While large language models and retrieval-augmented gen-
eration (RAG) are rapidly permeating the therapeutic AI
landscape, a critical barrier persists: context fragility—the
phenomenon whereby the meaning of a molecular label
changes when assay semantics, endpoint definitions, deci-
sion thresholds, or data provenance shift, even for the iden-
tical molecule. We reframe this problem through the lens
of agentic AI and propose AssayKG-RAG, a provenance-
aware typed knowledge graph retrieval framework in which
the agent actively plans admissible evidence, criticizes the
coherence between the query context and the retrieved
items, and verifies the directional validity of predictions.
The system is built on three pillars: (i) canonicalization
of the assay context into seven typed fields, (ii) prove-
nance tags on every evidence edge, and (iii) a determinis-
tic planner–critic–verifier loop that emits both predictions
and inspectable audit signals.
On a held-out-source synthetic benchmark and
a targeted real-molecule concept-conflict stress test,
AssayKG-RAG achieves a perfect Directional Correct-
ness Coe!cient (DCC = 1.000), an error-detection
AUROCerr = 0.777, and a Zero leakage rate
(LeakageRate = 0.000). These results empirically
demonstrate that the agent can surface and report
context-dependent failure modes that average AUROC
alone would render invisible. The core contribution is not
a leaderboard refresh, but the formalization of an explicitly
decoupled plan–criticize–verify loop with provenance-gated
auditability into a reproducible, executable contract for
therapeutic agentic AI.
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