Selen Bozkurt

Saima Rathore, Jatin Chaudhary, Boning Tong et al.

Cerebral microbleeds, markers of brain damage from vascular and amyloid pathologies, are linked to cognitive decline in aging, but their role in Alzheimer's disease (AD) onset and progression remains unclear. This study aimed to explore whether the presence and location of lobar microbleeds are associated with amyloid-$β$ (A$β$)-PET, tau tangle formation (tau-PET), and longitudinal cognitive decline. We analyzed 1,573 ADNI participants with MR imaging data and information on the number and location of microbleeds. Associations between lobar microbleeds and pathology, cerebrospinal fluid (CSF), genetics, and cognition were examined, focusing on regional microbleeds and domain-specific cognitive decline using ordinary least-squares regression while adjusting for covariates. Cognitive decline was assessed with ADAS-Cog11 and its domain-specific sub-scores. Participants underwent neuropsychological testing at least twice, with a minimum two-year interval between assessments. Among the 1,573 participants (692 women, mean age 71.23 years), 373 participants had microbleeds. The presence of microbleeds was linked to cognitive decline, particularly in the semantic, language, and praxis domains for those with temporal lobe microbleeds. Microbleeds in the overall cortex were associated with language decline. Pathologically, temporal lobe microbleeds were associated with increased tau in the overall cortex, while cortical microbleeds were linked to elevated A$β$ in the temporal, parietal, and frontal regions. In this mixed population, microbleeds were connected to longitudinal cognitive decline, especially in semantic and language domains, and were associated with higher baseline A$β$ and tau pathology. These findings suggest that lobar microbleeds should be included in AD diagnostic and prognostic evaluations.

JaMor Hairston, Ritvik Ranjan, Sahithi Lakamana et al.

Background Large language models (LLMs) face challenges in inductive thematic analysis, a task requiring deep interpretive and domain-specific expertise. We evaluated the feasibility of using LLMs to replicate expert-driven thematic analysis of social media data. Methods Using two temporally non-intersecting Reddit datasets on xylazine (n=286 and n=686, for model optimization and validation, respectively) with twelve expert-derived themes, we evaluated five LLMs against expert coding. We modeled the task as a series of binary classifications, rather than a single, multi-label classification, employing zero-, single-, and few-shot prompting strategies and measuring performance via accuracy, precision, recall, and F1-score. Results On the validation set, GPT-4o with two-shot prompting performed best (accuracy: 90.9%; F1-score: 0.71). For high-prevalence themes, model-derived thematic distributions closely mirrored expert classifications (e.g., xylazine use: 13.6% vs. 17.8%; MOUD use: 16.5% vs. 17.8%). Conclusions Our findings suggest that few-shot LLM-based approaches can automate thematic analyses, offering a scalable supplement for qualitative research. Keywords: thematic analysis, large language models, natural language processing, qualitative analysis, social media, prompt engineering, public health

Seibi Kobara, Alireza Rafiei, Masoud Nateghi et al.

Breast cancer is a significant public health concern and is the leading cause of cancer-related deaths among women. Despite advances in breast cancer treatments, medication non-adherence remains a major problem. As electronic health records do not typically capture patient-reported outcomes that may reveal information about medication-related experiences, social media presents an attractive resource for enhancing our understanding of the patients' treatment experiences. In this paper, we developed natural language processing (NLP) based methodologies to study information posted by an automatically curated breast cancer cohort from social media. We employed a transformer-based classifier to identify breast cancer patients/survivors on X (Twitter) based on their self-reported information, and we collected longitudinal data from their profiles. We then designed a multi-layer rule-based model to develop a breast cancer therapy-associated side effect lexicon and detect patterns of medication usage and associated side effects among breast cancer patients. 1,454,637 posts were available from 583,962 unique users, of which 62,042 were detected as breast cancer members using our transformer-based model. 198 cohort members mentioned breast cancer medications with tamoxifen as the most common. Our side effect lexicon identified well-known side effects of hormone and chemotherapy. Furthermore, it discovered a subject feeling towards cancer and medications, which may suggest a pre-clinical phase of side effects or emotional distress. This analysis highlighted not only the utility of NLP techniques in unstructured social media data to identify self-reported breast cancer posts, medication usage patterns, and treatment side effects but also the richness of social data on such clinical questions.

Yuxin Zhu, Sahithi Lakamana, Masoud Rouhizadeh et al.

Treatment-resistant depression (TRD) is a severe form of major depressive disorder in which patients do not achieve remission despite multiple adequate treatment trials. Evidence across pharmacologic options for TRD remains limited, and trials often do not fully capture patient-reported tolerability. Large-scale online peer-support narratives therefore offer a complementary lens on how patients describe and evaluate medications in real-world use. In this study, we curated a corpus of 5,059 Reddit posts explicitly referencing TRD from 3,480 subscribers across 28 mental health-related subreddits from 2010 to 2025. Of these, 3,839 posts mentioned at least one medication, yielding 23,399 mentions of 81 generic-name medications after lexicon-based normalization of brand names, misspellings, and colloquialisms. We developed an aspect-based sentiment classifier by fine-tuning DeBERTa-v3 on the SMM4H 2023 therapy-sentiment Twitter corpus with large language model based data augmentation, achieving a micro-F1 score of 0.800 on the shared-task test set. Applying this classifier to Reddit, we quantified sentiment toward individual medications across three categories: positive, neutral, and negative, and tracked patterns by drug, subscriber, subreddit, and year. Overall, 72.1% of medication mentions were neutral, 14.8% negative, and 13.1% positive. Conventional antidepressants, especially SSRIs and SNRIs, showed consistently higher negative than positive proportions, whereas ketamine and esketamine showed comparatively more favorable sentiment profiles. These findings show that normalized medication extraction combined with aspect-based sentiment analysis can help characterize patient-perceived treatment experiences in TRD-related Reddit discourse, complementing clinical evidence with large-scale patient-generated perspectives.

Yao Ge, Yuting Guo, Sudeshna Das et al.

We present HILGEN, a Hierarchically-Informed Data Generation approach that combines domain knowledge from the Unified Medical Language System (UMLS) with synthetic data generated by large language models (LLMs), specifically GPT-3.5. Our approach leverages UMLS's hierarchical structure to expand training data with related concepts, while incorporating contextual information from LLMs through targeted prompts aimed at automatically generating synthetic examples for sparsely occurring named entities. The performance of the HILGEN approach was evaluated across four biomedical NER datasets (MIMIC III, BC5CDR, NCBI-Disease, and Med-Mentions) using BERT-Large and DANN (Data Augmentation with Nearest Neighbor Classifier) models, applying various data generation strategies, including UMLS, GPT-3.5, and their best ensemble. For the BERT-Large model, incorporating UMLS led to an average F1 score improvement of 40.36%, while using GPT-3.5 resulted in a comparable average increase of 40.52%. The Best-Ensemble approach using BERT-Large achieved the highest improvement, with an average increase of 42.29%. DANN model's F1 score improved by 22.74% on average using the UMLS-only approach. The GPT-3.5-based method resulted in a 21.53% increase, and the Best-Ensemble DANN model showed a more notable improvement, with an average increase of 25.03%. Our proposed HILGEN approach improves NER performance in few-shot settings without requiring additional manually annotated data. Our experiments demonstrate that an effective strategy for optimizing biomedical NER is to combine biomedical knowledge curated in the past, such as the UMLS, and generative LLMs to create synthetic training instances. Our future research will focus on exploring additional innovative synthetic data generation strategies for further improving NER performance.