Deep learning model creates patient representations for scalable EHR-based stratification.
problem Challenges in summarizing and representing patient data from EHRs prevent scalable stratification analysis.
method Unsupervised framework based on deep learning (ConvAE) using word embeddings, CNNs, and autoencoders.
result ConvAE significantly outperformed baselines in clustering diverse patient cohorts, identifying clinically relevant subtypes.
CLOCS uses contrastive learning to improve cardiac signal representations.
problem Lack of labelled data in cardiac signal analysis.
method Contrastive learning across space, time, and patients.
result CLOCS outperforms state-of-the-art methods and achieves strong generalization.
Widespread adoption of electronic health records (EHRs) has fueled the development of using machine learning to build prediction models for various clinical outcomes. This process is often constrained by having a relatively small number of patient records for training the model. We demonstrate that using patient repres…
Enhances understanding of patient healthcare journeys using self-attention.
problem Capturing hidden dependencies in multi-level patient journey data.
method Proposes a multi-level self-attention network (MusaNet) for encoding patient journeys.
result MusaNet produces higher-quality representations than state-of-the-art methods.
Study proposes a model to improve patient subtyping from EHR data.
problem Challenges in subtyping temporal EHR datasets.
method Self-supervised Mamba-based model for learning EHR representations.
result Model outperforms baseline models in EHR data subtyping.
Novel framework detects CKD in diabetic patients using sparse EHR representations.
problem Early detection of CKD in diabetic patients.
method Sparse longitudinal representations of EHR data.
result Proposed model achieves higher predictive performance than baselines.
MCU-Net combines U-Net and Monte Carlo Dropout for uncertainty in medical image segmentation.
problem Lack of uncertainty representation in deep learning methods for patient-centered healthcare decisions.
method MCU-Net framework using U-Net and Monte Carlo Dropout with four uncertainty metrics.
result MCU-Net maximizes automated performance and refers truly uncertain cases.
Deep learning clusters patient time-series data for better prognosis.
problem Clustering time-series data for patient phenotyping and prognosis.
method Deep predictive clustering with novel loss functions for future outcome distribution.
result Model achieves superior clustering performance and identifies meaningful patient subgroups.
We study the behavior of a Time-Aware Long Short-Term Memory Autoencoder, a state-of-the-art method, in the context of learning latent representations from irregularly sampled patient data. We identify a key issue in the way such recurrent neural network models are being currently used and show that the solution of the…
Effective representation learning of electronic health records is a challenging task and is becoming more important as the availability of such data is becoming pervasive. The data contained in these records are irregular and contain multiple modalities such as notes, and medical codes. They are preempted by medical co…
Evaluating the clinical similarities between pairwise patients is a fundamental problem in healthcare informatics. A proper patient similarity measure enables various downstream applications, such as cohort study and treatment comparative effectiveness research. One major carrier for conducting patient similarity resea…
New model captures patient-level EHR data efficiently.
problem Irregular EHR code timing and lack of temporal structure.
method Latent factor point process model with Fourier-Eigen embedding.
result Efficiently captures subgroup-specific temporal patterns.
Massive electronic health records (EHRs) enable the success of learning accurate patient representations to support various predictive health applications. In contrast, doctor representation was not well studied despite that doctors play pivotal roles in healthcare. How to construct the right doctor representations? Ho…
Distributed representations have been used to support downstream tasks in healthcare recently. Healthcare data (e.g., electronic health records) contain multiple modalities of data from heterogeneous sources that can provide complementary information, alongside an added dimension to learning personalized patient repres…
Effective modeling of electronic health records presents many challenges as they contain large amounts of irregularity most of which are due to the varying procedures and diagnosis a patient may have. Despite the recent progress in machine learning, unsupervised learning remains largely at open, especially in the healt…
Computational models that forecast the progression of Alzheimer's disease at the patient level are extremely useful tools for identifying high risk cohorts for early intervention and treatment planning. The state-of-the-art work in this area proposes models that forecast by using latent representations extracted from t…
Proposes a tool to contrast global vs personalized models in clinical prediction.
problem Balancing global vs personalized models in clinical prediction.
method Localized regression approach using autoencoder for dimension reduction.
result Identification of patient subgroups where global models fall short.
