Heart failure (HF) is one of the leading causes of rehospitalization among older adults in the United States. Although clinical notes contain rich, detailed patient information and make up a large portion of electronic health records (EHRs), they remain underutilized for HF readmission risk analysis. Traditional computational models for HF readmission often rely on expert-crafted rules, medical thesauri, and ontologies to interpret clinical notes, which are typically written under time pressure and may contain misspellings, abbreviations, and domain-specific jargon. We present ClinNoteAgents, an LLM-based multi-agent framework that transforms free-text clinical notes into (1) structured representations of clinical and social risk factors for association analysis and (2) clinician-style abstractions for HF 30-day readmission prediction. We evaluate ClinNoteAgents on 3,544 notes from 2,065 patients (readmission rate=35.16%), demonstrating strong performance in extracting risk factors from free-text, identifying key contributing factors, and predicting readmission risk. By reducing reliance on structured fields and minimizing manual annotation and model training, ClinNoteAgents provides a scalable and interpretable approach to note-based HF readmission risk modeling in data-limited healthcare systems.

Understanding how individuals with Parkinson's disease (PD) describe cognitive experiences in their daily lives can offer valuable insights into disease-related cognitive and emotional changes. However, extracting such information from unstructured patient narratives is challenging due to the subtle, overlapping nature of cognitive constructs. This study developed and evaluated natural language processing (NLP) models to automatically identify categories that reflect various cognitive processes from de-identified first-person narratives. Three model families, a Bio_ClinicalBERT-based span categorization model for nested entity recognition, a fine-tuned Meta-Llama-3-8B-Instruct model using QLoRA for instruction following, and GPT-4o mini evaluated under zero- and few-shot settings, were compared on their performance on extracting seven categories. Our findings indicated that model performance varied substantially across categories and model families. The fine-tuned Meta-Llama-3-8B-Instruct achieved the highest overall F1-scores (0.74 micro-average and 0.59 macro-average), particularly excelling in context-dependent categories such as thought and social interaction. Bio_ClinicalBERT exhibited high precision but low recall and performed comparable to Llama for some category types such as location and time but failed on other categories such as thought, emotion and social interaction. Compared to conventional information extraction tasks, this task presents a greater challenge due to the abstract and overlapping nature of narrative accounts of complex cognitive processes. Nonetheless, with continued refinement, these NLP systems hold promise for enabling low-burden, longitudinal monitoring of cognitive function and serving as a valuable complement to formal neuropsychological assessments in PD.

De-identification in the healthcare setting is an application of NLP where automated algorithms are used to remove personally identifying information of patients (and, sometimes, providers). With the recent rise of generative large language models (LLMs), there has been a corresponding rise in the number of papers that apply LLMs to de-identification. Although these approaches often report near-perfect results, significant challenges concerning reproducibility and utility of the research papers persist. This paper identifies three key limitations in the current literature: inconsistent reporting metrics hindering direct comparisons, the inadequacy of traditional classification metrics in capturing errors which LLMs may be more prone to (i.e., altering clinically relevant information), and lack of manual validation of automated metrics which aim to quantify these errors. To address these issues, we first present a survey of LLM-based de-identification research, highlighting the heterogeneity in reporting standards. Second, we evaluated a diverse set of models to quantify the extent of inappropriate removal of clinical information. Next, we conduct a manual validation of an existing evaluation metric to measure the removal of clinical information, employing clinical experts to assess their efficacy. We highlight poor performance and describe the inherent limitations of such metrics in identifying clinically significant changes. Lastly, we propose a novel methodology for the detection of clinically relevant information removal.

The advent of large language models (LLMs) has opened new avenues for analyzing complex, unstructured data, particularly within the medical domain. Electronic Health Records (EHRs) contain a wealth of information in various formats, including free text clinical notes, structured lab results, and diagnostic codes. This paper explores the application of advanced language models to leverage these diverse data sources for improved clinical decision support. We will discuss how text-based features, often overlooked in traditional high dimensional EHR analysis, can provide semantically rich representations and aid in harmonizing data across different institutions. Furthermore, we delve into the challenges and opportunities of incorporating medical codes and ensuring the generalizability and fairness of AI models in healthcare.

Common factors and microcounseling skills are critical to the effectiveness of psychotherapy. Understanding and measuring these elements provides valuable insights into therapeutic processes and outcomes. However, automatic identification of these change principles from textual data remains challenging due to the nuanced and context-dependent nature of therapeutic dialogue. This paper introduces CFiCS, a hierarchical classification framework integrating graph machine learning with pretrained contextual embeddings. We represent common factors, intervention concepts, and microcounseling skills as a heterogeneous graph, where textual information from ClinicalBERT enriches each node. This structure captures both the hierarchical relationships (e.g., skill-level nodes linking to broad factors) and the semantic properties of therapeutic concepts. By leveraging graph neural networks, CFiCS learns inductive node embeddings that generalize to unseen text samples lacking explicit connections. Our results demonstrate that integrating ClinicalBERT node features and graph structure significantly improves classification performance, especially in fine-grained skill prediction. CFiCS achieves substantial gains in both micro and macro F1 scores across all tasks compared to baselines, including random forests, BERT-based multi-task models, and graph-based methods.

