The temporal complexity of electronic health record (EHR) data presents significant challenges for predicting clinical outcomes using machine learning. This paper proposes ChronoFormer, an innovative transformer based architecture specifically designed to encode and leverage temporal dependencies in longitudinal patient data. ChronoFormer integrates temporal embeddings, hierarchical attention mechanisms, and domain specific masking techniques. Extensive experiments conducted on three benchmark tasks mortality prediction, readmission prediction, and long term comorbidity onset demonstrate substantial improvements over current state of the art methods. Furthermore, detailed analyses of attention patterns underscore ChronoFormer's capability to capture clinically meaningful long range temporal relationships.
Hospital readmission prediction is critical for clinical decision support, aiming to identify patients at risk of returning within 30 days post-discharge. High readmission rates often indicate inadequate treatment or post-discharge care, making effective prediction models essential for optimizing resources and improving patient outcomes. We propose PT, a Transformer-based model that integrates Electronic Health Records (EHR), medical images, and clinical notes to predict 30-day all-cause hospital readmissions. PT extracts features from raw data and uses specialized Transformer blocks tailored to the data's complexity. Enhanced with Random Forest for EHR feature selection and test-time ensemble techniques, PT achieves superior accuracy, scalability, and robustness. It performs well even when temporal information is missing. Our main contributions are: (1)Simplicity: A powerful and efficient baseline model outperforming existing ones in prediction accuracy; (2)Scalability: Flexible handling of various features from different modalities, achieving high performance with just clinical notes or EHR data; (3)Robustness: Strong predictive performance even with missing or unclear temporal data.
Readmissions among Medicare beneficiaries are a major problem for the US healthcare system from a perspective of both healthcare operations and patient caregiving outcomes. Our study analyzes Medicare hospital readmissions using LSTM networks with feature engineering to assess feature contributions. We selected variables from admission-level data, inpatient medical history and patient demography. The LSTM model is designed to capture temporal dynamics from admission-level and patient-level data. On a case study on the MIMIC dataset, the LSTM model outperformed the logistic regression baseline, accurately leveraging temporal features to predict readmission. The major features were the Charlson Comorbidity Index, hospital length of stay, the hospital admissions over the past 6 months, while demographic variables were less impactful. This work suggests that LSTM networks offers a more promising approach to improve Medicare patient readmission prediction. It captures temporal interactions in patient databases, enhancing current prediction models for healthcare providers. Adoption of predictive models into clinical practice may be more effective in identifying Medicare patients to provide early and targeted interventions to improve patient outcomes.
Developing novel predictive models with complex biomedical information is challenging due to various idiosyncrasies related to heterogeneity, standardization or sparseness of the data. We previously introduced a person-centric ontology to organize information about individual patients, and a representation learning framework to extract person-centric knowledge graphs (PKGs) and to train Graph Neural Networks (GNNs). In this paper, we propose a systematic approach to examine the results of GNN models trained with both structured and unstructured information from the MIMIC-III dataset. Through ablation studies on different clinical, demographic, and social data, we show the robustness of this approach in identifying predictive features in PKGs for the task of readmission prediction.
Integrating modern machine learning and clinical decision-making has great promise for mitigating healthcare's increasing cost and complexity. We introduce the Enhanced Transformer for Health Outcome Simulation (ETHOS), a novel application of the transformer deep-learning architecture for analyzing high-dimensional, heterogeneous, and episodic health data. ETHOS is trained using Patient Health Timelines (PHTs)-detailed, tokenized records of health events-to predict future health trajectories, leveraging a zero-shot learning approach. ETHOS represents a significant advancement in foundation model development for healthcare analytics, eliminating the need for labeled data and model fine-tuning. Its ability to simulate various treatment pathways and consider patient-specific factors positions ETHOS as a tool for care optimization and addressing biases in healthcare delivery. Future developments will expand ETHOS' capabilities to incorporate a wider range of data types and data sources. Our work demonstrates a pathway toward accelerated AI development and deployment in healthcare.
