Abstract
Clinical risk prediction based on machine learning algorithms plays a vital role in modern healthcare. A crucial component in developing a reliable prediction model is collecting high-quality time series clinical events. In this work, we release such a dataset that consists of 22,588,586 Clinical Time Series events, which we term MIMIC-IV-Ext-22MCTS. Our source data are discharge summaries selected from the well-known yet unstructured MIMIC-IV-Note [1]. We then extract clinical events as short text span from the discharge summaries, along with the timestamps of these events as temporal information. The general-purpose MIMIC-IV-Note pose specific challenges for our work: it turns out that the discharge summaries are too lengthy for typical natural language models to process, and the clinical events of interest often are not accompanied with explicit timestamps. Therefore, we propose a new framework that works as follows: 1) we break each discharge summary into manageably small text chunks; 2) we apply contextual BM25 and contextual semantic search to retrieve chunks that have a high potential of containing clinical events; and 3) we carefully design prompts to teach the recently released Llama-3.1-8B [4] model to identify or infer temporal information of the chunks. We show that the obtained dataset is so informative and transparent that standard models fine-tuned on our dataset are achieving significant improvements in healthcare applications. In particular, the BERT model fine-tuned based on our dataset achieves 10% improvement in accuracy on medical question answering task, and 3% improvement in clinical trial matching task compared with the classic BERT. The GPT-2 model, fine-tuned on our dataset, produces more clinically reliable results for clinical questions.