The recognition of medical entities from natural language is an ubiquitous problem in the medical field, with applications ranging from medical act coding to the analysis of electronic health data for public health. It is however a complex task usually requiring human expert intervention, thus making it expansive and time consuming. The recent advances in artificial intelligence, specifically the raise of deep learning methods, has enabled computers to make efficient decisions on a number of complex problems, with the notable example of neural sequence models and their powerful applications in natural language processing. They however require a considerable amount of data to learn from, which is typically their main limiting factor. However, the CépiDc stores an exhaustive database of death certificates at the French national scale, amounting to several millions of natural language examples provided with their associated human coded medical entities available to the machine learning practitioner. This article investigates the applications of deep neural sequence models to the medical entity recognition from natural language problem.
We present a new corpus comprising annotations of medical entities in case reports, originating from PubMed Central's open access library. In the case reports, we annotate cases, conditions, findings, factors and negation modifiers. Moreover, where applicable, we annotate relations between these entities. As such, this is the first corpus of this kind made available to the scientific community in English. It enables the initial investigation of automatic information extraction from case reports through tasks like Named Entity Recognition, Relation Extraction and (sentence/paragraph) relevance …
TOBB University of Economics and Technology（TOBB经济与技术大学）
Early prediction of mortality and length of stay(LOS) of a patient is vital for saving a patient's life and management of hospital resources. Availability of electronic health records(EHR) makes a huge impact on the healthcare domain and there has seen several works on predicting clinical problems. However, many studies did not benefit from the clinical notes because of the sparse, and high dimensional nature. In this work, we extract medical entities from clinical notes and use them as additional features besides time-series features to improve our predictions. We propose a convolution based …
Performant ASR Models for Medical Entities in Accented Speech
CISPA Helmholtz Center for Information Security（CISPA亥姆霍兹信息安全中心）；Intron Health；Université de Lorraine（洛林大学）；CNRS（法国国家科学研究中心）；Inria（法国国家信息与自动化研究所）；LORIA（洛林计算机科学与应用实验室）；University of Minnesota - Twin Cities（明尼苏达大学双城分校）；African Masters of Machine Intelligence（非洲机器智能硕士项目）；AIMS/AMMI（非洲数学科学研究所/非洲机器智能硕士项目）；AI Saturdays Lagos（拉各斯AI周六）；Masakhane NLP（Masakhane自然语言处理项目）
This paper presents a novel approach to machine translation by combining the state of art name entity translation scheme. Improper translation of name entities lapse the quality of machine translated output. In this work, name entities are transliterated by using statistical rule based approach. This paper describes the translation and transliteration of name entities from English to Punjabi. We have experimented on four types of name entities which are: Proper names, Location names, Organization names and miscellaneous. Various rules for the purpose of syllabification have been constructed. T…
Clinical text provides essential information to estimate the acuity of a patient during hospital stays in addition to structured clinical data. In this study, we explore how clinical text can complement a clinical predictive learning task. We leverage an internal medical natural language processing service to perform named entity extraction and negation detection on clinical notes and compose selected entities into a new text corpus to train document representations. We then propose a multimodal neural network to jointly train time series signals and unstructured clinical text representations …
MIRACL, University of Sfax（斯法克斯大学MIRACL研究所）；Marin Mersenne, University Paris1（巴黎第一大学马林·梅森研究所）；Panthéon Sorbonne（先贤祠-索邦大学）；LASELDI, University of Franche-Comte（弗朗什-孔泰大学LASELDI实验室）
The recognition of Arabic Named Entities (NE) is a problem in different domains of Natural Language Processing (NLP) like automatic translation. Indeed, NE translation allows the access to multilingual in-formation. This translation doesn't always lead to expected result especially when NE contains a person name. For this reason and in order to ameliorate translation, we can transliterate some part of NE. In this context, we propose a method that integrates translation and transliteration together. We used the linguis-tic NooJ platform that is based on local grammars and transducers. In this p…
Indiana University Purdue University Indianapolis（印第安纳大学与普渡大学印第安纳波利斯联合分校）
Extracting cause-effect entities from medical literature is an important task in medical information retrieval. A solution for solving this task can be used for compilation of various causality relations, such as, causality between disease and symptoms, between medications and side effects, between genes and diseases, etc. Existing solutions for extracting cause-effect entities work well for sentences where the cause and the effect phrases are name entities, single-word nouns, or noun phrases consisting of two to three words. Unfortunately, in medical literature, cause and effect phrases in a …
University of British Columbia（不列颠哥伦比亚大学）；Curai（Curai公司）；Vatic Investments（Vatic投资公司）
Medical entity span extraction and linking are critical steps for many healthcare NLP tasks. Most existing entity extraction methods either have a fixed vocabulary of medical entities or require span annotations. In this paper, we propose a method for linking an open set of entities that does not require any span annotations. Our method, Open Set Label Attention Transformer (OSLAT), uses the label-attention mechanism to learn candidate-entity contextualized text representations. We find that OSLAT can not only link entities but is also able to implicitly learn spans associated with entities. W…
