Jiawei Sun

Jiyue Jiang, Pengan Chen, Jiuming Wang et al.

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of these LLMs. However, current benchmarks can hardly evaluate the performance of these models across diverse tasks effectively. In this paper, we introduce a comprehensive prompting-based benchmarking framework, termed Bio-benchmark, which includes 30 key bioinformatics tasks covering areas such as proteins, RNA, drugs, electronic health records, and traditional Chinese medicine. Using this benchmark, we evaluate six mainstream LLMs, including GPT-4o and Llama-3.1-70b, etc., using 0-shot and few-shot Chain-of-Thought (CoT) settings without fine-tuning to reveal their intrinsic capabilities. To improve the efficiency of our evaluations, we demonstrate BioFinder, a new tool for extracting answers from LLM responses, which increases extraction accuracy by round 30% compared to existing methods. Our benchmark results show the biological tasks suitable for current LLMs and identify specific areas requiring enhancement. Furthermore, we propose targeted prompt engineering strategies for optimizing LLM performance in these contexts. Based on these findings, we provide recommendations for the development of more robust LLMs tailored for various biological applications. This work offers a comprehensive evaluation framework and robust tools to support the application of LLMs in bioinformatics.

Haojun Jiang, Jiawei Sun, Jie Li et al.

Graph representation learning (GRL) makes considerable progress recently, which encodes graphs with topological structures into low-dimensional embeddings. Meanwhile, the time-consuming and costly process of annotating graph labels manually prompts the growth of self-supervised learning (SSL) techniques. As a dominant approach of SSL, Contrastive learning (CL) learns discriminative representations by differentiating between positive and negative samples. However, when applied to graph data, it overemphasizes global patterns while neglecting local structures. To tackle the above issue, we propose \underline{Local}-aware \underline{G}raph \underline{C}ontrastive \underline{L}earning (\textbf{\methnametrim}), a self-supervised learning framework that supplementarily captures local graph information with masking-based modeling compared with vanilla contrastive learning. Extensive experiments validate the superiority of \methname against state-of-the-art methods, demonstrating its promise as a comprehensive graph representation learner.