
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.
TREC
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
2006 Misc conf
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.
Pacific Symposium on Biocomputing
Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter
2006 Misc conf
Finding GeneRIFs via Gene Ontology Annotations.
Pacific Symposium on Biocomputing
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
2005 Misc conf
GO Molecular Function Terms Are Predictive of Subcellular Localization.
Pacific Symposium on Biocomputing
Zhiyong Lu, Lawrence Hunter
2004 J jnl
Predicting subcellular localization of proteins using machine-learned classifiers.
Bioinform.
Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner
2004 J jnl
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations.
Nucleic Acids Res.
Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, David Meeuwis
2003 B conf
Automatic Extraction of Clusters from Hierarchical Clustering Representations.
PAKDD
Jörg Sander, Xuejie Qin, Zhiyong Lu, Nan Niu, Alex Kovarsky
1999 J jnl
Artificial neural networks model of share analysis specialist system.
Appl. Math. Comput.
Ping He, Zheng Chen, Zhiyong Lu