Author

Ling Li

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Preprint Aug 2026

ATHENA: Knowledge-guided agentic neural architecture search for AutoFormer-based electronic health record modeling

Transformer-based models are widely used for clinical prediction from electronic health records (EHRs), yet their architectures require manual tuning, and the optimal configuration may vary across tasks and hospitals. Neural architecture search (NAS) automates architecture design, but conventional methods are computationally costly for Transformer-based EHR models. Recent large language model (LLM)-guided NAS methods reduce manual search design but conduct each search independently, without reusing architecture knowledge across hospitals. In this study, we propose ATHENA (Agentic Transfer across Hospitals for EHR Neural Architecture Search), a knowledge-guided agentic NAS framework for Transformer-based EHR modeling. ATHENA uses a weight-sharing supernet that is pretrained once per hospital, allowing candidate architectures to be instantiated as inherited subnetworks and evaluated through fine-tuning rather than independent pretraining. It incorporates a two-layer cross-hospital architecture prior. The first layer retrieves high-performing architecture examples from source sites based on task descriptors, while the second estimates the effects of architectural components using SHapley Additive exPlanations (SHAP)-based meta-regression. These priors guide a multi-agent LLM search using validation feedback from the target hospital. Across six clinical prediction tasks evaluated at one held-out OneFlorida+ site and one external MIMIC-IV site, ATHENA significantly outperforms all four baselines in 9 of 12 site-task evaluations under a strict equal-compute comparison. Using a common pretrained AutoFormer supernet for candidate evaluation, ATHENA ranks first in 9 of 12 evaluations at a search budget of 30. It also shows more consistent architecture selection across repeated searches. ATHENA provides a practical approach for reducing manual architecture tuning in Transformer-based EHR modeling.

Deyi Li, Qi Xu, Lingyao Li et al. · 0 citations

#artificial intelligence Preprint Jun 2026

Teaching agentic AI to learn expert reasoning for rare disease diagnosis

Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer; off-the-shelf large language models (LLMs) rank the correct disease first in only 35.4% of benchmark cases. Here we show that this expert reasoning can be converted into a scalable AI capability through a governed learning process rather than model training alone. We developed liteOdyssey through Policy Iteration with Human Feedback (PIHF), an in-context policy-learning method adapted from generalized policy iteration in reinforcement learning, in which model failures and expert corrections consolidate into an clinician-gated policy that turns an off-the-shelf LLM into an agentic diagnostic system. We demonstrated that such a policy improved diagnostic accuracy to match the best published systems at a fraction of their deployment footprint, generalized to unseen diseases, transferred across models, and remained under clinician control. Across 1,243 public benchmark cases spanning 722 rare diseases, liteOdyssey ranked the correct disease first in 59.3% of cases versus 26.5% without the policy, with nearly identical gains on the 1,193 cases and 679 diseases excluded from policy development. Ablations showed that gains exceeded automated prompting improvement and source access alone, and the policy transferred without modification across closed- and open-weight models. In 515 Undiagnosed Diseases Network patients, liteOdyssey again improved accuracy, and blinded physicians rated its differentials more often exact and less often unhelpful. Through PIHF, expert reasoning becomes an LLM capability that experts can inspect, revise, and transfer across models.

Minh-Ha Nguyen, Erica Gray, B. Schuler et al. · 0 citations