Medical knowledge bases (KBs), distilled from biomedical literature and regulatory actions, are expected to provide high-quality information to facilitate clinical decision making. Entity disambiguation (also referred to as entity linking) is considered as an essential task in unlocking the wealth of such medical KBs. However, existing medical entity disambiguation methods are not adequate due to word discrepancies between the entities in the KB and the text snippets in the source documents. Recently, graph neural networks (GNNs) have proven to be very effective and provide state-of-the-art results for many real-world applications with graph-structured data. In this paper, we introduce ED-GNN based on three representative GNNs (GraphSAGE, R-GCN, and MAGNN) for medical entity disambiguation. We develop two optimization techniques to fine-tune and improve ED-GNN. First, we introduce a novel strategy to represent entities that are mentioned in text snippets as a query graph. Second, we design an effective negative sampling strategy that identifies hard negative samples to improve the model's disambiguation capability. Compared to the best performing state-of-the-art solutions, our ED-GNN offers an average improvement of 7.3% in terms of F1 score on five real-world datasets.
Named Entity Disambiaguation (NED) is a central task for applications dealing with natural language text. Assume that we have a graph based knowledge base (subsequently referred as Knowledge Graph) where nodes represent various real world entities such as people, location, organization and concepts. Given data sources such as social media streams and web pages Entity Linking is the task of mapping named entities that are extracted from the data to those present in the Knowledge Graph. This is an inherently difficult task due to several reasons. Almost all these data sources are generated witho…
Entity disambiguation (ED) is the last step of entity linking (EL), when candidate entities are reranked according to the context they appear in. All datasets for training and evaluating models for EL consist of convenience samples, such as news articles and tweets, that propagate the prior probability bias of the entity distribution towards more frequently occurring entities. It was previously shown that the performance of the EL systems on such datasets is overestimated since it is possible to obtain higher accuracy scores by merely learning the prior. To provide a more adequate evaluation b…
Entity Linking is one of the essential tasks of information extraction and natural language understanding. Entity linking mainly consists of two tasks: recognition and disambiguation of named entities. Most studies address these two tasks separately or focus only on one of them. Moreover, most of the state-of-the -art entity linking algorithms are either supervised, which have poor performance in the absence of annotated corpora or language-dependent, which are not appropriate for multi-lingual applications. In this paper, we introduce an Unsupervised Language-Independent Entity Disambiguation…
University of California, Irvine（加州大学欧文分校）；Apple（苹果公司）
Retrieval is a core component for open-domain NLP tasks. In open-domain tasks, multiple entities can share a name, making disambiguation an inherent yet under-explored problem. We propose an evaluation benchmark for assessing the entity disambiguation capabilities of these retrievers, which we call Ambiguous Entity Retrieval (AmbER) sets. We define an AmbER set as a collection of entities that share a name along with queries about those entities. By covering the set of entities for polysemous names, AmbER sets act as a challenging test of entity disambiguation. We create AmbER sets for three p…
University of Bonn（波恩大学）；Fraunhofer IAIS（弗劳恩霍夫应用信息技术研究所）；Ruhr University Bochum（波鸿鲁尔大学）
Entity linking - connecting entity mentions in a natural language utterance to knowledge graph (KG) entities is a crucial step for question answering over KGs. It is often based on measuring the string similarity between the entity label and its mention in the question. The relation referred to in the question can help to disambiguate between entities with the same label. This can be misleading if an incorrect relation has been identified in the relation linking step. However, an incorrect relation may still be semantically similar to the relation in which the correct entity forms a triple wit…
A challenge for named entity disambiguation (NED), the task of mapping textual mentions to entities in a knowledge base, is how to disambiguate entities that appear rarely in the training data, termed tail entities. Humans use subtle reasoning patterns based on knowledge of entity facts, relations, and types to disambiguate unfamiliar entities. Inspired by these patterns, we introduce Bootleg, a self-supervised NED system that is explicitly grounded in reasoning patterns for disambiguation. We define core reasoning patterns for disambiguation, create a learning procedure to encourage the self-…
