Shamim Nemati

Xiaolei Lu, Shamim Nemati

Early prediction of respiratory failure is critical for timely clinical intervention in intensive care units. Existing electronic health record (EHR)-based models can continuously monitor physiologic deterioration, but they may not fully capture pulmonary pathophysiology reflected in chest radiographs (CXRs). In this study, we ask whether CXR information improves prospective prediction of invasive mechanical ventilation beyond EHR signals alone. We develop a gated multimodal framework that integrates structured EHR time-series data with CXR foundation-model representations. The gating module adaptively controls the contribution of imaging features based on patient-specific clinical context, allowing the model to selectively rely on imaging information when it is informative. We prospectively evaluate the framework for predicting invasive mechanical ventilation within 24 hours in ICU patients and compare it with an established EHR-only model (Vent.io), physician predictions obtained at matched clinical time points, and alternative multimodal variants. The gated multimodal models achieved higher discrimination than the EHR-only baseline, with AUROC values of 0.860 and 0.858 using REMEDIS and MedInsight CXR representations, respectively, compared with 0.752 for Vent.io. Relative to physician predictions, the multimodal framework substantially improved sensitivity while maintaining favorable specificity. Compared with the EHR-only model, multimodal integration increased specificity and positive predictive value, suggesting that CXR information can refine risk estimation in selected patients. These findings support adaptive multimodal fusion as a practical strategy for incorporating imaging into prospective respiratory failure prediction.

Anwesh Mohanty, Supreeth P. Shashikumar, Jonathan Y. Lam et al.

In the intensive care unit, the capability to predict the need for mechanical ventilation (MV) facilitates more timely interventions to improve patient outcomes. Recent works have demonstrated good performance in this task utilizing machine learning models. This paper explores the novel application of a deep learning model with multi-head attention (FFNN-MHA) to make more accurate MV predictions and reduce false positives by learning personalized contextual information of individual patients. Utilizing the publicly available MIMIC-IV dataset, FFNN-MHA demonstrates an improvement of 0.0379 in AUC and a 17.8\% decrease in false positives compared to baseline models such as feed-forward neural networks. Our results highlight the potential of the FFNN-MHA model as an effective tool for accurate prediction of the need for mechanical ventilation in critical care settings.

Xiaolei Lu, Shamim Nemati

Accurate prediction of the need for invasive mechanical ventilation (IMV) in intensive care units (ICUs) patients is crucial for timely interventions and resource allocation. However, variability in patient populations, clinical practices, and electronic health record (EHR) systems across institutions introduces domain shifts that degrade the generalization performance of predictive models during deployment. Test-Time Training (TTT) has emerged as a promising approach to mitigate such shifts by adapting models dynamically during inference without requiring labeled target-domain data. In this work, we introduce Adaptive Test-Time Training (AdaTTT), an enhanced TTT framework tailored for EHR-based IMV prediction in ICU settings. We begin by deriving information-theoretic bounds on the test-time prediction error and demonstrate that it is constrained by the uncertainty between the main and auxiliary tasks. To enhance their alignment, we introduce a self-supervised learning framework with pretext tasks: reconstruction and masked feature modeling optimized through a dynamic masking strategy that emphasizes features critical to the main task. Additionally, to improve robustness against domain shifts, we incorporate prototype learning and employ Partial Optimal Transport (POT) for flexible, partial feature alignment while maintaining clinically meaningful patient representations. Experiments across multi-center ICU cohorts demonstrate competitive classification performance on different test-time adaptation benchmarks.

Ayse Cakmak, Erik Reinertsen, Shamim Nemati et al.

The pattern of state changes in a biomedical time series can be related to health or disease. This work presents a principled approach for selecting a changepoint detection algorithm for a specific task, such as disease classification. Eight key algorithms were compared, and the performance of each algorithm was evaluated as a function of temporal tolerance, noise, and abnormal conduction (ectopy) on realistic artificial cardiovascular time series data. All algorithms were applied to real data (cardiac time series of 22 patients with REM-behavior disorder (RBD) and 15 healthy controls) using the parameters selected on artificial data. Finally, features were derived from the detected changepoints to classify RBD patients from healthy controls using a K-Nearest Neighbors approach. On artificial data, Modified Bayesian Changepoint Detection algorithm provided superior positive predictive value for state change identification while Recursive Mean Difference Maximization (RMDM) achieved the highest true positive rate. For the classification task, features derived from the RMDM algorithm provided the highest leave one out cross validated accuracy of 0.89 and true positive rate of 0.87. Automatically detected changepoints provide useful information about subject's physiological state which cannot be directly observed. However, the choice of change point detection algorithm depends on the nature of the underlying data and the downstream application, such as a classification task. This work represents the first time change point detection algorithms have been compared in a meaningful way and utilized in a classification task, which demonstrates the effect of changepoint algorithm choice on application performance.

