arXiv subjects

Selen Bozkurt

Publications and source records attributed to Selen Bozkurt.

8 recordsLinked to original sources

arXiv2026

LLM-Augmented Therapy Normalization and Aspect-Based Sentiment Analysis for Treatment-Resistant Depression on Reddit

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.

cs.CL↗

arXiv2026

Patient-Centered, Graph-Augmented Artificial Intelligence-Enabled Passive Surveillance for Early Stroke Risk Detection in High-Risk Individuals

Stroke affected millions annually, yet poor symptom recognition often delayed care-seeking. To address risk recognition gap, we developed a passive surveillance system for early stroke risk detection using patient-reported symptoms among individuals with diabetes. Constructing a symptom taxonomy grounded in patients own language and a dual machine learning pipeline (heterogeneous GNN and EN/LASSO), we identified symptom patterns associated with subsequent stroke. We translated findings into a hybrid risk screening system integrating symptom relevance and temporal proximity, evaluated across 3-90 day windows through EHR-based simulations. Under conservative thresholds, intentionally designed to minimize false alerts, the screening system achieved high specificity (1.00) and prevalence-adjusted positive predictive value (1.00), with good sensitivity (0.72), an expected trade-off prioritizing precision, that was highest in 90-day window. Patient-reported language alone supported high-precision, low-burden early stroke risk detection, that could offer a valuable time window for clinical evaluation and intervention for high-risk individuals.

cs.LG↗

arXiv2025

Automated Thematic Analyses Using LLMs: Xylazine Wound Management Social Media Chatter Use Case

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

cs.AI↗

arXiv2025

HILGEN: Hierarchically-Informed Data Generation for Biomedical NER Using Knowledgebases and Large Language Models

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.

cs.CL↗

arXiv2025

A Mixed-Methods Evaluation of LLM-Based Chatbots for Menopause

The integration of Large Language Models (LLMs) into healthcare settings has gained significant attention, particularly for question-answering tasks. Given the high-stakes nature of healthcare, it is essential to ensure that LLM-generated content is accurate and reliable to prevent adverse outcomes. However, the development of robust evaluation metrics and methodologies remains a matter of much debate. We examine the performance of publicly available LLM-based chatbots for menopause-related queries, using a mixed-methods approach to evaluate safety, consensus, objectivity, reproducibility, and explainability. Our findings highlight the promise and limitations of traditional evaluation metrics for sensitive health topics. We propose the need for customized and ethically grounded evaluation frameworks to assess LLMs to advance safe and effective use in healthcare.

cs.CY↗

arXiv2025

Two-Layer Retrieval-Augmented Generation Framework for Low-Resource Medical Question Answering Using Reddit Data: Proof-of-Concept Study

The increasing use of social media to share lived and living experiences of substance use presents a unique opportunity to obtain information on side effects, use patterns, and opinions on novel psychoactive substances. However, due to the large volume of data, obtaining useful insights through natural language processing technologies such as large language models is challenging. This paper aims to develop a retrieval-augmented generation (RAG) architecture for medical question answering pertaining to clinicians' queries on emerging issues associated with health-related topics, using user-generated medical information on social media. We proposed a two-layer RAG framework for query-focused answer generation and evaluated a proof of concept for the framework in the context of query-focused summary generation from social media forums, focusing on emerging drug-related information. Our modular framework generates individual summaries followed by an aggregated summary to answer medical queries from large amounts of user-generated social media data in an efficient manner. We compared the performance of a quantized large language model (Nous-Hermes-2-7B-DPO), deployable in low-resource settings, with GPT-4. For this proof-of-concept study, we used user-generated data from Reddit to answer clinicians' questions on the use of xylazine and ketamine. Our framework achieves comparable median scores in terms of relevance, length, hallucination, coverage, and coherence when evaluated using GPT-4 and Nous-Hermes-2-7B-DPO, evaluated for 20 queries with 76 samples. There was no statistically significant difference between the two for coverage, coherence, relevance, length, and hallucination. A statistically significant difference was noted for the Coleman-Liau Index. Our RAG framework can effectively answer medical questions about targeted topics and can be deployed in resource-constrained settings.

cs.CL↗

arXiv2024

Cerebral microbleeds: Association with cognitive decline and pathology build-up

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.

q-bio.NC↗

arXiv2024

Social Media as a Sensor: Analyzing Twitter Data for Breast Cancer Medication Effects Using Natural Language Processing

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.

cs.CL↗