We propose two neural network architectures for nested named entity recognition (NER), a setting in which named entities may overlap and also be labeled with more than one label. We encode the nested labels using a linearized scheme. In our first proposed approach, the nested labels are modeled as multilabels corresponding to the Cartesian product of the nested labels in a standard LSTM-CRF architecture. In the second one, the nested NER is viewed as a sequence-to-sequence problem, in which the input sequence consists of the tokens and output sequence of the labels, using hard attention on the word whose label is being predicted. The proposed methods outperform the nested NER state of the art on four corpora: ACE-2004, ACE-2005, GENIA and Czech CNEC. We also enrich our architectures with the recently published contextual embeddings: ELMo, BERT and Flair, reaching further improvements for the four nested entity corpora. In addition, we report flat NER state-of-the-art results for CoNLL-2002 Dutch and Spanish and for CoNLL-2003 English.
HwaMei Hospital, University of Chinese Academy of Sciences（中国科学院大学华美医院）；Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences（中国科学院大学宁波生命与健康产业研究院）
Many recent named entity recognition (NER) studies criticize flat NER for its non-overlapping assumption, and switch to investigating nested NER. However, existing nested NER models heavily rely on training data annotated with nested entities, while labeling such data is costly. This study proposes a new subtask, nested-from-flat NER, which corresponds to a realistic application scenario: given data annotated with flat entities only, one may still desire the trained model capable of recognizing nested entities. To address this task, we train span-based models and deliberately ignore the spans …
Named entity recognition (NER) is one of the best studied tasks in natural language processing. However, most approaches are not capable of handling nested structures which are common in many applications. In this paper we introduce a novel neural network architecture that first merges tokens and/or entities into entities forming nested structures, and then labels each of them independently. Unlike previous work, our merge and label approach predicts real-valued instead of discrete segmentation structures, which allow it to combine word and nested entity embeddings while maintaining differenti…
This paper studies the effect of the order of depth of mention on nested named entity recognition (NER) models. NER is an essential task in the extraction of biomedical information, and nested entities are common since medical concepts can assemble to form larger entities. Conventional NER systems only predict disjointed entities. Thus, iterative models for nested NER use multiple predictions to enumerate all entities, imposing a predefined order from largest to smallest or smallest to largest. We design an order-agnostic iterative model and a procedure to choose a custom order during training…
Lomonosov Moscow State University（莫斯科国立大学）；HSE University（高等经济大学）；Novosibirsk State University（新西伯利亚国立大学）；Ural Federal University（乌拉尔联邦大学）；Innopolis University（因诺波利斯大学）；Wiseyak（Wiseyak公司）；Kazan Federal University（喀山联邦大学）；Sber AI
In this paper, we present NEREL, a Russian dataset for named entity recognition and relation extraction. NEREL is significantly larger than existing Russian datasets: to date it contains 56K annotated named entities and 39K annotated relations. Its important difference from previous datasets is annotation of nested named entities, as well as relations within nested entities and at the discourse level. NEREL can facilitate development of novel models that can extract relations between nested named entities, as well as relations on both sentence and document levels. NEREL also contains the annot…
In this report, we describe our participant named-entity recognition system at VLSP 2018 evaluation campaign. We formalized the task as a sequence labeling problem using BIO encoding scheme. We applied a feature-based model which combines word, word-shape features, Brown-cluster-based features, and word-embedding-based features. We compare several methods to deal with nested entities in the dataset. We showed that combining tags of entities at all levels for training a sequence labeling model (joint-tag model) improved the accuracy of nested named-entity recognition.
