Tao, Cui

Abstract Anthracycline-induced cardiotoxicity (AIC) remains a dose-limiting complication of cancer treatment, often leading to irreversible heart failure, yet effective cardioprotective therapies remain limited. Graph-driven drug repurposing offers a rapid pathway to identify cardioprotective therapies, but different computational models often generate divergent candidate lists that exceed experimental validation capacity. We applied a novel "Union-then-Filter" framework to prioritize therapeutics for AIC using AI-based approaches and evaluated candidates in zebrafish models. Three state-of-the-art graph learning models (TxGNN, CompGCN, and RLR) were trained on the PrimeKG to generate an initial candidate pool. A Large Language Model (LLM) agent automated evidence synthesis across 4,286 PubMed abstracts for the top 50 drugs from each model. Candidates were stratified using dual decision criteria and filtered against existing clinical trials. The pipeline narrowed 150 initial candidates to four novel candidates: Cysteine, Dasatinib, Tranilast, and Tretinoin. Prospective in vivo validation was subsequently conducted using an adult AIC (aAIC) zebrafish model. Phenotypic screening via echocardiography revealed that Cysteine, Tranilast, and Tretinoin significantly restored ejection fraction (EF) (overall one-way ANOVA: \(\:F\left(\text{4,95}\right)=47.66,\:\:p<0.0001\); Tukey's post hoc: \(\:\:\:p<0.01\) for all three treatments vs. DOX+ control) and normalized cardiac remodeling markers in doxorubicin-treated subjects (Kruskal-Wallis: \(\:{\chi\:}^{2}\left(4\right)=17.21,\:\:p=0.0018\); Dunn’s post hoc: \(\:\:\:p<0.01\) for all three comparisons vs. DOX control). This study demonstrates the translational utility of an LLM-integrated AI pipeline for drug repurposing and highlights zebrafish AIC as an efficient bridge between in silico prediction and in vivo phenotypic validation in cardio-oncology.

Study objectives To evaluate and compare the performance of two proprietary frontier large language models (LLMs), ChatGPT-5 and Grok-4, on diagnostic reasoning and foundational knowledge tasks within the specialty domain of sleep medicine. Methods The models were evaluated on two tasks: case-based reasoning using 79 clinical vignettes from the AASM Case Book of Sleep Medicine and knowledge assessment using 897 multiple-choice questions (MCQs) from board review materials. For vignettes, final diagnosis was scored by concept-level exact match, and differential diagnosis (DDx) was scored on a fixed top-5 output using concept-level matching with synonym normalization to compute precision, recall, and F 1-score. MCQ performance was the proportion correct. Inter-model performance was compared using the Mann–Whitney U test. Results Both models achieved high accuracy for final diagnosis (92.4% for both; 95% CI 86.4, 98.4) and MCQs (ChatGPT-5: 93.0%; Grok-4: 92.8%). However, performance on generating a comprehensive differential diagnosis was suboptimal, with modest F 1-scores for both ChatGPT-5 (0.55 ± 0.20) and Grok-4 (0.59 ± 0.20). There were no statistically significant differences in performance between the two models across any metric ( p &gt; 0.05). Conclusions Frontier LLMs demonstrated high accuracy in sleep medicine tasks requiring knowledge recall and direct pattern recognition but showed more limited performance in complex clinical reasoning tasks such as generating a comprehensive differential diagnosis. These findings suggest that current general-purpose models may be more reliable for focused knowledge support than for broad hypothesis generation. Future studies should evaluate whether domain-adapted models or clinician-in-the-loop workflows can improve real-world diagnostic usefulness and safety.

Abstract Objective Evaluate how RAG architecture, including corpus structure, retrieval strategy, and pipeline complexity, affects LLM-based medical problem solving and knowledge retrieval in sleep medicine. Materials and Methods We benchmarked four open-source LLMs (Llama-3-8B, Llama -3 -70B, Qwen 2.5-14B, and Qwen 2.5-235B) using a knowledge base of five sleep medicine textbooks. We compared performance across three dimensions: corpus structure (raw text vs table-of-contents aligned.), retrieval strategy (dense embedding vs hybrid sparse-dense), and pipeline complexity (baseline vs augmented). Evaluation metrics included board-style multiple choice question (MCQ) accuracy and clinical case vignette diagnostic ranking. Results RAG improved MCQ accuracy for all models. Llama-8B saw the largest gain of 10.6% (61.8% to 72.4%), while Qwen-235B reached 87.3%. In clinical cases, Llama-8B accuracy dropped by 7.1% when using raw text and dense retrieval due to context noise. This was corrected by using structured hybrid configurations. Hybrid retrieval consistently outperformed dense-only methods. Overall, structured corpora improved primary diagnosis accuracy by 6.1% on average, with Qwen-235B reaching a peak 10.2% increase. Discussion RAG effectiveness depends on the balance between model size and data structure. Large models handle uncurated text well, but smaller models are easily distracted by irrelevant data. Hybrid retrieval is necessary to maintain precision with specialized medical terms. A structured corpus paired with a baseline hybrid pipeline offers the best stability and speed for clinical use. Conclusion Rigorous data curation and hybrid retrieval are as essential as model scale for deploying safe, guideline-compliant AI in sleep medicine.

ABSTRACT Behavioral and social factors (BSFs) substantially influence the risk, onset, and progression of Alzheimer’s disease and related dementias (ADRD), yet BSF-related knowledge remains scattered across heterogeneous sources, posing critical challenges for data harmonization and evidence synthesis. To address this gap, we present the B ehavioral S ocial Data and Knowledge O ntology for AD RD (BSO-AD), a FAIR-compliant semantic resource for representing and harmonizing BSFs and ADRD-related knowledge. BSO-AD was developed following established ontology design principles with reuse of existing ontologies and controlled terminologies, including the Social Determinants of Health Ontology, Drug Repurposing-Oriented Alzheimer’s Disease Ontology, AD-Onto, ICD-9-CM, and ICD-10-CM. Relationships between BSFs and ADRD were derived through literature mining. BSO-AD contains 1,690 classes, 152 object properties, 49 data properties, and 40 annotation properties. Ontology evaluation through Hootation-based domain expert review and a scalable LLM-assisted ontology assessment framework demonstrated high domain coverage and strong semantic coherence. BSO-AD provides a semantic foundation for data harmonization and knowledge integration in BSF-related ADRD research, while the LLM-assisted evaluation framework supports scalable and automated ontology assessment.

Abstract Models that estimate the probability of an adverse clinical outcome require an operational cutoff to translate continuous estimated probabilities into discrete labels that can trigger clinical action. Although statistical methods identify ‘optimal’ cut-offs, threshold selection ultimately reflects value judgments regarding harm tolerance, resource allocation, and workflow feasibility. We describe a governance-informed approach to selecting a deployment threshold for an asthma exacerbation (AE) prediction model integrated into clinical workflows. Using prevalence-adjusted performance metrics and real-world provider capacity modeling, we evaluated multiple candidate thresholds and quantified downstream workload and missed-event trade-offs. We demonstrate that statistically optimal thresholds may produce operationally infeasible alert volumes or unacceptable miss rates. We propose a structured threshold governance framework integrating statistical performance, clinical utility, stakeholder input, and human oversight safeguards. This case illustrates how threshold decisions should be treated as organizational governance processes rather than purely technical optimizations.