LLMs-based Few-Shot Disease Predictions using EHR: A Novel Approach Combining Predictive Agent Reasoning and Critical Agent Instruction

Electronic health records (EHRs) contain valuable patient data for health-related prediction tasks, such as disease prediction. Traditional approaches rely on supervised learning methods that require large labeled datasets, which can be expensive and challenging to obtain. In this study, we investigate the feasibility of applying Large Language Models (LLMs) to convert structured patient visit data (e.g., diagnoses, labs, prescriptions) into natural language narratives. We evaluate the zero-shot and few-shot performance of LLMs using various EHR-prediction-oriented prompting strategies. Furthermore, we propose a novel approach that utilizes LLM agents with different roles: a predictor agent that makes predictions and generates reasoning processes and a critic agent that analyzes incorrect predictions and provides guidance for improving the reasoning of the predictor agent. Our results demonstrate that with the proposed approach, LLMs can achieve decent few-shot performance compared to traditional supervised learning methods in EHR-based disease predictions, suggesting its potential for health-oriented applications.

CASPER: Causality-Aware Spatiotemporal Graph Neural Networks for Spatiotemporal Time Series Imputation

Spatiotemporal time series is the foundation of understanding human activities and their impacts, which is usually collected via monitoring sensors placed at different locations. The collected data usually contains missing values due to various failures, which have significant impact on data analysis. To impute the missing values, a lot of methods have been introduced. When recovering a specific data point, most existing methods tend to take into consideration all the information relevant to that point regardless of whether they have a cause-and-effect relationship. During data collection, it is inevitable that some unknown confounders are included, e.g., background noise in time series and non-causal shortcut edges in the constructed sensor network. These confounders could open backdoor paths between the input and output, in other words, they establish non-causal correlations between the input and output. Over-exploiting these non-causal correlations could result in overfitting and make the model vulnerable to noises. In this paper, we first revisit spatiotemporal time series imputation from a causal perspective, which shows the causal relationships among the input, output, embeddings and confounders. Next, we show how to block the confounders via the frontdoor adjustment. Based on the results of the frontdoor adjustment, we introduce a novel Causality-Aware SPatiotEmpoRal graph neural network (CASPER), which contains a novel Spatiotemporal Causal Attention (SCA) and a Prompt Based Decoder (PBD). PBD could reduce the impact of confounders and SCA could discover the sparse causal relationships among embeddings. Theoretical analysis reveals that SCA discovers causal relationships based on the values of gradients. We evaluate Casper on three real-world datasets, and the experimental results show that Casper outperforms the baselines and effectively discovers causal relationships.

MuseGraph: Graph-oriented Instruction Tuning of Large Language Models for Generic Graph Mining

Graphs with abundant attributes are essential in modeling interconnected entities and improving predictions in various real-world applications. Traditional Graph Neural Networks (GNNs), which are commonly used for modeling attributed graphs, need to be re-trained every time when applied to different graph tasks and datasets. Although the emergence of Large Language Models (LLMs) has introduced a new paradigm in natural language processing, the generative potential of LLMs in graph mining remains largely under-explored. To this end, we propose a novel framework MuseGraph, which seamlessly integrates the strengths of GNNs and LLMs and facilitates a more effective and generic approach for graph mining across different tasks and datasets. Specifically, we first introduce a compact graph description via the proposed adaptive input generation to encapsulate key information from the graph under the constraints of language token limitations. Then, we propose a diverse instruction generation mechanism, which distills the reasoning capabilities from LLMs (e.g., GPT-4) to create task-specific Chain-of-Thought-based instruction packages for different graph tasks. Finally, we propose a graph-aware instruction tuning with a dynamic instruction package allocation strategy across tasks and datasets, ensuring the effectiveness and generalization of the training process. Our experimental results demonstrate significant improvements in different graph tasks, showcasing the potential of our MuseGraph in enhancing the accuracy of graph-oriented downstream tasks while keeping the generation powers of LLMs.

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records

We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at \url{https://github.com/ritaranx/RAM-EHR}.

Are Synthetic Time-series Data Really not as Good as Real Data?

Time-series data presents limitations stemming from data quality issues, bias and vulnerabilities, and generalization problem. Integrating universal data synthesis methods holds promise in improving generalization. However, current methods cannot guarantee that the generator's output covers all unseen real data. In this paper, we introduce InfoBoost -- a highly versatile cross-domain data synthesizing framework with time series representation learning capability. We have developed a method based on synthetic data that enables model training without the need for real data, surpassing the performance of models trained with real data. Additionally, we have trained a universal feature extractor based on our synthetic data that is applicable to all time-series data. Our approach overcomes interference from multiple sources rhythmic signal, noise interference, and long-period features that exceed sampling window capabilities. Through experiments, our non-deep-learning synthetic data enables models to achieve superior reconstruction performance and universal explicit representation extraction without the need for real data.

