In biomedical fields, one named entity may consist of a series of non-adjacent tokens and overlap with other entities. Previous methods recognize discontinuous entities by connecting entity fragments or internal tokens, which face challenges of error propagation and decoding ambiguity due to the wide variety of span or word combinations. To address these issues, we deeply explore discontinuous entity structures and propose an effective Gap-aware grid tagging model for Discontinuous Named Entity Recognition, named GapDNER. Our GapDNER innovatively applies representation learning on the context gaps between entity fragments to resolve decoding ambiguity and enhance discontinuous NER performance. Specifically, we treat the context gap as an additional type of span and convert span classification into a token-pair grid tagging task. Subsequently, we design two interactive components to comprehensively model token-pair grid features from both intra- and inter-span perspectives. The intra-span regularity extraction module employs the biaffine mechanism along with linear attention to capture the internal regularity of each span, while the inter-span relation enhancement module utilizes criss-cross attention to obtain semantic relations among different spans. At the inference stage of entity decoding, we assign a directed edge to each entity fragment and context gap, then use the BFS algorithm to search for all valid paths from the head to tail of grids with entity tags. Experimental results on three datasets demonstrate that our GapDNER achieves new state-of-the-art performance on discontinuous NER and exhibits remarkable advantages in recognizing complex entity structures.

In this work, we present a manually annotated corpus for Adverse Event (AE) extraction from discharge summaries of elderly patients, a population often underrepresented in clinical NLP resources. The dataset includes 14 clinically significant AEs-such as falls, delirium, and intracranial haemorrhage, along with contextual attributes like negation, diagnosis type, and in-hospital occurrence. Uniquely, the annotation schema supports both discontinuous and overlapping entities, addressing challenges rarely tackled in prior work. We evaluate multiple models using FlairNLP across three annotation granularities: fine-grained, coarse-grained, and coarse-grained with negation. While transformer-based models (e.g., BERT-cased) achieve strong performance on document-level coarse-grained extraction (F1 = 0.943), performance drops notably for fine-grained entity-level tasks (e.g., F1 = 0.675), particularly for rare events and complex attributes. These results demonstrate that despite high-level scores, significant challenges remain in detecting underrepresented AEs and capturing nuanced clinical language. Developed within a Trusted Research Environment (TRE), the dataset is available upon request via DataLoch and serves as a robust benchmark for evaluating AE extraction methods and supporting future cross-dataset generalisation.

Named Entity Recognition has traditionally been a key task in natural language processing, aiming to identify and extract important terms from unstructured text data. However, a notable challenge for contemporary deep-learning NER models has been identifying discontinuous entities, which are often fragmented within the text. To date, methods to address Discontinuous Named Entity Recognition have not been explored using ensemble learning to the best of our knowledge. Furthermore, the rise of large language models, such as ChatGPT in recent years, has shown significant effectiveness across many NLP tasks. Most existing approaches, however, have primarily utilized ChatGPT as a problem-solving tool rather than exploring its potential as an integrative element within ensemble learning algorithms. In this study, we investigated the integration of ChatGPT as an arbitrator within an ensemble method, aiming to enhance performance on DNER tasks. Our method combines five state-of-the-art NER models with ChatGPT using custom prompt engineering to assess the robustness and generalization capabilities of the ensemble algorithm. We conducted experiments on three benchmark medical datasets, comparing our method against the five SOTA models, individual applications of GPT-3.5 and GPT-4, and a voting ensemble method. The results indicate that our proposed fusion of ChatGPT with the ensemble learning algorithm outperforms the SOTA results in the CADEC, ShARe13, and ShARe14 datasets, showcasing its potential to enhance NLP applications in the healthcare domain.

Discontinuous Named Entity Recognition (DNER) presents a challenging problem where entities may be scattered across multiple non-adjacent tokens, making traditional sequence labelling approaches inadequate. Existing methods predominantly rely on custom tagging schemes to handle these discontinuous entities, resulting in models tightly coupled to specific tagging strategies and lacking generalisability across diverse datasets. To address these challenges, we propose TriG-NER, a novel Triplet-Grid Framework that introduces a generalisable approach to learning robust token-level representations for discontinuous entity extraction. Our framework applies triplet loss at the token level, where similarity is defined by word pairs existing within the same entity, effectively pulling together similar and pushing apart dissimilar ones. This approach enhances entity boundary detection and reduces the dependency on specific tagging schemes by focusing on word-pair relationships within a flexible grid structure. We evaluate TriG-NER on three benchmark DNER datasets and demonstrate significant improvements over existing grid-based architectures. These results underscore our framework's effectiveness in capturing complex entity structures and its adaptability to various tagging schemes, setting a new benchmark for discontinuous entity extraction.

