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

Knowledge graphs (KGs) are increasingly used as structured context for Large Language Models (LLMs), but industrial KG-RAG systems often need to integrate public and domain-specific KGs constructed from heterogeneous databases. This integration relies on Entity Alignment (EA), where lexical matching alone is insufficient under predicate-name variation and incomplete local neighborhoods. We address EA for KG integration by constructing a pairwise EA dataset and proposing two complementary modules: Predicate Importance Estimation (PIE) and Decoupled Rationale-Score Distillation (DRSD). PIE is a compact embedding-based approach that removes the subject information from each 1-hop triple, encodes the resulting subjectless triples, and aggregates them with learnable predicate-importance weights to build predicate-aware entity embeddings. DRSD trains a distilled small language model (SLM) with pseudo-answers produced by a teacher LLM through distinct prompts. By converting binary EA labels into text-based supervision and decoupling confidence-score estimation from label-consistent rationales, DRSD enables the SLM to learn task-specific reasoning while retaining a less label-biased confidence signal. Experiments show that PIE and DRSD improve EA classification. Moreover, because DRSD decouples confidence-score estimation from the decision, a discrepancy between the two flags an uncertain prediction for human review, thereby enabling a practical discrepancy between automatic acceptance and human-in-the-loop verification.

Entity alignment (EA) aims to identify equivalent entities across heterogeneous knowledge graphs (KGs) and is a key component of knowledge fusion and cross-KG reasoning. The recent EA foundation model demonstrates that alignment knowledge, once pretrained, can be directly applied to diverse previously unseen KG pairs. However, it still underuses structural context in two places: cross-KG interaction is weak during encoding, and final candidate ranking still relies too heavily on coarse similarity. We address these limitations with ContextEA, an enhanced encoder-decoder framework for transferable EA. On the encoder side, we introduce a cross-KG interaction encoder that unifies the two KGs with anchor bridges and performs earlier relation-aware cross-graph propagation. On the decoder side, we introduce a structural calibration decoder that calibrates alignment scores with entity-level, neighborhood-level, relation-level, and anchor-aware structural evidence. This design strengthens both structural context construction and structural context exploitation while remaining lightweight. Experiments on 29 EA datasets in OpenEA, SRPRS, and DBP show consistent gains over strong transferable baselines. Notably, the pretrained ContextEA already surpasses the finetuned baselines on all three benchmark groups, demonstrating substantially stronger transfer to unseen KGs. These results suggest that explicitly harnessing structural context is an effective direction for improving EA foundation models.

Knowledge graphs (KGs) have emerged as a promising solution for integrating and reasoning over complex biomedical and clinical data in healthcare. By representing structured relationships among entities such as diseases, drugs, symptoms, and patient records, KGs provide a semantic backbone for decision-making, prediction, recommendation, and personalized care. Recent advances have demonstrated their utility across diverse medical applications--including clinical decision support systems, disease and treatment outcome prediction, health recommender systems, precision medicine, and medical question answering--where KGs often enhance interpretability, semantic coherence, and patient-specific reasoning. In parallel, a growing body of work focuses on medical KG generation itself, proposing frameworks that construct graphs from EHRs, clinical narratives, biomedical literature, and web resources using ontologies, semantic web technologies, deep-learning-based information extraction, and hybrid neuro-symbolic pipelines. Despite this progress, significant challenges remain, including limited and fragmented knowledge coverage, difficulties in aligning heterogeneous data sources, the fragility of current reasoning and representation-learning methods on dense multi-relational graphs, and unresolved issues related to privacy, bias, and accountability. This survey reviews and categorizes current research on KGs in medicine along both application-oriented and methodology-oriented dimensions, discusses their benefits and technical foundations, and outlines key limitations and open research directions. By analyzing trends, architectures, and evaluation practices, this work aims to guide future developments in KG-driven medical AI systems and support their safe and effective integration into healthcare environments.