The article proposes a framework called quantitative evidence mining to transform biomedical findings into structured, context-rich evidence units. It outlines core elements such as claim, measured entity, value, comparator, population, conditions, temporal context, uncertainty, provenance, validation, and expert review. The authors present an eight-stage reference architecture and emphasize that plausibility should remain multidimensional rather than collapsed into a single truth label, linking extraction to evidence synthesis for applications like clinical trials, biomarker research, and knowledge-graph construction.
arXiv:2608.30393v1 Announce Type: new Abstract: Biomedical artificial intelligence (AI) systems increasingly extract, organize, and reuse scientific claims from literature, clinical trials, and regul...
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
The article presents a new semantic model for representing scientific evidence, specifically tailored to genetics, that extends existing standards by adding fine‑grained, domain‑specific structure. It aligns with FHIR Evidence and SEPIO, incorporates a compact vocabulary validated by SHACL, and was tested in a human‑AI annotation pilot on six genetics papers, producing 28 evidence items and 95 source‑anchored assertions. The authors argue that this model advances trustworthy, AI‑ready infrastructure for variant interpretation by providing a reference data model and validation schema for genetic evidence.
arXiv:2607. 21859v2 Announce Type: replace Abstract: Constructing causal directed acyclic graphs (DAGs) is a core step in biomedical causal analysis, yet it remains a largely manual process.
arXiv:2607. 22574v1 Announce Type: new Abstract: Evidence-based clinical decision making requires specialists to identify, evaluate and synthesize relevant scientific literature.
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:2606. 20164v1 Announce Type: cross Abstract: Real-world clinical decision support requires reasoning over heterogeneous and longitudinal patient information rather than answering isolated medical questions.
arXiv:2608. 07796v1 Announce Type: new Abstract: Large language models perform strongly on medical knowledge benchmarks, but reliable clinical deployment requires agents to conduct defensible investigations over heterogeneous, longitudinal records: determining what evidence is needed, retrieving and reconciling structured and free-text data, grounding conclusions in verifiable evidence, and deferring cases that cannot be resolved reliably.
arXiv:2608.28974v1 Announce Type: new Abstract: Clinically relevant oncology information is distributed across heterogeneous, longitudinal documentation, creating substantial abstraction burden and r...
arXiv:2606. 08093v1 Announce Type: new Abstract: Pathology is the cornerstone of modern medicine, where accurate decision-making relies heavily on evidence-based practices.
PathPocket is a multimodal AI co‑pilot that grounds pathology decision‑making in evidence. It builds the largest pathology evidence corpus (≈110,472 documents) and a hypergraph of 4.55 million entities and 7.10 million relations to support traceable reasoning. The system handles text and multimodal queries, including ROI and gigapixel whole‑slide images, and outperforms current state‑of‑the‑art models on a benchmark of over 200,000 real‑world cases, improving pathologists’ diagnostic accuracy and confidence.
The paper introduces Clinical Graph-JEPA, a framework for building and refining predictive patient-state knowledge graphs from clinical records. It combines multi-agent relation proposal, ontology-aware normalization, deterministic evidence scoring, and JEPA-based latent refinement to construct evidence-scored graphs from MIMIC-IV data and recover missing clinical relations. Experiments show that injecting discharge-note representations into note-grounded entities boosts leave-one-out MRR by 31% relative improvement.