Deep Representation Learning-Based Dynamic Trajectory Phenotyping for Acute Respiratory Failure in Medical Intensive Care Units

Sepsis-induced acute respiratory failure (ARF) is a serious complication with a poor prognosis. This paper presents a deep representation learningbased phenotyping method to identify distinct groups of clinical trajectories of septic patients with ARF. For this retrospective study, we created a dataset from electronic medical records (EMR) consisting of data from sepsis patients admitted to medical intensive care units who required at least 24 hours of invasive mechanical ventilation at a quarternary care academic hospital in southeast USA for the years 2016-2021. A total of N=3349 patient encounters were included in this study. Clustering Representation Learning on Incomplete Time Series Data (CRLI) algorithm was applied to a parsimonious set of EMR variables in this data set. To validate the optimal number of clusters, the K-means algorithm was used in conjunction with dynamic time warping. Our model yielded four distinct patient phenotypes that were characterized as liver dysfunction/heterogeneous, hypercapnia, hypoxemia, and multiple organ dysfunction syndrome by a critical care expert. A Kaplan-Meier analysis to compare the 28-day mortality trends exhibited significant differences (p < 0.005) between the four phenotypes. The study demonstrates the utility of our deep representation learning-based approach in unraveling phenotypes that reflect the heterogeneity in sepsis-induced ARF in terms of different mortality outcomes and severity. These phenotypes might reveal important clinical insights into an effective prognosis and tailored treatment strategies.

Social Media as a Sensor: Analyzing Twitter Data for Breast Cancer Medication Effects Using Natural Language Processing

Breast cancer is a significant public health concern and is the leading cause of cancer-related deaths among women. Despite advances in breast cancer treatments, medication non-adherence remains a major problem. As electronic health records do not typically capture patient-reported outcomes that may reveal information about medication-related experiences, social media presents an attractive resource for enhancing our understanding of the patients' treatment experiences. In this paper, we developed natural language processing (NLP) based methodologies to study information posted by an automatically curated breast cancer cohort from social media. We employed a transformer-based classifier to identify breast cancer patients/survivors on X (Twitter) based on their self-reported information, and we collected longitudinal data from their profiles. We then designed a multi-layer rule-based model to develop a breast cancer therapy-associated side effect lexicon and detect patterns of medication usage and associated side effects among breast cancer patients. 1,454,637 posts were available from 583,962 unique users, of which 62,042 were detected as breast cancer members using our transformer-based model. 198 cohort members mentioned breast cancer medications with tamoxifen as the most common. Our side effect lexicon identified well-known side effects of hormone and chemotherapy. Furthermore, it discovered a subject feeling towards cancer and medications, which may suggest a pre-clinical phase of side effects or emotional distress. This analysis highlighted not only the utility of NLP techniques in unstructured social media data to identify self-reported breast cancer posts, medication usage patterns, and treatment side effects but also the richness of social data on such clinical questions.

Robust Meta-Model for Predicting the Need for Blood Transfusion in Non-traumatic ICU Patients

Objective: Blood transfusions, crucial in managing anemia and coagulopathy in ICU settings, require accurate prediction for effective resource allocation and patient risk assessment. However, existing clinical decision support systems have primarily targeted a particular patient demographic with unique medical conditions and focused on a single type of blood transfusion. This study aims to develop an advanced machine learning-based model to predict the probability of transfusion necessity over the next 24 hours for a diverse range of non-traumatic ICU patients. Methods: We conducted a retrospective cohort study on 72,072 adult non-traumatic ICU patients admitted to a high-volume US metropolitan academic hospital between 2016 and 2020. We developed a meta-learner and various machine learning models to serve as predictors, training them annually with four-year data and evaluating on the fifth, unseen year, iteratively over five years. Results: The experimental results revealed that the meta-model surpasses the other models in different development scenarios. It achieved notable performance metrics, including an Area Under the Receiver Operating Characteristic (AUROC) curve of 0.97, an accuracy rate of 0.93, and an F1-score of 0.89 in the best scenario. Conclusion: This study pioneers the use of machine learning models for predicting blood transfusion needs in a diverse cohort of critically ill patients. The findings of this evaluation confirm that our model not only predicts transfusion requirements effectively but also identifies key biomarkers for making transfusion decisions.

