This paper studies the problem of dynamical system modeling, which involves the evolution of multiple interacting objects. Recent data-driven methods often utilize graph neural networks (GNNs) to learn these interactions by optimizing the neural network in an end-to-end fashion. While large language models (LLMs) have shown exceptional zero-shot performance across various applications, their potential for modeling dynamical systems has not been extensively explored. In this work, we design prompting techniques for dynamical system modeling and systematically evaluate the capabilities of LLMs on two tasks, including dynamic forecasting and relational reasoning. An extensive benchmark LLM4DS across nine datasets is built for performance comparison. Our extensive experiments yield several key findings: (1) LLMs demonstrate competitive performance without training compared to state-of-the-art methods in dynamical system modeling. (2) LLMs effectively infer complex interactions among objects to capture system evolution. (3) Prompt engineering plays a crucial role in enabling LLMs to accurately understand and predict the evolution of systems.

Protein-specific large language models (ProteinLLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of ProteinLLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art ProteinLLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning ProteinLLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.