CRN model estimates treatment effects over time using adversarial balancing.
problem Estimating treatment effects over time in medical settings.
method Adversarial domain balancing to remove time-varying confounders.
result CRN achieves lower error in estimating counterfactuals and treatment timing.
Extracting actionable insight from Electronic Health Records (EHRs) poses several challenges for traditional machine learning approaches. Patients are often missing data relative to each other; the data comes in a variety of modalities, such as multivariate time series, free text, and categorical demographic informatio…
Many computational models were proposed to extract temporal patterns from clinical time series for each patient and among patient group for predictive healthcare. However, the common relations among patients (e.g., share the same doctor) were rarely considered. In this paper, we represent patients and clinicians relati…
Paper uses optimal transport for low-dimensional representation of leukemia flow cytometry data.
problem Detecting minimal residual disease in leukemia patients using flow cytometry data.
method Optimal transport for dimensionality reduction and visualization of multi-patient flow cytometry datasets.
result OT-based approach provides a more informative two-dimensional representation of leukemia MRD.
Electronic medical record (EMR) data contains historical sequences of visits of patients, and each visit contains rich information, such as patient demographics, hospital utilisation and medical codes, including diagnosis, procedure and medication codes. Most existing EMR embedding methods capture visit-code associatio…
Adaptive prediction timing improves healthcare outcomes by predicting patient events at the right frequency.
problem Inconsistent prediction granularity in healthcare models.
method Introduces a novel approach using Bayesian recurrent models and a new aggregation method to adapt prediction frequency based on uncertainty.
result Adaptive prediction timing leads to improved predictive performance, especially in the critical first 12 hours of patient stay.
Method reconstructs aneurysm growth history from patient parameters using physics-informed autoencoder.
problem Predicting arterial aneurysm rupture due to inaccessible growth time series.
method Physics-informed autoencoder combined with neural network for mapping patient parameters to aneurysm growth time history.
result Incorporating physical model constraints improves time series reconstruction, especially in noisy data.
Aims to integrate AI and modelling for patient health forecasting.
problem Personalized, precise treatment plans for patients.
method Graph neural network (GNNs) and generative adversarial network (GANs) for probabilistic simulations.
result Demonstrated integration of molecular data for predicting physiological state evolution.
Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribu…
Information in electronic health records (EHR), such as clinical narratives, examination reports, lab measurements, demographics, and other patient encounter entries, can be transformed into appropriate data representations that can be used for downstream clinical machine learning tasks using representation learning. L…
Framework integrates mental disorder measurements for personalized treatment.
problem Optimizing treatment for mental disorders with latent mental states and heterogeneity.
method Measurement theory and multi-layer neural network for complex treatment effects.
result Learned treatment policies outperform alternatives on heterogeneous treatment effects.
Disease progression models are instrumental in predicting individual-level health trajectories and understanding disease dynamics. Existing models are capable of providing either accurate predictions of patients prognoses or clinically interpretable representations of disease pathophysiology, but not both. In this pape…
We show how to learn low-dimensional representations (embeddings) of patient visits from the corresponding electronic health record (EHR) where International Classification of Diseases (ICD) diagnosis codes are removed. We expect that these embeddings will be useful for the construction of predictive statistical models…
Patients who suffer an acute coronary syndrome are at elevated risk for adverse cardiovascular events such as myocardial infarction and cardiovascular death. Accurate assessment of this risk is crucial to their course of care. We focus on estimating a patient's risk of cardiovascular death after an acute coronary syndr…
Deep network clusters hospital patients' vital signs.
problem Sparse and irregularly collected vital sign data.
method Deep interpolation network for latent representation extraction.
result Extracted 7 distinct clusters from vital sign data.
