Shamim Nemati

Shamim Nemati
Massachusetts Institute of Technology | MIT

PhD

About

76
Publications
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3,866
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Introduction

Publications

Publications (76)
Article
Full-text available
Objectives: Sepsis is a major public health concern with significant morbidity, mortality, and healthcare expenses. Early detection and antibiotic treatment of sepsis improve outcomes. However, although professional critical care societies have proposed new clinical criteria that aid sepsis recognition, the fundamental need for early detection and...
Preprint
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 pat...
Article
\emph{Objective:} Ventricular contractions in healthy individuals normally follow the contractions of atria to facilitate more efficient pump action and cardiac output. With a ventricular ectopic beat (VEB), volume within the ventricles are pumped to the body's vessels before receiving blood from atria, thus causing inefficient blood circulation. V...
Preprint
Full-text available
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 w...
Article
Objective: This study classifies sleep stages from a single lead electrocardiogram (ECG) using beat detection, cardiorespiratory coupling in the time-frequency domain and a deep convolutional neural network (CNN). Approach: An ECG-derived respiration (EDR) signal and synchronous beat-to-beat heart rate variability (HRV) time series were derived...
Article
\textit{Objective.} Changes in heart rate (HR) and locomotor activity reflect changes in autonomic physiology, behavior, and mood. These systems may involve interrelated neural circuits that are altered in psychiatric illness, yet their interactions are poorly understood. We hypothesized interactions between HR and locomotor activity could be used...
Article
Objective: This work aims to validate a set of data processing methods for variability metrics, which hold promise as potential indicators for autonomic function, prediction of adverse cardiovascular outcomes, psychophysiological status, and general wellness. Although the investigation of heart rate variability (HRV) has been prevalent for several...
Conference Paper
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 detect...
Conference Paper
Sepsis is a common disease with very costly, potentially deadly implications. Early prediction of Sepsis and initiation of antibiotic is widely considered as an important determinant of patient survival. Cross-institutional validation and implementation of algorithms for early prediction of Sepsis at a minimum require common data formats, streaming...
Conference Paper
The judgment of intensive care unit (ICU) providers is difficult to measure using conventional structured electronic medical record (EMR) data. However, provider sentiment may be a proxy for such judgment. Utilizing 10 years of EMR data, this study evaluates the association between provider sentiment and diagnostic imaging utilization. We extracted...
Conference Paper
Medication dosing in a critical care environment is a complex task that involves close monitoring of relevant physiologic and laboratory biomarkers and corresponding sequential adjustment of the prescribed dose. Misdosing of medications with narrow therapeutic windows (such as intravenous [IV] heparin) can result in preventable adverse events, decr...
Article
The judgment of intensive care unit (ICU) providers is difficult to measure using conventional structured electronic medical record (EMR) data. However, provider sentiment may be a proxy for such judgment. Utilizing 10 years of EMR data, this study evaluates the association between provider sentiment and diagnostic imaging utilization. We extracted...
Preprint
Full-text available
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 surrogate...
Article
This study focused on the comparison of single entropy measures for the ventricular response analysis-based AF detection. To enhance the performance of entropy-based AF detectors, we developed a normalized fuzzy entropy, H <sup>θ</sup><sub>N</sub> , a novel metric that: 1) uses a fuzzy function to determine vector similarity, 2) replaces probabilit...
Preprint
Full-text available
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 detect...
Article
Objectives: Sepsis is among the leading causes of morbidity, mortality, and cost overruns in critically ill patients. Early intervention with antibiotics improves survival in septic patients. However, no clinically validated system exists for real-time prediction of sepsis onset. We aimed to develop and validate an Artificial Intelligence Sepsis E...
Article
Main results: We show that features derived from a multiscale heart rate and blood pressure time series network provide approximately 20% improvement in the area under the receiver operating characteristic (AUROC) for four-hour advance prediction of sepsis over traditional indices of heart rate entropy ([Formula: see text] versus [Formula: see tex...
Article
Background: Heart rate variability (HRV) metrics hold promise as potential indicators for autonomic function, prediction of adverse cardiovascular outcomes, psychophysiological status, and general wellness. Although the investigation of HRV has been prevalent for several decades, the methods used for preprocessing, windowing, and choosing appropri...
Article
Sepsis remains a leading cause of morbidity and mortality among intensive care unit (ICU) patients. For each hour treatment initiation is delayed after diagnosis, sepsis-related mortality increases by approximately 8%. Therefore, maximizing effective care requires early recognition and initiation of treatment protocols. Antecedent signs and symptom...
Article
Full-text available
Objective. Heart rate variability (HRV) characterizes changes in autonomic nervous system function and varies with posttraumatic stress disorder (PTSD). In this study we developed a classifier based on heart rate (HR) and HRV measures, and improved classifier performance using a novel HR-based window segmentation. Approach. Single-channel ECG data...
Article
