Xue Gong

Joshua Zhi En Tan, JunJie Wee, Xue Gong et al.

Recently, therapeutic peptides have demonstrated great promise for cancer treatment. To explore powerful anticancer peptides, artificial intelligence (AI)-based approaches have been developed to systematically screen potential candidates. However, the lack of efficient featurization of peptides has become a bottleneck for these machine-learning models. In this paper, we propose a topology-enhanced machine learning model (Top-ML) for anticancer peptides prediction. Our Top-ML employs peptide topological features derived from its sequence "connection" information characterized by vector and spectral descriptors. Our Top-ML model, employing an Extra-Trees classifier, has been validated on the AntiCP 2.0 and mACPpred 2.0 benchmark datasets, achieving state-of-the-art performance or results comparable to existing deep learning models, while providing greater interpretability. Our results highlight the potential of leveraging novel topology-based featurization to accelerate the identification of anticancer peptides.

Xue Gong, Qi Yi, Ziyuan Nan et al.

Training Large Language Models (LLMs) for reasoning tasks is increasingly driven by Reinforcement Learning with Verifiable Rewards (RLVR), where Proximal Policy Optimization (PPO) provides a principled framework for stable policy updates. However, the practical application of PPO is hindered by unreliable advantage estimation in the sparse-reward RLVR regime. This issue arises because the sparse rewards in RLVR lead to inaccurate intermediate value predictions, which in turn introduce significant bias when aggregated at every token by Generalized Advantage Estimation (GAE). To address this, we introduce Segmental Advantage Estimation (SAE), which mitigates the bias that GAE can incur in RLVR. Our key insight is that aggregating $n$-step advantages at every token(as in GAE) is unnecessary and often introduces excessive bias, since individual tokens carry minimal information. Instead, SAE first partitions the generated sequence into coherent sub-segments using low-probability tokens as heuristic boundaries. It then selectively computes variance-reduced advantage estimates only from these information-rich segment transitions, effectively filtering out noise from intermediate tokens. Our experiments demonstrate that SAE achieves superior performance, with marked improvements in final scores, training stability, and sample efficiency. These gains are shown to be consistent across multiple model sizes, and a correlation analysis confirms that our proposed advantage estimator achieves a higher correlation with an approximate ground-truth advantage, justifying its superior performance.

Guanhua Huang, Tingqiang Xu, Mingze Wang et al.

Reinforcement Learning with Verifiable Rewards (RLVR) has propelled Large Language Models in complex reasoning, yet its scalability is often hindered by a training bottleneck where performance plateaus as policy entropy collapses, signaling a loss of exploration. Previous methods typically address this by maintaining high policy entropy, yet the precise mechanisms that govern meaningful exploration have remained underexplored. Our analysis suggests that an unselective focus on entropy risks amplifying irrelevant tokens and destabilizing training. This paper investigates the exploration dynamics within RLVR and identifies a key issue: the gradual elimination of valuable low-probability exploratory tokens, which we term \textbf{\textit{reasoning sparks}}. We find that while abundant in pre-trained models, these sparks are systematically extinguished during RLVR due to over-penalization, leading to a degeneracy in exploration. To address this, we introduce Low-probability Regularization (Lp-Reg). Its core mechanism regularizes the policy towards a heuristic proxy distribution. This proxy is constructed by filtering out presumed noise tokens and re-normalizing the distribution over the remaining candidates. The result is a less-noisy proxy where the probability of \textit{reasoning sparks} is amplified, which then serves as a soft regularization target to shield these valuable tokens from elimination via KL divergence. Experiments show that Lp-Reg enables stable on-policy RL, sustaining continuous scaling across $3,000$ training steps and $81,204$ GPU-hours, where baseline entropy-control methods collapse. This sustained exploration leads to state-of-the-art performance, achieving a $60.17\%$ average accuracy on five math benchmarks, an improvement of $2.66\%$ over prior methods. Code is available at https://github.com/CarlanLark/Lp-Reg.