In healthcare, thousands of safety incidents occur every year, but learning from these incidents is not effectively aggregated. Analysing incident reports using AI could uncover critical insights to prevent harm by identifying recurring patterns and contributing factors. To aggregate and extract valuable information, natural language processing (NLP) and machine learning techniques can be employed to summarise and mine unstructured data, potentially surfacing systemic issues and priority areas for improvement. This paper presents I-SIRch:CS, a framework designed to facilitate the aggregation and analysis of safety incident reports while ensuring traceability throughout the process. The framework integrates concept annotation using the Safety Intelligence Research (SIRch) taxonomy with clustering, summarisation, and analysis capabilities. Utilising a dataset of 188 anonymised maternity investigation reports annotated with 27 SIRch human factors concepts, I-SIRch:CS groups the annotated sentences into clusters using sentence embeddings and k-means clustering, maintaining traceability via file and sentence IDs. Summaries are generated for each cluster using offline state-of-the-art abstractive summarisation models (BART, DistilBART, T5), which are evaluated and compared using metrics assessing summary quality attributes. The generated summaries are linked back to the original file and sentence IDs, ensuring traceability and allowing for verification of the summarised information. Results demonstrate BART's strengths in creating informative and concise summaries.

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformers (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks. We evaluated the performance of PPI identification of multiple GPT and BERT models using three manually curated gold-standard corpora: Learning Language in Logic (LLL) with 164 PPIs in 77 sentences, Human Protein Reference Database with 163 PPIs in 145 sentences, and Interaction Extraction Performance Assessment with 335 PPIs in 486 sentences. BERT-based models achieved the best overall performance, with BioBERT achieving the highest recall (91.95%) and F1-score (86.84%) and PubMedBERT achieving the highest precision (85.25%). Interestingly, despite not being explicitly trained for biomedical texts, GPT-4 achieved commendable performance, comparable to the top-performing BERT models. It achieved a precision of 88.37%, a recall of 85.14%, and an F1-score of 86.49% on the LLL dataset. These results suggest that GPT models can effectively detect PPIs from text data, offering promising avenues for application in biomedical literature mining. Further research could explore how these models might be fine-tuned for even more specialized tasks within the biomedical domain.

A typical information extraction pipeline consists of token- or span-level classification models coupled with a series of pre- and post-processing scripts. In a production pipeline, requirements often change, with classes being added and removed, which leads to nontrivial modifications to the source code and the possible introduction of bugs. In this work, we evaluate sequence-to-sequence models as an alternative to token-level classification methods for information extraction of legal and registration documents. We finetune models that jointly extract the information and generate the output already in a structured format. Post-processing steps are learned during training, thus eliminating the need for rule-based methods and simplifying the pipeline. Furthermore, we propose a novel method to align the output with the input text, thus facilitating system inspection and auditing. Our experiments on four real-world datasets show that the proposed method is an alternative to classical pipelines.