arXiv:2607. 27651v1 Announce Type: new Abstract: Adaptive laboratories choose measurements during experiments, yet most methods begin after adaptation is permitted.
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arXiv:2607. 27651v2 Announce Type: replace Abstract: Learned rules select samples for follow-up measurements in high-throughput experiments.
The paper introduces OPAL, a held‑out decision test that evaluates follow‑up measurement rules in biological screens by freezing a rule and assessing unnecessary measurement, coverage, and value after cost against pre‑defined archive‑specific criteria. Using a six‑rule Cell Painting battery, the authors show that a high‑value rule would re‑image 96.01% of the library with a 97.14% false‑activation upper bound, illustrating that predicted value alone cannot justify replacing a fixed plan. In development, a sparse Cell Painting rule reduced added‑well burden 18.2‑fold but had a false‑discovery bound above 35%, leading the fixed plan to remain; similar analyses for LINCS–LJP and CTRP highlighted the need for fallback strategies and the importance of separating optimization from evidence. "whyItMatters":"OPAL provides a systematic way to determine whether a new measurement strategy truly improves experimental efficiency without compromising data quality, as demonstrated across multiple biological screening datasets."
The paper introduces a framework to predict whether a compound’s potency can be quantified in dose‑response profiling, treating quantifiability as a separate triage goal from biological activity. It shows that features from low‑cost primary screens, rather than molecular structure, strongly predict quantifiability, and that this prediction holds across new chemical scaffolds and assay families. The authors argue that incorporating quantifiability predictions can better allocate expensive dose‑response resources.
The study evaluates whether a portfolio of compact, semantically named descriptor blocks can match the performance of a 2048‑dimensional CheMeleon embedding in low‑data molecular assays. Using a fixed 11‑dimensional physicochemical base and greedily adding provenance‑screened blocks, the portfolio achieves a mean test AUC of 0.762 across nine ADME/Tox assays, comparable to CheMeleon’s 0.764 and better than Mordred’s 0.756. The results meet a predeclared pooled parity threshold but not all per‑assay thresholds, and further analysis confirms the competitiveness of the auditable representation while highlighting unresolved assay‑level differences.
The study evaluates a frozen Geneformer representation for predicting CRISPRi perturbation effects under a tightly controlled, pre‑registered protocol. While the representation shows significant predictive power within the Virtual Cell Challenge dataset, it fails to transfer to external screens, with negative zero‑shot Spearman correlations. The analysis also reveals that the VCC endpoint is heavily influenced by sampling depth, as cell count alone explains most of the variance, indicating a sampling‑depth entanglement that could mask transfer failures in less controlled settings.
arXiv:2606. 02902v1 Announce Type: cross Abstract: Deep reinforcement learning (DRL) is increasingly applied to de novo molecular design, but choices in data, rewards, and evaluation can yield uneven performance across disease areas and chemotypes.