1 code implementation • EMNLP (ClinicalNLP) 2020 • Yifan Peng, SungWon Lee, Daniel C. Elton, Thomas Shen, Yu-Xing Tang, Qingyu Chen, Shuai Wang, Yingying Zhu, Ronald Summers, Zhiyong Lu
We then introduce an end-to-end approach based on the combination of rules and transformer-based methods to detect these abdominal lymph node mentions and classify their types from the MRI radiology reports.
no code implementations • NAACL (BioNLP) 2021 • Lana Yeganova, Won Gyu Kim, Donald Comeau, W John Wilbur, Zhiyong Lu
In this work we establish the connection between the BM25 score of a query term appearing in a section of a full text document and the probability of that document being clicked or identified as relevant.
no code implementations • 8 Mar 2024 • Qingqing Zhu, Benjamin Hou, Tejas S. Mathai, Pritam Mukherjee, Qiao Jin, Xiuying Chen, Zhizheng Wang, Ruida Cheng, Ronald M. Summers, Zhiyong Lu
The volume of CT exams being done in the world has been rising every year, which has led to radiologist burn-out.
no code implementations • 22 Feb 2024 • Xiuying Chen, Tairan Wang, Qingqing Zhu, Taicheng Guo, Shen Gao, Zhiyong Lu, Xin Gao, Xiangliang Zhang
Our findings confirm that FM offers a more logical approach to evaluating scientific summaries.
2 code implementations • 20 Feb 2024 • Guangzhi Xiong, Qiao Jin, Zhiyong Lu, Aidong Zhang
However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes.
no code implementations • 20 Feb 2024 • Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu
Clinical calculators play a vital role in healthcare by offering accurate evidence-based predictions for various purposes such as prognosis.
no code implementations • 13 Feb 2024 • Yifan Yang, Mingquan Lin, Han Zhao, Yifan Peng, Furong Huang, Zhiyong Lu
Such biases can occur before, during, or after the development of AI models, making it critical to understand and address potential biases to enable the accurate and reliable application of AI models in clinical settings.
no code implementations • 6 Feb 2024 • 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
Intelligent agents powered by large language models (LLMs) have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines.
no code implementations • 5 Feb 2024 • Ashley Shin, Qiao Jin, James Anibal, Zhiyong Lu
Our study suggests that repurposing user query logs of academic search engines can be a promising way to train state-of-the-art models for explaining literature recommendation.
no code implementations • 29 Jan 2024 • Qingqing Zhu, Xiuying Chen, Qiao Jin, Benjamin Hou, Tejas Sudharshan Mathai, Pritam Mukherjee, Xin Gao, Ronald M Summers, Zhiyong Lu
In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging.
no code implementations • 25 Jan 2024 • Yifan Yang, Xiaoyu Liu, Qiao Jin, Furong Huang, Zhiyong Lu
Large language models like GPT-3. 5-turbo and GPT-4 hold promise for healthcare professionals, but they may inadvertently inherit biases during their training, potentially affecting their utility in medical applications.
no code implementations • 23 Jan 2024 • Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu
Lab results are often confusing and hard to understand.
no code implementations • 19 Jan 2024 • Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
PubTator 3. 0 (https://www. ncbi. nlm. nih. gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases, and chemicals.
no code implementations • 16 Jan 2024 • 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
Recent studies indicate that Generative Pre-trained Transformer 4 with Vision (GPT-4V) outperforms human physicians in medical challenge tasks.
