Biomedical Entity Recognition by Detection and Matching

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data poses a significant challenge. In this study, we propose a novel BNER framework called DMNER. By leveraging existing entity representation models SAPBERT, we tackle BNER as a two-step process: entity boundary detection and biomedical entity matching. DMNER exhibits applicability across multiple NER scenarios: 1) In supervised NER, we observe that DMNER effectively rectifies the output of baseline NER models, thereby further enhancing performance. 2) In distantly supervised NER, combining MRC and AutoNER as span boundary detectors enables DMNER to achieve satisfactory results. 3) For training NER by merging multiple datasets, we adopt a framework similar to DS-NER but additionally leverage ChatGPT to obtain high-quality phrases in the training. Through extensive experiments conducted on 10 benchmark datasets, we demonstrate the versatility and effectiveness of DMNER.Comment: 9 pages content, 2 pages appendi

Named Entity Recognition via Machine Reading Comprehension: A Multi-Task Learning Approach

Named Entity Recognition (NER) aims to extract and classify entity mentions in the text into pre-defined types (e.g., organization or person name). Recently, many works have been proposed to shape the NER as a machine reading comprehension problem (also termed MRC-based NER), in which entity recognition is achieved by answering the formulated questions related to pre-defined entity types through MRC, based on the contexts. However, these works ignore the label dependencies among entity types, which are critical for precisely recognizing named entities. In this paper, we propose to incorporate the label dependencies among entity types into a multi-task learning framework for better MRC-based NER. We decompose MRC-based NER into multiple tasks and use a self-attention module to capture label dependencies. Comprehensive experiments on both nested NER and flat NER datasets are conducted to validate the effectiveness of the proposed Multi-NER. Experimental results show that Multi-NER can achieve better performance on all datasets

MNER-QG: An End-to-End MRC framework for Multimodal Named Entity Recognition with Query Grounding

Multimodal named entity recognition (MNER) is a critical step in information extraction, which aims to detect entity spans and classify them to corresponding entity types given a sentence-image pair. Existing methods either (1) obtain named entities with coarse-grained visual clues from attention mechanisms, or (2) first detect fine-grained visual regions with toolkits and then recognize named entities. However, they suffer from improper alignment between entity types and visual regions or error propagation in the two-stage manner, which finally imports irrelevant visual information into texts. In this paper, we propose a novel end-to-end framework named MNER-QG that can simultaneously perform MRC-based multimodal named entity recognition and query grounding. Specifically, with the assistance of queries, MNER-QG can provide prior knowledge of entity types and visual regions, and further enhance representations of both texts and images. To conduct the query grounding task, we provide manual annotations and weak supervisions that are obtained via training a highly flexible visual grounding model with transfer learning. We conduct extensive experiments on two public MNER datasets, Twitter2015 and Twitter2017. Experimental results show that MNER-QG outperforms the current state-of-the-art models on the MNER task, and also improves the query grounding performance.Comment: 13 pages, 6 figures, published to AAA

Mirror: A Universal Framework for Various Information Extraction Tasks

Sharing knowledge between information extraction tasks has always been a challenge due to the diverse data formats and task variations. Meanwhile, this divergence leads to information waste and increases difficulties in building complex applications in real scenarios. Recent studies often formulate IE tasks as a triplet extraction problem. However, such a paradigm does not support multi-span and n-ary extraction, leading to weak versatility. To this end, we reorganize IE problems into unified multi-slot tuples and propose a universal framework for various IE tasks, namely Mirror. Specifically, we recast existing IE tasks as a multi-span cyclic graph extraction problem and devise a non-autoregressive graph decoding algorithm to extract all spans in a single step. It is worth noting that this graph structure is incredibly versatile, and it supports not only complex IE tasks, but also machine reading comprehension and classification tasks. We manually construct a corpus containing 57 datasets for model pretraining, and conduct experiments on 30 datasets across 8 downstream tasks. The experimental results demonstrate that our model has decent compatibility and outperforms or reaches competitive performance with SOTA systems under few-shot and zero-shot settings. The code, model weights, and pretraining corpus are available at https://github.com/Spico197/Mirror .Comment: Accepted to EMNLP23 main conferenc

LightNER: A Lightweight Tuning Paradigm for Low-resource NER via Pluggable Prompting

Most NER methods rely on extensive labeled data for model training, which struggles in the low-resource scenarios with limited training data. Existing dominant approaches usually suffer from the challenge that the target domain has different label sets compared with a resource-rich source domain, which can be concluded as class transfer and domain transfer. In this paper, we propose a lightweight tuning paradigm for low-resource NER via pluggable prompting (LightNER). Specifically, we construct the unified learnable verbalizer of entity categories to generate the entity span sequence and entity categories without any label-specific classifiers, thus addressing the class transfer issue. We further propose a pluggable guidance module by incorporating learnable parameters into the self-attention layer as guidance, which can re-modulate the attention and adapt pre-trained weights. Note that we only tune those inserted module with the whole parameter of the pre-trained language model fixed, thus, making our approach lightweight and flexible for low-resource scenarios and can better transfer knowledge across domains. Experimental results show that LightNER can obtain comparable performance in the standard supervised setting and outperform strong baselines in low-resource settings. Code is in https://github.com/zjunlp/DeepKE/tree/main/example/ner/few-shot.Comment: Accepted by COLING 202

From Clozing to Comprehending: Retrofitting Pre-trained Language Model to Pre-trained Machine Reader

We present Pre-trained Machine Reader (PMR), a novel method to retrofit Pre-trained Language Models (PLMs) into Machine Reading Comprehension (MRC) models without acquiring labeled data. PMR is capable of resolving the discrepancy between model pre-training and downstream fine-tuning of existing PLMs, and provides a unified solver for tackling various extraction tasks. To achieve this, we construct a large volume of general-purpose and high-quality MRC-style training data with the help of Wikipedia hyperlinks and design a Wiki Anchor Extraction task to guide the MRC-style pre-training process. Although conceptually simple, PMR is particularly effective in solving extraction tasks including Extractive Question Answering and Named Entity Recognition, where it shows tremendous improvements over previous approaches especially under low-resource settings. Moreover, viewing sequence classification task as a special case of extraction task in our MRC formulation, PMR is even capable to extract high-quality rationales to explain the classification process, providing more explainability of the predictions