An Open-Source Feature Extraction Tool for the Analysis of Peripheral Physiological Data

Publication guidelines for human heart rate and heart rate variability studies in psychophysiology-Part 1: Physiological underpinnings and foundations of measurement

This Committee Report provides methodological, interpretive, and reporting guidance for researchers who use measures of heart rate (HR) and heart rate variability (HRV) in psychophysiological research. We provide brief summaries of best practices in measuring HR and HRV via electrocardiographic and photoplethysmographic signals in laboratory, field (ambulatory), and brain-imaging contexts to address research questions incorporating measures of HR and HRV. The Report emphasizes evidence for the strengths and weaknesses of different recording and derivation methods for measures of HR and HRV. Along with this guidance, the Report reviews what is known about the origin of the heartbeat and its neural control, including factors that produce and influence HRV metrics. The Report concludes with checklists to guide authors in study design and analysis considerations, as well as guidance on the reporting of key methodological details and characteristics of the samples under study. It is expected that rigorous and transparent recording and reporting of HR and HRV measures will strengthen inferences across the many applications of these metrics in psychophysiology. The prior Committee Reports on HR and HRV are several decades old. Since their appearance, technologies for human cardiac and vascular monitoring in laboratory and daily life (i.e., ambulatory) contexts have greatly expanded. This Committee Report was prepared for the Society for Psychophysiological Research to provide updated methodological and interpretive guidance, as well as to summarize best practices for reporting HR and HRV studies in humans.

QRS detection in single-lead, telehealth electrocardiogram signals: Benchmarking open-source algorithms

BACKGROUND AND OBJECTIVES

A key step in electrocardiogram (ECG) analysis is the detection of QRS complexes, particularly for arrhythmia detection. Telehealth ECGs present a new challenge for automated analysis as they are noisier than traditional clinical ECGs. The aim of this study was to identify the best-performing open-source QRS detector for use with telehealth ECGs.

METHODS

The performance of 18 open-source QRS detectors was assessed on six datasets. These included four datasets of ECGs collected under supervision, and two datasets of telehealth ECGs collected without clinical supervision. The telehealth ECGs, consisting of single-lead ECGs recorded between the hands, included a novel dataset of 479 ECGs collected in the SAFER study of screening for atrial fibrillation (AF). Performance was assessed against manual annotations.

RESULTS

A total of 12 QRS detectors performed well on ECGs collected under clinical supervision (F1 score ≥0.96). However, fewer performed well on telehealth ECGs: five performed well on the TELE ECG Database; six performed well on high-quality SAFER data; and performance was poorer on low-quality SAFER data (three QRS detectors achieved F1 of 0.78-0.84). The presence of AF had little impact on performance.

CONCLUSIONS

The Neurokit and University of New South Wales QRS detectors performed best in this study. These performed sufficiently well on high-quality telehealth ECGs, but not on low-quality ECGs. This demonstrates the need to handle low-quality ECGs appropriately to ensure only ECGs which can be accurately analysed are used for clinical decision making.

Beyond the Game: Multimodal Emotion Recognition Before, During, and After Gameplay

In the era of Human-Computer Interaction (HCI), understanding emotional responses through multimodal signals during interactive experiences, such as serious games (SG), is of high importance. In this work, we explore emotion recognition (ER) by analyzing multimodal data from the 2nd Study in Bio-Reactions and Faces for Emotion-based Personalization for AI Systems (BIRAFFE-2) dataset, including data from 76 participants engaged in dynamic gameplay and pre-post audiovisual stimulations. Utilizing features derived from electrocardiogram (ECG), electrodermal activity (EDA), accelerometer, gyroscope, game logs (GL), affect dynamics and personality traits (PT) fed in different machine learning models, our study focuses on ER, achieving state-of-the-art performance across different experimental scenarios (accuracy: 0.967 for Negative Affect in Optimal Game using Support Vector Machines). This highlights the importance of emotional states as indicators for personalized HCI. Our approach offers valuable insights to understanding the interplay between multimodal physiological signals, GL, user's emotional states and PT, which could add to the design of adaptive, affect-sensitive SG. Distinct patterns in the data are revealed, particularly emphasizing the role of ECG-Derived Respiration features and the impact of past affectivity to current emotional state.Clinical relevance-By introducing innovative perspectives in affect-sensitive SG design, leveraging the analysis of multimodal signals, we foresee objective digital biomarkers that hold promise to broaden the clinical understanding of patients' emotional behavior during SG-based interventions.