Physiological variables, such as heart rate (HR), blood pressure (BP) and respiration (RESP), are tightly regulated and coupled under healthy conditions, and a break-down in the coupling has been associated with aging and disease. We present an approach that incorporates physiological modeling within a switching linear dynamical systems (SLDS) fram...
Article
Rationale: In patients with chronic heart failure, daytime oscillatory breathing at rest is associated with a high risk of mortality. Experimental evidence, including exaggerated ventilatory responses to CO2 and prolonged circulation time, implicates the ventilatory control system and suggests feedback instability (loop gain > 1) is responsible. H...
Conference Paper
Misdosing medications with sensitive therapeutic windows, such as heparin, can place patients at unnecessary risk, increase length of hospital stay, and lead to wasted hospital resources. In this work, we present a clinician-in-the-loop sequential decision making framework, which provides an individualized dosing policy adapted to each patient's ev...
Conference Paper
Atrial fibrillation (AFib) is diagnosed by analysis of the morphological and rhythmic properties of the electrocardiogram. It was recently shown that accurate detection of AFib is possible using beat-to-beat interval variations. This raises the question of whether AFib detection can be performed using a pulsatile waveform such as the Photoplethysmo...
Article
Full-text available
Clinical data management systems typically provide caregiver teams with useful information, derived from large, sometimes highly heterogeneous, data sources that are often changing dynamically. Over the last decade there has been a significant surge in interest in using these data sources, from simply reusing the standard clinical databases for eve...
Conference Paper
Our objective in this paper was to visualize the evolution of clinical language and sentiment with respect to several common population-level categories including: time in the hospital, age, mortality, gender and race. Our analysis utilized seven years of unstructured free text notes from the Multiparameter Intelligent Monitoring in Intensive Care...
Conference Paper
In a critical care setting, shock and resuscitation end-points are often defined based on arterial blood pressure values. Patient-specific fluctuations and interactions between heart rate (HR) and blood pressure (BP), however, may provide additional prognostic value to stratify individual patients' risks for adverse outcomes at different blood pres...
Conference Paper
In this work, we propose a stacked switching vector-autoregressive (SVAR)-CNN architecture to model the changing dynamics in physiological time series for patient prognosis. The SVAR-layer extracts dynamical features (or modes) from the time-series, which are then fed into the CNN-layer to extract higher-level features representative of transition...
Article
Full-text available
Elevated loop gain, consequent to hypersensitive ventilatory control, is a primary nonanatomical cause of obstructive sleep apnoea (OSA) but it is not possible to quantify this in the clinic. Here we provide a novel method to estimate loop gain in OSA patients using routine clinical polysomnography alone. We use the concept that spontaneous ventila...
Article
Full-text available
Cardiovascular variables such as heart rate (HR) and blood pressure (BP) are regulated by an underlying control system, and therefore the time series of these vital signs exhibit rich dynamical patterns of interaction in response to external perturbations (e.g., drug administration) as well as pathological states (e.g., onset of sepsis and hypotens...
Article
Full-text available
Physiologic systems generate complex dynamics in their output signals that reflect the changing state of the underlying control systems. In this work, we used a switching vector autoregressive (switching VAR) framework to systematically learn and identify a collection of vital sign dynamics, which can possibly be recurrent within the same patient a...
Article
Model identification for physiological systems is complicated by changes between operating regimes and measurement artifacts. We present a solution to these problems by assuming that a cohort of physiological time series is generated by switching among a finite collection of physiologically-constrained dynamical models and artifactual segments. We...
Article
Full-text available
We previously published a method for measuring several traits causing OSA. The method, however, had a relatively low success rate (76%) and required modeling, potentially limiting its application. This paper presents a revision of that technique. To make the measurements, CPAP was manipulated during sleep to quantify: 1) eupneic ventilation, 2) lev...
Article
Full-text available
Modern clinical databases include time series of vital signs, which are often recorded continuously during a hospital stay. Over several days, these recordings may yield many thousands of samples. In this work, we explore the feasibility of characterizing the "state of health" of a patient using the physiological dynamics inferred from these time s...
Article
Full-text available
Cardiovascular variables such as heart rate (HR) and blood pressure (BP) are robustly regulated by an underlying control system. Time series of HR and BP exhibit distinct dynamical patterns of interaction in response to perturbations (e.g., drugs or exercise) as well as in pathological states (e.g., excessive sympathetic activation). A question of...
Article
Full-text available
The detection of change in magnitude of directional coupling between two non-linear time series is a common subject of interest in the biomedical domain, including studies involving the respiratory chemoreflex system. Although transfer entropy is a useful tool in this avenue, no study to date has investigated how different transfer entropy estimati...
Article
Full-text available
We present a nonparametric adaptive surrogate test that allows for the differentiation of statistically significant T-wave alternans (TWA) from alternating patterns that can be solely explained by the statistics of noise. The proposed test is based on estimating the distribution of noise-induced alternating patterns in a beat sequence from a set of...
Article
Full-text available