Peking University（北京大学）；Microsoft Azure AI（微软Azure人工智能）；Harbin Institute of Technology（哈尔滨工业大学）；Microsoft Research（微软研究院）
While named entity recognition (NER) is a key task in natural language processing, most approaches only target flat entities, ignoring nested structures which are common in many scenarios. Most existing nested NER methods traverse all sub-sequences which is both expensive and inefficient, and also don't well consider boundary knowledge which is significant for nested entities. In this paper, we propose a joint entity mention detection and typing model via prior boundary knowledge (BoningKnife) to better handle nested NER extraction and recognition tasks. BoningKnife consists of two modules, Me…
As a fundamental natural language processing task and one of core knowledge extraction techniques, named entity recognition (NER) is widely used to extract information from texts for downstream tasks. Nested NER is a branch of NER in which the named entities (NEs) are nested with each other. However, most of the previous studies on nested NER usually apply linear structure to model the nested NEs which are actually accommodated in a hierarchical structure. Thus in order to address this mismatch, this work models the full nested NEs in a sentence as a holistic structure, then we propose a holis…
Named entity recognition (NER) is the task to detect and classify the entity spans in the text. When entity spans overlap between each other, this problem is named as nested NER. Span-based methods have been widely used to tackle the nested NER. Most of these methods will get a score $n \times n$ matrix, where $n$ means the length of sentence, and each entry corresponds to a span. However, previous work ignores spatial relations in the score matrix. In this paper, we propose using Convolutional Neural Network (CNN) to model these spatial relations in the score matrix. Despite being simple, exp…
University of Sydney（悉尼大学）；CSIRO Data61（澳大利亚联邦科学与工业研究组织数据61研究所）；Digital Health CRC（数字健康合作研究中心）
Named entity recognition (NER) is widely used in natural language processing applications and downstream tasks. However, most NER tools target flat annotation from popular datasets, eschewing the semantic information available in nested entity mentions. We describe NNE---a fine-grained, nested named entity dataset over the full Wall Street Journal portion of the Penn Treebank (PTB). Our annotation comprises 279,795 mentions of 114 entity types with up to 6 layers of nesting. We hope the public release of this large dataset for English newswire will encourage development of new techniques for n…
Nested named entity recognition (nested NER) is a fundamental task in natural language processing. Various span-based methods have been proposed to detect nested entities with span representations. However, span-based methods do not consider the relationship between a span and other entities or phrases, which is helpful in the NER task. Besides, span-based methods have trouble predicting long entities due to limited span enumeration length. To mitigate these issues, we present the Propose-and-Refine Network (PnRNet), a two-stage set prediction network for nested NER. In the propose stage, we u…
Fudan University（复旦大学）；New York University（纽约大学）；Pazhou Lab（琶洲实验室）
Named Entity Recognition (NER) is the task of identifying spans that represent entities in sentences. Whether the entity spans are nested or discontinuous, the NER task can be categorized into the flat NER, nested NER, and discontinuous NER subtasks. These subtasks have been mainly solved by the token-level sequence labelling or span-level classification. However, these solutions can hardly tackle the three kinds of NER subtasks concurrently. To that end, we propose to formulate the NER subtasks as an entity span sequence generation task, which can be solved by a unified sequence-to-sequence (…
Named entity recognition (NER) is a widely studied task in natural language processing. Recently, a growing number of studies have focused on the nested NER. The span-based methods, considering the entity recognition as a span classification task, can deal with nested entities naturally. But they suffer from the huge search space and the lack of interactions between entities. To address these issues, we propose a novel sequence-to-set neural network for nested NER. Instead of specifying candidate spans in advance, we provide a fixed set of learnable vectors to learn the patterns of the valuabl…
Siemens AG（西门子股份公司）；University of Munich (LMU)（慕尼黑大学（LMU））
Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity Recognition including nested entities extraction, Entity Normalization and Relation Extraction. Our proposed approach of Named Entities can be generalized to different languages and we have shown it's effectiveness for English and Spanish text. We investigated linguistic features, hybrid loss including ranking and Conditional Random Fields (CRF), multi-task o…
Shandong Normal University（山东师范大学）；Shandong University（山东大学）