Automated Heart Rate Detection in Seismocardiograms Using Electrocardiogram-Based Algorithms-A Feasibility Study

In recent decades, much work has been implemented in heart rate (HR) analysis using electrocardiographic (ECG) signals. We propose that algorithms developed to calculate HR based on detected R-peaks using ECG can be applied to seismocardiographic (SCG) signals, as they utilize common knowledge regarding heart rhythm and its underlying physiology. We implemented the experimental framework with methods developed for ECG signal processing and peak detection to be applied and evaluated on SCGs. Furthermore, we assessed and chose the best from all combinations of 15 peak detection and 6 preprocessing methods from the literature on the CEBS dataset available on Physionet. We then collected experimental data in the lab experiment to measure the applicability of the best-selected technique to the real-world data; the abovementioned method showed high precision for signals recorded during sitting rest (HR difference between SCG and ECG: 0.12 ± 0.35 bpm) and a moderate precision for signals recorded with interfering physical activity-reading out a book loud (HR difference between SCG and ECG: 6.45 ± 3.01 bpm) when compared to the results derived from the state-of-the-art photoplethysmographic (PPG) methods described in the literature. The study shows that computationally simple preprocessing and peak detection techniques initially developed for ECG could be utilized as the basis for HR detection on SCG, although they can be further improved.

PPG and EDA dataset collected with Empatica E4 for stress assessment

In response to challenging circumstances, the human body can experience marked levels of anxiety and distress. Wearable devices offer a means of real-time and ongoing data collection, facilitating personalized stress monitoring. Therefore, we collected physiological signals (blood pressure volume and electrodermal activities), using Empatica E4, from 29 subjects. A personalized protocol was developed to cause cognitive, mental, and psychological stressors since they are the ones that can be experienced in working or academic environment. We also propose a pipeline to clean and process these two signals to maximize the quality of further analysis. This study aids in the comprehension of the complex connection between stress and working situations by offering a sizable dataset made up of different physiological data. It additionally enables them to create cutting-edge stress-reduction techniques and improving professional achievement while lessening the negative impact of stress on welfare.

Completing the Cabrera Circle: deriving adaptable leads from ECG limb leads by combining constraints with a correction factor

Objective.We present a concept for processing 6-lead electrocardiography (ECG) signals which can be applied to various use cases in quantitative electrocardiography.Approach.Our work builds upon the mathematics of the well-known Cabrera sequence which is a re-sorting of the six limb leads (I,II,III,aVR,aVL,aVF) into a clockwise and physiologically-interpretable order. By deriving correction factors for harmonizing lead strengths and choosing an appropriate basis for the leads, we extend this concept towards what we call the 'Cabrera Circle' based on a mathematically sound foundation.Main results.To demonstrate the practical effectiveness and relevance of this concept, we analyze its suitability for deriving interpolated leads between the six limb leads and a 'radial' lead which both can be useful for specific use cases. We focus on the use cases of i) determination of the electrical heart axis by proposing a novel interactive tool for reconstructing the heart's vector loop and ii) improving accuracy in time of automatic R-wave detection and T-wave delineation in 6-lead ECG. For the first use case, we derive an equation which allows projections of the 2-dimensional vector loops to arbitrary angles of the Cabrera Circle. For the second use case, we apply several state-of-the-art algorithms to a freely-available 12-lead dataset (Lobachevsky University Database). Out-of-the-box results show that the derived radial lead outperforms the other limb leads (I,II,III,aVR,aVL,aVF) by improving F1 scores of R-peak and T-peak detection by 0.61 and 2.12, respectively. Results of on- and offset computations are also improved but on a smaller scale.Significance.In summary, the Cabrera Circle offers a methodology that might be useful for quantitative electrocardiography of the 6-lead subsystem-especially in the digital age.

Multimodal, Idiographic Ambulatory Sensing Will Transform our Understanding of Emotion

Emotions are inherently complex - situated inside the brain while being influenced by conditions inside the body and outside in the world - resulting in substantial variation in experience. Most studies, however, are not designed to sufficiently sample this variation. In this paper, we discuss what could be discovered if emotion were systematically studied within persons 'in the wild', using biologically-triggered experience sampling: a multimodal and deeply idiographic approach to ambulatory sensing that links body and mind across contexts and over time. We outline the rationale for this approach, discuss challenges to its implementation and widespread adoption, and set out opportunities for innovation afforded by emerging technologies. Implementing these innovations will enrich method and theory at the frontier of affective science, propelling the contextually situated study of emotion into the future.

