Escaping Local Optima in the Waddington Landscape: A Two-Stage TRPO-PPO Approach for Single-Cell Perturbation Analysis

Abstract

Modeling cellular responses to genetic and chemical perturbations remains a central challenge in single-cell biology. Existing data-driven frameworks have advanced perturbation prediction through variational autoencoders, chemically conditioned autoencoders, and large-scale transformer pretraining. However, most existing models rely exclusively on either in silico perturbation data or experimental perturbation data but rarely integrate both, limiting their ability to generalize and validate predictions across simulated and real biological contexts in a digital twin system. Moreover, the models are prone to local optima in the nonconvex Waddington landscape of cell fate decisions, where poor initialization can trap trajectories in spurious lineages. In this work, we introduce a two-stage reinforcement learning algorithm for modeling single-cell perturbation. We first compute an explicit natural gradient update using Fisher-vector products and a conjugate gradient solver, scaled by a KL trust-region constraint to provide a safe, curvature-aware first step for the policy. Starting with these preconditioned parameters, we then apply a second phase of proximal policy optimization (PPO) with a KL penalty, exploiting minibatch efficiency to refine the policy. We demonstrate that this initialization strategy substantially improves generalization on Single-cell RNA sequencing (scRNA-seq) perturbation analysis in a digital twin system.