A large number of embeddings trained on medical data have emerged, but it remains unclear how well they represent medical terminology, in particular whether the close relationship of semantically similar medical terms is encoded in these embeddings. To date, only small datasets for testing medical term similarity are available, not allowing to draw conclusions about the generalisability of embeddings to the enormous amount of medical terms used by doctors. We present multiple automatically created large-scale medical term similarity datasets and confirm their high quality in an annotation study with doctors. We evaluate state-of-the-art word and contextual embeddings on our new datasets, comparing multiple vector similarity metrics and word vector aggregation techniques. Our results show that current embeddings are limited in their ability to adequately encode medical terms. The novel datasets thus form a challenging new benchmark for the development of medical embeddings able to accurately represent the whole medical terminology.
The University of Surrey（萨里大学）；The University of Sheffield（谢菲尔德大学）
Medical dialogue generation aims to generate responses according to a history of dialogue turns between doctors and patients. Unlike open-domain dialogue generation, this requires background knowledge specific to the medical domain. Existing generative frameworks for medical dialogue generation fall short of incorporating domain-specific knowledge, especially with regard to medical terminology. In this paper, we propose a novel framework to improve medical dialogue generation by considering features centered on domain-specific terminology. We leverage an attention mechanism to incorporate term…
MeDiSumQA: Patient-Oriented Question-Answer Generation from Discharge Letters
Institute for AI in Medicine (IKIM), University Hospital Essen（埃森大学医院人工智能医学研究所（IKIM））；NVIDIA（英伟达公司）；Cancer Research Center Cologne Essen (CCCE), University Medicine Essen（埃森大学医学院科隆埃森癌症研究中心（CCCE））；German Cancer Consortium (DKTK, Partner site Essen)（德国癌症联盟（DKTK，埃森合作站点））；TU Dortmund（多特蒙德工业大学）
DeviceBERT: Applied Transfer Learning With Targeted Annotations and Vocabulary Enrichment to Identify Medical Device and Component Terminology in FDA Recall Summaries
University of California, Santa Barbara（加州大学圣塔芭芭拉分校）
Expert-layman text style transfer technologies have the potential to improve communication between members of scientific communities and the general public. High-quality information produced by experts is often filled with difficult jargon laypeople struggle to understand. This is a particularly notable issue in the medical domain, where layman are often confused by medical text online. At present, two bottlenecks interfere with the goal of building high-quality medical expert-layman style transfer systems: a dearth of pretrained medical-domain language models spanning both expert and layman t…
In this paper, we investigate a new approach to Population, Intervention and Outcome (PIO) element detection, a common task in Evidence Based Medicine (EBM). The purpose of this study is two-fold: to build a training dataset for PIO element detection with minimum redundancy and ambiguity and to investigate possible options in utilizing state of the art embedding methods for the task of PIO element detection. For the former purpose, we build a new and improved dataset by investigating the shortcomings of previously released datasets. For the latter purpose, we leverage the state of the art text…
Medical University of Vienna（维也纳医科大学）；University of Alicante（阿利坎特大学）；Medical University of Graz（格拉茨医科大学）
BACKGROUND: The amount of biomedical literature is rapidly growing and it is becoming increasingly difficult to keep manually curated knowledge bases and ontologies up-to-date. In this study we applied the word2vec deep learning toolkit to medical corpora to test its potential for identifying relationships from unstructured text. We evaluated the efficiency of word2vec in identifying properties of pharmaceuticals based on mid-sized, unstructured medical text corpora available on the web. Properties included relationships to diseases ('may treat') or physiological processes ('has physiological …
The First Affiliated Hospital of Jinan University（暨南大学附属第一医院）；The Fifth Affiliated Hospital of Sun Yat-sen University（中山大学附属第五医院）；Shenzhen Research Institute of Big Data（深圳大数据研究院）；The Chinese University of Hong Kong（香港中文大学）；Future Network of Intelligence Institute (FNii)（未来智能网络研究院）；Sun Yat-sen University（中山大学）；Jinan University（暨南大学）；Guangdong Provincial Key Laboratory of Big Data Computing（广东省大数据计算重点实验室）
Medical imaging technologies, including computed tomography (CT) or chest X-Ray (CXR), are largely employed to facilitate the diagnosis of the COVID-19. Since manual report writing is usually too time-consuming, a more intelligent auxiliary medical system that could generate medical reports automatically and immediately is urgently needed. In this article, we propose to use the medical visual language BERT (Medical-VLBERT) model to identify the abnormality on the COVID-19 scans and generate the medical report automatically based on the detected lesion regions. To produce more accurate medical …
CardioEmbed: Domain-Specialized Text Embeddings for Clinical Cardiology
University of Nevada Las Vegas, Department of Neuroscience（内华达大学拉斯维加斯分校神经科学系）；Concorde Career Colleges, Department of Cardiovascular and Medical Diagnostic Sonography（康科德职业学院心血管与医学诊断超声系）
landmarker: a Toolkit for Anatomical Landmark Localization in 2D/3D Images
IDLab；Department of Electronics and Information Systems（电子与信息系统系）；Ghent University（根特大学）；imec；Biometrics Research Group（生物识别研究组）；Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition（解剖学、成像、骨科、康复和营养系）