Integration of MRI and somatosensory evoked potentials facilitate diagnosis of spinal cord compression

This study aimed to integrate magnetic resonance imaging (MRI) and related somatosensory evoked potential (SSEP) features to assist in the diagnosis of spinal cord compression (SCC). MRI scans were graded from 0 to 3 according to the changes in the subarachnoid space and scan signals to confirm differences in SCC levels. The amplitude, latency, and time-frequency analysis (TFA) power of preoperative SSEP features were extracted and the changes were used as standard judgments to detect neurological function changes. Then the patient distribution was quantified according to the SSEP feature changes under the same and different MRI compression grades. Significant differences were found in the amplitude and TFA power between MRI grades. We estimated three degrees of amplitude anomalies and power loss under each MRI grade and found the presence or absence of power loss occurs after abnormal changes in amplitude only. For SCC, few integrated approach combines the advantages of both MRI and evoked potentials. However, integrating the amplitude and TFA power changes of SSEP features with MRI grading can help in the diagnosis and speculate progression of SCC.

A Method for Stress Detection Using Empatica E4 Bracelet and Machine-Learning Techniques

In response to challenging circumstances, the human body can experience marked levels of anxiety and distress. To prevent stress-related complications, timely identification of stress symptoms is crucial, necessitating the need for continuous stress monitoring. Wearable devices offer a means of real-time and ongoing data collection, facilitating personalized stress monitoring. Based on our protocol for data pre-processing, this study proposes to analyze signals obtained from the Empatica E4 bracelet using machine-learning algorithms (Random Forest, SVM, and Logistic Regression) to determine the efficacy of the abovementioned techniques in differentiating between stressful and non-stressful situations. Photoplethysmographic and electrodermal activity signals were collected from 29 subjects to extract 27 features which were then fed into three different machine-learning algorithms for binary classification. Using MATLAB after applying the chi-square test and Pearson's correlation coefficient on WEKA for features' importance ranking, the results demonstrated that the Random Forest model has the highest stability (accuracy of 76.5%) using all the features. Moreover, the Random Forest applying the chi-test for feature selection reached consistent results in terms of stress evaluation based on precision, recall, and F1-measure (71%, 60%, 65%, respectively).

A New Method of Identifying Characteristic Points in the Impedance Cardiography Signal Based on Empirical Mode Decomposition

The accurate detection of fiducial points in the impedance cardiography signal (ICG) has a decisive impact on the proper estimation of diagnostic parameters such as stroke volume or cardiac output. It is, therefore, necessary to find an algorithm that is able to assess their positions with great precision. The solution to this problem is, however, quite challenging with regard to the high sensitivity of the ICG technique to the noise and varying morphology of the acquired signals. The aim of this study is to propose a novel method that allows us to overcome these limitations. The developed algorithm is based on Empirical Mode Decomposition (EMD)-an effective technique for processing and analyzing various types of non-stationary signals. We find high correlations between the results obtained from the algorithm and annotated by an expert. This, in turn, implies that the difference in estimation of the diagnostic-relevant parameters is small, which suggests that the method can automatically provide precise clinical information.

Data-driven approach for automatic detection of aortic valve opening: B point detection from impedance cardiogram

Pre-ejection period (PEP), an indicator of sympathetic nervous system activity, is useful in psychophysiology and cardiovascular studies. Accurate PEP measurement is challenging and relies on robust identification of the timing of aortic valve opening, marked as the B point on impedance cardiogram (ICG) signals. The ICG sensitivity to noise and its waveform's morphological variability makes automated B point detection difficult, requiring inefficient and cumbersome expert visual annotation. In this article, we propose a machine learning-based automated algorithm to detect the aortic valve opening for PEP measurement, which is robust against noise and ICG morphological variations. We analyzed over 60 hr of synchronized ECG and ICG records from 189 subjects. A total of 3657 averaged beats were formed using our recently developed ICG noise removal algorithm. Features such as the averaged ICG waveform, its first and second derivatives, as well as high-level morphological and critical hemodynamic parameters were extracted and fed into the regression algorithms to estimate the B point location. The morphological features were extracted from our proposed "variable" physiologically valid search-window related to diverse B point shapes. A subject-wise nested cross-validation procedure was performed for parameter tuning and model assessment. After examining multiple regression models, Adaboost was selected, which demonstrated superior performance and higher robustness to five state-of-the-art algorithms that were evaluated in terms of low mean absolute error of 3.5 ms, low median absolute error of 0.0 ms, high correlation with experts' estimates (Pearson coefficient = 0.9), and low standard deviation of errors of 9.2 ms. For reproducibility, an open-source toolbox is provided.

