scholarly journals On the Calculation of Sample Entropy Using Continuous and Discrete Human Gait Data

Entropy ◽  
2018 ◽  
Vol 20 (10) ◽  
pp. 764 ◽  
Author(s):  
John McCamley ◽  
William Denton ◽  
Andrew Arnold ◽  
Peter Raffalt ◽  
Jennifer Yentes
Keyword(s):  
Range Of Motion ◽  
Sampling Rate ◽  
Discrete Data ◽  
Sample Entropy ◽  
Biological Data ◽  
Human Gait ◽  
Joint Angles ◽  
Data Types ◽  
Data Points ◽  
Differential Relationship

Sample entropy (SE) has relative consistency using biologically-derived, discrete data >500 data points. For certain populations, collecting this quantity is not feasible and continuous data has been used. The effect of using continuous versus discrete data on SE is unknown, nor are the relative effects of sampling rate and input parameters m (comparison vector length) and r (tolerance). Eleven subjects walked for 10-minutes and continuous joint angles (480 Hz) were calculated for each lower-extremity joint. Data were downsampled (240, 120, 60 Hz) and discrete range-of-motion was calculated. SE was quantified for angles and range-of-motion at all sampling rates and multiple combinations of parameters. A differential relationship between joints was observed between range-of-motion and joint angles. Range-of-motion SE showed no difference; whereas, joint angle SE significantly decreased from ankle to knee to hip. To confirm findings from biological data, continuous signals with manipulations to frequency, amplitude, and both were generated and underwent similar analysis to the biological data. In general, changes to m, r, and sampling rate had a greater effect on continuous compared to discrete data. Discrete data was robust to sampling rate and m. It is recommended that different data types not be compared and discrete data be used for SE.

scholarly journals Sample Entropy of Human Gait Center of Pressure Displacement: A Systematic Methodological Analysis

Entropy ◽  
2018 ◽  
Vol 20 (8) ◽  
pp. 579 ◽  
Author(s):  
Samira Ahmadi ◽  
Nariman Sepehri ◽  
Christine Wu ◽  
Tony Szturm
Keyword(s):  
Time Series Data ◽  
Inertial Sensors ◽  
Center Of Pressure ◽  
Sampling Rate ◽  
Sample Entropy ◽  
Human Gait ◽  
Series Data ◽  
Low Pass ◽  
Data Points ◽  
Parameter Values

Sample entropy (SampEn) has been used to quantify the regularity or predictability of human gait signals. There are studies on the appropriate use of this measure for inter-stride spatio-temporal gait variables. However, the sensitivity of this measure to preprocessing of the signal and to variant values of template size (m), tolerance size (r), and sampling rate has not been studied when applied to “whole” gait signals. Whole gait signals are the entire time series data obtained from force or inertial sensors. This study systematically investigates the sensitivity of SampEn of the center of pressure displacement in the mediolateral direction (ML COP-D) to variant parameter values and two pre-processing methods. These two methods are filtering the high-frequency components and resampling the signals to have the same average number of data points per stride. The discriminatory ability of SampEn is studied by comparing treadmill walk only (WO) to dual-task (DT) condition. The results suggest that SampEn maintains the directional difference between two walking conditions across variant parameter values, showing a significant increase from WO to DT condition, especially when signals are low-pass filtered. Moreover, when gait speed is different between test conditions, signals should be low-pass filtered and resampled to have the same average number of data points per stride.

scholarly journals HeatMapViewer: interactive display of 2D data in biology

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 48 ◽  
Author(s):  
Guy Yachdav ◽  
Maximilian Hecht ◽  
Metsada Pasmanik-Chor ◽  
Adva Yeheskel ◽  
Burkhard Rost
Keyword(s):  
Web Applications ◽  
Biological Data ◽  
Expression Data ◽  
Data Types ◽  
Heat Maps ◽  
Microarray Experiments ◽  
Link Type ◽  
Interactive Display ◽  
Data Points ◽  
2D Data

Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis.Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.

scholarly journals Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing

2012 ◽  
Vol 9 (2) ◽  
pp. 53-67 ◽  
Author(s):  
Peng Sun ◽  
Jiong Guo ◽  
Jan Baumbach
Keyword(s):  
Association Studies ◽  
Exact Algorithm ◽  
Biological Data ◽  
Genome Wide Association Studies ◽  
Biomedical Data ◽  
Data Types ◽  
Cluster Editing ◽  
Main Challenge ◽  
Different Types ◽  
Data Points

Summary The explosion of biological data has largely influenced the focus of today’s biology research. Integrating and analysing large quantity of data to provide meaningful insights has become the main challenge to biologists and bioinformaticians. One major problem is the combined data analysis of data from different types, such as phenotypes and genotypes. This data is modelled as bi-partite graphs where nodes correspond to the different data points, mutations and diseases for instance, and weighted edges relate to associations between them. Bi-clustering is a special case of clustering designed for partitioning two different types of data simultaneously. We present a bi-clustering approach that solves the NP-hard weighted bi-cluster editing problem by transforming a given bi-partite graph into a disjoint union of bi-cliques. Here we contribute with an exact algorithm that is based on fixed-parameter tractability. We evaluated its performance on artificial graphs first. Afterwards we exemplarily applied our Java implementation to data of genome-wide association studies (GWAS) data aiming for discovering new, previously unobserved geno-to-pheno associations. We believe that our results will serve as guidelines for further wet lab investigations. Generally our software can be applied to any kind of data that can be modelled as bi-partite graphs. To our knowledge it is the fastest exact method for weighted bi-cluster editing problem.

Multi-Objective Optimization of Human Gait With a Discomfort Function

2016 ◽  
Author(s):  
Hyun-Jung Kwon ◽  
Hyun-Joon Chung ◽  
Yujiang Xiang
Keyword(s):  
Joint Torque ◽  
Upper Body ◽  
Whole Body ◽  
Human Gait ◽  
Multi Objective Optimization ◽  
Joint Angles ◽  
Backward Walking ◽  
Multi Objective ◽  
Body Model ◽  
Neutral Angle

The objective of this study was to develop a discomfort function for including a high DOF upper body model during walking. A multi-objective optimization (MOO) method was formulated by minimizing dynamic effort and the discomfort function simultaneously. The discomfort function is defined as the sum of the squares of deviation of joint angles from their neutral angle positions. The dynamic effort is the sum of the joint torque squared. To investigate the efficacy of the proposed MOO method, backward walking simulation was conducted. By minimizing both dynamic effort and the discomfort function, a 3D whole body model with a high DOF upper body for walking was demonstrated successfully.

Implementation of “Epic Healthy Planet” registry for survivorship care coordination.

2021 ◽  
Vol 39 (28_suppl) ◽  
pp. 337-337
Author(s):  
Karen Kinahan ◽  
Bijal Desai ◽  
Michele Volpentesta ◽  
Margo Klein ◽  
Melissa Duffy ◽  
...  
Keyword(s):  
Medical Oncology ◽  
Discrete Data ◽  
Mandatory Reporting ◽  
Survivorship Care ◽  
Management Tools ◽  
Noticeable Increase ◽  
Episode Of Care ◽  
Data Points ◽  
User Friendly