East China University of Science and Technology（华东理工大学）
Medical terminology normalization aims to map the clinical mention to terminologies come from a knowledge base, which plays an important role in analyzing Electronic Health Record(EHR) and many downstream tasks. In this paper, we focus on Chinese procedure terminology normalization. The expression of terminologies are various and one medical mention may be linked to multiple terminologies. Previous study explores some methods such as multi-class classification or learning to rank(LTR) to sort the terminologies by literature and semantic information. However, these information is inadequate to …
Satisfactory Medical Consultation based on Terminology-Enhanced Information Retrieval and Emotional In-Context Learning
School of Mechanical Science and Engineering, Huazhong University of Science and Technology（华中科技大学机械科学与工程学院）；School of Computer Science, University of Warwick（华威大学计算机学院）；School of Software and Microelectronics, Peking University（北京大学软件与微电子学院）；MRC Weatherall Institute of Molecular Medicine, University of Oxford（牛津大学MRC Weatherall分子医学研究所）
Unidad Mixta de Imagen Biomédica FISABIO-CIPF（FISABIO-CIPF生物医学成像联合单元）；Universidad de Alicante（阿利坎特大学）；Medbravo；Hospital San Juan de Alicante（阿利坎特圣胡安医院）；Universidad Miguel Hernández（米格尔·埃尔南德斯大学）；Sierra Research SL（Sierra Research有限公司）；Bioinformatics & Biostatistics Unit, Principe Felipe Research Center（费利佩王子研究中心生物信息学与生物统计学单元）
This paper describes BIMCV COVID-19+, a large dataset from the Valencian Region Medical ImageBank (BIMCV) containing chest X-ray images CXR (CR, DX) and computed tomography (CT) imaging of COVID-19+ patients along with their radiological findings and locations, pathologies, radiological reports (in Spanish), DICOM metadata, Polymerase chain reaction (PCR), Immunoglobulin G (IgG) and Immunoglobulin M (IgM) diagnostic antibody tests. The findings have been mapped onto standard Unified Medical Language System (UMLS) terminology and cover a wide spectrum of thoracic entities, unlike the considerab…
East China University of Science and Technology（华东理工大学）；Shanghai Hospital Development Center（上海医院发展中心）
Enriching existing medical terminology knowledge bases (KBs) is an important and never-ending work for clinical research because new terminology alias may be continually added and standard terminologies may be newly renamed. In this paper, we propose a novel automatic terminology enriching approach to supplement a set of terminologies to KBs. Specifically, terminology and entity characters are first fed into pre-trained language model to obtain semantic embedding. The pre-trained model is used again to initialize the terminology and entity representations, then they are further embedded throug…
Georgia Institute of Technology（佐治亚理工学院）；Google Brain（谷歌大脑）；IBM Research（IBM研究院）；Sutter Health（萨特医疗）；HINT Consultants（HINT咨询公司）
Deep learning models exhibit state-of-the-art performance for many predictive healthcare tasks using electronic health records (EHR) data, but these models typically require training data volume that exceeds the capacity of most healthcare systems. External resources such as medical ontologies are used to bridge the data volume constraint, but this approach is often not directly applicable or useful because of inconsistencies with terminology. To solve the data insufficiency challenge, we leverage the inherent multilevel structure of EHR data and, in particular, the encoded relationships among…
Wayne State University（韦恩州立大学）；Oak Ridge National Laboratory（橡树岭国家实验室）；Louisiana State University Health Sciences Center（路易斯安那州立大学健康科学中心）；University of Kentucky（肯塔基大学）；University of Utah School of Medicine（犹他大学医学院）
A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external know…
Recent advancements in medical entity linking have been applied in the area of scientific literature and social media data. However, with the adoption of telemedicine and conversational agents such as Alexa in healthcare settings, medical name inference has become an important task. Medication name inference is the task of mapping user friendly medication names from a free-form text to a concept in a normalized medication list. This is challenging due to the differences in the use of medical terminology from health care professionals and user conversations coming from the lay public. We begin …
The collection of narrative spontaneous reports is an irreplaceable source for the prompt detection of suspected adverse drug reactions (ADRs): qualified domain experts manually revise a huge amount of narrative descriptions and then encode texts according to MedDRA standard terminology. The manual annotation of narrative documents with medical terminology is a subtle and expensive task, since the number of reports is growing up day-by-day. MagiCoder, a Natural Language Processing algorithm, is proposed for the automatic encoding of free-text descriptions into MedDRA terms. MagiCoder procedure…
Background: Clear language makes communication easier between any two parties. A layman may have difficulty communicating with a professional due to not understanding the specialized terms common to the domain. In healthcare, it is rare to find a layman knowledgeable in medical terminology which can lead to poor understanding of their condition and/or treatment. To bridge this gap, several professional vocabularies and ontologies have been created to map laymen medical terms to professional medical terms and vice versa. Objective: Many of the presented vocabularies are built manually or semi-a…
