arXiv:2604.27269cs.AI2026-04被引 1

构建跨分子、临床等领域的多模态生物医学知识图谱,支持精准推理与新假说生成。

Unifying biomedical knowledge in a modern multimodal graph

论文配图:Unifying biomedical knowledge in a modern multimodal graph
图 1 · 摘自论文原文
  • 融合结构化与半结构化数据,构建带类型元信息的统一知识图谱
  • 包含超2100万条边和6700万属性实例,90%以上真实边有文献支持
  • 适合用于大模型知识检索、药物发现与科研假说生成

生物医学知识图谱在生命科学中广泛应用,但多数来自非结构化文档,缺乏模式约束;而来自结构化资源的图谱又难以统一。我们提出OptimusKG,一种基于结构化与半结构化资源构建的多模态标注属性图(LPG),覆盖分子、解剖、临床和环境等多个领域,保留事实性与类型特异性元数据。OptimusKG包含190,939个节点(10类实体)、21,818,752条边(27种关系)和67,070,490个属性实例,涵盖145个属性键的109,665,797个取值,源自18个本体与受控词汇表。图谱采用顶层模式规范节点与边,并保留细粒度属性、交叉引用与来源信息。通过多模态代理PaperQA3评估其有效性:采样边中70.0%有文献支持,83.4%的虚假边无支持证据。缺乏文献支持的边主要来自实验与功能基因组学资源,表明OptimusKG捕捉了尚未被文献整合的前沿生物医学知识。该图谱以Apache Parquet格式发布,可作为图神经网络、大模型知识检索及假说生成等应用的标准化资源。

原文摘要 · Abstract (English)

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constraints, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,939 nodes across 10 entity types, 21,818,752 edges across 27 edge types, and 67,070,490 property instances encoding 109,665,797 values across 145 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

知识图谱生物医学多模态假说生成

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