337 Background: The evolving Commission on Cancer (CoC) reporting mandate and institution’s growing survivorship program led to identifying the need for systematic tracking of survivorship patients, surveillance tests, return appointments and referrals placed. Our aim was to develop an electronic medical record (EMR) integrated registry utilizing discrete data fields to assist our team in tracking key elements of high-quality survivorship care. Methods: Stakeholders from our survivorship team (APP/RN), medical oncology, psychology, research, operations and IT analytics reached consensus on essential discrete EMR fields to be included in the registry. For implementation we utilized the EPIC module, “Healthy Planet”, where patients enter the registry by initiating an “Episode of Care” at their initial survivorship visit. SmartForm fields create unique discrete patient data points identified by the stakeholders. Results: The following domains were identified as important elements of care that require tracking in a dedicated survivorship program. The registry domains populate from two sources: 1) currently existing EMR data fields, 2) domains with no currently discrete data (e.g. lymphedema, peripheral neuropathy) were captured in the developed SmartForm (see Table). From January 1, 2019 to June 1, 2021, 778 patients were entered into the registry. Since September 4, 2020, 112 patient follow-up appointment reminders were sent via EMR which has led to a noticeable increase in return appointments. SmartForm data fields are being amended as additional malignancy types are added to our survivorship program. Conclusions: The utilization of Healthy Planet is an effective and user-friendly way to track survivorship return appointments, remind providers of diagnostic tests that are due, and track referrals for CoC reporting. As the numbers of cancer survivors continues to increase, systematic population management tools are essential to ensure adherence to survivorship guideline recommendations, follow-up care and mandatory reporting.[Table: see text]

A Model of the Human Spine: Forward and Inverse Kinematics

1992 ◽  
Author(s):  
Sunil Kumar Agrawal ◽  
Siyan Li ◽  
Glen Desmier
Keyword(s):  
Range Of Motion ◽  
Inverse Kinematics ◽  
Degrees Of Freedom ◽  
Kinematic Model ◽  
Joint Angles ◽  
Human Spine ◽  
Forward And Inverse Kinematics ◽  
Position And Orientation ◽  
Three Degrees Of Freedom ◽  
Adjacent Vertebra

Abstract The human spine is a sophisticated mechanism consisting of 24 vertebrae which are arranged in a series-chain between the pelvis and the skull. By careful articulation of these vertebrae, a human being achieves fine motion of the skull. The spine can be modeled as a series-chain with 24 rigid links, the vertebrae, where each vertebra has three degrees-of-freedom relative to an adjacent vertebra. From the studies in the literature, the vertebral geometry and the range of motion between adjacent vertebrae are well-known. The objectives of this paper are to present a kinematic model of the spine using the available data in the literature and an algorithm to compute the inter vertebral joint angles given the position and orientation of the skull. This algorithm is based on the observation that the backbone can be described analytically by a space curve which is used to find the joint solutions..

Human Gait Analysis Method Based on Sample Entropy Fusion AlphaPose Algorithm

2021 ◽  
Author(s):  
Xinyu Lv ◽  
Shengying Wang ◽  
Tao Chen ◽  
Jing Zhao ◽  
Desheng Chen ◽  
...  
Keyword(s):  
Gait Analysis ◽  
Sample Entropy ◽  
Human Gait ◽  
Analysis Method ◽  
Human Gait Analysis

Projected Clustering for Biological Data Analysis

2011 ◽  
pp. 1617-1622
Author(s):  
Ping Deng ◽  
Qingkai Ma ◽  
Weili Wu
Keyword(s):  
Nearest Neighbor ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Biological Data ◽  
High Dimensional ◽  
Projected Clustering ◽  
Cluster Data ◽  
Biological Data Analysis ◽  
Data Points ◽  
Entire Dataset