Clinical Question Answering (CQA) plays a crucial role in medical decision-making, enabling physicians to extract relevant information from Electronic Medical Records (EMRs). While transformer-based models such as BERT, BioBERT, and ClinicalBERT have demonstrated state-of-the-art performance in CQA, existing models lack the ability to categorize extracted answers, which is critical for structured retrieval, content filtering, and medical decision support. To address this limitation, we introduce a Multi-Task Learning (MTL) framework that jointly trains CQA models for both answer extraction and medical categorization. In addition to predicting answer spans, our model classifies responses into five standardized medical categories: Diagnosis, Medication, Symptoms, Procedure, and Lab Reports. This categorization enables more structured and interpretable outputs, making clinical QA models more useful in real-world healthcare settings. We evaluate our approach on emrQA, a large-scale dataset for medical question answering. Results show that MTL improves F1-score by 2.2% compared to standard fine-tuning, while achieving 90.7% accuracy in answer categorization. These findings suggest that MTL not only enhances CQA performance but also introduces an effective mechanism for categorization and structured medical information retrieval.

Medication Extraction and Mining play an important role in healthcare NLP research due to its practical applications in hospital settings, such as their mapping into standard clinical knowledge bases (SNOMED-CT, BNF, etc.). In this work, we investigate state-of-the-art LLMs in text mining tasks on medications and their related attributes such as dosage, route, strength, and adverse effects. In addition, we explore different ensemble learning methods (\textsc{Stack-Ensemble} and \textsc{Voting-Ensemble}) to augment the model performances from individual LLMs. Our ensemble learning result demonstrated better performances than individually fine-tuned base models BERT, RoBERTa, RoBERTa-L, BioBERT, BioClinicalBERT, BioMedRoBERTa, ClinicalBERT, and PubMedBERT across general and specific domains. Finally, we build up an entity linking function to map extracted medical terminologies into the SNOMED-CT codes and the British National Formulary (BNF) codes, which are further mapped to the Dictionary of Medicines and Devices (dm+d), and ICD. Our model's toolkit and desktop applications are publicly available (at \url{https://github.com/HECTA-UoM/ensemble-NER}).

This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that BioBERT achieved the best performance in both precision and F1 score, verifying its applicability and superiority in the medical field. BioBERT enhances its ability to understand professional terms and complex medical texts through pre-training on biomedical data, providing a powerful tool for medical information extraction and clinical decision support. The study also explored the privacy and compliance challenges of BioBERT when processing medical data, and proposed future research directions for combining other medical-specific models to improve generalization and robustness. With the development of deep learning technology, the potential of BioBERT in application fields such as intelligent medicine, personalized treatment, and disease prediction will be further expanded. Future research can focus on the real-time and interpretability of the model to promote its widespread application in the medical field.

Clinical language models are important for many applications in healthcare, but their development depends on access to extensive clinical text for pretraining. However, obtaining clinical notes from electronic health records (EHRs) at scale is challenging due to patient privacy concerns. In this study, we rephrase existing clinical notes using LLMs to generate synthetic pretraining corpora, drawing inspiration from previous work on rephrasing web data. We examine four popular small-sized LLMs (<10B) to create synthetic clinical text to pretrain both decoder-based and encoder-based language models. The method yields better results in language modeling and downstream tasks than previous synthesis approaches without referencing real clinical text. We find that augmenting original clinical notes with synthetic corpora from different LLMs improves performances even at a small token budget, showing the potential of this method to support pretraining at the institutional level or be scaled to synthesize large-scale clinical corpora.

This work focuses on the efficiency of the knowledge distillation approach in generating a lightweight yet powerful BERT based model for natural language processing applications. After the model creation, we applied the resulting model, LastBERT, to a real-world task classifying severity levels of Attention Deficit Hyperactivity Disorder (ADHD)-related concerns from social media text data. Referring to LastBERT, a customized student BERT model, we significantly lowered model parameters from 110 million BERT base to 29 million, resulting in a model approximately 73.64% smaller. On the GLUE benchmark, comprising paraphrase identification, sentiment analysis, and text classification, the student model maintained strong performance across many tasks despite this reduction. The model was also used on a real-world ADHD dataset with an accuracy and F1 score of 85%. When compared to DistilBERT (66M) and ClinicalBERT (110M), LastBERT demonstrated comparable performance, with DistilBERT slightly outperforming it at 87%, and ClinicalBERT achieving 86% across the same metrics. These findings highlight the LastBERT model's capacity to classify degrees of ADHD severity properly, so it offers a useful tool for mental health professionals to assess and comprehend material produced by users on social networking platforms. The study emphasizes the possibilities of knowledge distillation to produce effective models fit for use in resource-limited conditions, hence advancing NLP and mental health diagnosis. Furthermore underlined by the considerable decrease in model size without appreciable performance loss is the lower computational resources needed for training and deployment, hence facilitating greater applicability. Especially using readily available computational tools like Google Colab. This study shows the accessibility and usefulness of advanced NLP methods in pragmatic world applications.