Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens
TL;DR - AssayLoop combines a transformer-based acquisition policy with LLM-derived biological priors to prioritize CRISPR perturbations across sequential experiments. It discovers 27.7% of hits while testing about 5% of candidates, potentially making constrained biological screens substantially more efficient.
- AssayBench-Loop includes 1,389 CRISPR screens spanning five phenotype categories.
- AssayFormer learns adaptive acquisition strategies from historical screens and updates them using experimental feedback.
- An adaptive handoff integrates LLM priors, while AssayLLM extends the approach through task-specific LLM post-training.
- On temporally held-out screens, AssayLoop achieved 5.67Ă— enrichment over random selection and transferred to phenotype categories excluded from training.