3 code implementations • 28 Nov 2023 • Rui Yang, Qingcheng Zeng, Keen You, Yujie Qiao, Lucas Huang, Chia-Chun 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
This study introduces Ascle, a pioneering natural language processing (NLP) toolkit designed for medical text generation.
no code implementations • 19 Nov 2023 • 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
Evidence-based medicine promises to improve the quality of healthcare by empowering medical decisions and practices with the best available evidence.
no code implementations • 24 Oct 2023 • 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
Many real-world image recognition problems, such as diagnostic medical imaging exams, are "long-tailed" $\unicode{x2013}$ there are a few common findings followed by many more relatively rare conditions.
no code implementations • 27 Jul 2023 • Qiao Jin, Zifeng Wang, Charalampos S. Floudas, Jimeng Sun, Zhiyong Lu
Second, the aggregated trial-level TrialGPT scores are highly correlated with expert eligibility annotations.
no code implementations • 18 Jul 2023 • Qiao Jin, Robert Leaman, Zhiyong Lu
In response, we present a survey of literature search tools tailored to both general and specific information needs in biomedicine, with the objective of helping readers efficiently fulfill their information needs.
no code implementations • 14 Jul 2023 • Zhaoyi Sun, Mingquan Lin, Qingqing Zhu, Qianqian Xie, Fei Wang, Zhiyong Lu, Yifan Peng
In this scoping review, we aim to provide a comprehensive overview of the current state of the field and identify key concepts, types of studies, and research gaps with a focus on biomedical images and texts joint learning, mainly because these two were the most commonly available data types in MDL research.
2 code implementations • 2 Jul 2023 • Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
In response, we introduce MedCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot semantic IR in biomedicine.
1 code implementation • 19 Jun 2023 • Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, Zhiyong Lu
State-of-the-art methods were used primarily to train machine learning models on individual RE datasets, such as protein-protein interaction and chemical-induced disease relation.
no code implementations • 15 Jun 2023 • 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
In this work, we examine the diverse applications of large language models (LLMs), such as ChatGPT, in biomedicine and health.
1 code implementation • 14 Jun 2023 • Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee, Yifan Peng, Ronald M. Summers, Zhiyong Lu
Pre-filling a radiology report holds promise in mitigating reporting errors, and despite efforts in the literature to generate medical reports, there exists a lack of approaches that exploit the longitudinal nature of patient visit records in the MIMIC-CXR dataset.
1 code implementation • 10 May 2023 • Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu
Biomedical literature is growing rapidly, making it challenging to curate and extract knowledge manually.
1 code implementation • 19 Apr 2023 • Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions.
no code implementations • 10 Apr 2023 • Qiao Jin, Andrew Shin, Zhiyong Lu
On all queries, LADER can improve the performance of a dense retriever by 24%-37% relative NDCG@10 while not requiring additional training, and further performance improvement is expected from more logs.
1 code implementation • 29 Mar 2023 • 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
Results: Using baseline prompts, GPT-3. 5 and GPT-4 achieved relaxed F1 scores of 0. 634, 0. 804 for MTSamples, and 0. 301, 0. 593 for VAERS.
no code implementations • 19 Feb 2023 • Xinyue Hu, Lin Gu, Kazuma Kobayashi, Qiyuan An, Qingyu Chen, Zhiyong Lu, Chang Su, Tatsuya Harada, Yingying Zhu
Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images.
1 code implementation • 3 Feb 2023 • Li Fang, Qingyu Chen, Chih-Hsuan Wei, Zhiyong Lu, Kai Wang
We thoroughly evaluated the performance of Bioformer as well as existing biomedical BERT models including BioBERT and PubMedBERT on 15 benchmark datasets of four different biomedical NLP tasks: named entity recognition, relation extraction, question answering and document classification.
1 code implementation • 30 Nov 2022 • Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu
Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction and question answering.
no code implementations • 27 Sep 2022 • Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
LitCovid (https://www. ncbi. nlm. nih. gov/research/coronavirus/), first launched in February 2020, is a first-of-its-kind literature hub for tracking up-to-date published research on COVID-19.
no code implementations • 16 Sep 2022 • Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
A significant percentage of COVID-19 survivors experience ongoing multisystemic symptoms that often affect daily living, a condition known as Long Covid or post-acute-sequelae of SARS-CoV-2 infection.
