Multi-source knowledge graphs (KGs) need query mechanisms that expose reliability and exploit domain structure. This paper presents TCMaster, a property-graph query substrate for confidence-aware trav...
arXiv:2608. 06713v1 Announce Type: new Abstract: Biomedical knowledge graphs (KGs) accelerate drug discovery, but standard pipelines assume query molecules already exist as graph entities, leaving unregistered molecules disconnected.
By Yiming Zhang, Hikaru Shindo, Shuan Chen, Kaushalya Madhawa, Jun Jin Choong, Yuna Oikawa, Takashi Fujiwara, Keisuke Ozawa
OptimusKG is a multimodal biomedical labeled property graph that integrates structured and semi‑structured resources to preserve detailed, type‑specific metadata across molecular, anatomical, clinical, and environmental domains. The graph contains nearly 191,000 nodes, over 21.8 million edges, and more than 67 million property instances derived from 18 ontologies, with a top‑level schema that enforces node and edge constraints while retaining granular provenance. Validation using the PaperQA3 agent found that 70.0% of sampled edges are supported by literature evidence, and the graph offers a standardized resource for machine learning, knowledge‑grounded retrieval, and hypothesis generation in biomedical research.
By Lucas Vittor, Ayush Noori, I\~naki Arango, Joaqu\'in Polonuer, Sam Rodriques, Andrew White, David A. Clifton, Marinka Zitnik
The paper evaluates seven graph database engines, including Corvic AI, on a synthetic biomedical property graph with 1.02 million nodes and 5.34 million rows. It benchmarks query latency, bulk‑ingest throughput, point‑update latency, and correctness across a twenty‑query workload that covers neighborhood lookups, bounded paths, set intersections, anti‑joins, aggregation, ranking, temporal filters, full scans, and relational joins. The study finds that no single engine is universally fastest; performance depends on query shape, and the largest cost difference arises from bulk‑ingest throughput, which varies by three orders of magnitude and dominates total cost for workloads with fewer than about 10⁵ queries per data refresh.
By Donald Nguyen, Gurbinder Gill, Hadi Ahmadi, Christopher J. Rossbach
arXiv:2605. 07022v3 Announce Type: replace Abstract: Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage.
By Haydn Jones, Yimeng Zeng, Alden Rose, Li S. Yifei, Yining Huang, Kaiwen Wu, Jiaming Liang, Maggie Ziyu Huan, Yoseph Barash, Cesar de la Fuente-Nunez, Osbert Bastani, Zachary Ives, Mark Yatskar, Jacob R. Gardner
The paper introduces a novel LLM‑driven multi‑agent pipeline that converts relational databases into graph databases by standardizing table and column names and iteratively refining the graph schema through ETL, Analyzer, and Graph agents. The resulting graph database meets accuracy, groundedness, and faithfulness criteria and shows significant performance gains, achieving 85.6% Q&A accuracy—12.12% higher than an SQL agent on PostgreSQL—and reducing latency by roughly threefold on a BFSI dataset. This demonstrates an efficient, automated method for transforming tabular data into a more intuitive and faster‑executing graph format.
By Dinh-Khanh Pham, Quy-Anh Dang, Lam Mai Thanh, Khanh Bui, Truong-Son Hy