Large Language Models (LLMs) are increasingly deployed in medicine. However, their utility in non-generative clinical prediction, often presumed inferior to specialized models, remains under-evaluated, leading to ongoing debate within the field and potential for misuse, misunderstanding, or over-reliance due to a lack of systematic benchmarking. Our ClinicRealm study addresses this by benchmarking 9 GPT-based LLMs, 5 BERT-based models, and 7 traditional methods on unstructured clinical notes and structured Electronic Health Records (EHR). Key findings reveal a significant shift: for clinical note predictions, leading LLMs (e.g., DeepSeek R1/V3, GPT o3-mini-high) in zero-shot settings now decisively outperform finetuned BERT models. On structured EHRs, while specialized models excel with ample data, advanced LLMs (e.g., GPT-4o, DeepSeek R1/V3) show potent zero-shot capabilities, often surpassing conventional models in data-scarce settings. Notably, leading open-source LLMs can match or exceed proprietary counterparts. These results establish modern LLMs as powerful non-generative clinical prediction tools, particularly with unstructured text and offering data-efficient structured data options, thus necessitating a re-evaluation of model selection strategies. This research should serve as an important insight for medical informaticists, AI developers, and clinical researchers, potentially prompting a reassessment of current assumptions and inspiring new approaches to LLM application in predictive healthcare.
Background: Accurate short-term readmission prediction of ICU patients is significant in improving the efficiency of resource assignment by assisting physicians in making discharge decisions. Clinically, both individual static static and multivariate temporal data collected from ICU monitors play critical roles in short-term readmission prediction. Informative static and multivariate temporal feature representation capturing and fusion present challenges for accurate readmission prediction. Methods:We propose a novel static and multivariate-temporal attentive fusion transformer (SMTAFormer) to predict short-term readmission of ICU patients by fully leveraging the potential of demographic and dynamic temporal data. In SMTAFormer, we first apply an MLP network and a temporal transformer network to learn useful static and temporal feature representations, respectively. Then, the well-designed static and multivariate temporal feature fusion module is applied to fuse static and temporal feature representations by modeling intra-correlation among multivariate temporal features and constructing inter-correlation between static and multivariate temporal features. Results: We construct a readmission risk assessment (RRA) dataset based on the MIMIC-III dataset. The extensive experiments show that SMTAFormer outperforms advanced methods, in which the accuracy of our proposed method is up to 86.6%, and the area under the receiver operating characteristic curve (AUC) is up to 0.717. Conclusion: Our proposed SMTAFormer can efficiently capture and fuse static and multivariate temporal feature representations. The results show that SMTAFormer significantly improves the short-term readmission prediction performance of ICU patients through comparisons to strong baselines.
Social determinants of health (SDOH) $-$ the myriad of circumstances in which people live, grow, and age $-$ play an important role in health outcomes. However, existing outcome prediction models often only use proxies of SDOH as features. Recent open data initiatives present an opportunity to construct a more comprehensive view of SDOH, but manually integrating the most relevant data for individual patients becomes increasingly challenging as the volume and diversity of public SDOH data grows. Large language models (LLMs) have shown promise at automatically annotating structured data. Here, we conduct an end-to-end case study evaluating the feasibility of using LLMs to integrate SDOH data, and the utility of these SDOH features for clinical prediction. We first manually label 700+ variables from two publicly-accessible SDOH data sources to one of five semantic SDOH categories. Then, we benchmark performance of 9 open-source LLMs on this classification task. Finally, we train ML models to predict 30-day hospital readmission among 39k heart failure (HF) patients, and we compare the prediction performance of the categorized SDOH variables with standard clinical variables. Additionally, we investigate the impact of few-shot LLM prompting on LLM annotation performance, and perform a metadata ablation study on prompts to evaluate which information helps LLMs accurately annotate these variables. We find that some open-source LLMs can effectively, accurately annotate SDOH variables with zero-shot prompting without the need for fine-tuning. Crucially, when combined with standard clinical features, the LLM-annotated Neighborhood and Built Environment subset of the SDOH variables shows the best performance predicting 30-day readmission of HF patients.