The Entity Disambiguation and Linking (EDL) task matches entity mentions in text to a unique Knowledge Base (KB) identifier such as a Wikipedia or Freebase id. It plays a critical role in the construction of a high quality information network, and can be further leveraged for a variety of information retrieval and NLP tasks such as text categorization and document tagging. EDL is a complex and challenging problem due to ambiguity of the mentions and real world text being multi-lingual. Moreover, EDL systems need to have high throughput and should be lightweight in order to scale to large datas…
University of California, San Diego（加州大学圣地亚哥分校）；Meta AI
We propose an autoregressive entity linking model, that is trained with two auxiliary tasks, and learns to re-rank generated samples at inference time. Our proposed novelties address two weaknesses in the literature. First, a recent method proposes to learn mention detection and then entity candidate selection, but relies on predefined sets of candidates. We use encoder-decoder autoregressive entity linking in order to bypass this need, and propose to train mention detection as an auxiliary task instead. Second, previous work suggests that re-ranking could help correct prediction errors. We ad…
InfAI, University of Leipzig（莱比锡大学 InfAI）；AKSW, University of Leipzig（莱比锡大学 AKSW）；SDA Research Group, University of Bonn（波恩大学 SDA 研究组）
Named Entity Recognition and Disambiguation (NERD) systems have recently been widely researched to deal with the significant growth of the Web. NERD systems are crucial for several Natural Language Processing (NLP) tasks such as summarization, understanding, and machine translation. However, there is no standard interface specification, i.e. these systems may vary significantly either for exporting their outputs or for processing the inputs. Thus, when a given company desires to implement more than one NERD system, the process is quite exhaustive and prone to failure. In addition, industrial s…
University of Sheffield（谢菲尔德大学）；EURECOM；Università di Torino（都灵大学）；VU University Amsterdam（阿姆斯特丹自由大学）
Applying natural language processing for mining and intelligent information access to tweets (a form of microblog) is a challenging, emerging research area. Unlike carefully authored news text and other longer content, tweets pose a number of new challenges, due to their short, noisy, context-dependent, and dynamic nature. Information extraction from tweets is typically performed in a pipeline, comprising consecutive stages of language identification, tokenisation, part-of-speech tagging, named entity recognition and entity disambiguation (e.g. with respect to DBpedia). In this work, we descri…
Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text spans to be annotated as more than one type when simultaneously recognizing multiple entity types. The straightforward solution is a rule-based approach applying a priority order based on the precision of each entity tagger (from highest to lowest). While this method is straightforward and useful, imprecise disambiguation remains a significant source of error. W…
Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate a large volume of clinical records and biomedical literature, to standardized concepts described in an ontology such as Unified Medical Language System (UMLS). We observe that with precise type information, entity disambiguation becomes a straightforward task. However, fine-grained type information is usually not available in biomedical domain. Thus, we prop…
A typical architecture for end-to-end entity linking systems consists of three steps: mention detection, candidate generation and entity disambiguation. In this study we investigate the following questions: (a) Can all those steps be learned jointly with a model for contextualized text-representations, i.e. BERT (Devlin et al., 2019)? (b) How much entity knowledge is already contained in pretrained BERT? (c) Does additional entity knowledge improve BERT's performance in downstream tasks? To this end, we propose an extreme simplification of the entity linking setup that works surprisingly well:…
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）
We propose an 'end-to-end' character-based recurrent neural network that extracts disease named entities from a Japanese medical text and simultaneously judges its modality as either positive or negative; i.e., the mentioned disease or symptom is affirmed or negated. The motivation to adopt neural networks is to learn effective lexical and structural representation features for Entity Recognition and also for Positive/Negative classification from an annotated corpora without explicitly providing any rule-based or manual feature sets. We confirmed the superiority of our method over previous cha…
BlackRock（贝莱德）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
We propose yet another entity linking model (YELM) which links words to entities instead of spans. This overcomes any difficulties associated with the selection of good candidate mention spans and makes the joint training of mention detection (MD) and entity disambiguation (ED) easily possible. Our model is based on BERT and produces contextualized word embeddings which are trained against a joint MD and ED objective. We achieve state-of-the-art results on several standard entity linking (EL) datasets.