Nested named entity recognition (NER) aims to identify the entity boundaries and recognize categories of the named entities in a complex hierarchical sentence. Some works have been done using character-level, word-level, or lexicon-level based models. However, such researches ignore the role of the complementary annotations. In this paper, we propose a trigger-based graph neural network (Trigger-GNN) to leverage the nested NER. It obtains the complementary annotation embeddings through entity trigger encoding and semantic matching, and tackle nested entity utilizing an efficient graph message …
Zhejiang University（浙江大学）；University of Science and Technology of China（中国科学技术大学）
Named entity recognition (NER) is a well-studied task in natural language processing. Traditional NER research only deals with flat entities and ignores nested entities. The span-based methods treat entity recognition as a span classification task. Although these methods have the innate ability to handle nested NER, they suffer from high computational cost, ignorance of boundary information, under-utilization of the spans that partially match with entities, and difficulties in long entity recognition. To tackle these issues, we propose a two-stage entity identifier. First we generate span prop…
In this paper, we propose a novel bipartite flat-graph network (BiFlaG) for nested named entity recognition (NER), which contains two subgraph modules: a flat NER module for outermost entities and a graph module for all the entities located in inner layers. Bidirectional LSTM (BiLSTM) and graph convolutional network (GCN) are adopted to jointly learn flat entities and their inner dependencies. Different from previous models, which only consider the unidirectional delivery of information from innermost layers to outer ones (or outside-to-inside), our model effectively captures the bidirectional…
ShanghaiTech University（上海科技大学）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉成像工程研究中心）
Constituency parsing and nested named entity recognition (NER) are similar tasks since they both aim to predict a collection of nested and non-crossing spans. In this work, we cast nested NER to constituency parsing and propose a novel pointing mechanism for bottom-up parsing to tackle both tasks. The key idea is based on the observation that if we traverse a constituency tree in post-order, i.e., visiting a parent after its children, then two consecutively visited spans would share a boundary. Our model tracks the shared boundaries and predicts the next boundary at each step by leveraging a p…
This paper introduces DaN+, a new multi-domain corpus and annotation guidelines for Danish nested named entities (NEs) and lexical normalization to support research on cross-lingual cross-domain learning for a less-resourced language. We empirically assess three strategies to model the two-layer Named Entity Recognition (NER) task. We compare transfer capabilities from German versus in-language annotation from scratch. We examine language-specific versus multilingual BERT, and study the effect of lexical normalization on NER. Our results show that 1) the most robust strategy is multi-task lear…
Hefei University of Technology（合肥工业大学）；Umeå University（于默奥大学）
While Named Entity Recognition (NER) is a widely studied task, making inferences of entities with only a few labeled data has been challenging, especially for entities with nested structures. Unlike flat entities, entities and their nested entities are more likely to have similar semantic feature representations, drastically increasing difficulties in classifying different entity categories in the few-shot setting. Although prior work has briefly discussed nested structures in the context of few-shot learning, to our best knowledge, this paper is the first one specifically dedicated to studyin…
This paper presents Wojood, a corpus for Arabic nested Named Entity Recognition (NER). Nested entities occur when one entity mention is embedded inside another entity mention. Wojood consists of about 550K Modern Standard Arabic (MSA) and dialect tokens that are manually annotated with 21 entity types including person, organization, location, event and date. More importantly, the corpus is annotated with nested entities instead of the more common flat annotations. The data contains about 75K entities and 22.5% of which are nested. The inter-annotator evaluation of the corpus demonstrated a str…
ShanghaiTech University（上海科技大学）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉成像工程研究中心）
Nested named entity recognition (NER) has been receiving increasing attention. Recently, (Fu et al, 2021) adapt a span-based constituency parser to tackle nested NER. They treat nested entities as partially-observed constituency trees and propose the masked inside algorithm for partial marginalization. However, their method cannot leverage entity heads, which have been shown useful in entity mention detection and entity typing. In this work, we resort to more expressive structures, lexicalized constituency trees in which constituents are annotated by headwords, to model nested entities. We lev…
Popular solutions to Named Entity Recognition (NER) include conditional random fields, sequence-to-sequence models, or utilizing the question-answering framework. However, they are not suitable for nested and overlapping spans with large ontologies and for predicting the position of the entities. To fill this gap, we introduce a new model for NER task -- an RNN transducer (RNN-T). These models are trained using paired input and output sequences without explicitly specifying the alignment between them, similar to other seq-to-seq models. RNN-T models learn the alignment using a loss function th…
