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Fan-Yu Yen

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Review Jul 2026

EviDAG: Auditable Causal DAG Authoring with Biomedical Literature

Constructing causal directed acyclic graphs (DAGs) is a core step in biomedical causal analysis, yet it remains a largely manual process. Analysts must connect study variables to prior literature, evaluate uncertain causal claims, and preserve sufficient provenance for expert review. We present EviDAG, a browser-based system for authoring causal DAGs as auditable, evidence-linked artifacts from biomedical literature. Given free-text descriptions of study concepts, EviDAG creates a reproducible literature snapshot, uses an LLM-based reasoning module to generate structured pairwise causal judgments, links literature-supported judgments to verbatim evidence excerpts, and assembles the judgments into a constraint-checked graph. Each proposed edge includes confidence estimates, provenance, and a reviewable rationale. The interface supports study specification, progress monitoring, evidence review, graph comparison, adjustment-set computation, and export. In evaluations against both compact benchmark DAGs and reference DAGs derived from published literature, EviDAG achieves high edge recall on the literature-based cohort while retaining verifiable evidence trails absent from LLM-only baselines. EviDAG thus reduces the burden of causal DAG curation while making the resulting assumptions auditable, supporting the design, analysis, and interpretation of biomedical studies.

Y. Sheu, Michael R. Steigman, Yu Zhou et al. · 0 citations
Open access Jul 2026

Using large language models for enhancing accessibility for Monte Carlo photon transport simulations and beyond

This work investigates the use of LLMs in quantitative biophotonics simulation tools, with a goal of enabling novice users to build complex photon simulations using intuitive natural-language-based problem descriptions and provides a pathway to making complex scientific tools accessible while ensuring the reliability and technical correctness required for rigorous scientific research.

Fan-Yu Yen, Yiyi Liu, Qianqian Fang · 0 citations

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