Carnegie Mellon University（卡内基梅隆大学）；University of Pittsburgh（匹兹堡大学）
Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate concepts, and finally (3) picking the best concept among them. In this paper, we probe into alleviating the problem of overgeneration of candidate concepts in the candidate generation module, the most under-studied component of medical entity linking. For this, we present MedType, a fully modular system that prunes out irrelevant candidate concepts based on…
Weill Cornell Medical College, Cornell University（康奈尔大学威尔康奈尔医学院）；University of California Berkeley（加州大学伯克利分校）；Harbin Institute of Technology（哈尔滨工业大学）
State-of-the-art studies have demonstrated the superiority of joint modelling over pipeline implementation for medical named entity recognition and normalization due to the mutual benefits between the two processes. To exploit these benefits in a more sophisticated way, we propose a novel deep neural multi-task learning framework with explicit feedback strategies to jointly model recognition and normalization. On one hand, our method benefits from the general representations of both tasks provided by multi-task learning. On the other hand, our method successfully converts hierarchical tasks in…
Named entities recognition (NER) and disambiguation (NED) can add semantic context to the recognized named entities in texts. Named entity linkage in texts, regardless of a domain, provides links between the entities mentioned in unstructured texts and individual instances of real-world objects. In this poster, we present a tool - protagonistTagger - for person NER and NED in texts. The tool was tested on texts extracted from classic English novels and Polish Internet news. The tool's performance (both precision and recall) fluctuates between 78% and even 88%.
University of Amsterdam（阿姆斯特丹大学）；University of Edinburgh（爱丁堡大学）
Generative approaches have been recently shown to be effective for both Entity Disambiguation and Entity Linking (i.e., joint mention detection and disambiguation). However, the previously proposed autoregressive formulation for EL suffers from i) high computational cost due to a complex (deep) decoder, ii) non-parallelizable decoding that scales with the source sequence length, and iii) the need for training on a large amount of data. In this work, we propose a very efficient approach that parallelizes autoregressive linking across all potential mentions and relies on a shallow and efficient …
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 …
University of Rostock（罗斯托克大学）；GESIS - Leibniz Institute for the Social Sciences（莱布尼茨社会科学研究所）；Heinrich-Heine-University（海因里希·海涅大学）
Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but rather mentioned informally within the scholarly description of the investigation, raising the need for automatic information extraction and disambiguation. Given the lack of reliable ground truth data, we present SoMeSci (Software Mentions in Science) a gold standard knowledge graph of software mentions in scientific articles. It contains high quality annot…
Ubiquitous Knowledge Processing Lab (UKP)（普适知识处理实验室（UKP））；Research Training Group AIPHES（AIPHES研究培训小组）；Department of Computer Science, Technische Universität Darmstadt（达姆施塔特工业大学计算机科学系）
The first stage of every knowledge base question answering approach is to link entities in the input question. We investigate entity linking in the context of a question answering task and present a jointly optimized neural architecture for entity mention detection and entity disambiguation that models the surrounding context on different levels of granularity. We use the Wikidata knowledge base and available question answering datasets to create benchmarks for entity linking on question answering data. Our approach outperforms the previous state-of-the-art system on this data, resulting in an…
Pre-trained Language Models and Few-shot Learning for Medical Entity Extraction
Santa Clara University（圣克拉拉大学）；San Francisco State University（旧金山州立大学）；Cornell University（康奈尔大学）；The Chinese University of Hong Kong（香港中文大学）；Stevens Institute of Technology（史蒂文斯理工学院）
Universität Hamburg（汉堡大学）；Indian Institute of Technology (BHU)（印度理工学院（瓦拉纳西））
In this work, we present an end-to-end Knowledge Graph Question Answering (KGQA) system named GETT-QA. GETT-QA uses T5, a popular text-to-text pre-trained language model. The model takes a question in natural language as input and produces a simpler form of the intended SPARQL query. In the simpler form, the model does not directly produce entity and relation IDs. Instead, it produces corresponding entity and relation labels. The labels are grounded to KG entity and relation IDs in a subsequent step. To further improve the results, we instruct the model to produce a truncated version of the KG…
Labex Observatoire de la vie littéraire (OBVIL)（文学生活观察实验室）；Laboratoire d’Informatique de Paris 6 (LIP6), Pierre and Marie Curie University（巴黎第六大学计算机实验室）