Detecting algorithmic bias in medical AI-models

With the growing prevalence of machine learning and artificial intelligence-based medical decision support systems, it is equally important to ensure that these systems provide patient outcomes in a fair and equitable fashion. This paper presents an innovative framework for detecting areas of algorithmic bias in medical-AI decision support systems. Our approach efficiently identifies potential biases in medical-AI models, specifically in the context of sepsis prediction, by employing the Classification and Regression Trees (CART) algorithm. We verify our methodology by conducting a series of synthetic data experiments, showcasing its ability to estimate areas of bias in controlled settings precisely. The effectiveness of the concept is further validated by experiments using electronic medical records from Grady Memorial Hospital in Atlanta, Georgia. These tests demonstrate the practical implementation of our strategy in a clinical environment, where it can function as a vital instrument for guaranteeing fairness and equity in AI-based medical decisions.

Mixed-Integer Projections for Automated Data Correction of EMRs Improve Predictions of Sepsis among Hospitalized Patients

Machine learning (ML) models are increasingly pivotal in automating clinical decisions. Yet, a glaring oversight in prior research has been the lack of proper processing of Electronic Medical Record (EMR) data in the clinical context for errors and outliers. Addressing this oversight, we introduce an innovative projections-based method that seamlessly integrates clinical expertise as domain constraints, generating important meta-data that can be used in ML workflows. In particular, by using high-dimensional mixed-integer programs that capture physiological and biological constraints on patient vitals and lab values, we can harness the power of mathematical "projections" for the EMR data to correct patient data. Consequently, we measure the distance of corrected data from the constraints defining a healthy range of patient data, resulting in a unique predictive metric we term as "trust-scores". These scores provide insight into the patient's health status and significantly boost the performance of ML classifiers in real-life clinical settings. We validate the impact of our framework in the context of early detection of sepsis using ML. We show an AUROC of 0.865 and a precision of 0.922, that surpasses conventional ML models without such projections.

Meta-learning in healthcare: A survey

As a subset of machine learning, meta-learning, or learning to learn, aims at improving the model's capabilities by employing prior knowledge and experience. A meta-learning paradigm can appropriately tackle the conventional challenges of traditional learning approaches, such as insufficient number of samples, domain shifts, and generalization. These unique characteristics position meta-learning as a suitable choice for developing influential solutions in various healthcare contexts, where the available data is often insufficient, and the data collection methodologies are different. This survey discusses meta-learning broad applications in the healthcare domain to provide insight into how and where it can address critical healthcare challenges. We first describe the theoretical foundations and pivotal methods of meta-learning. We then divide the employed meta-learning approaches in the healthcare domain into two main categories of multi/single-task learning and many/few-shot learning and survey the studies. Finally, we highlight the current challenges in meta-learning research, discuss the potential solutions and provide future perspectives on meta-learning in healthcare.

Transfer Causal Learning: Causal Effect Estimation with Knowledge Transfer

A novel problem of improving causal effect estimation accuracy with the help of knowledge transfer under the same covariate (or feature) space setting, i.e., homogeneous transfer learning (TL), is studied, referred to as the Transfer Causal Learning (TCL) problem. While most recent efforts in adapting TL techniques to estimate average causal effect (ACE) have been focused on the heterogeneous covariate space setting, those methods are inadequate for tackling the TCL problem since their algorithm designs are based on the decomposition into shared and domain-specific covariate spaces. To address this issue, we propose a generic framework called $\ell_1$-TCL, which incorporates $\ell_1$ regularized TL for nuisance parameter estimation and downstream plug-in ACE estimators, including outcome regression, inverse probability weighted, and doubly robust estimators. Most importantly, with the help of Lasso for high-dimensional regression, we establish non-asymptotic recovery guarantees for the generalized linear model (GLM) under the sparsity assumption for the proposed $\ell_1$-TCL. From an empirical perspective, $\ell_1$-TCL is a generic learning framework that can incorporate not only GLM but also many recently developed non-parametric methods, which can enhance robustness to model mis-specification. We demonstrate this empirical benefit through extensive numerical simulation by incorporating both GLM and recent neural network-based approaches in $\ell_1$-TCL, which shows improved performance compared with existing TL approaches for ACE estimation. Furthermore, our $\ell_1$-TCL framework is subsequently applied to a real study, revealing that vasopressor therapy could prevent 28-day mortality within septic patients, which all baseline approaches fail to show.

