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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 valuable spans. We utilize a non-autoregressive decoder to predict the final set of entities in one pass, in which we are able to capture dependencies between entities. Compared with the sequence-to-sequence method, our model is more suitable for such unordered recognition task as it is insensitive to the label order. In addition, we utilize the loss function based on bipartite matching to compute the overall training loss. Experimental results show that our proposed model achieves state-of-the-art on three nested NER corpora: ACE 2004, ACE 2005 and KBP 2017. | NER for Nested Entities |
Here we describe a new clinical corpus rich in nested entities and a series of neural models to identify them. The corpus comprises de-identified referrals from the waiting list in Chilean public hospitals. A subset of 5,000 referrals (58.6% medical and 41.4% dental) was manually annotated with 10 types of entities, six attributes, and pairs of relations with clinical relevance. In total, there are 110,771 annotated tokens. A trained medical doctor or dentist annotated these referrals, and then, together with three other researchers, consolidated each of the annotations. The annotated corpus has 48.17% of entities embedded in other entities or containing another one. We use this corpus to build models for Named Entity Recognition (NER). The best results were achieved using a Multiple Single-entity architecture with clinical word embeddings stacked with character and Flair contextual embeddings. The entity with the best performance is abbreviation, and the hardest to recognize is finding. NER models applied to this corpus can leverage statistics of diseases and pending procedures. This work constitutes the first annotated corpus using clinical narratives from Chile and one of the few in Spanish. The annotated corpus, clinical word embeddings, annotation guidelines, and neural models are freely released to the community. | NER for Nested Entities |
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, MentionTagger and TypeClassifier. MentionTagger better leverages boundary knowledge beyond just entity start/end to improve the handling of nesting levels and longer spans, while generating high quality mention candidates. TypeClassifier utilizes a two-level attention mechanism to decouple different nested level representations and better distinguish entity types. We jointly train both modules sharing a common representation and a new dual-info attention layer, which leads to improved representation focus on entity-related information. Experiments over different datasets show that our approach outperforms previous state of the art methods and achieves 86.41, 85.46, and 94.2 F1 scores on ACE2004, ACE2005, and NNE, respectively. | NER for Nested Entities |
Named Entity Recognition (NER) is a well and widely studied task in natural language processing. Recently, the nested NER has attracted more attention since its practicality and difficulty. Existing works for nested NER ignore the recognition order and boundary position relation of nested entities. To address these issues, we propose a novel seq2seq model named GPRL, which formulates the nested NER task as an entity triplet sequence generation process. GPRL adopts the reinforcement learning method to generate entity triplets de-coupling the entity order in gold labels and expects to learn a reasonable recognition order of entities via trial and error. Based on statistics of boundary distance for nested entities, GPRL designs a Gaussian prior to represent the boundary distance distribution between nested entities and adjust the out-put probability distribution of nested boundary tokens. Experiments on three nested NER datasets demonstrate that GPRL outperforms previous nested NER models. | NER for Nested Entities |
In this article, we propose a new encoding scheme for named entity recognition (NER) called Joined Type-Length encoding (JoinedTL). Unlike most existing named entity encoding schemes, which focus on flat entities, JoinedTL can label nested named entities in a single sequence. JoinedTL uses a packed encoding to represent both type and span of a named entity, which not only results in less tagged tokens compared to existing encoding schemes, but also enables it to support nested NER. We evaluate the effectiveness of JoinedTL for nested NER on three nested NER datasets: GENIA in English, GermEval in German, and PerNest, our newly created nested NER dataset in Persian. We apply CharLSTM+WordLSTM+CRF, a three-layer sequence tagging model on three datasets encoded using JoinedTL and two existing nested NE encoding schemes, i.e., JoinedBIO and JoinedBILOU. Our experiment results show that CharLSTM+WordLSTM+CRF trained with JoinedTL encoded datasets can achieve competitive F1 scores as the ones trained with datasets encoded by two other encodings, but with 27%–48% less tagged tokens. To leverage the power of three different encodings, i.e., JoinedTL, JoinedBIO, and JoinedBILOU, we propose an encoding-based ensemble method for nested NER. Evaluation results show that the ensemble method achieves higher F1 scores on all datasets than the three models each trained using one of the three encodings. By using nested NE encodings including JoinedTL with CharLSTM+WordLSTM+CRF, we establish new state-of-the-art performance with an F1 score of 83.7 on PerNest, 74.9 on GENIA, and 70.5 on GermEval, surpassing two recent neural models specially designed for nested NER. | NER for Nested Entities |
