The paper introduces HypoKG, a unified biochemical knowledge graph built from KEGG, Rhea, and UniProt, and uses it to benchmark 13,200 biomedical hypotheses generated by six large language models (LLMs). By varying the biological information provided—source enzyme only, full biological path, or source and disease endpoint—the study finds that LLMs produce higher-scoring hypotheses when given minimal information, but these are less evidence‑grounded. When supplied with the full biological path, the models generate hypotheses that align more closely with known mechanistic relationships, a phenomenon the authors term evidence‑disciplined reasoning, which is confirmed by shuffling intermediate path steps. "whyItMatters":"The study demonstrates that knowledge graphs can both uncover novel disease–enzyme pairs and guide LLMs to reason more accurately from evidence, improving the reliability of AI‑generated biomedical hypotheses."
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
arXiv:2608. 05982v1 Announce Type: new Abstract: Inadequate target--disease linkage accounts for 40--50\% of Phase~II efficacy failures, so anticipating which programmes will advance would let sponsors back the hypotheses most likely to reach patients.
Hakken is a domain‑agnostic system that predicts and explains future scientific discoveries by combining transformer‑based models trained on temporal knowledge graphs with large language model semantic knowledge. It identifies novel relationships between scientific concepts that extend beyond the deductive hull of existing knowledge and provides explanations to help scientists assess these predictions. In the biomedical domain, Hakken set a new benchmark for time‑aware multi‑label relation prediction, generated 1.5 million high‑confidence hypotheses about aging, and experimentally confirmed two predictions that revealed previously undocumented interactions relevant to drug discovery.
arXiv:2606. 08532v1 Announce Type: new Abstract: A scientific hypothesis is the first step in research and undergoes experimental validation, yet it also reflects a deep understanding of and reasoning about scientific phenomena.
arXiv:2609.06779v1 Announce Type: cross Abstract: Drug repurposing aims to identify new therapeutic uses for existing compounds and, compared with de novo drug discovery, offers a faster and more cos...
arXiv:2607. 26397v1 Announce Type: cross Abstract: Enzyme function prediction is a hierarchical, knowledge-intensive form of protein function classification.
Scientific knowledge graphs organize entities and relations extracted from scientific literature, but they remain inherently incomplete. Missing typed links in such graphs can therefore represent plau...
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:2608.30393v1 Announce Type: new Abstract: Biomedical artificial intelligence (AI) systems increasingly extract, organize, and reuse scientific claims from literature, clinical trials, and regul...
arXiv:2601. 12805v4 Announce Type: replace-cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks.
HyGRAIL is a framework for discovering scientific hypotheses in incomplete knowledge graphs by combining a graph neural network (GNN) triage with large language model (LLM) review. The GNN scores candidate hypotheses and routes only ambiguous cases to the LLM, which receives structured evidence from the graph converted into natural language. Experiments on MatKG show HyGRAIL achieves the highest F1 score, improves over baselines, and cuts LLM calls by over 54%.
arXiv:2609.15938v1 Announce Type: new Abstract: Scientific agents contribute to hypothesis discovery by synthesizing evidence, assessing proposals, and developing new explanations. Recent systems com...