Causal Graph Discovery from Self and Mutually Exciting Time Series

We present a generalized linear structural causal model, coupled with a novel data-adaptive linear regularization, to recover causal directed acyclic graphs (DAGs) from time series. By leveraging a recently developed stochastic monotone Variational Inequality (VI) formulation, we cast the causal discovery problem as a general convex optimization. Furthermore, we develop a non-asymptotic recovery guarantee and quantifiable uncertainty by solving a linear program to establish confidence intervals for a wide range of non-linear monotone link functions. We validate our theoretical results and show the competitive performance of our method via extensive numerical experiments. Most importantly, we demonstrate the effectiveness of our approach in recovering highly interpretable causal DAGs over Sepsis Associated Derangements (SADs) while achieving comparable prediction performance to powerful ``black-box'' models such as XGBoost. Thus, the future adoption of our proposed method to conduct continuous surveillance of high-risk patients by clinicians is much more likely.

ALRt: An Active Learning Framework for Irregularly Sampled Temporal Data

Sepsis is a deadly condition affecting many patients in the hospital. Recent studies have shown that patients diagnosed with sepsis have significant mortality and morbidity, resulting from the body's dysfunctional host response to infection. Clinicians often rely on the use of Sequential Organ Failure Assessment (SOFA), Systemic Inflammatory Response Syndrome (SIRS), and the Modified Early Warning Score (MEWS) to identify early signs of clinical deterioration requiring further work-up and treatment. However, many of these tools are manually computed and were not designed for automated computation. There have been different methods used for developing sepsis onset models, but many of these models must be trained on a sufficient number of patient observations in order to form accurate sepsis predictions. Additionally, the accurate annotation of patients with sepsis is a major ongoing challenge. In this paper, we propose the use of Active Learning Recurrent Neural Networks (ALRts) for short temporal horizons to improve the prediction of irregularly sampled temporal events such as sepsis. We show that an active learning RNN model trained on limited data can form robust sepsis predictions comparable to models using the entire training dataset.

UnfoldML: Cost-Aware and Uncertainty-Based Dynamic 2D Prediction for Multi-Stage Classification

Machine Learning (ML) research has focused on maximizing the accuracy of predictive tasks. ML models, however, are increasingly more complex, resource intensive, and costlier to deploy in resource-constrained environments. These issues are exacerbated for prediction tasks with sequential classification on progressively transitioned stages with ''happens-before'' relation between them.We argue that it is possible to ''unfold'' a monolithic single multi-class classifier, typically trained for all stages using all data, into a series of single-stage classifiers. Each single-stage classifier can be cascaded gradually from cheaper to more expensive binary classifiers that are trained using only the necessary data modalities or features required for that stage. UnfoldML is a cost-aware and uncertainty-based dynamic 2D prediction pipeline for multi-stage classification that enables (1) navigation of the accuracy/cost tradeoff space, (2) reducing the spatio-temporal cost of inference by orders of magnitude, and (3) early prediction on proceeding stages. UnfoldML achieves orders of magnitude better cost in clinical settings, while detecting multi-stage disease development in real time. It achieves within 0.1% accuracy from the highest-performing multi-class baseline, while saving close to 20X on spatio-temporal cost of inference and earlier (3.5hrs) disease onset prediction. We also show that UnfoldML generalizes to image classification, where it can predict different level of labels (from coarse to fine) given different level of abstractions of a image, saving close to 5X cost with as little as 0.4% accuracy reduction.