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 nested inside labeled entities, since these spans are possibly unlabeled entities. With nested entities removed from the training data, our model achieves 54.8%, 54.2% and 41.1% F1 scores on the subset of spans within entities on ACE 2004, ACE 2005 and GENIA, respectively. This suggests the effectiveness of our approach and the feasibility of the task. In addition, the model's performance on flat entities is entirely unaffected. We further manually annotate the nested entities in the test set of CoNLL 2003, creating a nested-from-flat NER benchmark. Analysis results show that the main challenges stem from the data and annotation inconsistencies between the flat and nested entities. | NER for Nested Entities |
Named entity recognition (NER) aims to extract entities from unstructured text, and a nested structure often exists between entities. However, most previous studies paid more attention to flair named entity recognition while ignoring nested entities. The importance of words in the text should vary for different entity categories. In this paper, we propose a head-to-tail linker for nested NER. The proposed model exploits the extracted entity head as conditional information to locate the corresponding entity tails under different entity categories. This strategy takes part of the symmetric boundary information of the entity as a condition and effectively leverages the information from the text to improve the entity boundary recognition effectiveness. The proposed model considers the variability in the semantic correlation between tokens for different entity heads under different entity categories. To verify the effectiveness of the model, numerous experiments were implemented on three datasets: ACE2004, ACE2005, and GENIA, with F1-scores of 80.5%, 79.3%, and 76.4%, respectively. The experimental results show that our model is the most effective of all the methods used for comparison. | NER for Nested Entities |
Nested named entity recognition (NER) is a task in which named entities may overlap with each other. Span-based approaches regard nested NER as a two-stage span enumeration and classification task, thus having the innate ability to handle this task. However, they face the problems of error propagation, ignorance of span boundary, difficulty in long entity recognition and requirement on large-scale annotated data. In this paper, we propose Extract-Select, a span selection framework for nested NER, to tackle these problems. Firstly, we introduce a span selection framework in which nested entities with different input categories would be separately extracted by the extractor, thus naturally avoiding error propagation in two-stage span-based approaches. In the inference phase, the trained extractor selects final results specific to the given entity category. Secondly, we propose a hybrid selection strategy in the extractor, which not only makes full use of span boundary but also improves the ability of long entity recognition. Thirdly, we design a discriminator to evaluate the extraction result, and train both extractor and discriminator with generative adversarial training (GAT). The use of GAT greatly alleviates the stress on the dataset size. Experimental results on four benchmark datasets demonstrate that Extract-Select outperforms competitive nested NER models, obtaining state-of-the-art results. The proposed model also performs well when less labeled data are given, proving the effectiveness of GAT. | NER for Nested Entities |
Nested named entity recognition (Nested NER) aims to identify entities with nested structures from the given text, which is a fundamental task in Natural Language Processing. The region-based approach is the current mainstream approach, which first generates candidate spans and then classifies them into predefined categories. However, this method suffers from several drawbacks, including over-reliance on span representation, vulnerability to unbalanced category distribution, and inaccurate span boundary detection. To address these problems, we propose to model the nested NER problem into a head-tail mapping problem, namely, HTMapper, which detects head boundaries first and then models a conditional mapping from head to tail under a given category. Based on this mapping, we can find corresponding tails under different categories for each detected head by enumerating all entity categories. Our approach directly models the head boundary and tail boundary of entities, avoiding over-reliance on the span representation. Additionally, Our approach utilizes category information as an indicator signal to address the imbalance of category distribution during category prediction. Furthermore, our approach enhances the detection of span boundaries by capturing the correlation between head and tail boundaries. Extensive experiments on three nested NER datasets and two flat NER datasets demonstrate that our HTMapper achieves excellent performance with F1 scores of 89.09%, 88.30%, 81.57% on ACE2004,ACE2005, GENIA, and 94.26%, 91.40% on CoNLL03, OntoNotes, respectively. | NER for Nested Entities |
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. | NER for Nested Entities |
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