Automatic identification and expansion of ambiguous abbreviations are essential for biomedical natural language processing applications, such as information retrieval and question answering systems. In this paper, we present DEep Contextualized Biomedical. Abbreviation Expansion (DECBAE) model. DECBAE automatically collects substantial and relatively clean annotated contexts for 950 ambiguous abbreviations from PubMed abstracts using a simple heuristic. Then it utilizes BioELMo to extract the contextualized features of words, and feed those features to abbreviation-specific bidirectional LSTMs, where the hidden states of the ambiguous abbreviations are used to assign the exact definitions. Our DECBAE model outperforms other baselines by large margins, achieving average accuracy of 0.961 and macro-F1 of 0.917 on the dataset. It also surpasses human performance for expanding a sample abbreviation, and remains robust in imbalanced, low-resources and clinical settings.
Manipal Institute of Technology（马尼帕尔理工学院）；Elsevier Labs（爱思唯尔实验室）
Biomedical Named Entity Recognition (NER) is a challenging problem in biomedical information processing due to the widespread ambiguity of out of context terms and extensive lexical variations. Performance on bioNER benchmarks continues to improve due to advances like BERT, GPT, and XLNet. FLAIR (1) is an alternative embedding model which is less computationally intensive than the others mentioned. We test FLAIR and its pretrained PubMed embeddings (which we term BioFLAIR) on a variety of bio NER tasks and compare those with results from BERT-type networks. We also investigate the effects of a…
City University London（伦敦城市大学）；Centre for Health Informatics（健康信息学中心）
BADREX uses dynamically generated regular expressions to annotate term definition-term abbreviation pairs, and corefers unpaired acronyms and abbreviations back to their initial definition in the text. Against the Medstract corpus BADREX achieves precision and recall of 98% and 97%, and against a much larger corpus, 90% and 85%, respectively. BADREX yields improved performance over previous approaches, requires no training data and allows runtime customisation of its input parameters. BADREX is freely available from https://github.com/philgooch/BADREX-Biomedical-Abbreviation-Expander as a plug…
Chemical patents are an important resource for chemical information. However, few chemical Named Entity Recognition (NER) systems have been evaluated on patent documents, due in part to their structural and linguistic complexity. In this paper, we explore the NER performance of a BiLSTM-CRF model utilising pre-trained word embeddings, character-level word representations and contextualized ELMo word representations for chemical patents. We compare word embeddings pre-trained on biomedical and chemical patent corpora. The effect of tokenizers optimized for the chemical domain on NER performance…
LingShu: A Large-Scale Symptom-Centric Contextualized Knowledge Graph Bridging Traditional Chinese Medicine and Modern Biomedicine
Beijing Jiaotong University（北京交通大学）；Hubei Provincial Hospital of Traditional Chinese Medicine（湖北省中医院）；Hubei University of Chinese Medicine（湖北中医药大学）；Hubei Province Academy of Traditional Chinese Medicine（湖北省中医药研究院）；China Academy of Chinese Medical Sciences（中国中医科学院）；Xiyuan Hospital（西苑医院）；National Clinical Research Center for Chinese Medicine Cardiology（国家中医心血管病临床医学研究中心）；Hubei Provincial Clinical Research Center for Acupuncture and Moxibustion in Obesity Treatment（湖北省肥胖病针灸临床研究中心）；Hubei Shizhen Laboratory（湖北时珍实验室）；Tianjin Ta（天津（此处原文未完整，按原文提取））
UMass Amherst（马萨诸塞大学阿默斯特分校）；UMass Lowell（马萨诸塞大学洛厄尔分校）；UMass Medical School（马萨诸塞大学医学院）；U.S. Department of Veterans Affairs（美国退伍军人事务部）
This paper proposes a new natural language processing (NLP) application for identifying medical jargon terms potentially difficult for patients to comprehend from electronic health record (EHR) notes. We first present a novel and publicly available dataset with expert-annotated medical jargon terms from 18K+ EHR note sentences ($MedJ$). Then, we introduce a novel medical jargon extraction ($MedJEx$) model which has been shown to outperform existing state-of-the-art NLP models. First, MedJEx improved the overall performance when it was trained on an auxiliary Wikipedia hyperlink span dataset, w…
Pontificia Universidad Católica de Chile（智利天主教大学）；Millennium Institute for Foundational Research on Data (IMFD)（千禧基础数据研究所）；Elsevier（爱思唯尔）
