EpiKG2DAG is introduced, a framework that supports evidence-anchored candidate DAG generation by transforming unstructured biomedical abstracts into structured epidemiological associations and enables the automated identification of candidate confounders, mediators, and colliders based on graph-theoretic motifs and literature-derived evidence.
Abstract
While Directed Acyclic Graphs (DAGs) are essential for causal inference, their construction often relies on expert heuristics, which bypasses systematic evidence synthesis and creates a critical "evidence retrieval gap" in causal modeling. This study introduces EpiKG2DAG, a framework that supports evidence-anchored candidate DAG generation by transforming unstructured biomedical abstracts into structured epidemiological associations. We utilized DeepSeek-V3 to extract exposure-outcome association triplets from 189,266 abstracts and employed SapBERT for semantic normalization against UMLS concepts. The resulting Epidemiological Knowledge Graph (EpiKG) enables the automated identification of candidate confounders, mediators, and colliders based on graph-theoretic motifs and literature-derived evidence. A case study on COVID-19 and AKI demonstrates that the framework uncovers non-obvious confounders, such as air pollution, while ensuring evidence traceability. This work contributes to the field by mitigating the knowledge-acquisition bottleneck and providing a transparent, reproducible foundation for evidence-based causal modeling.
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.· arXiv.org· 0 citations
Initial experiments on heart-failure-focused clinical question answering show that CGX improves evidence retrieval quality and perceived answer reliability over conventional retrieval methods, while reducing total graph construction time by 69.7% under the same input corpus and hardware setting.
Dat Nguyen, Anh N. Le, Binh T. D. Trinh et al.· Journal of Biomedical Inform...· 0 citations
DAG-FM is proposed, a novel foundation model architecture that amortizes causal discovery and introduces Mixture-of-Leaf-Experts (MoLE) to handle diverse and unknown Functional Causal Model (FCM) assumptions in real-world scenarios.
THGAgents utilizes collaborative and dynamically updating agents to build a Traceable Causal Knowledge Graph, which serves as the foundation for the evidence-based knowledge structure and employs an LLM-driven heuristic search algorithm to traverse the complex network, balancing both novelty and rigor to deduce strict, evidence-based mechanistic causal chains.
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Amy K. Glen, D. Witherington, Trent Leslie et al.· bioRxiv· 0 citations
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