Jiayi Yuan

Yue Wan, Jiayi Yuan, Zhiwei Feng et al.

Antigenic epitope presented by major histocompatibility complex II (MHC-II) proteins plays an essential role in immunotherapy. However, compared to the more widely studied MHC-I in computational immunotherapy, the study of MHC-II antigenic epitope poses significantly more challenges due to its complex binding specificity and ambiguous motif patterns. Consequently, existing datasets for MHC-II interactions are smaller and less standardized than those available for MHC-I. To address these challenges, we present a well-curated dataset derived from the Immune Epitope Database (IEDB) and other public sources. It not only extends and standardizes existing peptide-MHC-II datasets, but also introduces a novel antigen-MHC-II dataset with richer biological context. Leveraging this dataset, we formulate three major machine learning (ML) tasks of peptide binding, peptide presentation, and antigen presentation, which progressively capture the broader biological processes within the MHC-II antigen presentation pathway. We further employ a multi-scale evaluation framework to benchmark existing models, along with a comprehensive analysis over various modeling designs to this problem with a modular framework. Overall, this work serves as a valuable resource for advancing computational immunotherapy, providing a foundation for future research in ML guided epitope discovery and predictive modeling of immune responses.

Feng Luo, Yu-Neng Chuang, Guanchu Wang et al. · tencent-ai, tsinghua

The reasoning-capable large language models (LLMs) demonstrate strong performance on complex reasoning tasks but often suffer from overthinking, generating unnecessarily long chain-of-thought (CoT) reasoning paths for easy reasoning questions, thereby increasing inference cost and latency. Recent approaches attempt to address this challenge by manually deciding when to apply long or short reasoning. However, they lack the flexibility to adapt CoT length dynamically based on question complexity. In this paper, we propose Auto Long-Short Reasoning (AutoL2S), a dynamic and model-agnostic framework that enables LLMs to dynamically compress their generated reasoning path based on the complexity of the reasoning question. AutoL2S enables a learned paradigm, in which LLMs themselves can decide when longer reasoning is necessary and when shorter reasoning suffices, by training on data annotated with our proposed method, which includes both long and short CoT paths and a special <EASY> token. We then use <EASY> token to indicate when the model can skip generating lengthy CoT reasoning. This proposed annotation strategy can enhance the LLMs' ability to generate shorter CoT reasoning paths with improved quality after training. Extensive evaluation results show that AutoL2S reduces the length of reasoning generation by up to 57% without compromising performance, demonstrating the effectiveness of AutoL2S for scalable and efficient LLM reasoning.