scholarly journals SleepPy: A python package for sleep analysis from accelerometer data

2019 ◽  
Vol 4 (44) ◽  
pp. 1663
Author(s):  
Yiorgos Christakis ◽  
Nikhil Mahadevan ◽  
Shyamal Patel
Keyword(s):  
Accelerometer Data ◽  
Sleep Analysis ◽  
Python Package

scholarly journals DPSleep: Open-Source Longitudinal Sleep Analysis From Accelerometer Data (Preprint)

10.2196/29849 ◽  
2021 ◽  
Author(s):  
Habiballah Rahimi-Eichi ◽  
Garth Coombs 3rd ◽  
Constanza M. Vidal Bustamante ◽  
Jukka-Pekka Onnela ◽  
Justin T. Baker ◽  
...  
Keyword(s):  
Open Source ◽  
Accelerometer Data ◽  
Sleep Analysis

DPSleep: Open-Source Longitudinal Sleep Analysis From Accelerometer Data (Preprint)

2021 ◽  
Author(s):  
Habiballah Rahimi-Eichi ◽  
Garth Coombs 3rd ◽  
Constanza M. Vidal Bustamante ◽  
Jukka-Pekka Onnela ◽  
Justin T. Baker ◽  
...  
Keyword(s):  
Open Source ◽  
Self Report ◽  
Activity Levels ◽  
Accelerometer Data ◽  
Time Zone ◽  
Sleep Episode ◽  
Sleep Timing ◽  
Sleep Analysis ◽  
Smartphone Use ◽  
Deep Phenotyping

UNSTRUCTURED Wearable devices are now widely available to collect continuous objective behavioral data from individuals and to measure sleep. Here we introduce an open-source pipeline for the deep phenotyping of sleep, "DPSleep", that uses algorithms to detect missing data, calculate activity levels, and finally estimate the major Sleep Episode onset and offset. The pipeline allows for manual quality control adjustment and correction for time zone changes. We illustrate the utility of the pipeline with data from participants studied for more than 200 days. Actigraphy-based measures of sleep duration are associated with self-report rating of sleep quality. Simultaneous measures of smartphone use and GPS data support the sleep timing inferences and reveal how phone measures of sleep can differ from actigraphy data. We discuss the uses of DPSleep in relation to other available sleep estimation approaches and provide example use cases that include multi-dimensional, deep dynamic longitudinal phenotyping associated with mental illness.

The Effect of Sensor Placement and Number on Physical Activity Recognition and Energy Expenditure Estimation (Preprint)

2020 ◽  
Author(s):  
Anis Davoudi ◽  
Mamoun T. Mardini ◽  
Dave Nelson ◽  
Fahd Albinali ◽  
Sanjay Ranka ◽  
...  
Keyword(s):  
Physical Activity ◽  
Older Adults ◽  
Energy Expenditure ◽  
Activity Recognition ◽  
Recognition Accuracy ◽  
Body Position ◽  
Computer Work ◽  
Accelerometer Data ◽  
Upper Arm ◽  
Lifestyle Activities

BACKGROUND Research shows the feasibility of human activity recognition using Wearable accelerometer devices. Different studies have used varying number and placement for data collection using the sensors. OBJECTIVE To compare accuracy performance between multiple and variable placement of accelerometer devices in categorizing the type of physical activity and corresponding energy expenditure in older adults. METHODS Participants (n=93, 72.2±7.1 yrs) completed a total of 32 activities of daily life in a laboratory setting. Activities were classified as sedentary vs. non-sedentary, locomotion vs. non-locomotion, and lifestyle vs. non-lifestyle activities (e.g. leisure walk vs. computer work). A portable metabolic unit was worn during each activity to measure metabolic equivalents (METs). Accelerometers were placed on five different body positions: wrist, hip, ankle, upper arm, and thigh. Accelerometer data from each body position and combinations of positions were used in developing Random Forest models to assess activity category recognition accuracy and MET estimation. RESULTS Model performance for both MET estimation and activity category recognition strengthened with additional accelerometer devices. However, a single accelerometer on the ankle, upper arm, hip, thigh, or wrist had only a 0.03 to 0.09 MET increase in prediction error as compared to wearing all five devices. Balanced accuracy showed similar trends with slight decreases in balanced accuracy for detection of locomotion (0-0.01 METs), sedentary (0.13-0.05 METs) and lifestyle activities (0.08-0.04 METs) compared to all five placements. The accuracy of recognizing activity categories increased with additional placements (0.15-0.29). Notably, the hip was the best single body position for MET estimation and activity category recognition. CONCLUSIONS Additional accelerometer devices only slightly enhance activity recognition accuracy and MET estimation in older adults. However, given the extra burden of wearing additional devices, single accelerometers with appropriate placement appear to be sufficient for estimating energy expenditure and activity category recognition in older adults.

scholarly journals Identifying resting locations of a small elusive forest carnivore using a two-stage model accounting for GPS measurement error and hidden behavioral states

