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Register a new userBiomedical Named Entity Recognition via Reference-Set Augmented Bootstrapping
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Joel Mathew
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER) model over a small seed of fully-labeled examples. Second, we use a reference set of entity names (e.g., proteins in UniProt) to identify entity mentions with high precision, but low recall, on an unlabeled corpus. Third, we use the NNER model to assign weak labels to the corpus. Finally, we retrain our NNER model iteratively over the augmented training set, including the seed, the reference-set examples, and the weakly-labeled examples, which improves model performance. We show empirically that this augmented bootstrapping process significantly improves NER performance, and discuss the factors impacting the efficacy of the approach.
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In this paper we describe our submissions to the 2nd and 3rd SlavNER Shared Tasks held at BSNLP 2019 and BSNLP 2021, respectively. The tasks focused on the analysis of Named Entities in multilingual Web documents in Slavic languages with rich inflection. Our solution takes advantage of large collections of both unstructured and structured documents. The former serve as data for unsupervised training of language models and embeddings of lexical units. The latter refers to Wikipedia and its structured counterpart - Wikidata, our source of lemmatization rules, and real-world entities. With the aid of those resources, our system could recognize, normalize and link entities, while being trained with only small amounts of labeled data.
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. The code is available at https://github.com/zqtan1024/sequence-to-set.
We study learning named entity recognizers in the presence of missing entity annotations. We approach this setting as tagging with latent variables and propose a novel loss, the Expected Entity Ratio, to learn models in the presence of systematically missing tags. We show that our approach is both theoretically sound and empirically useful. Experimentally, we find that it meets or exceeds performance of strong and state-of-the-art baselines across a variety of languages, annotation scenarios, and amounts of labeled data. In particular, we find that it significantly outperforms the previous state-of-the-art methods from Mayhew et al. (2019) and Li et al. (2021) by +12.7 and +2.3 F1 score in a challenging setting with only 1,000 biased annotations, averaged across 7 datasets. We also show that, when combined with our approach, a novel sparse annotation scheme outperforms exhaustive annotation for modest annotation budgets.
Named Entity Recognition (NER) in Few-Shot setting is imperative for entity tagging in low resource domains. Existing approaches only learn class-specific semantic features and intermediate representations from source domains. This affects generalizability to unseen target domains, resulting in suboptimal performances. To this end, we present CONTaiNER, a novel contrastive learning technique that optimizes the inter-token distribution distance for Few-Shot NER. Instead of optimizing class-specific attributes, CONTaiNER optimizes a generalized objective of differentiating between token categories based on their Gaussian-distributed embeddings. This effectively alleviates overfitting issues originating from training domains. Our experiments in several traditional test domains (OntoNotes, CoNLL03, WNUT 17, GUM) and a new large scale Few-Shot NER dataset (Few-NERD) demonstrate that on average, CONTaiNER outperforms previous methods by 3%-13% absolute F1 points while showing consistent performance trends, even in challenging scenarios where previous approaches could not achieve appreciable performance.
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. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.
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