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.

Irregularly Sampled Medical Time Series (ISMTS) are commonly found in the healthcare domain, where different variables exhibit unique temporal patterns while interrelated. However, many existing methods fail to efficiently consider the differences and correlations among medical variables together, leading to inadequate capture of fine-grained features at the variable level in ISMTS. We propose Knowledge-Empowered Dynamic Graph Network (KEDGN), a graph neural network empowered by variables' textual medical knowledge, aiming to model variable-specific temporal dependencies and inter-variable dependencies in ISMTS. Specifically, we leverage a pre-trained language model to extract semantic representations for each variable from their textual descriptions of medical properties, forming an overall semantic view among variables from a medical perspective. Based on this, we allocate variable-specific parameter spaces to capture variable-specific temporal patterns and generate a complete variable graph to measure medical correlations among variables. Additionally, we employ a density-aware mechanism to dynamically adjust the variable graph at different timestamps, adapting to the time-varying correlations among variables in ISMTS. The variable-specific parameter spaces and dynamic graphs are injected into the graph convolutional recurrent network to capture intra-variable and inter-variable dependencies in ISMTS together. Experiment results on four healthcare datasets demonstrate that KEDGN significantly outperforms existing methods.

Electronic health record (EHR) data has emerged as a valuable resource for analyzing patient health status. However, the prevalence of missing data in EHR poses significant challenges to existing methods, leading to spurious correlations and suboptimal predictions. While various imputation techniques have been developed to address this issue, they often obsess difficult-to-interpolate details and may introduce additional noise when making clinical predictions. To tackle this problem, we propose SMART, a Self-Supervised Missing-Aware RepresenTation Learning approach for patient health status prediction, which encodes missing information via missing-aware temporal and variable attentions and learns to impute missing values through a novel self-supervised pre-training approach which reconstructs missing data representations in the latent space rather than in input space as usual. By adopting elaborated attentions and focusing on learning higher-order representations, SMART promotes better generalization and robustness to missing data.

Large language models (LLMs) have shown impressive capabilities in solving a wide range of tasks based on human instructions. However, developing a conversational AI assistant for electronic health record (EHR) data remains challenging due to (1) the lack of large-scale instruction-following datasets and (2) the limitations of existing model architectures in handling complex and heterogeneous EHR data. In this paper, we introduce MIMIC-Instr, a dataset comprising over 400K open-ended instruction-following examples derived from the MIMIC-IV EHR database. This dataset covers various topics and is suitable for instructiontuning general-purpose LLMs for diverse clinical use cases. Additionally, we propose Llemr, a general framework that enables LLMs to process and interpret EHRs with complex data structures. Llemr demonstrates competitive performance in answering a wide range of patient-related questions based on EHR data. Furthermore, our evaluations on clinical predictive modeling benchmarks reveal that the fine-tuned Llemr achieves performance comparable to state-of-the-art (SOTA) baselines using curated features. The dataset and code are available at https://github.com/zzachw/llemr.

Large language models (LLMs) have shown impressive capabilities in solving a wide range of tasks based on human instructions. However, developing a conversational AI assistant for electronic health record (EHR) data remains challenging due to (1) the lack of large-scale instruction-following datasets and (2) the limitations of existing model architectures in handling complex and heterogeneous EHR data. In this paper, we introduce MIMIC-Instr, a dataset comprising over 400K open-ended instruction-following examples derived from the MIMIC-IV EHR database. This dataset covers various topics and is suitable for instructiontuning general-purpose LLMs for diverse clinical use cases. Additionally, we propose Llemr, a general framework that enables LLMs to process and interpret EHRs with complex data structures. Llemr demonstrates competitive performance in answering a wide range of patient-related questions based on EHR data. Furthermore, our evaluations on clinical predictive modeling benchmarks reveal that the fine-tuned Llemr achieves performance comparable to state-of-the-art (SOTA) baselines using curated features. The dataset and code are available at https://github.com/zzachw/llemr.

