The paper introduces an open, reproducible biomedical knowledge graph ecosystem built on the Rust-native Samyama graph database. It details three foundational knowledge graphs—Pathways, Clinical Trials, and Drug Interactions—along with their expansion into a 22‑graph, 2‑cohort biomedical store containing over 328 million nodes and 1.44 billion edges, including synthetic patient data. The authors describe a reproducible ETL workflow, cross‑graph integration via query‑time joins and identifier deduplication, and a schema‑driven Model Context Protocol that achieves high accuracy on the BiomedQA benchmark.
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.
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.
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.
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.
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.
The paper introduces a modular agentic-AI platform that transforms heterogeneous CMC process-development documents into a dual-layer knowledge graph. The base layer creates a lexical Document‑Section‑Chunk hierarchy, while the intelligence layer extracts ontology‑aligned entities and links cross‑document concepts, all anchored by provenance. LLM agents navigate these layers to answer queries, and a novel three‑tier evaluation protocol demonstrates high retrieval‑augmented generation performance on proprietary data from a Sanofi program.
arXiv:2608. 14228v1 Announce Type: new Abstract: Life science knowledge graphs make large collections of structured data available through SPARQL, but each resource uses its own schema, identifiers, and links.
arXiv:2606. 11562v1 Announce Type: new Abstract: Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood.
post-graph-rag is an open‑source PostgreSQL‑native engine that unifies chunks, embeddings, a canonical entity graph, and community summaries in a single database, using pgvector for search and edge tables for traversal. It validates extraction output—rejecting vague predicates, normalising predicates, resolving entities to unique vertices, and flagging negations—before writing, and employs a bi‑temporal layer to record when a relation held and when the system believed it, superseding incompatible earlier assertions. In benchmarks against LightRAG, it builds denser, more queryable graphs and achieves higher scores on LongMemEval, largely due to its temporal grounding in prompts.
arXiv:2608.21418v1 Announce Type: new Abstract: Manufacturing knowledge graphs that integrate data from heterogeneous industrial systems face a trust deficit: consumers cannot determine whether queri...
arXiv:2602. 01086v3 Announce Type: replace Abstract: Generative AI can encode substantial medical knowledge, but patient-specific answers remain constrained by the context supplied at inference time.