Many Entity Linking systems use collective graph-based methods to disambiguate the entity mentions within a document. Most of them have focused on graph construction and initial weighting of the candidate entities, less attention has been devoted to compare the graph ranking algorithms. In this work, we focus on the graph-based ranking algorithms, therefore we propose to apply five centrality measures: Degree, HITS, PageRank, Betweenness and Closeness. A disambiguation graph of candidate entities is constructed for each document using the popularity method, then centrality measures are applied…
University of Zagreb（萨格勒布大学）；University of Konstanz（康斯坦茨大学）；EPFL（洛桑联邦理工学院）
Named entity linking (NEL) in news is a challenging endeavour due to the frequency of unseen and emerging entities, which necessitates the use of unsupervised or zero-shot methods. However, such methods tend to come with caveats, such as no integration of suitable knowledge bases (like Wikidata) for emerging entities, a lack of scalability, and poor interpretability. Here, we consider person disambiguation in Quotebank, a massive corpus of speaker-attributed quotations from the news, and investigate the suitability of intuitive, lightweight, and scalable heuristics for NEL in web-scale corpora…
University of Amsterdam（阿姆斯特丹大学）；Sapienza University of Rome（罗马第一大学）；Babelscape；Amazon Alexa AI（亚马逊Alexa AI）
Entity disambiguation (ED) is the task of mapping an ambiguous entity mention to the corresponding entry in a structured knowledge base. Previous research showed that entity overshadowing is a significant challenge for existing ED models: when presented with an ambiguous entity mention, the models are much more likely to rank a more frequent yet less contextually relevant entity at the top. Here, we present NICE, an iterative approach that uses entity type information to leverage context and avoid over-relying on the frequency-based prior. Our experiments show that NICE achieves the best perfo…
We introduce ReFinED, an efficient end-to-end entity linking model which uses fine-grained entity types and entity descriptions to perform linking. The model performs mention detection, fine-grained entity typing, and entity disambiguation for all mentions within a document in a single forward pass, making it more than 60 times faster than competitive existing approaches. ReFinED also surpasses state-of-the-art performance on standard entity linking datasets by an average of 3.7 F1. The model is capable of generalising to large-scale knowledge bases such as Wikidata (which has 15 times more en…
Tsinghua University（清华大学）；Microsoft Research Asia（微软亚洲研究院）
Medical named entity recognition (NER) has wide applications in intelligent healthcare. Sufficient labeled data is critical for training accurate medical NER model. However, the labeled data in a single medical platform is usually limited. Although labeled datasets may exist in many different medical platforms, they cannot be directly shared since medical data is highly privacy-sensitive. In this paper, we propose a privacy-preserving medical NER method based on federated learning, which can leverage the labeled data in different platforms to boost the training of medical NER model and remove …
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…
Accurate Medical Named Entity Recognition Through Specialized NLP Models
Tulane University（杜兰大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；University of Pennsylvania（宾夕法尼亚大学）；New York University（纽约大学）；University of Houston（休斯顿大学）
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）
Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the same time, the language model has achieved excellent results in more and more natural language processing tasks. In this paper, we present a focused attention model for the joint entity and relation extraction task. Our model integrates well-known BERT language model into joint learning through dynamic range attention mechanism, thus improving the feature repre…
We present a new local entity disambiguation system. The key to our system is a novel approach for learning entity representations. In our approach we learn an entity aware extension of Embedding for Language Model (ELMo) which we call Entity-ELMo (E-ELMo). Given a paragraph containing one or more named entity mentions, each mention is first defined as a function of the entire paragraph (including other mentions), then they predict the referent entities. Utilizing E-ELMo for local entity disambiguation, we outperform all of the state-of-the-art local and global models on the popular benchmarks…
Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also be used for merging different medical and clinical ontologies. In this paper, we center around the problem of disease linking or normalization. This task is executed in two phases: candidate generation and candidate scoring. In this paper, we present an approach to rank the candidate Knowledge Base entries based on their similarity with disease mention. We …
Entity Linking (EL) is an essential task for semantic text understanding and information extraction. Popular methods separately address the Mention Detection (MD) and Entity Disambiguation (ED) stages of EL, without leveraging their mutual dependency. We here propose the first neural end-to-end EL system that jointly discovers and links entities in a text document. The main idea is to consider all possible spans as potential mentions and learn contextual similarity scores over their entity candidates that are useful for both MD and ED decisions. Key components are context-aware mention embeddi…
