Improving biomedical entity linking for complex entity mentions with LLM-based text simplification.

Large amounts of important medical information are captured in free-text documents in biomedical research and within healthcare systems, which can be made accessible through natural language processing (NLP). A key component in most biomedical NLP pipelines is entity linking, i.e. grounding textual mentions of named entities to a reference of medical concepts, usually derived from a terminology system, such as the Systematized Nomenclature of Medicine Clinical Terms. However, complex entity mentions, spanning multiple tokens, are notoriously hard to normalize due to the difficulty of finding appropriate candidate concepts. In this work, we propose an approach to preprocess such mentions for candidate generation, building upon recent advances in text simplification with generative large language models. We evaluate the feasibility of our method in the context of the entity linking track of the BioCreative VIII SympTEMIST shared task. We find that instructing the latest Generative Pre-trained Transformer model with a few-shot prompt for text simplification results in mention spans that are easier to normalize. Thus, we can improve recall during candidate generation by 2.9 percentage points compared to our baseline system, which achieved the best score in the original shared task evaluation. Furthermore, we show that this improvement in recall can be fully translated into top-1 accuracy through careful initialization of a subsequent reranking model. Our best system achieves an accuracy of 63.6% on the SympTEMIST test set. The proposed approach has been integrated into the open-source xMEN toolkit, which is available online via https://github.com/hpi-dhc/xmen.

Relapsing upper bleeding in non-Hodgkin's oesophageal lymphoma associated with achalasia.

Achalasia is a disease of unknown origin in which there is a denervation of the myenteric plexus on the smooth muscle of the lower oesophageal sphincter, causing a cardial stenosis and a loss of efficacy of oesophageal peristalsis. The predominant symptoms are dysphagia for solids and liquids and regurgitation of the retained food. Occasionally, there may be oesophageal haemorrhage as a consequence of oesophagitis and stasis ulcers. An important but uncommon complication is the development of oesophageal cancer, which is typically squamous cell carcinoma. We report an exceptional case of a 77-year-old woman with a long-term achalasia and mega-oesophagus who presented four episodes of upper gastrointestinal bleeding in a 2 month period. The patient underwent surgical resection of the 10 cm of distal oesophagus, performing a partial fundoplication, and the pathological study revealed an oesophageal infiltration by a low-grade non-Hodgkin's lymphoma. After an insidious outcome, she died on the 47th day after admission.

[Clinical and endoscopic prognostic factors in patients with bleeding peptic ulcer]. / Estudio de los factores pronósticos clínicos y endoscópicos en los pacientes con hemorragia digestiva de origen gastroduodenal.

BACKGROUND: The main objectives of this study were to review the clinic and endoscopic variables of patients with upper gastrointestinal bleeding (UGB) due to peptic gastroduodenal lesions who were evaluated in our hospital during one year, to identify the characteristics associated with a negative evolution of the UGB and to analyse the characteristics of those patients who were discharged immediately after the endoscopy was performed. PATIENTS AND METHOD: A one-year retrospective analysis of all UGB episodes was performed. Patients having gastroduodenal ulcer or erosive gastritis/duodenitis at endoscopy were included. The prognostic value of several clinic, laboratory and endoscopic variables was evaluated. Persistence or recurrence of bleeding, surgery and mortality were considered as outcome variables (the variable evolution was categorized as negative when any of these was observed). RESULTS: 156 patients were identified, with a mean (SD) age of 61 (17) years. Melena was the most frequent UGB presentation (79%). 46% patients had associated diseases and 50% were taking gastroerosive drugs. Duodenal ulcer was the commonest cause of UGB (52%), followed by gastric ulcer (30%). The evolution of UGB was negative in 7% cases. Variables associated with a negative evolution in the multivariate analysis were: age, red hematemesis, systolic blood pressure >= 100 mmHg, heart rate >= 100 b.p.m. and a more severe Forrest endoscopic classification. 11% patients were discharged immediately, without complications afterwards. If predictive variables obtained in the multivariate analysis would have been applied, hospitalization would have been avoided in 59 patients (38%) without subsequent complications. CONCLUSIONS: A number of clinic and endoscopic variables (UGB presentation form, blood pressure, heart rate, and Forrest endoscopic classification) with prognostic value have been identified in this study. These variables are easy to obtain and apply in clinical practice, allowing a precise estimate of the UGB evolution. Thus, a relatively high number of patients with UGB susceptible of ambulatory treatment and management can be reliably identified.