Polish Japanese Academy of Information Technology（波兰日本信息技术学院）
The quality of machine translation is rapidly evolving. Today one can find several machine translation systems on the web that provide reasonable translations, although the systems are not perfect. In some specific domains, the quality may decrease. A recently proposed approach to this domain is neural machine translation. It aims at building a jointly-tuned single neural network that maximizes translation performance, a very different approach from traditional statistical machine translation. Recently proposed neural machine translation models often belong to the encoder-decoder family in whi…
Fondazione Bruno Kessler（布鲁诺·凯斯勒基金会）；University of Trento（特伦托大学）
Automatic translation systems are known to struggle with rare words. Among these, named entities (NEs) and domain-specific terms are crucial, since errors in their translation can lead to severe meaning distortions. Despite their importance, previous speech translation (ST) studies have neglected them, also due to the dearth of publicly available resources tailored to their specific evaluation. To fill this gap, we i) present the first systematic analysis of the behavior of state-of-the-art ST systems in translating NEs and terminology, and ii) release NEuRoparl-ST, a novel benchmark built fro…
Indian Institute of Technology Patna（印度理工学院巴特那分校）；ezDI, INC（ezDI公司）
Owing to the exponential rise in the electronic medical records, information extraction in this domain is becoming an important area of research in recent years. Relation extraction between the medical concepts such as medical problem, treatment, and test etc. is also one of the most important tasks in this area. In this paper, we present an efficient relation extraction system based on the shortest dependency path (SDP) generated from the dependency parsed tree of the sentence. Instead of relying on many handcrafted features and the whole sequence of tokens present in a sentence, our system r…
Incorporating tagging into neural machine translation (NMT) systems has shown promising results in helping translate rare words such as named entities (NE). However, translating NE in low-resource setting remains a challenge. In this work, we investigate the effect of using tags and NE hypernyms from knowledge graphs (KGs) in parallel corpus in different levels of resource conditions. We find the tag-and-copy mechanism (tag the NEs in the source sentence and copy them to the target sentence) improves translation in high-resource settings only. Introducing copying also results in polarizing eff…
Zhejiang University（浙江大学）；Peking University（北京大学）；University of Cambridge（剑桥大学）；Harvard Medical School（哈佛医学院）；Westlake University（西湖大学）
The COVID-19 pandemic continues to bring up various topics discussed or debated on social media. In order to explore the impact of pandemics on people's lives, it is crucial to understand the public's concerns and attitudes towards pandemic-related entities (e.g., drugs, vaccines) on social media. However, models trained on existing named entity recognition (NER) or targeted sentiment analysis (TSA) datasets have limited ability to understand COVID-19-related social media texts because these datasets are not designed or annotated from a medical perspective. This paper releases METS-CoV, a data…
On Creating an English-Thai Code-switched Machine Translation in Medical Domain
Bangkok Christian International School（曼谷基督教国际学校）；Vidyasirimedhi Institute of Science and Technology（维迪亚西密提科技学院）；Chulalongkorn University（朱拉隆功大学）；Mahidol University（玛希隆大学）
Medical Dialogue Generation via Dual Flow Modeling
The Hong Kong Polytechnic University（香港理工大学）；Southern University of Science and Technology（南方科技大学）；Research Institute of Trustworthy Autonomous Systems（可信自主系统研究院）
The processing of entities in natural language is essential to many medical NLP systems. Unfortunately, existing datasets vastly under-represent the entities required to model public health relevant texts such as health advice often found on sites like WebMD. People rely on such information for personal health management and clinically relevant decision making. In this work, we release a new annotated dataset, HealthE, consisting of 6,756 health advice. HealthE has a more granular label space compared to existing medical NER corpora and contains annotation for diverse health phrases. Additiona…
Northeastern University（东北大学）；University of Pennsylvania（宾夕法尼亚大学）
The best evidence concerning comparative treatment effectiveness comes from clinical trials, the results of which are reported in unstructured articles. Medical experts must manually extract information from articles to inform decision-making, which is time-consuming and expensive. Here we consider the end-to-end task of both (a) extracting treatments and outcomes from full-text articles describing clinical trials (entity identification) and, (b) inferring the reported results for the former with respect to the latter (relation extraction). We introduce new data for this task, and evaluate mod…
Université de Nantes（南特大学）；LINA FRE CNRS 2729（法国国家科学研究中心LINA联合研究室（FRE 2729））；Lingua et Machina（语言与机器（机构））；Inria（法国国家信息与自动化研究所）
This paper defines a method for lexicon in the biomedical domain from comparable corpora. The method is based on compositional translation and exploits morpheme-level translation equivalences. It can generate translations for a large variety of morphologically constructed words and can also generate 'fertile' translations. We show that fertile translations increase the overall quality of the extracted lexicon for English to French translation.
