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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:2608. 00152v1 Announce Type: new Abstract: Predicting the magnitude of a CRISPRi perturbation's transcriptomic effect on held-out target genes is an important open problem in single-cell biology.
The paper introduces CELLAUDIT, a method for auditing whether inputs claimed to influence predictive models actually do so. By testing if an input can enter the computation, whether predictions depend on it, and if that dependence improves observed responses, the authors evaluate agent-generated predictors on a morphology‑transcriptomics benchmark (BBBC047). Their findings show that many models claim compound contributions that are not supported by the data, and that falsification‑guided revisions can recover genuine input effects while improving performance.
arXiv:2608. 10145v1 Announce Type: new Abstract: LeWorldModel trains a latent world model with a prediction loss and a single anti-collapse regulariser, and reports approximately 87% of goals reached on TwoRoom, its simplest diagnostic environment.
SCALE is a conditional transport model that treats cells as unordered sets to predict treated cell populations without requiring cell-level matching. It uses a shared set-aware encoder and a conditional DiT backbone to learn latent transport, enabling endpoint supervision that is directly delta-aligned. Across diverse perturbation types—including genetic, chemical, developmental, and immune—SCALE accurately recovers gene‑expression changes, response directions, and population structure, outperforming competing methods on CRISPR data and successfully prioritizing cytokines that elicit distinct immune responses.
arXiv:2607. 04926v1 Announce Type: cross Abstract: How does the way information reaches a transformer -- as symbolic tokens, a clean per-factor "oracle" code, or an entangled perceptual vector -- shape whether it binds that information compositionally?