Abul Hasan

Abul Hasan, Mark Levene, David Weston

We investigate the potential benefit of incorporating dictionary information into a neural network architecture for natural language processing. In particular, we make use of this architecture to extract several concepts related to COVID-19 from an on-line medical forum. We use a sample from the forum to manually curate one dictionary for each concept. In addition, we use MetaMap, which is a tool for extracting biomedical concepts, to identify a small number of semantic concepts. For a supervised concept extraction task on the forum data, our best model achieved a macro $F_1$ score of 90\%. A major difficulty in medical concept extraction is obtaining labelled data from which to build supervised models. We investigate the utility of our models to transfer to data derived from a different source in two ways. First for producing labels via weak learning and second to perform concept extraction. The dataset we use in this case comprises COVID-19 related tweets and we achieve an $F_1$ score 81\% for symptom concept extraction trained on weakly labelled data. The utility of our dictionaries is compared with a COVID-19 symptom dictionary that was constructed directly from Twitter. Further experiments that incorporate BERT and a COVID-19 version of BERTweet demonstrate that the dictionaries provide a commensurate result. Our results show that incorporating small domain dictionaries to deep learning models can improve concept extraction tasks. Moreover, models built using dictionaries generalize well and are transferable to different datasets on a similar task.

Imane Guellil, Salomé Andres, Atul Anand et al.

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.

Jinge Wu, Abul Hasan, Honghan Wu

Radiology report summarization is a crucial task that can help doctors quickly identify clinically significant findings without the need to review detailed sections of reports. This study proposes RadBARTsum, a domain-specific and ontology facilitated adaptation of the BART model for abstractive radiology report summarization. The approach involves two main steps: 1) re-training the BART model on a large corpus of radiology reports using a novel entity masking strategy to improving biomedical domain knowledge learning, and 2) fine-tuning the model for the summarization task using the Findings and Background sections to predict the Impression section. Experiments are conducted using different masking strategies. Results show that the re-training process with domain knowledge facilitated masking improves performances consistently across various settings. This work contributes a domain-specific generative language model for radiology report summarization and a method for utilising medical knowledge to realise entity masking language model. The proposed approach demonstrates a promising direction of enhancing the efficiency of language models by deepening its understanding of clinical knowledge in radiology reports.