University of Science and Technology of China（中国科学技术大学）；Tsinghua University（清华大学）
Recognizing useful named entities plays a vital role in medical information processing, which helps drive the development of medical area research. Deep learning methods have achieved good results in medical named entity recognition (NER). However, we find that existing methods face great challenges when dealing with the nested named entities. In this work, we propose a novel method, referred to as ASAC, to solve the dilemma caused by the nested phenomenon, in which the core idea is to model the dependency between different categories of entity recognition. The proposed method contains two key…
Kyoto University（京都大学）；Nara Institute of Science and Technology（奈良先端科学技术大学院大学）
We present an open-access natural language processing toolkit for Japanese medical information extraction. We first propose a novel relation annotation schema for investigating the medical and temporal relations between medical entities in Japanese medical reports. We experiment with the practical annotation scenarios by separately annotating two different types of reports. We design a pipeline system with three components for recognizing medical entities, classifying entity modalities, and extracting relations. The empirical results show accurate analyzing performance and suggest the satisfac…
The goal of Question Answering over Knowledge Graphs (KGQA) is to find answers for natural language questions over a knowledge graph. Recent KGQA approaches adopt a neural machine translation (NMT) approach, where the natural language question is translated into a structured query language. However, NMT suffers from the out-of-vocabulary problem, where terms in a question may not have been seen during training, impeding their translation. This issue is particularly problematic for the millions of entities that large knowledge graphs describe. We rather propose a KGQA approach that delegates th…
Although over 100 languages are supported by strong off-the-shelf machine translation systems, only a subset of them possess large annotated corpora for named entity recognition. Motivated by this fact, we leverage machine translation to improve annotation-projection approaches to cross-lingual named entity recognition. We propose a system that improves over prior entity-projection methods by: (a) leveraging machine translation systems twice: first for translating sentences and subsequently for translating entities; (b) matching entities based on orthographic and phonetic similarity; and (c) i…
Polish Japanese Institute of Information Technology（波兰日本信息技术学院）
This new research explores the effects of various training methods on a Polish to English Statistical Machine Translation system for medical texts. Various elements of the EMEA parallel text corpora from the OPUS project were used as the basis for training of phrase tables and language models and for development, tuning and testing of the translation system. The BLEU, NIST, METEOR, RIBES and TER metrics have been used to evaluate the effects of various system and data preparations on translation results. Our experiments included systems that used POS tagging, factored phrase models, hierarchic…
University of Oregon（俄勒冈大学）；Auburn University（奥本大学）；Peking University（北京大学）
Cross-lingual entity alignment, which aims to precisely connect the same entities in different monolingual knowledge bases (KBs) together, often suffers challenges from feature inconsistency to sequence context unawareness. This paper presents a dual adversarial learning framework for cross-lingual entity alignment, DAEA, with two original contributions. First, in order to address the structural and attribute feature inconsistency between entities in two knowledge graphs (KGs), an adversarial kernel embedding technique is proposed to extract graph-invariant information in an unsupervised manne…
The Natural Language Processing (NLP) community has recently seen outstanding progress, catalysed by the release of different Neural Network (NN) architectures. Neural-based approaches have proven effective by significantly increasing the output quality of a large number of automated solutions for NLP tasks (Belinkov and Glass, 2019). Despite these notable advancements, dealing with entities still poses a difficult challenge as they are rarely seen in training data. Entities can be classified into two groups, i.e., proper nouns and common nouns. Proper nouns are also known as Named Entities (N…
Multilingual Neural Machine Translation (MNMT) models leverage many language pairs during training to improve translation quality for low-resource languages by transferring knowledge from high-resource languages. We study the quality of a domain-adapted MNMT model in the medical domain for English-Romanian with automatic metrics and a human error typology annotation which includes terminology-specific error categories. We compare the out-of-domain MNMT with the in-domain adapted MNMT. The in-domain MNMT model outperforms the out-of-domain MNMT in all measured automatic metrics and produces few…
