no code implementations • 1 Oct 2024 • Qiuhao Lu, Rui Li, Elham Sagheb, Andrew Wen, Jinlian Wang, LiWei Wang, Jungwei W. Fan, Hongfang Liu
Diagnosis prediction is a critical task in healthcare, where timely and accurate identification of medical conditions can significantly impact patient outcomes.
no code implementations • 27 Sep 2024 • Zehan Li, Yan Hu, Scott Lane, Salih Selek, Lokesh Shahani, Rodrigo Machado-Vieira, Jair Soares, Hua Xu, Hongfang Liu, Ming Huang
We evaluated the performance of four BERT-based models using two fine-tuning strategies (multiple single-label and single multi-label) for detecting coexisting suicidal events from 500 annotated psychiatric evaluation notes.
1 code implementation • 30 Jun 2024 • Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, LiWei Wang, Hongfang Liu
However, there is a significant research gap when it comes to employing token-level NER for clinical texts, especially with the use of local open-source LLMs.
no code implementations • 15 Jun 2024 • Mingchen Li, Jiatan Huang, Jeremy Yeung, Anne Blaes, Steven Johnson, Hongfang Liu, Hua Xu, Rui Zhang
Medical Large Language Models (LLMs) such as ClinicalCamel 70B, Llama3-OpenBioLLM 70B have demonstrated impressive performance on a wide variety of medical NLP task. However, there still lacks a large language model (LLM) specifically designed for cancer domain.
no code implementations • 14 Aug 2023 • Xiaoyang Ruan, LiWei Wang, Charat Thongprayoon, Wisit Cheungpasitporn, Hongfang Liu
Our findings demonstrate the considerable potential of GRU-D-Weibull as the next-generation architecture for endpoint risk management, capable of generating various endpoint estimates for real-time monitoring using clinical data.
1 code implementation • 26 May 2023 • Kai Zhang, Rong Zhou, Eashan Adhikarla, Zhiling Yan, Yixin Liu, Jun Yu, Zhengliang Liu, Xun Chen, Brian D. Davison, Hui Ren, Jing Huang, Chen Chen, Yuyin Zhou, Sunyang Fu, Wei Liu, Tianming Liu, Xiang Li, Yong Chen, Lifang He, James Zou, Quanzheng Li, Hongfang Liu, Lichao Sun
Traditional biomedical artificial intelligence (AI) models, designed for specific tasks or modalities, often exhibit limited flexibility in real-world deployment and struggle to utilize holistic information.
Ranked #1 on
Text Summarization
on MeQSum
no code implementations • 15 Mar 2023 • Sicheng Zhou, Nan Wang, LiWei Wang, Ju Sun, Anne Blaes, Hongfang Liu, Rui Zhang
We developed three types of NLP models (i. e., conditional random field, bi-directional long short-term memory and CancerBERT) to extract cancer phenotypes from clinical texts.
no code implementations • 3 Feb 2023 • Ziyi Chen, Ren Yang, Sunyang Fu, Nansu Zong, Hongfang Liu, Ming Huang
In this work, we propose a hybrid deep learning model which combines a pretrained sentence BERT (SBERT) and convolutional neural network (CNN) to detect individuals with depression with their Reddit posts.
no code implementations • 19 Dec 2022 • Xiaoyang Ruan, LiWei Wang, Michelle Mai, Charat Thongprayoon, Wisit Cheungpasitporn, Hongfang Liu
Real-time individual endpoint prediction has always been a challenging task but of great clinic utility for both patients and healthcare providers.
no code implementations • 28 Jun 2022 • Yao Yan, Thomas Yu, Kathleen Muenzen, Sijia Liu, Connor Boyle, George Koslowski, Jiaxin Zheng, Nicholas Dobbins, Clement Essien, Hongfang Liu, Larsson Omberg, Meliha Yestigen, Bradley Taylor, James A Eddy, Justin Guinney, Sean Mooney, Thomas Schaffter
Discussion We demonstrated the feasibility of using the NLP Sandbox to conduct a multi-site evaluation of clinical text de-identification models without the sharing of data.
no code implementations • 7 Jan 2022 • Sungrim Moon, Huan He, Hongfang Liu, Jungwei W. Fan
Specifically, the 1-to-N, M-to-1, and M-to-N drug-reason relations were included to form the multi-answer and multi-focus QA entries, which represent more complex and natural challenges in addition to the basic one-drug-one-reason cases.
no code implementations • 20 Oct 2021 • Sijia Liu, Andrew Wen, LiWei Wang, Huan He, Sunyang Fu, Robert Miller, Andrew Williams, Daniel Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-el-rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S Hong, Joel H Saltz, Thomas Schaffter, Emily Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu, Natural Language Processing, Subgroup, National COVID Cohort Collaborative
Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP.