With the development of machine learning techniques, the attention of research has been moved from single-modal learning to multi-modal learning, as real-world data exist in the form of different modalities. However, multi-modal models often carry more information than single-modal models and they are usually applied in sensitive scenarios, such as medical report generation or disease identification. Compared with the existing membership inference against machine learning classifiers, we focus on the problem that the input and output of the multi-modal models are in different modalities, such as image captioning. This work studies the privacy leakage of multi-modal models through the lens of membership inference attack, a process of determining whether a data record involves in the model training process or not.

A.1 Motivation For what purpose was the dataset created? We created EHRXQA to provide a valuable resource for advancing machine learning applications in multi-modal question answering systems on structured electronic health records (EHRs) and chest X-ray images. As an affiliated dataset, we created MIMIC-CXR-VQA to provide a benchmark for medical visual question answering systems. Who created the dataset (e.g., which team, research group) and on behalf of which entity (e.g., company, institution, organization)? Who funded the creation of the dataset? If there is an associated grant, please provide the name of the grantor and the grant name and number. A.2 Composition What do the instances that comprise the dataset represent (e.g., documents, photos, people, countries)? EHRXQA contains natural questions and corresponding SQL/NeuralSQL queries (text). MIMIC-CXR-VQA contains the image ID of the MIMIC-CXR dataset and their related natural questions. How many instances are there in total (of each type, if appropriate)? In MIMIC-CXR-VQA, there are about 377.4K instances. Does the dataset contain all possible instances or is it a sample (not necessarily random) of instances from a larger set? EHRXQA contains (Question, SQL/NeuralSQL, Answer) pair for each instance. MIMIC-CXR-VQA contains (Question, CXR image ID, Answer) pair for each instance. Is there a label or target associated with each instance? The answer (label) is provided for each question. Is any information missing from individual instances? If so, please provide a description, explaining why this information is missing (e.g., because it was unavailable). This does not include intentionally removed information, but might include, e.g., redacted text. No. Are relationships between individual instances made explicit (e.g., users' movie ratings, social network links)? No. Are there recommended data splits (e.g., training, development/validation, testing)? See Appendix B.2.2, and Appendix C.3.3. Questions are created by filling the slots in the templates with pre-defined values and records from the database. Thus, some questions can be grammatically incorrect but not critical (e.g., verb tense).

Electronic Health Records (EHRs), which contain patients' medical histories in various multi-modal formats, often overlook the potential for joint reasoning across imaging and table modalities underexplored in current EHR Question Answering (QA) systems. In this paper, we introduce EHRXQA, a novel multi-modal question answering dataset combining structured EHRs and chest X-ray images. To develop our dataset, we first construct two uni-modal resources: 1) The MIMIC-CXR-VQA dataset, our newly created medical visual question answering (VQA) benchmark, specifically designed to augment the imaging modality in EHR QA, and 2) EHRSQL (MIMIC-IV), a refashioned version of a previously established table-based EHR QA dataset. By integrating these two uni-modal resources, we successfully construct a multi-modal EHR QA dataset that necessitates both uni-modal and cross-modal reasoning. To address the unique challenges of multimodal questions within EHRs, we propose a NeuralSQL-based strategy equipped with an external VQA API. This pioneering endeavor enhances engagement with multi-modal EHR sources and we believe that our dataset can catalyze advances in real-world medical scenarios such as clinical decision-making and research.

Explanations of time series models are useful for high stakes applications like healthcare but have received little attention in machine learning literature. We propose FIT, a framework that evaluates the importance of observations for a multivariate time-series black-box model by quantifying the shift in the predictive distribution over time. FIT defines the importance of an observation based on its contribution to the distributional shift under a KL-divergence that contrasts the predictive distribution against a counterfactual where the rest of the features are unobserved. We also demonstrate the need to control for time-dependent distribution shifts. We compare with state-of-the-art baselines on simulated and real-world clinical data and demonstrate that our approach is superior in identifying important time points and observations throughout the time series.