Medical entity extraction (EE) is a standard procedure used as a first stage in medical texts processing. Usually Medical EE is a two-step process: named entity recognition (NER) and named entity normalization (NEN). We propose a novel method of doing medical EE from electronic health records (EHR) as a single-step multi-label classification task by fine-tuning a transformer model pretrained on a large EHR dataset. Our model is trained end-to-end in an distantly supervised manner using targets automatically extracted from medical knowledge base. We show that our model learns to generalize for …
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）；NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London（英国国立卫生研究院生物医学研究中心（位于南伦敦和莫兹利 NHS 基金会信托与伦敦国王学院））
Biomedical documents such as Electronic Health Records (EHRs) contain a large amount of information in an unstructured format. The data in EHRs is a hugely valuable resource documenting clinical narratives and decisions, but whilst the text can be easily understood by human doctors it is challenging to use in research and clinical applications. To uncover the potential of biomedical documents we need to extract and structure the information they contain. The task at hand is Named Entity Recognition and Linking (NER+L). The number of entities, ambiguity of words, overlapping and nesting make th…
Previous studies have shown that health reports in social media, such as DailyStrength and Twitter, have potential for monitoring health conditions (e.g. adverse drug reactions, infectious diseases) in particular communities. However, in order for a machine to understand and make inferences on these health conditions, the ability to recognise when laymen's terms refer to a particular medical concept (i.e.\ text normalisation) is required. To achieve this, we propose to adapt an existing phrase-based machine translation (MT) technique and a vector representation of words to map between a social…
Comparing Large Language Models and Traditional Machine Translation Tools for Translating Medical Consultation Summaries: A Pilot Study
Faculty of Information Technology, Monash University（信息技术学院，莫纳什大学）；Faculty of Medicine, Nursing and Health Sciences, Monash University（医学、护理与健康科学学院，莫纳什大学）；Supportive and Palliative Care Unit, Monash Health（支持与姑息护理单元，莫纳什健康）
Qatar Computing Research Institute, HBKU（卡塔尔计算研究所，哈马德·本·哈利法大学）；Texas A&M University in Qatar（卡塔尔德州农工大学）
We present research towards bridging the language gap between migrant workers in Qatar and medical staff. In particular, we present the first steps towards the development of a real-world Hindi-English machine translation system for doctor-patient communication. As this is a low-resource language pair, especially for speech and for the medical domain, our initial focus has been on gathering suitable training data from various sources. We applied a variety of methods ranging from fully automatic extraction from the Web to manual annotation of test data. Moreover, we developed a method for autom…
Text mining and information extraction for the medical domain has focused on scientific text generated by researchers. However, their direct access to individual patient experiences or patient-doctor interactions can be limited. Information provided on social media, e.g., by patients and their relatives, complements the knowledge in scientific text. It reflects the patient's journey and their subjective perspective on the process of developing symptoms, being diagnosed and offered a treatment, being cured or learning to live with a medical condition. The value of this type of data is therefore…
When comparing entities extracted by a medical entity recognition system with gold standard annotations over a test set, two types of mismatches might occur, label mismatch or span mismatch. Here we focus on span mismatch and show that its severity can vary from a serious error to a fully acceptable entity extraction due to the subjectivity of span annotations. For a domain-specific BERT-based NER system, we showed that 25% of the errors have the same labels and overlapping span with gold standard entities. We collected expert judgement which shows more than 90% of these mismatches are accepte…
MultiMed-ST: Large-scale Many-to-many Multilingual Medical Speech Translation
University of Toronto（多伦多大学）；University Health Network（大学健康网络）；Knovel Engineering Lab（Knovel 工程实验室）；Hanoi University of Science and Technology（河内科技大学）；KU Leuven（鲁汶大学）；Eötvös Loránd University（罗兰大学）；HCMC Open University（胡志明市开放大学）；IÉSEG School of Management（IÉSEG 管理学院）；Technische Universität Dortmund（多特蒙德工业大学）；University of Hertfordshire（赫特福德大学）；UC Berkeley（加州大学伯克利分校）；New Jersey Institute of Technology（新泽西理工学院）
Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integr…
