arXiv subjects

Yutang Ge

Publications and source records attributed to Yutang Ge.

6 recordsLinked to original sources

arXiv2026

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design

Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is data- and compute-hungry. With limited supervision, LLMs can produce coherent plans in text yet fail to reliably realize them as sequences. This plan-execute gap motivates ProtoCycle, an agentic framework for protein design that uses LLMs primarily to drive a multi-round, feedback-driven decision cycle. ProtoCycle couples an LLM planner with a lightweight tool environment designed to emulate the iterative workflow of human protein engineering and uses LLM-driven reflection on tool feedback to revise plans. Trained with supervised trajectories and online reinforcement learning, ProtoCycle achieves strong language alignment while maintaining competitive foldability, and ablations show that reflection substantially improves sequence quality.

q-bio.QM↗

arXiv2026

SpecXMaster Technical Report

Intelligent spectroscopy serves as a pivotal element in AI-driven closed-loop scientific discovery, functioning as the critical bridge between matter structure and artificial intelligence. However, conventional expert-dependent spectral interpretation encounters substantial hurdles, including susceptibility to human bias and error, dependence on limited specialized expertise, and variability across interpreters. To address these challenges, we propose SpecXMaster, an intelligent framework leveraging Agentic Reinforcement Learning (RL) for NMR molecular spectral interpretation. SpecXMaster enables automated extraction of multiplicity information from both 1H and 13C spectra directly from raw FID (free induction decay) data. This end-to-end pipeline enables fully automated interpretation of NMR spectra into chemical structures. It demonstrates superior performance across multiple public NMR interpretation benchmarks and has been refined through iterative evaluations by professional chemical spectroscopists. We believe that SpecXMaster, as a novel methodological paradigm for spectral interpretation, will have a profound impact on the organic chemistry community.

cs.LG↗

arXiv2026

Latent Poincar\'e Shaping for Agentic Reinforcement Learning

We propose LaPha, a method for training AlphaZero-like LLM agents in a Poincar\'e latent space. Under LaPha, the search process can be visualized as a tree rooted at the prompt and growing outward from the origin toward the boundary of the Poincar\'e ball, where negative curvature provides exponentially increasing capacity with radius. Using hyperbolic geodesic distance to rule-verified correctness, we define a node potential and assign dense process rewards by potential differences. We further attach a lightweight value head on the same shared latent space, enabling self-guided test-time scaling with almost no additional overhead. On MATH-500, LaPha improves Qwen2.5-Math-1.5B from 66.0% to 88.2%. With value-head-guided search, LaPha-1.5B reaches 56.7% accuracy on AIME'24, and LaPha-7B further achieves 60.0% on AIME'24 and 53.3% on AIME'25.

cs.LG↗

arXiv2026

T$^\star$: Progressive Block Scaling for Masked Diffusion Language Models Through Trajectory Aware Reinforcement Learning

We present T$^\star$, a simple TraceRL-based training curriculum for progressive block-size scaling in masked diffusion language models (MDMs). Starting from an AR-initialized small-block MDM, T$^\star$ transitions smoothly to larger blocks, enabling higher-parallelism decoding with minimal performance degradation on math reasoning benchmarks. Moreover, further analysis suggests that T$^\star$ may actually converge to an alternative decoding schedule that achieves comparable performance.

cs.CL↗

arXiv2025

MolReasoner: Toward Effective and Interpretable Reasoning for Molecular LLMs

Large Language Models (LLMs) have shown impressive performance across various domains, but their ability to perform molecular reasoning remains underexplored. Existing methods mostly rely on general-purpose prompting, which lacks domain-specific molecular semantics, or fine-tuning, which faces challenges in interpretability and reasoning depth, often leading to structural and textual hallucinations. To address these issues, we introduce MolReasoner, a two-stage framework that transitions LLMs from memorization to high-fidelity chemical reasoning. In the Mol-SFT stage, knowledge-enhanced Chain-of-Thought (CoT) data provides a strong foundation, while the Mol-RL stage refines reasoning using a novel, task-adaptive reward system to mitigate hallucinations. Extensive evaluations demonstrate that MolReasoner significantly outperforms a wide range of strong baselines in both molecule generation and captioning tasks. Further analyses highlight the framework's synergistic design and its ability to produce more interpretable outputs. Our work presents a principled and effective new approach for advancing high-fidelity molecular reasoning.

cs.LG↗

arXiv2024

How Out-of-Distribution Detection Learning Theory Enhances Transformer: Learnability and Reliability

Transformers excel in natural language processing and computer vision tasks. However, they still face challenges in generalizing to Out-of-Distribution (OOD) datasets, i.e. data whose distribution differs from that seen during training. OOD detection aims to distinguish outliers while preserving in-distribution (ID) data performance. This paper introduces the OOD detection Probably Approximately Correct (PAC) Theory for transformers, which establishes the conditions for data distribution and model configurations for the OOD detection learnability of transformers. It shows that outliers can be accurately represented and distinguished with sufficient data under conditions. The theoretical implications highlight the trade-off between theoretical principles and practical training paradigms. By examining this trade-off, we naturally derived the rationale for leveraging auxiliary outliers to enhance OOD detection. Our theory suggests that by penalizing the misclassification of outliers within the loss function and strategically generating soft synthetic outliers, one can robustly bolster the reliability of transformer networks. This approach yields a novel algorithm that ensures learnability and refines the decision boundaries between inliers and outliers. In practice, the algorithm consistently achieves state-of-the-art (SOTA) performance across various data formats.

cs.LG↗