Hospital readmission, defined as patients being re-hospitalized shortly after discharge, is a critical concern as it impacts patient outcomes and healthcare costs. Identifying patients at risk of readmission allows for timely interventions, reducing re-hospitalization rates and overall treatment costs. This study focuses on predicting patient readmission within less than 30 days using text mining techniques applied to discharge report texts from electronic health records (EHR). Various machine learning and deep learning methods were employed to develop a classification model for this purpose. A novel aspect of this research involves leveraging the Bio-Discharge Summary Bert (BDSS) model along with principal component analysis (PCA) feature extraction to preprocess data for deep learning model input. Our analysis of the MIMIC-III dataset indicates that our approach, which combines the BDSS model with a multilayer perceptron (MLP), outperforms state-of-the-art methods. This model achieved a recall of 94% and an area under the curve (AUC) of 75%, showcasing its effectiveness in predicting patient readmissions. This study contributes to the advancement of predictive modeling in healthcare by integrating text mining techniques with deep learning algorithms to improve patient outcomes and optimize resource allocation.
Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.
Hospital readmission prediction is considered an essential approach to decreasing readmission rates, which is a key factor in assessing the quality and efficacy of a healthcare system. Previous studies have extensively utilized three primary modalities, namely electronic health records (EHR), medical images, and clinical notes, to predict hospital readmissions. However, the majority of these studies did not integrate information from all three modalities or utilize the spatiotemporal relationships present in the dataset. This study introduces a novel model called the Multimodal Spatiotemporal Graph-Transformer (MuST) for predicting hospital readmissions. By employing Graph Convolution Networks and temporal transformers, we can effectively capture spatial and temporal dependencies in EHR and chest radiographs. We then propose a fusion transformer to combine the spatiotemporal features from the two modalities mentioned above with the features from clinical notes extracted by a pre-trained, domain-specific transformer. We assess the effectiveness of our methods using the latest publicly available dataset, MIMIC-IV. The experimental results indicate that the inclusion of multimodal features in MuST improves its performance in comparison to unimodal methods. Furthermore, our proposed pipeline outperforms the current leading methods in the prediction of hospital readmissions.
With the increasing availability of patients' data, modern medicine is shifting towards prospective healthcare. Electronic health records contain a variety of information useful for clinical patient description and can be exploited for the construction of predictive models, given that similar medical histories will likely lead to similar progressions. One example is unplanned hospital readmission prediction, an essential task for reducing hospital costs and improving patient health. Despite predictive models showing very good performances especially with deep-learning models, they are often criticized for the poor interpretability of their results, a fundamental characteristic in the medical field, where incorrect predictions might have serious consequences for the patient health. In this paper we propose a novel, interpretable deep-learning framework for predicting unplanned hospital readmissions, supported by NLP findings on word embeddings and by neural-network models (ConvLSTM) for better handling temporal data. We validate our system on the two predictive tasks of hospital readmission within 30 and 180 days, using real-world data. In addition, we introduce and test a model-dependent technique to make the representation of results easily interpretable by the medical staff. Our solution achieves better performances compared to traditional models based on machine learning, while providing at the same time more interpretable results.
The intensive care unit (ICU) comprises a complex hospital environment, where decisions made by clinicians have a high level of risk for the patients' lives. A comprehensive care pathway must then be followed to reduce p complications. Uncertain, competing and unplanned aspects within this environment increase the difficulty in uniformly implementing the care pathway. Readmission contributes to this pathway's difficulty, occurring when patients are admitted again to the ICU in a short timeframe, resulting in high mortality rates and high resource utilisation. Several works have tried to predict readmission through patients' medical information. Although they have some level of success while predicting readmission, those works do not properly assess, characterise and understand readmission prediction. This work proposes a standardised and explainable machine learning pipeline to model patient readmission on a multicentric database (i.e., the eICU cohort with 166,355 patients, 200,859 admissions and 6,021 readmissions) while validating it on monocentric (i.e., the MIMIC IV cohort with 382,278 patients, 523,740 admissions and 5,984 readmissions) and multicentric settings. Our machine learning pipeline achieved predictive performance in terms of the area of the receiver operating characteristic curve (AUC) up to 0.7 with a Random Forest classification model, yielding an overall good calibration and consistency on validation sets. From explanations provided by the constructed models, we could also derive a set of insightful conclusions, primarily on variables related to vital signs and blood tests (e.g., albumin, blood urea nitrogen and hemoglobin levels), demographics (e.g., age, and admission height and weight), and ICU-associated variables (e.g., unit type). These insights provide an invaluable source of information during clinicians' decision-making while discharging ICU patients.