Cyclic ventilatory instabilities are widely attributed to an increase in the sensitivity or loop gain of the chemoreflex feedback loop controlling ventilation. A major limitation in the conventional characterization of this feedback loop is the need for labor-intensive methodologies. To overcome this limitation, we developed a method based on triva...
Article
Full-text available
We present an application of a modified Kalman-Filter (KF) framework for data fusion to the estimation of respiratory rate from multiple physiological sources which is robust to background noise. A novel index of the underlying signal quality of respiratory signals is presented and then used to modify the noise covariance matrix of the KF which dis...
Article
Background: T-wave alternans (TWA) activity is known to be a function of heart rate and condition, as well as perhaps physiological state. A recently published nonparametric nonstationary TWA analysis method has been shown to reject nonstationary noise accurately using phase-randomized surrogates and has been shown to estimate TWA accurately. This...
Article
Full-text available
We present generalizations of our previously published artificial models for generating multi-channel ECG to provide simulations of abnormal cardiac rhythms. Using a three-dimensional vectorcardiogram (VCG) formulation, we generate the normal cardiac dipole for a patient using a sum of Gaussian kernels, fitted to real VCG recordings. Abnormal beats...
Article
In this paper, a support vector machine (SVM) classifier was designed to identify tornado vortices based on their characteristics that were determined from the Doppler spectra and eigenvalues that were calculated from the data that were collected in the vicinity of these vortices. To collect these data, weather surveillance radar (WSR-88D) was empl...
Article
We describe an open source algorithm suite for T-Wave Alternans (TWA) detection and quantification. The software consists of Matlab implementations of the widely used Spectral Method and Modified Moving Average with libraries to read both WFDB and ASCII data under windows and Linux. The software suite can run in both batch mode and with a provided...
Article
Full-text available
We present generalizations of our previously published artificial models for generating multi-channel ECG so that the simulation of abnormal rhythms is possible. Using a three-dimensional vectorcardiogram (VCG) formulation, we generate the normal cardiac dipole for a patient using a sum of Gaussian kernels, fitted to real VCG recordings. Abnormal b...
Article
Tornado vortices observed from Doppler radars are often associated with strong azimuthal shear and Doppler spectra that are wide and flattened. The current operational tornado detection algorithm (TDA) primarily searches for shear signatures that are larger than the predefined thresholds. In this work, a tornado detection procedure based on a fuzzy...
Article
Full-text available
One of the essential components of a neuromotor prosthetic device is a neural decoder that translates the activity of a set of neurons into an estimate of the intended movement of the prosthetic limb. Wiener filter style approaches model this transformation as a linear function of the number of spikes observed from a set of neurons and over a range...
Article
Full-text available
Quite recently, it has become possible to use signals recorded simultaneously from large numbers of cortical neurons for real-time control. Such brain machine interfaces (BMIs) have allowed animal subjects and human patients to control the position of a computer cursor or robotic limb under the guidance of visual feedback. Although impressive, such...
Article
The research Weather Surveillance Radar-1988 Doppler locally operated by the National Severe Storms Laboratory in Norman, OK, has the unique capability of collecting massive volumes of Level I time-series data over many hours, which provides a rich environment for evaluating our new postprocessing algorithms. In this letter, an approach of identify...
Conference Paper
Full-text available
The research WSR-88D (weather surveillance radar) locally operated by the National Severe Storm Laboratory (NSSL) in Norman has the unique capability of collecting massive volumes of Level I time series data over many hours which provides a rich environment for evaluating our new post-processing algorithms. In this work, a Support Vector Machine (S...
Conference Paper
This paper describes a new visual target tracking algorithm which can be applied to intelligent video surveillance systems. We model the target under track as a nonlinear switching dynamic system, which is often referred as a jump Markov process. More specifically, we assume the target operates according to one dynamic model from a finite set of hy...
Conference Paper
Full-text available
In this paper, we present a new particle filtering (PF) algorithm for visual target tracking where Galerkin's projection method is used to generate the proposal distribution. Galerkin's method is a numerical approach to approximate the solution of a partial differential equation (PDE). By leveraging this method in concert with L<sup>2</sup> theory...
Conference Paper
A summary of results from linear algebra pertaining to orthogonal projections onto subspaces of an inner product space is presented. A formal definition and a sufficient condition for the existence of a fractional transform given a unitary periodic operator is given. Next, using an orthogonal projection formula the class of weighted discrete fracti...
Article
Enhanced tornado detection and tracking can prevent loss of life and property damage. The research weather surveillance radar (WSR)-88D locally operated by the National Severe Storms Laboratory (NSSL) in Norman, OK, has the unique capability of collecting massive volumes of time-series data over many hours, which provides a rich environment for eva...
Conference Paper
Remote sensing radar has shown to be an important tool to observe severe and hazardous weather and to provide operational forecasters prompt information of such rapidly evolving phenomena. Although the history of tornado measurements is long, there have been only a few successes in obtaining spectral signatures. This is largely because neither the...

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