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.
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. 13669v1 Announce Type: new Abstract: Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration.
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.
arXiv:2607. 11464v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions.
LingShu is a large-scale, symptom‑centric knowledge graph that bridges Traditional Chinese Medicine (TCM) and modern biomedicine. It contains 17.33 million entity records and 39.47 million relation records, combining 17.19 million semantic triples with 22.29 million contextualized quadruples to encode conditional medical associations. The graph integrates data from electronic medical records, TCM texts, biomedical ontologies, and curated knowledge bases, and is supported by a web platform offering visualization, reasoning, and evidence‑grounded question answering.
arXiv:2608. 08056v1 Announce Type: new Abstract: Medical data, by its nature, exhibit a high degree of heterogeneity on multiple levels ranging from (a) different modalities like images, text and time series, (b) diverse tabular schemata introduced by institutions and (c) completely unstructured textual information data provided by healthcare professionals.
arXiv:2609.02056v1 Announce Type: new Abstract: Scientific knowledge graphs organize entities and relations extracted from scientific literature, but they remain inherently incomplete. Missing typed...
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.
arXiv:2608. 02692v1 Announce Type: new Abstract: Access to holistic, multimodal data improves the performance of Artificial Intelligence (AI) in medical classification tasks compared to utilizing single modalities or data sources.
The paper introduces a unified framework for aligning biomedical text with knowledge graphs using a lightweight projection learned via contrastive learning, keeping the text encoder and KG embedding model frozen. It evaluates six design choices—text encoder, KG embedding, projection head, triple composition, training direction, and hard‑negative sampling—on a newly created CTD‑Align corpus of 22K chemical‑gene interaction pairs linked to PubMed passages. The study finds that triple composition and training direction have the largest impact, while simpler linear projections over concatenated subject, predicate, and object embeddings yield the best performance.
arXiv:2606. 09105v1 Announce Type: new Abstract: Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery.
arXiv:2608. 15193v1 Announce Type: cross Abstract: As large language model (LLM) agents are increasingly adopted in scientific research, external knowledge bases, knowledge graphs, and long-term memory have improved information retrieval and task continuity.