1 code implementation • 8 May 2022 • Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj Doğan, Zhiyong Lu
The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or identifier by a text-mining algorithm.
no code implementations • 20 Apr 2022 • Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Doğan, Jingcheng Du, Li Fang, Kai Wang, 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 Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu
To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature.
1 code implementation • 19 Apr 2022 • Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
However, it has been a primary curation bottleneck due to the nature of the task and the rapid literature growth.
1 code implementation • 8 Apr 2022 • Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Cecilia N Arighi, Zhiyong Lu
However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e. g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine.
Ranked #1 on Named Entity Recognition (NER) on BioRED
no code implementations • 7 Apr 2022 • Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP.
no code implementations • 31 Mar 2022 • Tejas Sudharshan Mathai, SungWon Lee, Thomas C. Shen, Zhiyong Lu, Ronald M. Summers
Results: Experiments on 122 test T2 MRI volumes revealed that VFNet achieved a 51. 1% mAP and 78. 7% recall at 4 false positives (FP) per volume, while the one-stage model ensemble achieved a mAP of 52. 3% and sensitivity of 78. 7% at 4FP.
1 code implementation • 19 Mar 2022 • Song Wang, Mingquan Lin, Ying Ding, George Shih, Zhiyong Lu, Yifan Peng
Analyzing radiology reports is a time-consuming and error-prone task, which raises the need for an efficient automated radiology report analysis system to alleviate the workloads of radiologists and encourage precise diagnosis.
no code implementations • 18 Jan 2022 • Qiyuan An, Ruijiang Li, Lin Gu, Hao Zhang, Qingyu Chen, Zhiyong Lu, Fei Wang, Yingying Zhu
To evaluate our proposed method's utility and privacy loss, we apply our model on a medical report disease label classification task using two noisy challenging clinical text datasets.
1 code implementation • 18 Nov 2021 • Tian Ye, Mingchao Jiang, Yunchen Zhang, Liang Chen, ErKang Chen, Pen Chen, Zhiyong Lu
However, due to the paradox caused by the variation of real captured haze and the fixed degradation parameters of the current networks, the generalization ability of recent dehazing methods on real-world hazy images is not ideal. To address the problem of modeling real-world haze degradation, we propose to solve this problem by perceiving and modeling density for uneven haze distribution.
Ranked #5 on Image Dehazing on Haze4k
no code implementations • 9 Nov 2021 • Tejas Sudharshan Mathai, SungWon Lee, Daniel C. Elton, Thomas C. Shen, Yifan Peng, Zhiyong Lu, Ronald M. Summers
Identification of lymph nodes (LN) in T2 Magnetic Resonance Imaging (MRI) is an important step performed by radiologists during the assessment of lymphoproliferative diseases.
no code implementations • BioCreative VII Challenge Evaluation Workshop 2021 • Robert Leaman, Rezarta Islamaj, Zhiyong Lu
The BioCreative NLM-Chem track calls for a community effort to fine-tune automated recognition of chemical names in biomedical literature.
1 code implementation • 12 Oct 2021 • Wenbin Zou, Mingchao Jiang, Yunchen Zhang, Liang Chen, Zhiyong Lu, Yi Wu
On this basis, we reduce the number of up-sampling and down-sampling and design a simple network structure.
Ranked #1 on Image Deblurring on RealBlur-R(trained on GoPro)
no code implementations • 11 Jan 2021 • Po-Ting Lai, Zhiyong Lu
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation.
Ranked #2 on Relation Extraction on BioRED
no code implementations • 9 Nov 2020 • 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
The objective was to develop and evaluate the performance of a novel 'M3' deep learning framework on RPD detection.