Institute of Computer Science, Polish Academy of Sciences（波兰科学院计算机科学研究所）
In this paper an open-domain factoid question answering system for Polish, RAFAEL, is presented. The system goes beyond finding an answering sentence; it also extracts a single string, corresponding to the required entity. Herein the focus is placed on different approaches to entity recognition, essential for retrieving information matching question constraints. Apart from traditional approach, including named entity recognition (NER) solutions, a novel technique, called Deep Entity Recognition (DeepER), is introduced and implemented. It allows a comprehensive search of all forms of entity ref…
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…
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…
Rutgers University–New Brunswick（罗格斯大学新伯朗士威校区）；Hasso Plattner Institute（哈索·普拉特纳研究所）；University of Potsdam（波茨坦大学）
Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a retrieve and rerank paradigm, where the candidate entities are first selected using a retriever model, and then the retrieved candidates are ranked by a reranker model. While this paradigm produces state-of-the-art results, they are slow both at training and test time as they can process only one mention at a time. To mitigate these issues, we propose a BERT-bas…
Language Technology Group, Universität Hamburg（汉堡大学语言技术组）；Fraunhofer IAIS（弗劳恩霍夫智能分析与信息系统研究所）；Smart Data Analytics Group, University of Bonn（波恩大学智能数据分析组）
Question Answering systems are generally modelled as a pipeline consisting of a sequence of steps. In such a pipeline, Entity Linking (EL) is often the first step. Several EL models first perform span detection and then entity disambiguation. In such models errors from the span detection phase cascade to later steps and result in a drop of overall accuracy. Moreover, lack of gold entity spans in training data is a limiting factor for span detector training. Hence the movement towards end-to-end EL models began where no separate span detection step is involved. In this work we present a novel a…
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 …
University of Wisconsin – Eau Claire（威斯康星大学欧克莱尔分校）
Physicians provide expert opinion to legal courts on the medical state of patients, including determining if a patient is likely to have permanent or non-permanent injuries or ailments. An independent medical examination (IME) report summarizes a physicians medical opinion about a patients health status based on the physicians expertise. IME reports contain private and sensitive information (Personally Identifiable Information or PII) that needs to be removed or randomly encoded before further research work can be conducted. In our study the IME is an orthopedic surgeon from a private practice…
We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for …
Named Entity Recognition and Disambiguation (NERD) systems are foundational for information retrieval, question answering, event detection, and other natural language processing (NLP) applications. We introduce TweetNERD, a dataset of 340K+ Tweets across 2010-2021, for benchmarking NERD systems on Tweets. This is the largest and most temporally diverse open sourced dataset benchmark for NERD on Tweets and can be used to facilitate research in this area. We describe evaluation setup with TweetNERD for three NERD tasks: Named Entity Recognition (NER), Entity Linking with True Spans (EL), and End…
University of Cambridge（剑桥大学）；University College London（伦敦大学学院）
Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language. Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain. To address this we introduce a new corpus called COMETA, consisting of 20k English biomedical entity mentions from Reddit expert-annotated with links to SNOMED CT, a widely-used medical knowledge graph. Our corpus satisfies a combination of desirable properties, from scale and coverage to diversity and qu…
This paper summarizes the CLaC submission for SMM4H 2022 Task 10 which concerns the recognition of diseases mentioned in Spanish tweets. Before classifying each token, we encode each token with a transformer encoder using features from Multilingual RoBERTa Large, UMLS gazetteer, and DISTEMIST gazetteer, among others. We obtain a strict F1 score of 0.869, with competition mean of 0.675, standard deviation of 0.245, and median of 0.761.
Bell Labs, Nokia（诺基亚贝尔实验室）；University College Dublin（都柏林大学学院）
Entity disambiguation, or mapping a phrase to its canonical representation in a knowledge base, is a fundamental step in many natural language processing applications. Existing techniques based on global ranking models fail to capture the individual peculiarities of the words and hence, either struggle to meet the accuracy requirements of many real-world applications or they are too complex to satisfy real-time constraints of applications. In this paper, we propose a new disambiguation system that learns specialized features and models for disambiguating each ambiguous phrase in the English la…
