Eugenia Alleva

Eugenia Alleva, Isotta Landi, Leslee J Shaw et al.

Clinical note classification is a common clinical NLP task. However, annotated data-sets are scarse. Prompt-based learning has recently emerged as an effective method to adapt pre-trained models for text classification using only few training examples. A critical component of prompt design is the definition of the template (i.e. prompt text). The effect of template position, however, has been insufficiently investigated. This seems particularly important in the clinical setting, where task-relevant information is usually sparse in clinical notes. In this study we develop a keyword-optimized template insertion method (KOTI) and show how optimizing position can improve performance on several clinical tasks in a zero-shot and few-shot training setting.

Isotta Landi, Eugenia Alleva, Alissa A. Valentine et al.

Despite being a unique source of information on patients' status and disease progression, clinical notes are characterized by high levels of duplication and information redundancy. In general domain text, it has been shown that deduplication does not harm language model (LM) pretraining, thus helping reduce the training cost. Although large LMs have proven to learn medical knowledge, they still require specialized domain adaptation for improved downstream clinical tasks. By leveraging large real-world clinical corpora, we first provided a fine-grained characterization of duplicates stemming from common writing practices and clinical relevancy. Second, we demonstrated that deduplicating clinical text can help clinical LMs encode less redundant information in a more efficient manner and do not harm classification tasks via prompt-based learning.

Shengjia Chen, Ruchika Verma, Kevin Clare et al.

Artificial Intelligence (AI) has demonstrated success in computational pathology (CPath) for disease detection, biomarker classification, and prognosis prediction. However, its potential to learn unintended demographic biases, particularly those related to social determinants of health, remains understudied. This study investigates whether deep learning models can predict self-reported race from digitized dermatopathology slides and identifies potential morphological shortcuts. Using a multisite dataset with a racially diverse population, we apply an attention-based mechanism to uncover race-associated morphological features. After evaluating three dataset curation strategies to control for confounding factors, the final experiment showed that White and Black demographic groups retained high prediction performance (AUC: 0.799, 0.762), while overall performance dropped to 0.663. Attention analysis revealed the epidermis as a key predictive feature, with significant performance declines when these regions were removed. These findings highlight the need for careful data curation and bias mitigation to ensure equitable AI deployment in pathology. Code available at: https://github.com/sinai-computational-pathology/CPath_SAIF.

Anna Shopova, Cristoph Lippert, Leslee J. Shaw et al.

Menstrual health is a critical yet often overlooked aspect of women's healthcare. Despite its clinical relevance, detailed data on menstrual characteristics is rarely available in structured medical records. To address this gap, we propose a novel Natural Language Processing pipeline to extract key menstrual cycle attributes -- dysmenorrhea, regularity, flow volume, and intermenstrual bleeding. Our approach utilizes the GatorTron model with Multi-Task Prompt-based Learning, enhanced by a hybrid retrieval preprocessing step to identify relevant text segments. It out- performs baseline methods, achieving an average F1-score of 90% across all menstrual characteristics, despite being trained on fewer than 100 annotated clinical notes. The retrieval step consistently improves performance across all approaches, allowing the model to focus on the most relevant segments of lengthy clinical notes. These results show that combining multi-task learning with retrieval improves generalization and performance across menstrual charac- teristics, advancing automated extraction from clinical notes and supporting women's health research.