Evaluation of General Large Language Models in Contextually Assessing Semantic Concepts Extracted from Adult Critical Care Electronic Health Record Notes

The field of healthcare has increasingly turned its focus towards Large Language Models (LLMs) due to their remarkable performance. However, their performance in actual clinical applications has been underexplored. Traditional evaluations based on question-answering tasks don't fully capture the nuanced contexts. This gap highlights the need for more in-depth and practical assessments of LLMs in real-world healthcare settings. Objective: We sought to evaluate the performance of LLMs in the complex clinical context of adult critical care medicine using systematic and comprehensible analytic methods, including clinician annotation and adjudication. Methods: We investigated the performance of three general LLMs in understanding and processing real-world clinical notes. Concepts from 150 clinical notes were identified by MetaMap and then labeled by 9 clinicians. Each LLM's proficiency was evaluated by identifying the temporality and negation of these concepts using different prompts for an in-depth analysis. Results: GPT-4 showed overall superior performance compared to other LLMs. In contrast, both GPT-3.5 and text-davinci-003 exhibit enhanced performance when the appropriate prompting strategies are employed. The GPT family models have demonstrated considerable efficiency, evidenced by their cost-effectiveness and time-saving capabilities. Conclusion: A comprehensive qualitative performance evaluation framework for LLMs is developed and operationalized. This framework goes beyond singular performance aspects. With expert annotations, this methodology not only validates LLMs' capabilities in processing complex medical data but also establishes a benchmark for future LLM evaluations across specialized domains.

Contrastive Unlearning: A Contrastive Approach to Machine Unlearning

Machine unlearning aims to eliminate the influence of a subset of training samples (i.e., unlearning samples) from a trained model. Effectively and efficiently removing the unlearning samples without negatively impacting the overall model performance is still challenging. In this paper, we propose a contrastive unlearning framework, leveraging the concept of representation learning for more effective unlearning. It removes the influence of unlearning samples by contrasting their embeddings against the remaining samples so that they are pushed away from their original classes and pulled toward other classes. By directly optimizing the representation space, it effectively removes the influence of unlearning samples while maintaining the representations learned from the remaining samples. Experiments on a variety of datasets and models on both class unlearning and sample unlearning showed that contrastive unlearning achieves the best unlearning effects and efficiency with the lowest performance loss compared with the state-of-the-art algorithms.

Deep Efficient Private Neighbor Generation for Subgraph Federated Learning

Behemoth graphs are often fragmented and separately stored by multiple data owners as distributed subgraphs in many realistic applications. Without harming data privacy, it is natural to consider the subgraph federated learning (subgraph FL) scenario, where each local client holds a subgraph of the entire global graph, to obtain globally generalized graph mining models. To overcome the unique challenge of incomplete information propagation on local subgraphs due to missing cross-subgraph neighbors, previous works resort to the augmentation of local neighborhoods through the joint FL of missing neighbor generators and GNNs. Yet their technical designs have profound limitations regarding the utility, efficiency, and privacy goals of FL. In this work, we propose FedDEP to comprehensively tackle these challenges in subgraph FL. FedDEP consists of a series of novel technical designs: (1) Deep neighbor generation through leveraging the GNN embeddings of potential missing neighbors; (2) Efficient pseudo-FL for neighbor generation through embedding prototyping; and (3) Privacy protection through noise-less edge-local-differential-privacy. We analyze the correctness and efficiency of FedDEP, and provide theoretical guarantees on its privacy. Empirical results on four real-world datasets justify the clear benefits of proposed techniques.

EHRAgent: Code Empowers Large Language Models for Complex Tabular Reasoning on Electronic Health Records

Large language models (LLMs) have demonstrated exceptional capabilities in planning and tool utilization as autonomous agents, but few have been developed for medical problem-solving. We propose EHRAgent1, an LLM agent empowered with a code interface, to autonomously generate and execute code for complex clinical tasks within electronic health records (EHRs). First, we formulate an EHR question-answering task into a tool-use planning process, efficiently decomposing a complicated task into a sequence of manageable actions. By integrating interactive coding and execution feedback, EHRAgent learns from error messages and improves the originally generated code through iterations. Furthermore, we enhance the LLM agent by incorporating long-term memory, which allows EHRAgent to effectively select and build upon the most relevant successful cases from past experiences. Experiments on two real-world EHR datasets show that EHRAgent outperforms the strongest LLM agent baseline by 36.48% and 12.41%, respectively. EHRAgent leverages the emerging few-shot learning capabilities of LLMs, enabling autonomous code generation and execution to tackle complex clinical tasks with minimal demonstrations.