HyDaP clusters mixed-type data efficiently.
problem Clustering data with mixed types (continuous and categorical).
method Two-step hybrid approach: density-based and partition-based for continuous variables, partition-based for mixed data.
result HyDaP outperforms existing methods in clustering electronic health records.
Study identifies sepsis subpopulations for better ICU prediction.
problem Lack of stratified sepsis subpopulations in ICU EHR predictions.
method Stratified sepsis subpopulations identified using machine learning.
result Machine learning models perform better with stratified subpopulations.
Sepsis is a dangerous condition that is a leading cause of patient mortality. Treating sepsis is highly challenging, because individual patients respond very differently to medical interventions and there is no universally agreed-upon treatment for sepsis. In this work, we explore the use of continuous state-space mode…
Characterizing a patient's progression through stages of sepsis is critical for enabling risk stratification and adaptive, personalized treatment. However, commonly used sepsis diagnostic criteria fail to account for significant underlying heterogeneity, both between patients as well as over time in a single patient. W…
New dataset from clinicians improves sepsis prediction models.
problem Circularity in previous sepsis prediction models.
method Developed an independent dataset from clinical judgments, avoiding circularity.
result Achieved state-of-the-art AUROC scores.
Deep learning and lazy learner improve early sepsis detection.
problem Detecting sepsis early in high-resolution ICU records.
method Deep learning model with temporal convolutional network and Gaussian Process Adapter; lazy learner with dynamic time warping.
result Improves sepsis detection from 0.25 to 0.40 AUPRC 7 hours before onset.
DeepAISE predicts sepsis onset with high accuracy and low false alarms.
problem Early prediction of sepsis in ICU patients to improve clinical situational awareness.
method Recurrent neural survival model that combines clinical criteria and treatment policies.
result DeepAISE produces the most accurate predictions (AUC=0.90 and 0.87) and lowest false alarm rates (FAR=0.20 and 0.26) compared to baseline models.
We study multiple rule-based and machine learning (ML) models for sepsis detection. We report the first neural network detection and prediction results on three categories of sepsis. We have used the retrospective Medical Information Mart for Intensive Care (MIMIC)-III dataset, restricted to intensive care unit (ICU) p…
EHR-MPC optimizes sepsis treatment using digital twins and inference-time control.
problem Optimal sepsis treatment policies are contested and difficult to adapt during inference.
method EHR-MPC decouples learning patient dynamics from treatment optimization, enabling inference-time control over learned digital twins.
result EHR-MPC achieves comparable off-policy performance and improved simulation performance compared to RL baselines.
Simulates sepsis treatment decisions using a world model approach.
problem Predicting optimal sepsis treatment actions based on noisy EHR data.
method Uses a Variational Auto-Encoder and Mixture Density Network (MDN-RNN) to model sepsis patient trajectories.
result Simulator learns from MIMIC dataset to predict patient states.
Paper uses a mix of deep and kernel learning to personalize sepsis treatment.
problem Managing sepsis in ICU patients due to individual variability.
method A mixture-of-experts framework combining kernel-based and deep reinforcement learning.
result The mixture-based approach outperforms individual methods on a large sepsis patient cohort.
Deep learning detects sepsis early, improving patient outcomes.
problem Improving timeliness of sepsis detection in various healthcare settings.
method Deep learning model on electronic health records, combining CNN and LSTM networks.
result Model performance ranges from 0.856 to 0.756 AUROC, detecting sepsis up to 24 hours in advance.
Paper uses ensemblers to predict sepsis early from patient records.
problem Early detection of sepsis in patients.
method Imputation and weak ensembler technique applied to 40k patient records.
result Model achieved 93.45% accuracy and 0.271 utility score.
Model predicts sepsis early with high accuracy.
problem Early detection of sepsis to reduce mortality.
method MGP-AttTCN: Gaussian Process and attention-based deep learning.
result Model outperforms state-of-the-art with AUROC 0.660 and AUPR 0.483.
