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.
By Pui Chung Siu, Claudia Cabrera, Mani Mudaliar, Arkaitz Zubiaga
ForeSCITE is a framework that uses large language models to analyze temporal patterns in biomedical conclusions. It clusters published conclusions, estimates a direction that separates earlier from more recent findings within each cluster, and projects conclusion embeddings along these directions. The projected coordinates are decoded into natural‑language hypotheses, and retrospective evaluations show that ForeSCITE expands semantic coverage, introduces novel biomedical entity pairs, and identifies plausible CAR‑T hypotheses that experts deem biologically relevant.
By Chia-Hsuan Chang, Brian Ondov, Jiang Lv, Lan Jiang, Yunmai Wang, Haerin Song, Xueqing Peng, Qiaozhu Mei, Xiaolei Su, Hua Xu
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."
By Dominic Okonkwo, Adetayo Okunoye, Ismailcem Budak Arpinar
arXiv:2609.22174v1 Announce Type: cross
Abstract: Anticipating emerging research directions is a critical goal of AI-assisted science. Existing methods mainly predict which concepts will co-occur in...
By Jingze Wang, Fred Sun, Shangqi Guo
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.
By Xinyu Yuan, Xixian Liu, Jianan Zhao, Yashi Zhang, Hongyu Guo, Jian Tang
AI co-scientists have expanded the use of large language models for generating scientific hypotheses and guiding experimental investigation. Here we investigate whether temporal patterns in the semant...