Timing errors and temporal uncertainty in clinical databases-A narrative review

A firm concept of time is essential for establishing causality in a clinical setting. Review of critical incidents and generation of study hypotheses require a robust understanding of the sequence of events but conducting such work can be problematic when timestamps are recorded by independent and unsynchronized clocks. Most clinical models implicitly assume that timestamps have been measured accurately and precisely, but this custom will need to be re-evaluated if our algorithms and models are to make meaningful use of higher frequency physiological data sources. In this narrative review we explore factors that can result in timestamps being erroneously recorded in a clinical setting, with particular focus on systems that may be present in a critical care unit. We discuss how clocks, medical devices, data storage systems, algorithmic effects, human factors, and other external systems may affect the accuracy and precision of recorded timestamps. The concept of temporal uncertainty is introduced, and a holistic approach to timing accuracy, precision, and uncertainty is proposed. This quantitative approach to modeling temporal uncertainty provides a basis to achieve enhanced model generalizability and improved analytical outcomes.

PulseLab: An Integrated and Expandable Toolbox for Pulse Wave Velocity-based Blood Pressure Estimation

In this paper, we introduce PulseLab, a comprehensive MATLAB toolbox that enables estimating the blood pressure (BP) from electrocardiogram (ECG) and photoplethysmogram (PPG) signals using pulse wave velocity (PWV)-based models. This universal framework consists of 6 sequential modules, covering end-to-end procedures that are needed for estimating BP from raw PPG/ECG data. These modules are "dataset formation", "signal pre-processing", "segmentation", "characteristic-points detection", "pulse transit time (PTT)/ pulse arrival time (PAT) calculation", and "model validation". The toolbox is expandable and its application programming interface (API) is built such that newly-derived PWV-BP models can be easily included. The toolbox also includes a user-friendly graphical user interface (GUI) offering visualization for step-by-step processing of physiological signals, position of characteristic points, PAT/PTT values, and the BP regression results. To the best of our knowledge, PulseLab is the first comprehensive toolbox that enables users to optimize their model by considering several factors along the process for obtaining the most accurate model for cuff-less BP estimation.

FLIRT: A feature generation toolkit for wearable data

BACKGROUND AND OBJECTIVE

Researchers use wearable sensing data and machine learning (ML) models to predict various health and behavioral outcomes. However, sensor data from commercial wearables are prone to noise, missing, or artifacts. Even with the recent interest in deploying commercial wearables for long-term studies, there does not exist a standardized way to process the raw sensor data and researchers often use highly specific functions to preprocess, clean, normalize, and compute features. This leads to a lack of uniformity and reproducibility across different studies, making it difficult to compare results. To overcome these issues, we present FLIRT: A Feature Generation Toolkit for Wearable Data; it is an open-source Python package that focuses on processing physiological data specifically from commercial wearables with all its challenges from data cleaning to feature extraction.

METHODS

FLIRT leverages a variety of state-of-the-art algorithms (e.g., particle filters, ML-based artifact detection) to ensure a robust preprocessing of physiological data from wearables. In a subsequent step, FLIRT utilizes a sliding-window approach and calculates a feature vector of more than 100 dimensions - a basis for a wide variety of ML algorithms.

RESULTS

We evaluated FLIRT on the publicly available WESAD dataset, which focuses on stress detection with an Empatica E4 wearable. Preprocessing the data with FLIRT ensures that unintended noise and artifacts are appropriately filtered. In the classification task, FLIRT outperforms the preprocessing baseline of the original WESAD paper.

CONCLUSION

FLIRT provides functionalities beyond existing packages that can address unmet needs in physiological data processing and feature generation: (a) integrated handling of common wearable file formats (e.g., Empatica E4 archives), (b) robust preprocessing, and (c) standardized feature generation that ensures reproducibility of results. Nevertheless, while FLIRT comes with a default configuration to accommodate most situations, it offers a highly configurable interface for all of its implemented algorithms to account for specific needs.

