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Xiaoxue Cheng

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NeurIPS Conference 2025 Conference Paper

Incentivizing Dual Process Thinking for Efficient Large Language Model Reasoning

Xiaoxue Cheng
Junyi Li
Zhenduo Zhang
Xinyu Tang
Xin Zhao
Xinyu Kong
Zhiqiang Zhang

Large reasoning models (LRMs) have demonstrated strong performance on complex reasoning tasks, but often suffer from overthinking, generating redundant content regardless of task difficulty. Inspired by the dual process theory in cognitive science, we propose Adaptive Cognition Policy Optimization (ACPO), a reinforcement learning framework that enables LRMs to achieve efficient reasoning through adaptive cognitive allocation and dynamic system switch. ACPO incorporates two key components: (1) introducing system-aware reasoning tokens to explicitly represent the thinking modes thereby making the model's cognitive process transparent, and (2) integrating online difficulty estimation and token length budget to guide adaptive system switch and reasoning during reinforcement learning. To this end, we propose a two-stage training strategy. The first stage begins with supervised fine-tuning to cold start the model, enabling it to generate reasoning paths with explicit thinking modes. In the second stage, we apply ACPO to further enhance adaptive system switch for difficulty-aware reasoning. Experimental results demonstrate that ACPO effectively reduces redundant reasoning while adaptively adjusting cognitive allocation based on task complexity, achieving efficient hybrid reasoning.

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NeurIPS Conference 2025 Conference Paper

ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search

Mengdi Liu
Xiaoxue Cheng
Zhangyang Gao
Hong Chang
Cheng Tan
Shiguang Shan
Xilin Chen

Designing protein sequences that fold into a target 3D structure—known as protein inverse folding—is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of the problem: multiple diverse sequences can fold into the same structure. This motivates the need for a generative model capable of designing diverse sequences while preserving structural consistency. To address this trade-off, we introduce ProtInvTree, the first reward-guided tree-search framework for protein inverse folding. ProtInvTree reformulates sequence generation as a deliberate, step-wise decision-making process, enabling the exploration of multiple design paths and exploitation of promising candidates through self-evaluation, lookahead, and backtracking. We propose a two-stage focus-and-grounding action mechanism that decouples position selection and residue generation. To efficiently evaluate intermediate states, we introduce a jumpy denoising strategy that avoids full rollouts. Built upon pretrained protein language models, ProtInvTree supports flexible test-time scaling by adjusting the search depth and breadth without retraining. Empirically, ProtInvTree outperforms state-of-the-art baselines across multiple benchmarks, generating structurally consistent yet diverse sequences, including those far from the native ground truth. The code is available at https: //github. com/A4Bio/ProteinInvBench/.

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