The success of pretrained word embeddings has motivated their use in the biomedical domain, with contextualized embeddings yielding remarkable results in several biomedical NLP tasks. However, there is a lack of research on quantifying their behavior under severe "stress" scenarios. In this work, we systematically evaluate three language models with adversarial examples -- automatically constructed tests that allow us to examine how robust the models are. We propose two types of stress scenarios focused on the biomedical named entity recognition (NER) task, one inspired by spelling errors and …
In recent years, summarizers that incorporate domain knowledge into the process of text summarization have outperformed generic methods, especially for summarization of biomedical texts. However, construction and maintenance of domain knowledge bases are resource-intense tasks requiring significant manual annotation. In this paper, we demonstrate that contextualized representations extracted from the pre-trained deep language model BERT, can be effectively used to measure the similarity between sentences and to quantify the informative content. The results show that our BERT-based summarizer c…
The recognition of pharmacological substances, compounds and proteins is an essential preliminary work for the recognition of relations between chemicals and other biomedically relevant units. In this paper, we describe an approach to Task 1 of the PharmaCoNER Challenge, which involves the recognition of mentions of chemicals and drugs in Spanish medical texts. We train a state-of-the-art BiLSTM-CRF sequence tagger with stacked Pooled Contextualized Embeddings, word and sub-word embeddings using the open-source framework FLAIR. We present a new corpus composed of articles and papers from Spani…
Comprehensive Study on German Language Models for Clinical and Biomedical Text Understanding
University of Applied Sciences and Arts Dortmund（多特蒙德应用科学与艺术大学）；University Hospital Essen（埃森大学医院）；Institute for AI in Medicine (IKIM)（医学人工智能研究所）；University Medicine Essen（埃森大学医学中心）；FernUniversität in Hagen（哈根函授大学）；NVIDIA（英伟达公司）；College of Medicine, University of Florida（佛罗里达大学医学院）；University of Florida Health Cancer Center（佛罗里达大学健康癌症中心）；University of Marburg（马尔堡大学）；University of Mannheim（曼海姆大学）；TU Dortmund（多特蒙德工业大学）
HeFei University of Technology（合肥工业大学）；CSIRO（澳大利亚联邦科学与工业研究组织）；Shanghai Engineering Center for Microsatellites（上海微卫星工程中心）；Xi’an Jiaotong University（西安交通大学）；College of Computer and Information Engineering, Tianjin Normal University（天津师范大学计算机与信息工程学院）；School of Mechatronic Engineering and Automation, Shanghai University（上海大学机电工程与自动化学院）；Faculty of Business Information, Shanghai Business School（上海商学院商务信息学院）；School of Information Technology, Deakin University（迪肯大学信息技术学院）
Named entity recognition (NER) of chemicals and drugs is a critical domain of information extraction in biochemical research. NER provides support for text mining in biochemical reactions, including entity relation extraction, attribute extraction, and metabolic response relationship extraction. However, the existence of complex naming characteristics in the biomedical field, such as polysemy and special characters, make the NER task very challenging. Here, we propose a hybrid deep learning approach to improve the recognition accuracy of NER. Specifically, our approach applies the Bidirectiona…
University of Pittsburgh（匹兹堡大学）；Carnegie Mellon University（卡内基梅隆大学）；Google, Inc.（谷歌公司）
Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance. In this paper, we conduct probing experiments to determine what additional information is carried intrinsically by the in-domain trained contextualized embeddings. For this we use the pre-trained LMs as fixed feature extractors and restrict the downstream task models to not have additional sequence modeling layers. We compare BERT, ELMo, BioBERT and BioELMo, …
Weill Cornell Medical College, Cornell University（康奈尔大学威尔康奈尔医学院）；Weill Cornell Medicine（威尔康奈尔医学中心）
Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR. GRAPHENE consists of three main different modules 1) graph-augmented document representation learning; 2) query expansion and representation learning and 3) learning to rank biomedical articles. The graph-augmented document representation learning module constructs a document-concept graph containing biomedical concept nodes and document nodes so that global biomedical related concept from external …
