Yichen He, Guanhua Huang, Peiyuan Feng, Yuan Lin, Yuchen Zhang, Hang Li, Weinan E. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

We introduce a novel reinforcement learning framework of LLM agents named AGILE (AGent that Interacts and Learns from Environments) designed to perform complex conversational tasks with users, leveraging LLMs, memory, tools, and interactions with experts. The agent possesses capabilities beyond conversation, including reflection, tool usage, and expert consultation. We formulate the construction of such an LLM agent as a reinforcement learning (RL) problem, in which the LLM serves as the policy model. We fine-tune the LLM using labeled data of actions and the PPO algorithm. We focus on question answering and release a dataset for agents called ProductQA, comprising challenging questions in online shopping. Our extensive experiments on ProductQA, MedMCQA and HotPotQA show that AGILE agents based on 7B and 13B LLMs trained with PPO can outperform GPT-4 agents. Our ablation study highlights the indispensability of memory, tools, consultation, reflection, and reinforcement learning in achieving the agent's strong performance. Datasets and code are available at https://github.com/bytarnish/AGILE.

MOTIVATION: The prediction of the binding between peptides and major histocompatibility complex (MHC) molecules plays an important role in neoantigen identification. Although a large number of computational methods have been developed to address this problem, they produce high false-positive rates in practical applications, since in most cases, a single residue mutation may largely alter the binding affinity of a peptide binding to MHC which cannot be identified by conventional deep learning methods. RESULTS: We developed a differential boundary tree-based model, named DBTpred, to address this problem. We demonstrated that DBTpred can accurately predict MHC class I binding affinity compared to the state-of-art deep learning methods. We also presented a parallel training algorithm to accelerate the training and inference process which enables DBTpred to be applied to large datasets. By investigating the statistical properties of differential boundary trees and the prediction paths to test samples, we revealed that DBTpred can provide an intuitive interpretation and possible hints in detecting important residue mutations that can largely influence binding affinity. AVAILABILITY AND IMPLEMENTATION: The DBTpred package is implemented in Python and freely available at: https://github.com/fpy94/DBT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.