Framework predicts patient risk progression over time.
problem Predicting how patient risk changes over time.
method Supervised contrastive learning framework with embedding properties.
result Framework outperforms baselines in mortality and cognitive impairment datasets.
Clinical notes are a rich source of information about patient state. However, using them to predict clinical events with machine learning models is challenging. They are very high dimensional, sparse and have complex structure. Furthermore, training data is often scarce because it is expensive to obtain reliable labels…
Dynamic assessment of patient status (e.g. by an automated, continuously updated assessment of outcome) in the Intensive Care Unit (ICU) is of paramount importance for early alerting, decision support and resource allocation. Extraction and cleaning of expert-selected clinical variables discards information and protrac…
Sepsis is a life-threatening disease and one of the major causes of death in hospitals. Imaging of microcirculatory dysfunction is a promising approach for automated diagnosis of sepsis. We report a machine learning classifier capable of distinguishing non-septic and septic images from dark field microcirculation video…
In rare disease physician targeting, a major challenge is how to identify physicians who are treating diagnosed or underdiagnosed rare diseases patients. Rare diseases have extremely low incidence rate. For a specified rare disease, only a small number of patients are affected and a fractional of physicians are involve…
Missing values, irregularly collected samples, and multi-resolution signals commonly occur in multivariate time series data, making predictive tasks difficult. These challenges are especially prevalent in the healthcare domain, where patients' vital signs and electronic records are collected at different frequencies an…
Neural networks are capable of learning rich, nonlinear feature representations shown to be beneficial in many predictive tasks. In this work, we use such models to explore different geographical feature representations in the context of predicting colorectal cancer survival curves for patients in the state of Iowa, sp…
Multi-omic data provides multiple views of the same patients. Integrative analysis of multi-omic data is crucial to elucidate the molecular underpinning of disease etiology. However, multi-omic data has the "big p, small N" problem (the number of features is large, but the number of samples is small), it is challenging…
We link disjoint longitudinal data for rare disease patients using latent representations and mixed-effects regression.
problem Analyzing treatment switches in rare diseases with limited data and changing measurement instruments.
method We embed item values into a shared latent space using variational autoencoders and apply mixed-effects regression to quantify treatment effects.
result Our approach allows for statistical inference and quantifies the impact of treatment switches in spinal muscular atrophy.
Laboratory test results are an important and generally high dimensional component of a patient's Electronic Health Record (EHR). We train embedding representations (via Word2Vec and GloVe) for LOINC codes of laboratory tests from the EHRs of about 80,000 patients at a cancer center. To include information about lab tes…
A model learns symptom-drug relations for PD patients.
problem Automatic prescription recommendation for Parkinson's Disease patients.
method Builds a dataset of PD symptoms and prescriptions, learns latent symptom space, uses alternating optimization.
result Effective in recommending suitable prescription drugs for new PD patients.
This paper develops explainable treatment policies for RPM using clinical knowledge.
problem Barriers to adoption of DHIs and lack of interpretability in purely black-box algorithms.
method Developed a pipeline for learning explainable treatment policies using clinician-informed representations.
result Policies learned from clinician-informed representations are more efficacious and efficient than black-box policies.
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. We report that our…
Veterans with mild traumatic brain injury (mTBI) have reported auditory and visual dysfunction that persists beyond the acute incident. The etiology behind these symptoms is difficult to characterize with current clinical imaging. These functional deficits may be caused by shear injury or micro-bleeds, which can be det…
Deep learning models predict postoperative complications more accurately than random forests.
problem Predicting postoperative complications to inform patient care decisions.
method Multi-task deep neural networks integrating intraoperative physiological data.
result Deep learning models improved prediction accuracy and provided interpretable risk factors.
Framework predicts clinical severity from rs-fMRI data using network optimization.
problem Predicting clinical severity from rs-fMRI data.
method Joint network optimization framework combining sparse subnetworks and linear regression.
result Framework outperforms standard methods and identifies clinically relevant ASD networks.