The development of conversational agents to interact with patients and deliver clinical advice has attracted the interest of many researchers, particularly in light of the COVID-19 pandemic. The training of an end-to-end neural based dialog system, on the other hand, is hampered by a lack of multi-turn medical dialog corpus. We make the very first attempt to release a high-quality multi-turn Medical Dialog dataset relating to Covid-19 disease named CDialog, with over 1K conversations collected from the online medical counselling websites. We annotate each utterance of the conversation with sev…
Machine Transliteration has come out to be an emerging and a very important research area in the field of machine translation. Transliteration basically aims to preserve the phonological structure of words. Proper transliteration of name entities plays a very significant role in improving the quality of machine translation. In this paper we are doing machine transliteration for English-Punjabi language pair using rule based approach. We have constructed some rules for syllabification. Syllabification is the process to extract or separate the syllable from the words. In this we are calculating …
University of Paderborn（帕德博恩大学）；Insight Centre for Data Analytics, Data Science Institute National University of Ireland Galway（爱尔兰国立高威大学数据科学研究院洞察数据分析中心）
While neural networks have been used extensively to make substantial progress in the machine translation task, they are known for being heavily dependent on the availability of large amounts of training data. Recent efforts have tried to alleviate the data sparsity problem by augmenting the training data using different strategies, such as back-translation. Along with the data scarcity, the out-of-vocabulary words, mostly entities and terminological expressions, pose a difficult challenge to Neural Machine Translation systems. In this paper, we hypothesize that knowledge graphs enhance the sem…
MedCOD: Enhancing English-to-Spanish Medical Translation of Large Language Models Using Enriched Chain-of-Dictionary Framework
Center for Healthcare Organization and Implementation Research, VA Bedford Health Care（医疗组织与实施研究中心，VA贝德福德医疗中心）；Miner School of Computer and Information Sciences, University of Massachusetts Lowell（矿物计算机与信息科学学院，马萨诸塞州立大学洛厄尔分校）；Manning College of Information and Computer Sciences, University of Massachusetts Amherst（曼宁信息与计算机科学学院，马萨诸塞州立大学阿姆赫斯特分校）
Neural Machine Translation (NMT) has been shown to struggle with grammatical gender that is dependent on the gender of human referents, which can cause gender bias effects. Many existing approaches to this problem seek to control gender inflection in the target language by explicitly or implicitly adding a gender feature to the source sentence, usually at the sentence level. In this paper we propose schemes for incorporating explicit word-level gender inflection tags into NMT. We explore the potential of this gender-inflection controlled translation when the gender feature can be determined fr…
Comprehend Medical is a stateless and Health Insurance Portability and Accountability Act (HIPAA) eligible Named Entity Recognition (NER) and Relationship Extraction (RE) service launched under Amazon Web Services (AWS) trained using state-of-the-art deep learning models. Contrary to many existing open source tools, Comprehend Medical is scalable and does not require steep learning curve, dependencies, pipeline configurations, or installations. Currently, Comprehend Medical performs NER in five medical categories: Anatomy, Medical Condition, Medications, Protected Health Information (PHI) and …
Llettuce: An Open Source Natural Language Processing Tool for the Translation of Medical Terms into Uniform Clinical Encoding
Centre for Health Informatics, School of Medicine, The University of Nottingham（诺丁汉大学医学院健康信息学中心）；Digital Research Service, The University of Nottingham（诺丁汉大学数字研究服务）；NIHR Nottingham Biomedical Research Centre（尼日利亚生物医学研究中心）；Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore（南洋理工大学新加坡李科贤医学院）；Department of Software Engineering, Andalusian Institute of Data Science and Computational Intelligence (DaSCI), University of Granada, 18012, Granada, Spain（安达卢西亚数据科学与计算智能研究所（DaSCI）软件工程系，格拉纳达大学，18012，格拉纳达，西班牙）
East China University of Science and Technology（华东理工大学）；Tongji University（同济大学）
The medical dialogue system is a promising application that can provide great convenience for patients. The dialogue state tracking (DST) module in the medical dialogue system which interprets utterances into the machine-readable structure for downstream tasks is particularly challenging. Firstly, the states need to be able to represent compound entities such as symptoms with their body part or diseases with degrees of severity to provide enough information for decision support. Secondly, these named entities in the utterance might be discontinuous and scattered across sentences and speakers. …
