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

UCPhrase: Unsupervised Context-aware Quality Phrase Tagging

Identifying and understanding quality phrases from context is a fundamental task in text mining. The most challenging part of this task arguably lies in uncommon, emerging, and domain-specific phrases. The infrequent nature of these phrases significantly hurts the performance of phrase mining methods that rely on sufficient phrase occurrences in the input corpus. Context-aware tagging models, though not restricted by frequency, heavily rely on domain experts for either massive sentence-level gold labels or handcrafted gazetteers. In this work, we propose UCPhrase, a novel unsupervised context-aware quality phrase tagger. Specifically, we induce high-quality phrase spans as silver labels from consistently co-occurring word sequences within each document. Compared with typical context-agnostic distant supervision based on existing knowledge bases (KBs), our silver labels root deeply in the input domain and context, thus having unique advantages in preserving contextual completeness and capturing emerging, out-of-KB phrases. Training a conventional neural tagger based on silver labels usually faces the risk of overfitting phrase surface names. Alternatively, we observe that the contextualized attention maps generated from a transformer-based neural language model effectively reveal the connections between words in a surface-agnostic way. Therefore, we pair such attention maps with the silver labels to train a lightweight span prediction model, which can be applied to new input to recognize (unseen) quality phrases regardless of their surface names or frequency. Thorough experiments on various tasks and datasets, including corpus-level phrase ranking, document-level keyphrase extraction, and sentence-level phrase tagging, demonstrate the superiority of our design over state-of-the-art pre-trained, unsupervised, and distantly supervised methods.