Hehe Fan

Chao Wang, Hehe Fan, Ruijie Quan et al.

Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending task-specific knowledge, suggesting the potential for ChatGPT-like systems specialized in protein to facilitate basic research. In this work, we introduce ProtChatGPT, which aims at learning and understanding protein structures via natural languages. ProtChatGPT enables users to upload proteins, ask questions, and engage in interactive conversations to produce comprehensive answers. The system comprises protein encoders, a Protein-Language Pertaining Transformer (PLP-former), a projection adapter, and an LLM. The protein first undergoes protein encoders and PLP-former to produce protein embeddings, which are then projected by the adapter to conform with the LLM. The LLM finally combines user questions with projected embeddings to generate informative answers. Experiments show that ProtChatGPT can produce promising responses to proteins and their corresponding questions. We hope that ProtChatGPT could form the basis for further exploration and application in protein research. Code and our pre-trained model will be publicly available.

Yubo Dong, Hehe Fan

Recent Large Language Models (LLMs) have significantly advanced natural language processing and automated decision-making. However, these models still encounter difficulties when performing complex reasoning tasks involving logical deduction and systematic planning, primarily due to their reliance on implicit statistical relationships without structured knowledge representation.Inspired by cognitive science and neurosymbolic AI, we introduce a novel approach to enhance LLMs through explicit structured reasoning. First, we convert unstructured data into structured formats by explicitly annotating reasoning steps. We then employ this structured dataset to train LLMs through Supervised Fine-Tuning (SFT). Additionally, we enhance the structured reasoning capabilities of LLMs using Group Relative Policy Optimization (GRPO), incorporating two innovative algorithms--MAX-Flow and Longest Common Subsequence (LCS)--which notably improve reasoning effectiveness and reduce computational complexity. Experimental results from fine-tuning a DeepSeek-R1-Distill-Qwen-1.5B model demonstrate concise reasoning, robust performance across various scenarios, and improved compatibility with optimization techniques, validating the efficacy of structured reasoning integration in LLMs.