End-to-end relation extraction (E2ERE) is an important and realistic application of natural language processing (NLP) in biomedicine. In this paper, we aim to compare three prevailing paradigms for E2ERE using a complex dataset focused on rare diseases involving discontinuous and nested entities. We use the RareDis information extraction dataset to evaluate three competing approaches (for E2ERE): NER $\rightarrow$ RE pipelines, joint sequence to sequence models, and generative pre-trained transformer (GPT) models. We use comparable state-of-the-art models and best practices for each of these approaches and conduct error analyses to assess their failure modes. Our findings reveal that pipeline models are still the best, while sequence-to-sequence models are not far behind; GPT models with eight times as many parameters are worse than even sequence-to-sequence models and lose to pipeline models by over 10 F1 points. Partial matches and discontinuous entities caused many NER errors contributing to lower overall E2E performances. We also verify these findings on a second E2ERE dataset for chemical-protein interactions. Although generative LM-based methods are more suitable for zero-shot settings, when training data is available, our results show that it is better to work with more conventional models trained and tailored for E2ERE. More innovative methods are needed to marry the best of the both worlds from smaller encoder-decoder pipeline models and the larger GPT models to improve E2ERE. As of now, we see that well designed pipeline models offer substantial performance gains at a lower cost and carbon footprint for E2ERE. Our contribution is also the first to conduct E2ERE for the RareDis dataset.

Named Entity Recognition (NER) remains challenging due to the complex entities, like nested, overlapping, and discontinuous entities. Existing approaches, such as sequence-to-sequence (Seq2Seq) generation and span-based classification, have shown impressive performance on various NER subtasks, but they are difficult to scale to datasets with longer input text because of either exposure bias issue or inefficient computation. In this paper, we propose a novel Sequence-to-Forest generation paradigm, S2F-NER, which can directly extract entities in sentence via a Forest decoder that decode multiple entities in parallel rather than sequentially. Specifically, our model generate each path of each tree in forest autoregressively, where the maximum depth of each tree is three (which is the shortest feasible length for complex NER and is far smaller than the decoding length of Seq2Seq). Based on this novel paradigm, our model can elegantly mitigates the exposure bias problem and keep the simplicity of Seq2Seq. Experimental results show that our model significantly outperforms the baselines on three discontinuous NER datasets and on two nested NER datasets, especially for discontinuous entity recognition.

So far, discontinuous named entity recognition (NER) has received increasing research attention and many related methods have surged such as hypergraph-based methods, span-based methods, and sequence-to-sequence (Seq2Seq) methods, etc. However, these methods more or less suffer from some problems such as decoding ambiguity and efficiency, which limit their performance. Recently, grid-tagging methods, which benefit from the flexible design of tagging systems and model architectures, have shown superiority to adapt for various information extraction tasks. In this paper, we follow the line of such methods and propose a competitive grid-tagging model for discontinuous NER. We call our model TOE because we incorporate two kinds of Tag-Oriented Enhancement mechanisms into a state-of-the-art (SOTA) grid-tagging model that casts the NER problem into word-word relationship prediction. First, we design a Tag Representation Embedding Module (TREM) to force our model to consider not only word-word relationships but also word-tag and tag-tag relationships. Concretely, we construct tag representations and embed them into TREM, so that TREM can treat tag and word representations as queries/keys/values and utilize self-attention to model their relationships. On the other hand, motivated by the Next-Neighboring-Word (NNW) and Tail-Head-Word (THW) tags in the SOTA model, we add two new symmetric tags, namely Previous-Neighboring-Word (PNW) and Head-Tail-Word (HTW), to model more fine-grained word-word relationships and alleviate error propagation from tag prediction. In the experiments of three benchmark datasets, namely CADEC, ShARe13 and ShARe14, our TOE model pushes the SOTA results by about 0.83%, 0.05% and 0.66% in F1, demonstrating its effectiveness.