AI for Biomedicine in the Era of Large Language Models

Abstract: The capabilities of AI for biomedicine span a wide spectrum, from the atomic level, where it solves partial differential equations for quantum systems, to the molecular level, predicting chemical or protein structures, and further extending to societal predictions like infectious disease outbreaks. Recent advancements in LLMs, exemplified by models like ChatGPT, have showcased significant prowess in natural language tasks, such as translating languages, constructing chatbots, and answering questions. When we consider biomedical data, we observe a resemblance to natural language in terms of sequences: biomedical literature and health records presented as text, biological sequences or sequencing data arranged in sequences, or sensor data like brain signals as time series. The question arises: Can we harness the potential of recent LLMs to drive biomedical knowledge discoveries? In this survey, we will explore the application of LLMs to three crucial categories of biomedical data: 1) textual data, 2) biological sequences, and 3) brain signals. Furthermore, we will delve into LLM challenges in biomedical research, including ensuring trustworthiness, achieving personalization, and adapting to multi-modal data representation