Med-gte-hybrid: A contextual embedding transformer model for extracting actionable information from clinical texts

We introduce a novel contextual embedding model med-gte-hybrid that was derived from the gte-large sentence transformer to extract information from unstructured clinical narratives. Our model tuning strategy for med-gte-hybrid combines contrastive learning and a denoising autoencoder. To evaluate the performance of med-gte-hybrid, we investigate several clinical prediction tasks in large patient cohorts extracted from the MIMIC-IV dataset, including Chronic Kidney Disease (CKD) patient prognosis, estimated glomerular filtration rate (eGFR) prediction, and patient mortality prediction. Furthermore, we demonstrate that the med-gte-hybrid model improves patient stratification, clustering, and text retrieval, thus outperforms current state-of-the-art models on the Massive Text Embedding Benchmark (MTEB). While some of our evaluations focus on CKD, our hybrid tuning of sentence transformers could be transferred to other medical domains and has the potential to improve clinical decision-making and personalised treatment pathways in various healthcare applications.

A Bayesian Approach to Rule Mining

In this paper, we introduce the increasing belief criterion in association rule mining. The criterion uses a recursive application of Bayes' theorem to compute a rule's belief. Extracted rules are required to have their belief increase with their last observation. We extend the taxonomy of association rule mining algorithms with a new branch for Bayesian rule mining~(BRM), which uses increasing belief as the rule selection criterion. In contrast, the well-established frequent association rule mining~(FRM) branch relies on the minimum-support concept to extract rules. We derive properties of the increasing belief criterion, such as the increasing belief boundary, no-prior-worries, and conjunctive premises. Subsequently, we implement a BRM algorithm using the increasing belief criterion, and illustrate its functionality in three experiments: (1)~a proof-of-concept to illustrate BRM properties, (2)~an analysis relating socioeconomic information and chemical exposure data, and (3)~mining behaviour routines in patients undergoing neurological rehabilitation. We illustrate how BRM is capable of extracting rare rules and does not suffer from support dilution. Furthermore, we show that BRM focuses on the individual event generating processes, while FRM focuses on their commonalities. We consider BRM's increasing belief as an alternative criterion to thresholds on rule support, as often applied in FRM, to determine rule usefulness.