Salman Seyedi, Li Xiong, Shamim Nemati et al.

The increasing complexity of algorithms for analyzing medical data, including de-identification tasks, raises the possibility that complex algorithms are learning not just the general representation of the problem, but specifics of given individuals within the data. Modern legal frameworks specifically prohibit the intentional or accidental distribution of patient data, but have not addressed this potential avenue for leakage of such protected health information. Modern deep learning algorithms have the highest potential of such leakage due to complexity of the models. Recent research in the field has highlighted such issues in non-medical data, but all analysis is likely to be data and algorithm specific. We, therefore, chose to analyze a state-of-the-art free-text de-identification algorithm based on LSTM (Long Short-Term Memory) and its potential in encoding any individual in the training set. Using the i2b2 Challenge Data, we trained, then analyzed the model to assess whether the output of the LSTM, before the compression layer of the classifier, could be used to estimate the membership of the training data. Furthermore, we used different attacks including membership inference attack method to attack the model. Results indicate that the attacks could not identify whether members of the training data were distinguishable from non-members based on the model output. This indicates that the model does not provide any strong evidence into the identification of the individuals in the training data set and there is not yet empirical evidence it is unsafe to distribute the model for general use.

Chao Yu, Jiming Liu, Shamim Nemati

As a subfield of machine learning, reinforcement learning (RL) aims at empowering one's capabilities in behavioural decision making by using interaction experience with the world and an evaluative feedback. Unlike traditional supervised learning methods that usually rely on one-shot, exhaustive and supervised reward signals, RL tackles with sequential decision making problems with sampled, evaluative and delayed feedback simultaneously. Such distinctive features make RL technique a suitable candidate for developing powerful solutions in a variety of healthcare domains, where diagnosing decisions or treatment regimes are usually characterized by a prolonged and sequential procedure. This survey discusses the broad applications of RL techniques in healthcare domains, in order to provide the research community with systematic understanding of theoretical foundations, enabling methods and techniques, existing challenges, and new insights of this emerging paradigm. By first briefly examining theoretical foundations and key techniques in RL research from efficient and representational directions, we then provide an overview of RL applications in healthcare domains ranging from dynamic treatment regimes in chronic diseases and critical care, automated medical diagnosis from both unstructured and structured clinical data, as well as many other control or scheduling domains that have infiltrated many aspects of a healthcare system. Finally, we summarize the challenges and open issues in current research, and point out some potential solutions and directions for future research.

Supreeth P. Shashikumar, Christopher Josef, Ashish Sharma et al.

Sepsis, a dysregulated immune system response to infection, is among the leading causes of morbidity, mortality, and cost overruns in the Intensive Care Unit (ICU). Early prediction of sepsis can improve situational awareness amongst clinicians and facilitate timely, protective interventions. While the application of predictive analytics in ICU patients has shown early promising results, much of the work has been encumbered by high false-alarm rates. Efforts to improve specificity have been limited by several factors, most notably the difficulty of labeling sepsis onset time and the low prevalence of septic-events in the ICU. Here, we present DeepAISE (Deep Artificial Intelligence Sepsis Expert), a recurrent neural survival model for the early prediction of sepsis. We show that by coupling a clinical criterion for defining sepsis onset time with a treatment policy (e.g., initiation of antibiotics within one hour of meeting the criterion), one may rank the relative utility of various criteria through offline policy evaluation. Given the optimal criterion, DeepAISE automatically learns predictive features related to higher-order interactions and temporal patterns among clinical risk factors that maximize the data likelihood of observed time to septic events. DeepAISE has been incorporated into a clinical workflow, which provides real-time hourly sepsis risk scores. A comparative study of four baseline models indicates that DeepAISE produces the most accurate predictions (AUC=0.90 and 0.87) and the lowest false alarm rates (FAR=0.20 and 0.26) in two separate cohorts (internal and external, respectively), while simultaneously producing interpretable representations of the clinical time series and risk factors.

Russell Jeter, Christopher Josef, Supreeth Shashikumar et al.