Although timely sepsis diagnosis and prompt interventions in Intensive Care Unit (ICU) patients are associated with reduced mortality, early clinical recognition is frequently impeded by non-specific signs of infection and failure to detect signs of sepsis-induced organ dysfunction in a constellation of dynamically cha…
Study identifies subphenotypes of pediatric sepsis to improve ML predictive performance.
problem Enhance machine learning predictive performance in pediatric sepsis.
method Latent profile analysis of clinical data to identify subphenotypes, followed by ML experiments.
result Improved predictive performance of ML models targeting specific subphenotypes of pediatric sepsis.
New method identifies sepsis-related patient features in EMR data.
problem Identify sepsis-related patient features in EMR data.
method Linear multivariate Hawkes process model with ReLU link function, coupled with gradient-based method.
result Identifies several interpretable GC chains that precede sepsis.
Sepsis is a poorly understood and potentially life-threatening complication that can occur as a result of infection. Early detection and treatment improves patient outcomes, and as such it poses an important challenge in medicine. In this work, we develop a flexible classifier that leverages streaming lab results, vita…
Predict sepsis early from EHR data with aggregated clinical events.
problem Predict sepsis from clinical data in EHR with temporal interactions.
method Aggregates heterogeneous clinical events, captures temporal interactions with LSTM.
result Achieved high utility score (0.321) in PhysioNet/Computing in Cardiology Challenge 2019.
Disease phenotyping algorithms process observational clinical data to identify patients with specific diseases. Supervised phenotyping methods require significant quantities of expert-labeled data, while unsupervised methods may learn non-disease phenotypes. To address these limitations, we propose the Semi-Supervised …
Electronic phenotyping is the task of ascertaining whether an individual has a medical condition of interest by analyzing their medical record and is foundational in clinical informatics. Increasingly, electronic phenotyping is performed via supervised learning. We investigate the effectiveness of multitask learning fo…
VBphenoR uses variational Bayes for EHR-based patient phenotyping.
problem Phenotyping patients from EHR data for targeted treatments.
method Variational Bayes Gaussian Mixture Model (GMM) and logistic regression.
result Closed-form inference for efficient patient phenotype determination.
It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the su…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of phenotypes makes high-throughput phenotype profiling a very difficult and labor…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we …
Study evaluates how framing affects machine learning models for sepsis prediction.
problem Understanding and reporting framing is crucial for AI technology success.
method Four different approaches applied to AI models of sepsis prediction.
result On-clinical-demand framing showed the lowest missing values and best temporal dependencies.
Bayesian model enhances phenotype discovery in asthma EHRs.
problem Lack of interpretability in unsupervised learning phenotyping of EHR data.
method Operationalized a Bayesian latent class framework with clinical knowledge priors.
result Identified an asthma sub-phenotype with elevated eosinophil levels and allergy markers.
Model identifies key problems in HIV patients' records.
problem Complex and time-consuming task of identifying patient problems from electronic health records.
method Unsupervised phenotyping approach that jointly learns phenotypes from structured and unstructured data.
result Learned phenotypes and their relatedness are clinically valid and surpass existing methods.
Active learning with Gaussian processes improves crop phenotype data collection.
problem Scalability issue in high throughput phenotyping for crop improvement.
method Active learning algorithm with Gaussian Process model.
result Superior performance compared to current practices on sorghum data.
Deep learning quantifies butterfly phenotypes, validating evolutionary theory.
problem Capturing comprehensive phenotypic information of butterflies.
method Deep convolutional triplet network for phenotypic distance calculation.
result Euclidean phenotypic distances support classical mimicry theory.
This paper reviews methods for discovering patient subgroups from EHR data.
problem Discovering subgroups of patients and co-occurring medical conditions from EHR data.
method Low-rank data approximation methods like matrix and tensor decompositions.
result These methods provide transparent and interpretable insights into patient phenotypes.
Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We ass…
Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospi…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
ODBAE detects complex phenotypes in biological data.
problem Challenges in identifying complex phenotypes from high-dimensional biological data.
method ODBAE (Outlier Detection using Balanced Autoencoders) identifies influential and high leverage points in latent relationships among multiple physiological parameters.
result ODBAE reveals novel metabolism-related genes and uncovers coordinated abnormalities across metabolic indicators.
TASTE combines static and temporal data for phenotyping EHRs.
problem Phenotyping EHRs with both static and temporal data.
method Jointly models static and temporal tensors using PARAFAC2 and non-negative matrix factorization, alternatingly solving sub-problems.
result TASTE outperforms existing methods in speed and clinical meaningfulness of phenotypes.
Study identifies three sub-phenotypes of AKI with different severity.
problem Tackles the heterogeneity of AKI to improve targeted interventions.
method Used a memory network-based deep learning approach on EHR data.
result Identified three distinct sub-phenotypes of AKI with varying severity.
Study uses LCA to identify ARDS sub-phenotypes improving predictive models.
problem Complex and heterogeneous nature of ARDS makes early recognition difficult.
method Applied latent class analysis to identify sub-groups, then built predictive models.
result Significantly improved prediction performance for two sub-phenotypes of ARDS.
SWoTTeD discovers hidden temporal patterns in EHR data.
problem Complex temporal patterns in EHR data.
method Sliding Window for Temporal Tensor Decomposition (SWoTTeD) with constraints and regularizations.
result SWoTTeD achieves at least as accurate reconstruction as state-of-the-art models and extracts meaningful temporal phenotypes.
Paper introduces tCNNS model for predicting drug cell line interactions.
problem Predicting phenotypic drug responses on cancer cell lines.
method tCNNS model using SMILES format for drugs and cancer cell lines.
result Achieves 0.84 for R2 and 0.92 for Rp. WEST uses EHRs and expert cases to improve rare disease phenotyping.
problem Limited labeled data for rare diseases.
method Weakly supervised transformer model trained on probabilistic silver-standard labels.
result WEST outperforms existing methods in phenotype classification and subphenotyping.
OMTL uses ontology to learn from imbalanced EHR data.
problem Imbalanced and small usable data for phenotypes in EHRs.
method Ontology-driven multi-task learning framework.
result Improved learning performance on phenotypes.
We develop a model to cluster time-series data with interval censoring, improving disease phenotyping.
problem Noise and interval censoring hinder clustering in disease phenotyping.
method Deep generative, continuous-time model that clusters time-series data while correcting for censorship.
result Our model corrects for interval censoring and recovers known clinical subtypes.
We present a scalable end-to-end classifier that uses streaming physiological and medication data to accurately predict the onset of sepsis, a life-threatening complication from infections that has high mortality and morbidity. Our proposed framework models the multivariate trajectories of continuous-valued physiologic…
Study develops electronic phenotypes of ICU patient acuity.
problem Limited time for patient acuity assessments and imprecise clinical trajectory prediction.
method Developed electronic phenotypes using automated variable retrieval in electronic health records.
result Identified three phenotypes: persistently stable, persistently unstable, and transitioning from unstable to stable.
Baseline injury categorization is important to traumatic brain injury (TBI) research and treatment. Current categorization is dominated by symptom-based scores that insufficiently capture injury heterogeneity. In this work, we apply unsupervised clustering to identify novel TBI phenotypes. Our approach uses a generaliz…
New methods for evaluating and optimizing policies in offline RL with unobserved confounders.
problem Evaluating and optimizing policies in the presence of unobserved confounders.
method Characterized settings and algorithms for consistent value estimates and lower bounds, with sample complexity guarantees.
result Proved local convergence guarantees for offline policy improvement.
Binary PheNorm extends phenotype labeling for EHRs using binary silver labels.
problem Lack of gold-standard phenotype labels in EHR studies.
method Proposes Binary PheNorm, an extension that uses binary silver labels directly in phenotype scoring.
result Binary PheNorm achieved strong discrimination using binary labels alone and improved performance when combined with count labels.