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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.
arXiv:2606. 15412v1 Announce Type: cross Abstract: Biomedical relation extraction (BioRE) is a key step in transforming biomedical literature into structured knowledge.
CONSISTRE is a consistency‑aware framework for document‑level relation extraction that tackles contradictions in large language model predictions. It offers two tracks: an inference‑time track that refines black‑box LLM outputs through constraint‑aware prompting, verification, and self‑reflection, and a training‑time track that distills consistency knowledge into smaller open‑source models via supervised fine‑tuning and reinforcement learning. Experiments on DocRED show both tracks outperform baselines, with the inference‑time track matching competitive F1 scores and the training‑time track narrowing the performance gap to proprietary LLMs while reducing inference cost.
Document-level relation extraction (DocRE) aims to extract relations among multiple entities across extended contexts while maintaining consistency across predicted triples. Although large language models (LLMs) show remarkable reasoning capabilities in information extraction, their predictions are typically generated independently for each candidate triple and may violate fundamental relational constraints such as transitivity, symmetry, and functional uniqueness, leading to contradictory and unreliable outputs.
The paper presents an automated framework for building ontology networks by discovering typed semantic links between concepts across domains. It uses domain‑adapted DistilBERT embeddings, clustering to prune candidates, and GPT‑4o for generating interpretable relationships, reducing 800k raw pairs to 95k high‑quality candidates. Human validation on 429 links shows an 80.19% precision and 0.890 F1, outperforming five similarity‑based baselines and demonstrating the need for LLM reasoning in ontology link construction.
arXiv:2511.21075v4 Announce Type: replace-cross Abstract: Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text...