arXiv:2606. 12838v1 Announce Type: cross Abstract: Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks.
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:2608. 06824v1 Announce Type: cross Abstract: A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships.
The paper introduces scEGFlow, an energy‑guided flow matching framework that predicts how single cells respond to perturbations by modeling continuous transitions from control to perturbed states. It uses conditional flow matching and condition‑specific energy gradients to dynamically adjust predictions without retraining, achieving superior performance on imaging and transcriptomic benchmarks, even for unseen perturbations or limited data. The method preserves cellular manifold geometry, heterogeneity, and accurately recapitulates gene‑expression regulatory patterns.
arXiv:2610.04945v2 Announce Type: replace-cross Abstract: Destructive single-cell measurements provide unpaired population snapshots rather than observations of the same cells across conditions. Loca...
arXiv:2606.27752v2 Announce Type: replace Abstract: Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions. Recent adva...
arXiv:2608.23114v1 Announce Type: cross Abstract: Predicting transcriptome-wide responses to unseen genetic perturbations remains a major computational challenge because accurate prediction requires...
arXiv:2606. 27752v1 Announce Type: new Abstract: Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions.
arXiv:2606. 11286v1 Announce Type: cross Abstract: High-content imaging assays quantify cellular responses to chemical and genetic perturbations, yet continuous trajectories of individual cells are unobservable because cells are chemically fixed at acquisition.
arXiv:2511. 02986v2 Announce Type: replace-cross Abstract: Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge.
Generative modeling has shown increasing promise for predicting cellular perturbation effects under chemical compound treatments. Existing approaches either model perturbation as a distribution-to-dis...
arXiv:2610.18456v1 Announce Type: cross Abstract: AI-based cellular perturbation prediction is essential to accelerate drug discovery and therapeutic identification. However, perturbation-specific si...