We present Clinical Prediction with Large Language Models (CPLLM), a method that involves fine-tuning a pre-trained Large Language Model (LLM) for clinical disease and readmission prediction. We utilized quantization and fine-tuned the LLM using prompts. For diagnosis prediction, we predict whether patients will be diagnosed with a target disease during their next visit or in the subsequent diagnosis, leveraging their historical diagnosis records. We compared our results to various baselines, including RETAIN, and Med-BERT, the current state-of-the-art model for disease prediction using temporal structured EHR data. In addition, We also evaluated CPLLM for patient hospital readmission prediction and compared our method's performance with benchmark baselines. Our experiments have shown that our proposed method, CPLLM, surpasses all the tested models in terms of PR-AUC and ROC-AUC metrics, showing state-of-the-art results for diagnosis prediction and patient hospital readmission prediction. Such a method can be easily implemented and integrated into the clinical process to help care providers estimate the next steps of patients
A hospital readmission is when a patient who was discharged from the hospital is admitted again for the same or related care within a certain period. Hospital readmissions are a significant problem in the healthcare domain, as they lead to increased hospitalization costs, decreased patient satisfaction, and increased risk of adverse outcomes such as infections, medication errors, and even death. The problem of hospital readmissions is particularly acute in intensive care units (ICUs), due to the severity of the patients' conditions, and the substantial risk of complications. Predicting Unplanned Readmissions in ICUs is a challenging task, as it involves analyzing different data modalities, such as static data, unstructured free text, sequences of diagnoses and procedures, and multivariate time-series. Here, we investigate the effectiveness of each data modality separately, then alongside with others, using state-of-the-art machine learning approaches in time-series analysis and natural language processing. Using our evaluation process, we are able to determine the contribution of each data modality, and for the first time in the context of readmission, establish a hierarchy of their predictive value. Additionally, we demonstrate the impact of Temporal Abstractions in enhancing the performance of time-series approaches to readmission prediction. Due to conflicting definitions in the literature, we also provide a clear definition of the term Unplanned Readmission to enhance reproducibility and consistency of future research and to prevent any potential misunderstandings that could result from diverse interpretations of the term. Our experimental results on a large benchmark clinical data set show that Discharge Notes written by physicians, have better capabilities for readmission prediction than all other modalities.
Knowledge graphs (KGs) are a popular way to organise information based on ontologies or schemas and have been used across a variety of scenarios from search to recommendation. Despite advances in KGs, representing knowledge remains a non-trivial task across industries and it is especially challenging in the biomedical and healthcare domains due to complex interdependent relations between entities, heterogeneity, lack of standardization, and sparseness of data. KGs are used to discover diagnoses or prioritize genes relevant to disease, but they often rely on schemas that are not centred around a node or entity of interest, such as a person. Entity-centric KGs are relatively unexplored but hold promise in representing important facets connected to a central node and unlocking downstream tasks beyond graph traversal and reasoning, such as generating graph embeddings and training graph neural networks for a wide range of predictive tasks. This paper presents an end-to-end representation learning framework to extract entity-centric KGs from structured and unstructured data. We introduce a star-shaped ontology to represent the multiple facets of a person and use it to guide KG creation. Compact representations of the graphs are created leveraging graph neural networks and experiments are conducted using different levels of heterogeneity or explicitness. A readmission prediction task is used to evaluate the results of the proposed framework, showing a stable system, robust to missing data, that outperforms a range of baseline machine learning classifiers. We highlight that this approach has several potential applications across domains and is open-sourced. Lastly, we discuss lessons learned, challenges, and next steps for the adoption of the framework in practice.