Clustering can be considered as the most important unsupervised learning problem. It has been discussed thoroughly by both statistics and database communities due to its numerous applications in problems such as classification, machine learning, and data mining. A summary of clustering techniques can be found in (Berkhin, 2002). Most known clustering algorithms such as DBSCAN (Easter, Kriegel, Sander, & Xu, 1996) and CURE (Guha, Rastogi, & Shim, 1998) cluster data points based on full dimensions. When the dimensional space grows higher, the above algorithms lose their efficiency and accuracy because of the so-called “curse of dimensionality”. It is shown in (Beyer, Goldstein, Ramakrishnan, & Shaft, 1999) that computing the distance based on full dimensions is not meaningful in high dimensional space since the distance of a point to its nearest neighbor approaches the distance to its farthest neighbor as dimensionality increases. Actually, natural clusters might exist in subspaces. Data points in different clusters may be correlated with respect to different subsets of dimensions. In order to solve this problem, feature selection (Kohavi & Sommerfield, 1995) and dimension reduction (Raymer, Punch, Goodman, Kuhn, & Jain, 2000) have been proposed to find the closely correlated dimensions for all the data and the clusters in such dimensions. Although both methods reduce the dimensionality of the space before clustering, the case where clusters may exist in different subspaces of full dimensions is not handled well. Projected clustering has been proposed recently to effectively deal with high dimensionalities. Finding clusters and their relevant dimensions are the objectives of projected clustering algorithms. Instead of projecting the entire dataset on the same subspace, projected clustering focuses on finding specific projection for each cluster such that the similarity is reserved as much as possible.

A Latent Feature Model Approach to Biclustering

2016 ◽  
Vol 6 (2) ◽  
pp. 11-28
Author(s):  
José Caldas ◽  
Samuel Kaski
Keyword(s):  
Expectation Maximization Algorithm ◽  
Learning Task ◽  
Biological Data ◽  
Feature Model ◽  
Data Matrix ◽  
Data Types ◽  
Data Set ◽  
Modelling Framework ◽  
Number Variation ◽  
Mirna Expression Data

Biclustering is the unsupervised learning task of mining a data matrix for useful submatrices, for instance groups of genes that are co-expressed under particular biological conditions. As these submatrices are expected to partly overlap, a significant challenge in biclustering is to develop methods that are able to detect overlapping biclusters. The authors propose a probabilistic mixture modelling framework for biclustering biological data that lends itself to various data types and allows biclusters to overlap. Their framework is akin to the latent feature and mixture-of-experts model families, with inference and parameter estimation being performed via a variational expectation-maximization algorithm. The model compares favorably with competing approaches, both in a binary DNA copy number variation data set and in a miRNA expression data set, indicating that it may potentially be used as a general-problem solving tool in biclustering.

Bio-Inspired Algorithms in Bioinformatics I

2011 ◽  
pp. 236-240
Author(s):  
José Antonio Seoane Fernández ◽  
Mónica Miguélez Rico
Keyword(s):  
Human Genome ◽  
Heterogeneous Data ◽  
Genome Project ◽  
Biological Data ◽  
Organizational Level ◽  
Data Types ◽  
Proteomic Data ◽  
New Information ◽  
Cell Tissue ◽  
The Human Genome Project

Large worldwide projects like the Human Genome Project, which in 2003 successfully concluded the sequencing of the human genome, and the recently terminated Hapmap Project, have opened new perspectives in the study of complex multigene illnesses: they have provided us with new information to tackle the complex mechanisms and relationships between genes and environmental factors that generate complex illnesses (Lopez, 2004; Dominguez, 2006). Thanks to these new genomic and proteomic data, it becomes increasingly possible to develop new medicines and therapies, establish early diagnoses, and even discover new solutions for old problems. These tasks however inevitably require the analysis, filtration, and comparison of a large amount of data generated in a laboratory with an enormous amount of data stored in public databases, such as the NCBI and the EBI. Computer sciences equip biomedicine with an environment that simplifies our understanding of the biological processes that take place in each and every organizational level of live matter (molecular level, genetic level, cell, tissue, organ, individual, and population) and the intrinsic relationships between them. Bioinformatics can be described as the application of computational methods to biological discoveries (Baldi, 1998). It is a multidisciplinary area that includes computer sciences, biology, chemistry, mathematics, and statistics. The three main tasks of bioinformatics are the following: develop algorithms and mathematical models to test the relationships between the members of large biological datasets, analyze and interpret heterogeneous data types, and implement tools that allow the storage, retrieve, and management of large amounts of biological data.

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