University of Edinburgh（爱丁堡大学）；Alibaba Group（阿里巴巴集团）
Named entity recognition (NER) is a well-studied task in natural language processing. However, the widely-used sequence labeling framework is difficult to detect entities with nested structures. In this work, we view nested NER as constituency parsing with partially-observed trees and model it with partially-observed TreeCRFs. Specifically, we view all labeled entity spans as observed nodes in a constituency tree, and other spans as latent nodes. With the TreeCRF we achieve a uniform way to jointly model the observed and the latent nodes. To compute the probability of partial trees with partia…
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；University at Buffalo（布法罗大学）；Zhejiang Lab（之江实验室）；Tencent Medical AI Lab（腾讯医疗AI实验室）；Alibaba Group（阿里巴巴集团）；Tencent America（腾讯美国）
This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities.…
S2F-NER: Exploring Sequence-to-Forest Generation for Complex Entity Recognition
School of Cyber Security, University of Chinese Academy of Sciences（中国科学院大学网络空间安全学院）；School of Computer Science and Technology, Beijing Institute of Technology（北京理工大学计算机科学与技术学院）
Nested Named Entity Recognition in Plasma Physics Research Articles
TIB---Leibniz Information Centre for Science and Technology（蒂宾根—莱布尼茨科学与技术信息中心）；Leibniz University Hannover（莱布尼茨汉诺威大学）；Leibniz Institute for Plasma Science and Technology (INP)（莱布尼茨等离子科学与技术研究所）
Queen Mary University（伦敦玛丽女王大学）；Google Research（谷歌研究院）
Named Entity Recognition (NER) is a fundamental task in Natural Language Processing, concerned with identifying spans of text expressing references to entities. NER research is often focused on flat entities only (flat NER), ignoring the fact that entity references can be nested, as in [Bank of [China]] (Finkel and Manning, 2009). In this paper, we use ideas from graph-based dependency parsing to provide our model a global view on the input via a biaffine model (Dozat and Manning, 2017). The biaffine model scores pairs of start and end tokens in a sentence which we use to explore all spans, so…
Beihang University（北京航空航天大学）；Meituan（美团）；Meta AI；Harbin Institute of Technology（哈尔滨工业大学）
Named entity recognition (NER) is an important research problem in natural language processing. There are three types of NER tasks, including flat, nested and discontinuous entity recognition. Most previous sequential labeling models are task-specific, while recent years have witnessed the rising of generative models due to the advantage of unifying all NER tasks into the seq2seq model framework. Although achieving promising performance, our pilot studies demonstrate that existing generative models are ineffective at detecting entity boundaries and estimating entity types. This paper proposes …
Lucerne University of Applied Sciences and Arts（卢塞恩应用科学与艺术大学）
Entity Recognition (ER) within a text is a fundamental exercise in Natural Language Processing, enabling further depending tasks such as Knowledge Extraction, Text Summarisation, or Keyphrase Extraction. An entity consists of single words or of a consecutive sequence of terms, constituting the basic building blocks for communication. Mainstream ER approaches are mainly limited to flat structures, concentrating on the outermost entities while ignoring the inner ones. This paper introduces a partly-layered network architecture that deals with the complexity of overlapping and nested cases. The p…
We present a bi-encoder framework for named entity recognition (NER), which applies contrastive learning to map candidate text spans and entity types into the same vector representation space. Prior work predominantly approaches NER as sequence labeling or span classification. We instead frame NER as a representation learning problem that maximizes the similarity between the vector representations of an entity mention and its type. This makes it easy to handle nested and flat NER alike, and can better leverage noisy self-supervision signals. A major challenge to this bi-encoder formulation for…
Nested Named-Entity Recognition on Vietnamese COVID-19: Dataset and Experiments
School of Applied Mathematics and Informatics, Hanoi University of Science and Technology（1 工程数学与信息学院，河内科学技术大学）；Financial Deep Mind（2 财务深度智能）；National Economics University（3 国家经济大学）；Faculty of Information Technology, Hanoi Open University（4 信息学院，河内开放大学）
In this work, we propose a two-stage method for named entity recognition (NER), especially for nested NER. We borrowed the idea from the two-stage Object Detection in computer vision and the way how they construct the loss function. First, a region proposal network generates region candidates and then a second-stage model discriminates and classifies the entity and makes the final prediction. We also designed a special loss function for the second-stage training that predicts the entityness and entity type at the same time. The model is built on top of pretrained BERT encoders, and we tried bo…
NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entities
Lomonosov Moscow State University（莫斯科罗蒙诺索夫国立大学）；Madan Bhandari University of Science and Technology（马丹·班达里科技大学）；Ural Federal University（乌拉尔联邦大学）；HSE University（高等经济大学）；Innopolis University（因诺波利斯大学）；A.P. Ershov Institute of Informatics Systems（A.P. 埃尔绍夫信息学系统研究所）；Artificial Intelligence Research Institute（人工智能研究所）；Sber AI
Nested entities are observed in many domains due to their compositionality, which cannot be easily recognized by the widely-used sequence labeling framework. A natural solution is to treat the task as a span classification problem. To learn better span representation and increase classification performance, it is crucial to effectively integrate heterogeneous factors including inside tokens, boundaries, labels, and related spans which could be contributing to nested entities recognition. To fuse these heterogeneous factors, we propose a novel triaffine mechanism including triaffine attention a…
University of Chinese Academy of Sciences（中国科学院大学）；Institute of Software, Chinese Academy of Sciences（中国科学院软件研究所）
Sequential labeling-based NER approaches restrict each word belonging to at most one entity mention, which will face a serious problem when recognizing nested entity mentions. In this paper, we propose to resolve this problem by modeling and leveraging the head-driven phrase structures of entity mentions, i.e., although a mention can nest other mentions, they will not share the same head word. Specifically, we propose Anchor-Region Networks (ARNs), a sequence-to-nuggets architecture for nested mention detection. ARNs first identify anchor words (i.e., possible head words) of all mentions, and …
There has been a growing academic interest in the recognition of nested named entities in many domains. We tackle the task with a novel local hypergraph-based method: We first propose start token candidates and generate corresponding queries with their surrounding context, then use a query-based sequence labeling module to form a local hypergraph for each candidate. An end token estimator is used to correct the hypergraphs and get the final predictions. Compared to span-based approaches, our method is free of the high computation cost of span sampling and the risk of losing long entities. Sequ…
In this work, we formulate the NER task as a multi-answer knowledge guided QA task (KGQA) which helps to predict entities only by assigning B, I and O tags without associating entity types with the tags. We provide different knowledge contexts, such as, entity types, questions, definitions and examples along with the text and train on a combined dataset of 18 biomedical corpora. This formulation (a) enables systems to jointly learn NER specific features from varied NER datasets, (b) can use knowledge-text attention to identify words having higher similarity to provided knowledge, improving per…
Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University（武汉大学网络空间安全学院，空天信息安全与可信计算教育部重点实验室）；Institute of Computing and Intelligence, Harbin Institute of Technology (Shenzhen)（哈尔滨工业大学（深圳）计算与智能研究院）
So far, named entity recognition (NER) has been involved with three major types, including flat, overlapped (aka. nested), and discontinuous NER, which have mostly been studied individually. Recently, a growing interest has been built for unified NER, tackling the above three jobs concurrently with one single model. Current best-performing methods mainly include span-based and sequence-to-sequence models, where unfortunately the former merely focus on boundary identification and the latter may suffer from exposure bias. In this work, we present a novel alternative by modeling the unified NER a…
In this paper, we propose a new strategy for the task of named entity recognition (NER). We cast the task as a query-based machine reading comprehension task: e.g., the task of extracting entities with PER is formalized as answering the question of "which person is mentioned in the text ?". Such a strategy comes with the advantage that it solves the long-standing issue of handling overlapping or nested entities (the same token that participates in more than one entity categories) with sequence-labeling techniques for NER. Additionally, since the query encodes informative prior knowledge, this …
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…
Named entity recognition is a fundamental task in natural language processing, identifying the span and category of entities in unstructured texts. The traditional sequence labeling methodology ignores the nested entities, i.e. entities included in other entity mentions. Many approaches attempt to address this scenario, most of which rely on complex structures or have high computation complexity. The representation learning of the heterogeneous star graph containing text nodes and type nodes is investigated in this paper. In addition, we revise the graph attention mechanism into a hybrid form …
Biomedical Nested NER with Large Language Model and UMLS Heuristics
Georgia Institute of Technology（佐治亚理工学院）；Peoples' Friendship University of Russia (RUDN University)（俄罗斯人民友谊大学（RUDN大学））；Joint Institute for Nuclear Research（联合核研究所）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）；University of Skövde（舍夫德大学）