1 code implementation • EMNLP (NLP-COVID19) 2020 • Robert Leaman, Zhiyong Lu
In this manuscript we present an extensive dictionary of terms used in the literature to refer to SARS-CoV-2 and COVID-19.
no code implementations • 9 Oct 2020 • Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
The COVID-19 pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread.
no code implementations • 17 Sep 2020 • Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text.
no code implementations • 7 Aug 2020 • Lana Yeganova, Rezarta Islamaj, Qingyu Chen, Robert Leaman, Alexis Allot, Chin-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu
In this study we analyze the LitCovid collection, 13, 369 COVID-19 related articles found in PubMed as of May 15th, 2020 with the purpose of examining the landscape of literature and presenting it in a format that facilitates information navigation and understanding.
no code implementations • 19 Jul 2020 • Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
By 2040, age-related macular degeneration (AMD) will affect approximately 288 million people worldwide.
1 code implementation • 11 Jun 2020 • Yifan Peng, Yu-Xing Tang, Sung-Won Lee, Yingying Zhu, Ronald M. Summers, Zhiyong Lu
(1) We show that COVID-19-CT-CXR, when used as additional training data, is able to contribute to improved DL performance for the classification of COVID-19 and non-COVID-19 CT. (2) We collected CT images of influenza and trained a DL baseline to distinguish a diagnosis of COVID-19, influenza, or normal or other types of diseases on CT. (3) We trained an unsupervised one-class classifier from non-COVID-19 CXR and performed anomaly detection to detect COVID-19 CXR.
1 code implementation • WS 2020 • Yifan Peng, Qingyu Chen, Zhiyong Lu
Multi-task learning (MTL) has achieved remarkable success in natural language processing applications.
1 code implementation • 24 Apr 2020 • Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu
Manually annotated data is key to developing text-mining and information-extraction algorithms.
1 code implementation • 23 Dec 2019 • Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery.
no code implementations • 23 Sep 2019 • Chih-Hsuan Wei, Kyubum Lee, Robert Leaman, Zhiyong Lu
The priority ordering rule-based approach demonstrated F1-scores of 71. 29% (micro-averaged) and 41. 19% (macro-averaged), while the new disambiguation method demonstrated F1-scores of 91. 94% (micro-averaged) and 85. 42% (macro-averaged), a very substantial increase.
no code implementations • 6 Sep 2019 • Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
For the post challenge, the performance of both Random Forest and the Encoder Network was improved; in particular, the correlation of the Encoder Network was improved by ~13%.
14 code implementations • 12 Aug 2019 • Ke Yan, You-Bao Tang, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
When reading medical images such as a computed tomography (CT) scan, radiologists generally search across the image to find lesions, characterize and measure them, and then describe them in the radiological report.
Ranked #7 on Medical Object Detection on DeepLesion
1 code implementation • 7 Jun 2019 • Tiarnan D. Keenan, Shazia Dharssi, Yifan Peng, Qingyu Chen, Elvira Agrón, Wai T. Wong, Zhiyong Lu, Emily Y. Chew
Results: The deep learning models (GA detection, CGA detection from all eyes, and centrality detection from GA eyes) had AUC of 0. 933-0. 976, 0. 939-0. 976, and 0. 827-0. 888, respectively.
no code implementations • 30 Apr 2019 • Yifan Peng, Ke Yan, Veit Sandfort, Ronald M. Summers, Zhiyong Lu
In radiology, radiologists not only detect lesions from the medical image, but also describe them with various attributes such as their type, location, size, shape, and intensity.
3 code implementations • CVPR 2019 • Ke Yan, Yifan Peng, Veit Sandfort, Mohammadhadi Bagheri, Zhiyong Lu, Ronald M. Summers
In radiologists' routine work, one major task is to read a medical image, e. g., a CT scan, find significant lesions, and describe them in the radiology report.
no code implementations • 4 Mar 2019 • Ke Yan, Yifan Peng, Zhiyong Lu, Ronald M. Summers
To address this problem, we define a set of 145 labels based on RadLex to describe a large variety of lesions in the DeepLesion dataset.
no code implementations • 21 Jan 2019 • Alistair E. W. Johnson, Tom J. Pollard, Nathaniel R. Greenbaum, Matthew P. Lungren, Chih-ying Deng, Yifan Peng, Zhiyong Lu, Roger G. Mark, Seth J. Berkowitz, Steven Horng
Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's thorax, but requiring specialized training for proper interpretation.