Traditional evaluation metrics for classification in natural language processing such as accuracy and area under the curve fail to differentiate between models with different predictive behaviors despite their similar performance metrics. We introduce sensitivity score, a metric that scrutinizes models' behaviors at the vocabulary level to provide insights into disparities in their decision-making logic. We assess the sensitivity score on a set of representative words in the test set using two classifiers trained for hospital readmission classification with similar performance statistics. Our experiments compare the decision-making logic of clinicians and classifiers based on rank correlations of sensitivity scores. The results indicate that the language model's sensitivity score aligns better with the professionals than the xgboost classifier on tf-idf embeddings, which suggests that xgboost uses some spurious features. Overall, this metric offers a novel perspective on assessing models' robustness by quantifying their discrepancy with professional opinions. Our code is available on GitHub (https://github.com/nyuolab/Model_Sensitivity).
Transformers are powerful text representation learners, useful for all kinds of clinical decision support tasks. Although they outperform baselines on readmission prediction, they are not infallible. Here, we look into one such failure case, and report patterns that lead to inferior predictive performance.
Artificial intelligence, and particularly machine learning (ML), is increasingly developed and deployed to support healthcare in a variety of settings. However, clinical decision support (CDS) technologies based on ML need to be portable if they are to be adopted on a broad scale. In this respect, models developed at one institution should be reusable at another. Yet there are numerous examples of portability failure, particularly due to naive application of ML models. Portability failure can lead to suboptimal care and medical errors, which ultimately could prevent the adoption of ML-based CDS in practice. One specific healthcare challenge that could benefit from enhanced portability is the prediction of 30-day readmission risk. Research to date has shown that deep learning models can be effective at modeling such risk. In this work, we investigate the practicality of model portability through a cross-site evaluation of readmission prediction models. To do so, we apply a recurrent neural network, augmented with self-attention and blended with expert features, to build readmission prediction models for two independent large scale claims datasets. We further present a novel transfer learning technique that adapts the well-known method of born-again network (BAN) training. Our experiments show that direct application of ML models trained at one institution and tested at another institution perform worse than models trained and tested at the same institution. We further show that the transfer learning approach based on the BAN produces models that are better than those trained on just a single institution's data. Notably, this improvement is consistent across both sites and occurs after a single retraining, which illustrates the potential for a cheap and general model transfer mechanism of readmission risk prediction.
Measures to predict 30-day readmission are considered an important quality factor for hospitals as accurate predictions can reduce the overall cost of care by identifying high risk patients before they are discharged. While recent deep learning-based studies have shown promising empirical results on readmission prediction, several limitations exist that may hinder widespread clinical utility, such as (a) only patients with certain conditions are considered, (b) existing approaches do not leverage data temporality, (c) individual admissions are assumed independent of each other, which is unrealistic, (d) prior studies are usually limited to single source of data and single center data. To address these limitations, we propose a multimodal, modality-agnostic spatiotemporal graph neural network (MM-STGNN) for prediction of 30-day all-cause hospital readmission that fuses multimodal in-patient longitudinal data. By training and evaluating our methods using longitudinal chest radiographs and electronic health records from two independent centers, we demonstrate that MM-STGNN achieves AUROC of 0.79 on both primary and external datasets. Furthermore, MM-STGNN significantly outperforms the current clinical reference standard, LACE+ score (AUROC=0.61), on the primary dataset. For subset populations of patients with heart and vascular disease, our model also outperforms baselines on predicting 30-day readmission (e.g., 3.7 point improvement in AUROC in patients with heart disease). Lastly, qualitative model interpretability analysis indicates that while patients' primary diagnoses were not explicitly used to train the model, node features crucial for model prediction directly reflect patients' primary diagnoses. Importantly, our MM-STGNN is agnostic to node feature modalities and could be utilized to integrate multimodal data for triaging patients in various downstream resource allocation tasks.