pharmaceutical research teams

Abstract: Longitudinal single cell atlases now capture matched pre treatment and post treatment states from responders and non responders, presenting an opportunity to mechanistically explain why two patients on the same drug diverge. We introduce scDEFT (single cell Drug EFfect Transducer), which treats a drug as a conditioning operator on cell representations, enabling prediction and explanation. In scDEFT, feature wise linear modulation produces drug conditioned cell latents, learned under abundant per cell supervision and then frozen. Two independent heads aggregate those latents over shared transcriptional neighborhoods to predict drug induced state change and responder status. A backward stage ranks the latent dimensions by how strongly they separate responders from non responders and maps them to genes under a cell composition control. On a harmonized inflammatory bowel disease atlas of 1.16 million cells, three cohorts and two drug classes, scDEFT predicts state change at 45% of the baseline to reproducibility ceiling headroom and stratifies responders before treatment at AUROC 0.70, where standard predictors remain at chance. These predictions and the drivers behind them support target and co target nomination, patient stratification, and counterfactual prediction of unseen drug cohort effects.

Abstract: Scientific ideation is the capacity to formulate novel and testable hypotheses from scientific evidence, and autonomous AI scientists depend on it. Existing evaluations largely assess it by asking models to generate ideas from a static, curated set of reference papers. That passive setup departs from the retrieval-and-reasoning workflow of modern AI scientists, and it becomes less discriminative as models improve. We introduce AgentIdeaBench, a multidisciplinary benchmark that evaluates scientific ideation under two matched settings, static observation and active exploration. We report matched Static-Active evaluations for 33 LLMs across 40 densely scored subfields spanning five disciplines, using a multidimensional, literature-verified scoring framework whose critics assess originality against retrieved prior art. Active exploration reveals considerably more capability headroom, and that headroom is unevenly distributed across models. Performance scales about twice as fast as under static observation, and the exploration gain is capability-gated, favoring the strongest models over the weakest. The gain reflects better grounding, improving feasibility, clarity, and specificity while leaving measured originality unchanged under our critics. We further explore Scientific World Modeling, a generation-time loop that refines a draft hypothesis through structured thought experiments. It benefits mid-capability models, and its impact diminishes among frontier models that appear to have internalized such reasoning patterns already. AgentIdeaBench gives future work on scientific ideation a measurement basis suited to the agent era.