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-based dual encoder model that resolves multiple mentions in a document in one shot. We show that our proposed model is multiple times faster than existing BERT-based models while being competitive in accuracy for biomedical entity linking. Additionally, we modify our dual encoder model for end-to-end biomedical entity linking that performs both mention span detection and entity disambiguation and out-performs two recently proposed models.
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；Megagon Labs（Megagon实验室）
We introduce BioCoM, a contrastive learning framework for biomedical entity linking that uses only two resources: a small-sized dictionary and a large number of raw biomedical articles. Specifically, we build the training instances from raw PubMed articles by dictionary matching and use them to train a context-aware entity linking model with contrastive learning. We predict the normalized biomedical entity at inference time through a nearest-neighbor search. Results found that BioCoM substantially outperforms state-of-the-art models, especially in low-resource settings, by effectively using th…
Korea University（高丽大学）；AIRS Company, Hyundai Motor Group（现代汽车集团AIRS公司）；AIGEN Sciences（AIGEN科学公司）
In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical…
This paper introduces a new model that uses named entity recognition, coreference resolution, and entity linking techniques, to approach the task of linking people entities on Wikipedia people pages to their corresponding Wikipedia pages if applicable. Our task is different from general and traditional entity linking because we are working in a limited domain, namely, people entities, and we are including pronouns as entities, whereas in the past, pronouns were never considered as entities in entity linking. We have built 2 models, both outperforms our baseline model significantly. The purpose…
College of Information and Computer Sciences University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校信息与计算机科学学院）；Chan Zuckerberg Initiative（陈-扎克伯格倡议）
Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using learned representations of entities. Previous approaches link each mention independently, ignoring the relationships within and across documents between the entity mentions. These relations can be very useful for linking mentions in biomedical text where linking decisions are often difficult due mentions having a generic or a highly specialized form. In this pa…
Institut Polytechnique de Paris（巴黎综合理工学院）；Inria（法国国家信息与自动化研究所）；CEA（法国原子能和替代能源委员会）
Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names, including synonyms, morphological variations, and names with different word orderings. Recently, BERT-based methods have advanced the state-of-the-art by allowing for rich representations of word sequences. However, they often have hundreds of millions of parameters and require heavy computing resources, which limits their applications in resource-limited s…
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…
Fine-grained entity typing is a challenging problem since it usually involves a relatively large tag set and may require to understand the context of the entity mention. In this paper, we use entity linking to help with the fine-grained entity type classification process. We propose a deep neural model that makes predictions based on both the context and the information obtained from entity linking results. Experimental results on two commonly used datasets demonstrates the effectiveness of our approach. On both datasets, it achieves more than 5\% absolute strict accuracy improvement over the …
This paper describes the system proposed by Sabancı University Natural Language Processing Group in the SemEval-2022 MultiCoNER task. We developed an unsupervised entity linking pipeline that detects potential entity mentions with the help of Wikipedia and also uses the corresponding Wikipedia context to help the classifier in finding the named entity type of that mention. Our results showed that our pipeline improved performance significantly, especially for complex entities in low-context settings.
University of Edinburgh（爱丁堡大学）；University of Amsterdam（阿姆斯特丹大学）
Entity linking involves aligning textual mentions of named entities to their corresponding entries in a knowledge base. Entity linking systems often exploit relations between textual mentions in a document (e.g., coreference) to decide if the linking decisions are compatible. Unlike previous approaches, which relied on supervised systems or heuristics to predict these relations, we treat relations as latent variables in our neural entity-linking model. We induce the relations without any supervision while optimizing the entity-linking system in an end-to-end fashion. Our multi-relational model…
Zhejiang Gongshang University（浙江工商大学）；Massey University（梅西大学）；National University of Defense Technology（国防科技大学）；Shanghai Research Center for Brain Science and Brain-Inspired Intelligence（上海脑科学与类脑研究中心）；Zhangjiang Lab（张江实验室）
Entity embeddings, which represent different aspects of each entity with a single vector like word embeddings, are a key component of neural entity linking models. Existing entity embeddings are learned from canonical Wikipedia articles and local contexts surrounding target entities. Such entity embeddings are effective, but too distinctive for linking models to learn contextual commonality. We propose a simple yet effective method, FGS2EE, to inject fine-grained semantic information into entity embeddings to reduce the distinctiveness and facilitate the learning of contextual commonality. FGS…
We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction t…
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…
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…
Harbin Institute of Technology（哈尔滨工业大学）；Microsoft Research Asia（微软亚洲研究院）；Peng Cheng Laboratory（鹏城实验室）
Existing state of the art neural entity linking models employ attention-based bag-of-words context model and pre-trained entity embeddings bootstrapped from word embeddings to assess topic level context compatibility. However, the latent entity type information in the immediate context of the mention is neglected, which causes the models often link mentions to incorrect entities with incorrect type. To tackle this problem, we propose to inject latent entity type information into the entity embeddings based on pre-trained BERT. In addition, we integrate a BERT-based entity similarity score into…
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.
Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-tra…
We consider the task of document-level entity linking (EL), where it is important to make consistent decisions for entity mentions over the full document jointly. We aim to leverage explicit "connections" among mentions within the document itself: we propose to join the EL task with that of coreference resolution (coref). This is complementary to related works that exploit either (i) implicit document information (e.g., latent relations among entity mentions, or general language models) or (ii) connections between the candidate links (e.g, as inferred from the external knowledge base). Specifi…
Instituto de Telecomunicações（电信研究所）；Priberam Labs（Priberam实验室）；Institute of Systems and Robotics（系统与机器人研究所）；Unbabel
Named entity recognition (NER) and entity linking (EL) are two fundamentally related tasks, since in order to perform EL, first the mentions to entities have to be detected. However, most entity linking approaches disregard the mention detection part, assuming that the correct mentions have been previously detected. In this paper, we perform joint learning of NER and EL to leverage their relatedness and obtain a more robust and generalisable system. For that, we introduce a model inspired by the Stack-LSTM approach (Dyer et al., 2015). We observe that, in fact, doing multi-task learning of NER…
The number of biomedical literature on new biomedical concepts is rapidly increasing, which necessitates a reliable biomedical named entity recognition (BioNER) model for identifying new and unseen entity mentions. However, it is questionable whether existing models can effectively handle them. In this work, we systematically analyze the three types of recognition abilities of BioNER models: memorization, synonym generalization, and concept generalization. We find that although current best models achieve state-of-the-art performance on benchmarks based on overall performance, they have limita…
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；Megagon Labs（Megagon实验室）
Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual benefits. While this approach achieves high performance, disease concepts that do not appear in the training dataset cannot be accurately predicted. This study introduces a novel end-to-end approach that combines span representations with dictionary-matching features to address this problem. Our model handles unseen concepts by referring to a dictionary while mai…
We introduce and make publicly available an entity linking dataset from Reddit that contains 17,316 linked entities, each annotated by three human annotators and then grouped into Gold, Silver, and Bronze to indicate inter-annotator agreement. We analyze the different errors and disagreements made by annotators and suggest three types of corrections to the raw data. Finally, we tested existing entity linking models that are trained and tuned on text from non-social media datasets. We find that, although these existing entity linking models perform very well on their original datasets, they per…
Facebook AI Research（Facebook人工智能研究（Facebook AI Research））；University College London（伦敦大学学院）；Ecole Polytechnique Federale de Lausanne（洛桑联邦理工学院）
This paper introduces a conceptually simple, scalable, and highly effective BERT-based entity linking model, along with an extensive evaluation of its accuracy-speed trade-off. We present a two-stage zero-shot linking algorithm, where each entity is defined only by a short textual description. The first stage does retrieval in a dense space defined by a bi-encoder that independently embeds the mention context and the entity descriptions. Each candidate is then re-ranked with a cross-encoder, that concatenates the mention and entity text. Experiments demonstrate that this approach is state of t…
Previous work on Entity Linking has focused on resources targeting non-nested proper named entity mentions, often in data from Wikipedia, i.e. Wikification. In this paper, we present and evaluate WikiGUM, a fully wikified dataset, covering all mentions of named entities, including their non-named and pronominal mentions, as well as mentions nested within other mentions. The dataset covers a broad range of 12 written and spoken genres, most of which have not been included in Entity Linking efforts to date, leading to poor performance by a pretrained SOTA system in our evaluation. The availabili…
Microsoft Research（微软研究院）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision ($\…
BioMNER: A Dataset for Biomedical Method Entity Recognition
University of Surrey（萨里大学）；The University of Manchester（曼彻斯特大学）；University of Pittsburgh（匹兹堡大学）；Chinese Academy of Sciences（中国科学院）；Durham University（杜伦大学）