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dalton J. Hance ◽  
Katie M. Moriarty ◽  
Bruce A. Hollen ◽  
Russell W. Perry
Keyword(s):  
Time Series ◽  
Measurement Error ◽  
Gaussian State ◽  
Parameter Estimates ◽  
Accelerometer Data ◽  
Two Stage ◽  
Location Data ◽  
Gps Measurement ◽  
Activity Measurements ◽  
Behavioral States

Abstract Background Studies of animal movement using location data are often faced with two challenges. First, time series of animal locations are likely to arise from multiple behavioral states (e.g., directed movement, resting) that cannot be observed directly. Second, location data can be affected by measurement error, including failed location fixes. Simultaneously addressing both problems in a single statistical model is analytically and computationally challenging. To both separate behavioral states and account for measurement error, we used a two-stage modeling approach to identify resting locations of fishers (Pekania pennanti) based on GPS and accelerometer data. Methods We developed a two-stage modelling approach to estimate when and where GPS-collared fishers were resting for 21 separate collar deployments on 9 individuals in southern Oregon. For each deployment, we first fit independent hidden Markov models (HMMs) to the time series of accelerometer-derived activity measurements and apparent step lengths to identify periods of movement and resting. Treating the state assignments as given, we next fit a set of linear Gaussian state space models (SSMs) to estimate the location of each resting event. Results Parameter estimates were similar across collar deployments. The HMMs successfully identified periods of resting and movement with posterior state assignment probabilities greater than 0.95 for 97% of all observations. On average, fishers were in the resting state 63% of the time. Rest events averaged 5 h (4.3 SD) and occurred most often at night. The SSMs allowed us to estimate the 95% credible ellipses with a median area of 0.12 ha for 3772 unique rest events. We identified 1176 geographically distinct rest locations; 13% of locations were used on > 1 occasion and 5% were used by > 1 fisher. Females and males traveled an average of 6.7 (3.5 SD) and 7.7 (6.8 SD) km/day, respectively. Conclusions We demonstrated that if auxiliary data are available (e.g., accelerometer data), a two-stage approach can successfully resolve both problems of latent behavioral states and GPS measurement error. Our relatively simple two-stage method is repeatable, computationally efficient, and yields directly interpretable estimates of resting site locations that can be used to guide conservation decisions.

scholarly journals Automatic Identification of Upper Extremity Rehabilitation Exercise Type and Dose Using Body-Worn Sensors and Machine Learning: A Pilot Study

2021 ◽  
pp. 158-166
Author(s):  
Noah Balestra ◽  
Gaurav Sharma ◽  
Linda M. Riek ◽  
Ania Busza
Keyword(s):  
Machine Learning ◽  
Upper Extremity ◽  
Sensor Data ◽  
Inpatient Setting ◽  
Accelerometer Data ◽  
Data Set ◽  
Machine Learning Classification ◽  
Exercise Type ◽  
Exercise Dose ◽  
Rehabilitation Exercises

<b><i>Background:</i></b> Prior studies suggest that participation in rehabilitation exercises improves motor function poststroke; however, studies on optimal exercise dose and timing have been limited by the technical challenge of quantifying exercise activities over multiple days. <b><i>Objectives:</i></b> The objectives of this study were to assess the feasibility of using body-worn sensors to track rehabilitation exercises in the inpatient setting and investigate which recording parameters and data analysis strategies are sufficient for accurately identifying and counting exercise repetitions. <b><i>Methods:</i></b> MC10 BioStampRC® sensors were used to measure accelerometer and gyroscope data from upper extremities of healthy controls (<i>n</i> = 13) and individuals with upper extremity weakness due to recent stroke (<i>n</i> = 13) while the subjects performed 3 preselected arm exercises. Sensor data were then labeled by exercise type and this labeled data set was used to train a machine learning classification algorithm for identifying exercise type. The machine learning algorithm and a peak-finding algorithm were used to count exercise repetitions in non-labeled data sets. <b><i>Results:</i></b> We achieved a repetition counting accuracy of 95.6% overall, and 95.0% in patients with upper extremity weakness due to stroke when using both accelerometer and gyroscope data. Accuracy was decreased when using fewer sensors or using accelerometer data alone. <b><i>Conclusions:</i></b> Our exploratory study suggests that body-worn sensor systems are technically feasible, well tolerated in subjects with recent stroke, and may ultimately be useful for developing a system to measure total exercise “dose” in poststroke patients during clinical rehabilitation or clinical trials.

scholarly journals GriSPy: A Python package for fixed-radius nearest neighbors search

2020 ◽  
pp. 100443
Author(s):  
M. Chalela ◽  
E. Sillero ◽  
L. Pereyra ◽  
M.A. Garcia ◽  
J.B. Cabral ◽  
...  
Keyword(s):  
Nearest Neighbors ◽  
Fixed Radius ◽  
Python Package

scholarly journals Detection of foraging behavior from accelerometer data using U-Net type convolutional networks

2021 ◽  
pp. 101275
Author(s):  
Mạnh Cường Ngô ◽  
Raghavendra Selvan ◽  
Outi Tervo ◽  
Mads Peter Heide-Jørgensen ◽  
Susanne Ditlevsen
Keyword(s):  
Foraging Behavior ◽  
Accelerometer Data ◽  
Convolutional Networks
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