no code implementations • 25 Aug 2021 • Sicheng Zhou, LiWei Wang, Nan Wang, Hongfang Liu, Rui Zhang
This data used in the study included 21, 291 breast cancer patients diagnosed from 2010 to 2020, patients' clinical notes and pathology reports were collected from the University of Minnesota Clinical Data Repository (UMN).
no code implementations • 4 Aug 2021 • Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz, Jake Vasilakes, Jacob C. Solinsky, Reed McEwan, Benjamin C. Knoll, Christopher J. Tignanelli, Hongfang Liu, Hua Xu, Xiaoqian Jiang, Genevieve B. Melton, Serguei VS Pakhomov
Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts.
1 code implementation • 30 Mar 2021 • David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
Cancer is responsible for millions of deaths worldwide every year.
no code implementations • 24 Feb 2021 • Hongfang Liu, Ji-Kun Zhou, Bing-Lan Wu, Zhi-Qiang Zhang, Hua Jiang
We study the characterization and realization of higher-order topological Anderson insulator (HOTAI) in non-Hermitian systems, where the non-Hermitian mechanism ensures extra symmetries as well as gain and loss disorder. We illuminate that the quadrupole moment $Q_{xy}$ can be used as the real space topological invariant of non-Hermitian higher-order topological insulator (HOTI).
Disordered Systems and Neural Networks Mesoscale and Nanoscale Physics
no code implementations • 14 Jan 2021 • David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
We applied and compared eight GNN models including AGNN, ChebNet, GAT, GCN, GIN, GraphSAGE, SGC, and TAGCN on the Mayo Clinic cancer disease dataset and assessedtheir performance as well as compared them with each other and with more conventional machinelearning models such as decision tree, gradient boosting, multi-layer perceptron, naive bayes, andrandom forest which we used as the baselines.
no code implementations • 24 Oct 2019 • Sunyang Fu, David Chen, Huan He, Sijia Liu, Sungrim Moon, Kevin J Peterson, Feichen Shen, Li-Wei Wang, Yanshan Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu
Background Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement.
no code implementations • 21 Aug 2019 • Krishna B. Soundararajan, Sunyang Fu, Luke A. Carlson, Rebecca A. Smith, David S. Knopman, Hongfang Liu, Yanshan Wang
The total lifetime cost of care for someone with dementia is estimated to be $350, 174 in 2018, 70% of which is associated with family-provided care.
no code implementations • 23 Jun 2019 • Jun Jiang, Shumao Pang, Xia Zhao, Li-Wei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng
In order to train a generalizable model, a large volume of text must be collected.
no code implementations • WS 2019 • Sijia Liu, Li-Wei Wang, Vipin Chaudhary, Hongfang Liu
Neural network models have shown promise in the temporal relation extraction task.
no code implementations • 17 May 2019 • Yanshan Wang, Yiqing Zhao, Terry M. Therneau, Elizabeth J. Atkinson, Ahmad P. Tafti, Nan Zhang, Shreyasee Amin, Andrew H. Limper, Hongfang Liu
Both unsupervised machine learning approaches could be leveraged to discover patient subgroups using EHRs but with different foci.
5 code implementations • 28 Aug 2018 • Yanshan Wang, Naveed Afzal, Sunyang Fu, Li-Wei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu
A subset of MedSTS (MedSTS_ann) containing 1, 068 sentence pairs was annotated by two medical experts with semantic similarity scores of 0-5 (low to high similarity).
2 code implementations • 1 Feb 2018 • Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Li-Wei Wang, Feichen Shen, Paul Kingsbury, Hongfang Liu
First, the word embeddings trained on clinical notes and biomedical publications can capture the semantics of medical terms better, and find more relevant similar medical terms, and are closer to human experts' judgments, compared to these trained on Wikipedia and news.
Information Retrieval
no code implementations • SEMEVAL 2017 • Sijia Liu, Feichen Shen, Vipin Chaudhary, Hongfang Liu
We explored semantic similarities and patterns of keyphrases in scientific publications using pre-trained word embedding models.
no code implementations • LREC 2016 • Stephen Wu, Tamara Timmons, Amy Yates, Meikun Wang, Steven Bedrick, William Hersh, Hongfang Liu
Privacy concerns have often served as an insurmountable barrier for the production of research and resources in clinical information retrieval (IR).
no code implementations • LREC 2016 • Stephen Wu, Chung-Il Wi, Sunghwan Sohn, Hongfang Liu, Young Juhn
Domain-specific annotations for NLP are often centered on real-world applications of text, and incorrect annotations may be particularly unacceptable.