Query-Conditioned Knowledge Alignment for Reliable Cross-System Medical Reasoning

• URL: http://arxiv.org/abs/2605.18570v1
• Date: Mon, 18 May 2026 15:49:46 GMT
• Title: Query-Conditioned Knowledge Alignment for Reliable Cross-System Medical Reasoning
• Abstract summary: Cross-domain knowledge alignment is essential for integrating heterogeneous medical systems.<n>We propose Query-Conditioned Entity Alignment (QCEA), which reformulates entity alignment as a query-conditioned correspondence problem.<n>We evaluate QCEA on TCM--WM knowledge graphs derived from SymMap, covering both symptom alignment and herb--molecule alignment tasks.
• Score: 8.331524801839162
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Cross-domain knowledge alignment is essential for integrating heterogeneous medical systems, yet existing approaches typically treat entity alignment as a static matching problem, ignoring query context and cross-system asymmetry. This limitation is particularly critical in integrative medical settings, where correspondence between concepts is inherently context-dependent, non-bijective, and direction-sensitive. In this paper, we propose Query-Conditioned Entity Alignment (QCEA), which reformulates entity alignment as a query-conditioned correspondence problem. Instead of learning a fixed mapping between entity representations, QCEA treats the textual description of a source entity as a query and ranks candidate entities in the target graph, enabling context-dependent alignment. The framework integrates semantic encoding, graph-based representation learning, and a direction-aware transformation module to capture asymmetric and many-to-many correspondence across heterogeneous knowledge systems. We evaluate QCEA on TCM--WM knowledge graphs derived from SymMap, covering both symptom alignment and herb--molecule alignment tasks. Experimental results show consistent improvements over representative baselines, particularly on rank-sensitive metrics such as Hit@K and MRR. Furthermore, downstream retrieval-augmented generation (RAG) experiments demonstrate that improved alignment leads to better evidence retrieval, stronger grounding, and higher answer accuracy. These findings highlight that alignment is not merely a data integration step, but a key factor that shapes knowledge accessibility and reliability in cross-system medical reasoning.

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