Discharge summaries in Electronic Health Records (EHRs) are crucial for clinical decision-making, but their length and complexity make information extraction challenging, especially when dealing with accumulated summaries across multiple patient admissions.

Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Longitudinal data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differences in the way these diseases progress over time. In this paper, we focus on answering two questions that can be asked using these databases of longitudinal EHR data. First, we want to understand whether there are individuals with similar disease trajectories and whether there are a small number of degrees of freedom that account for differences in trajectories across the population. Second, we want to understand how important clinical outcomes are associated with disease trajectories. To answer these questions, we propose the Disease Trajectory Map (DTM), a novel probabilistic model that learns low-dimensional representations of sparse and irregularly sampled longitudinal data. We propose a stochastic variational inference algorithm for learning the DTM that allows the model to scale to large modern medical datasets. To demonstrate the DTM, we analyze data collected on patients with the complex autoimmune disease, scleroderma. We find that DTM learns meaningful representations of disease trajectories and that the representations are significantly associated with important clinical outcomes.

In recent years, there has been a proliferation of ready-to-use large language models (LLMs) designed for various applications, both general-purpose and domainspecific. Instead of advocating for the development of a new model or continuous pretraining of an existing one, this paper introduces a pragmatic teacher-teacher framework to facilitate mutual learning between two pre-existing models. By leveraging two teacher models possessing complementary knowledge, we introduce a LIghtweight kNowledge alignmEnt (LINE) module aimed at harmonizing their knowledge within a unified representation space. This framework is particularly valuable in clinical settings, where stringent regulations and privacy considerations dictate the handling of detailed clinical notes. Our trained LINE module excels in capturing critical information from clinical notes, leveraging highly de-identified data. Validation and downstream tasks further demonstrate the effectiveness of the proposed framework.

Estimating patient's clinical state from multiple concurrent physiological streams plays an important role in determining if a therapeutic intervention is necessary and for triaging patients in the hospital. In this paper we construct a non-parametric learning algorithm to estimate the clinical state of a patient. The algorithm addresses several known challenges with clinical state estimation such as eliminating the bias introduced by therapeutic intervention censoring, increasing the timeliness of state estimation while ensuring a sufficient accuracy, and the ability to detect anomalous clinical states. These benefits are obtained by combining the tools of non-parametric Bayesian inference, permutation testing, and generalizations of the empirical Bernstein inequality. The algorithm is validated using real-world data from a cancer ward in a large academic hospital.

A.1 Motivation For what purpose was the dataset created? EHRs are integral for storing comprehensive patient medical records, combining structured data with detailed clinical notes. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon. Who created the dataset (e.g., which team, research group) and on behalf of which entity (e.g., company, institution, organization)?

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 4,101 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings.

Electronic health records (EHRs) are stored in various database systems with different database models on heterogeneous storage architectures, such as relational databases, document stores, or graph databases. These different database models have a big impact on query complexity and performance. While this has been a known fact in database research, its implications for the growing number of Text-to-Query systems have surprisingly not been investigated so far. In this paper, we present SM3-Text-to-Query, the first multi-model medical Text-to-Query benchmark based on synthetic patient data from Synthea, following the SNOMED-CT taxonomy--a widely used knowledge graph ontology covering medical terminology. SM3-Text-to-Query provides data representations for relational databases (PostgreSQL), document stores (MongoDB), and graph databases (Neo4j and GraphDB (RDF)), allowing the evaluation across four popular query languages, namely SQL, MQL, Cypher, and SPARQL. We systematically and manually develop 408 template questions, which we augment to construct a benchmark of 10K diverse natural language question/query pairs for these four query languages (40K pairs overall). On our dataset, we evaluate several common in-context-learning (ICL) approaches for a set of representative closed and open-source LLMs.

Large language models (LLMs) have demonstrated remarkable capabilities in language understanding and generation, leading to their widespread adoption across various fields. Among these, the medical field is particularly well-suited for LLM applications, as many medical tasks can be enhanced by LLMs. Despite the existence of benchmarks for evaluating LLMs in medical question-answering and exams, there remains a notable gap in assessing LLMs' performance in supporting patients throughout their entire hospital visit journey in real-world clinical practice. In this paper, we address this gap by dividing a typical patient's clinical journey into four stages: planning, access, delivery and ongoing care. For each stage, we introduce multiple tasks and corresponding datasets, resulting in a comprehensive benchmark comprising 12 datasets, of which five are newly introduced, and seven are constructed from existing datasets. This proposed benchmark facilitates a thorough evaluation of LLMs' effectiveness across the entire patient journey, providing insights into their practical application in clinical settings. Additionally, we evaluate three categories of LLMs against this benchmark: 1) proprietary LLM services such as GPT-4; 2) public LLMs like QWen; and 3) specialized medical LLMs, like HuatuoGPT2. Through this extensive evaluation, we aim to provide a better understanding of LLMs' performance in the medical domain, ultimately contributing to their more effective deployment in healthcare settings.

Foundation models are becoming valuable tools in medicine. Yet despite their promise, the best way to leverage Large Language Models (LLMs) in complex medical tasks remains an open question. We introduce a novel multi-agent framework, named Medical Decision-making Agents (MDAgents) that helps to address this gap by automatically assigning a collaboration structure to a team of LLMs. The assigned solo or group collaboration structure is tailored to the medical task at hand, a simple emulation inspired by the way real-world medical decision-making processes are adapted to tasks of different complexities. We evaluate our framework and baseline methods using state-of-the-art LLMs across a suite of real-world medical knowledge and medical diagnosis benchmarks, including a comparison of LLMs' medical complexity classification against human physicians

The California Department of Corrections and Rehabilitation is reviewing hundreds of state parole hearings to see if any inmates who were denied parole were rejected because of faulty drug tests. Nearly 6,000 drug tests in California prisons are believed to have yielded false positives between April and July last year, and attorneys for the Board of Parole are now conducting a review of inmate files to determine if any of them need to appear before the parole board again to be reconsidered, according to officials with CDCR. If any inmates were denied parole because of the faulty tests, they could be owed a new hearing before the parole board, said attorneys representing inmates affected by the defective drug tests. The review is already underway and will determine if "without the positive drug screening, there is sufficient evidence to support an incarcerated person's denial of parole," said CDCR spokesperson Emily Humpal in a statement. If there isn't enough evidence to support incarceration other than the drug test, a new hearing will be scheduled.