ReBeatICG: Real-time Low-Complexity Beat-to-beat Impedance Cardiogram Delineation Algorithm

This work presents ReBeatICG, a real-time, low-complexity beat-to-beat impedance cardiography (ICG) delineation algorithm that allows hemodynamic parameters monitoring. The proposed procedure relies only on the ICG signal compared to most algorithms found in the literature that rely on synchronous electrocardiogram signal (ECG) recordings. ReBeatICG was designed with implementation on an ultra-low-power microcontroller (MCU) in mind. The detection accuracy of the developed algorithm is tested against points manually labeled by cardiologists. It achieves a detection Gmean accuracy of 94.9%, 98.6%, 90.3%, and 84.3% for the B, C, X, and O characteristic points, respectively. Furthermore, several hemodynamic parameters were calculated based on annotated characteristic points and compared with values generated from the cardiologists' annotations. ReBeatICG achieved mean error rates of 0.11 ms, 9.72 ms, 8.32 ms, and 3.97% for HR, LVET, IVRT, and relative C-point amplitude, respectively.

Investigating the relationship between emotional granularity and cardiorespiratory physiological activity in daily life

Emotional granularity describes the ability to create emotional experiences that are precise and context-specific. Despite growing evidence of a link between emotional granularity and mental health, the physiological correlates of granularity have been under-investigated. This study explored the relationship between granularity and cardiorespiratory physiological activity in everyday life, with particular reference to the role of respiratory sinus arrhythmia (RSA), an estimate of vagal influence on the heart often associated with positive mental and physical health outcomes. Participants completed a physiologically triggered experience-sampling protocol including ambulatory recording of electrocardiogram, impedance cardiogram, movement, and posture. At each prompt, participants generated emotion labels to describe their current experience. In an end-of-day survey, participants elaborated on each prompt by rating the intensity of their experience on a standard set of emotion adjectives. Consistent with our hypotheses, individuals with higher granularity exhibited a larger number of distinct patterns of physiological activity during seated rest, and more situationally precise patterns of activity during emotional events: granularity was positively correlated with the number of clusters of cardiorespiratory physiological activity discovered in seated rest data, as well as with the performance of classifiers trained on event-related changes in physiological activity. Granularity was also positively associated with RSA during seated rest periods, although this relationship did not reach significance in this sample. These findings are consistent with constructionist accounts of emotion that propose concepts as a key mechanism underlying individual differences in emotional experience, physiological regulation, and physical health.

Context-aware experience sampling reveals the scale of variation in affective experience

Emotion research typically searches for consistency and specificity in physiological activity across instances of an emotion category, such as anger or fear, yet studies to date have observed more variation than expected. In the present study, we adopt an alternative approach, searching inductively for structure within variation, both within and across participants. Following a novel, physiologically-triggered experience sampling procedure, participants' self-reports and peripheral physiological activity were recorded when substantial changes in cardiac activity occurred in the absence of movement. Unsupervised clustering analyses revealed variability in the number and nature of patterns of physiological activity that recurred within individuals, as well as in the affect ratings and emotion labels associated with each pattern. There were also broad patterns that recurred across individuals. These findings support a constructionist account of emotion which, drawing on Darwin, proposes that emotion categories are populations of variable instances tied to situation-specific needs.

PaWFE: Fast Signal Feature Extraction Using Parallel Time Windows

Motivation: Hand amputations can dramatically affect the quality of life of a person. Researchers are developing surface electromyography and machine learning solutions to control dexterous and robotic prosthetic hands, however long computational times can slow down this process.

Objective: This paper aims at creating a fast signal feature extraction algorithm that can extract widely used features and allow researchers to easily add new ones.

Methods: PaWFE (Parallel Window Feature Extractor) extracts the signal features from several time windows in parallel. The MATLAB code is publicly available and supports several time domain and frequency features. The code was tested and benchmarked using 1,2,4,8,16,32, and 48 threads on a server with four Xeon E7- 4820 and 128 GB RAM using the first 5 datasets of the Ninapro database, that are recorded with different acquisition setups.

Results: The parallel time window analysis approach allows to reduce the computational time up to 20 times when using 32 cores, showing a very good scalability. Signal features can be extracted in few seconds from an entire data acquisition and in <100 ms from a single time window, easily reducing of up to over 15 times the feature extraction procedure in comparison to traditional approaches. The code allows users to easily add new signal feature extraction scripts, that can be added to the code and on the Ninapro website upon request.

Significance: The code allows researchers in machine learning and biosignals data analysis to easily and quickly test modern machine learning approaches on big datasets and it can be used as a resource for real time data analysis too.