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

arXiv: https://arxiv.org/abs/2605.18570 · HTML: https://mlsanity.com/paper/2605.18570/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 40 references that are in the map.
- First posted on arXiv 18 May 2026.

## Builds on (most cited first, 19 of 19)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
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- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [gpt-oss-120b & gpt-oss-20b Model Card](https://mlsanity.com/paper/2508.10925/) (2025)
- [ColBERT: Efficient and Effective Passage Search via Contextualized Late Interaction over BERT](https://mlsanity.com/paper/2004.12832/) (2020)
- [When Not to Trust Language Models: Investigating Effectiveness of Parametric and Non-Parametric Memories](https://mlsanity.com/paper/2212.10511/) (2022)
- [Word Translation Without Parallel Data](https://mlsanity.com/paper/1710.04087/) (2017)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Multilingual Knowledge Graph Embeddings for Cross-lingual Knowledge Alignment](https://mlsanity.com/paper/1611.03954/) (2016)
- [Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding](https://mlsanity.com/paper/1708.05045/) (2017)
- [A Deep Relevance Matching Model for Ad-hoc Retrieval](https://mlsanity.com/paper/1711.08611/) (2017)
- [Zhongjing: Enhancing the Chinese Medical Capabilities of Large Language Model through Expert Feedback and Real-world Multi-turn Dialogue](https://mlsanity.com/paper/2308.03549/) (2023)
- [MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs](https://mlsanity.com/paper/2504.00993/) (2025)
- [Relation-Aware Entity Alignment for Heterogeneous Knowledge Graphs](https://mlsanity.com/paper/1908.08210/) (2019)
- [Multi-view Knowledge Graph Embedding for Entity Alignment](https://mlsanity.com/paper/1906.02390/) (2019)
- [Aligning Cross-Lingual Entities with Multi-Aspect Information](https://mlsanity.com/paper/1910.06575/) (2019)
- [TCM-SD: A Benchmark for Probing Syndrome Differentiation via Natural Language Processing](https://mlsanity.com/paper/2203.10839/) (2022)

## Abstract (arXiv)

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.