Entity Linking aims to link entity mentions in texts to knowledge bases, and neural models have achieved recent success in this task. However, most existing methods rely on local contexts to resolve entities independently, which may usually fail due to the data sparsity of local information. To address this issue, we propose a novel neural model for collective entity linking, named as NCEL. NCEL applies Graph Convolutional Network to integrate both local contextual features and global coherence information for entity linking. To improve the computation efficiency, we approximately perform grap…
A key challenge in entity linking is making effective use of contextual information to disambiguate mentions that might refer to different entities in different contexts. We present a model that uses convolutional neural networks to capture semantic correspondence between a mention's context and a proposed target entity. These convolutional networks operate at multiple granularities to exploit various kinds of topic information, and their rich parameterization gives them the capacity to learn which n-grams characterize different topics. We combine these networks with a sparse linear model to a…
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…
Humboldt-Universität zu Berlin（柏林洪堡大学）；GFZ German Research Centre for Geosciences（德国地学研究中心）
Summary: Named Entity Recognition (NER) is an important step in biomedical information extraction pipelines. Tools for NER should be easy to use, cover multiple entity types, highly accurate, and robust towards variations in text genre and style. To this end, we propose HunFlair, an NER tagger covering multiple entity types integrated into the widely used NLP framework Flair. HunFlair outperforms other state-of-the-art standalone NER tools with an average gain of 7.26 pp over the next best tool, can be installed with a single command and is applied with only four lines of code. Availability: H…
Automated entity relation extraction (RE) from literature provides an important source for constructing biomedical database, which is more efficient and extensible than manual curation. However, existing RE models usually ignore the information contained in sentence structures and target entities. In this paper, we propose BERE, a deep learning based model which uses Gumbel Tree-GRU to learn sentence structures and joint embedding to incorporate entity information. It also employs word-level attention for improved relation extraction and sentence-level attention to suit the distantly supervise…
Fraunhofer IAIS, University of Bonn, Germany（德国波恩大学弗劳恩霍夫研究所人工智能研究所（Fraunhofer IAIS））；Cerence GmbH, and Zerotha Research, Germany（德国Cerence GmbH公司，以及Zerotha Research）；TIB, Hannover, Germany（德国汉诺威技术信息中心（TIB））；University of Dayton, USA（美国代顿大学）
The collaborative knowledge graphs such as Wikidata excessively rely on the crowd to author the information. Since the crowd is not bound to a standard protocol for assigning entity titles, the knowledge graph is populated by non-standard, noisy, long or even sometimes awkward titles. The issue of long, implicit, and nonstandard entity representations is a challenge in Entity Linking (EL) approaches for gaining high precision and recall. Underlying KG, in general, is the source of target entities for EL approaches, however, it often contains other relevant information, such as aliases of entit…
This paper describes the University of Sheffield's entry in the 2011 TAC KBP entity linking and slot filling tasks. We chose to participate in the monolingual entity linking task, the monolingual slot filling task and the temporal slot filling tasks. We set out to build a framework for experimentation with knowledge base population. This framework was created, and applied to multiple KBP tasks. We demonstrated that our proposed framework is effective and suitable for collaborative development efforts, as well as useful in a teaching environment. Finally we present results that, while very mode…
We propose a simple and practical method for named entity linking (NEL), based on entity representation by multiple embeddings. To explore this method, and to review its dependency on parameters, we measure its performance on Namesakes, a highly challenging dataset of ambiguously named entities. Our observations suggest that the minimal number of mentions required to create a knowledge base (KB) entity is very important for NEL performance. The number of embeddings is less important and can be kept small, within as few as 10 or less. We show that our representations of KB entities can be adjus…