no code implementations • 18 Jan 2019 • Yijia Zhang, Zhiyong Lu
Experimental results show that our method effectively exploits the unlabeled data to improve the performance and reduce the dependence on labeled data.
no code implementations • 2 Dec 2018 • Qingyu Chen, Yifan Peng, Tiarnan Keenan, Shazia Dharssi, Elvira Agron, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
Built on our previous work DeepSeeNet, we developed a novel deep learning model for automated classification of images into the 9-step scale.
Age-Related Macular Degeneration Classification Classification +2
1 code implementation • 19 Nov 2018 • Yifan Peng, Shazia Dharssi, Qingyu Chen, Tiarnan D. Keenan, Elvira Agrón, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
DeepSeeNet simulates the human grading process by first detecting individual AMD risk factors (drusen size, pigmentary abnormalities) for each eye and then calculating a patient-based AMD severity score using the AREDS Simplified Severity Scale.
4 code implementations • 13 Nov 2018 • Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu
Due to this nature, the multi-label text classification task is often considered to be more challenging compared to the binary or multi-class text classification problems.
4 code implementations • 22 Oct 2018 • Qingyu Chen, Yifan Peng, Zhiyong Lu
Sentence embeddings have become an essential part of today's natural language processing (NLP) systems, especially together advanced deep learning methods.
Ranked #1 on Sentence Embeddings For Biomedical Texts on MedSTS (using extra training data)
no code implementations • WS 2018 • Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu
A search that is targeted at finding a specific document in databases is called a Single Citation search.
no code implementations • WS 2018 • Won Gyu Kim, Lana Yeganova, Donald Comeau, W. John Wilbur, Zhiyong Lu
Creating simulated search environments has been of a significant interest in infor-mation retrieval, in both general and bio-medical search domains.
no code implementations • NAACL 2018 • Nicolas Fiorini, Zhiyong Lu
Query auto completion (QAC) systems are a standard part of search engines in industry, helping users formulate their query.
no code implementations • 26 Feb 2018 • Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
Publications in the life sciences are characterized by a large technical vocabulary, with many lexical and semantic variations for expressing the same concept.
no code implementations • 5 Feb 2018 • Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu
Text mining the relations between chemicals and proteins is an increasingly important task.
no code implementations • CVPR 2018 • Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Ronald M. Summers
Chest X-rays are one of the most common radiological examinations in daily clinical routines.
1 code implementation • 16 Dec 2017 • Yifan Peng, Xiaosong Wang, Le Lu, Mohammadhadi Bagheri, Ronald Summers, Zhiyong Lu
Negative and uncertain medical findings are frequent in radiology reports, but discriminating them from positive findings remains challenging for information extraction.
no code implementations • WS 2017 • Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
We describe a Deep Learning approach to modeling the relevance of a document{'}s text to a query, applied to biomedical literature.
no code implementations • WS 2017 • Rezarta Islamaj Do{\u{g}}an, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald Comeau, Zhiyong Lu
The Precision Medicine Track in BioCre-ative VI aims to bring together the Bi-oNLP community for a novel challenge focused on mining the biomedical litera-ture in search of mutations and protein-protein interactions (PPI).
no code implementations • WS 2017 • Yifan Peng, Zhiyong Lu
State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information.
25 code implementations • CVPR 2017 • Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, Mohammadhadi Bagheri, Ronald M. Summers
The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases.
no code implementations • 5 Aug 2016 • Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu
Here we present a query-document similarity measure motivated by the Word Mover's Distance.
no code implementations • Journal of Biomedical Informatics 2015 • Robert Leaman, Ritu Khare, Zhiyong Lu
Conclusion Disorder mentions in text from clinical narratives use a rich vocabulary that results in high term variation, which we believe to be one of the primary causes of reduced performance in clinical narrative.