AI for Biomedicine in the Era of Large Language Models

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 large language models, 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 large language models to drive biomedical knowledge discoveries? In this survey, we will explore the application of large language models to three crucial categories of biomedical data: 1) textual data, 2) biological sequences, and 3) brain signals. Furthermore, we will delve into large language model challenges in biomedical research, including ensuring trustworthiness, achieving personalization, and adapting to multi-modal data representation

XAI-CLASS: Explanation-Enhanced Text Classification with Extremely Weak Supervision

Text classification aims to effectively categorize documents into pre-defined categories. Traditional methods for text classification often rely on large amounts of manually annotated training data, making the process time-consuming and labor-intensive. To address this issue, recent studies have focused on weakly-supervised and extremely weakly-supervised settings, which require minimal or no human annotation, respectively. In previous methods of weakly supervised text classification, pseudo-training data is generated by assigning pseudo-labels to documents based on their alignment (e.g., keyword matching) with specific classes. However, these methods ignore the importance of incorporating the explanations of the generated pseudo-labels, or saliency of individual words, as additional guidance during the text classification training process. To address this limitation, we propose XAI-CLASS, a novel explanation-enhanced extremely weakly-supervised text classification method that incorporates word saliency prediction as an auxiliary task. XAI-CLASS begins by employing a multi-round question-answering process to generate pseudo-training data that promotes the mutual enhancement of class labels and corresponding explanation word generation. This pseudo-training data is then used to train a multi-task framework that simultaneously learns both text classification and word saliency prediction. Extensive experiments on several weakly-supervised text classification datasets show that XAI-CLASS outperforms other weakly-supervised text classification methods significantly. Moreover, experiments demonstrate that XAI-CLASS enhances both model performance and explainability.