Universität Hamburg（汉堡大学）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Lomonosov Moscow State University（莫斯科罗蒙诺索夫国立大学）；AIRI（AIRI（人工智能研究所））；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；FIZ Karlsruhe - Leibniz Institute for Information Infrastructure（FIZ卡尔斯鲁厄——莱布尼茨信息基础设施研究所）；Université Sorbonne Paris Nord（巴黎索邦北大学）；Vrije University of Amsterdam（阿姆斯特丹自由大学）；The Open University（开放大学）；University of Cagliari（卡利亚里大学）
This survey presents a comprehensive description of recent neural entity linking (EL) systems developed since 2015 as a result of the "deep learning revolution" in natural language processing. Its goal is to systemize design features of neural entity linking systems and compare their performance to the remarkable classic methods on common benchmarks. This work distills a generic architecture of a neural EL system and discusses its components, such as candidate generation, mention-context encoding, and entity ranking, summarizing prominent methods for each of them. The vast variety of modificat…
In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce a novel, subword approach for named entity recognition (NER) that uses byte-pair encodings (BPE) in combination with convolutional and recurrent neural networks to produce byte-level tags of entities. We present experimental results on several standard biomedical datasets, namely the BioCreative VI Bio-ID, JNLPBA, and GENETAG datasets. We demonstrate competi…
University of Iceland（冰岛大学）；Reykjavík University（雷克雅未克大学）；Quick Lookup（快速查询公司）
In this paper, we present the first Entity Linking corpus for Icelandic. We describe our approach of using a multilingual entity linking model (mGENRE) in combination with Wikipedia API Search (WAPIS) to label our data and compare it to an approach using WAPIS only. We find that our combined method reaches 53.9% coverage on our corpus, compared to 30.9% using only WAPIS. We analyze our results and explain the value of using a multilingual system when working with Icelandic. Additionally, we analyze the data that remain unlabeled, identify patterns and discuss why they may be more difficult to …
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Entity linking (EL) is the task of linking entity mentions in a document to referent entities in a knowledge base (KB). Many previous studies focus on Wikipedia-derived KBs. There is little work on EL over Wikidata, even though it is the most extensive crowdsourced KB. The scale of Wikidata can open up many new real-world applications, but its massive number of entities also makes EL challenging. To effectively narrow down the search space, we propose a novel candidate retrieval paradigm based on entity profiling. Wikidata entities and their textual fields are first indexed into a text search …
German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心）
We present MobIE, a German-language dataset, which is human-annotated with 20 coarse- and fine-grained entity types and entity linking information for geographically linkable entities. The dataset consists of 3,232 social media texts and traffic reports with 91K tokens, and contains 20.5K annotated entities, 13.1K of which are linked to a knowledge base. A subset of the dataset is human-annotated with seven mobility-related, n-ary relation types, while the remaining documents are annotated using a weakly-supervised labeling approach implemented with the Snorkel framework. To the best of our kn…
Humans use language to refer to entities in the external world. Motivated by this, in recent years several models that incorporate a bias towards learning entity representations have been proposed. Such entity-centric models have shown empirical success, but we still know little about why. In this paper we analyze the behavior of two recently proposed entity-centric models in a referential task, Entity Linking in Multi-party Dialogue (SemEval 2018 Task 4). We show that these models outperform the state of the art on this task, and that they do better on lower frequency entities than a counterp…
School of Artificial Intelligence, University of Chinese Academy of Sciences（中国科学院大学人工智能学院）；National Laboratory of Pattern Recognition, Institute of Automation, CAS（中国科学院自动化研究所模式识别国家重点实验室）；Beijing Fanyu Technology Co., Ltd（北京梵语科技有限公司）
Entity linking aims to establish a link between entity mentions in a document and the corresponding entities in knowledge graphs (KGs). Previous work has shown the effectiveness of global coherence for entity linking. However, most of the existing global linking methods based on sequential decisions focus on how to utilize previously linked entities to enhance the later decisions. In those methods, the order of mention is fixed, making the model unable to adjust the subsequent linking targets according to the previously linked results, which will cause the previous information to be unreasonab…
