arXiv:2607. 18249v1 Announce Type: cross Abstract: Constraint-based metabolic modeling is a powerful way to study the mechanistic basis of cellular states and disease, but its effective use demands substantial computational expertise and careful coordination of multi-step analyses.
arXiv:2606. 03435v1 Announce Type: new Abstract: Cell Painting combines multiplexed fluorescent staining, high-content imaging, and quantitative analysis to generate high-dimensional phenotypic readouts to support diverse downstream tasks such as mechanism-of-action (MoA) inference, toxicity prediction, and construction of drug-disease atlases.
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...
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:2610.16975v1 Announce Type: new Abstract: Drug discovery remains a resource-intensive and time-consuming process, involving billions of dollars and a decade of development to advance a drug to...
arXiv:2606. 31085v1 Announce Type: new Abstract: Drug-drug interaction (DDI) prediction is essential for medication safety, yet it requires reasoning over heterogeneous biomedical evidence whose relevance changes across interaction mechanisms.
arXiv:2507.07426v4 Announce Type: replace Abstract: Recent advances in large language models have demonstrated considerable potential in scientific domains such as drug repositioning. However, their...
CellCanon is an agentic cellular world model that integrates single‑cell expression prediction, evidence‑grounded explanation, and observation‑driven updating. Its predictive core reuses condition‑level biological evidence to generate gene‑specific readouts, while a shared world state links predictions, measurements, and source‑linked claims to support explanation and revision. On 339 held‑out SciPlex3 conditions across three cell lines, CellCanon outperforms baselines in differential‑expression AUPRC, Macro‑F1, and direction Macro‑F1, and its explanation module correctly answers all answerable questions with supporting proofs.
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:2602.00663v3 Announce Type: replace Abstract: Optimizing molecules to achieve desired properties is a central bottleneck across the chemical sciences, particularly in the pharmaceutical industr...
arXiv:2603. 11872v3 Announce Type: replace-cross Abstract: Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models remain opaque to natural language.
The paper introduces CellForge, a team of autonomous agents that can autonomously generate, train, and validate predictive models for single‑cell perturbation data across transcriptomic, epigenomic, and proteomic contexts. By surveying literature, parsing data, and engaging in critic‑mediated discussions among specialized agents, CellForge produces end‑to‑end model architectures and code without human specification, achieving performance competitive with state‑of‑the‑art hand‑crafted methods. Human evaluators found CellForge’s research plans to be more scientifically sound and innovative than those produced by single large language models or deep‑research systems.