arXiv:2603.04135v1 Announce Type: cross Abstract: Group Relative Policy Optimization (GRPO) effectively scales LLM reasoning but incurs prohibitive computational costs due to its extensive group-based sampling requirement. While recent selective data utilization methods can mitigate this overhead, they could induce estimation bias by altering the underlying sampling distribution, compromising theoretical rigor and convergence behavior. To address this limitation, we propose Dynamic Pruning Policy Optimization (DPPO), a framework that enables dynamic pruning while preserving unbiased gradient estimation through importance sampling-based correction. By incorporating mathematically derived rescaling factors, DPPO significantly accelerates GRPO training without altering the optimization objective of the full-batch baseline. Furthermore, to mitigate the data sparsity induced by pruning, we introduce Dense Prompt Packing, a window-based greedy strategy that maximizes valid token density and hardware utilization. Extensive experiments demonstrate that DPPO consistently accelerates training across diverse models and benchmarks. For instance, on Qwen3-4B trained on MATH, DPPO achieves 2.37$\times$ training speedup and outperforms GRPO by 3.36% in average accuracy across six mathematical reasoning benchmarks.

arXiv:2603.02406v1 Announce Type: cross Abstract: Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.