Tasks such as chronic disease Large language models (LLMs) have emerged management, multi-visit care planning, and patient history as promising tools for assisting in medical tasks, synthesis require clinicians to understand complex relationships yet processing Electronic Health Records (EHRs) between different record entries and how past events presents unique challenges due to their longitudinal influence current and future clinical decisions (Wornow nature. While LLMs' capabilities to perform et al., 2024). The cognitive demands of processing such medical tasks continue to improve, their ability lengthy documentation are significant. While biomedical to reason over temporal dependencies across LLMs have shown promising results on well-structured multiple patient visits and time frames remains tasks like answering USMLE questions and medical knowledge unexplored. We introduce TIMER (Temporal retrieval (Singhal et al., 2023; Lu et al., 2024; Lucas Instruction Modeling and Evaluation for Longitudinal et al., 2024), recent evaluations reveal their significant limitations Clinical Records), a framework that incorporate in processing longitudinal patient information and in instruction-response pairs grounding to making clinical decisions over time (Hager et al., 2024; Bedi different parts of a patient's record as a critical et al., 2024). The gap between isolated question-answering dimension in both instruction evaluation and tuning performance and temporal reasoning ability impacts the for longitudinal clinical records. We develop practical utility of LLMs in healthcare. While there is some TIMER-Bench, the first time-aware benchmark prior work that has explored temporal understanding abilities that evaluates temporal reasoning capabilities over of general LLMs (Wang & Zhao, 2024; Fatemi et al., longitudinal EHRs, as well as TIMER-Instruct, 2024; Herel et al., 2024), how these capabilities scale to an instruction-tuning methodology for LLMs to longer contexts remains understudied, particularly in healthcare learn reasoning over time. We demonstrate that where longitudinal reasoning is important.

Prescription contraceptives play a critical role in supporting women's reproductive health. With nearly 50 million women in the United States using contraceptives, understanding the factors that drive contraceptives selection and switching is of significant interest. However, many factors related to medication switching are often only captured in unstructured clinical notes and can be difficult to extract. Here, we evaluate the zero-shot abilities of a recently developed large language model, GPT-4 (via HIPAA-compliant Microsoft Azure API), to identify reasons for switching between classes of contraceptives from the UCSF Information Commons clinical notes dataset. We demonstrate that GPT-4 can accurately extract reasons for contraceptive switching, outperforming baseline BERT-based models with microF1 scores of 0.849 and 0.881 for contraceptive start and stop extraction, respectively. Human evaluation of GPT-4-extracted reasons for switching showed 91.4% accuracy, with minimal hallucinations. Using extracted reasons, we identified patient preference, adverse events, and insurance as key reasons for switching using unsupervised topic modeling approaches. Notably, we also showed using our approach that "weight gain/mood change" and "insurance coverage" are disproportionately found as reasons for contraceptive switching in specific demographic populations. Our code and supplemental data are available at https://github.com/BMiao10/contraceptive-switching.

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges: subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SubGNN, a subgraph neural network to learn disentangled subgraph representations. We propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SubGNN specifies three channels, each designed to capture a distinct aspect of subgraph topology, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SubGNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 19.8% over the strongest baseline. SubGNN performs exceptionally well on challenging biomedical datasets where subgraphs have complex topology and even comprise multiple disconnected components.

Intimate partner violence (IPV) is an urgent, prevalent, and under-detected public health issue. We present machine learning models to assess patients for IPV and injury. We train the predictive algorithms on radiology reports with 1) IPV labels based on entry to a violence prevention program and 2) injury labels provided by emergency radiology fellowship-trained physicians. Our dataset includes 34,642 radiology reports and 1479 patients of IPV victims and control patients. Our best model predicts IPV a median of 3.08 years before violence prevention program entry with a sensitivity of 64% and a specificity of 95%. We conduct error analysis to determine for which patients our model has especially high or low performance and discuss next steps for a deployed clinical risk model.

Patient summarization is essential for clinicians to provide coordinated care and practice effective communication. Automated summarization has the potential to save time, standardize notes, aid clinical decision making, and reduce medical errors. Here we provide an upper bound on extractive summarization of discharge notes and develop an LSTM model to sequentially label topics of history of present illness notes. We achieve an F1 score of 0.876, which indicates that this model can be employed to create a dataset for evaluation of extractive summarization methods.