From 2017 to 2018 the number of scientific publications found via PubMed search using the keyword "Machine Learning" increased by 46% (4,317 to 6,307). The results of studies involving machine learning, artificial intelligence (AI), and big data have captured the attention of healthcare practitioners, healthcare managers, and the public at a time when Western medicine grapples with unmitigated cost increases and public demands for accountability. The complexity involved in healthcare applications of machine learning and the size of the associated data sets has afforded many researchers an uncontested opportunity to satisfy these demands with relatively little oversight. In a recent Nature Medicine article, "The Artificial Intelligence Clinician learns optimal treatment strategies for sepsis in intensive care," Komorowski and his coauthors propose methods to train an artificial intelligence clinician to treat sepsis patients with vasopressors and IV fluids. In this post, we will closely examine the claims laid out in this paper. In particular, we will study the individual treatment profiles suggested by their AI Clinician to gain insight into how their AI Clinician intends to treat patients on an individual level.

Justus T. C. Schwabedal, John C. Snyder, Ayse Cakmak et al.

Randomizing the Fourier-transform (FT) phases of temporal-spatial data generates surrogates that approximate examples from the data-generating distribution. We propose such FT surrogates as a novel tool to augment and analyze training of neural networks and explore the approach in the example of sleep-stage classification. By computing FT surrogates of raw EEG, EOG, and EMG signals of under-represented sleep stages, we balanced the CAPSLPDB sleep database. We then trained and tested a convolutional neural network for sleep stage classification, and found that our surrogate-based augmentation improved the mean F1-score by 7%. As another application of FT surrogates, we formulated an approach to compute saliency maps for individual sleep epochs. The visualization is based on the response of inferred class probabilities under replacement of short data segments by partial surrogates. To quantify how well the distributions of the surrogates and the original data match, we evaluated a trained classifier on surrogates of correctly classified examples, and summarized these conditional predictions in a confusion matrix. We show how such conditional confusion matrices can qualitatively explain the performance of surrogates in class balancing. The FT-surrogate augmentation approach may improve classification on noisy signals if carefully adapted to the data distribution under analysis.

Supreeth P. Shashikumar, Amit J. Shah, Gari D. Clifford et al.

Detection of atrial fibrillation (AF), a type of cardiac arrhythmia, is difficult since many cases of AF are usually clinically silent and undiagnosed. In particular paroxysmal AF is a form of AF that occurs occasionally, and has a higher probability of being undetected. In this work, we present an attention based deep learning framework for detection of paroxysmal AF episodes from a sequence of windows. Time-frequency representation of 30 seconds recording windows, over a 10 minute data segment, are fed sequentially into a deep convolutional neural network for image-based feature extraction, which are then presented to a bidirectional recurrent neural network with an attention layer for AF detection. To demonstrate the effectiveness of the proposed framework for transient AF detection, we use a database of 24 hour Holter Electrocardiogram (ECG) recordings acquired from 2850 patients at the University of Virginia heart station. The algorithm achieves an AUC of 0.94 on the testing set, which exceeds the performance of baseline models. We also demonstrate the cross-domain generalizablity of the approach by adapting the learned model parameters from one recording modality (ECG) to another (photoplethysmogram) with improved AF detection performance. The proposed high accuracy, low false alarm algorithm for detecting paroxysmal AF has potential applications in long-term monitoring using wearable sensors.

Hongteng Xu, Weichang Wu, Shamim Nemati et al.

Over the past decade the rate of care unit (CU) use in the United States has been increasing. With an aging population and ever-growing demand for medical care, effective management of patients' transitions among different care facilities will prove indispensible for shortening the length of hospital stays, improving patient outcomes, allocating critical care resources, and reducing preventable re-admissions. In this paper, we focus on an important problem of predicting the so-called "patient flow" from longitudinal electronic health records (EHRs), which has not been explored via existing machine learning techniques. By treating a sequence of transition events as a point process, we develop a novel framework for modeling patient flow through various CUs and jointly predicting patients' destination CUs and duration days. Instead of learning a generative point process model via maximum likelihood estimation, we propose a novel discriminative learning algorithm aiming at improving the prediction of transition events in the case of sparse data. By parameterizing the proposed model as a mutually-correcting process, we formulate the estimation problem via generalized linear models, which lends itself to efficient learning based on alternating direction method of multipliers (ADMM). Furthermore, we achieve simultaneous feature selection and learning by adding a group-lasso regularizer to the ADMM algorithm. Additionally, for suppressing the negative influence of data imbalance on the learning of model, we synthesize auxiliary training data for the classes with extremely few samples, and improve the robustness of our learning method accordingly. Testing on real-world data, we show that our method obtains superior performance in terms of accuracy of predicting the destination CU transition and duration of each CU occupancy.